gebhart/patrepeval huggingface dataset:
Student research award in the undergraduate, Master candidate category, or health science degree candidate category, 17th annual meeting of the society for biomaterials, scottsdale, AZ may 1–5,1991. Characterization of the interface in the plasma‐sprayed HA coating/Ti‐6Al‐4V implant system (1991)

The successful use of plasma-sprayed hydroxyapatite (HA) coatings on Ti-alloy implants for implant-to-bone fixation requires strong adherence of the ceramic coating to the underlying metal substrate. In this study, the metal-ceramic interface was evaluated using mechanical, chemical, and structural characterization methods. Evaluations of an HA-coated Ti-6Al-4V implant system using a modified short bar technique for interfacial fracture toughness determination revealed relatively low fracture toughness values. Additionally, conventional tensile bond strength testing indicated much lower values than previously reported. Using high resolution electron spectroscopic imaging, evidence of chemical bonding was revealed at the plasma-sprayed HA/Ti-6Al-4V interface, though bonding was primarily due to mechanical interlock at the interface. This study illustrates the benefits of, and the need for, a multilevel approach to evaluate and improve these plasma-sprayed ceramic-metal substrate interfaces.
Cryptochrome 1 interacts with PIF4 to regulate high temperature-mediated hypocotyl elongation in response to blue light (2015)

Cryptochrome 1 (CRY1) is a blue light receptor that mediates primarily blue-light inhibition of hypocotyl elongation. Very little is known of the mechanisms by which CRY1 affects growth. Blue light and temperature are two key environmental signals that profoundly affect plant growth and development, but how these two abiotic factors integrate remains largely unknown. Here, we show that blue light represses high temperature-mediated hypocotyl elongation via CRY1. Furthermore, CRY1 interacts directly with PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) in a blue light-dependent manner to repress the transcription activity of PIF4. CRY1 represses auxin biosynthesis in response to elevated temperature through PIF4. Our results indicate that CRY1 signal by modulating PIF4 activity, and that multiple plant photoreceptors [CRY1 and PHYTOCHROME B (PHYB)] and ambient temperature can mediate morphological responses through the same signaling component-PIF4.
Genome wide expression profiling identifies specific deregulated pathways in meningioma (2008)

Genome-wide expression signatures improve the understanding of tumor biology. We performed expression profiling of 24 meningioma including 8 of each WHO grade and 2 dura controls analyzing 55.000 transcripts including 18.300 known genes. We compared expression in meningioma vs. dura, expression of low grade (WHO I) vs. higher-grade (WHO II and WHO III) tumors and expression of meningothelial and syncytial meningioma vs. fibroblastic meningioma. Overall expression was significantly decreased in meningioma compared to dura and in meningothelial and syncytial compared to fibroblastic meningioma. Gene expression was exemplarily confirmed by immunohistochemistry using independent samples. Applying our statistical gene set analysis toolkit "GeneTrail", we identified significantly deregulated biochemical pathways using Kyoto encyclopedia of genes and genomes and Transpath databases. Kyoto encyclopedia of genes and genomes pathways with decreased expression in meningioma included cell adhesion molecules (p<0.0001) and cytokine-cytokine receptor interactions (p<0.0001). Pathways with increased expression included several metabolic pathways. Extended expression profiling by a novel statistical gene set enrichment identified pathways that have previously not been associated with meningioma.
Machine-guided cell-fate engineering (2022)

A bstract The creation of induced pluripotent stem cells (iPSCs) has enabled scientists to explore the derivation of many types of cells. While there are diverse general approaches for cell-fate engineering, one of the fastest and most efficient approaches is transcription factor (TF) over-expression. However, finding the right combination of TFs to over-express to differentiate iPSCs directly into other cell-types is a difficult task. Here were describe a machine-learning (ML) pipeline, called CellCartographer , for using chromatin accessibility data to design multiplex TF pooled-screens for cell type conversions. We validate this method by differentiating iPSCs into twelve diverse cell types at low efficiency in preliminary screens and then iteratively refining our TF combinations to achieve high efficiency differentiation for six of these cell types in &lt; 6 days. Finally, we functionally characterized engineered iPSC-derived cytotoxic T-cells (iCytoT), regulatory T-cells (iTReg), type II astrocytes (iAstII), and hepatocytes (iHep) to validate functionally accurate differentiation.
Distributed Accelerated Proximal Coordinate Gradient Methods (2017)

We develop a general accelerated proximal coordinate descent algorithm in distributed settings (Dis- APCG) for the optimization problem that minimizes the sum of two convex functions: the first part f is smooth with a gradient oracle, and the other one Ψ is separable with respect to blocks of coordinate and has a simple known structure (e.g., L1 norm). Our algorithm gets new accelerated convergence rate in the case that f is strongly con- vex by making use of modern parallel structures, and includes previous non-strongly case as a special case. We further present efficient implementations to avoid full-dimensional operations in each step, significantly reducing the computation cost. Experiments on the regularized empirical risk minimization problem demonstrate the effectiveness of our algorithm and match our theoretical findings.
Materials and Processes for Emerging Memories (2018)

Resistive memories such as STT-MRAM, RERAM and PCRAM use many elements, alloys and compounds that are not used in traditional semiconductor memory and even logic devices. Even newer FERAM materials based on doped HfOx, require optimizing crystal structure to get ferro-electric properties, that are not typically preferred for logic devices. For all these materials, requirements such as precise thickness in sub Angstrom values, precise composition control, surface smoothness and texture control become very critical. In addition, etching of these materials provide new challenges because halogens used in traditional RIE are in many cases too aggressive for some of these materials. The focus of this paper is on status of deposition (PVD and ALD) and etching approaches used for resistive memories. Blanket film data as well as some typical electrical behavior obtained from metalinsulator-metal (MIM) pillar structures is presented.
Constraints on Higgs boson production with large transverse momentum using H→bb¯ decays in the ATLAS detector (2022)

This paper reports constraints on Higgs boson production with transverse momentum above 1 TeV. The analyzed data from proton-proton collisions at a center-of-mass energy of 13 TeV were recorded with the ATLAS detector at the Large Hadron Collider from 2015 to 2018 and correspond to an integrated luminosity of 136 fb -1 . Higgs bosons decaying into b b are reconstructed as single large-radius jets recoiling against a hadronic system and are identified by the experimental signature of two b-hadron decays. The experimental techniques are validated in the same kinematic regime using the Z b b process.
A deterministic compensation method for near surface attenuation and its application (2011)

This paper describes a deterministic method to compensate the attenuation of seismic wave caused by near surface , the compensation includes amplitude, frequency and phase, the compensation has two steps, first, An accurate near surface Q was estimated from uphole survey in double hole, then a wide band , stable inverse Q filter was proposed and applied. The method has been tested in Daqing Oilfield, the result shown that the near surface Q estimation method is accurate and stable, the estimated Q‐factor is reliable, the proposed inverse Q filer was applied to 3D seismic data, after inverse Q filter, the attenuated high frequency by near surface has been recovered reasonably ,the resolution of seismic data was enhanced ,signal to noise ratio was not decreased. Compared the result with OMEGA processing system , the proposed inverse Q filter has the more widen and flatten spectrum ,means the result has higher resolution.
Auto-Personalization: Theory, Practice and Cross-Platform Implementation (2012)

In an increasing digital society, access to information and communication technologies (ICT) is no longer just helpful but has become a necessity. However, the human interfaces appearing on these ICT (and increasingly, even common household products) are beyond of the abilities of many people with disability, digital literacy, or aging related limitations. Access to these ICT is essential to these individuals yet it is not possible to create an interface that is usable by all. This paper introduces a new approach to auto-personalization that is based on the development of the Global Public Inclusive Infrastructure (GPII). The GPII is a new international collaborative effort between users, developers and industry to build a sustainable infrastructure to make access to all digital technologies technically and economically possible, including access by users who are unable to use or understand today’s technologies. Based on a one-size-fits-one approach, the GPII uses auto-adapting mainstream interfaces, and ubiquitous access to assistive technologies when mainstream interfaces cannot adapt enough, to provide each user with the interface they need. The GPII has three main components: a mechanism to allow individuals to easily discover which interface variations they need and then store it in a secure way on a token or in the cloud; a mechanism to allow them to use these stored needs and preferences to automatically adapt the interfaces on the digital technologies they encounter, anywhere and anytime; and a resource for developers (mainstream and assistive technology) providing the information and tools required to develop, disseminate, and support new access solutions more simply, more quickly, and at lower cost.
Scanning Tunneling Spectroscopy on a Disordered Superconductor (2006)

Thin disordered TiN films display a multiple reentrant superconductor‐insulator transition. By combining very low temperature scanning tunneling microscopy and spectroscopy on TiN films we have observed a non uniform state made of superconducting and normal areas. These inhomogeneities can be related to fluctuations driven quantum superconductor‐metal transition models recently developed. When the disorder of the film is increased or its thickness reduced, electronic interactions begin to take over and the LDOS develops a zero bias anomaly (ZBA). We observed smooth spatial transitions between areas displaying a superconducting LDOS and other ones with a ZBA in the excitation spectrum.
ChemInform Abstract: Adenosine Deaminase Inhibitors: Synthesis, Diastereoisomeric Resolution and Biological Activity of 1‐(2‐Hydroxy‐3‐nonyl)‐1,2,4‐triazole‐3‐carboxamide. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
ORA1, a Zebrafish Olfactory Receptor Ancestral to All Mammalian V1R Genes, Recognizes 4-Hydroxyphenylacetic Acid, a Putative Reproductive Pheromone (2014)

The teleost v1r-related ora genes are a small, highly conserved olfactory receptor gene family of only six genes, whose direct orthologues can be identified in lineages as far as that of cartilaginous fish. However, no ligands for fish olfactory receptor class A related genes (ORA) had been uncovered so far. Here we have deorphanized the ORA1 receptor using heterologous expression and calcium imaging. We report that zebrafish ORA1 recognizes with high specificity and sensitivity 4-hydroxyphenylacetic acid. The carboxyl group of this compound is required in a particular distance from the aromatic ring, whereas the hydroxyl group in the para-position is not essential, but strongly enhances the binding efficacy. Low concentrations of 4-hydroxyphenylacetic acid elicit increases in oviposition frequency in zebrafish mating pairs. This effect is abolished by naris closure. We hypothesize that 4-hydroxyphenylacetic acid might function as a pheromone for reproductive behavior in zebrafish. ORA1 is ancestral to mammalian V1Rs, and its putative function as pheromone receptor is reminiscent of the role of several mammalian V1Rs as pheromone receptors.
Differential expression of P2X/P2Y genes in conventional swine tissues (2007)

The aim of this study was to address the differential expression of purinergic receptor encoding gene and their bioactivity profiles in tissues of neonatal pigs. Neonatal piglets of either sex on day 1 and 5 were sacrificed. Dissected organs were used for molecular analysis of gene and protein for purinergic receptors. In addition, functional analysis of P2X/P2Y receptor by pharmacophysiological skill in swine renal artery was performed. As results, Differences exist in specific P2X/P2Y gene expression between 1 day‐ and 5 day‐old neonatal pig tissues of either sex, especially brain tissue. No significant differences of P2X/P2Y protein expression in brain, heart, kidney under with/without ATP, a P2 receptor agonist were observed. In functional analysis of P2Y receptor for vascular relaxation, 2 msATP, a strong agonist of P2Y receptor, induced relaxation of NA‐precontracted renal artery in a dose‐dependent manner. Vascular relaxative effect of ATP, 2 msATP, agonists of P2Y receptor, abolished by treatment of reactive blue 2 (RB‐2), a putative P2Y‐receptor antagonist. These findings reveal a tissue‐specific differential gene expression of purinergic receptors that were modulated by developmental stages in swine. Finally, the relationship between molecular and functional characteristic of P2X/P2Y during developmental stage in conventional pig should be applied to clinical fields. This work was supported by the Research Project on the Production of Bio‐organs (No. 200508010801), Ministry of Agriculture and Forestry, Republic of Korea.
Soft x-ray images of the laser entrance hole of ignition hohlraums (2012)

Hohlraums are employed at the national ignition facility to convert laser energy into a thermal x-radiation drive, which implodes a fusion capsule, thus compressing the fuel. The x-radiation drive is measured with a low spectral resolution, time-resolved x-ray spectrometer, which views the region around the hohlraum's laser entrance hole. This measurement has no spatial resolution. To convert this to the drive inside the hohlraum, the size of the hohlraum's opening ("clear aperture") and fraction of the measured x-radiation, which comes from this opening, must be known. The size of the clear aperture is measured with the time integrated static x-ray imager (SXI). A soft x-ray imaging channel has been added to the SXI to measure the fraction of x-radiation emitted from inside the clear aperture. A multilayer mirror plus filter selects an x-ray band centered at 870 eV, near the peak of the x-ray spectrum of a 300 eV blackbody. Results from this channel and corrections to the x-radiation drive are discussed.
NMR Studies of Protein–Ligand Interactions (2011)

Nuclear magnetic resonance (NMR) has evolved into a powerful tool for characterizing protein-ligand interactions in solution under near physiological conditions. It is now frequently harnessed to assess the affinity and specificity of interactions; to identify binding epitopes on proteins and ligands; and to characterize the structural rearrangements induced by binding.The first section of this chapter provides a general overview of the NMR study of protein-ligand interactions. The section is divided according to two main categories of experiments: those based on observing protein signals and those based on observing ligand signals. The next section explains two case studies performed in the authors' laboratory. The first of these deals with the interaction between vascular endothelial growth factor and a peptidic ligand, and includes a detailed protocol of chemical shift perturbation experiments. The second one reports on the interaction between prolyl oligopeptidase and a small molecule as monitored by ligand saturation transfer difference (STD), and illustrates how NMR can be used to confirm binding and to identify the binding epitope of a ligand.
A sustainable wood biorefinery for low–carbon footprint chemicals production (2020)

The profitability and sustainability of future biorefineries are dependent on efficient feedstock use. Therefore, it is essential to valorize lignin when using wood. We have developed an integrated biorefinery that converts 78 weight % (wt %) of birch into xylochemicals. Reductive catalytic fractionation of the wood produces a carbohydrate pulp amenable to bioethanol production and a lignin oil. After extraction of the lignin oil, the crude, unseparated mixture of phenolic monomers is catalytically funneled into 20 wt % of phenol and 9 wt % of propylene (on the basis of lignin weight) by gas-phase hydroprocessing and dealkylation; the residual phenolic oligomers (30 wt %) are used in printing ink as replacements for controversial <i>para</i>-nonylphenol. A techno-economic analysis predicts an economically competitive production process, and a life-cycle assessment estimates a lower carbon dioxide footprint relative to that of fossil-based production.
Mycobacterium tuberculosis HN878 Infection Induces Human-Like B-Cell Follicles in Mice (2019)

Specific spatial organization of granulomas within the lungs is crucial for protective anti-tuberculosis (TB) immune responses. However, only large animal models such as macaques are thought to reproduce the morphological hallmarks of human TB granulomas. In this study, we show that infection of mice with clinical "hypervirulent" Mycobacterium tuberculosis (Mtb) HN878 induces human-like granulomas composed of bacilli-loaded macrophages surrounded by lymphocytes and organized localization of germinal centers and B-cell follicles. Infection with laboratory-adapted Mtb H37Rv resulted in granulomas that are characterized by unorganized clusters of macrophages scattered between lymphocytes. An in-depth exploration of the functions of B cells within these follicles suggested diverse roles and the activation of signaling pathways associated with antigen presentation and immune cell recruitment. These findings support the use of clinical Mtb HN878 strain for infection in mice as an appropriate model to study immune parameters associated with human TB granulomas.
Passivity-based PI control of three-phase switched power converters (2005)

This paper addresses the practically important question of when a nonlinear system can be asymptotically stabilized with a linear PI control, and show that it is possible if the system can be passified with constant control actions. This result is used to propose a constructive methodology to design PI schemes for switched power converters, which are viewed from a novel perspective: with the switches acting as effective "port variables" that establishes a passive mapping with a suitably defined outputs. Detailed calculations are given for the three-phase rectifier and experimental results that compare the performance of the proposed PI with other linear and nonlinear designs.
Sulfamate Acetamides as Self-Immolative Electrophiles for Covalent Ligand-Directed Release Chemistry (2023)

Electrophiles for covalent inhibitors that are suitable for in vivo administration are rare. While acrylamides are prevalent in FDA-approved covalent drugs, chloroacetamides are considered too reactive for such purposes. We report sulfamate-based electrophiles that maintain chloroacetamide-like geometry with tunable reactivity. In the context of the BTK inhibitor ibrutinib, sulfamate analogues showed low reactivity with comparable potency in protein labeling, in vitro, and cellular kinase activity assays and were effective in a mouse model of CLL. In a second example, we converted a chloroacetamide Pin1 inhibitor to a potent and selective sulfamate acetamide with improved buffer stability. Finally, we show that sulfamate acetamides can be used for covalent ligand-directed release (CoLDR) chemistry, both for the generation of "turn-on" probes as well as for traceless ligand-directed site-specific labeling of proteins. Taken together, this chemistry represents a promising addition to the list of electrophiles suitable for in vivo covalent targeting.
Li Metal‐Free Rechargeable LiMn2 O 4 / Carbon Cells: Their Understanding and Optimization (1992)

So‐called "rocking‐chair" rechargeable batteries that use lithium intercalation compounds for the positive and negative electrodes should be safer than batteries that contain free‐lithium metal. Such a cell, using the spinel as the positive electrode and carbon as the negative electrode, was optimized as a function of various operating parameters. These cells reversibly insert 0.32 Li atoms per Mn at an average output voltage of 3.7 V, yielding an effective specific energy of 250 mWh/g of electrode materials (3 times that of Ni‐Cd). They can sustain high current rates similar to Ni‐Cd batteries, and can be discharged to 0 V without any degradation of their operating conditions. By systematically studying the stability of several electrolyte systems, we were able to minimize electrolyte decomposition (by controlling drastically the charge cut‐off voltage) so that these cells show a promising cycle life even at 55°C while maintaining 75% of their initial capacity.
Reversible thermal gelation of soft semi‐crystalline polyethylene microparticles with surface interactions in squalane (2007)

Abstract The effect of temperature on the steady‐shear viscosity of a soft semi‐crystalline crosslinked‐polyethylene microparticle suspension in squalane was studied using rotational rheometry. The results show a sharp increase in the viscosity of the system occurring at about 86°C. The magnitude of this spike is dependent on the concentration of the suspension and is reproducible over multiple heating and cooling cycles. This phenomenon has been attributed to the melting of the crystalline regions within the particles, causing them to swell by soaking up squalane. The Mooney equation was used to model the viscosity data based on swelling data obtained from separate experiments. The results showed that the model is inadequate for describing the observed phenomenon, suggesting the possibility of additional interactions existing among the particles. POLYM. ENG. SCI., 2008. © 2007 Society of Plastics Engineers