gebhart/patrepeval huggingface dataset:
Subunit structure and chromophore composition of rhodophytan phycoerythrins. Porphyridium cruentum B-phycoerythrin and b-phycoerythrin. (1977)

A comparative study is presented of the two phycoerythrins of the unicellular red alga Porphyridium cruentum. Native B-phycoerythrin has a molecular weight of 236,000 +/- 18,000 in 0.05 M potassium phosphate at pH 7.0, and an absorption spectrum with maxima at 545 nm (epsilonM = 2.41 X 10(6) M-1 cm-1) and 563 nm, and a shoulder at 498 nm. The protein carries 38 phycoerythrobilin and at least two phycourobilin prosthetic groups per 240,000 daltons. B-Phycoerythrin is composed of three dissimilar subunits, alpha and beta, each of 17,500 daltons, and gamma of 30,200 daltons. Physical, chemical, and spectroscopic data are consistent with a subunit structure (alphabeta)6gamma for B-phycoerythrin. The alpha and beta subunits carry solely phycoerythrobilin chromophores, while the gamma subunit carries both phycoerythrobilin and phycourobilin groups. The NH2-terminal sequences of the alpha and beta subunits determined by sequential Edman degradation, are shown below: alpha subunit: Met-Lys-Ser-Val-Ile-(Gly-Arg-Phe: beta subunit: Met-Leu-Asp-Ala-Phe-(Thr)-Arg-Val-Val-Val-Asn-Ala-Asx-Ala-( )-Ala-Ala-Tyr-Val. The NH2 terminus of the gamma subunit is blocked. b-Phycoerythrin is polydisperse and exhibits native molecular weights ranging from approximately 40,000 to approximately 260,000, depending on pH, ionic strength, and protein concentration. The absorption spectrum is characterized by maxima at 543 nm (epsilonM = 3.41 X 10(5) M-1 cm-1/35,000 daltons) and 563 nm. The protein carries six phycoerythrobilin groups per 35,000 daltons. b-Phycoerythrin is made up of two dissimilar types of subunits, alpha and beta, of 17,500 daltons each. The alpha and beta subunits derived from b-phycoerythrin appeared equivalent to the corresponding subunits of B-phycoerythrin on the basis of the following criteria: (a) identical chromatographic behavior on Bio-Rex 70 in acid urea; (b) similar amino acid compositions; (c) identical mobilities on polyacrylamide gels in the presence of sodium dodecyl sulfate; (d) similar phycoerythrobilin contents; (e) identical NH2-terminal sequences. These data support, but do not establish unambiguously, the conclusion that b-phycoerythrin may be a component of B-phycoerythrin. The absence or presence, and relative height, of an absorption peak (or shoulder) at 498 nm represents the major difference among the absorption spectra of different classes of phycoerythrins. The present study shows that this spectral feature is dependent on the presence and amount of phycourobilin chromophores in the native protein and is correlated with the presence of the gamma subunit.
Abstract 4608: Colchicine binding site agents as potent tubulin inhibitors suppressing triple negative breast cancer (2019)

Triple-negative breast cancer (TNBC) cases account for about 15% of all breast cancers in the United States and have poorer overall prognosis relative to other molecular subtypes, partially due to the rapid development of drug resistance to chemotherapies and the increased risk of visceral metastasis. One of the standard treatment regimens for TNBC is the use of a taxane-based chemotherapy, such as paclitaxel, which stabilizes microtubules. However, drug resistance and neurotoxicities often limit the clinical efficacy of taxanes. Therefore, there are continuous needs to develop more effective therapies that could overcome resistance to taxanes. In this study, a novel series of structurally related pyridine analogs based on our previously reported lead compound ABI-274, was designed and synthesized to identify a molecule with improved antiproliferative potency. Most of these pyridine compounds exhibited potent cytotoxicity when tested in a panel of melanoma and breast cancer cell lines, with IC50 values in the low nanomolar range. Among them, CH-II-77 is the most potent compound with an IC50 value of 1−3 nM against these cancer cell lines, including paclitaxel-resistant sublines. The high-resolution X-ray crystal structure of CH-II-77 in complex with tubulin protein confirmed its direct binding to the colchicine-binding site. It strongly induced apoptosis and produced G2/M phase cell cycle arrest in TNBC cells in a dose-dependent manner in vitro. In vivo, CH-II-77 inhibited tumor growth in A375 melanoma xenografts and MDA-MB-231 TNBC xenografts in a dose-dependent manner. CH-II-77 was able to induce tumor necrosis and apoptosis in vivo. Collectively, these studies strongly suggest that CH-II-77 is a potent inhibitor of the growth of TNBC in vitro and in vivo. Thus, CH-II-77 and optimization of this analog are promising new generation of tubulin inhibitors for the treatment of TNBC and other types of cancers where tubulin inhibitors are currently being used clinically.Citation Format: Shanshan Deng, Hao Chen, Raisa Krutilina, Najah G. Albadari, Tiffany N. Seagroves, Duane D. Miller, Wei Li. Colchicine binding site agents as potent tubulin inhibitors suppressing triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4608.
Increased liquid droplet erosion resistance of steam turbine blades (2007)

Alloys used for the blades of steam turbines usually do not show a satisfactory resistance to erosion and require surface protection with suitable coatings. Starting from the results obtained with Stellite 6 coatings on AISI 420 stainless steel blades, this research has been developed with the aim to increase erosion resistance by modifying the chemical composition of the coatings. Several samples have been coated by laser cladding and exposed to liquid erosion tests. In particular, concentrations of carbide forming and solid solution strengthening elements have been varied in order to establish their effects against liquid droplet erosion. Results of the tests and EDX analyses on the samples are reported, with a discussion on the various effects on erosion resistance. Two directions have appeared as the most promising, either increasing the concentration of carbide forming elements, or increasing the concentration of nickel in the coatings.
Optimizing electrostatic affinity in ligand–receptor binding: Theory, computation, and ligand properties (1998)

The design of a tight-binding molecular ligand involves a tradeoff between an unfavorable electrostatic desolvation penalty incurred when the ligand binds a receptor in aqueous solution and the generally favorable intermolecular interactions made in the bound state. Using continuum electrostatic models we have developed a theoretical framework for analyzing this problem and have shown that the ligand-charge distribution can be optimized to produce the most favorable balance of these opposing free energy contributions [L.-P. Lee and B. Tidor, J. Chem. Phys. 106, 8681 (1997)]. Herein the theoretical framework is extended and calculations are performed for a wide range of model receptors. We examine methods for computing optimal ligands (including cases where there is conformational change) and the resulting properties of optimized ligands. In particular, indicators are developed to aid in the determination of the deficiencies in a specific ligand or basis. A connection is established between the optimization problem here and a generalized image problem, from which an inverse-image basis set can be defined; this basis is shown to perform very well in optimization calculations. Furthermore, the optimized ligands are shown to have favorable electrostatic binding free energies (in contrast to many natural ligands), there is a strong correlation between the receptor desolvation penalty and the optimized binding free energy for fixed geometry, and the ligand and receptor cannot generally be mutually optimal. Additionally, we introduce the display of complementary desolvation and interaction potentials and the deviation of their relationship from ideal as a useful tool for judging effective complementarity. Scripts for computing and displaying these potentials with GRASP are available at http://mit.edu/tidor.
162 Supplementation of Fibroblast Growth Factor 2, Leukemia Inhibitory Factor, and Insulin-Like Growth Factor 1 (FLI) Enables Efficient Production of Competent Porcine Oocytes Without Gonadotropins in the Maturation Medium (2017)

In vitro maturation (IVM) of oocytes is a critical step in assisted reproductive technologies carried out in species such as cattle and swine, for generating oocytes capable of being fertilized in vitro and providing healthy offspring useful for biomedical and agricultural purposes. Cumulus-oocyte complexes (COC) collected from abattoir ovaries for IVM often respond poorly to gonadotropins, resulting in compromised oocyte competence. Our previous work demonstrated that the combination of fibroblast growth factor 2, leukemia inhibitory factor, and insulin-like growth factor 1 (FGF2, LIF, and IGF1; FLI) significantly improved nuclear maturation of porcine oocytes and their developmental competence. However, it is unclear whether the benefits of FLI are mediated through increased gonadotropin sensitivity of COC or improved downstream signalling. Here we investigated the effect of FLI supplementation of IVM medium with and without gonadotropins. The COC, collected from 2- to 6-mm follicles from prepubertal ovaries, were matured in 5% CO2/air at 38.5°C for 42 h in chemically defined TCM-199 medium (supplemented with 0.1% polyvinyl alcohol, 3.05 mM d-glucose, 0.91 mM pyruvate, 0.57 mM cysteine, 10 ng mL-1 epidermal growth factor), with or without FLI (40 ng mL-1 FGF2, 20 ng mL-1 LIF, and 20 ng mL-1 IGF1), and with or without gonadotropins (0.5 µg mL-1 LH, 0.5 µg mL-1 FSH), in a 2 × 2 factorial design experiment. After IVM, oocytes were fertilized in vitro and cultured under standard conditions until Day 6 when blastocyst formation was assessed. The experiment was replicated 4 times with a total of 792 oocytes. Percentage data were arcsin transformed and analysed by ANOVA to detect differences (significance, P &amp;lt; 0.05). When FLI was absent from the maturation medium, oocytes matured in presence of gonadotropins demonstrated improved nuclear maturation (67.0 ± 2.2% v. 52.7 ± 5.3%) and blastocyst formation (23.7 ± 3.3% v. 10.2 ± 2.3%) relative to oocytes matured without gonadotropins, respectively. However, when FLI was present in the medium, the extent of oocyte maturation and subsequent blastocyst development was unaffected by gonadotrophin addition (maturation: 84.2 ± 1.8% with and 79.2 ± 3.4% without; blastocyst formation: 29.5 ± 4.3% with and 24.9 ± 4.3% without). In summary, these results suggest that FLI, rather than enhancing COC sensitivity to gonadotrophins, may activate certain downstream signalling pathways that are normally controlled by gonadotropins during IVM, thereby enhancing oocyte quality. Therefore, FLI appears able to substitute for gonadotropins in the maturation medium and supports porcine oocyte competence in the absence of FSH and LH. These observations will help us better understand the mechanisms whereby FLI enhances oocyte nuclear maturation and improves developmental competency. Supported by NIH R01HD69979, U42OD011140, and University of Missouri Food for the 21st Century Program.
ENDOSCOPIC SUBMUCOSAL DISSECTION OF A SOLITARY GASTRIC PLASMOCYTOMA: 'THIRD SPACE ODDITY' (2022)

A 35-year-old woman underwent esophagogastroduodenoscopy for progressive epigastralgia. A 10mm subepithelial antral lesion contained plasmocytoma tissue. Diagnostic work up was negative apart from a gastric focus on PET.
COMMERCIAL APPLICATIONS OF EXPERT SYSTEMS IN APPLE PRODUCTION (1990)

Apple orchards are highly diversified and complex ecological and economic systems. Production is affected by a wide range of insects, diseases, weeds, and mammalian pests. The incidence of these pests is often dependant upon climatological effects; and the microclimate within orchards. An expert system, a form of artificial intelligence, has been developed and commercially released to apple growers that utilizes weather data to make recommendations regarding production decisions. Users of the system are instructed on how to establish a weather station, and to collect, and input weather data from the farm. The information is utilized to calculate disease infection periods and pesticide residues to arrive at a control recommendation. Other weather dependant modules include the scheduling of trickle irrigation as well as water application rates during a frost. An interactive demonstration of the system will be presented to the group.
3D Structure of the Complex of MDL 63,246 with the Cell Wall Model Peptide Ac2-Lys-d-Ala-d-Ala (1996)

The complex between the glycopeptide MDL 62,346 and the model cell wall analog Ac2-Lys-d-Ala-d-Ala was studied by NMR spectroscopy in DMSO solution. A complete assignment of proton and carbon resonances was achieved, and the data were compared with the results observed for the free glycopeptide. NOE buildup rates were determined to calculate interproton distances which were used as constraints to model the 3D structure of the complex. Molecular dynamics simulations were performed in DMSO to gain further insight into the stability of the complex and the dynamical behavior of structural features. The structure of the glycopeptide backbone and the attractive interactions in the intermolecular interface are very well defined. The complex is stabilized by the formation of five intermolecular hydrogen bonds between the glycopeptide and the tripeptide.
Geophysical exploration of the Midcontinent Rift, Southwestern Iowa—A parting of the way (1985)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1985Geophysical exploration of the Midcontinent Rift, Southwestern Iowa—A parting of the wayAuthors: Alan W. HinksJeffrey M. YarusIndependent ConsultantEdward F. SimmonsIndependent GeologistAlan W. HinksThree‐D Gravity Inc., Jeffrey M. Yarus, and Edward F. Simmonshttps://doi.org/10.1190/1.1892722 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail FiguresReferencesRelatedDetails SEG Technical Program Expanded Abstracts 1985ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1985 Pages: 643 publication data© 1985 Copyright © 1985 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 07 Mar 2005 CITATION INFORMATION Alan W. Hinks, Jeffrey M. Yarus, and Edward F. Simmons, (1985), "Geophysical exploration of the Midcontinent Rift, Southwestern Iowa—A parting of the way," SEG Technical Program Expanded Abstracts : 199-202. https://doi.org/10.1190/1.1892722 Plain-Language Summary PDF DownloadLoading ...
Adaptive SSFE Near-ML MIMO Detector with Dynamic Search Range and 80-103Mbps Flexible Implementation (2008)

In this paper, we will present a near-ML (maximum likelihood) MIMO (multiple input multiple output) detector explicitly optimized for parallel programmable baseband architectures, such as DSPs (digital signal processors) with VLIW (very long instruction word), SIMD (single instruction multiple data) or vector processing features. First, we propose the SSFE (selective spanning with fast enumeration) algorithm as an architecture friendly near-ML MIMO detector. The SSFE has a distributed and greedy algorithmic structure that brings a completely deterministic and regular dataflow. This enables efficient parallelization on programmable architectures. More importantly, in order to exploit the abundant flexibility enabled by programmable architectures, we propose an efficient online algorithm to adaptively adjust the search range of the SSFE according to the numerical properties of MIMO channel matrixes. Such adaptiveness brings significant throughput improvements at negligible performance degradations. Specifically, on VLIW DSP TI TMS320C6416, such a dynamic adaptation brings 2.62 times to 28.6 times improvements (comparing to the static SSFE) for 1/2 turbo-coded 4 times 4 64 QAM transmissions over 3GPP suburban macro channels, delivering 80 - 103 Mbps average throughput.
Comparison of a gonadotropin releasing-hormone antagonist plus testosterone (T) versus T alone as potential male contraceptive regimens. (1993)

Efforts to develop a hormonal contraceptive regimen for men have focused on administration of testosterone (T), alone or together with other agents. Previous regimens have successfully induced azoospermia in only 50-70% of subjects, however. GnRH antagonists, alone or in combination with T, have been shown to induce azoospermia in a very high percentage of nonhuman primates. We tested the hypothesis that the addition of a GnRH antagonist to a high-dose T regimen would lead to a higher percentage of men developing azoospermia than would T alone. We administered the GnRH antagonist, Nal-Glu (100 micrograms/kg.day sc), plus T enanthate, 200 mg im weekly or placebo sc injections daily plus T enanthate, 200 mg im weekly, to separate groups of healthy men for 16-20 weeks. Seven of 10 men who received Nal-Glu plus T and 6 of 9 men who received T alone became azoospermic; gonadotropin levels were suppressed and T levels were increased similarly in both groups. There was a trend toward higher pretreatment gonadotropin levels and lower sperm counts in men who became azoospermic. Weight gain, development of acne, and increases in hematocrit and hemoglobin were similar in the two groups. In the majority of the men, sperm counts returned to the baseline levels within 4-5 months after treatment ended. We conclude that with the dosages of Nal-Glu and T we used in this study, the addition of GnRH antagonist to a high-dose T regimen does not increase the ability of T to suppress spermatogenesis in healthy men. Use of a higher dose of Nal-Glu, a lower dose of T, delaying the start of T replacement until several weeks after Nal-Glu injections are initiated, or prolonged hormonal administration might lead to a combination regimen that will suppress spermatogenesis more fully than does T alone.
Ge-on-Si Bufferless Epitaxial Growth for Photonic Devices (2013)

Demonstration of bufferless fully crystalline Ge-on-Si is shown. Si-Ge interdiffusion is limited to 10nm. One dimension lateral constrain provides a mechanism to prevent the formation of polycrystalline material. TEM, SEM and XRD analysis confirms Ge crystallinity. PL shows that dopant concentration is retained avoiding the dopant sink that the Ge buffer provides. Dopant concentration is retained at high levels of 1019cm-3 for n-type. Preliminary results exhibit a dopant surfactant effect determining changing the required channel dimensions for crystallinity with the dopant concentration and type used.
Single-pulse x-ray diffraction using polycapillary optics for in situ dynamic diffraction (2016)

Diagnostic use of single-pulse x-ray diffraction (XRD) at pulsed power facilities can be challenging due to factors such as the high flux and brightness requirements for diffraction and the geometric constraints of experimental platforms. By necessity, the x-ray source is usually positioned very close, within a few inches of the sample. On dynamic compression platforms, this puts the x-ray source in the debris field. We coupled x-ray polycapillary optics to a single-shot needle-and-washer x-ray diode source using a laser-based alignment scheme to obtain high-quality x-ray diffraction using a single 16 ns x-ray pulse with the source >1 m from the sample. The system was tested on a Mo sample in reflection geometry using 17 keV x-rays from a Mo anode. We also identified an anode conditioning effect that increased the x-ray intensity by 180%. Quantitative measurements of the x-ray focal spot produced by the polycapillary yielded a total x-ray flux on the sample of 3.3 ± 0.5 × 10(7) molybdenum Kα photons.
Optimal User Scheduling and Rate Selection for REMA Broadcast-Channel Transmission (2016)

Superposed transmission on the broadcast channel delivers multiple private messages simultaneously to the intended users. Superposed transmission is employed in non-orthogonal multiple access to increase the aggregate throughput and connectivity of wireless cellular systems. Rate-adaptive constellation Expansion Multiple Access (REMA, a.k.a. RA-CEMA) is a non-orthogonal multiple access scheme which exhibits performance similar to the conventional superposed transmission schemes for transmission on the degraded broadcast channel, while requiring less complex signal processing and scheduling algorithms. This paper solves the problem of user scheduling and rate allocation for REMA. We pose the problem as a weighted sum-rate optimization and develop provably optimal algorithms for user selection and rate allocation with REMA broadcast-channel transmission. System-level evaluations show that our schemes outperform an LTE-A compliant orthogonal multiple access system and exhibit similar or better performance compared to other known non-orthogonal multiple access schemes.
Guided-Mode Resonance Enhanced Mid-Wave Infrared Detector (2020)

We present an all-epitaxial guided mode resonance MWIR photodetector consisting of a type-II superlattice absorber between a highly-doped low index virtual substrate and a high-index patterned grating layer. Angle and polarization dependent responsivities are measured, and enhanced absorption is observed compared to an unpatterned control.
Ion Channel Toxins and Therapeutics: From Cone Snail Venoms to Ciguatera (2000)

Ion channels are intimately linked to all neurotransmission and neurotransmitter release processes, but in disease states often contribute adversely to disease pathology. The diversity and distribution of ion channel types and subtypes being uncovered through the use of molecular biology and toxin probes present an exciting opportunity for the discovery of new, more selective drugs. Among ion channels targeted by cone shell venom peptides (conotoxins) are the voltage-sensitive sodium, calcium, and potassium channels which open and then close (inactivate) in response to membrane depolarization, and thus regulate neurotransmission and the neurotransmitter release process. Conotoxins also target ligand-gated ion channels, including the NMDA-glutamate channel and the nicotinic acetylcholine receptor channel. The diversity of subtypes, especially those subtypes upregulated in disease states, makes ion channels a rapidly expanding therapeutic area. Conotoxins represent some of the most selective inhibitors of ion channel subtypes and have often been used as the defining ligand. In this overview, the structures and therapeutic potential of conotoxins active at ion channels are highlighted. The activity and structures are then contrasted with ciguatoxins, which are responsible for the food poisoning known as ciguatera. A universal liquid chromatography/mass spectrometry approach to the detection of these classes of toxins is briefly discussed.
Characterization of a γ‐adaptin ear‐binding motif in enthoprotin (2003)

Enthoprotin, a newly identified component of clathrin-coated vesicles, interacts with the trans-Golgi network (TGN) clathrin adapters AP-1 and GGA2. Here we perform a multi-faceted analysis of the site in enthoprotin that is responsible for the binding to the gamma-adaptin ear (gamma-ear) domain of AP-1. Alanine scan mutagenesis and nuclear magnetic resonance (NMR) studies reveal the full extent of the site as well as critical residues for this interaction. NMR studies of the gamma-ear in complex with a synthetic peptide from enthoprotin provide structural details of the binding site for TGN accessory proteins within the gamma-ear.