gebhart/patrepeval huggingface dataset:
Chitinolytic Activity in Chromobacterium violaceum : Substrate Analysis and Regulation by Quorum Sensing (1998)

Quorum sensing control mediated by N-acyl homoserine lactone (AHL) signaling molecules has been established as a key feature of the regulation of exoenzyme production in many gram-negative bacteria. In Chromobacterium violaceum ATCC 31532 a number of phenotypic characteristics, including production of the purple pigment violacein, hydrogen cyanide, antibiotics, and exoproteases are known to be regulated by the endogenous AHL N-hexanoyl-L-homoserine lactone (HHL). In this study we show that C. violaceum produces a set of chitinolytic enzymes whose production is regulated by HHL. The chitinolytic activity was induced in strains grown in the presence of chitin as the sole carbon source and quantitated in the secreted proteins by using p-nitrophenol analogs of disaccharide, trisaccharide, and tetrasaccharide oligomers of N-acetylglucosamine. By using 4-methylumbelliferyl analogs of the same oligomers of N-acetylglucosamine as substrates for proteins separated and renatured by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, at least six enzymes were detected: a chitobiase with high specificity to a dimeric substrate of 87 kDa, two N-acetylglucosaminidases with apparent molecular masses of 162 and 133 kDa, two endochitinases of 108 and 67 kDa, and a chitobiosidase of 56 kDa. In addition, two unidentified bands of >205 kDa were found where a tetrameric chitin derivative was used as a substrate. A pleiotropic mini-Tn5 mutant of C. violaceum (CV026) that is defective in HHL production and other quorum-sensing-regulated factors was also found to be completely deficient in chitinolytic activity. Growth of this mutant on minimal medium with chitin supplemented with culture supernatant from the C. violaceum wild-type strain or 10 microM synthetic HHL restored chitinase production to the level shown by the parental strain. These results constitute the most complete evidence so far for regulation of chitinolytic activity by AHL signaling in a gram-negative bacterium.
Solid-phase synthesis of CD40L mimetics (2006)

The C3-symmetric molecule has been previously shown to mimic CD40 ligand (CD40L) homotrimers and to display effector functions. This molecule consists of a cyclic hexapeptide core containing the repetition of the D-Ala-L-Lys motif. The side chains of the lysine residues have been modified by appending the CD40L-derived sequence 143Lys-Gly-Tyr-Tyr146 via a 6-aminohexanoic acid residue as a spacer. The present report describes a general solid-phase synthesis approach to and related trimeric architectures. In addition, their CD40 binding properties as well as their effector functions have been evaluated.
High-frequency plastid transformation in tobacco by selection for a chimeric aadA gene. (1993)

We report here a 100-fold increased frequency of plastid transformation in tobacco by selection for a chimeric aadA gene encoding aminoglycoside 3"-adenylyltransferase, as compared with that obtained with mutant 16S rRNA genes. Expression of aadA confers resistance to spectinomycin and streptomycin. In transforming plasmid pZS197, a chimeric aadA is cloned between rbcL and open reading frame ORF512 plastid gene sequences. Selection was for spectinomycin resistance after biolistic delivery of pZS197 DNA into leaf cells. DNA gel-blot analysis confirmed incorporation of the chimeric aadA gene into the plastid genome by two homologous recombination events via the flanking plastid gene sequences. The chimeric gene became homoplasmic in the recipient cells and is uniformly transmitted to the maternal seed progeny. The ability to transform routinely plastids of land plants opens the way to manipulate the process of photosynthesis and to incorporate novel genes into the plastid genome of crops.
Mechanosensitive mechanisms in transcriptional regulation (2012)

Transcriptional regulation contributes to the maintenance of pluripotency, self-renewal and differentiation in embryonic cells and in stem cells. Therefore, control of gene expression at the level of transcription is crucial for embryonic development, as well as for organogenesis, functional adaptation, and regeneration in adult tissues and organs. In the past, most work has focused on how transcriptional regulation results from the complex interplay between chemical cues, adhesion signals, transcription factors and their co-regulators during development. However, chemical signaling alone is not sufficient to explain how three-dimensional (3D) tissues and organs are constructed and maintained through the spatiotemporal control of transcriptional activities. Accumulated evidence indicates that mechanical cues, which include physical forces (e.g. tension, compression or shear stress), alterations in extracellular matrix (ECM) mechanics and changes in cell shape, are transmitted to the nucleus directly or indirectly to orchestrate transcriptional activities that are crucial for embryogenesis and organogenesis. In this Commentary, we review how the mechanical control of gene transcription contributes to the maintenance of pluripotency, determination of cell fate, pattern formation and organogenesis, as well as how it is involved in the control of cell and tissue function throughout embryogenesis and adult life. A deeper understanding of these mechanosensitive transcriptional control mechanisms should lead to new approaches to tissue engineering and regenerative medicine.
Midkine as a novel target gene for the Wilms' tumor suppressor gene (WT1). (1996)

Midkine (MK) is a heparin-binding growth factor which is strongly expressed during the midgestation period of mouse embryogenesis. Wilms' tumor is an embryonal kidney malignancy in infants, and WT1 has been identified as its tumor suppressor gene. The high expression level of MK in all Wilms' tumor specimens so far examined and the presence of two WT1 elements (5'-GCGGGGGCG-3') in the human MK promoter region led us to examine the possible role of the WT1 gene product in the regulation of MK gene expression. A gel shift assay verified the complex formation between the WT1 gene product and WT1 consensus sequence of MK gene. DNase1 footprint analysis also demonstrated that the downstream WT1 element was protected from DNase1 cleavage by the addition of the WT1 protein. The human MK promoter fused with the chloramphenicol acetyltransferase gene (phMK2.3kCAT) was co-transfected with an effector plasmid containing the WT1 gene into several cell lines. Transient transfection assays showed suppression of the MK promoter by WT1 co-transfection in recipient cells; deletion of the WT1 binding site abolished the suppression. The evidence reported in this study indicates that MK gene is a newly identified WT1 target gene.
Hyaluronan Enters Keratinocytes by a Novel Endocytic Route for Catabolism (2001)

Hyaluronan synthesized in the epidermis has an exceptionally short half-life, indicative of its catabolism by epidermal keratinocytes. An intracellular pool of endogenously synthesized hyaluronan, from 1 to 20 fg/cell, inversely related to cell density, was observed in cultured rat epidermal keratinocytes. More than 80% of the intracellular hyaluronan was small (<90 kDa). Approximately 25% of newly synthesized hyaluronan was endocytosed by the keratinocytes and had a half-life of 2-3 h. A biotinylated aggrecan G(1) domain/link protein probe demonstrated hyaluronan in small vesicles of approximately 100 nm diameter close to the plasma membrane, and in large vesicles and multivesicular bodies up to 1300 nm diameter around the nucleus. Hyaluronan did not co-localize with markers of lysosomes. However, inhibition of lysosomal acidification with NH(4)Cl or chloroquine, or treating the cells with the hyaluronidase inhibitor apigenin increased intracellular hyaluronan staining, suggesting that it resided in prelysosomal endosomes. Competitive displacement of hyaluronan from surface receptors using hyaluronan decasaccharides, resulted in a rapid disappearance of this endosomal hyaluronan (t(12) approximately 5 min), indicating its transitory nature. The ultrastructure of the hyaluronan-containing vesicles, co-localization with marker proteins for different vesicle types, and application of specific uptake inhibitors demonstrated that the formation of hyaluronan-containing vesicles did not involve clathrin-coated pits or caveolae. Treatment of rat epidermal keratinocytes with the OX50 monoclonal antibody against the hyaluronan receptor CD44 increased endosomal hyaluronan. However, no CD44-hyaluronan co-localization was observed intracellularly unless endosomal trafficking was retarded by monensin, or cultivation at 20 degrees C, suggesting CD44 recycling. Rat epidermal keratinocytes thus internalize a large proportion of their newly synthesized hyaluronan into non-clathrin-coated endosomes in a receptor mediated way, and rapidly transport it to slower degradation in the endosomal/lysosomal system.
Semantic Technologies in IBM Watson (2013)

This paper describes a seminar course designed by IBM and Columbia University on the topic of Semantic Technologies, in particular as used in IBM Watson TM — a large scale Question Answering system which famously won at Jeopardy! R against two human grand champions. It was first offered at Columbia University during the 2013 spring semester, and will be offered at other institutions starting in the fall semester. We describe the course’s first successful run and its unique features: a class centered around a specific industrial technology; a large-scale class project which student teams can choose to participate in and which serves as the basis for an open source project that will continue to grow each time the course is offered; publishable papers, demos and start-up ideas; evidence that the course can be self-evaluating, which makes it potentially appropriate for an online setting; and a unique model where a large company trains instructors and contributes to creating educational material at no charge to qualifying institutions.
Mightier than the sickle cell (2010)

In this issue of Blood , Chang and colleagues demonstrate that a synthetic small molecule inhibitor designed to displace ligand binding to E-selectin disrupts key signaling and activation events leading to vaso-occlusion in SCD.[1][1]

The age-old adage “the pen is mightier than the sword”
A versatile LabVIEW and field-programmable gate array-based scanning probe microscope for in operando electronic device characterization (2014)

Understanding the complex properties of electronic and spintronic devices at the micro- and nano-scale is a topic of intense current interest as it becomes increasingly important for scientific progress and technological applications. In operando characterization of such devices by scanning probe techniques is particularly well-suited for the microscopic study of these properties. We have developed a scanning probe microscope (SPM) which is capable of both standard force imaging (atomic, magnetic, electrostatic) and simultaneous electrical transport measurements. We utilize flexible and inexpensive FPGA (field-programmable gate array) hardware and a custom software framework developed in National Instrument's LabVIEW environment to perform the various aspects of microscope operation and device measurement. The FPGA-based approach enables sensitive, real-time cantilever frequency-shift detection. Using this system, we demonstrate electrostatic force microscopy of an electrically biased graphene field-effect transistor device. The combination of SPM and electrical transport also enables imaging of the transport response to a localized perturbation provided by the scanned cantilever tip. Facilitated by the broad presence of LabVIEW in the experimental sciences and the openness of our software solution, our system permits a wide variety of combined scanning and transport measurements by providing standardized interfaces and flexible access to all aspects of a measurement (input and output signals, and processed data). Our system also enables precise control of timing (synchronization of scanning and transport operations) and implementation of sophisticated feedback protocols, and thus should be broadly interesting and useful to practitioners in the field.
Bacterial HA1 Vaccine against Pandemic H5N1 Influenza Virus: Evidence of Oligomerization, Hemagglutination, and Cross-Protective Immunity in Ferrets (2010)

The impending influenza virus pandemic requires global vaccination to prevent large-scale mortality and morbidity, but traditional influenza virus vaccine production is too slow for rapid responses. We have developed bacterial systems for expression and purification of properly folded functional hemagglutinin as a rapid response to emerging pandemic strains. A recombinant H5N1 (A/Vietnam/1203/2004) hemagglutinin globular domain (HA1) was produced in Escherichia coli under controlled redox refolding conditions. Importantly, the properly folded HA1(1-320), i.e., HA1 lacking amino acids 321 to 330, contained ≥75% functional oligomers without addition of foreign oligomerization sequence. Site-directed mutagenesis mapped the oligomerization signal to the HA1 N-terminal Ile-Cys-Ile residues at positions 3 to 5. The purified HA1 oligomers (but not monomers) bound fetuin and agglutinated red blood cells. Upon immunization of rabbits, the oligomeric HA1(1-320) elicited potent neutralizing antibodies against homologous and heterologous H5N1 viruses more rapidly than HA1(28-320) containing only monomers. Ferrets vaccinated with oligomeric HA1 (but not monomeric HA1 with the N terminus deleted) at 15 and 3 μg/dose were fully protected from lethality and weight loss after challenge with homologous H5N1 (A/Vietnam/1203/2004, clade 1) virus, as well as heterologous clade 2.2 H5N1 (A/WooperSwan/Mongolia/244/2005) virus. Protection was associated with a significant reduction in viral loads in the nasal washes of homologous and heterologous virus challenged ferrets. This is the first study that describes the presence of an N-terminal oligomerization sequence in the globular domain of influenza virus hemagglutinin. Our findings suggest that functional oligomeric rHA1-based vaccines can be produced efficiently in bacterial systems and can be easily upscaled in response to a pandemic influenza virus threat.
Multidrug resistance modulators and doxorubicin synergize to elevate ceramide levels and elicit apoptosis in drug-resistant cancer cells (1999)

These results demonstrate that MDR modulators can be used separately, in combination, or in conjunction with chemotherapy at clinically relevant concentrations to manipulate cellular ceramide levels and restore sensitivity in the drug resistant setting. As such, this represents a new direction in the treatment of cancer.
Simplified Rules and Theoretical Analysis for Information Bottleneck Optimization and PCA with Spiking Neurons (2007)

We show that under suitable assumptions (primarily linearization) a simple and perspicuous online learning rule for Information Bottleneck optimization with spiking neurons can be derived. This rule performs on common benchmark tasks as well as a rather complex rule that has previously been proposed [1]. Furthermore, the transparency of this new learning rule makes a theoretical analysis of its convergence properties feasible. A variation of this learning rule (with sign changes) provides a theoretically founded method for performing Principal Component Analysis (PCA) with spiking neurons. By applying this rule to an ensemble of neurons, different principal components of the input can be extracted. In addition, it is possible to preferentially extract those principal components from incoming signals X that are related or are not related to some additional target signal YT. In a biological interpretation, this target signal YT (also called relevance variable) could represent proprioceptive feedback, input from other sensory modalities, or top-down signals. 1
782 PD-L1-targeted ISAC combines myeloid cell activation, immune-checkpoint inhibition and ADCP to improve anti-tumor efficacy over anti-PD-L1 antibodies in preclinical models (2021)

<h3>Background</h3> PD-L1 is an immune checkpoint that regulates anti-tumor T cell responses and is expressed on tumor cells as well as tumor-infiltrating immune cells across many tumor types. Immune-stimulating antibody conjugates (ISACs) consist of tumor-targeting antibodies conjugated to immune stimulants and are designed to activate the innate and adaptive immune systems against tumor cells following systemic administration. Here we show that PD-L1-targeted TLR7/8 ISACs elicit robust myeloid cell activation which leads to improved anti-tumor responses compared to anti-PD-L1 treatment in pre-clinical tumor models. <h3>Methods</h3> A panel of proprietary anti-PD-L1 antibodies was identified through a phage display screen and subsequently tested for PD-L1 binding affinity and specificity, PD-L1/PD-1 blocking, antibody-dependent cellular phagocytosis (ADCP) by myeloid cells, and anti-tumor efficacy. Lead antibodies were conjugated to proprietary TLR7/8 agonists, and the resulting PD-L1 ISACs were evaluated for in vitro myeloid cell activation and in vivo efficacy against syngeneic and xenograft tumors. <h3>Results</h3> Anti-PD-L1 antibodies induced robust ADCP by myeloid effector cells and medium to strong PD-L1/PD-1 blockade in vitro. Selected antibodies inhibited the growth of syngeneic MC38-hPD-L1 tumors in vivo, confirming efficient immune-checkpoint blockade. The conjugated PD-L1 ISACs induced robust, target-dependent activation of myeloid cells when co-cultured with PD-L1-expressing tumor cells, as measured by increased secretion of such cytokines as IL-12p70, IFN-alpha, and TNF-alpha. Importantly, myeloid activation was observed following co-culture with tumor cells having various levels of endogenous PD-L1 expression that was within the range of PD-L1 expression observed in human tumors. Systemically administered surrogate PD-L1 ISACs were well tolerated in mice and showed improved anti-tumor efficacy over anti-PD-L1 antibodies, with significant tumor growth delay or complete responses frequently observed in syngeneic (e.g. MB49, MC38-hPD-L1) as well as xenograft (e.g. HCC1954-hPD-L1) tumor models. <h3>Conclusions</h3> These data demonstrate the potential of a PD-L1-targeted ISAC as a multifunctional therapeutic that may improve efficacy of PD-L1/PD-1 inhibition by combining three mechanisms of action into a single molecule: TLR-mediated myeloid cell activation, T cell activation through immune-checkpoint inhibition as well as ADCP. <h3>Ethics Approval</h3> All animal studies were performed in accordance with Institutional Animal Care and Use Committee (IACUC)-approved protocols.
Generating Factoid Questions With Recurrent Neural Networks: The 30M Factoid Question-Answer Corpus (2016)

Iulian Vlad Serban, Alberto García-Durán, Caglar Gulcehre, Sungjin Ahn, Sarath Chandar, Aaron Courville, Yoshua Bengio. Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2016.
State of the Art Lecture: Erythropoietin receptor: application in drug development (1995)

Erythropoietin (EPO) is the primary hormone responsible for the growth and maturation of red blood cells in mammals. In contrast to many other growth factors, the specificity of EPO for mature erythroid cells has lead to its development as a safe and efficacious therapeutic, EPREX. The medical benefits of EPREX have been well established in the treatment of anaemic chronic renal failure patients, anaemic HIV patients treated with AZT, cancer chemotherapy patients, and patients wishing to donate their own blood prior to elective surgery (autologous predonation). Due to the chronic nature of EPO therapy, it would be desirable to have an orally administered 'second generation' molecule. An understanding of the structural basis of the interaction of EPO with its receptor will aid in the design of an oral anaemia drug. In this study, a series of mutations have been generated in a truncated form of the receptor comprising the extracellular region, termed EPO binding protein (EBP). One mutant, in which alanine replaces phenylalanine at position 93 (F93A) has a 500-fold reduction in binding compared to wild-type EBP. A neutralizing anti-EBP antibody binds poorly to the F93A mutant, while a non-neutralizing anti-EBP antibody binds wild-type and F93A equally well. Information from this mutational analysis can be applied to a receptor 3-D model and ultimately used in drug development.
Molecular architecture of a light-harvesting antenna. Quaternary interactions in the Synechococcus 6301 phycobilisome core as revealed by partial tryptic digestion and circular dichroism studies. (1983)

The core of the phycobilisomes of Synechococcus 6301 (Anacystis nidulans) strain AN112 consists of two cylindrical elements each made up of the same four distinct subcomplexes: A (alpha AP beta AP)3; B (alpha AP beta AP)2 . 18.3K . 75K; C (alpha 1APB alpha 2AP beta 3AP) . 10.5K; and D (alpha AP beta AP)3 . 10.5K, where alpha AP and beta AP are the subunits of allophycocyanin, alpha APB is the subunit of allophycocyanin B, and 18.3K, 75K, and 10.5K are polypeptides of 18,300, 75,000, and 10,500 Da, respectively. An 18 S subassembly containing subcomplexes A and B has previously been characterized (Yamanaka, G., Lundell, D. J., and Glazer, A. N. (1982) J. Biol. Chem. 257, 4077-4086; Lundell, D. J., and Glazer, A. N. (1983) J. Biol. Chem. 258, 894-901, 902-908). A ternary core subassembly, containing complexes A, B, and C, was isolated from a limited tryptic digest of AN112 phycobilisomes and characterized with respect to composition and spectroscopic properties. Isolation of this ternary subassembly also establishes that subcomplex D must occupy a terminal position in each of the two core cylinders. Spectroscopic studies of the individual complexes, A-D, of the subassemblies AB and ABC, and of intact AN112 phycobilisomes showed core assembly-dependent changes in the circular dichroism spectra indicative of changes in the environment and/or conformation of the bilin chromophores within the individual subcomplexes. Two terminal energy acceptors are present in the phycobilisome core, alpha APB and 75K. No indication of interaction between the chromophores on these polypeptides was detected by circular dichroism spectroscopy. This result indicates that the bilins on alpha APB and 75K act as independent energy acceptors rather than as exciton pairs.
Synthesis of the Novel Antidepressant (R)-(-)-Rolipram (1997)

Abstract Enantioselective synthesis of (R)-Rolipram 1 has been achieved through a conjugate addition of cyanide to enantiomerically pure 2-(2-aryl ethenyl)oxazoline 2, followed by selective reduction of the adduct with NaBH4-NiCl2.