gebhart/patrepeval huggingface dataset:
Amphiphilic Diblock Dendrimers:  Synthesis and Incorporation in Langmuir and Langmuir−Blodgett Films (2001)

A new dendron with peripheral long alkyl chains and containing five C(60) units in the branching shell has been prepared and attached to a Fréchet-type dendron functionalized with ethylene glycol chains. The peripheral substitution of the resulting globular dendrimer with hydrophobic chains on one hemisphere and hydrophilic groups on the other provides the perfect hydrophobic/hydrophilic balance allowing the formation of stable Langmuir films. Furthermore, a perfect reversibility has been observed in successive compression/decompression cycles. The diblock structure of the dendrimer has been also crucial for the efficient transfer of the Langmuir films in order to obtain well-ordered multilayered Langmuir-Blodgett films. This approach appears particularly interesting since functional groups not well adapted for the preparation of Langmuir and Langmuir-Blodgett films such as fullerenes can be attached into the branching shell of the dendritic structure and, thus, efficiently incorporated in thin ordered films.
Two amino acid mutations in an anti-human CD3 single chain Fv antibody fragment that affect the yield on bacterial secretion but not the affinity (1997)

Recombinant antibody fragments directed against cell surface antigens have facilitated the development of novel therapeutic agents. As a first step in the creation of cytotoxic immunoconjugates, we constructed a single-chain Fv fragment derived from the murine hybridoma OKT3, that recognizes an epitope on the epsilon-subunit of the human CD3 complex. Two amino acid residues were identified that are critical for the high level production of this scFv in Escherichia coli. First, the substitution of glutamic acid encoded by a PCR primer at position 6 of VH framework 1 by glutamine led to a more than a 30-fold increase in the production of soluble scFv. Second, the substitution of cysteine by a serine in the middle of CDR-H3 additionally doubled the yield of soluble antibody fragment without any adverse effect on its affinity for the CD3 antigen. The double mutant scFv (Q,S) proved to be very stable in vitro: no loss of activity was observed after storage for 1 month at 4 degrees C, while the activity of scFv containing a cysteine residue in CDR-H3 decreased by more than half. The results of production yield, affinity, stability measurements and analysis of three-dimensional models of the structure suggest that the sixth amino acid influences the correct folding of the VH domain, presumably by affecting a folding intermediate, but has no effect on antigen binding.
Structural basis for the interaction between human milk oligosaccharides and the bacterial lectin PA-IIL of Pseudomonas aeruginosa (2005)

One of the mechanisms contributing to the protection by breast-feeding of the newborn against enteric diseases is related to the ability of human milk oligosaccharides to prevent the attachment of pathogenic bacteria to the duodenual epithelium. Indeed, a variety of fucosylated oligosaccharides, specific to human milk, form part of the innate immune system. In the present study, we demonstrate the specific blocking of PA-IIL, a fucose-binding lectin of the human pathogen Pseudomonas aeruginosa, by milk oligosaccharides. Two fucosylated epitopes, Lewis a and 3-fucosyl-lactose (Lewis x glucose analogue) bind to the lectin with dissociation constants of 2.2×10−7 M and 3.6×10−7 M respectively. Thermodynamic studies indicate that these interactions are dominated by enthalpy. The entropy contribution is slightly favourable when binding to fucose and to the highest-affinity ligand, Lewis a. The high-resolution X-ray structures of two complexes of PA-IIL with milk oligosaccharides allow the precise determination of the conformation of a trisaccharide and a pentasaccharide. The different types of interaction between the oligosaccharides and the protein involve not only hydrogen bonding, but also calcium- and water-bridged contacts, allowing a rationalization of the thermodynamic data. This study provides important structural information about compounds that could be of general application in new therapeutic strategies against bacterial infections.
Prolonged sensory-selective nerve blockade (2010)

Sensory-selective local anesthesia has long been a key goal in local anesthetic development. For example, it allows women to be pain-free during labor without compromising their ability to push. Here we show that prolonged sensory-selective nerve block can be produced by specific concentrations of surfactants-such as are used to enhance drug flux across skin-in combination with QX-314, a lidocaine derivative that has relative difficulty penetrating nerves. For example, injection of 25 mM QX-314 in 30 mM octyltrimethylammonium bromide (OTAB) lasted up to 7 h. Sensory selectivity was imparted to varying degrees by cationic, neutral, and anionic surfactants, and also was achieved with another lidocaine derivative, QX-222. Simultaneous injection of OTAB at a s.c. injection site remote from the sciatic nerve did not result in prolonged sensory-specific nerve blockade from QX-314, suggesting that the observed effect is due to a local interaction between the surfactant and the lidocaine derivative, not a systemic effect.
CS-MUVI: Video compressive sensing for spatial-multiplexing cameras (2012)

Compressive sensing (CS)-based spatial-multiplexing cameras (SMCs) sample a scene through a series of coded projections using a spatial light modulator and a few optical sensor elements. SMC architectures are particularly useful when imaging at wavelengths for which full-frame sensors are too cumbersome or expensive. While existing recovery algorithms for SMCs perform well for static images, they typically fail for time-varying scenes (videos). In this paper, we propose a novel CS multi-scale video (CS-MUVI) sensing and recovery framework for SMCs. Our framework features a co-designed video CS sensing matrix and recovery algorithm that provide an efficiently computable low-resolution video preview. We estimate the scene's optical flow from the video preview and feed it into a convex-optimization algorithm to recover the high-resolution video. We demonstrate the performance and capabilities of the CS-MUVI framework for different scenes.
Transforming growth factor β1 dysregulation in a human oral carcinoma tumour progression model (2002)

A human oral tumour progression model was established that consists of normal epithelial cells and three cell lines representing stages from dysplastic to metastatic cells. To investigate the impact of exogenous transforming growth factor-beta 1 on this model system, we analysed the responsiveness of those cells to transforming growth factor-beta 1 and explored the potential mechanism underlying the transforming growth factor-beta 1 activity. We found that the growth of all cell types, regardless of their stage of tumour progression, is inhibited by transforming growth factor-beta 1, although to different degrees. Transforming growth factor-beta 1 induced the expression of cyclin-dependent kinase inhibitors p15(INK4B), p21WAF1/(CIP1) and p27(KIP1). In contrast, transforming growth factor-beta 1 was found to stimulate the invasive potential of one cell type that represents the most advanced stage of tumour phenotype, suggesting that the impact of transforming growth factor-beta 1 on functional features of tumour cells other than cellular proliferation may play a significant role in the process of oral tumour progression.
Interferons: Rationale for Clinical Trials in Neoplastic Disease (1979)

Interferons, cell glycoproteins synthesized in response to viral infections and various nonviral inducers, have proved therapeutically effective for viral infections in experimental models and in humans. Current evidence suggests interferons may also prove effective as antitumor agents in humans. Potent effects on cellular function result from interferons. Cell surface structure and enzyme levels are altered. Immunologic responses thought to be important in tumor immunity are augmented. Interferons have antiproliferative effects on the replication of normal and neoplastic cells. Interferons are effective in animals against tumors of both viral and nonviral origin. Clinical trials in cancer have been limited by the availability and cost of human interferons. However, results in small numbers of patients have been encouraging. This paper review experimental and clinical findings regarding the rationale for use of interferons in neoplastic disease.
Separation of dansyl-dl-amino acids by open tubular capillary chromatography based on tube radial distribution phenomenon of the ternary mixed carrier solvents (2012)

Separation of enantiomers, dansyl-DL-amino acids, was carried out by open-tubular capillary chromatography based on the tube radial distribution of the carrier solvents. An untreated poly(tetrafluoroethylene) capillary tube (100 μm inner diameter and 90 cm effective length) as a separation column and a water–acetonitrile–ethyl acetate mixture containing cyclodextrin as a carrier solution were used in the chromatography. An analyte solution of dansyl-DL-amino acids, such as dansyl-DL-methionine, was injected into the capillary tube by a gravity method. The analyte solution was subsequently delivered through the capillary tube with the carrier solution by a microsyringe pump. The ternary mixed carrier solution (water-rich carrier solution) was radially distributed in the capillary tube based on the tube radial distribution phenomenon, causing the formation of inner (water-rich) and outer (organic solvent-rich) phases. The outer or capillary wall phase acted as a pseudo-stationary phase in the chromatography. The analytes were separated through the capillary tube with on-capillary detection by an absorption or a fluorescence detector. The D-enantiomer and the L-enantiomer were eluted in this order with a baseline separation. The separation mechanism of the enantiomers in the open-tubular capillary using cyclodextrin was discussed.
INTERACTIONS OF LIPOSOMES WITH MAMMALIAN CELLS (1978)

In this review we have attempted to highlight each of the major areas of interest in liposome-cell interactions: the purely physical chemical, the cell biological, and the medical. Liposomes can be generated in a number of ways and are classified as small unilamellar, large unilamellar, and multilamellar vesicles. Although liposomes are easy to prepare, it is important to consider the effects of impurities, and also the possible changes in liposome properties with time (particularly at or below the phase transition temperature). Intelligent application of liposomes to cell biological and clinical problems requires an understanding of their mechanisms of interaction with cells. The mechanisms thus far delineated, largely by studies in vitro, are fusion, endocytosis, lipid transfer, and stable adsorption. In practice, demonstrating the occurrence of a given mechanism in an actual system is difficult because these are not mutually exclusive. Cell type, conditions of incubation, and liposome properties (charge, fluidity, size) are important in determining mechanism and appear to organize the literature effectively. However, this may be an oversimplification resulting from the sketchiness of current information. Liposomes have been used in cell biology to alter the phospholipid and cholesterol composition of cells, to bypass the membrane permeability barrier to normally impermeant solutes, and to promote cell-cell fusion. Perhaps the most fruitful of these applications has been the alteration of cholesterol, which can result in changes in cell permeability and morphology. On the other hand, delivery into cells of liposome-entrapped, water-soluble materials has not yet proved an effective tool in cell biology; delivery, and consequent physiological changes, have been demonstrated, but generally to answer questions about liposome-cell interactions, not to answer questions about the cells. Much of the current interest in liposomes derives from their potential applications in vivo. Liposomes are envisioned as pharmacological capsules for delivery of therapeutic agents in treatment of such conditions as diabetes, enzyme deficiencies, heavy metal poisoning, and neoplasms. Although much of the literature to date has been concerned with the end applications, it seems clear that a more systematic approach to the pharmacokinetics of liposomes will be necessary. In particular, such aspects as their leakage rates and their ability to cross cell and anatomical barriers require further study. Targeting of liposomes to particular cells or tissues will be essential for many applications. Finally, it must be remembered that all of these in vivo applications of liposomes are future tense; as with other technologies, passage from demonstration of the phenomenon to practical application is likely to be arduous.
Functional Effect of Deletion and Mutation of theEscherichia coli Ribosomal RNA and tRNA Pseudouridine Synthase RluA (1999)

The Escherichia coli gene rluA, coding for the pseudouridine synthase RluA that forms 23 S rRNA pseudouridine 746 and tRNA pseudouridine 32, was deleted in strains MG1655 and BL21/DE3. The rluA deletion mutant failed to form either 23 S RNA pseudouridine 746 or tRNA pseudouridine 32. Replacement of rluA in trans on a rescue plasmid restored both pseudouridines. Therefore, RluA is the sole protein responsible for the in vivo formation of 23 S RNA pseudouridine 746 and tRNA pseudouridine 32. Plasmid rescue of both rluA- strains using an rluA gene carrying asparagine or threonine replacements for the highly conserved aspartate 64 demonstrated that neither mutant could form 23 S RNA pseudouridine 746 or tRNA pseudouridine 32 in vivo, showing that this conserved aspartate is essential for enzyme-catalyzed formation of both pseudouridines. In vitro assays using overexpressed wild-type and mutant synthases confirmed that only the wild-type protein was active despite the overexpression of wild-type and mutant synthases in approximately equal amounts. There was no difference in exponential growth rate between wild-type and MG1655(rluA-) either in rich or minimal medium at 24, 37, or 42 degrees C, but when both strains were grown together, a strong selection against the deletion strain was observed.
Dual-tier thin film polymer polarization imaging sensor (2010)

Traditional imaging systems capture and replicate the imaged environment in terms of color and intensity. One important property of light, which the human eye is blind to and is ignored by traditional imaging systems, is polarization. In this paper we present a novel, low power imaging sensor capable of recording the optical properties of partially linearly polarized light in real-time. The imaging sensor combines polymer polarization filters with a CMOS image sensor in order to compute the first three Stokes parameters at the focal plane. The imaging array contains 100 x 100 pixels and consumes 48 mW at 30 fps.
Partial Escape Analysis and Scalar Replacement for Java (2014)

Escape Analysis allows a compiler to determine whether an object is accessible outside the allocating method or thread. This information is used to perform optimizations such as Scalar Replacement, Stack Allocation and Lock Elision, allowing modern dynamic compilers to remove some of the abstractions introduced by advanced programming models.
Preimplantation diagnosis: Gender preselection in humans? Flow cytometric separation of X and Y spermatozoa for the prevention of X-linked diseases (1993)

Human X- and Y-chromosome-bearing spermatozoa were separated based on their DNA content, using modified flow cytometric cell sorting technology. The resulting separation purity of the X-bearing from Y-bearing spermatozoa was evaluated using in-situ hybridization with alpha satellite DNA probes for the X- and Y-chromosomes. In the putative X-enriched-sorted populations, an average of 82% of the spermatozoa showed a hybridization signal with the X probe. Similarly, in the Y-sorted population 75% gave a signal with the Y probe. Sorted X- and Y-bearing spermatozoa were found to maintain their viability for several hours after sorting. These results demonstrate that the human sperm sex ratio can be significantly shifted to favour the selection of female-producing (X) spermatozoa or male-producing (Y) spermatozoa when spermatozoa are flow cytometrically sorted on the basis of DNA content. We propose that flow cytometrically sorted human spermatozoa, used in conjunction with in-vitro fertilization or intra-oviductal insemination, could be used by families who are at risk for X-linked diseases to preferentially produce female offspring. Sorted spermatozoa could also be used to pre-select for male offspring if that were medically indicated.
Engineered Botulinum Neurotoxins as New Therapeutics (2013)

Botulinum neurotoxins (BoNTs) cause flaccid paralysis by inhibiting neurotransmission at cholinergic nerve terminals. Each BoNT consists of three domains that are essential for toxicity: the binding domain, the translocation domain, and the catalytic light-chain domain. BoNT modular architecture is associated with a multistep mechanism that culminates in the intracellular proteolysis of SNARE (soluble N-ethylmaleimide-sensitive-fusion-protein attachment protein receptor) proteins, which prevents synaptic vesicle exocytosis. As the most toxic proteins known, BoNTs have been extensively studied and are used as pharmaceutical agents to treat an increasing variety of disorders. This review summarizes the level of sophistication reached in BoNT engineering and highlights the diversity of approaches taken to utilize the modularity of the toxin. Improved efficiency and applicability have been achieved by direct mutagenesis and interserotype domain rearrangement. The scope of BoNT activity has been extended to nonneuronal cells and offers the basis for novel biomolecules in the treatment of secretion disorders.
Real-time 2D/3D registration using kV-MV image pairs for tumor motion tracking in image guided radiotherapy (2013)

Intra-fractional respiratory motion during radiotherapy leads to a larger planning target volume (PTV). Real-time tumor motion tracking by two-dimensional (2D)/3D registration using on-board kilo-voltage (kV) imaging can allow for a reduction of the PTV though motion along the imaging beam axis cannot be resolved using only one projection image. We present a retrospective patient study investigating the impact of paired portal mega-voltage (MV) and kV images on registration accuracy. Material and methods. We used data from 10 patients suffering from non-small cell lung cancer (NSCLC) undergoing stereotactic body radiation therapy (SBRT) lung treatment. For each patient we acquired a planning computed tomography (CT) and sequences of kV and MV images during treatment. We compared the accuracy of motion tracking in six degrees-of-freedom (DOF) using the anterior-posterior (AP) kV sequence or the sequence of kV-MV image pairs. Results. Motion along cranial-caudal direction could accurately be extracted when using only the kV sequence but in AP direction we obtained large errors. When using kV-MV pairs, the average error was reduced from 2.9 mm to 1.5 mm and the motion along AP was successfully extracted. Mean registration time was 188 ms. Conclusion. Our evaluation shows that using kV-MV image pairs leads to improved motion extraction in six DOF and is suitable for real-time tumor motion tracking with a conventional LINAC.
Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm. (2001)

Biochemical analysis of amylose-extender (ae) mutant of rice (Oryza sativa) revealed that the mutation in the gene for starch-branching enzyme IIb (BEIIb) specifically altered the structure of amylopectin in the endosperm by reducing short chains with degree of polymerization of 17 or less, with the greatest decrease in chains with degree of polymerization of 8 to 12. The extent of such change was correlated with the gelatinization properties of the starch granules, as determined in terms of solubility in urea solution. The ae mutation caused a dramatic reduction in the activity of BEIIb. The activity of soluble starch synthase I (SSI) in the ae mutant was significantly lower than in the wild type, suggesting that the mutation had a pleiotropic effect on the SSI activity. In contrast, the activities of BEI, BEIIa, ADP-Glc pyrophosphorylase, isoamylase, isoamylase, pullulanase, and Suc synthase were not affected by the mutation. Therefore, it is stressed that the function of BEIIb cannot be complemented by BEIIa and BEI. These results strongly suggest that BEIIb plays a specific role in the transfer of short chains, which might then be extended by SS to form the A and B(1) chains of amylopectin cluster in rice endosperm.
Comprehensive Expression Profiling of Tumor Cell Lines Identifies Molecular Signatures of Melanoma Progression (2007)

We conclude that tumor cell lines are a valuable resource for the early identification of gene signatures associated with malignant progression in tumors with significant heterogeneity like melanoma. We further conclude that the development of novel data reduction algorithms for analysis of microarray studies is critical to allow for optimized mining of important, clinically-relevant datasets. It is expected that subsequent validation studies in primary human tissues using such an approach will lead to more rapid translation of such studies to the identification of novel tumor biomarkers and therapeutic targets.