gebhart/patrepeval huggingface dataset:
Aqueous Phase Synthesized CdSe Magic-Sized Clusters: Solution Composition Dependence of Adsorption Layer Structure (2012)

We report dispersion solution composition dependence of the adsorption layer structure and the physical and optical properties of aqueous phase-synthesized semiconductor nanoparticles (NPs). We synthesized cysteine (Cys)-capped CdSe NPs with well-defined core structures, dispersed them in a series of aqueous solutions with different compositions, and then investigated their adsorption layer structure and physical and optical properties. Each CdSe NP consisted of a (CdSe)33 or (CdSe)34 magic-sized cluster (d - 1.45 nm) core, a ligand-Cys shell, and an adsorption layer. The dispersion solution composition strongly affected the adsorption layer structure of the CdSe NPs. The solution with a composition close to that of the as-prepared solution stabilized the physical and optical properties of the NPs. The solution with a composition different from that of the as-prepared solution, however, resulted in large changes in their adsorption layer structure and thus their physical and optical properties. The solution composed of neutral or weakly charged Cys and Cd-Cys complexes led to the adsorption layer with low charge density and that destabilized the NPs. The solution containing only neutral or weakly charged forms of Cys, without Cd-Cys complexes, was favorable to the formation of a thick adsorption layer with low charge density and that destabilized the NPs. The amount of adsorbed Cys in the adsorption layer depended on the dispersion solution composition. However, the amount of adsorbed Cd-Cys complexes in the adsorption layer was almost constant regardless of the dispersion solution composition.
Growth hormone promotes skeletal muscle cell fusion independent of insulin-like growth factor 1 up-regulation (2006)

Growth hormone (GH) participates in the postnatal regulation of skeletal muscle growth, although the mechanism of action is unclear. Here we show that the mass of skeletal muscles lacking GH receptors is reduced because of a decrease in myofiber size with normal myofiber number. GH signaling controls the size of the differentiated myotubes in a cell-autonomous manner while having no effect on size, proliferation, and differentiation of the myoblast precursor cells. The GH hypertrophic action leads to an increased myonuclear number, indicating that GH facilitates fusion of myoblasts with nascent myotubes. NFATc2, a transcription factor regulating this phase of fusion, is required for GH action because GH is unable to induce hypertrophy of NFATc2-/- myotubes. Finally, we provide three lines of evidence suggesting that GH facilitates cell fusion independent of insulin-like growth factor 1 (IGF-1) up-regulation. First, GH does not regulate IGF-1 expression in myotubes; second, GH action is not mediated by a secreted factor in conditioned medium; third, GH and IGF-1 hypertrophic effects are additive and rely on different signaling pathways. Taken together, these data unravel a specific function of GH in the control of cell fusion, an essential process for muscle growth.
Suboptimality of Nonlocal Means for Images with Sharp Edges (2011)

We conduct an asymptotic risk analysis of the nonlocal means image denoising algorithm for the Horizon class of images that are piecewise constant with a sharp edge discontinuity. We prove that the mean square risk of an optimally tuned nonlocal means algorithm decays according to $n^{-1}\log^{1/2+ε} n$, for an $n$-pixel image with $ε&gt;0$. This decay rate is an improvement over some of the predecessors of this algorithm, including the linear convolution filter, median filter, and the SUSAN filter, each of which provides a rate of only $n^{-2/3}$. It is also within a logarithmic factor from optimally tuned wavelet thresholding. However, it is still substantially lower than the the optimal minimax rate of $n^{-4/3}$.
Towards A Swarm of Agile Micro Quadrotors (2012)

We describe a prototype 73 gram, 21 cm diameter micro quadrotor with onboard attitude estimation and control that operates autonomously with an external localization system. We argue that the reduction in size leads to agility and the ability to operate in tight formations and provide experimental arguments in support of this claim. The robot is shown to be capable of 1850 /sec roll and pitch, performs a 360 flip in 0.4 seconds and exhibits a lateral step response of 1 body length in 1 second. We describe the architecture and algorithms to coordinate a team of quadrotors, organize them into groups and fly through known three-dimensional environments. We provide experimental results for a team of 20 micro quadrotors.
Localization of a novel septin protein, hCDCrel-1, in neurons of human brain (1998)

Synaptic function is critical for cell-cell communication and the characterization of proteins that function during vesicle formation, transport and fusion events will yield further insight into the mechanisms of synaptic transmission. We have cloned and characterized a gene product expressed in human brain called hCDCrel-1. This protein is a new member of the septin family of gene products that functions during cytokinesis in lower eukaryotes. In this study we characterize the expression of the hCDCrel-1 gene and localize the hCDCrel-1 protein to neurons in adult human brain. hCDCrel-1 co-purifies with SNAP-25 and synaptophysin marked synaptosomes, suggesting a novel function for this gene family in the brain. Our data indicate that members of the septin family of proteins may function in synaptic vesicle transport, fusion or recycling events in the human brain.
CD20 and CD37 antibodies synergize to activate complement by Fc-mediated clustering (2019)

CD20 monoclonal antibody therapies have significantly improved the outlook for patients with B-cell malignancies. However, many patients acquire resistance, demonstrating the need for new and improved drugs. We previously demonstrated that the natural process of antibody hexamer formation on targeted cells allows for optimal induction of complement-dependent cytotoxicity. Complement-dependent cytotoxicity can be potentiated by introducing a single point mutation such as E430G in the IgG Fc domain that enhances intermolecular Fc-Fc interactions between cell-bound IgG molecules, thereby facilitating IgG hexamer formation. Antibodies specific for CD37, a target that is abundantly expressed on healthy and malignant B cells, are generally poor inducers of complement-dependent cytotoxicity. Here we demonstrate that introduction of the hexamerization-enhancing mutation E430G in CD37-specific antibodies facilitates highly potent complement-dependent cytotoxicity in chronic lymphocytic leukemia cells <i>ex vivo</i> Strikingly, we observed that combinations of hexamerization-enhanced CD20 and CD37 antibodies cooperated in C1q binding and induced superior and synergistic complement-dependent cytotoxicity in patient-derived cancer cells compared to the single agents. Furthermore, CD20 and CD37 antibodies colocalized on the cell membrane, an effect that was potentiated by the hexamerization-enhancing mutation. Moreover, upon cell surface binding, CD20 and CD37 antibodies were shown to form mixed hexameric antibody complexes consisting of both antibodies each bound to their own cognate target, so-called hetero-hexamers. These findings provide novel insights into the mechanisms of synergy in antibody-mediated complement-dependent cytotoxicity and provide a rationale to explore Fc-engineering and antibody hetero-hexamerization as a tool to enhance the cooperativity and therapeutic efficacy of antibody combinations.
A Highly Efficient Recombinant Laccase from the Yeast Yarrowia lipolytica and Its Application in the Hydrolysis of Biomass (2015)

A modified thermal asymmetric interlaced polymerase chain reaction was performed to obtain the first yeast laccase gene (YlLac) from the isolated yeast Yarrowia lipolytica. The 1557-bp full-length cDNA of YlLac encoded a mature laccase protein containing 519 amino acids preceded by a signal peptide of 19 amino acids, and the YlLac gene was expressed in the yeast Pichia pastoris. YlLac is a monomeric glycoprotein with a molecular mass of ~55 kDa as determined by polyacrylamide-gel electrophoresis. It showed a higher catalytic efficiency towards 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (kcat/Km = 17.5 s(-1) μM(-1)) and 2,6-dimethoxyphenol (kcat/Km = 16.1 s(-1) μM(-1)) than other reported laccases. The standard redox potential of the T1 site of the enzyme was found to be 772 mV. The highest catalytic efficiency of the yeast recombinant laccase, YlLac, makes it a good candidate for industrial applications: it removes phenolic compounds in acid-pretreated woody biomass (Populus balsamifera) and enhanced saccharification.
Serine phosphorylation of NPM-ALK, which is dependent on the auto-activation of the kinase activation loop, contributes to its oncogenic potential (2010)

It is well established that the tumorigenic potential of nucleophosmin (NPM)-anaplastic lymphoma kinase (ALK), an oncogenic tyrosine kinase, is dependent on its tyrosine phosphorylation. Using tandem affinity purification-mass spectrometry, we found evidence of phosphorylation of three serine residues of NPM-ALK (Serine¹³⁵, Serine¹⁶⁴ and Serine⁴⁹⁷) ectopically expressed in GP293 cells. Using a specific anti-phosphoserine antibody and immunoprecipitation, we confirmed the presence of serine phosphorylation of NPM-ALK in all three NPM-ALK-expressing cell lines examined. Similar to the tyrosine phosphorylation, phosphorylation of these serine residues was dependent on the activation status of the kinase activation loop of ALK. All of these three serine residues are biologically important as mutation of any one of these residues resulted in a significant reduction in the tumorigenicity of NPM-ALK (assessed by cell viability and clonogenic assay), which correlated with a substantial reduction in the phosphorylation of extracellular signal-regulated kinase 1/2, c-jun N-terminal kinase and signal transducer and activator of transcription 6. Serine phosphorylation of NPM-ALK appears to be regulated by multiple serine kinases since it was markedly reduced by pharmacologic inhibitors for glycogen synthase kinase-3, casein kinase I or mitogen-activated protein kinases. In summary, our study is the first to identify serine phosphorylation of NPM-ALK and to provide evidence that it enhances the tumorigenic potential of this oncogenic protein.
Breaking the Softmax Bottleneck: A High-Rank RNN Language Model (2017)

We formulate language modeling as a matrix factorization problem, and show that the expressiveness of Softmax-based models (including the majority of neural language models) is limited by a Softmax bottleneck. Given that natural language is highly context-dependent, this further implies that in practice Softmax with distributed word embeddings does not have enough capacity to model natural language. We propose a simple and effective method to address this issue, and improve the state-of-the-art perplexities on Penn Treebank and WikiText-2 to 47.69 and 40.68 respectively. The proposed method also excels on the large-scale 1B Word dataset, outperforming the baseline by over 5.6 points in perplexity.
Fabrication of Hierarchical Zeolitic Material from Zeolite Nanoprecursors and Macromolecular Template (2005)

Abstract Hierarchical zeolitic material possessing three generations of micro-, meso-, and macroporosities was fabricated under controlled steaming at 145 °C through a dual-template approach using tetrapropylammonium hydroxide (TPAOH) and poly(methyl methacrylate) (PMMA) latex particles as micropore and macropore templates, respectively.
Assessment of extracellular glucose distribution and glucose transport activity in conscious rats (1995)

The effects of insulin on extracellular glucose distribution and cellular glucose transport activity were studied by simultaneously analyzing the plasma kinetics of L-[1-14C]glucose and 3-O-[3H]methylglucose after an intravenous injection during saline or insulin infusion (euglycemic glucose clamp) in conscious rats (n = 7 for each). The time profiles of plasma L-glucose were almost superimposable in the two protocols, and compartmental analysis showed that neither distribution volumes nor distribution rate constants were affected with insulin (P > 0.05 for all), suggesting that glucose distribution within the extracellular space was not influenced with insulin. In contrast, the time profile of plasma 3-O-methylglucose (3-MG) was markedly altered with insulin; the initial decrease was much faster during insulin infusion than during saline infusion, indicating stimulation of 3-MG transport into intracellular spaces with insulin. The 3-MG data were analyzed using a comprehensive model separately describing extracellular distribution and cellular transport of 3-MG by incorporating information on extracellular distribution kinetics obtained from L-glucose data. The combined L-glucose and 3-MG kinetic analysis precisely estimated insulin's effect in vivo to stimulate glucose transport into and out of intracellular spaces. We conclude that 1) insulin does not affect extracellular glucose distribution kinetics or volumes in conscious rats and 2) insulin's effects on cellular glucose transport in vivo can be assessed by simultaneous analysis of plasma L-glucose and 3-MG kinetics.
A CMOS-VLSI rate conversion digital filter for digital audio signal processing (2005)

This paper describes CMOS-VLSI architecture for a rate conversion digital filter which interpolates an input discrete-time audio signal at the twice times higher sampling rate. In the proposed architecture, two discrete-time audio signals with 16-bit word length are multiplexed into a serial bit stream and are simultaneously interpolated through parallel table look up array multiplications. Based on the architecture study, the VLSI interpolator which contains 34,000 transistors has been fabricated with 3 µm CMOS technologies. Its power consumption is less than 100 mW and the maximum input sampling rate is 50 kHz. The interpolator quality is specified in terms of in-band amplitude ripple and out-band attenuation each of which is ± 0.13 dB or 80 dB, respectively.
High aspect ratio nano-structures (HARNS) for photonic mems based on vertical DBR architecture (2005)

High aspect ratio nano-structures (HARNS), having an aspect ratio of up to 107, were fabricated by DRIE (deep reactive ion etching). Sidewall surface roughness was reduced to a level less than 20 nm peak-to-valley. These technological advances are applied to photonic MEMS based on in-plane, free-space propagation of light. As an illustration, a Fabry-Perot cavity is presented. It uses vertical distributed Bragg reflectors (DBRs), which consist of thin silicon walls separated by small air gaps, the widths being an even multiple of quarter wavelengths of light in silicon and in air, respectively.
Analysis of Decision-Feedback Based Broadband OFDM Systems (2006)

In wireless communications, about 25% of the bandwidth is dedicated to training symbols for channel estimation. By using a semi-blind approach, the training sequence length can be reduced while improving performance. The principle is as follows: the detected symbols (hard decision) are fed back to the channel estimator in order to re-estimate the channel more accurately. However, semi-blind approach can significantly deteriorate the performance if the bit error rate is high. In this paper, we propose to determine analytically the minimum signal to noise ratio (SNR) from which a semi-blind method starts to outperform a training sequence based only system
P‐33: Cu‐Mn Electrodes for a‐Si TFT and Its Electrical Characteristics (2010)

Abstract Cu‐Mn alloy was used for electrode materials for amorphous Si TFT. The gate electrode showed a good adhesion to glass and low resistivity. The source/drain electrodes showed a good diffusion barrier property, Ohmic contact, and a low contact resistivity. TFT structure showed the ON/OFF ratio of better than 10 6 .
High-throughput experimentation based kinetic modeling of selective hydrodesulfurization of gasoline model molecules catalyzed by CoMoS/Al2O3 (2023)

The selective hydrodesulfurization (HDS) of fluidized catalytic cracking gasoline still represents a challenging step to minimize hydrogen overconsumption and maintain high octane numbers.
Evidence for differential viral oncolytic efficacy in an in vitro model of epithelial ovarian cancer metastasis (2015)

Epithelial ovarian cancer is unique among most carcinomas in that metastasis occurs by direct dissemination of malignant cells traversing throughout the intraperitoneal fluid. Accordingly, we test new therapeutic strategies using an in vitro three-dimensional spheroid suspension culture model that mimics key steps of this metastatic process. In the present study, we sought to uncover the differential oncolytic efficacy among three different viruses-Myxoma virus, double-deleted vaccinia virus, and Maraba virus-using three ovarian cancer cell lines in our metastasis model system. Herein, we demonstrate that Maraba virus effectively infects, replicates, and kills epithelial ovarian cancer (EOC) cells in proliferating adherent cells and with slightly slower kinetics in tumor spheroids. Myxoma virus and vaccinia viruses infect and kill adherent cells to a much lesser extent than Maraba virus, and their oncolytic potential is almost completely attenuated in spheroids. Myxoma virus and vaccinia are able to infect and spread throughout spheroids, but are blocked in the final stages of the lytic cycle, and oncolytic-mediated cell killing is reactivated upon spheroid reattachment. Alternatively, Maraba virus has a remarkably reduced ability to initially enter spheroid cells, yet rapidly infects and spreads throughout spheroids generating significant cell killing effects. We show that low-density lipoprotein receptor expression in ovarian cancer spheroids is reduced and this controls efficient Maraba virus binding and entry into infected cells. Taken together, these results are the first to implicate the potential impact of differential viral oncolytic properties at key steps of ovarian cancer metastasis.
Surgical Versus Nonsurgical Management of Rotator Cuff Tears (2019)

Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Induction of heat-stable enterotoxin receptor activity by a human Alu repeat (1994)

The heat-stable enterotoxins (ST) elaborated by enterotoxigenic Escherichia coli are a family of small cysteine-rich peptides that bind to specific epithelial receptors in the mammalian intestine, causing a secretory diarrhea. The expression of ST receptors is tightly regulated; they are found primarily in intestine, and their expression is developmentally modulated. One receptor for ST has been cloned, and its cDNA encodes a approximately 120-kDa particulate guanylyl cyclase (guanylyl cyclase-C). Recent studies suggest that there are additional ST receptors that are not homologous to guanylyl cyclase-C. We used an expression cloning strategy to identify intestinal mRNAs that lead to expression of ST receptor activity in transfected cells. Using an ST-specific affinity panning system, we identified a novel 1891-base pair cDNA that does not encode a receptor protein, but instead, consists primarily of untranslated sequence. This cDNA induced receptor activity in both COS and 293 embryonic kidney cells. Northern analysis of the T84 human intestinal cell line, from which this cDNA was cloned, suggests that it is part of a 7.8-kilobase mRNA transcript. This transcript was also identified in human small intestine and colon, as well as in several extra-intestinal tissues. Functional analysis of subcloned fragments reveals that ST binding activity is induced by a 457-base pair human Alu repetitive sequence within the cDNA and that the phenotype is independent of orientation. These findings suggest that a human Alu element induces expression of a unique ST receptor by a transacting mechanism. An unrelated Alu-rich genomic clone did not confer ST binding, suggesting that there may be structural and functional specificity within individual Alu sequences.
BARReL: Bottleneck Attention for Adversarial Robustness in Vision-Based Reinforcement Learning (2022)

Robustness to adversarial perturbations has been explored in many areas of computer vision. This robustness is particularly relevant in vision-based reinforcement learning, as the actions of autonomous agents might be safety-critic or impactful in the real world. We investigate the susceptibility of vision-based reinforcement learning agents to gradient-based adversarial attacks and evaluate a potential defense. We observe that Bottleneck Attention Modules (BAM) included in CNN architectures can act as potential tools to increase robustness against adversarial attacks. We show how learned attention maps can be used to recover activations of a convolutional layer by restricting the spatial activations to salient regions. Across a number of RL environments, BAM-enhanced architectures show increased robustness during inference. Finally, we discuss potential future research directions.
A role of respiratory infections in exacerbations of asthma (2007)

Nineteen patients aged 18–65 years with moderate and severe exacerbations of atopic asthma were examined for respiratory viruses, Mycoplasma pneumoniae, and Chlamydophila pneumoniae. Interferon system, IL-4 and γ-IFN serum levels were also investigated. Viral infections (RS-virus, adenovirus, influenza types A (H1N1, H3N2) and B viruses, parainfluenza types 1 and 3 viruses) were diagnosed serologically or using PCR with direct detection of viral nucleic acids in 73.6 % of the patients. Diagnostic level of Mycoplasma pneumoniae antigen was found in 78.9 % of the patients, anti-Chlamydophila pneumoniae antibodies were detected in 31.6 %. Leukocyte interferon-producing function was decreased in all the patients.
ChemInform Abstract: STRUCTURE‐ACTIVITY RELATIONSHIPS OF C‐TERMINAL TRI‐ AND TETRAPEPTIDE FRAGMENTS THAT INHIBIT GASTRIN ACTIVITY (1985)

Abstract Tri‐ und Tetrapeptide wie (I) und (II) werden dargestellt und auf Gastiin‐inhibierende Aktivität untersucht; sie sind 20 ‐ 30mal wirksamer als Proglumide und Benzotript.
Nickel-BINAP Catalyzed Enantioselective α-Arylation of α-Substituted γ-Butyrolactones (2002)

A Ni(0)-BINAP system is utilized for the highly enantioselective alpha-arylation of alpha-substituted gamma-butyrolactones with aryl chlorides and bromides. alpha-Quaternization is achieved in moderate to excellent yields. Furthermore, the rate accelerating effect caused by the addition of Zn(II) salts is investigated.