gebhart/patrepeval huggingface dataset:
Spin on glass (SOG) etch-back planarization process: an industrial solution for 0.5-μm CMOS TLM technology (1993)

A SOG/etch-back process has been developed in order to be compatible with a 0.5 micrometers triple level metal technology with plugged vias. Four SOG are compared in terms of planarization level after coating but also after etch-back. The etching process is studied in order to reach the low selectivities required to compensate the microloading effects of patterned wafers. The compromise between high planarization level and low surface roughness is obtained by adjusting selectivity and etching time. Planarization level and complete SOG consumption, required to avoid vias poisoning, can be controlled by measuring TEOS1 consumption after etch-back. Vias and metal yield are measured on different topographies. Results illustrate the planarization efficiency.
Design and fabrication of a polymer gradient-index optical element for a high-performance eyepiece (2013)

A 40-deg full field-of-view high-performance eyepiece design utilizing a polymer spherical gradient-index (GRIN) optical element is presented. In the design process, the GRIN lens material is constrained to current manufacturing capabilities. Several spherical GRIN lens blanks are fabricated from a thermoformable axial GRIN polymethyl methacrylate polystyrene copolymer material. One is diamond turned into a lens for the eyepiece, and the additional blanks are used to characterize the fabrication process. The spherical GRIN profile is evaluated in the original design, and a tolerance analysis is provided.
Abstract 4614: Progesterone receptor and ErbB-2 crosstalk in breast cancer (2010)

Abstract Progesterone receptor (PR) and ErbB-2, a member of the ErbBs family of receptor tyrosine kinases, play key roles in breast cancer development. Here, we identified a new mechanism of PR and ErbB-2 interaction in breast cancer cells. Our findings demonstrated that progestin stimulates the rapid activation of ErbB-2, its nuclear translocation, and a striking nuclear colocalization of ErbB-2 with signal transducer and activator of transcription 3 (Stat3) in human T47D breast cancer cells and C4HD cells, from a murine progestin-dependent mammary tumor. By using quantitative chromatin immunoprecipitation (ChIP) and sequential ChIP, we demonstrated that progestin induces the recruitment of Stat3 and ErbB-2 to Stat3 response elements (GAS sites) in the cyclin D1 promoter, which lacks ErbB-2 response elements (HAS sites). Through a series of experimental approaches including transient transfection with cyclin D1 promoter luciferase constructs and RNA interfering-reconstitution strategies employing functional ErbB-2 and Stat3 mutants, we revealed ErbB-2 role as a transcriptional coactivator of Stat3 in progestin-induced cyclin D1 promoter activation. Inhibition of ErbB-2 nuclear migration by transfection of breast cancer cells with the ErbB-2 nuclear localization domain mutant ErbB-2ΔNLS (Mol Cell Biol, 24: 11005-11018, 2005), which we here found that functions as a dominant negative inhibitor of endogenous ErbB-2 nuclear translocation, resulted in complete abrogation of progestin-induced in vitro and in vivo breast cancer growth. Our findings reveal a novel therapeutic intervention in PR- and ErbB-2- positive breast tumors via the specific blockage of ErbB-2 nuclear translocation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4614.
A New Reagent for Direct Difluoromethylation (2012)

Molecular scaffolds containing alkylfluorine substituents are desired in many areas of chemical research from materials to pharmaceuticals. Herein, we report the invention of a new reagent (Zn(SO(2)CF(2)H)(2), DFMS) for the innate difluoromethylation of organic substrates via a radical process. This mild, operationally simple, chemoselective, and scalable difluoromethylation method is compatible with a range of nitrogen-containing heteroarene substrates of varying complexity as well as select classes of conjugated π-systems and thiols. Regiochemical comparisons suggest that the CF(2)H radical generated from the new reagent possesses nucleophilic character.
HIV‐1 NNRTIs: structural diversity, pharmacophore similarity, and impliations for drug design (2011)

Nonnucleoside reverse transcriptase inhibitors (NNRTIs) nowadays represent very potent and most promising anti-AIDS agents that specifically target the HIV-1 reverse transcriptase (RT). However, the effectiveness of NNRTI drugs can be hampered by rapid emergence of drug-resistant viruses and severe side effects upon long-term use. Therefore, there is an urgent need to develop novel, highly potent NNRTIs with broad spectrum antiviral activity and improved pharmacokinetic properties, and more efficient strategies that facilitate and shorten the drug discovery process would be extremely beneficial. Fortunately, the structural diversity of NNRTIs provided a wide space for novel lead discovery, and the pharmacophore similarity of NNRTIs gave valuable hints for lead discovery and optimization. More importantly, with the continued efforts in the development of computational tools and increased crystallographic information on RT/NNRTI complexes, structure-based approaches using a combination of traditional medicinal chemistry, structural biology, and computational chemistry are being used increasingly in the design of NNRTIs. First, this review covers two decades of research and development for various NNRTI families based on their chemical scaffolds, and then describes the structural similarity of NNRTIs. We have attempted to assemble a comprehensive overview of the general approaches in NNRTI lead discovery and optimization reported in the literature during the last decade. The successful applications of medicinal chemistry strategies, crystallography, and computational tools for designing novel NNRTIs are highlighted. Future directions for research are also outlined.
Large-Scale Synthesis of a Key Catalytic Reagent for Phosphorus Protection in Building Blocks for Isopolar Phosphonate Oligonucleotide Preparation (2000)

A simple procedure for the large-scale synthesis of 4-methoxy-2-pyridinemethanol 1-oxide (5), a key compound in modern triester synthesis of oligonucleotides, employing Büchi R 152 evaporator as a reaction apparatus was elaborated. Two crucial reaction steps, both strongly exothermic, were satisfactorily handled. Our procedure provides a high-purity, light- and heat-stable product in a satisfactory yield.
Polyhydroxyurethane covalent adaptable networks: looking for suitable catalysts (2023)

Various bases (DMAP, DBU, TBD, t -BuOK), acid ( p -TSA), thiourea (TU) and organometallic Lewis acid (DBTDL) were investigated as potential catalysts for the preparation of polyhydroxyurethane covalent adaptable networks.
Kinesin-1 and mitochondrial motility control by discrimination of structurally equivalent but distinct subdomains in Ran-GTP-binding domains of Ran-binding protein 2 (2013)

The pleckstrin homology (PH) domain is a versatile fold that mediates a variety of protein-protein and protein-phosphatidylinositol lipid interactions. The Ran-binding protein 2 (RanBP2) contains four interspersed Ran GTPase-binding domains (RBD(n = 1-4)) with close structural homology to the PH domain of Bruton's tyrosine kinase. The RBD2, kinesin-binding domain (KBD) and RBD3 comprise a tripartite domain (R2KR3) of RanBP2 that causes the unfolding, microtubule binding and biphasic activation of kinesin-1, a crucial anterograde motor of mitochondrial motility. However, the interplay between Ran GTPase and R2KR3 of RanBP2 in kinesin-1 activation and mitochondrial motility is elusive. We use structure-function, biochemical, kinetic and cell-based assays with time-lapse live-cell microscopy of over 260,000 mitochondrial-motility-related events to find mutually exclusive subdomains in RBD2 and RBD3 towards Ran GTPase binding, kinesin-1 activation and mitochondrial motility regulation. The RBD2 and RBD3 exhibit Ran-GTP-independent, subdomain and stereochemical-dependent discrimination on the biphasic kinetics of kinesin-1 activation or regulation of mitochondrial motility. Further, KBD alone and R2KR3 stimulate and suppress, respectively, multiple biophysical parameters of mitochondrial motility. The regulation of the bidirectional transport of mitochondria by either KBD or R2KR3 is highly coordinated, because their kinetic effects are accompanied always by changes in mitochondrial motile events of either transport polarity. These studies uncover novel roles in Ran GTPase-independent subdomains of RBD2 and RBD3, and KBD of RanBP2, that confer antagonizing and multi-modal mechanisms of kinesin-1 activation and regulation of mitochondrial motility. These findings open new venues towards the pharmacological harnessing of cooperative and competitive mechanisms regulating kinesins, RanBP2 or mitochondrial motility in disparate human disorders.
Single Step Isolation and Activation of Primary CD3+ T Lymphocytes Using Alcohol-Dispersed Electrospun Magnetic Nanofibers (2012)

Electrospun polymer nanofibers with entrapped magnetic nanoparticles (magnetic NP–NF) represent a novel scaffold substrate that can be functionalized for single-step isolation and activation of specific lymphocyte subsets. Using a surface-embedded T cell receptor ligand/trigger (anti-CD3 monoclonal antibody), we demonstrate, as proof of principle, the use of magnetic NP–NF to specifically isolate, enrich, and activate CD3+ T cells from a heterogeneous cell mixture, leading to preferential expansion of CD8+CD3+ T cells. The large surface area, adjustable antibody density, and embedded paramagnetic properties of the NP–NF permitted enhanced activation and expansion; its use represents a strategy that is amenable to an efficient selection process for adoptive cellular therapy as well as for the isolation of other cellular subsets for downstream translational applications.
Golden Berry-Derived 4β-hydroxywithanolide E for Selectively Killing Oral Cancer Cells by Generating ROS, DNA Damage, and Apoptotic Pathways (2013)

Together, the findings of this study, particularly the improved understanding of the selective killing mechanisms of 4βHWE, can be used to improve efficiency in killing oral cancer cells during chemoprevention and therapy.
Quinazolin-4-one Derivatives as Selective Histone Deacetylase-6 Inhibitors for the Treatment of Alzheimer’s Disease (2013)

Novel quinazolin-4-one derivatives containing a hydroxamic acid moiety were designed and synthesized. All compounds were subjected to histone deacetylase (HDAC) enzymatic assays to identify selective HDAC6 inhibitors with nanomolar IC50 values. (E)-3-(2-Ethyl-7-fluoro-4-oxo-3-phenethyl-3,4-dihydroquinazolin-6-yl)-N-hydroxyacrylamide, 4b, is the most potent HDAC6 inhibitor (IC50, 8 nM). In vitro, these compounds induced neurite outgrowth accompanied by growth-associated protein 43 expression, and they enhanced the synaptic activities of PC12 and SH-SY5Y neuronal cells without producing toxic or mitogenic effects. Several of the compounds dramatically increased nonhistone protein acetylation, specifically of α-tubulin. Some of the more potent HDAC6 inhibitors decreased zinc-mediated β-amyloid aggregation in vitro. N-Hydroxy-3-(2-methyl-4-oxo-3-phenethyl-3,4-dihydro-quinazolin-7-yl)-acrylamide, 3f, the most promising drug candidate, selectively inhibits HDAC6 (IC50, 29 nM), practically does not affect human ether-a-go-go-related membrane channel activity (IC50 >10 μM) or cytochrome P450 activity (IC50 >6.5 μM) in vitro, and significantly improves learning-based performances of mice with β-amyloid-induced hippocampal lesions.
Estrogen Does Not Induce the Calcium-Dependent Nitric Oxide Synthase in Cultured Human Uterine Endothelial and Myometrial Smooth Muscle Cells (1997)

In many tissues, estrogen-induced vasodilatation is mediated, at least in part, by the release of nitric oxide (NO). We determined whether human myometrial endothelial and smooth muscle cells express estrogen receptors (ERs) and whether endothelial NO synthase (eNOS) expression in these cells was affected by 17beta-estradiol (10[-13]-10[-6]M). ER was strongly expressed in myometrial smooth muscle cells but was absent from endothelial cells. Expression of eNOS mRNA was strong in endothelial cells, but weak in muscle cells. 17beta-estradiol administration for 24 or 72 h failed to increase eNOS in both cell types. Thus, an increase of human uterine blood flow by estrogens appears not to be mediated by stimulation of myometrial eNOS expression.
New word acquisition using subword modeling (2007)

In this paper, we use subword modeling to learn the pronunciations and spellings of new words. The subwords are generated with a context-free grammar, and are intermediate units between phonemes and syllables. We first evaluate the effectiveness of the subword model in automatically generating the spelling and pronunciation of new words. Then the subword model is embedded in a multi-stage recognizer which consists of word, subword, and letter recognizers. In a preliminary set of experiments, the hybrid system outperforms a large-vocabulary isolated word recognizer. The subword model is also used to improve the performance of the letter recognizer by generating a spelling cohort which is used to train a small letter n-gram. The small letter n-gram has a reduced perplexity compared to a much larger n-gram, and can be used by the letter recognizer for the spoken spelling mode. This could translate to an improved letter error rate in future letter recognition experiments. Index Terms: subword modeling, new word acquisition
A phase II clinical study of dendritoma vaccination combined with low dose interleukin-2 in advanced melanoma patients (2007)

3051 Background: The use of the fusion product of dendritic cells (DC) and tumor cells as a tumor vaccine represents one of the most promising approaches for cancer immunotherapy. We have developed a novel technology that instantly isolates the hybrids (Dendritomas) from the fusion mixture of DCs and tumor cells and thereby maintains tumor cellular diversity. Animal studies demonstrated that Dendritomas are superior activators of tumor cell specific antitumor immunity compared to fusion mixtures; and phase I clinical studies in advanced melanoma and renal cell carcinoma patients demonstrated that Dendritomas can be safely administered to cancer patients and are able to stimulate immunological and clinical responses in some of the patients. Methods: In order to determine the efficacy of Dendritoma vaccines, we designed a small phase II clinical trial in which individualized Dendritomas are manufactured from and injected into 15 stage IV melanoma patients. In order to boost the antitumor immune responses, a low dose interleukin-2 regime was followed only after the first Dendritoma vaccine. The patients received various numbers of vaccines (1 to 6) at six-week intervals. Clinical responses defined as complete response (CR), partial response (PR), stable disease (SD), mixed response (MR), progressive disease (PD), and no evidence of disease (NED) are monitored. The survival of the patients are monitored as well. Results: Twelve weeks after the first vaccine, three patients were NED; four patients were SD; two patients were PD/MR; and six patients were PD. At the time of the submission of this abstract, two patients were still NED and the median survival was 684 days with twelve of the fifteen patients (80%) surviving more than 431 days and eleven of fifteen patients (73%) surviving more than 519 days. Seven out of fifteen patients (47%) are still alive. Conclusions: The data from this small phase II study demonstrated that Dendritoma therapy combined with low dose IL-2 or other adjuvants may represent an effective therapy for melanoma patients and/or other cancer patients. No significant financial relationships to disclose.
Combining digital watermarks and collusion secure fingerprints for digital images (2000)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
Age- and Race-Related Differences in Human Scleral Material Properties (2014)

The age- and race-related differences in scleral material properties result in a loss of scleral compliance due to a higher shear stiffness and a lower level of stretch at which the collagen fibrils uncrimp. The loss of compliance should lead to larger high frequency IOP fluctuations and changes in the optic nerve head (ONH) biomechanical response in the elderly and in persons of African ancestry, and may contribute to the higher susceptibility to glaucoma in these at-risk populations.
Low profile wideband embedded dielectric resonator (2007)

A dielectric resonator antenna (DRA) made of high dielectric constant substrate is studied. Embedding a higher dielectric disk inside the substrate disk enhances the bandwidth. A narrow slot excites the DRA. Embedded DRAs of different shapes are considered for wideband applications. An eye-shaped DRA made with a circular dielectric resonator disk embedded in an elliptical-shaped ‘host’ DRA is found to have an impedance bandwidth of 28% with stable broadside patterns.
A Multivariate Analysis of Determinants of Survival for Patients with Squamous Cell Carcinoma of the Head and Neck (1989)

The prognosis for patients with squamous cell carcinoma of the head and neck remains poor, despite refinements in conventional therapy and experimental protocols using alternative treatment modalities. Clinical characteristics reported to influence survival have included age and sex of the patient, the therapy used, location of the primary tumor, and stage at initial presentation. However, such variables are highly correlated, and previous reports have lacked sufficient statistical analysis to assess the independent influence of these competing variables on survival. To better define the principal determinants of survival, we used a Cox multivariate regression analysis of 542 patients with invasive squamous cell carcinoma of the head and neck treated exclusively at our institution from 1962 to 1976. All patients were followed for a minimum of 5 years after diagnosis, with 98% complete follow-up achieved. Stage at initial presentation was the single-most important factor influencing survival for all tumor locations (p less than 0.0001). Advanced age (p = 0.001) and location of the primary tumor in the tonsillar area (p = 0.01) were also independently associated with an inferior survival. The type of therapy used and sex of the patient did not significantly influence survival after controlling for stage. These data emphasize the need for early diagnosis and treatment of squamous cell carcinoma of the head and neck and underscore the limitations of current therapeutic approaches. Future investigations should incorporate multivariate statistical techniques whenever possible, and additional efforts must be directed at basic research into the biology and immunologic characteristics of these tumors in an attempt to identify innovative therapeutic modalities.
Effective SSD caching for high-performance home cloud server (2015)

In this paper, we propose a novel SSD caching scheme and virtual disk image format, named SVD (Sequential Virtual Disk). Our proposed techniques are based on workload characteristics in home cloud server, in which synchronous random writes dominate. Unlike previous studies, we use SSD as a read-write cache in order to effectively mitigate performance degradation of synchronous random writes.
Wnt1 Boosts Fracture Healing by Enhancing Bone Formation in the Fracture Callus (2020)

Despite considerable improvement in fracture care, 5%-10% of all fractures still heal poorly or result in nonunion formation. Therefore, there is an urgent need to identify new molecules that can be used to improve bone fracture healing. One activator of the Wnt-signaling cascade, Wnt1, has recently gained attention for its intense osteoanabolic effect on the intact skeleton. The aim of the present study was to investigate whether Wnt1 might be a promising molecule to accelerate fracture healing both in skeletally healthy and osteoporotic mice that display a diminished healing capacity. Transgenic mice for a temporary induction of Wnt1 specifically in osteoblasts (Wnt1-tg) were subjected to femur osteotomy. Non-ovariectomized and ovariectomized Wnt1-tg mice displayed significantly accelerated fracture healing based on a strong increase in bone formation in the fracture callus. Transcriptome profiling revealed that Hippo/yes1-associated transcriptional regulator (YAP)-signaling and bone morphogenetic protein (BMP) signaling pathways were highly enriched in the fracture callus of Wnt1-tg animals. Immunohistochemical staining confirmed increased activation of YAP1 and expression of BMP2 in osteoblasts in the fracture callus. Therefore, our data indicate that Wnt1 boosts bone formation during fracture healing via YAP/BMP signaling both under healthy and osteoporotic conditions. To further test a potential translational application of Wnt1, we applied recombinant Wnt1 embedded into a collagen gel during critical-size bone-defect repair. Mice treated with Wnt1 displayed increased bone regeneration compared to control mice accompanied by increased YAP1/BMP2 expression in the defect area. These findings are of high clinical relevance because they indicate that Wnt1 could be used as a new therapeutic agent to treat orthopedic complications in the clinic. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
Special issue on Nanomaterials for energy and environmental applications (2016)

Citation: Smagul Karazhanov, Ana Cremades. Special issue on Nanomaterials for energy and environmental applications[J]. AIMS Materials Science, 2016, 3(3): 1125-1125. doi: 10.3934/matersci.2016.3.1125
Partial Disruption of Translational and Posttranslational Machinery Reshapes Growth Rates of Bartonella birtlesii (2013)

Here, we show that specialization in a specific niche could be caused by the disruption of critical genes. Most of these genes were involved in translation, and we show that evolution of obligate parasitism bacteria was specifically associated with disruption of translation system-encoding genes.
Hydrogen Peroxide Versus Hydrogen Generation at Bipolar Pd/Au Nano-catalysts Grown into an Intrinsically Microporous Polyamine (PIM-EA-TB) (2021)

Abstract Binding of PdCl 4 2− into the polymer of intrinsic microporosity PIM-EA-TB (on a Nylon mesh substrate) followed by borohydride reduction leads to uncapped Pd(0) nano-catalysts with typically 3.2 ± 0.2 nm diameter embedded within the microporous polymer host structure. Spontaneous reaction of Pd(0) with formic acid and oxygen is shown to result in the competing formation of (i) hydrogen peroxide (at low formic acid concentration in air; with optimum H 2 O 2 yield at 2 mM HCOOH), (ii) water, or (iii) hydrogen (at higher formic acid concentration or under argon). Next, a spontaneous electroless gold deposition process is employed to attach gold (typically 10- to 35-nm diameter) to the nano-palladium in PIM-EA-TB to give an order of magnitude enhanced production of H 2 O 2 with high yields even at higher HCOOH concentration (suppressing hydrogen evolution). Pd and Au work hand-in-hand as bipolar electrocatalysts. A Clark probe method is developed to assess the catalyst efficiency (based on competing oxygen removal and hydrogen production) and a mass spectrometry method is developed to monitor/optimise the rate of production of hydrogen peroxide. Heterogenised Pd/Au@PIM-EA-TB catalysts are effective and allow easy catalyst recovery and reuse for hydrogen peroxide production. Graphical abstract