gebhart/patrepeval huggingface dataset:
Fluorescent imaging probes of nitrogen-containing bone active drugs: design, synthesis and applications (2013)

Bisphosphonates (BPs) are therapeutic agents for treatment of bone disorders such as osteoporosis and Paget?s disease. Several nitrogen-containing bisphosphonates (N-BPs) and phosphonocarboxylate (PC) analogues also have potential as anti-cancer agents. However, details of the skeletal distribution, cellular uptake and mechanisms of these drugs remain to be elucidated, stimulating the creation of imaging probes which mimic some or all of their pharmacological properties. ? A fluorescent imaging "toolkit" with more than 20 probes derived from all three heterocyclic N-BP drugs (risedronate, zoledronate and minodronate) and related analogues have been successfully synthesized. A linking strategy with two routes was applied under exceedingly mild conditions and introduced a terminal amino group in drug-linker intermediates capable to conjugate with the commercially available activated ester of fluorescent dyes. All the fluorescent probes were prepared in good yield (50-77%) and high purity (> 95%), and are fully characterized by HPLC, UV-VIS and fluorescence emission spectroscopy, �H and ��P NMR and high-resolution MS. ? The "toolkit" contains a series of fluorescent probes ranging from visible to near infrared optical window and the probes generally retain substantial affinity for bone mineral reflecting the varying affinities of their parent drug components, depending on the structure of the conjugating fluorescent dye. In addition, we have obtained evidence that certain probes (e.g. the FAM- and ROX- conjugates) have anti-prenylation and anti-resorptive effects in vitro and in vivo, demonstrating that the probes could retain biological activities of the parent BP drugs. ? Due to their diverse spectroscopic and pharmacological properties, the fluorescent imaging probe "toolkit" has been successfully utilized in various biological researches including osteoclast imaging, drug distribution at bone skeleton and cellular level, mechanism studies of osteonecrosis of the jaw (ONJ), cancer imaging, et al., and several papers have been published based on the obtained results, demonstrating the versatility of the imaging probe "toolkit". ? The first example of a bifunctional amino/azido-containing N-heterocyclic bisphosphonate (amino-azido-para-dRIS, compound 7 in Chapter 5) has been synthesized
Anion Effects in (BEDT‐TTF)2X Salts: Symmetry Induced Superstructures (1986)

Abstract The structural and electrical properties of a series of (BEDT‐TTF) 2 X salts are systematized in terms of a substructure‐superstructure relationship which is induced by variation in anion symmetry and pictorially represented as a crystallographic family tree. Importantly, it is recognized that the ambient‐pressure superconductors α‐(BEDT‐TTF) 2 I 3 , α‐(BEDT‐TTF) 2 IBr 2 , and α‐(BEDT‐TTF) 2 AuI 2 have crystal structures coincident with the parent subcell of this crystallographic family tree. Moreover, all first‐generation supercells (doubling of any one subcell vector) are exclusively populated by salts with non‐centrosymmetric anions of tetrahedral symmetry, and, apparently, second‐generation supercells (doubling of any two subcell vectors) are populated by salts with centrosymmetric anions of octahedral symmetry. Finally, trends in structural properties with anion size are briefly considered.
Nanotechnology promotes the full-thickness diabetic wound healing effect of recombinant human epidermal growth factor in diabetic rats (2010)

We utilized a modified double-emulsion method with poly(lactic-co-glycolic acid) as the carrier to prepare recombinant human epidermal growth factor (rhEGF) nanoparticles. The morphology of the nanoparticles was detected by a transmission electron microscope. The particle size distribution was measured by a laser analyzer with a zeta potential meter. Enzyme-linked immunosorbent assays were performed to determine the rhEGF encapsulation efficiency and release model, and the proliferation of the mouse fibroblasts was analyzed by the MTT method. Diabetic rats with full-thickness wounds were divided into four groups according to different treatments: rhEGF nanoparticles, rhEGF stock solution, empty nanoparticles, and phosphate-buffered saline. Photographs were taken after the treatments to calculate the wound healing rates, and the granulation tissue of the wounds was sampled for pathologic slides. Proliferating cell nuclear antigen was assayed by immunohistochemistry. Our results showed that the rhEGF nanoparticles were around 193.5 nm (diameter), and the particle size distribution was uniform and dispersible. The encapsulation efficiency was 85.6% and rhEGF release lasted 24 hours. Compared with other groups, the rhEGF nanoparticles promoted the highest level of fibroblast proliferation, and this group showed the fastest healing rate. The number of proliferating cell nuclear antigen positive cells in the rhEGF nanoparticles group was higher than the other groups. We concluded that controlled release of rhEGF encapsulated in the nanoparticles enhanced rhEGF effects to stimulate cell proliferation and shorten the wound healing time.
The Growth of Complex Garnet Epitaxial Films with a Coaxially Arranged CVD Reactor (1973)

A coaxially arranged CVD reactor has proved versatile in the epitaxial growth of several complex magnetic garnet films. Gallium substituted gadolinium yttrium iron garnet (Ga‐GdYIG) and gallium substituted yttrium iron garnet (Ga‐YIG) have been grown on gadolinium gallium garnet (GGG) and dysprosium gadolinium gallium garnet (DyGGG) substrates, respectively. Features in the reactor design pertinent to the growth of good quality complex garnet films as well as deposition conditions are presented. Among these are precise control of reactant and carrier gas flow, provision for well‐mixed reactant gases at the substrate surface, and the suitable presentation of the substrate to the CVD reactants.
Engagement of CD99 triggers the exocytic transport of ganglioside GM1 and the reorganization of actin cytoskeleton (2003)

We studied the role of lipid rafts and actin cytoskeleton in CD99-mediated signaling to elucidate the mechanism of protein transport upon CD99 engagement. CD99 engagement in Jurkat cells elicited the exocytic transport of GM1 as well as several surface molecules closely related with CD99 functions. In addition, CD99 molecules were rapidly incorporated into lipid rafts and appeared to rearrange the actin cytoskeleton upon CD99 stimulation. Association of CD99 with actin cytoskeleton was inhibited by methyl-beta-cyclodextrin, while CD99-mediated GM1 clustering was inhibited by cytochalasin D. Therefore, we suggest that CD99 may play a role in the vesicular transport of transmembrane proteins and lipid rafts from the intracellular location to the cell surface, possibly by effecting actin cytoskeleton reorganization.
Supplementary Figure 1 from Adjuvant Therapy with Oncolytic Adenovirus Delta-24-RGDOX After Intratumoral Adoptive T-cell Therapy Promotes Antigen Spread to Sustain Systemic Antitumor Immunity (2023)

&lt;p&gt;gp100 and ovalbumin (OVA) expression in indicated mouse melanoma cell lines. Cell lysates were analyzed with immunoblotting. GAPDH levels are shown as a protein loading control.&lt;/p&gt;
An Astigmatic Detection System for Polymeric Cantilever-Based Sensors (2011)

We demonstrate the use of an astigmatic detection system (ADS) for resonance frequency identification of polymer microcantilever sensors. The ADS technology is based on a DVD optical head combined with an optical microscope (OM). The optical head has a signal bandwidth of 80 MHz, allowing thermal fluctuation measurements on cantilever beams with a subnanometer resolution. Furthermore, an external excitation can intensify the resonance amplitude, enhancing the signal- to-noise ratio. The full width at half maximum (FWHM) of the laser spot is 568 nm, which facilitates read-out on potentially submicrometer-sized cantilevers. The resonant frequency of SU-8 microcantilevers is measured by both thermal fluctuation and excited vibration measurement modes of the ADS.
Enhancing Arabic text steganography for personal usage utilizing pseudo-spaces (2019)

Steganography is the process of hiding data within multimedia communication between parties by embedding the secret data inside a carrier file to be protected during its transmission. This paper addresses the problem of hiding information within the Arabic text as it is currently a challenging research area. Two methods are presented for text steganography: utilizing pseudo-spaces alone and combining them with Kashida (extension character). Experimental results have shown that the proposed algorithms achieved high capacity and security ratio as compared to state-of-the-art steganography methods presented for the Arabic language. The proposed techniques are of great benefit and can be further used for languages similar to Arabic, such as Urdu and Persian, as well as opening the direction of text-stego research for other languages of the world.
Using Structured Lighting and Shadow for Leaf Segmentation (2007)

Leaves in arrangements of tomato and bean plants were segmented using an edge detection technique that used shadows from multiple, differently illuminated images to identify shadow edges and compared the results with those of a more conventional single image technique that identified intensity gradient edges. Images were taken in a 10 nm waveband centred at 766 nm and segmented by both techniques. Shadow edges produced segmentation percentages of 7% for bean and 18% for tomato for partially occluded leaves. Gradient edges segmented 12% for bean and 10% for tomato for partially occluded leaves. The results are poor when compared with existing work but the different modes of failure show potential for hybrid imaging techniques
Solvent dependence of rotational energetics and formyl-proton long-range spin-spin coupling behavior of 2,6-dichloro- and 2,6-dinitrobenzaldehydes using dipolar couplings and temperature dependence of long-range couplings (1999)

The formyl rotational energetics, solvent effects on the energetics and formyl-proton spin-spin coupling behavior of 2,6-dichlorobenzaldehyde were studied by using dipolar couplings analysis and the temperature dependence of the spin-spin couplings. The general form of the rotational potential was taken from molecular mechanics and the conjugative sin 2 Θ-type component (where Θ is the formyl-ring dihedral angle) was then optimized using the dipolar couplings obtained by analyzing 1 H NMR and 13 C proton satellite spectra in a liquid crystal solvent. The optimization based on the dipolar couplings gave the following rotational free energy potential: V(Θ) = 4.5 cos 6 Θ + 10.7 (± 2.0) sin 2 Θ, in kJ/mol. The analysis based on the temperature dependence of 6 J data allowed estimation of solvent effects on the potential. For example, the potentials in acetone and in acetonitrile differ by a 1.0 sin 2 2Θ (in kJ/mol). The chloroform solvent effect can be described by term of -1.0 cos 6 Θ. When the formyl-proton six-bond coupling data was fit, assuming it obeyed the expression 6 J(Θ) = 6 J 90 sin 2 Θ + 6 J 0 and assuming 6 J 0 = 0.015 Hz, the analysis yielded 6 J 90 of -0.48 (± 0.03) Hz. The scalar coupling temperature dependence method was applied also to the conformational analysis of 2,6-dinitrobenzaldehyde.Key words: spin-spin coupling, dipolar coupling, solvent effect, rotational barrier, benzaldehyde.
Early and aggressive treatment of rheumatoid arthritis patients affects the association of HLA class II antigens with progression of joint damage (2002)

Early and aggressive antirheumatic drug treatment affects the association of HLA class II alleles with progression of joint damage in RA.
Discovery of estrogen receptor modulators: a review of virtual screening and SAR efforts (2009)

With the goal of reducing toxicity and/or improving efficacy, challenges to the successful modeling of endocrine agents are proposed, providing new paradigms for the design of ER inhibitors.
Fabrication of hybrid nanocomposite scaffolds by incorporating ligand-free hydroxyapatite nanoparticles into biodegradable polymer scaffolds and release studies (2015)

We report on the optical fabrication approach of preparing free-standing composite thin films of hydroxyapatite (HA) and biodegradable polymers by combining pulsed laser ablation in liquid and mask-projection excimer laser stereolithography (MPExSL). Ligand-free HA nanoparticles were prepared by ultrafast laser ablation of a HA target in a solvent, and then the nanoparticles were dispersed into the liquid polymer resin prior to the photocuring process using MPExSL. The resin is poly(propylene fumarate) (PPF), a photo-polymerizable, biodegradable material. The polymer is blended with diethyl fumarate in 7:3 w/w to adjust the resin viscosity. The evaluation of the structural and mechanical properties of the fabricated hybrid thin film was performed by means of SEM and nanoindentation, respectively, while the chemical and degradation studies were conducted through thermogravimetric analysis, and FTIR. The photocuring efficiency was found to be dependent on the nanoparticle concentration. The MPExSL process yielded PPF thin films with a stable and homogenous dispersion of the embedded HA nanoparticles. Here, it was not possible to tune the stiffness and hardness of the scaffolds by varying the laser parameters, although this was observed for regular PPF scaffolds. Finally, the gradual release of the hydroxyapatite nanoparticles over thin film biodegradation is reported.
ChemInform Abstract: Synthesis and Characterization of the Phosphorus Halide—Boron Halide Complexes X3PBY3 (X: Cl, Br, I; Y: Br, I) by 31P MAS NMR, IR, and Raman Spectroscopy and the Crystal Structure of Br3PBBr3. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Amplification of an adenylosuccinate synthetase gene in alanosine-resistant murine T-lymphoma cells. Molecular cloning of a cDNA encoding the “non-muscle” isozyme. (1994)

Adenylosuccinate synthetase (EC 6.3.4.4) catalyzes the initial step in the conversion of IMP to AMP. Two isoforms of this enzyme have been observed in vertebrates. A muscle isozyme is highly abundant in cardiac and skeletal muscle tissue and is thought to play a role in muscle energy metabolism. The non-muscle isozyme, which is present at low levels in most tissues, likely functions in de novo AMP biosynthesis. The analysis of the non-muscle isozyme has been hampered by its low abundance and instability during purification. In this study a genetic selection scheme was used to generate a murine T-lymphoma cell line which was at least 100-fold enriched for the non-muscle isozyme, as a result of amplification of the non-muscle synthetase gene. This cell line made possible the purification of the non-muscle isozyme, and the subsequent isolation of isozyme-specific peptides. Based on peptide sequence information a degenerate oligonucleotide probe was designed and used to screen a mouse kidney cDNA library. A 1.5-kilobase cDNA encoding the non-muscle isozyme was cloned and found to contain an open reading frame of 1368 base pairs encoding 456 amino acids. Gene transfer experiments showed that the cDNA encoded a 50-kDa protein, the size expected for mammalian synthetases, that correlated with the presence of high levels of synthetase activity. The deduced amino acid sequence of the mouse non-muscle synthetase is approximately 75% identical to the previously reported mouse muscle synthetase. Southern blot analysis of mouse genomic DNA with the isozyme-specific cDNA probes revealed that the synthetase isozymes are encoded by separate genes. The non-muscle gene is expressed in most tissues but is virtually undetectable in striated muscle tissues. Three different transcripts (1.7, 2.8, and 3.4 kilobases) are detected for the non-muscle isozyme which show a similar tissue distribution. The availability of a cDNA for the non-muscle isozyme of adenylosuccinate synthetase will facilitate further comparative analyses with the previously cloned muscle isozyme.
Vibrational Spectroscopy of the Multianion Mineral Kemmlitzite (Sr,Ce)Al3(AsO4)(SO4)(OH)6 (2012)

ABSTRACT Some minerals are colloidal and show no X-ray diffraction patterns. Vibrational spectroscopy offers one of the few methods for the assessment of the structure of these types of minerals. Among this group of minerals is kemmlitzite (Sr,Ce)Al3(AsO4)(SO4)(OH)6. The objective of this research is to determine the molecular structure of the mineral kemmlitzite using vibrational spectroscopy. Raman microscopy offers a useful method for the analysis of such colloidal minerals. Raman and infrared bands are attributed to the , , and water stretching vibrations. The Raman spectrum is dominated by a very intense sharp band at 984 cm−1 assigned to the symmetric stretching mode. Raman bands at 690, 772, and 825 cm−1 may be assigned to the antisymmetric and symmetric stretching modes. Raman bands observed at 432 and 465 cm−1 are attributable to the doubly degenerate ν2(SO4)2− bending mode. Vibrational spectroscopy is important in the assessment of the molecular structure of the kemmlitzite, especially when the mineral is nondiffracting or poorly diffracting.
Pathophysiological power of improper tonic GABAA conductances in mature and immature models (2013)

High-affinity extrasynaptic gamma-aminobutyric acid A (GABA(A)) receptors are tonically activated by low and consistent levels of ambient GABA, mediating chronic inhibition against neuronal excitability (tonic inhibition) and the modulation of neural development. Synaptic (phasic) inhibition is spatially and temporally precise compared with tonic inhibition, which provides blunt yet strong integral inhibitory force by shunting electrical signaling. Although effects of acute modification of tonic inhibition are known, its pathophysiological significance remains unclear because homeostatic regulation of neuronal excitability can compensate for long-term deficit of extrasynaptic GABA(A) receptor activation. Nevertheless, tonic inhibition is of great interest for its pathophysiological involvement in central nervous system (CNS) diseases and thus as a therapeutic target. Together with the development of experimental models for various pathological states, recent evidence demonstrates such pathological involvements of tonic inhibition in neuronal dysfunction. This review focuses on the recent progress of tonic activation of GABA(A) conductance on the development and pathology of the CNS. Findings indicate that neuronal function in various brain regions are exacerbated with a gain or loss of function of tonic inhibition by GABA spillover. Disturbance of tonic GABA(A) conductance mediated by non-synaptic ambient GABA may result in brain mal-development. Therefore, various pathological states (epilepsy, motor dysfunctions, psychiatric disorders, and neurodevelopmental disorders) may be partly attributable to abnormal tonic GABA(A) conductances. Thus, the tone of tonic conductance and level of ambient GABA may be precisely tuned to maintain the regular function and development of the CNS. Therefore, receptor expression and factors for regulating the ambient GABA concentration are highlighted to gain a deeper understanding of pathology and therapeutic strategy for CNS diseases.
Interpretable Convolutional Filters with SincNet (2018)

Deep learning is currently playing a crucial role toward higher levels of artificial intelligence. This paradigm allows neural networks to learn complex and abstract representations, that are progressively obtained by combining simpler ones. Nevertheless, the internal "black-box" representations automatically discovered by current neural architectures often suffer from a lack of interpretability, making of primary interest the study of explainable machine learning techniques. This paper summarizes our recent efforts to develop a more interpretable neural model for directly processing speech from the raw waveform. In particular, we propose SincNet, a novel Convolutional Neural Network (CNN) that encourages the first layer to discover more meaningful filters by exploiting parametrized sinc functions. In contrast to standard CNNs, which learn all the elements of each filter, only low and high cutoff frequencies of band-pass filters are directly learned from data. This inductive bias offers a very compact way to derive a customized filter-bank front-end, that only depends on some parameters with a clear physical meaning. Our experiments, conducted on both speaker and speech recognition, show that the proposed architecture converges faster, performs better, and is more interpretable than standard CNNs.
Deep Distribution Regression (2019)

Due to their flexibility and predictive performance, machine-learning based regression methods have become an important tool for predictive modeling and forecasting. However, most methods focus on estimating the conditional mean or specific quantiles of the target quantity and do not provide the full conditional distribution, which contains uncertainty information that might be crucial for decision making. In this article, we provide a general solution by transforming a conditional distribution estimation problem into a constrained multi-class classification problem, in which tools such as deep neural networks. We propose a novel joint binary cross-entropy loss function to accomplish this goal. We demonstrate its performance in various simulation studies comparing to state-of-the-art competing methods. Additionally, our method shows improved accuracy in a probabilistic solar energy forecasting problem.
Lead Optimization Using Matched Molecular Pairs: Inclusion of Contextual Information for Enhanced Prediction of hERG Inhibition, Solubility, and Lipophilicity (2010)

Previous studies of the analysis of molecular matched pairs (MMPs) have often assumed that the effect of a substructural transformation on a molecular property is independent of the context (i.e., the local structural environment in which that transformation occurs). Experiments with large sets of hERG, solubility, and lipophilicity data demonstrate that the inclusion of contextual information can enhance the predictive power of MMP analyses, with significant trends (both positive and negative) being identified that are not apparent when using conventional, context-independent approaches.
Robust fabrication of μ-patterns with tunable and durable wetting properties: hydrophilic to ultrahydrophobic via a vacuum process (2017)

Tunable and durable lotus effect on laser-patterned stainless steel <italic>via</italic> a vacuum process in a very short time interval.