gebhart/patrepeval huggingface dataset:
Hydrogel formulation determines cell fate of fetal and adult neural progenitor cells (2013)

Hydrogels provide a unique tool for neural tissue engineering. These materials can be customized for certain functions, i.e. to provide cell/drug delivery or act as a physical scaffold. Unfortunately, hydrogel complexities can negatively impact their biocompatibility, resulting in unintended consequences. These adverse effects may be combated with a better understanding of hydrogel chemical, physical, and mechanical properties, and how these properties affect encapsulated neural cells. We defined the polymerization and degradation rates and compressive moduli of 25 hydrogels formulated from different concentrations of hyaluronic acid (HA) and poly(ethylene glycol) (PEG). Changes in compressive modulus were driven primarily by the HA concentration. The in vitro biocompatibility of fetal-derived (fNPC) and adult-derived (aNPC) neural progenitor cells was dependent on hydrogel formulation. Acute survival of fNPC benefited from hydrogel encapsulation. NPC differentiation was divergent: fNPC differentiated into mostly glial cells, compared with neuronal differentiation of aNPC. Differentiation was influenced in part by the hydrogel mechanical properties. This study indicates that there can be a wide range of HA and PEG hydrogels compatible with NPC. Additionally, this is the first study comparing hydrogel encapsulation of NPC derived from different aged sources, with data suggesting that fNPC and aNPC respond dissimilarly within the same hydrogel formulation.
Investigation of the differences in stability of the OC⋅⋅⋅HF and CO⋅⋅⋅HF complexes (1985)

The structure and energetics of the isomeric H-bonded complexes OC⋅⋅⋅HF and CO⋅⋅⋅HF have been investigated by ab initio molecular orbital theory and by natural bond orbital analysis. Only with the inclusion of electron correlation is a significant preference for the experimentally observed OC⋅⋅⋅HF isomer found. The large effect of correlation upon the relative stability of the two isomers is apparently entirely an electrostatic effect caused by the correlation-induced sign reversal of the dipole moment of CO. Nevertheless, a molecular multipole expansion is found inadequate to account for the principal features of these H-bonded complexes and their relative stability. Contrary to a recent study, we find that ‘‘charge transfer’’ effects are highly significant contributions to the binding in these complexes. The differences in stability of OC⋅⋅⋅HF and CO⋅⋅⋅HF are attributed primarily to differences in the interaction of carbon and oxygen lone pairs of CO donating into the unfilled antibond on HF, i.e., to differences in nC→σHF* and nO→σHF* matrix elements.
Characterizing naturalistic driving patterns for Plug-in Hybrid Electric Vehicle analysis (2009)

While much of the previous research relies on Federal Driving Schedules originally developed for emission certification tests of conventional vehicles, consumer acceptance and market penetration will depend on PHEV performance under realistic driving conditions. Therefore, characterizing the actual driving is essential for PHEV design and control studies, and for establishing realistic forecasts pertaining to vehicle energy consumption and charging requirements. To achieve this goal, we analyze naturalistic driving data generated in Field Operational Tests (FOT) of passenger vehicles in Southeast Michigan. The FOT were originally conceived for evaluating driver interaction with advanced safety systems, but the databases are rich with information pertaining to vehicle energy. After the initial statistical analysis of the vehicle speed histories, the naturalistic driving schedules are used as input to the PHEV computer simulation to predict energy usage as a function of trip length. The highest specific energy, i.e. energy per mile, is critical for battery and motor sizing. As an illustration of the impact of actual driving, the low-energy and high-energy driving patterns would require PHEV20 battery sizes of 6.12 kWh and 13.6 kWh, respectively. This is determined assuming that the minimum state of charge (SOC) is 40%. In addition, the naturalistic driving databases are mined for information about vehicle resting time, i.e. time spent at typical locations during the 24-hour period. The locations include ldquohomerdquo, ldquoworkrdquo, ldquolarge-businessrdquo such as a large retail store, and ldquosmall businessrdquo, such as a gas station, and finally ldquoresidentialrdquo other than home. The characterization of vehicle daily missions supports analysis of charging schedules, as it indicates times spent at given locations as well as the likely battery SOC at the time of arrival.
Factorized Contrastive Learning: Going Beyond Multi-view Redundancy (2023)

In a wide range of multimodal tasks, contrastive learning has become a particularly appealing approach since it can successfully learn representations from abundant unlabeled data with only pairing information (e.g., image-caption or video-audio pairs). Underpinning these approaches is the assumption of multi-view redundancy - that shared information between modalities is necessary and sufficient for downstream tasks. However, in many real-world settings, task-relevant information is also contained in modality-unique regions: information that is only present in one modality but still relevant to the task. How can we learn self-supervised multimodal representations to capture both shared and unique information relevant to downstream tasks? This paper proposes FactorCL, a new multimodal representation learning method to go beyond multi-view redundancy. FactorCL is built from three new contributions: (1) factorizing task-relevant information into shared and unique representations, (2) capturing task-relevant information via maximizing MI lower bounds and removing task-irrelevant information via minimizing MI upper bounds, and (3) multimodal data augmentations to approximate task relevance without labels. On large-scale real-world datasets, FactorCL captures both shared and unique information and achieves state-of-the-art results on six benchmarks
Machine Learning enables Ultra-Compact Integrated Photonics through Silicon-Nanopattern Digital Metamaterials (2020)

In this work, we demonstrate three ultra-compact integrated-photonics devices, which are designed via a machine-learning algorithm coupled with finite-difference time-domain (FDTD) modeling. Through digitizing the design domain into "binary pixels" these digital metamaterials are readily manufacturable as well. By showing a variety of devices (beamsplitters and waveguide bends), we showcase the generality of our approach. With an area footprint smaller than ${λ_0}^2$, our designs are amongst the smallest reported to-date. Our method combines machine learning with digital metamaterials to enable ultra-compact, manufacturable devices, which could power a new "Photonics Moore's Law."
The Role of TLR2 and Bacterial Lipoprotein in Enhancing Airway Inflammation and Immunity (2011)

Non-typeable Haemophilus influenzae (NTHI) colonizes the lower respiratory tract of patients with chronic obstructive pulmonary disease and also causes exacerbations of the disease. The 16-kDa lipoprotein P6 has been widely studied as a potential vaccine antigen due to its highly conserved expression amongst NTHI strains. Although P6 is known to induce potent inflammatory responses, its role in the pathogenesis of NTHI infection in vivo has not been examined. Additionally, the presence of an amino-terminal lipid motif on P6 serves to activate host Toll-like receptor 2 (TLR2) signaling. The role of host TLR2 and NTHI expression of the lipoprotein P6 on the induction of airway inflammation and generation of adaptive immune responses following chronic NTHI stimulation was evaluated with TLR2-deficient mice and a P6-deficient NTHI strain. Absence of either host TLR2 or bacterial P6 resulted in diminished levels of immune cell infiltration within lungs of mice exposed to NTHI. Pro-inflammatory cytokine secretion was also reduced in lungs that did not express TLR2 or were exposed to NTHI devoid of P6. Induction of specific antibodies to P6 was severely limited in TLR2-deficient mice. Although mice exposed to the P6-deficient NTHI strain were capable of generating antibodies to other surface antigens of NTHI, these levels were lower compared to those observed in mice exposed to P6-expressing NTHI. Therefore, cognate interaction between host TLR2 and bacterial P6 serves to enhance lung inflammation and elicit robust adaptive immune responses during NTHI exposure. Strategies to limit NTHI inflammation while simultaneously promoting robust immune responses may benefit from targeting the TLR2:P6 signaling axis.
Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations (2015)

The present work provides a methodology to generate a robust signature using copy number data that can be potentially used to any cancer. Using it, we found new prognostic scores based on tumor DNA that, jointly with clinical information, are able to predict overall survival (OS) in patients with early-stage ADC and SCC.
Catalytic Microcontact Printing on Chemically Functionalized H-Terminated Silicon (2009)

We report a novel inkless soft lithographic fabrication protocol that permits uniform parallel patterning of hydrogen-terminated silicon surfaces using catalytic elastomeric stamps. Pattern transfer is achieved catalytically via reaction between sulfonic acid moieties covalently bound to an elastomeric stamp and a Boc-functionalized SAM grafted to passivated silicon. The approach represents the first example of a soft lithographic printing technique that creates patterns of chemically distinctive SAMs on oxide-free silicon substrates.
The Use of Carboranes in Electrolyte Design and Ligand Development (2018)

The discovery of polyhedral boranes in the early 1900âs by Alfred Stock and coworkers opened the door to an entirely new realm of structural chemistry. Boronâs rather unique property of catenation, the ability to build molecules of unlimited size by covalently bonding to itself, has been exploited to develop the field of polyhedral borane chemistry. In 1960 the first icosahedral carborane was synthesized, B12H122- dianion, by Pitochelli and Hawthorne. Aside from the interesting structure and bonding of the cluster it was found to be incredibly thermally stable, withstanding heats above 800 Â°C, and chemically inert to almost all reagents. These properties have led to the B12H122- being called the most stable molecule known. The isoelectronic analogues of this structure where one or more BH has been replaced by a CH+ are known as carboranes. The first of this family was prepared in the industrial setting in the 1950âs but went unreported until 1963. The post-World War II government programs (ZIP and HEF) were purposed with developing borane-based rocket fuel that would utilize the higher energies generated by the combustion of boron hydrides in contrast to hydrocarbons. In 1957 ortho-carborane, 1,2-C2B10H12 was isolated by Reaction Motors Inc, however this ground-breaking work on the o-carborane wasnât published until 1963 when the groups at Thiokol and Olin-Mathieson released a series of papers. Years later, the monoanionic cluster HCB11H111- was synthesized by Knoth in 1967. The related closed 10-vertex anion HCB9H91- was also prepared by Knoth in 1971 and displays many of the same characteristics as the 12-vertex mono-anion. These monoanionic closed cluster carboranes have found application most notably as weakly coordinating anions but are also used in medicine, material science, electrochemistry, and transition metal catalysis. It is these monoanionic carborane clusters that will be the primary focus of this thesis.A major part of this work is directed at functionalizing these carborane clusters and incorporating them into imidazolium salts. The imidazoliums bearing functionalized carboranes can then converted into the corresponding N-heterocyclic carbenes (NHC) to be used as ligands for transition metal complexes. This thesis will also contain work in the area of electrolyte development exploiting the weakly coordinating nature of the carborane anion. Both the 10- and 12-vertex carborane clusters can be paired with various cations for their implementation in secondary batteries. Magnesium electrolytes were developed and tested in collaboration with the Guo lab at UC Riverside. Solid-state electrolytes were also developed for various cations and tested by our collaborators at Sandia National Laboratory, Argonne National Laboratory, and the Jet Propulsion Laboratory.
Enamine chemistry. Part XVII. Reaction of αβ-unsaturated acid chlorides with enamines. Further mechanistic investigations. Effect of triethylamine on the reaction path (1973)

αα′-Annulation of enamines of cyclic ketones occurs on treatment with αβ-unsaturated acid chlorides in boiling benzene, to give bridged bicyclic ketones. Further evidence supports the contention that this occurs by initial N-acylation of the enamine followed by a [3,3]sigmatropic rearrangement. In the presence of triethylamine the course of the reaction is changed. C-Acylation of the enamine occurs, leading to a tetrahydrochromanone. This reaction has been shown to involve a vinylketen intermediate. The evidence available indicates that vinylketens react with enamines by a two-stage mechanism to give a zwitterionic intermediate, rather than by concerted [2 + 2] or [4 + 2] cycloaddition.
High Speed 2×2 GaAs-GaAlAs Electro-optic Switches Based on Multi-mode Interference Couplers (2006)

We have designed and fabricated 2×2 GaAs-GaAlAs electro-optic switches using multi-mode interference couplers. Prototype switches have demonstrated almost the same insertion-loss as straight waveguides, typically 0.3 dB/cm, and small channel-to-channel cross-talk better than – 22 dB.
ChemInform Abstract: Titanocene‐Catalyzed Asymmetric Ketone Hydrosilylation: The Effect of Catalyst Activation Protocol and Additives on the Reaction Rate and Enantioselectivity. (1999)

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.
Role of Gut-Associated Lymphoreticular Tissues in Antigen-Specific Intestinal IgA Immunity (2004)

This study assessed the roles of the postnatal lymphotoxin-beta receptor (LTbetaR)-mediated signals in the gut-associated lymphoreticular tissues of mice for subsequent regulation of Ag-specific intestinal IgA responses. Blockade of LTbetaR-dependent events by postnatal administration of the fusion protein of LTbetaR and IgG Fc (LTbetaR-Ig) reduced both the size and numbers of Peyer's patches (PP) without influencing the PP microarchitecture. Interestingly, inhibition of LTbetaR-dependent signaling revealed significant reductions in the formation of follicular dendritic cell clusters in mesenteric lymph nodes (MLN). Furthermore, these postnatal signaling events controlled the development of isolated lymphoid follicles (ILF) because treatment with LTbetaR-Ig eliminated the formation of ILF. LTbetaR-Ig-treated mice with altered microarchitecture of MLN and lacking ILF were still able to produce significant Ag-specific mucosal IgA responses after oral immunization; however, the levels were significantly lower than those seen in control mice. These results imply the importance of ILF for Ag-specific intestinal immunity. However, mice treated with both TNFR55-Ig and LTbetaR-Ig in utero, which lack PP and MLN, but retain intact ILF, failed to induce Ag-specific IgA responses after oral immunization. These findings demonstrate that ILF are not essential for induction of intestinal IgA Ab responses to orally administered Ag. Furthermore, the induction of intestinal IgA Ab responses requires the proper maintenance of the MLN microarchitecture, including a follicular dendritic cell network.
Thermal behavior of stearoylsphingomyelin-cholesterol dispersions (1981)

The thermotropic behavior of aqueous dispersions of stearoylsphingomyelin-cholesterol mixtures was examined by high-sensitivity differential scanning calorimetry. When less than 20 mol % cholesterol was mixed with the sphingomyelin and the samples were held at room temperature for 7-9 days before the initiation of calorimetric measurements, a sharp endotherm at 56-57 degrees C and a broad endotherm at 35-50 degrees C were observed. In addition, samples containing 15-20 mol % stearol exhibited a sharp endotherm at 43-45 degrees C. If samples were held at room temperature for less than 2 h before the initiation of calorimetric analysis, the 56-57 degrees C endotherm was usually not seen. Instead, a combination of broad and sharp endotherms over the range of 35-50 degrees C was observed. Occasionally, exotherms were also observed within this temperature range. These results, along with those from previous studies, imply that a cholesterol-rich phase coexists with a cholesterol-poor phase in which the sphingomyelin molecules may exist in two distinctly different gel states.
Emergence and evolution of agent-based referral networks (2002)

Numerous studies have shown that interpersonal communication acts as an important channel for gathering information. But if we wish to rely oninterpersonal communication, we still need to figure out how to determinethe right person to ask. Usually we cannot find the potential expert(s) directly, and we need some assistance from our friends or friends' friends to locate them. The phenomenon of Six Degrees of Separation indicates that it is possible to use some intelligent software agents, who can interpret the links between people and follow only therelevant one, to find the desired experts quickly. A computational model of agent-based referral networks was proposed to assist and simplify the users to find potential experts for a specified topic in a person-to-person social network, in which each user is assigned a softwareagent, and software agents help automate the process by a series of "referral chains''. Unlike most previous approaches, our architecture is fully distributed and includes agents who preserve the privacy and autonomy oftheir users. These agents learn models of each other in terms of expertise(ability to produce correct domain answers), and sociability (ability to produce accurate referrals). We study this framework experimentally to see the effects that the different variables have on each other and the efficiencyof the referral networks. Furthermore, a social mechanism of reputation management was proposed tohelp agents (users) avoid interaction with undesirable participants inthe referral networks. The mathematical theory of evidence is used torepresent and propagate the reputation information in a referral network.Our approach adjusts the ratings of agents based on their observations as well the testimony from others. Moreover, we conducted several experimentsto study the reputation management in different settings. Social mechanismsare even more important when some centralized reputation managementmechanisms, i.e., trusted third parties, are not available. Our specific approach to reputation management leads to a decentralized society in which agents help each other weed out undesirable players.
Synthesis of mononuclear paramagnetic zirconium(III) derivatives (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of mononuclear paramagnetic zirconium(III) derivativesMichael D. Fryzuk, Murugesapillai Mylvaganam, Michael J. Zaworotko, and Leonard R. MacGillivrayCite this: J. Am. Chem. Soc. 1993, 115, 22, 10360–10361Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/ja00075a062https://doi.org/10.1021/ja00075a062research-articleACS PublicationsRequest reuse permissionsArticle Views317Altmetric-Citations20LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (4)»Supporting Information Supporting Information Get e-Alerts
Retinal Vessel Geometry and the Incidence and Progression of Diabetic Retinopathy (2017)

Novel measures of retinal vascular geometry are associated with the incidence and progression of DR at 1 year. These geometric measures are likely to represent early dysfunction in the retinal microvasculature.
Increased mutation and gene conversion within human segmental duplications (2023)

Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data<sup>1,2</sup>. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions<sup>3,4</sup>. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have 'relocated' on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences<sup>5,6</sup>.
Hybrid molecular/enzymatic catalytic cascade for complete electro-oxidation of glycerol using a promiscuous NAD-dependent formate dehydrogenase from Candida boidinii (2017)

Glycerol is a common fuel considered for bioenergy applications. Computational docking studies were performed on formate dehydrogenase from Candida boidinii (cbFDH) that showed that mesoxalate can bind to the buried active site of the holo form predicting that mesoxalate, a byproduct of glycerol oxidation, may act as its substrate. Spectroscopic assays and characterization by HPLC and GC/TCD have shown for the first time that cbFDH can act as a decarboxylase with mesoxalate. From this assessment, cbFDH was combined with NH<sub>2</sub>-TEMPO to form a novel hybrid anode to oxidize glycerol to carbon dioxide at near-neutral pH.