gebhart/patrepeval huggingface dataset:
Overcoming conservation in TALE–DNA interactions: a minimal repeat scaffold enables selective recognition of an oxidized 5-methylcytosine (2018)

Transcription-activator-like effectors (TALEs) are repeat-based proteins featuring programmable DNA binding. The repulsion of TALE repeats by 5-methylcytosine (5mC) and its oxidized forms makes TALEs potential probes for their programmable analysis. However, this potential has been limited by the inability to engineer repeats capable of actual, fully selective binding of an (oxidized) 5mC: the extremely conserved and simple nucleobase recognition mode of TALE repeats and their extensive involvement in inter-repeat interactions that stabilize the TALE fold represent major engineering hurdles. We evaluated libraries of alternative, strongly truncated repeat scaffolds and discovered a repeat that selectively recognizes 5-carboxylcytosine (5caC), enabling construction of the first programmable receptors for an oxidized 5mC. In computational studies, this unusual scaffold executes a dual function <i>via</i> a critical arginine that provides inter-repeat stabilization and selectively interacts with the 5caC carboxyl group <i>via</i> a salt-bridge. These findings argue for an unexpected adaptability of TALE repeats and provide a new impulse for the design of programmable probes for nucleobases beyond A, G, T and C.
Supplementary Figure 2 from Combination of Two Insulin-Like Growth Factor-I Receptor Inhibitory Antibodies Targeting Distinct Epitopes Leads to an Enhanced Antitumor Response (2023)

Supplementary Figure 2 from Combination of Two Insulin-Like Growth Factor-I Receptor Inhibitory Antibodies Targeting Distinct Epitopes Leads to an Enhanced Antitumor Response
Analysis of orientation distribution in YBa2Cu3O7−x polycrystals by electron channeling patterns (1990)

A unit standard map for YBa2Cu3O7−x superconductors was constructed and indexed from a series of electron channeling patterns (ECPs). (001) pole figures of YBa2Cu3O7−x tapes and bulk specimens with various values of critical current density (Jc) were drawn by using the map covering [001-1̄1̄0-1̄10] stereographic quadrant and ECPs taken from individual grains of the specimens. It was found that preferred orientation of (001) formed in the tape with a decreasing thickness of the tape, which raised Jc significantly. It is concluded that the ECP technique is very useful for the analysis of orientation distribution in small-sized YBa2Cu3O7−x specimens such as tapes or thin films.
Plant E2F factors in cell cycle, development and DNA damage response (2008)

International audience
Direct measurement of charge transport through helical poly(ethyl propiolate) nanorods wired into gaps in single walled carbon nanotubes (2009)

We report the direct measurement of electrical transport through rod-like polymer molecules, of poly(ethyl propiolate) (PEP), utilizing single walled carbon nanotubes (SWNTs) as electrodes. The electrical properties of the devices were measured (i) before cutting a SWNT, (ii) when a SWNT was cut and (iii) after PEP deposition into the nanoscale gap in a cut SWNT. The gate-dependent electrical properties showed a reduction in current from I(on) = 2.4 x 10(-7) A for SWNT devices to I(on) = 3.6 x 10(-9) A for PEP bridge devices, both with the ON/OFF ratio of 10(4). Similarly, metallic SWNT devices showed a reduction in current from a few hundreds of microA for a SWNT device to a few nA for a PEP-SWNT structure. The current density of a single PEP molecule is 10(5)-10(6) A cm(-2), which is relatively high, indicating that the PEP molecule can carry significant current. Use of SWNT electrodes was seen to be an effective method of contacting PEP nanorods to facilitate electrical measurements.
Critical cooling rates during rapid solidification of an eutectic Al-Cu alloy (1987)

The microstructure and accompanying physical properties of metals are strongly influenced by the cooling rate during solidification. Conventional cooling rates of 10/sup 3/ K/s normally employed in industry result in crystalline phases which may be predicted from equilibrium phase diagrams. These rates may be greatly increased by employing a relatively new technique which consists of ejecting a small stream of molten alloy upon a water-cooled rotating drum. Cooling rates may be controlled by adjusting the rotational velocity of the drum while a forward-marching explicit finite difference solution was used to calculate specific rates. Comparison of theory and experiment show that, as the cooling rate is increased, the degree of crystallinity of the continuous equilibrium phase decreases and, at a cooling rate greater than 10/sup 10/ K/s, the continuous equilibrium phase disappears and an amorphous phase appears in its place.
Detergent Effects of Sodium Deoxycholate Are a Major Feature of an Injectable Phosphatidylcholine Formulation Used for Localized Fat Dissolution (2004)

BACKGROUND Phosphatidylcholine injections are becoming an increasingly popular technique to treat localized fat accumulation. This formula is composed primarily of phosphatidylcholine and sodium deoxycholate, a bile salt used to solubilize the natural phospholipid in water. The mechanism through which this injectable phosphatidylcholine formulation causes localized fat reduction is unknown. OBJECTIVE To investigate the active component and mechanism of action of an injectable phosphatidylcholine formulation in clinical use. METHODS Cell viability and cell membrane lysis assays were performed on cell cultures and porcine skin after treatment with the phosphatidylcholine formula, isolated sodium deoxycholate, or common laboratory detergents Triton-X 100 and Empigen BB. In addition, we described the histologic changes after injection of these substances into porcine tissue. RESULTS A significant and comparable loss of cell viability, cell membrane lysis, and disruption of fat and muscle architecture was seen in cell cultures and tissue specimens treated with the phosphatidylcholine formula and isolated sodium deoxycholate. These findings were similar to the effects produced after treatment with laboratory detergents. CONCLUSIONS The phosphatidylcholine formula popularly used in subcutaneous injections for fat dissolution works primarily as a detergent causing nonspecific lysis of cell membranes. Our findings suggest that sodium deoxycholate is the major active component responsible for cell lysis. Detergent substances may have a role in eliminating unwanted adipose tissue. It is advised that physicians use caution until adequate safety data are available.
Antibodies against Retroviral Proteins and Nuclear Antigens in a Subset of Idiopathic CD4 + T Lymphocytopenia Patients (1996)

Idiopathic CD4+ T lymphocytopenia (ICL) is an immunodeficiency syndrome characterized by severe depletion of CD4+ T lymphocytes, but in which human immunodeficiency virus cannot be detected. Peripheral blood mononuclear cells (BPMCs) from an ICL patient were cocultured with HUT78 T-lymphoblastoid cells, and an acute cytopathic effect and formation of multinucleated cells were observed. A human intracisternal A-type retroviral particle designated HIAP-II was detected in cells surviving the acute cytopathic effect. Eight of 13 ICL patients in a blinded screen of a serological panel provided by the National Centers for Disease Control and Prevention (CDC) had serum antibodies that specifically reacted with HIAP-II associated proteins by Western immunoblotting. None of 19 control sera in the panel that were unreactive with HIV Gag proteins produced a positive result on HIAP-II immunoblots. Comparable results were obtained in a blinded screen of a second CDC serological panel. Sera from 8 of 14 ICL patients in the second serological panel were positive for antinuclear autoantibodies (ANAs) commonly observed in patients with systemic autoimmune diseases. These results suggest the possible involvement of an A-type retrovirus or autoimmunity in development of ICL in a subset of patients.
Porcine Endothelial Cells Cocultured with Smooth Muscle Cells Became Procoagulant In Vitro (2010)

Endothelial cell (EC) seeding represents a promising approach to provide a nonthrombogenic surface on vascular grafts. In this study, we used a porcine EC/smooth muscle cell (SMC) coculture model that was previously developed to examine the efficacy of EC seeding. Expression of tissue factor (TF), a primary initiator in the coagulation cascade, and TF activity were used as indicators of thrombogenicity. Using immunostaining, primary cultures of porcine EC showed a low level of TF expression, but a highly heterogeneous distribution pattern with 14% of ECs expressing TF. Quiescent primary cultures of porcine SMCs displayed a high level of TF expression and a uniform pattern of staining. When we used a two-stage amidolytic assay, TF activity of ECs cultured alone was very low, whereas that of SMCs was high. ECs cocultured with SMCs initially showed low TF activity, but TF activity of cocultures increased significantly 7-8 days after EC seeding. The increased TF activity was not due to the activation of nuclear factor kappa-B on ECs and SMCs, as immunostaining for p65 indicated that nuclear factor kappa-B was localized in the cytoplasm in an inactive form in both ECs and SMCs. Rather, increased TF activity appeared to be due to the elevated reactive oxygen species levels and contraction of the coculture, thereby compromising the integrity of EC monolayer and exposing TF on SMCs. The incubation of cocultures with N-acetyl-cysteine (2 mM), an antioxidant, inhibited contraction, suggesting involvement of reactive oxygen species in regulating the contraction. The results obtained from this study provide useful information for understanding thrombosis in tissue-engineered vascular grafts.
ChemInform Abstract: Activation of sp3 C—H Bonds with Cobalt(I): Catalytic Synthesis of Enamines. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
‘Something so hard': a mixed-methods study of home sputum collection for tuberculosis contact investigation in Uganda (2018)

Home sputum collection by LHWs entails different challenges from sputum collection in clinical settings. More research is needed to develop interventions to mitigate stigma and increase success of home-based collection.
Invited: Investigation of the Solid Electrolyte Interface (SEI) on Silicon Nano-Particle Anodes (2014)

The surface reactions of electrolytes with a silicon anode in lithium ion cells have been investigated. The investigation utilizes two novel techniques that are enabled by the use of binder-free silicon (BF-Si) nanoparticle anodes. The first method, transmission electron microscopy with energyndispersive X-ray spectroscopy, allows straightforward analysis of the BF-Si solid electrolyte interphase (SEI). The second method utilizes multi-nuclear magnetic resonance spectroscopy of D2O extracts from the cycled anodes. The TEM and NMR data are complemented by XPS and FTIR data, which are routinely used for SEI studies. Coin cells (BF-Si/Li) were cycled in electrolytes containing LiPF6 salt and ethylene carbonate or fluoroethylene carbonate solvent. Capacity retention was significantly better for cells cycled with LiPF6/FEC electrolyte than for cells cycled with LiPF6/EC electrolyte. Our unique combination of techniques establishes that for LiPF6/EC electrolyte the BF-Si SEI continuously grows during the first 20 cycles and the SEI becomes integrated with the BF-Si nanoparticles. The SEI predominantly contains lithium ethylene dicarbonate, LiF, and LixSiOy. BF-Si electrodes cycled with LiPF6/FEC electrolyte have a different behavior; the BF-Si nanoparticles remain relatively distinct from the SEI. The SEI predominantly contains LiF, LixSiOy, and an insoluble polymeric species. The depth dependence of structure of the SEI was further investigated by Hard X-ray photoelectron spectroscopy (HAXPES). Finally, the effect of different binders including PVDF, CMC, and PAA on the surface of silicon nanoparticles and on the structure of the SEI will be discussed. We gratefully acknowledge funding from Department of Energy office of Basic Energy Sciences EPSCoR Implementation award (DE-SC0007074).
Depth-dependence of visual signals in the human superior colliculus: Comparison between 3T and 9.4T (2015)

The SC is composed of 7 layers where the most superficial layers process visual information. The intermediate layers contain neurons involved in oculomotor control, and the deep layers contain multisensory and visuomotor neurons. Until now there were several studies which demonstrated reliable activation in the SC after visual stimulation at 3T. In this study we investigated the benefits of using 9.4T MRI for humans to study small brain structures in the brainstem like the SC in a comparison with 3T data. Left or right-sided half circles of a flickering checkerboard (8Hz) were shown in a block design interleaved with fixation baseline periods with a duration of 15s. For the 3T measurements each participant underwent three experimental runs, in which each condition was repeated 10 times. For the 9.4T measurements each participant underwent two experimental runs, in which each condition was repeated 20 times. Regions-Of-Interest (ROI) of the SC were drawn manually for each subject considering specific anatomical landmarks. The SC was then divided in three zones: superficial zone (SZ), intermediate zone (IZ) and deep zone (DZ). With the data acquired in the 9.4T we were able to detect signal increases in the left and right SC and lateralization of BOLD responses consistent with the cortical signals in each subject. With the 3T data the same results were only apparent in a group analysis. Averages of the beta estimates of the GLM models were calculated within each of the three zones (SZ, IZ and DZ) for the 3T and the 9.4T data. For the 9.4T data the highest signals were localized in the SZ of the right and left colliculi as expected. Activations encountered in the SC were not present outside the structure (CSF) evidencing the localizing capacity of our technique. For the 3T data there is also a higher value for the SZ compared to the other zones. However, this difference was less clear compared to the results obtained for the 9.4T data. In summary, despite of several technical issues, e.g. larger B1 inhomogeneities and distortions, we demonstrated the feasibility of a functional mapping of the human brainstem with UHF neuroimaging and found a substantial benefit of the 9.4T in comparison with the 3T for the functional mapping of upper brainstem structures.
Demonstration of transponder aggregator based on silicon photonics for multi-degree color/direction-independent ROADM system (2011)

We fabricated 8-port transponder-aggregator modules based on silicon photonics for multi-degree color/direction-independent ROADM systems. The signal drop function of the module with four 43-Gbps NRZ signals was demonstrated.
Deep Learning with Partially Labeled Data for Radio Map Reconstruction (2023)

In this paper, we address the problem of Received Signal Strength map reconstruction based on location-dependent radio measurements and utilizing side knowledge about the local region; for example, city plan, terrain height, gateway position. Depending on the quantity of such prior side information, we employ Neural Architecture Search to find an optimized Neural Network model with the best architecture for each of the supposed settings. We demonstrate that using additional side information enhances the final accuracy of the Received Signal Strength map reconstruction on three datasets that correspond to three major cities, particularly in sub-areas near the gateways where larger variations of the average received signal power are typically observed.
Brachytherapy in the treatment of head and neck cancer. (2002)

Brachytherapy is a therapeutic modality that may provide a significant improvement in the therapeutic ratio when appropriately applied, and hence, is an appealing treatment strategy for the head and neck. For several tumor sites in the head and neck, the use of a brachytherapy implant has been demonstrated to be effective and is optimally provided within a multidisciplinary team setting. This enables meticulous attention to technical and treatment-related factors that have been demonstrated to influence the therapeutic ratio for low-dose-rate implants. Recent technologic advances have enabled the study of promising high-dose-rate and pulsed-dose-rate afterloading brachytherapy techniques, in an attempt to expand the role of brachytherapy in the head and neck. These techniques minimize radiation exposure hazards while offering the physical and biologic advantages of brachytherapy. Issues pertinent to members of the brachytherapy team providing multidisciplinary care of the implanted head and neck patient are discussed.
Synthesis of 2(3H)‐Benzoxazolone Derivatives as Potential Melatonin Receptor Ligands. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
An Alternative Method for the Highly Selective Iodination of Alcohols Using a CsI/BF3×Et2O System. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Ultralow-Loss SiC Floating Junction Schottky Barrier Diodes (Super-SBDs) (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We have applied the floating junction (FJ) structure, which has been confirmed to be effective in reducing the on-resistance of Si power devices, to SiC FJ Schottky barrier diodes (SiC Super-SBDs). Optimization of the device parameters, which are derived by making improvements in the device simulator, and development of the fabrication process have enabled realization of Super-SBDs with a breakdown voltage of 2700 V and a specific on-resistance of 2.57 <formula formulatype="inline"><tex>$\hbox{m}\Omega \cdot \hbox{cm}^{2}$</tex></formula>. These values correspond to the world record of 11.3 <formula formulatype="inline"><tex>$\hbox{GW}/\hbox{cm}^{2}$</tex></formula> for Baliga's figure-of-merit <formula formulatype="inline"><tex>$(\hbox{BFOM} = \hbox{4}V_{\rm bd}^{2}/R_{{\rm on} \hbox{-}{\rm sp}})$</tex></formula>. </para>
Deuterated docosahexaenoic acid protects against oxidative stress and geographic atrophy‐like retinal degeneration in a mouse model with iron overload (2022)

Oxidative stress plays a central role in age-related macular degeneration (AMD). Iron, a potent generator of hydroxyl radicals through the Fenton reaction, has been implicated in AMD. One easily oxidized molecule is docosahexaenoic acid (DHA), the most abundant polyunsaturated fatty acid in photoreceptor membranes. Oxidation of DHA produces toxic oxidation products including carboxyethylpyrrole (CEP) adducts, which are increased in the retinas of AMD patients. In this study, we hypothesized that deuterium substitution on the bis-allylic sites of DHA in photoreceptor membranes could prevent iron-induced retinal degeneration by inhibiting oxidative stress and lipid peroxidation. Mice were fed with either DHA deuterated at the oxidation-prone positions (D-DHA) or control natural DHA and then given an intravitreal injection of iron or control saline. Orally administered D-DHA caused a dose-dependent increase in D-DHA levels in the neural retina and retinal pigment epithelium (RPE) as measured by mass spectrometry. At 1 week after iron injection, D-DHA provided nearly complete protection against iron-induced retinal autofluorescence and retinal degeneration, as determined by in vivo imaging, electroretinography, and histology. Iron injection resulted in carboxyethylpyrrole conjugate immunoreactivity in photoreceptors and RPE in mice fed with natural DHA but not D-DHA. Quantitative PCR results were consistent with iron-induced oxidative stress, inflammation, and retinal cell death in mice fed with natural DHA but not D-DHA. Taken together, our findings suggest that DHA oxidation is central to the pathogenesis of iron-induced retinal degeneration. They also provide preclinical evidence that dosing with D-DHA could be a viable therapeutic strategy for retinal diseases involving oxidative stress.
<title>Large one-step holographic stereogram</title> (1991)

One-step holographic stereograms which can reconstruct large images have been produced by an extremely anamorphic optical system. One of the important lenses is the long and narrow cylindrical lens with small f-number. The lens is designed as a composite dual lens. Reference light is illuminated through this composite lens and the special configuration with cylindrical lenses is considered. But in the one-step holographic stereogram, if the series of conventional perspective original images are used without performing any anamorphic image processing, the reconstructed images are observed behind the hologram plane. In order to enhance the sense of perspective of the reconstructed images and minimize blur of the reconstructed image, an image processing technique is introduced. In this report, the authors describe their optical system and the image processing technique which can display a large and bright 3D image, with about 55 degree(s) viewing zone.
Adoptive transfer of BALb/c mouse splenocytes reduces lesion severity and induces intestinal pathophysiologic changes in the Mycobacterium avium Subspecies paratuberculosis beige/scid mouse model. (2002)

Successful immune reconstitution would enhance resistance of beige/scid mice to chronic infection with Mycobacterium avium subspecies paratuberculosis, but may cause damage to intestinal tissue. Therefore, we investigated the effect of adoptive transfer of BALB/c mouse splenocytes on lesion severity and intestinal physiology in beige/scid mice infected with M. paratuberculosis. Mice were inoculated intraperitoneally (i.p.) with M. paratuberculosis, and two weeks later were inoculated i.p. with viable spleen cells from immune-competent BALB/c mice. Mice were necropsied 12 weeks after infection when engraftment of lymphocytes, clinical disease, pathologic lesions, and intestinal electrophysiologic parameters were evaluated. Lymphocytes were rare in control beige/scid mice not inoculated with spleen cells. In contrast, high numbers of CD4+, CD8+, and B220+ lymphocytes were detected in the spleen of all beige/scid mice (n = 24) inoculated with spleen cells, indicating that adoptive transfer resulted in successful engraftment of donor lymphocytes (immune reconstitution). Immune reconstitution of M. paratuberculosis-infected beige/ scid mice significantly reduced the severity of clinical disease and pathologic lesions, and numbers of bacteria in the liver. However, intestinal electrophysiologic parameters studied in vitro indicated that intestinal tissues from reconstituted beige/scid mice had reduced short-circuit current responses (due to reduced ion secretion) following electrical, glucose, and forskolin stimulation. These abnormal responses suggested that neural or epithelial cells in the intestine were damaged. We conclude that successful immune reconstitution of beige/scid mice enhance their resistance to M. paratuberculosis infection, but may cause pathophysiologic changes associated with intestinal inflammation.
Cover Picture: Tunable n‐ and p‐type doping of single‐layer graphene by engineering its interaction with the SiO2 support (Phys. Status Solidi RRL 2/2012) (2012)

As shown by Amirhasan Nourbakhsh et al. (see their Letter on pp. 53–55), non-destructive n- and p-type doping of graphene has been achieved by tuning the interaction between graphene and a self-assembled monolayer of 3-aminopropyl triethoxy silane. The type of doping could be controlled by changing the pH value of the immersing solutions. The results of the experiments described in this work represent a convenient solution to the problem of tailoring the electronic properties of graphene for many applications which require a fine control of the charge density.