gebhart/patrepeval huggingface dataset:
Chemotactic recruitment of adult neural progenitor cells into multifunctional hydrogels providing sustained SDF‐1α release and compatible structural support (2012)

Without chemotactic cues and structural support, cavitary brain lesions typically fail to recruit endogenous neural progenitor cells (NPCs). Toward resolving this, we engineered multifunctional biomaterials comprising injectable gelatin-hydroxyphenylpropionic acid (Gtn-HPA) hydrogels and dextran sulfate/chitosan polyelectrolyte complex nanoparticles (PCNs) that delivered stromal cell-derived factor-1α (SDF-1α). Over 7 d of interface with in vitro tissue simulant containing adult rat hippocampal NPCs (aNPCs) and their neuronal progeny, Gtn-HPA/SDF-1α-PCN hydrogels promoted chemotactic recruitment to enhance infiltration of aNPCs by 3- to 45-fold relative to hydrogels that lacked SDF-1α or vehicles to sustain SDF-1α release. When cross-linked with 0.85-0.95 mM HO, Gtn-HPA/SDF-1α-PCN hydrogels provided optimally permissive structural support for migration of aNPCs. Specific matrix metalloproteinase (MMP) inhibitors revealed that 42, 30, and 55% of cell migration into Gtn-HPA/SDF-1α-PCN hydrogels involved MMP-2, 3, and 9, respectively, demonstrating the hydrogels to be compatible toward homing endogenous NPCs, given their expression of similar MMPs. Interestingly, PCNs utilized FGF-2 found in situ to induce chemokinesis, potentiate SDF-1α chemotactic recruitment, and increase proliferation of recruited cells, which collectively orchestrated a higher number of migrated aNPCs. Overall, Gtn-HPA/SDF-1α-PCN hydrogels prove to be promising biomaterials for injection into cavitary brain lesions to recruit endogenous NPCs and enhance neural tissue repair/regeneration.
Interaction between Radiation-Induced Adaptive Response and Bystander Mutagenesis in Mammalian Cells (2003)

Two conflicting phenomena, the bystander effect and the adaptive response, are important in determining biological responses at low doses of radiation and have the potential to have an impact on the shape of the dose-response relationship. Using the Columbia University charged-particle microbeam and the highly sensitive AL cell mutagenic assay, we reported previously that nonirradiated cells acquired mutagenesis through direct contact with cells whose nuclei had previously been traversed with either a single or 20 alpha particles each. Here we show that pretreatment of cells with a low dose of X rays 4 h before alpha-particle irradiation significantly decreased this bystander mutagenic response. Furthermore, bystander cells showed an increase in sensitivity after a subsequent challenging dose of X rays. Results from the present study address some of the pressing issues regarding both the actual target size and the radiation dose response and can improve on our current understanding of radiation risk assessment.
Increased sodium channel SNS/PN3 immunoreactivity in a causalgic finger (2001)

The sodium channels SNS/PN3 and NaN/SNS2 are regulated by the neurotrophic factors-nerve growth factor (NGF) and glial-derived neurotrophic factor (GDNF), and may play an important role in the development of pain after nerve injury or inflammation. These key molecules have been studied in an amputated causalgic finger and control tissues by immunohistochemistry. There was a marked increase in the number and intensity of SNS/PN3-immunoreactive nerve terminals in the affected finger, while GDNF-immunoreactivity was not observed, in contrast to controls. No differences were observed for NGF, trk A, NT-3 or NaN/SNS2-immunoreactivity. While further studies are required, these findings suggest that accumulation of SNS/PN3 and/or loss of GDNF may contribute to pain in causalgia, and that selective blockers of SNS/PN3 and/or rhGDNF may provide effective novel treatments.
A User-Friendly Model for Spray Drying to Aid Pharmaceutical Product Development (2013)

The aim of this study was to develop a user-friendly model for spray drying that can aid in the development of a pharmaceutical product, by shifting from a trial-and-error towards a quality-by-design approach. To achieve this, a spray dryer model was developed in commercial and open source spreadsheet software. The output of the model was first fitted to the experimental output of a Büchi B-290 spray dryer and subsequently validated. The predicted outlet temperatures of the spray dryer model matched the experimental values very well over the entire range of spray dryer settings that were tested. Finally, the model was applied to produce glassy sugars by spray drying, an often used excipient in formulations of biopharmaceuticals. For the production of glassy sugars, the model was extended to predict the relative humidity at the outlet, which is not measured in the spray dryer by default. This extended model was then successfully used to predict whether specific settings were suitable for producing glassy trehalose and inulin by spray drying. In conclusion, a spray dryer model was developed that is able to predict the output parameters of the spray drying process. The model can aid the development of spray dried pharmaceutical products by shifting from a trial-and-error towards a quality-by-design approach.
Ionic Liquid-Enhanced Photooxidation of Water Using the Polyoxometalate Anion [P<sub>2</sub>W<sub>18</sub>O<sub>62</sub>]<sup>6–</sup>as the Sensitizer (2011)

Simple polyoxometalate anions are known to be photoreduced in molecular solvents in the presence of 2-propanol or benzyl alcohol. The use of ionic liquids (ILs) as the solvent is now reported to also allow the photooxidation of water to be achieved. In particular, the photochemistry of the classic Dawson polyoxometalate salt K(6)[P(2)W(18)O(62)] has been studied in detail when water is present in the aprotic IL, 1-butyl-3-methylimidazolium tetrafluoroborate ([Bmim][BF(4)]) and the protic IL, diethanolamine hydrogen sulfate (DEAS). In these and other ILs, irradiation with white light (wavelength 275-750 nm) or UV light (wavelength 275-320 nm) leads to overall reduction of the [P(2)W(18)O(62)](6-) anion to [P(2)W(18)O(62)](7-) and concomitant oxidation of water to dioxygen and protons. The modified structure of bulk water present in ILs appears to facilitate its oxidation. Analogous results were obtained in aqueous solutions containing the protic IL as an electrolyte. The photoproducts (reduced polyoxometalate anion, dioxygen, and protons) were identified by, respectively, voltammetry, a Clark electrode, and monitoring of pH. The formal reversible potentials E(0)(F) for [P(2)W(18)O(62)](6-/7-/8-/9-/10-) couples are much more positive than in molecular solvents. The [P(2)W(18)O(62)](8-) and more reduced anions, if formed as intermediates, would efficiently reduce photoproducts H(+) or dioxygen to produce [P(2)W(18)O(62)](7-), rather than reform to [P(2)W(18)O(62)](6-). Thus, under photoirradiation conditions [P(2)W(18)O(62)](7-) acts as a kinetic sink so that in principle indirect splitting of water to produce dioxygen and dihydrogen can be achieved. The equivalent form of photooxidation does not occur in liquid water or in molecular solvents such as MeCN and MeCN/CH(2)Cl(2) containing added water, but does occur for solid K(6)[P(2)W(18)O(62)] in contact with water vapor.
Development and Characterization of a Novel Peptide—Drug Conjugate with DM1 for Treatment of FGFR2-Positive Tumors (2021)

A maytansin derivative, DM1, is a promising therapeutic compound for treating tumors, but is also a highly poisonous substance with various side effects. For clinical expansion, we tried to develop novel peptide-drug conjugates (PDCs) with DM1. In the study, a one-bead one-compound (OBOC) platform was used to screen and identify a novel, highly stable, non-natural amino acid peptide targeting the tyrosine receptor FGFR2. Then, the identified peptide, named LLC2B, was conjugated with the cytotoxin DM1. Our results show that LLC2B has high affinity for the FGFR2 protein according to an isothermal titration calorimetry (ITC) test. LLC2B-Cy5.5 binding to FGFR2-positive cancer cells was confirmed by fluorescent microscopic imaging and flow cytometry in vitro. Using xenografted nude mouse models established with breast cancer MCF-7 cells and esophageal squamous cell carcinoma KYSE180 cells, respectively, LLC2B-Cy5.5 was observed to specifically target tumor tissues 24 h after tail vein injection. Incubation assays, both in aqueous solution at room temperature and in human plasma at 37 °C, suggested that LLC2B has high stability and strong anti-proteolytic ability. Then, we used two different linkers, one of molecular disulfide bonds and another of a maleimide group, to couple LLC2B to the toxin DM1. The novel peptide-drug conjugates (PDCs) inhibited tumor growth and significantly increased the maximum tolerated dose of DM1 in xenografted mice. In brief, our results suggest that LLC2B-DM1 can be developed into a potential PDC for tumor treatment in the future.
Hemoadsorption removes tumor necrosis factor, interleukin-6, and interleukin-10, reduces nuclear factor-κB DNA binding, and improves short-term survival in lethal endotoxemia* (2004)

Hemoadsorption was associated with reduced inflammation and improved survival in this murine model of septic shock.
Expanded encyclopaedias of DNA elements in the human and mouse genomes (2020)

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE<sup>1</sup> and Roadmap Epigenomics<sup>2</sup> data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.
A view of the human idiotypic repertoire. Electron microscopic and immunologic analyses of spontaneous idiotype-anti-idiotype dimers in pooled human IgG. (1990)

It has previously been reported that up to 40% of the molecules of human IgG from pooled plasma (100,000 donations) spontaneously dimerize, whereas IgG prepared from a single donor contains only trace quantities of dimer. We have conducted immunoelectron microscopic analyses on such samples and have verified that the majority of dimers are composed of complexes in which two arms of each molecule are bound in a reciprocal fashion at or near the distal tips of their respective arms as previously seen in bona fide Id-anti-Id complexes. A significant role for Fc was ruled out by showing the formation of dimeric ring structures in purified F(ab')2 samples. Spontaneous dimerization was also observed in pooled bovine or mouse IgG, but not in that from single animals. Radiolabeled monomeric, single donor human IgG was used as a probe to investigate dimer formation; this material readily codimerized with IgG from other donors or from pooled plasma (either human or bovine), but did not dimerize with IgG from the same donor. Subclass analysis of multiple donor human IgG revealed that the most flexible subclass (IgG3) was overrepresented in the dimer fraction, whereas one of the less flexible subclasses (IgG2) was underrepresented. Although IgG2 could dimerize to some extent with IgG of other subclasses, it could not self-dimerize. These data suggest that structural constraints (hinge flexibility) may play a role in limiting dimerization. This suspicion was confirmed by showing that an additional 15.5% of the monomeric IgG fraction from a multidonor sample could dimerize after a chemically induced increase in hinge flexibility. Our results are interpreted to show that, although the number of functionally distinct Id produced by a species is immense, it is nontheless finite. Moreover, the Id repertoire of an individual is much smaller than that of the species. Pooling the IgG from a number of individuals increases the Id diversity, which increases the chance that any given Id-bearing molecular will encounter a complementary partner.
Histamine-Releasing Factor and Immunoglobulins in Asthma and Allergy (2013)

Factors that can induce the release of histamine from basophils have been studied for more than 30 years. A protein termed histamine-releasing factor (HRF) was purified and molecularly cloned in 1995. HRF can stimulate histamine release and IL-4 and IL-13 production from IgE-sensitized basophils and mast cells. HRF-like activities were found in bodily fluids during the late phase of allergic reactions, implicating HRF in allergic diseases. However, definitive evidence for the role of HRF in allergic diseases has remained elusive. On the other hand, we found effects of monomeric IgE on the survival and activation of mast cells without the involvement of a specific antigen, as well as heterogeneity of IgEs in their ability to cause such effects. The latter property of IgE molecules seemed to be similar to the heterogeneity of IgEs in their ability to prime basophils in response to HRF. This similarity led to our recent finding that ~30% of IgE molecules can bind to HRF via their Fab interactions with two binding sites within the HRF molecule. The use of peptide inhibitors that block HRF-IgE interactions revealed an essential role of HRF to promote skin hypersensitivity and airway inflammation. This review summarizes this and more recent findings and provides a perspective on how they impact our understanding of allergy pathogenesis and potentially change the treatment of allergic diseases.
The Australian and New Zealand registry of regional anaesthesia (AURORA) - results from our most recent 10,000 patients (2011)

s and Programme: EUROANAESTHESIA 2011: The European Anaesthesiology Congress: ESA Best Abstract Prize Competition (BAPC)
Mitigation of uncertainty in velocity and anisotropy estimation for prestack depth imaging (2004)

We present a workflow to reduce error in estimating anisotropy parameters when using vertical updating and integration of surface seismic, well logs and vertical checkshots. For a simplified model having a low velocity anomaly, we derive an analytical expression for residual moveout which demonstrates that vertical update cannot discriminate between lateral velocity heterogeneity and anisotropy. We have seen that this error in anisotropy estimation can lead to erroneous depth structures in anisotropic pre‐stack depth migrated images. We found that, imposing a constraint on the maximum lateral velocity gradient during model building can minimize error in anisotropy estimates. Finally we propose some alternative methods that may further reduce anisotropy estimation error.
Comparative single-dose kinetics and dynamics of lorazepam, alprazolam, prazepam, and placebo (1988)

Thirty-nine healthy volunteers received single oral doses of either alprazolam (1 mg), lorazepam (2 mg), prazepam (20 mg), or placebo in a randomized, double-blind, parallel group study. Plasma drug concentrations, subjective self-ratings, and the digit symbol substitution test (DSST) were evaluated during 24 hours after dosage. Alprazolam was absorbed rapidly and produced correspondingly rapid sedation and impaired DSST performance. These effects also resolved rapidly, being similar to placebo by 4 to 6 hours after dosage. Sedative and DSST-impairing effects of lorazepam were of slower onset but longer duration than those of alprazolam. After oral prazepam, appearance of desmethyldiazepam in plasma was slow, with minimal sedative and DSST-impairing effects. Twenty-four hours after dosage, both alprazolam and lorazepam significantly impaired recall of a list of 16 words learned previously 3 hours after dosage. Thus benzodiazepines with approximately equivalent clinical anxiolytic properties may have different sedative, performance-impairing, and amnesic profiles after single doses in healthy volunteers; these differences are explained at least in part by pharmacokinetic variations.
Mapping nanoscale domain patterns in ferroelectric ceramics by atomic force acoustic microscopy and piezoresponse force microscopy (2013)

In this paper, nanoscale domain patterns of ferroelectric ceramics were investigated by both atomic force acoustic microscopy (AFAM) and piezoresponse force microscopy (PFM). First, we applied the dual frequency resonance tracking (DFRT) technique on AFAM and realized nanoscale modulus mapping. Then we comparatively mapped the nanoscale domain patterns in a PZT ceramics using PFM, single-frequency AFAM, and DFRT AFAM in the same scanning area. Results show that PFM can give the best contrast domain patterns and is not sensitive to cantilever stiffness. In comparison, both modes of AFAM are sensitive to cantilever stiffness and can give good contrast of domains only using very stiff cantilevers. Furthermore, both modes of AFAM can map the subsurface domain structures and the grain boundaries clearly while PFM usually cannot. Based on the resonance-frequency image obtained by the DFRT AFAM, we also obtained the nanoscale modulus of the whole scanning area which may help understand the possible domain movement under mechanical or electric fields. Finally, we suggest that, to characterize the nanoscale domain properties in ferroelectrics, PFM plus resonance tracking AFAM is the best choice.
A high-speed neural analog circuit for computing the bit-level transform image coding (1991)

A Hopfield-type neural network approach is presented which leads to an analog circuit for implementing the bit-level transform image. The computation of a 2D DCT (discrete cosine transform)-based transform coding is shown to solve a quadratic nonlinear programming problem subject to the corresponding 2's complement binary variables of 2D DCT coefficients. A novel Hopfield-type neural analog circuit designed to perform the DCT-based quadratic nonlinear programming could obtain the desired coefficients of an 8*8 DCT in 2's complement code within 1 ns with RC=10/sup -8/. A programmable analog MOS implementation provides a flexible architecture to realize the DCT-based neural net.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Learning and inference via maximum inner product search (2016)

A large class of commonly used probabilistic models known as log-linear models are defined up to a normalization constant. Typical learning algorithms for such models require solving a sequence of probabilistic inference queries. These inferences are typically intractable, and are a major bottleneck for learning models with large output spaces. In this paper, we provide a new approach for amortizing the cost of a sequence of related inference queries, such as the ones arising during learning. Our technique relies on a surprising connection with algorithms developed in the past two decades for similarity search in large data bases. Our approach achieves improved running times with provable approximation guarantees. We show that it performs well both on synthetic data and neural language models with large output spaces.
Synthesis and Anti-inflammatory Evaluation of Novel Benzimidazole and Imidazopyridine Derivatives (2012)

Sepsis, an acute inflammatory disease, remains the most common cause of death in intensive care units. A series of benzimidazole and imidazopyridine derivatives were synthesized and screened for anti-inflammatory activities, and the imidazopyridine series showed excellent inhibition of the expression of inflammatory cytokines in LPS-stimulated macrophages. Compounds X10, X12, X13, X14, and X15 inhibited TNF-α and IL-6 release in a dose-dependent manner, and X12 showed no cytotoxicity in hepatic cells. Furthermore, X12 exhibited a significant protection against LPS-induced septic death in mouse models. Together, these data present a series of new imidazopyridines with potential therapeutic effects in acute inflammatory diseases.
Automatic setup deviation measurements with electronic portal images for pelvic fields (1998)

The purpose of this work was to develop a fully automatic tool for the detection of setup deviation for small pelvic field using, in external beam radiotherapy, an electronic portal imaging device (EPID). The algorithm processes electronic portal images of prostate cancer patients. No fiducial points or user interventions are needed. Deviation measurements are based on bone edge detection performed with Laplacian of a Gaussian (LoG) operator. Two bone edge images are then correlated, one of which is a reference image taken as the first fraction image for the purpose of this study. The electronic portal images (EPI) also show band artefacts which are removed using the morphological top-hat transform. The algorithm was first validated with 59 phantom images acquired in clinical treatment conditions with known displacements. The algorithm was then validated with 79 clinical images where bone contours were delineated manually. For the phantom images, the setup deviations were measured with a absolute mean error of 0.59 mm and 0.47 mm with a standard deviation of 0.64 mm and 0.42 mm, horizontally and vertically, respectively. A second validation was performed using clinical prostate cancer images. The measured patient displacements have an absolute mean error of 0.48 mm and 1.41 mm with a standard deviation of 0.58 mm and 1.30 mm in the X and Y directions, respectively. The algorithm execution time on a SUN workstation is 5 s. This algorithm shows good potential as a setup deviation measurement tool in clinical practice. The possibility of using this algorithm combined with decision rules based on statistical observations is very promising.
Optical phantoms for ultrasound-modulated optical tomography (2008)

Optical phantoms are widely used for simulating optical properties of biological tissues. Their accurate design and fabrication are important factors in validating and designing biomedical systems. We discuss fabrication and measurement of optical phantoms in ultrasound-modulated optical tomography. The optical properties of the phantoms are measured by an oblique-incidence diffuse reflectance spectrometer, which can accurately measure the wavelength-dependent absorption and reduced scattering coefficients of optical phantoms. In addition, the acoustic properties of the phantoms are discussed.