gebhart/patrepeval huggingface dataset:
Functional profiling of neurons through cellular neuropharmacology (2012)

We describe a functional profiling strategy to identify and characterize subtypes of neurons present in a peripheral ganglion, which should be extendable to neurons in the CNS. In this study, dissociated dorsal-root ganglion neurons from mice were exposed to various pharmacological agents (challenge compounds), while at the same time the individual responses of >100 neurons were simultaneously monitored by calcium imaging. Each challenge compound elicited responses in only a subset of dorsal-root ganglion neurons. Two general types of challenge compounds were used: agonists of receptors (ionotropic and metabotropic) that alter cytoplasmic calcium concentration (receptor-agonist challenges) and compounds that affect voltage-gated ion channels (membrane-potential challenges). Notably, among the latter are K-channel antagonists, which elicited unexpectedly diverse types of calcium responses in different cells (i.e., phenotypes). We used various challenge compounds to identify several putative neuronal subtypes on the basis of their shared and/or divergent functional, phenotypic profiles. Our results indicate that multiple receptor-agonist and membrane-potential challenges may be applied to a neuronal population to identify, characterize, and discriminate among neuronal subtypes. This experimental approach can uncover constellations of plasma membrane macromolecules that are functionally coupled to confer a specific phenotypic profile on each neuronal subtype. This experimental platform has the potential to bridge a gap between systems and molecular neuroscience with a cellular-focused neuropharmacology, ultimately leading to the identification and functional characterization of all neuronal subtypes at a given locus in the nervous system.
ChemInform Abstract: Preparation and Reactions of New Low‐Valent Samarium Reagents. (1994)

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.
The Krebs Cycle Enzyme Isocitrate Dehydrogenase 3A Couples Mitochondrial Metabolism to Synaptic Transmission (2017)

Neurotransmission is a tightly regulated Ca<sup>2+</sup>-dependent process. Upon Ca<sup>2+</sup> influx, Synaptotagmin1 (Syt1) promotes fusion of synaptic vesicles (SVs) with the plasma membrane. This requires regulation at multiple levels, but the role of metabolites in SV release is unclear. Here, we uncover a role for isocitrate dehydrogenase 3a (idh3a), a Krebs cycle enzyme, in neurotransmission. Loss of idh3a leads to a reduction of the metabolite, alpha-ketoglutarate (αKG), causing defects in synaptic transmission similar to the loss of syt1. Supplementing idh3a flies with αKG suppresses these defects through an ATP or neurotransmitter-independent mechanism. Indeed, αKG, but not glutamate, enhances Syt1-dependent fusion in a reconstitution assay. αKG promotes interaction between the C2-domains of Syt1 and phospholipids. The data reveal conserved metabolic regulation of synaptic transmission via αKG. Our studies provide a synaptic role for αKG, a metabolite that has been proposed as a treatment for aging and neurodegenerative disorders.
Maximally Recoverable LRCs: A field size lower bound and constructions for few heavy parities (2019)

The explosion in the volumes of data being stored online has resulted in distributed storage systems transitioning to erasure coding based schemes. Local Reconstruction Codes (LRCs) have emerged as the codes of choice for these applications. These codes can correct a small number of erasures (which is the typical case) by accessing only a small number of remaining coordinates. An (n, r, h, a, q)-LRC is a linear code over of length n, whose codeword symbols are partitioned into g = n/r local groups each of size r. Each local group has a local parity checks that allow recovery of up to a erasures within the group by reading the unerased symbols in the group. There are a further h “heavy” parity checks to provide fault tolerance from more global erasure patterns. Such an LRC is Maximally Recoverable (MR), if it corrects all erasure patterns which are information-theoretically correctable under the stipulated structure of local and global parity checks, namely patterns with up to a erasures in each local group and an additional h (or fewer) erasures anywhere in the codeword. The existing constructions require fields of size nΩ(h) while no superlinear lower bounds were known for any setting of parameters. Is it possible to get linear field size similar to the related MDS codes (e.g. Reed-Solomon codes)? In this work, we answer this question by showing superlinear lower bounds on the field size of MR LRCs. When a, h are constant and the number of local groups g  h, while r may grow with n, our lower bound simplifies to MR LRCs deployed in practice have a small number of global parities, typically h = 2, 3 [HSX+12]. We complement our lower bounds by giving constructions with small field size for h  3. When h = 2, we give a linear field size construction, whereas previous constructions required quadratic field size in some parameter ranges. Note that our lower bound is superlinear only if h  3. When h = 3, we give a construction with O(n3) field size, whereas previous constructions needed nΘ(a) field size. Our construction for h = 2 makes the choices r = 3, a = 1, h = 3 the next smallest setting to investigate regarding the existence of MR LRCs over fields of near-linear size. We answer this question in the positive via a novel approach based on elliptic curves and arithmetic progression free sets.
First-in-Human Study of the Radioligand 68Ga-N188 Targeting Nectin-4 for PET/CT Imaging of Advanced Urothelial Carcinoma (2023)

A clear correlation between PET SUV value and nectin-4 expression was observed, supporting the application of 68Ga-N188 PET as a companion diagnostic tool for optimizing treatments that target nectin-4. See related commentary by Jiang et al., p. 3259.
Human Retinal Pigment Epithelium: In Vivo Cell Morphometry, Multispectral Autofluorescence, and Relationship to Cone Mosaic (2018)

Improvements in AOSLO autofluorescence imaging permit efficient visualization of RPE cells with safe light exposures, allowing individual characterization of RPE cell morphometry that is variable between participants. The normative dataset and analysis of RPE cell IRAF and SWAF herein are essential for understanding microscopic characteristics of cell fluorescence and may assist in interpreting disease progression in RPE cells.
Cyano(methylthio)methyltrimethylsilane (2001)

[121221-45-2] C6H13NSSi (MW 159.32) InChI = 1S/C6H13NSSi/c1-8-6(5-7)9(2,3)4/h6H,1-4H3 InChIKey = SXNNRIVSRGIQNS-UHFFFAOYSA-N (reagent for the synthesis of α-cyano-substituted vinyl sulfides1) Physical Data: bp 72–74 °C/4 mmHg.1 Solubility: sol ether, THF, and CHCl3. Analysis of Reagent Purity: 1H NMR, IR.1 Preparative Method: prepared in 80–85% yield by the treatment of methylthioacetonitrile with Trimethylsilyl Trifluoromethanesulfonate and Triethylamine in ether at 0–5 °C for 3 h.1 Purification: distillation. Handling, Storage, and Precautions: use in a fume hood.
Transcriptional profiling of human amniotic fluid derived stem cells and their multilineage differentiation (2007)

Hipp, Jennifer; Tillman, Bryan MD, PhD; Hipp, Jason PhD; Hodges, Steve MD; Atala, Anthony MD; Soker, Shay PhD Author Information
Acoustic characterization of polymer-encapsulated microbubbles with different shell-thickness-to-radius ratios using in vitro attenuation and scattering: Comparison between different rheological models (2014)

Acoustic behaviors of five different polymer (polylactide) encapsulated microbubbles—PB127 (Point Biomedical), PH37, PH43, PH44, PH45 (Phillips Healthcare) with different shell-thickness-to-radius ratios (STRR) of 3.5, 30, 40, 65, and 100 nm/μm have been characterized. In vitro attenuation data were used to determine the interfacial rheological properties of their shells. Use of different models—Newtonian, viscoelastic, strain-softening, Marmottant, and Church—resulted in similar rheological properties. The shell elasticity and shell viscosity were found to increase with increasing shell thickness as expected. The nonlinear scattered response from these microbubbles were measured. Experimentally measured scattered subharmonic response were compared with the model predictions.
Replication (2004)

Replication is the process of copying and distributing user data and some objects (like views and stored procedures) from one database to another. The participating databases can exist on the same or different servers. Depending on the type of replication that you select, data can be modified on the copy of the database, and then resynchronized with the source database.KeywordsReplication AgentEnterprise ManagerServer RegistrationSubscriber ServerDistribution AgentThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
ChemInform Abstract: Polyene Macrolactam Construction Using a Stille Vinyl‐Vinyl Coupling Protocol: An Approach to the Antitumor Antibiotic Substance Leinamycin. (1994)

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.
Radiation inducible MafB gene is required for thymic regeneration (2021)

The thymus facilitates mature T cell production by providing a suitable stromal microenvironment. This microenvironment is impaired by radiation and aging which lead to immune system disturbances known as thymic involution. Young adult thymus shows thymic recovery after such involution. Although various genes have been reported for thymocytes and thymic epithelial cells in such processes, the roles of stromal transcription factors in these remain incompletely understood. MafB (v-maf musculoaponeurotic fibrosarcoma oncogene homolog B) is a transcription factor expressed in thymic stroma and its expression was induced a day after radiation exposure. Hence, the roles of mesenchymal MafB in the process of thymic regeneration offers an intriguing research topic also for radiation biology. The current study investigated whether MafB plays roles in the adult thymus. MafB/green fluorescent protein knock-in mutant (MafB<sup>+/GFP</sup>) mice showed impaired thymic regeneration after the sublethal irradiation, judged by reduced thymus size, total thymocyte number and medullary complexity. Furthermore, IL4 was induced after irradiation and such induction was reduced in mutant mice. The mutants also displayed signs of accelerated age-related thymic involution. Altogether, these results suggest possible functions of MafB in the processes of thymic recovery after irradiation, and maintenance during aging.
Conclusion (2009)

The International Law Commission considers that the topic of the aut dedere aut judicare obligation has achieved a sufficient substantial maturity for its codification, with a possibility of including some elements of progressive development. Zdzislaw Galicki, the Special Rapporteur, has submitted a preliminary and a second report on the topic. The examination of the topic by the ILC is welcomed: the topic is certainly ripe for a comprehensive study by a respected body of international lawyer...
Novel mechanism of hepatocyte growth factor against prevention of inflammation and oxidative stress (2013)

Hepatocyte growth factor (HGF) was originally identified as a potent mitogen stimulating hepatocyte growth. It also has mesenchyme-derived pleiotropic effects of regulating growth, motility, and morphogenesis of various types of cells, and is thus considered a humoral mediator of morphogenic tissue interactions. The protective effects of HGF against oxidative stress are important in the early stage of inflammation. Many studies suggest that epidermal growth factor receptor (EGFR) plays an important role in the production of oxidative stress. Some substances such as lipopolysaccharide (LPS) increase EGFR expression. LPS triggers sepsis shock and the systemic inflammatory response syndrome, which results in multiple organ failure. Recent reports demonstrated that HGF attenuated LPS- or angiotensin II (Ang II)-induced oxidative stress via EGFR degradation, and protected against vascular damage. Similarly, HGF inhibited the increase in expression of vascular cell adhesion molecule-1 in pathological conditions attributed LPS or Ang II. The protective effects of HGF are associated with the HGF/c-Met system. Since the HGF/c-Met system inhibits the translocation of SHIP2 to EGFR in pathological conditions, EGFR degradation is triggered via EGFR ubiquitination through SHIP2 binding to its own receptor, c-Met. This newly described mechanism of HGF to regulate SHIP2 recruitment to EGFR and inhibit LPS-induced inflammation via EGFR degradation may be useful for the development of anti-inflammatory agents.
Gold Nanorod-Mediated Photothermal Enhancement of the Biocatalytic Activity of a Polymer-Encapsulated Enzyme (2017)

The rational integration of biomolecules and functional nanostructures can enable remote-controlled biological processes such as molecular transport, catalysis, and molecular recognition. The photothermal ability of plasmonic nanostructures is highly attractive for optically modulating biomolecular processes such as biocatalysis. However, the studies pertaining to the photothermal enhancement of enzyme activity are mostly limited to thermophilic enzymes because of the thermal denaturation and loss of the activity of conventional enzymes at elevated temperatures. The lack of effective strategies for preserving the activity of immobilized enzymes at elevated temperatures hinders the potential use of plasmonic nanostructures as nanoheaters for the photothermal enhancement of enzyme activity. Here, we demonstrate a simple and highly effective strategy for stabilizing enzymes immobilized on plasmonic nanostructures by encapsulating them through in situ polymerization. Apart from enhanced thermal and biological stability, the encapsulation strategy provides enhancement of enzyme activity with an external optical trigger. The encapsulation strategy demonstrated here can be a highly attractive approach for designing remote-controlled biomolecular reactions.
An Online Microcredential Certification Program to Upskill Petrotechnical Professionals in Data Analytics and Machine Learning with an Upstream Oil and Gas Industry Focus (2021)

Abstract The upstream oil and gas industry's digital transformation over the last few years has accelerated because of the COVID-19 pandemic. Data analytics and machine learning are key components of this digital transformation and have become essential skills for experienced petrotechnical professionals (PTPs) and aspiring entrants into the field. The objective of our work was to design and deliver a practical, engaging, and online microcredential certification program in upstream energy data analytics for PTPs. The program was conceived as a collaboration between academia (University of Houston's UH Energy) and industry (NExT, a Schlumberger company). It was designed as three belt levels (Bronze, Silver, and Gold), each containing three stackable badges of 12 to 15 hours duration per badge. Key design points included Identifying an online platform for administration Delivering convenient, interactive, live online sessions Delivering hybrid classes blending lectures and hands-on laboratories Designing laboratories using upstream datasets across various stages of oilfield expertise Administering test and quizzes, Kaggle competitions, and team projects. The program contents were designed incorporating appropriate instructional design practices for effective online class delivery. The design and delivery of the laboratories using a code-free approach by leveraging visual programming offers PTPs and new entrants a unique opportunity to learn data analytics concepts without the traditional concern of learning to code. Additionally, the collaboration between academia and industry enables delivering a program that combines academic rigor with application of the skills and knowledge to solve problems facing the industry using the real-world datasets. As a pilot program, all three badges of the Bronze belt were scheduled and successfully delivered during July and August 2020, as six 2-hour sessions per badge. From a total of 26 students registered in badge 1, 24 completed it, resulting in a completion rate of 92%. Out of these students, 19 registered and completed badge 2 and badge 3, resulting in the completion rates of 100%. Based on the success of the pilot program, a second delivery of the Bronze belt with 18 participants was offered from October 2020 through January 2021. All 18 participants completed all three badges. Feedback from participants attests to the success of the pilot program as seen in the following excerpts: "A very good course and instructors. I have already recommended the course to a friend and I will continue to be an advocate for the course." "Teachers are very receptive to questions and it is a joy to hear their lectures." "I found the University of Houston course to be both highly engaging and incredibly informative. The course teaches basic principles of data science without being bogged down by the specific coding language."
Instrumentation for fast functional optical tomography (2002)

In this article, we describe the design rationale and performance features of an integrated multichannel continuous wave (cw) near-infrared (NIR) optical tomographic imager capable of collecting fast tomographic measurements over a large dynamic range. Fast data collection (∼70 Hz/channel/wavelength) is achieved using time multiplexed source illumination (up to 25 illumination sites) combined with frequency encoded wavelength discrimination (up to four-wavelength capability) and parallel detection (32 detectors). The described system features a computerized user interface that allows for automated system operation and is compatible with various previously described measuring heads. The results presented show that the system exhibits a linear response over the full dynamic measuring range (180 dB), and has excellent noise (∼10 pW noise equivalent power) and stability performance (&amp;lt;1% over 30 min). Recovered images of laboratory vessels show that dynamic behavior can be accurately defined and spatially localized.
Carbocationic Polymerizations for Profit and Fun (2004)

Abstract This presentation consists of two largely independent parts: The first åfor Profitα part concerns a bird's eye view of recently commercialized carbocationic processes and materials created by these processes in the author's laboratories whose marketing started during the past ∼5 years by various companies. These materials/processes include liquid telechelic polyisobutylene (PIB) for architectural sealants, poly(styrene‐ b ‐isobutylene‐ b ‐styrene) (PSt‐ b ‐PIB‐ b ‐PSt) triblocks for thermoplastic elastomers, PIB/PSt‐based blocks for coating of medical devices, and PIB‐based microemulsions for surface protection of painted metal surfaces. It is concluded that in order to enhance and solidify research in polymer synthesis it would behoove the scientific community to pay increased attention to intellectual property protection. Appropriately managed patenting and publishing activities are self‐reinforcing and may be quite profitable. The second “for Fun” part concerns a brief review of the design, synthesis and characterization of two novel fully aliphatic star‐block copolymers: ∅︁(PIB‐ b ‐PNBD) 3 and ∅︁(PNBD‐ b ‐PIB) 3 (where PNBD = polynorbornadiene). The constituent moieties of these star‐blocks are identical except their block sequences are reversed. Motivation for the synthesis of ∅︁(PIB‐ b ‐PNBD) 3 , consisting of a low Tg (∼‐73°C) PIB inner‐corona attached to a high Tg (∼320°C) PNBD outer corona, was the expectation that this star‐block would exhibit thermoplastic elastomer characteristics, and that it could be used in applications where similar polyaromatic‐based TPEs cannot be employed (e.g., magnetic signal storage). The other star‐block, ∅︁(PNBD‐ b ‐PIB) 3 , comprises the same building blocks with the PIB and PNBD sequences reversed. We found that the secondary chlorine at the PNBD chain end, in conjunction with TiCl 4 , is able to initiate the polymerization of isobutylene. Details of the carbocationic polymerization of NBD, together with the microstructure of PNBD, will be discussed.
Metabolic Engineering of Cephalosporin Biosynthesis in Streptomyces clavuligerusa (1996)

The biosynthesis of beta-lactams is one of the most thoroughly studied antibiotic pathways. The availability of the characteristics and the time profiles of activities of enzymes involved in the biosynthesis allows one to critically evaluate the potential rate-limiting steps in its production. Our approach to understanding the control of beta-lactam biosynthesis has been pursued using a two-stage strategy: (1) to predict the rate-limiting steps using a kinetic model and (2) to relax the rate-limiting steps by engineering the biosynthetic pathway or by altering the kinetic parameters of the predicted key rate-limiting enzyme. Kinetic analysis of the pathway dynamics of cephamycin C production in Streptomyces clavuligerus was performed using data obtained from wild type. Sensitivity analysis revealed that the availability of precursor alpha-aminoadipic acid and activity of ACV synthetase were the potential rate-limiting steps. Relaxation of the precursor limitation was accomplished by integration of an additional copy of the gene encoding lysine-epsilon-aminotransferase (lat) into the chromosome. The recombinant strain showed an increased level of cephamycin C production as expected. The intracellular levels of different intermediates in the pathway in batch cultures were analyzed.
IBM infosphere streams for scalable, real-time, intelligent transportation services (2010)

With the widespread adoption of location tracking technologies like GPS, the domain of intelligent transportation services has seen growing interest in the last few years. Services in this domain make use of real-time location-based data from a variety of sources, combine this data with static location-based data such as maps and points of interest databases, and provide useful information to end-users. Some of the major challenges in this domain include i) scalability, in terms of processing large volumes of real-time and static data; ii) extensibility, in terms of being able to add new kinds of analyses on the data rapidly, and iii) user interaction, in terms of being able to support different kinds of one-time and continuous queries from the end-user. In this paper, we demonstrate the use of IBM InfoSphere Streams, a scalable stream processing platform, for tackling these challenges. We describe a prototype system that generates dynamic, multi-faceted views of transportation information for the city of Stockholm, using real vehicle GPS and road-network data. The system also continuously derives current traffic statistics, and provides useful value-added information such as shortest-time routes from real-time observed and inferred traffic conditions. Our performance experiments illustrate the scalability of the system. For instance, our system can process over 120000 incoming GPS points per second, combine it with a map containing over 600,000 links, continuously generate different kinds of traffic statistics and answer user queries.