gebhart/patrepeval huggingface dataset:
Vibrational Entropic Stabilization of Layered Chalcogenides: From Ordered Vacancy Compounds to 2D Layers (2023)

Despite the rapid pace of computationally and experimentally discovering new two-dimensional layered materials, a general criteria for a given compound to prefer a layered structure over a non-layered one remains unclear. Articulating such criteria would allow one to identify materials at the verge of an inter-dimensional structural phase transition between a 2D layered phase and 3D bulk one, with potential applications in phase change memory devices. Here we identify a general stabilization effect driven by vibrational entropy that can favor 2D layered structures over 3D bulk structures at higher temperatures, which can manifest in ordered vacancy compounds where phase competition is tight. We demonstrate this vibrational-entropy stabilization effect for three prototypical ordered vacancy chalcogenides, ZnIn2S4 and In2S3, and Cu3VSe4, either by vacancy rearrangement or by cleaving through existing vacancies. The relative vibrational entropy advantage of the 2D layered phase originates mainly from softened out-of-plane dilation phonon modes.
Bulk Synthesis of Large Diameter Semiconducting Single-Walled Carbon Nanotubes by Oxygen-Assisted Floating Catalyst Chemical Vapor Deposition (2011)

Semiconducting single-walled carbon nanotubes (s-SWCNTs) with a mean diameter of 1.6 nm were synthesized on a large scale by using oxygen-assisted floating catalyst chemical vapor deposition. The oxygen introduced can selectively etch metallic SWCNTs in situ, while the sulfur growth promoter functions in promoting the growth of SWCNTs with a large diameter. The electronic properties of the SWCNTs were characterized by laser Raman spectroscopy, absorption spectroscopy, and field effect transistor measurements. It was found that the content of s-SWCNTs in the samples was highly sensitive to the amount of oxygen introduced. Under optimum synthesis conditions, enriched s-SWCNTs can be obtained in milligram quantities per batch.
Efficient collection and manipulation of laser diode output using refractive micro-optics (1995)

The collection efficiency and collimation ability of high numerical aperture circular and cylindrical GaP lenses were evaluated using single index-guided and gain-guided laser diode emitters. Comparisons were made between 200 micrometers focal length cylindrical lenses (NA equals 0.75) fabricated by an accurate repetitive step-wise etching method and 70 micrometers focal length cylindrical lenses (NA &gt; 1) fabricated by a simple resist reflow technique. Lens arrays (200 - 300 micrometers fl, 0.5 - 0.75 NA) fabricated by the repetitive resist-etch method were used to collimate the output of a diode bar consisting of 100 index-guided elements. Refocusing of the collimated light with a macro-optic (for pumping a Nd:YVO<SUB>4</SUB> laser) produced a spot that was on average 2 - 3 times larger than the diffraction limit and contained up to 88% of the total bar output. The deviation from the theoretical limit was examined in terms of lens fabrication accuracy and alignment tolerances between the diode and lens arrays, which were shown to be on the order of 1 - 2 micrometers .
Refractive‐index matching between liquid crystals and photopolymers (2005)

Abstract— Refractive indices of two photocurable polymers, NOA65 and NOA81 (Norland Optical Adhesive), and two series of Merck liquid crystals, E‐series (E44, E48, and E7) and BL‐series (BL038, BL003 and BL006), and two UCF high‐birefringence liquid‐crystal mixtures were measured using an Abbe refractometer in the visible spectral region and 15–55°C temperature range. Some liquid crystals have excellent index matching with NOA65 in the red, while some fit better in the blue spectral region. To validate this index‐matching property found in the material level, we prepared some polymer‐dispersed liquid‐crystal devices. Good correlations between material and device performances are obtained.
Supplementary Figures from Tumor Microenvironment–Derived R-spondins Enhance Antitumor Immunity to Suppress Tumor Growth and Sensitize for Immune Checkpoint Blockade Therapy (2023)

&lt;p&gt;Supplementary Figures&lt;/p&gt;
Real-time microbe detection based on director distortions around growing immune complexes in lyotropic chromonic liquid crystals (2005)

We describe director distortions in the nematic liquid crystal (LC) caused by a spherical particle with tangential surface orientation of the director and show that light transmittance through the distorted region is a steep function of the particle's size. The effect allows us to propose a real-time microbial sensor based on a nontoxic lyotropic chromonic LC (LCLC) that detects and amplifies the presence of immune complexes. A cassette is filled with LCLC, antibody, and antigen-bearing particles. Small and isolated particles cause no macroscopic distortions of the LCLC. Upon antibody-antigen binding, the growing immune complexes distort the director and cause detectable optical transmittance between crossed polarizers.
The tandem C2 domains of synaptotagmin contain redundant Ca2+ binding sites that cooperate to engage t-SNAREs and trigger exocytosis (2001)

Real-time voltammetry measurements from cracked PC12 cells were used to analyze the role of synaptotagmin-SNARE interactions during Ca2+-triggered exocytosis. The isolated C2A domain of synaptotagmin I neither binds SNAREs nor inhibits norepinephrine secretion. In contrast, two C2 domains in tandem (either C2A-C2B or C2A-C2A) bind strongly to SNAREs, displace native synaptotagmin from SNARE complexes, and rapidly inhibit exocytosis. The tandem C2 domains of synaptotagmin cooperate via a novel mechanism in which the disruptive effects of Ca2+ ligand mutations in one C2 domain can be partially alleviated by the presence of an adjacent C2 domain. Complete disruption of Ca2+-triggered membrane and target membrane SNARE interactions required simultaneous neutralization of Ca2+ ligands in both C2 domains of the protein. We conclude that synaptotagmin-SNARE interactions regulate membrane fusion and that cooperation between synaptotagmin's C2 domains is crucial to its function.
Human thrombin-derived host defense peptides inhibit neutrophil recruitment and tissue injury in severe acute pancreatitis (2014)

Severe acute pancreatitis (AP) is characterized by leukocyte infiltration and tissue injury. Herein, we wanted to examine the potential effects of thrombin-derived host defense peptides (TDPs) in severe AP. Pancreatitis was provoked by infusion of taurocholate into the pancreatic duct or by intraperitoneal administration of l-arginine in C57BL/6 mice. Animals were treated with the TDPs GKY20 and GKY25 or a control peptide WFF25 30 min before induction of AP. TDPs reduced blood amylase levels, neutrophil infiltration, hemorrhage, necrosis, and edema formation in the inflamed pancreas. Treatment with TDPs markedly attenuated the taurocholate-induced increase in plasma levels of CXCL2 and interleukin-6. Moreover, administration of TDPs decreased histone 3, histone 4, and myeloperoxidase levels in the pancreas in response to taurocholate challenge. Interestingly, administration of TDPs abolished neutrophil expression of Mac-1 in mice with pancreatitis. In addition, TDPs inhibited CXCL2-induced chemotaxis of isolated neutrophils in vitro. Fluorescent-labeled TDP was found to directly bind to isolated neutrophils. Finally, a beneficial effect of TDPs was confirmed in l-arginine-induced pancreatitis. Our novel results demonstrate that TDPs exert protective effects against pathological inflammation and tissue damage in AP. These findings suggest that TDPs might be useful in the management of patients with severe AP.
Esterolytic Activities of Rat Intestinal Mucosa (1976)

A glycerol‐ester hydrolase from rat intestinal cells has been purified using chromatography on carboxyhexanoyl‐Sepharose‐glyceryldioctanoate and preparative gel electrophoresis. The enzyme gives a single band by analytical gel electrophoresis; it is a monomer of molecular weight 68000. The optimum pH for its action on glyceryl tributyrate is between 8.0 and 8.5; the activation energy was calculated to be 8.7 kcal × mol −1 (36.4 kJ/mol). Its substrate specificity is mainly directed against esters of glycerol and of primary monoalcohols. Similarly to pancreatic lipase but contrary to liver esterase, it is inhibited by bile salts; relief of this inhibition by colipase is only observed for pancreatic lipase. The possible role of the glycerol‐ester hydrolase in the absorption of short and of medium chain triglycerides is discussed.
Neural network-based modeling of the plasma-enhanced chemical vapor deposition of silicon dioxide (2002)

The properties of plasma enhanced chemical vapor deposition (PECVD) silicon dioxide films are modeled using neural networks. This method is simple, extremely useful and readily applicable to the empirical modeling of such complex plasma processes. In characterizing the SiO/sub 2/ films, it is found that the dominant film property is its impurity concentration. The impurity concentration dictates the refractive index and permittivity, two critical figures of merit when these films are used as interlayer dielectric and in optoelectronic applications. The most important parameters in determining the impurity concentration of the films are substrate temperature and pressure. Increasing the substrate temperature causes the impurity concentration to decrease. This drop in impurity concentration causes an increase in refractive index and a decrease in permittivity. Increasing pressure has almost the same effect, causing a decrease in permittivity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Eye-selective fMRI activity in human primary visual cortex: Comparison between 3 T and 9.4 T, and effects across cortical depth (2020)

The primary visual cortex of humans contains patches of neurons responding preferentially to stimulation of one eye (the ocular dominance columns). Multiple previous studies attempted to detect their activity using fMRI. The majority of these fMRI studies used magnetic field strengths of 4 ​T and higher. However, there have been reports of reliable eye-selective activations at 3 ​T as well. In this study we investigated the possibility of detecting eye-selective V1 activity using high-resolution GE-EPI fMRI at 3 ​T and sub-millimeter resolution fMRI at ultrahigh 9.4 ​T magnetic field strengths with acquisition parameters optimized for each field strength. High-resolution fMRI at 9.4 ​T also allowed us to examine the eye-selectivity responses across the cortical depth, which are expected to be strongest in the middle layers. We observed a substantial increase in the percentage of eye-selective voxels, as well as a doubling in run-to-run consistency of eye preference at ultrahigh field compared to 3 ​T. We also found that across cortical depth, eye selectivity increased towards the superficial layers, and that signal contrast increased while noise remained nearly constant towards the surface. The depth-resolved results are consistent with a distortion of spatial specificity of the GE-EPI signal by ascending venules and large draining veins on the cortical surface. The effects of larger vessels cause increasing signal amplitude, but also displacement of the maximum BOLD signal relative to neural activity. In summary, our results show that increase in spatial resolution, reduced partial volume effects, and improved sensitivity at 9.4 ​T allow for better detection of eye-selective signals related to ocular dominance columns. However, although ultrahigh field yields higher sensitivity to the ocular dominance signal, GE-EPI still suffers from specificity issues, with a prominent signal contribution at shallow depths from larger cortical vessels.
X-Ray Microanalysis of the Fingernails in Cirrhotic Patients (1987)

The element content of clipped nails of 13 patients with liver cirrhosis was examined by X-ray microanalysis, and compared with that of 50 healthy subjects. The results showed a statistically significant increase in the percentage of Na, Mg and P and a slight, but statistically significant decrease in S and Cl. The percentage of K, Ca, Fe, Cu and Zn did not show any difference from that of the controls. The findings indicate that X-ray microanalysis may be a valuable tool for the simultaneous examination of a large number of elements in the fingernails.
Biotechnology for secure biocontainment designs in an emerging bioeconomy (2021)

Genetically modified organisms (GMOs) have emerged as an integral component of a sustainable bioeconomy, with an array of applications in agriculture, bioenergy, and biomedicine. However, the rapid development of GMOs and associated synthetic biology approaches raises a number of biosecurity concerns related to environmental escape of GMOs, detection thereof, and impact upon native ecosystems. A myriad of genetic safeguards have been deployed in diverse microbial hosts, ranging from classical auxotrophies to global genome recoding. However, to realize the full potential of microbes as biocatalytic platforms in the bioeconomy, a deeper understanding of the fundamental principles governing microbial responsiveness to biocontainment constraints, and interactivity of GMOs with the environment, is required. Herein, we review recent analytical biotechnological advances and strategies to assess biocontainment and microbial bioproductivity, as well as opportunities for predictive systems biodesigns towards securing a viable bioeconomy.
MAC inhibitors suppress mitochondrial apoptosis (2009)

MAC (mitochondrial apoptosis-induced channel) forms in the mitochondrial outer membrane and unleashes cytochrome c to orchestrate the execution of the cell. MAC opening is the commitment step of intrinsic apoptosis. Hence closure of MAC may prevent apoptosis. Compounds that blocked the release of fluorescein from liposomes by recombinant Bax were tested for their ability to directly close MAC and suppress apoptosis in FL5.12 cells. Low doses of these compounds (IC50 values ranged from 19 to 966 nM) irreversibly closed MAC. These compounds also blocked cytochrome c release and halted the onset of apoptotic markers normally induced by IL-3 (interleukin-3) deprivation or staurosporine. Our results reveal the tight link among MAC activity, cytochrome c release and apoptotic death, and indicate this mitochondrial channel is a promising therapeutic target.
Multifunctional volumetric meta-optics for color and polarization image sensors (2020)

Three-dimensional elements, with refractive index distribution structured at subwavelength scale, provide an expansive optical design space that can be harnessed for demonstrating multifunctional free-space optical devices. Here we present 3D dielectric elements, designed to be placed on top of the pixels of image sensors, that sort and focus light based on its color and polarization with efficiency significantly surpassing 2D absorptive and diffractive filters. The devices are designed via iterative gradient-based optimization to account for multiple target functions while ensuring compatibility with existing nanofabrication processes, and they are experimentally validated using a scaled device that operates at microwave frequencies. This approach combines arbitrary functions into a single compact element, even where there is no known equivalent in bulk optics, enabling novel integrated photonic applications.
Radiative coupling effects in GaInP/GaAs/Ge multijunction solar cells (2003)

Direct measurements of radiative coupling effects in GaInP/GaAs/Ge multijunction solar cells are presented. Radiative coupling between the GaInP and GaAs cells is observed by using isotype cells as well as specially fabricated 3-terminal device structures. Spectral response measurements of the GaAs cell in both isotype and 3-terminal approaches are shown to exhibit enhanced quantum efficiency in the short wavelength region under favorable radiative coupling conditions. Additionally, electroluminescence of the GaInP cell is shown to enhance the current output from the GaAs cell using a 3-terminal device structure. One consequence of this effect is the possible influence on the measured J-ratio of a multijunction cell. Consideration of radiative coupling may become increasingly important as multijunction III-V based solar cells - including 4- and 5- junction cells - continue to develop and improve in performance.
A Self‐Adjuvanting Supramolecular Vaccine Carrying a Folded Protein Antigen (2013)

This work illustrates a strategy for the design of molecularly defined immunotherapies, using a blend of supramolecular peptide self-assembly and active site-directed protein capture.
F2 -laser photosensitivity applications in germanosilicate fiber and planar waveguides (2002)

The energetic 7.9-eV photons of the F<sub>2</sub> laser directly access bandgap states in germanosilicate glasses to provide a strong and direct channel for inducing refractive index changes in optical fibers and planar waveguides. In this paper, we review our F<sub>2</sub>-laser photosensitivity studies with an aim to assess prospects for shaping useful photonics structures directly inside the germanosilicate waveguides. We describe strong photosensitivity responses in standard telecommunication fibers and planar optical waveguides without the need for hydrogen loading, and compare with responses provided by traditional ultraviolet lasers. Because of the strong 157-nm absorption in the germanium-doped guiding layers, large non-uniform changes to refractive index are noted that offer opportunities for trimming phase errors and correcting waveguide birefringence in planar optical circuits. With hydrogen soaking, modest 157-nm pre-irradiation was found to 'lock-in' a permanent photosensitivity enhancement in the germanosilicate guiding core, permitting the formation of strong (40-dB) and stable fiber Bragg gratings with 248-nm KrF laser light. The 157-nm 'lock-in' mechanism is associated with Si-OH and Ge-OH defect formation and permanently enhances the ultraviolet photosensitivity response by several orders of magnitude above that for an untreated fiber without the aging related disadvantages of conventional hydrogen soaking. The unique opportunities for F<sub>2</sub>-laser photosensitivity applications in shaping and trimming photonic components will be outlined in this presentation.
An optical technique for bit and packet synchronization (2002)

In this paper, we present and evaluate a new method for optical synchronization using the combined effect of wavelength tuning of the transmitter together with the dispersion in fibers. This scheme is suitable for time division multiplexing (TDM) at high bit rates employing asynchronous transfer mode (ATM) switches.
Heart Allograft Tolerance Induced By Hind-Limb Transplant in Rats: Findings of a Pilot Study (2023)

The present study shows that a short-term antilymphocyte serum + Cyclosporine A (ALS + CsA) treatment enabled indefinite vascularized hind-limb allograft survival, which induced secondary donor-strain skin and heart allograft tolerance. Transplanting organs or tissues has emerged as a successful treatment for terminal illnesses. Immunosuppression following transplantation, however, may have very negative side effects. To address this issue, donor-specific transplant tolerance was suggested. Here, we describe a novel technique for raising heart allograft tolerance in rats. First, we induced indefinite vascularized hind-limb allograft survival with a short-term antilymphocyte serum + Cyclosporine A treatment. Peripheral blood chimerism disappeared 6-7 weeks after immunosuppression was withdrawn. Then the recipients accepted secondary donor-strain skin and heart transplantation 200 days following vascularized hind-limb transplantation without any immunosuppression, but rejected third party skin allografts, a status of donor-specific tolerance. The ELISPOT results suggested a mechanism of clone deletion. The findings may open new perspectives for the role of vascularized bone transplant, especially vascularized bone marrow transplant, in the induction and maintenance of organ transplantation tolerance.
Lasing from dye-doped photonic crystals with graded layers in dichromate gelatin emulsions (2008)

We report on optically pumped lasing from dye-doped, graded-spacing layer structures of dichromate gelatin emulsions fabricated using two-beam holographic interference. The graded layers exhibited deep and wide photonic band gaps. Multimode lasing with both a low threshold and a high quality factor was observed at the band edge of the photonic band gap. We modeled the emissions from the dye-doped graded layer system using a finite difference time domain technique and achieved good agreement with experimental results.
Growth hormone stimulation of normal and leukemic human T-lymphocyte proliferation in vitro (1981)

In order to investigate the effect of human growth hormone on T lymphocytes, we utilized a clonogenic assay for mitogen-responsive human peripheral blood T lymphocytes. Lymphocytes were purified by density gradient centrifugation and incubated in the presence of phytohemagglutinin using a two-layer agar technique for CFU- T-lymphocyte culture. Nanogram concentrations of human growth hormone, ovine prolactin, human chorionic somatomammotropin, or growth hormone fragment were added to cell cultures. Growth hormone potentiated normal T-cell colony formation in a species-specific manner. Cells from a homogeneous T-lymphoblast line derived from a patient with a T-cell variant of hairy cell leukemia also showed augmentation of colony growth in the presence of human growth hormone. These studies provide evidence for a direct effect of growth hormone on normal and some neoplastic human T cells.
Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids (2023)

Pairs of pyrrolysyl-tRNA synthetase (PylRS) and tRNAPyl from Methanosarcina mazei and Methanosarcina barkeri are widely used for site-specific incorporations of non-canonical amino acids into proteins (genetic code expansion). Previously, we achieved full productivity of cell-free protein synthesis for bulky non-canonical amino acids, including Ne-((((E)-cyclooct-2-en-1-yl)oxy)carbonyl)-L-lysine (TCO*Lys), by using Methanomethylophilus alvus PylRS with structure-based mutations in and around the amino acid binding pocket (first-layer and second-layer mutations, respectively). Recently, the PylRS&amp;bull;tRNAPyl pair from a methanogenic archaeon ISO4-G1 was used for genetic code expansion. In the present study, we determined the crystal structure of the methanogenic archaeon ISO4-G1 PylRS (ISO4-G1 PylRS) and compared it with those of structure-known PylRSs. Based on the ISO4-G1 PylRS structure, we attempted the site-specific incorporation of Ne-(p-ethynylbenzyloxycarbonyl)-L-lysine (pEtZLys) into proteins, but it was much less efficient than that of TCO*Lys with M. alvus PylRS mutants. Thus, the first-layer mutations (Y125A and M128L) of ISO4-G1 PylRS, with no additional second-layer mutations, increased the protein productivity with pEtZLys up to 578% of that with TCO*Lys, at high enzyme concentrations in the cell-free protein synthesis.