gebhart/patrepeval huggingface dataset:
A new class of high affinity ligands for the neurokinin A NK2 receptor: .psi.(CH2NR) reduced peptide bond analogs of neurokinin A4-10 (1992)

Analogues of [Leu10]NKA4-10 were synthesized in which each of the amide bonds was sequentially replaced with the reduced amide psi (CH2NH) bond to determine the effect of this structural modification on the antagonism of NKA binding to the HUB NK2 receptor. [psi (CH2-NH)9,Leu10]NKA4-10 (6) retained significant affinity for the NK2 receptor (IC50 = 115 nM) and showed weak partial stimulation of PI turnover (approximately 10-15% of NKA maximum). 6 behaves as a competitive antagonist of NKA-stimulated PI turnover with a pA2 = 6.7. The secondary amine of the psi (CH2NH) moiety of 6 was converted to a tertiary amine by alkylation. This modification was found to have a small effect upon receptor affinity but did result in attenuation of partial agonist activity. A combination of amino acid substitutions and psi (CH2NH) alkylation yielded [beta Ala8,psi (CH2N(CH2)2CH3)9,Phe10]NKA4-10 (21) which has very high affinity for the HUB NK2 receptor. This compound inhibited [125I]NKA binding with an IC50 = 1 nM which is equal to the receptor affinity of NKA. Compound 21 also shows very weak partial agonism of PI turnover (< or = 5% of NKA maximum) which makes this the most potent member of a new class of NKA ligands: psi(CH2NR)9-NKA4-10 analogues which potently antagonize NKA binding and possess minimal partial agonist activity.
Localized Conformational Changes in the N-Terminal Domain of CD4 Identified in Competitive Binding Assay of Monoclonal Antibodies and HIV-1 Envelope Glycoprotein (1992)

The CD4 antigen is established as a major cellular receptor for the human immunodeficiency virus (HIV). Previous studies have suggested that certain anti-CD4 monoclonal antibodies (MAbs) can inhibit or enhance the binding of the viral envelope glycoprotein gp120 to CD4 by allosteric effects. In the study reported here, 17 anti-CD4 MAbs were tested for their ability to influence the binding of each other to recombinant soluble CD4 in a solid-phase radioimmunoassay. Marked enhancement of binding between specific pairs of MAbs was seen, as well as inhibition or lack of interaction. Enhancement was seen less often when CD4+ cells were used as the target antigen. Information on patterns of enhancement and inhibition permitted grouping of MAbs on the basis of epitope specificity, and this grouping was in agreement with published findings based on X-ray crystallographic studies. These results demonstrate connectivity between epitopes in the first domain of recombinant CD4 and suggest a high degree of flexibility of surface structure. These findings may be of physiological significance both in the normal function of CD4 and in the interaction of CD4 with HIV. The data have implications for research or therapeutic strategies based on recombinant CD4 or CD4 mutants and highlight the problems of interpreting experimental findings based on abrogation of MAb binding.
Anti-alpha4 integrin monoclonal antibody inhibits multiple myeloma growth in a murine model. (2005)

In a syngeneic murine model of multiple myeloma with many of the characteristics of the human disease, a monoclonal antibody (mAb) to the integrin very late antigen-4 (VLA-4), given after the myeloma has already homed to and begun to establish itself within the bone marrow compartment, produces statistically significant effects on multiple disease variables. These include reductions in circulating levels of IgG2b; percentage of IgG2b-positive myeloma cells circulating in blood; spleen weight; and myeloma cell burden in spleen, bone marrow, and liver. mAb therapy had no effect on nonmalignant hematopoietic cells. An acute 6-day regimen of mAb treatment, initiated very late in disease to avoid mAb elimination in the immunocompetent animals, still significantly reduced spleen and blood myeloma cell burden. The ability of the (VLA-4) mAb to affect multiple variables in this model, even as monotherapy, suggests this pathway plays a central role in disease progression.
Genetic Analysis of Werner Syndrome in a Family. (1995)

Werner syndrome (WRN) is a rare autosomal recessive disorder, one of the progeroid syndromes, and is characterized by features of premature aging. The incidence of WRN in the Japanese population, 1 in 200,000, is higher than than that in the Caucasian population. The genetic defect of WRN is unknown. But genetic linkage to several markers on the short arm of chromosome 8 has been reported recently. Here, we studied one family with WRN in which an affected individual had a papillary thyroid carcinoma and myelodysplastic syndrome. Using 4 microsatellites closely located to the WRN locus: D8S360, D8S1055, D8S339 and ANK1, we analyzed the genotypes of this patient, her three siblings and her parents, who were first cousins. The mutative haplotype, identified through the generations in pedigree, helps detect a carrier or a presymptomatic patient. The eldest sister inherited two normal haplotypes, but the second sister inherited one mutative haplotype. There was no difference in clinical signs and symptoms between these sisters. when the WRN gene is isolated, it will help us understand the mechanism of aging.
Zeolite-catalyzed biomass conversion to fuels and chemicals (2010)

Heterogeneous catalysts have been a central element in the efficient conversion of fossil resources to fuels and chemicals, but their role in biomass utilization is more ambiguous. Zeolites constitute a promising class of heterogeneous catalysts and developments in recent years have demonstrated their potential to find broad use in the conversion of biomass. In this perspective we review and discuss the developments that have taken place in the field of biomass conversion using zeolites. Emphasis is put on the conversion of lignocellulosic material to fuels using conventional zeolites as well as conversion of sugars using Lewis acidic zeolites to produce useful chemicals.
From toxicological to eco-toxicological effects : how matrix population models can help to assess population sensitivity to contaminants in ecosystems (2011)

The retrospective and prospective assessment of contaminant impacts at higher levels of biological organization (populations, communities) is today constrained by the difficulty to observe, detect and assess chemical effects directly at these integrated levels. This is because of both practical issues (time and spatial scale, extinction) and intrinsic properties of such complex biological systems (integration of multiple environmental influences, adaptability, stochasticity). To gain in sensitivity and specificity, the assessment of toxicity in the lab and in the field is thus performed considering effects on organisms (survival, fertility, growth, or sub-organism responses (biomarkers). The extrapolation from such lower tier toxicity tests to sensitivity of higher biological levels is therefore required to ensure the ecological relevance of toxicity assessment. In this framework, population modelling is proposed in order to bridge the gap between the alterations of individual performance traits and the potential impairment of population dynamics. In ecotoxicology, this modelling mechanistic demographic approach revealed theoretically and experimentally how toxic population impacts are deeply modulated by population life history. In this presentation based on examples from aquatic ecotoxicology, I illustrate how perturbation analysis of matrix population models allows to disclose key demographic transitions for population fitness and to recognize the interplay between these demographic sensitivities and toxicological sensitivities in the response of populations to chemical perturbations. I discuss how these modelling tools lead us to consider that between and within species differences in life history are key determinants of chemical effects in the ecosystems.
Electrical measure of cross-phase modulation impact in WDM optical systems (2003)

Spectral response of XPM impairments in WDM systems is evaluated by experimentally measuring NRZ signals XPM impact through a spectral electrical technique. The results are compared with classically adopted time domain measurements and found in good agreement also with the theoretical model.
Tetrafunctional aliphatic epoxy I. Synthesis and characterization (1998)

A low viscosity tetrafunctional epoxy resin was synthesized by reacting amino-terminated polydimethylsiloxane with epichlorohydrin followed by dehydrohalogenation. The synthesized tetrafunctional aliphatic epoxy resin had an epoxy equivalent weight of 382, Mn of 1492, Mw of 2296, and a viscosity of 4.2 poise at 25°C. The chemical structure of the tetrafunctional aliphatic epoxy resin was studied by gel permeation chromatography (GPC), Fourier transform infrared spectra (FTIR), and 1H-NMR spectra. Results showed the tetrafunctional aliphatic epoxy-blended aromatic epoxy resin possessed high impact strength and flexural strength. SEM photographs were investigated to study the compatibility of the blended epoxy system. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 69: 51–58, 1998
Early Detection of Steatohepatitis in Fatty Rat Liver by Using MR Elastography (2009)

http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.2523081817/-/DC1.
Senescence and Immortalization: Relationships to Telomeres and Telomerase (2006)

Cellular senescence is a general stress‐response program that restrains cellular proliferation. Under optimal growth conditions, the onset of senescence depends on telomere status. There is not a sentinel short human telomere that triggers senescence but a group of about 10% of the shortest telomeres that are involved. When a few telomeres are sufficiently short (uncapped), a DNA damage response‐induced growth arrest occurs. The senescence pathway involves the formation of telomere dysfunction induced foci that contain DNA damage response factors, such as 53BP1, gamma‐H2AX, and the Mre11complex. The signaling pathway responsible for establishing a senescent state in such cells involves primarily ATM, Chk1/Chk2 and p53, leading to a G1 phase arrest. Importantly, the DNA‐damage response observed in senescent cells is not a transient phenomenon, but consists of a permanent activation of the DNA damage checkpoint machinery. The long‐term growth arrest at senescence may be thought of as an initial anti‐tumor protection mechanism. In situations where normal cell cycle checkpoints are altered, cells can bypass the normal senescence signaling pathway and continue to grow until they reach a second growth arrest state known as crisis. In crisis, telomeres are terminally short and, in the presence of other genetic and epigenetic changes, can result in telomeric fusions, subsequent breakage‐fusion‐bridge cycles and in rare cells, up‐regulation or reactivation of telomerase, the cellular RNP that is able to add telomeric repeats to the ends of chromosomes and thus prevent their shortening. In both senescence and crisis ectopic expression of the catalytic subunit of telomerase (hTERT) leads directly to an immortal state demonstrating that telomeres are important in both replicative senescence and crisis.
Biologically-Derived Photonic Materials for Thermal Protection Systems (2014)

Space vehicles entering a planetary atmosphere at high velocity can be subject to substantial radiative heating from the shock layer in addition to the convective heating caused by the flow of hot gas past the vehicle surface. The radiative component can be very high but of a short duration. Approaches to combat this effect include investigation of various materials to reflect the radiation. Photonic materials can be used to reflect radiation. The wavelengths reflected depend on the length scale of the ordered microstructure. Fabricating photonic structures, such as layers, can be time consuming and expensive. We have used a biologically-derived material as the template for forming a high temperature photonic material that could be incorporated into a heatshield thermal protection material.
Enhanced Imaging Using Inverse Design of Nanophotonic Scintillators (2023)

Abstract Converting ionizing radiation into visible light is essential in a wide range of fundamental and industrial applications, such as electromagnetic calorimeters in high‐energy particle detectors, electron detectors, image intensifiers, and X‐ray imaging. These different areas of technology all rely on scintillators or phosphors, i.e., materials that emit light upon bombardment by high‐energy particles. In all cases, the emission is through spontaneous emission . The fundamental nature of spontaneous emission poses limitations on all these technologies, imposing an intrinsic trade‐off between efficiency and resolution in all imaging applications: thicker phosphors are more efficient due to their greater stopping power, which however comes at the expense of image blurring due to light spread inside the thicker phosphors. Here, the concept of inverse‐designed nanophotonic scintillators is proposed, which can overcome the trade‐off between resolution and efficiency by reshaping the intrinsic spontaneous emission. To exemplify the concept, multilayer phosphor nanostructures are designed and these nanostructures are compared to state‐of‐the‐art phosphor screens in image intensifiers, showing a threefold resolution enhancement simultaneous with a threefold efficiency enhancement. The enabling concept is applying the ubiquitous Purcell effect for the first time in a new context—for improving image resolution. Looking forward, this approach directly applies to a wide range of technologies, including X‐ray imaging applications.
Carbon dioxide laser treatment promotes repair of the three-dimensional network of elastic fibres in rat skin (2001)

These findings indicate that CO2 laser treatment has a therapeutic potential to repair wrinkles to non-irradiated levels through recovery of the three-dimensional structure of elastic fibres.
Polarization dependence of light intensity distribution near a nanometric aluminum slit (2004)

The near-field radiation pattern of a long thin slit (with a width much smaller than the excitation wavelength) in a uniform aluminum surface was measured and modeled by numerical computation. In particular, the interplay between the incident light polarization and the slit width is found to play an essential role in the near-field profile on the back side of the nanoslits. Two-dimensional finite-difference time-domain computer simulations were performed to calculate the near-field intensity profile for different slit widths and metal thicknesses. This method will allow the optimization of three-dimensional near-field radiation patterns for a variety of near-field molecular scanning schemes.
Integrative visual analytics for suspicious behavior detection (2009)

In the VAST Challenge 2009 suspicious behavior had to be detected applying visual analytics to heterogeneous data, such as network traffic, social network enriched with geo-spatial attributes, and finally video surveillance data. This paper describes some of the awarded parts from our solution entry.
Supplementary Table from Epigenetic Therapies in Ovarian Cancer Alter Repetitive Element Expression in a <i>TP53</i>-Dependent Manner (2023)

Supplementary Table from Epigenetic Therapies in Ovarian Cancer Alter Repetitive Element Expression in a &lt;i&gt;TP53&lt;/i&gt;-Dependent Manner
Damage Growth Analysis of Sandwich Structures Subjected to Combined Compression and Pressure Loading (2019)

Fluid-ingression phenomena in composite sandwich structures is a concern for components employed in the aerospace industry. Poor design/material selections, impact damages, thermomechanical loads occurring during ground-air-ground (GAG) cycling and changes to internal pressure within the sandwich structure all lead to localized transverse cracks, delaminations, facesheet/core disbonds and core damages which create more passageways for fluid migration. In some cases, damage growth due to latter two cases is stable and occurs over a period of flights, but may not be readily detected on the ground when the thermo-mechanical and internal pressure loads are released. Hence, the structure will continue to sustain load-carrying capabilities until the damage size reaches a critical damage threshold (CDT) which leads to catastrophic failure. Unless such damage is detected and repaired prior to reaching CDT, GAG effects will further increase the damage size and threaten the structural integrity and safety of the aircraft. Current research provides an analytical method to predict facesheet debond based on the Winkler foundation approach that agrees well with both numerical and experimental results and evaluates the capabilities of cohesive zone modeling to predict onset of damage growth. Also, a standardized procedure and test apparatus for GAG testing to simulate damage under a mixed-mode stress state caused by the pressure differential and in-plane mechanical loads is developed. Current phase of the research focusses on investigating the effects of GAG cycling on sandwich structures by subjecting them to combined pressure and in-plane mechanical loads and investigate the conditions leading to the onset of damage, and to develop a method to conduct GAG simulation based on SCB model calibration. The information gathered through this research will be instrumental in developing analytical methods and validating finite element analysis procedures to further investigate the damage growth mechanics of sandwich composite structures.
Statistical analysis of the autoregressive modeling of reverberant speech (2006)

Hands-free speech input is required in many modern telecommunication applications that employ autoregressive (AR) techniques such as linear predictive coding. When the hands-free input is obtained in enclosed reverberant spaces such as typical office rooms, the speech signal is distorted by the room transfer function. This paper utilizes theoretical results from statistical room acoustics to analyze the AR modeling of speech under these reverberant conditions. Three cases are considered: (i) AR coefficients calculated from a single observation; (ii) AR coefficients calculated jointly from an M-channel observation (M > 1); and (iii) AR coefficients calculated from the output of a delay-and sum beamformer. The statistical analysis, with supporting simulations, shows that the spatial expectation of the AR coefficients for cases (i) and (ii) are approximately equal to those from the original speech, while for case (iii) there is a discrepancy due to spatial correlation between the microphones which can be significant. It is subsequently demonstrated that at each individual source-microphone position (without spatial expectation), the M-channel AR coefficients from case (ii) provide the best approximation to the clean speech coefficients when microphones are closely spaced (<0.3m).
Covalent Modification of the Nucleotide Binding Domains of Cystic Fibrosis Transmembrane Conductance Regulator (1998)

The cytosolic nucleotide binding domains of cystic fibrosis transmembrane conductance regulator (NBD1 and NBD2) mediate ATP-dependent opening and closing of the Cl- channel pore. To learn more about NBD structure and function, we introduced a cysteine residue into the Walker A motif or the LSGGQ motif of each NBD and examined modification by N-ethylmaleimide (NEM). Covalent modification of either Walker A motif partially inhibited cystic fibrosis transmembrane conductance regulator channel activity, decreasing the open state probability by prolonging the long closed duration. An increase in cytosolic ATP concentration slowed the rate of modification. The data suggest that both NBDs interact with ATP to influence channel opening and that inhibition by NEM modification was in part due to decreased ATP binding. When cysteine was placed in the NBD2 Walker A motif, it was modified more rapidly than when it was placed in NBD1, suggesting that the NBDs are not structurally or functionally identical. Modification of a cysteine inserted in the LSGGQ motif of either NBD1 or NBD2 also inhibited channel activity. The rate of modification was comparable with that of a thiol in free solution, suggesting that the LSGGQ motif resides in a surface-exposed position in both NBDs.
P2‐361: AMYLOID AND TAU IMAGING IN PATIENTS WITH POSTERIOR CORTICAL ATROPHY (2018)

Posterior cortical atrophy (PCA) is a clinical syndrome characterized by progressive loss of higher visual function based on heterogeneous pathologies including Alzheimer's disease (AD) and non-AD tauopathies. 11C-labeled pyridinyl-butadienyl-benzothiazole3 (11C-PBB3) is a tau positron emission tomography (PET) lingand that can detect a broad range of tau inclusions. Aims of the present study are to investigate the pathological background using PET and its relation with clinical features of PCA. Three patients with PCA (age 56 ± 3 years), two early onset AD patients (51 and 60 years), and 12 healthy volunteers (71.8 ± 8.73 years) underwent PET scans with 11C-PBB3, 11C-PiB, and 18F-FDG for evaluating brain regional tau and amyloid demposition and glucose metabolism, as well as neurological exams. All PCA and early onset AD patients demonstrated PiB positive and all healthy volunteers were negative. Distribution patterns of PiB in PCA patients resembled those in AD patients. As for PBB3-PET, PCA patients showed higher PBB3 uptake around parieto-occipital lobe in addition to temporal lobe compared with healthy volunteers, while PBB3 uptake around occipital lobe was relatively spared in AD patients. Similary, PCA patients showed glucose hypometabolism around occipital lobe as well as AD specific regions such as posterior cingulate, precuneus and lateral parieto-occipital cortices. The present study demonstrated that tau pathology characteristically involved occipital lobe in PCA patients despite their commonplace distribution patterns of amyloid pathology, suggesting that tau pathology rather than amyloid pathology would closely associated with unique clinical features of PCA.
Isolation of Murine Retinal Endothelial Cells for Next-Generation Sequencing (2021)

Recent improvements in next-generation sequencing have advanced researchers' knowledge of molecular and cellular biology, with several studies revealing novel paradigms in vascular biology. Applying these methods to models of vascular development requires the optimization of cell isolation techniques from embryonic and postnatal tissues. Cell yield, viability, and purity all need to be maximal to obtain accurate and reproducible results from next-generation sequencing approaches. The neonatal mouse retinal vascularization model is used by researchers to study mechanisms of vascular development. Researchers have used this model to investigate mechanisms of angiogenesis and arterial-venous fate specification during blood vessel formation and maturation. Applying next-generation sequencing techniques to study the retinal vascular development model requires optimization of a method for the isolation of retinal endothelial cells that maximizes cell yield, viability, and purity. This protocol describes a method for murine retinal tissue isolation, digestion, and purification using fluorescence-activated cell sorting (FACS). The results indicate that the FACS-purified CD31+/CD45- endothelial cell population is highly enriched for endothelial cell gene expression and exhibits no change in viability for 60 min post-FACS. Included are representative results of next-generation sequencing approaches on endothelial cells isolated using this method, including bulk RNA sequencing and single-cell RNA sequencing, demonstrating that this method for retinal endothelial cell isolation is compatible with next-generation sequencing applications. This method of retinal endothelial cell isolation will allow for advanced sequencing techniques to reveal novel mechanisms of vascular development.