gebhart/patrepeval huggingface dataset:
Rejuvenation of β cells by epigenetic editing (2018)

Insulin-secreting β cell loss or dysfunction is a feature of both type 1 and type 2 diabetes. Strategies to restore β cell mass are limited, as sources of healthy islets are scarce and mature β cells are not readily expanded in vitro. In this issue of the JCI, Ou et al. report that mature β cell expansion can be induced in situ through epigenetic editing of regulatory elements in pancreatic tissue. Specifically, hypomethylation at imprinting control region 2 (ICR2) in human islets promoted β cell expansion. Importantly, transplantation of these epigenetically edited islets into diabetic mice reduced blood glucose levels. Together, these results support further evaluation of this strategy for restoring β cell mass in patients with diabetes.
Identification, Cloning, and Mutational Analysis of the Casein Kinase 1 cDNA of the Malaria Parasite, Plasmodium falciparum (1997)

The cDNA for casein kinase 1 (CK1) of Plasmodium falciparum was cloned, sequenced, and expressed in bacteria. The single major open reading frame of the 1.2-kilobase pair cDNA coded for a 324-amino acid polypeptide of approximately 37 kDa, the predicted sequence of which showed strong identity with known CK1 isoforms. The purified recombinant enzyme exhibited properties characteristic of CK1, such as inhibition by CK1-7, the ability to phosphorylate a highly specific peptide substrate, and a strong preference for ATP over GTP. A casein kinase activity, partially purified from soluble extracts of P. falciparum by affinity chromatography through CK1-7 columns displayed identical properties. The activity showed a stage-specific expression in the parasite, in the order trophozoite > ring >> schizont. Northern analysis indicated the existence of two major CK1 mRNAs, 2.4 and 3.2 kilobase pairs long, the levels of which were in the order ring > schizont > trophozoite. Mutagenesis of recombinant CK1 defined important amino acid residues and their potential role in the conformation of the enzyme. The malarial CK1 appeared to be the one of the smallest and perhaps the most primitive CK1 enzymes known, containing little sequence information beyond the minimal catalytic domain.
Phase-mediated locomotion of two self-propelled flexible plates in a tandem arrangement (2020)

Unique propulsion systems have evolved in fish that interact with the effects on the surrounding fluid of upstream fish. The downstream fish utilize these complex interactions to swim efficiently. The immersed boundary method is used to explore the phase-mediated locomotion of two self-propelled flexible plates in a tandem arrangement. The interactions caused by the phase difference are elucidated, and the hydrodynamic benefits obtained from the phase-mediated interactions are scrutinized. The variations with the phase difference (Δϕ) and initial gap distance (Gx,0) in the average cruising speed (ŪC), the average input power (P¯), the swimming efficiency (η), and the equilibrium gap distance (G¯x) are determined. Three flapping modes are identified: a tandem flapping mode, a closely mediated flapping mode, and an interfered flapping mode. The propulsion mechanisms in these modes are analyzed in detail in terms of Δϕ and Gx,0. ŪC and η are increased by more than 45% in the closely mediated flapping mode. The vortical structures are visualized to characterize the three flapping modes qualitatively.
Nucleation, absorption, or desorption of metal-vapor atoms on amorphous photochromic diarylethene films having a low glass transition temperature (2018)

Metal-vapor atoms with high or low intrinsic vapor-pressure were absorbed into or desorbed from the low-<italic>T</italic><sub>g</sub> colorless photochromic film, respectively.
Detection of Bacillus spores within 15 minutes by surface-enhanced Raman spectroscopy (2012)

Since the distribution of Bacillus anthracis causing spores through the US Postal System, there has been a persistent fear that biological warfare agents (BWAs) will be used by terrorists against our military abroad and our civilians at home. Despite the substantial effort to develop BWA analyzers, they remain either too slow, produce high falsealarm rates, lack sensitivity, or cannot be fielded. Consequently there remains a need for a portable analyzer that can overcome these limitations as expressed at the 2011 Biological Weapons Convention. To meet this need we have been developing a sample system that selectively binds BWAs and produce surface-enhanced Raman (SER) spectra using portable Raman spectrometers. Here we describe the use of a short peptide ligand functionalized on silver nanoparticles to selectively capture Bacillus cereus spores (a surrogate of B. anthracis) and their subsequent detection by SER spectroscopy. This technique was used to specifically detect B. cereus spores over closely related species like B. subtilis belonging to the same genus within 15 minutes. Sensitivity of the method was demonstrated by detecting 10<sup>4</sup> B. cereus spores/mL of water. The technology, once developed should prove invaluable for rapid monitoring of BWAs, which will immensely help first responders and emergency personnel in implementing appropriate counter measures.
Evaluation of Enantiomerically Pure Binaphthol-Based Molybdenum Catalysts for Asymmetric Olefin Metathesis Reactions that Contain 3,3‘-Diphenyl- or 3,3‘-Dimesityl-Substituted Binaphtholate Ligands. Generation and Decomposition of Unsubstituted Molybdacyclobutane Complexes (2001)

Enantiomerically pure molybdenum imido alkylidene complexes were prepared that contain binaphtholate ligands substituted in the 3 and 3‘ positions with either phenyl (4; Mo(NAr)(CHCMe2Ph)[Ph](THF)) or 2,4,6-trimethylphenyl groups (5; Mo(NAr)(CHCMe2Ph)[Mes](THF); Ar = 2,6-i-Pr2C6H3). Compound 5 was found to be an anti trigonal bipyramidal complex in an X-ray study. Asymmetric metatheses employing complex 5 were found to proceed to high conversion and to give high product % ee, while reactions that employed complex 4 were found to give lower conversion and lower % ee. One ring-closing reaction with 5 was shown to take place at a rate that was proportional to catalyst and substrate. Molybdacyclobutane complexes were observed in solution during ring-closing reactions. The molybdacyclobutane complex generated by treating 5 with ethylene was found to be a trigonal bipyramidal species which decomposed to yield some propylene; the metal-containing product or products of decomposition could not be identified. Molybdacyclobutane complexes were also formed upon adding ethylene to the analogous complex containing a 2,4,6-triisopropylphenyl-substituted binaphtholate ligand, or to 4. The detection of propylene as a product of decomposition of the molybdacyclobutane complexes examined here suggests that a decomposition pathway that consists of β hydride rearrangement can compete with bimolecular decomposition of methylene complexes under some conditions.
Relay-Assisted Interference Channel: Degrees of Freedom (2011)

This paper investigates the degrees of freedom of the interference channel in the presence of a dedicated MIMO relay. The relay is used to manage the interference at the receivers. It is assumed that all nodes including the relay have channel state information only for their own links and that the relay has M (greater than or equal to K) antennas in a K-user network. We pose the question: What is the benefit of exploiting the direct links from the source to destinations compared to a simpler two-hop strategy. To answer this question, we first establish the degrees of freedom of the interference channel with a MIMO relay, showing that a K-pair network with a MIMO relay has K/2 degrees of freedom. Thus, appropriate signaling in a two-hop scenario captures the degrees of freedom without the need for the direct links. We then consider more sophisticated encoding strategies in search of other ways to exploit the direct links. Using a number of hybrid encoding strategies, we obtain non-asymptotic achievable sum-rates. We investigate the case where the relay (unlike other nodes) has access to abundant power, showing that when sources have power P and the relay is allowed power proportional to O(P^2), the full degrees of freedom K are available to the network.
Formulas for the force and torque of axial couplings (1993)

Closed-form expressions are presented for computing the force and torque that is transmitted by synchronous axial couplings. These expressions enable rapid parametric studies of coupling performance relative to the selection of magnet material, dimensions, and spacings. They are also useful for testing three-dimensional numerically based field algorithms. The derived expressions are tested here using data taken from a ceramic coupling.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Numerical Study of Parabolic Pulse Generation in Backward-Pumped Erbium-Doped Fiber Amplifiers (2022)

In this paper, the actual shape of the gain spectrum and the whole dispersion curve of the Er-doped fiber are employed in the vectorial coupled nonlinear Schrödinger equation to model the parabolic pulse (similariton) generation in the backward-pumped Er-doped fiber amplifier. The input of the amplifier is Gaussian pulses of a high repetition rate. The numerical model is developed to account for the combination of input and amplified spontaneous emission powers to consider the average of all prior iterations in the present interaction to reach a converged solution rather than oscillating between two solutions. The excess kurtosis factor identifies the parabolic pulse among other pulse shapes. The effect of the input pulse width, peak power, and polarization and the impact of the input pump power and the fiber length on the similariton generation are studied.
ETSI Reconfigurable Radio System - System Aspects and Control Channels for Cognitive Radio (2012)

This paper introduces novel results in the area of Cognitive Radio System (CRS) aspects and Control Channels for Cognitive Information Sharing as they are currently elaborated in the framework of the ETSI Reconfigurable Radio Systems (RRS) Technical Body. An overview of the most relevant scenarios for CRS employing opportunistic spectrum usage in the TV White Spaces is given as well as an analysis of inherently required context information provisioning solutions. Finally, an overview on the related regulatory activities and future regulatory challenges are indicated with an emphasis on expected per-device certification mechanisms which will finally enable the introduction of “RadioApps”, i.e. software components provided to Mobile Devices (MD) which will affect the compliance of MDs to the essential requirements of the R&TTE Directive in Europe.
Dynamics of a pulsed single photon source (2012)

We propose and demonstrate a method for an independent verification of a degree of single photon purity and coherence applicable for all single-photon emitters used in pulsed mode. Using two-time second-order correlation measurements, we reconstruct the dynamics of the nonclassical photon wavepacket. This reveals the temporal evolution of the photon field during the excitation-relaxation cycle of an emitter. The technique allows for the simultaneous measurement of multiphoton content and decoherence. Here we applied this technique to characterize a nonclassical state produced from a single InAs quantum dot (QD). We experimentally observe variations in the degree of multiphoton content and coherence of the wavepacket. A rate equation is introduced to explain multiphoton variations of our source and is found to describe the observed two-dimensional second-order correlation function accurately.
Classification and clinical behavior of blastic plasmacytoid dendritic cell neoplasms according to their maturation-associated immunophenotypic profile (2015)

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare subtype of leukemia/lymphoma, whose diagnosis can be difficult to achieve due to its clinical and biological heterogeneity, as well as its overlapping features with other hematologic malignancies. In this study we investigated whether the association between the maturational stage of tumor cells and the clinico-biological and prognostic features of the disease, based on the analysis of 46 BPDCN cases classified into three maturation-associated subgroups on immunophenotypic grounds. Our results show that blasts from cases with an immature plasmacytoid dendritic cell (pDC) phenotype exhibit an uncommon CD56- phenotype, coexisting with CD34+ non-pDC tumor cells, typically in the absence of extramedullary (e.g. skin) disease at presentation. Conversely, patients with a more mature blast cell phenotype more frequently displayed skin/extramedullary involvement and spread into secondary lymphoid tissues. Despite the dismal outcome, acute lymphoblastic leukemia-type therapy (with central nervous system prophylaxis) and/or allogeneic stem cell transplantation appeared to be the only effective therapies. Overall, our findings indicate that the maturational profile of pDC blasts in BPDCN is highly heterogeneous and translates into a wide clinical spectrum -from acute leukemia to mature lymphoma-like behavior-, which may also lead to variable diagnosis and treatment.
Mineralization of Acephate, a Recalcitrant Organophosphate Insecticide Is Initiated by a Pseudomonad in Environmental Samples (2012)

An aerobic bacterium capable of breaking down the pesticide acephate (O,S-dimethyl acetyl phosphoramidothioic acid) was isolated from activated sludge collected from a pesticide manufacturing facility. A phylogenetic tree based on the 16 S rRNA gene sequence determined that the isolate lies within the Pseudomonads. The isolate was able to grow in the presence of acephate at concentrations up to 80 mM, with maximum growth at 40 mM. HPLC and LC-MS/MS analysis of spent medium from growth experiments and a resting cell assay detected the accumulation of methamidophos and acetate, suggesting initial hydrolysis of the amide linkage found between these two moieties. As expected, the rapid decline in acephate was coincident with the accumulation of methamidophos. Methamidophos concentrations were maintained over a period of days, without evidence of further metabolism or cell growth by the cultures. Considering this limitation, strains such as described in this work can promote the first step of acephate mineralization in soil microbial communities.
Supplementary Figure 2 from RKI-1447 Is a Potent Inhibitor of the Rho-Associated ROCK Kinases with Anti-Invasive and Antitumor Activities in Breast Cancer (2023)

&lt;p&gt;PDF file, 64K, Effect of RKI-1447 and RKI-1313 on anchorage dependent proliferation/survival of MDA-MB-231 cells. Cells were seeded in a 96-well plate and treated with increasing concentrations of RKI-1447 or RKI-1313. The effects of the compounds on cell viability under anchorage-dependent conditions were determined by MTT assay as described below. MTT Assay Method: MTT assay was performed exactly as described by us (see reference 41 in manuscript) to determine the effects of RKI-1447 on anchorage-dependent cell proliferation. Briefly, cells were plated in a 96 well tissue culture plate (1200 cells per well) and incubated for 24 hours. After incubation the cells were treated with vehicle or increasing concentrations of RKI-1447 or RKI-1313 for 72 hours. After incubation, freshly prepared MTT (2mg/ml) was added to each well and incubated for 3 hours. After incubation the plates were read at 540 nm.&lt;/p&gt;
Competitive SPR using an intracellular anti-LMO2 antibody identifies novel LMO2-interacting compounds (2021)

The use of intracellular antibodies as templates to derive surrogate compounds is an important objective because intracellular antibodies can be employed initially for target validation in pre-clinical assays and subsequently employed in compound library screens. LMO2 is a T cell oncogenic protein activated in the majority of T cell acute leukaemias. We have used an inhibitory intracellular antibody fragment as a competitor in a small molecule library screen using competitive surface plasmon resonance (cSPR) to identify compounds that bind to LMO2. We selected four compounds that bind to LMO2 but not when the anti-LMO2 intracellular antibody fragment is bound to it. These findings further illustrate the value of intracellular antibodies in the initial stages of drug discovery campaigns and more generally antibodies, or antibody fragments, can be the starting point for chemical compound development as surrogates of the antibody combining site.
PARP inhibitors affect growth, survival and radiation susceptibility of human alveolar and embryonal rhabdomyosarcoma cell lines (2018)

This study suggests that the combined exposure to PARPi and IR might display a role in the treatment of RMS tumours compared with single-agent exposure, since stronger cytotoxic effects are induced, and compensatory survival mechanisms are prevented.
Green Chemistry and the Health Implications of Nanoparticles (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Experimental identification of evaporator dynamics for vapor compression refrigeration cycle during phase transition (2010)

Experimental identification of the evaporator dynamics in a vapor compression cycle (VCC) subjected to imposed heat flux in the evaporator is studied. The imposed heat flux boundary condition represents a specific application of the VCC for electronics cooling. However, this application requires different models and control algorithms than traditional VCCs with fluid-to-fluid heat exchanges because of the faster time response of the imposed heat flux boundary condition and because the refrigerant flow at the exit of the evaporator is expected to be a two-phase mixture. First principle models are highly nonlinear and, hence, are not practical for system control. To obtain a simplified model, a dynamic identification of component response characteristics is performed by applying a pulse change in the system operating conditions (i.e., the heat load to the evaporator, the expansion valve opening, or the compressor speed). It is shown that for changes in expansion valve opening, the temperature of the refrigerant at the exit of the evaporator has opposite trends when the flow is initially in the two-phase region and when the flow is in the superheated region. This phenomena represents a challenge for controller design, and further investigation is required.
Quantitative determination of the lateral diffusion coefficients of the hormone-receptor complexes of insulin and epidermal growth factor on the plasma membrane of cultured fibroblasts. (1978)

Fluorescent derivatives of insulin and epidermal growth factor bound to 3T3 mouse fibroblasts are mobile on the cell surface, with similar diffusion coefficients, D approximately (3--5) x 10(-10) cm2/sec at 23 degrees C. Increasing the temperature to 37 degrees C results in rapid receptor immobilization. The immobilization is attributed to aggregation of hormone-receptor complexes, their internalization, or a combination of both processes.
Progestins Induce Down-Regulation of Insulin-Like Growth Factor-I (IGF-I) Receptors in Human Breast Cancer Cells: Potential Autocrine Role of IGF-II (1991)

Insulin-like growth factor-I (IGF-I) receptors are present in breast cancer cells and may play a role in breast cancer cell growth. We have studied the effect of progestins on IGF-I receptors in T47D human breast cancer cells. T47D cells constitutively express high levels of progesterone receptors and are a model for studying the regulation of cellular functions by progestins. Treatment of T47D cells with either progesterone or the synthetic progestin promegestone (R5020) decreased IGF-I receptor content by approximately 50%, as measured by Scatchard analysis and receptor biosynthesis studies. In contrast to progestins, estradiol, dexamethasone, and dihydrotestosterone did not influence IGF-I receptor content. No effect of R5020 was seen after 12 h of incubation, a near-maximal effect was seen after 24 h, and greatest effects were seen after 72 h. R5020 decreased IGF-I receptor mRNA abundance, indicating that progestins acted at the level of gene expression. However, progestins also increased the secretion of IGF-II, a ligand for the IGF-I receptor. In contrast to IGF-II, T47D cells did not express IGF-I. The addition of exogenous IGF-II to T47D cells down-regulated both IGF-I receptor binding and IGF-I receptor mRNA abundance. This study indicates, therefore, that progestins regulate IGF-I receptors in breast cancer cells and suggests that this regulation occurs via an autocrine pathway involving enhanced IGF-II secretion.
Immunogenicity and Safety of a Third COVID-19 BNT162b2 mRNA Vaccine Dose in 5- to 11-Year Olds (2023)

In this ongoing study, substantially increased ancestral SARS-CoV-2 neutralizing responses were observed 1 month after a third 10-µg BNT162b2 dose given to 5 to 11-year olds versus neutralizing responses post-dose 2. After dose 3, increased neutralizing responses against Omicron BA.1 and BA.4/BA.5 strains were also observed. The safety/tolerability profile was acceptable. (NCT04816643).
Gaussian versus flat-top spatial beam profiles for optical stimulation of the prostate nerves (2010)

The cavernous nerves (CN) course along the prostate surface and are responsible for erectile function. Improved identification and preservation of the CN's is critical to maintaining sexual potency after prostate cancer surgery. Noncontact optical nerve stimulation (ONS) of the CN's was recently demonstrated in a rat model, <i>in vivo</i>, as a potential alternative to electrical nerve stimulation (ENS) for identification of the CN's during prostate surgery. However, the therapeutic window for ONS is narrow, so optimal design of the fiber optic delivery system is critical for safe, reproducible stimulation. This study describes modeling, assembly, and testing of an ONS probe for delivering a small, collimated, flat-top laser beam for uniform CN stimulation. A direct comparison of the magnitude and response time of the intracavernosal pressure (ICP) for both Gaussian and flat-top spatial beam profiles was performed. Thulium fiber laser radiation (&lambda;=1870 nm) was delivered through a 200-&mu;m fiber, with distal fiber tip chemically etched to convert a Gaussian to flat-top beam profile. The laser beam was collimated to a 1-mm-diameter spot using an aspheric lens. Computer simulations of light propagation were used to optimize the probe design. The 10-Fr (3.4-mm-OD) laparoscopic probe provided a constant radiant exposure at the CN surface. The probe was tested in four rats, <i>in vivo</i>. ONS of the CN's was performed with a 1-mm-diameter spot, 5-ms pulse duration, and pulse rate of 20 Hz for a duration of 15-30 s. The flat-top laser beam profile consistently produced a faster and higher ICP response at a lower radiant exposure than the Gaussian beam profile due, in part, to easier alignment of the more uniform beam with nerve. The threshold for ONS was approximately 0.14 J/cm<sup>2</sup>, corresponding to a temperature increase of 6-8&deg;C at the CN surface after a stimulation time of 15 s. With further development, ONS may be used as a diagnostic tool for identification of CN's during prostate cancer surgery.