gebhart/patrepeval huggingface dataset:
Induction of murine autoimmune disease by chronic polyclonal B cell activation. (1983)

In vivo, prolonged polyclonal activation of B cells by the nonantigenic but potent mitogenic lipid A portion of lipopolysaccharide (LPS-R595) resulted in acceleration of the late life systemic lupus erythematosus disease of female MRL/n, BXSB, and NZW mice, mimicking the time, form, and histopathological features characteristic of their early life disease counterparts, i.e., MRL/l females, BXSB males, and (NZB X NZW)F1 females. Similar polyclonal B cell activation of "immunologically normal" mice has less effect and led to a limited expression of autoimmune disease. This R595-induced autoimmunity and immune complex-mediated disease seemed to be the direct result of activation of the immune system and not from other effects of endotoxin since C3H/HeJ, a strain lacking lymphocyte receptors for LPS-R595, had neither serological nor histological evidence of autoimmune disease despite identical treatment.
A Novel Metal-activated Pyridoxal Enzyme with a Unique Primary Structure, Low Specificity d-Threonine Aldolase fromArthrobacter sp. Strain DK-38 (1998)

The gene encoding low specificity D-threonine aldolase, catalyzing the interconversion of D-threonine/D-allo-threonine and glycine plus acetaldehyde, was cloned from the chromosomal DNA of Arthrobacter sp. strain DK-38. The gene contains an open reading frame consisting of 1,140 nucleotides corresponding to 379 amino acid residues. The enzyme was overproduced in recombinant Escherichia coli cells and purified to homogeneity by ammonium sulfate fractionation and three-column chromatography steps. The recombinant aldolase was identified as a pyridoxal enzyme with the capacity of binding 1 mol of pyridoxal 5'-phosphate per mol of subunit, and Lys59 of the enzyme was determined to be the cofactor binding site by chemical modification with NaBH4. In addition, Mn2+ ion was demonstrated to be an activator of the enzyme, although the purified enzyme contained no detectable metal ions. Equilibrium dialysis and atomic absorption studies revealed that the recombinant enzyme could bind 1 mol of Mn2+ ion per mol of subunit. Remarkably, the predicted amino acid sequence of the enzyme showed no significant similarity to those of the currently known pyridoxal 5'-phosphate-dependent enzymes, indicating that low specificity D-threonine aldolase is a new pyridoxal enzyme with a unique primary structure. Taken together, low specificity D-threonine aldolase from Arthrobacter sp. strain DK-38, with a unique primary structure, is a novel metal-activated pyridoxal enzyme.
The role of tumor rejection antigens in host antitumor defense mechanisms (1995)

Such findings have led to speculation that HSPs or their associated peptides may have a role in the diagnosis and/or treatment of specific cancers. Immunotherapy and bispecific antibodies in particular are areas in which HSPs may prove to be useful.
An engineered small RNA-mediated genetic switch based on a ribozyme expression platform (2013)

An important requirement for achieving many goals of synthetic biology is the availability of a large repertoire of reprogrammable genetic switches and appropriate transmitter molecules. In addition to engineering genetic switches, the interconnection of individual switches becomes increasingly important for the construction of more complex genetic networks. In particular, RNA-based switches of gene expression have become a powerful tool to post-transcriptionally program genetic circuits. RNAs used for regulatory purposes have the advantage to transmit, sense, process and execute information. We have recently used the hammerhead ribozyme to control translation initiation in a small molecule-dependent fashion. In addition, riboregulators have been constructed in which a small RNA acts as transmitter molecule to control translation of a target mRNA. In this study, we combine both concepts and redesign the hammerhead ribozyme to sense small trans-acting RNAs (taRNAs) as input molecules resulting in repression of translation initiation in Escherichia coli. Importantly, our ribozyme-based expression platform is compatible with previously reported artificial taRNAs, which were reported to act as inducers of gene expression. In addition, we provide several insights into key requirements of riboregulatory systems, including the influences of varying transcriptional induction of the taRNA and mRNA transcripts, 5'-processing of taRNAs, as well as altering the secondary structure of the taRNA. In conclusion, we introduce an RNA-responsive ribozyme-based expression system to the field of artificial riboregulators that can serve as reprogrammable platform for engineering higher-order genetic circuits.
Expansion of CD4+CD25+ regulatory T cells by intravenous immunoglobulin: a critical factor in controlling experimental autoimmune encephalomyelitis (2007)

The clinical use of intravenous immunoglobulin (IVIg) based on its immunomodulatory and anti-inflammatory potential remains an ongoing challenge. Fcgamma receptor-mediated effects of IVIg, although well elucidated in certain pathologies, cannot entirely account for its proven benefit in several autoimmune disorders mediated by autoreactive T cells. In this study, we show that prophylactic infusion of IVIg prevents the development of experimental autoimmune encephalomyelitis (EAE), an accepted animal model for multiple sclerosis (MS). The protection was associated with peripheral increase in CD4+CD25+Foxp3+ regulatory T cell (Treg) numbers and function. The protection was Treg-mediated because IVIg failed to protect against EAE in mice that were depleted of the Treg population. Rather than inducing de novo generation from conventional T cells, IVIg had a direct effect on proliferation of natural Treg. In conclusion, our results highlight a novel mechanism of action of IVIg and provide a rationale to test the use of IVIg as an immunomodulatory tool to enhance Treg in early onset MS and other autoimmune and inflammatory conditions.
Effect of nonparabolicity in GaAs/Ga1−xAlxAs semiconductor quantum wells (1989)

We investigate the effect of nonparabolicity in various bands of bulk semiconductors on the electronic-subband-edge energies in quantum wells. We compare the results from different versions of the model originally proposed by Bastard. We show that their efficacy in yielding the correct quantum-well energy levels for the conduction band can be characterized in terms of two parameters, namely, the effective mass ${m}^{\mathrm{*}}$ and the nonparabolicity parameter \ensuremath{\gamma}. We have performed this comparison of the models for a number of well widths for GaAs/${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Al}}_{\mathrm{x}}$As quantum-well structures using the results from an eight-band second-order k\ensuremath{\cdot}p Hamiltonian, in a transfer-matrix method derived earlier, as the benchmark. We confirm the observation made earlier that band nonparabolicity actually raises the lowest conduction-band energy level of the quantum well by a small amount while lowering the higher energy levels.
Characterization of the signal transduction pathways mediating noradrenaline-stimulated MAPK activation and c-fos expression in oligodendrocyte progenitors (1999)

In examining the signaling transduction pathway of adrenoceptors in oligodendrocyte progenitors, we have found that stimulation of alpha(1)-adrenoceptors with norepinephrine (NE), in the presence of 3 microM propranolol, increased the activity of mitogen-activated protein kinases (MAPKs). This stimulation was concentration- and time-dependent, with maximal response after 10 min of exposure to 10 microM NE. Pertussis toxin (PTX) blocked NE-mediated MAPK activation, suggesting that alpha(1)-adrenoceptor activates MAPK through a PTX-sensitive G-protein. In the presence of U73122, an inhibitor of phospholipase C (PLC), MAPK activation was blocked. In oligodendrocyte progenitor cultures, chronic treatment with phorbol-12-myristate-13-acetate (PMA) down-regulated protein kinase C (PKC) and blocked NE-mediated MAPK activation. The response to NE was also significantly decreased by the PKC inhibitors H7 and bisindolylmaleimide GF109203X. Similarly, the effect of NE on MAPK activation was not observed in a calcium-free medium. Furthermore, attenuation of MAPK activity was observed when cultures were pretreated with LY294002 and wortmannin, inhibitors of phosphatidylinositol-3 kinase (PI3K). These results suggest that alpha(1)-adrenoceptor-mediated activation of MAPK involves a PTX-sensitive G-protein, PLC, PI3K, and 1,2-diacyl glycerol (DAG)-dependent PKC isozyme. Stimulation of oligodendrocyte progenitors with NE also resulted in an increase in c-fos expression, which was mediated by both alpha(1)- and beta-adrenoceptor and was calcium-, PKC-, and protein kinase A (PKA)-dependent. Interestingly, in the presence of PD 098059, a specific inhibitor of MAPK kinase (MEK), both MAPK activity and c-fos expression were blocked. This suggests that MAPK is implicated in the transmission of the signal from alpha(1)-adrenoceptor to c-fos gene expression.
Biochemical and biophysical analysis of the GTPase activating proteins of the small guanine nucleotide binding protein Rap1 and RheB (2005)

This work covers biochemical characterization of GAP activation of the small GNBPs, Rap1 and RheB, which was achieved by a combination of techniques like infrared spectroscopy, mutational analysis and stopped flow kinetics. It was shown that RapGAP catalyzed reaction involves an additional intermediate GTP state, the chemical cleavage reaction is reversible and P\(_{i}\) release is rate limiting. The most important feature in GAP catalyzed reaction is a shift of negative charge towards the non-bridging oxygen of the \(\beta\) phosphate of GTP, which is more pronounced than Ras\(\cdot\)RasGAP system. A carboxyamide intermediate vibration was observed which in an independent study, turned out to be the catalytic asparagine residue of the GAP. RapGAP can down regulate mutations of position 61 and 12 of Rap and BeF\(_{3}\)\(^{-}\) is a better transition state mimic than AlF\(_{x}\), which indicates a dissociative mechanism. Also the \(\textit {in vitro}\) GAP activity of tuberin, a homolog could be demonstrated.
Training labels for hippocampal segmentation based on the EADC‐ADNI harmonized hippocampal protocol (2015)

This work provides reference hippocampal labels for the training and certification of automated segmentation algorithms. The publicly released labels will allow the widespread implementation of the standard segmentation protocol.
Ambient-temperature-stable molecular biology reagents. (1993)

We have processed biological materials to generate several reagents that are ambient temperature stable and ready to use. Stabilized biomolecules in a glassy matrix of carbohydrate polymers offer water-soluble reagents for complex molecular biology applications. This approach is particularly useful for reagent systems composed of enzymes, nucleotides and other components dispensed in single-use aliquots. Reconstitution of the glassy matrix delivers buffered enzymes and/or nucleotides for restriction, modification, sequencing and/or amplification of nucleic acids. These ambient-temperature-stable reagents allow a high level of reproducibility as they minimize the potential for pipetting errors. They also provide advantages in shipping, storage and subsequent handling. Added convenience includes elimination of setup time, cross contamination and refrigeration. Applications of ambient-temperature-stable biological reagents for routine molecular biology methods are presented.
Distinct Expression Patterns in Cytogenetically Normal Acute Myeloid Leukemia (CN-AML) Characterized by Uniparental Disomy. (2008)

Abstract Genome-wide single nucleotide polymorphism (SNP) analyses have revealed uniparental disomy (UPD) to be a common event in cytogenetically normal acute myeloid leukemia (CN-AML) occurring in approximately 20% of cases. Acquired UPD results in copy number neutral loss of heterozygosity (LOH). Comparing matched tumor and germline DNA samples recurrent acquired UPDs affecting chromosomes 11p and 13q were identified. As DNA microarray-based gene expression profiling (GEP) has recently been shown to powerfully capture the molecular heterogeneity of leukemia, we sought to identify gene expression patterns associated with recurrent UPD in CN-AML. We profiled a set of clinically annotated CN-AML specimens (n=66) entered on a multicenter trial for patients &amp;lt;60 years (AMLSG 07-04) which had been characterized by either 50k or 500k Affymetrix SNP microarrays. All cases were analyzed using Affymetrix microarrays (Human Genome U133 Plus 2.0 Arrays). In this data set we investigated 12 UPDs (affecting chromosomes 1p, 2p, 6p, 11p, 13q and 19q) and applied supervised analyses to define gene-expression patterns associated with UPDs on chromosome 11p and 13q. For the case with an acquired UPD on 19q a gene dosage effect could be demonstrated. Genes located in the 36 Mb large UPD region showed a significantly lower average expression (p&amp;lt;0.001; t-test). Similarly, we observed a gene dosage effect in one of the UPDs observed on chromosome 1 (p=0.0097; t-test), whereas for the other UPDs no significant association between LOH and gene expression levels could be identified. Despite small sample numbers supervised analyses revealed a biologically meaningful gene expression signatures associated with acquired UPD 11p and 13q. In accordance with the association of UPD 13q with FLT3-ITD, the UPD13q gene expression signature was enriched for genes associated with FLT3-ITD. The UPD11p expression pattern was characterized by genes found to be down-regulated in CEBPAmut CN-AML cases, such as down-regulation of homeobox genes HOXA9, HOXA10, HOXB2, and MEIS1. Notably, the UPD11p signature was also characterized by the expression of e.g. UGT2B28, P2RX5, PGDS, CAPN1, NDFIP1, and TRIB2, an expression profile that has been shown to be associated with CEBPAmut CN-AML as well as AML cases with epigenetic CEBPA silencing. Thus, our findings represent a starting point to further dissect CN-AML characterized by recurrent UPD, and ongoing analyses will provide additional insights into leukemia biology.
Medical Image Compression Based on Ordered Binary Decision Diagrams (2009)

A new approach for lossless compression of medical images has been proposed. After preprocessing, the image is split into bit planes to which the compressed technique is applied. These bit planes can be expressed as ordered binary decision diagrams (OBDD) and coding. This approach compared well with WINZIP in terms of compression ratio.
π-Nucleophile Traps for Metallonitrene/Alkyne Cascade Reactions: A Versatile Process for the Synthesis of α-Aminocyclopropanes and β-Aminostyrenes (2009)

The reaction of a sulfamate ester derived rhodium nitrenoid species with an alkyne produces a versatile intermediate, capable of cascading into a wide variety of secondary transformations. The nature of the intermediate has been probed by reactivity studies, and the synthetic utility of the cascade process, which facilitates the construction of complex heterocyclic structures from remarkably simple acyclic precursors, is highlighted.
Using link analysis to improve layout on mobile devices (2004)

Delivering web pages to mobile phones or personal digital assistants has become possible with the latest wireless technology. However, mobile devices have very small screen sizes and memory capacities. Converting web pages for delivery to a mobile device is an exciting new problem. In this paper, we propose to use a ranking algorithm similar to Google's PageRank algorithm to rank the content objects within a web page. This allows the extraction of only important parts of web pages for delivery to mobile devices. Experiments show that the new method is effective. In experiments on pages from randomly selected websites, the system needed to extract and deliver only 39% of the objects in a web page in order to provide 85% of a viewer's desired viewing content. This provides significant savings in the wireless traffic and downloading time while providing a satisfactory reading experience on the mobile device.
Morphine-3-Succinyl—Bovine Serum Albumin: An Immunogenic Hapten-Protein Conjugate (1972)

Morphine-3-hemisuccinate was synthesized by reaction of morphine with succinic anhydride. This compound was conjugated to bovine serum albumin by the mixed anhydride method, and the degree of conjugation was determined by base hydrolysis of the conjugate, extraction, and measurement of free morphine. An average of 6.5 molecules of morphine were conjugated to each molecule of protein. Eleven rabbits immunized with varying doses of the conjugate were producing antibody 8 weeks later, as determined by a modification of the ammonium sulfate method, which measures primary binding of antigen by antibody.
Optical patterning of GaN films (1996)

Patterned etching of GaN films was achieved with laser-induced thermal decomposition. High-energy laser pulses are used to locally heat the film above 900 °C, causing rapid nitrogen effusion. Excess gallium is then removed by conventional etching. At exposures of 0.4 J/cm2 with 355 nm light, etch rates of 50–70 nm per pulse were obtained. Illumination with an interference grating was used to produce trenches as narrow as 100 nm.
Persistent induction of cyclooxygenase in p60v-src-transformed 3T3 fibroblasts. (1990)

A BALB/c 3T3 cell line infected with the temperature-sensitive Rous sarcoma virus strain LA90 has been used to investigate early, p60v-src-dependent changes in gene expression (protein synthesis). Giant two-dimensional electrophoresis, which can resolve greater than 3000 polypeptides from [35S]methionine-labeled cell lysates, was used to detect the induction of a p72-74 (72-74 kDa) doublet (pI 7.5) after activation of p60v-src at 35 degrees C. Antiserum against cyclooxygenase (prostaglandin synthase or prostaglandin endoperoxide synthase) specifically immunoprecipitated the p72-74 doublet. The p72-74 doublet was also induced by platelet-derived growth factor and by phorbol 12-myristate 13-acetate and was elevated in an NIH 3T3 cell line transformed by wild-type src. Activation of p60v-src caused a persistent increase in p72-74, whereas the effect of the growth factor was transient. These dissimilar kinetics of induction were paralleled by changes in cyclooxygenase activity. Down-regulation of protein kinase C inhibited subsequent induction of cyclooxygenase by phorbol myristate acetate but did not block induction by p60v-src. The glucocorticoid agonist dexamethasone inhibited induction of cyclooxygenase by p60v-src. Although induction of this enzyme may not be directly involved in transformation, the data support the view that oncogenic transformation may result, not from expression of transformation-specific genes, but from persistent changes in the expression of genes normally induced only transiently during passage from the G0 stage of the cell cycle.
16S and 23S plastid rDNA phylogenies of Prototheca species and their auxanographic phenotypes (2014)

Because algae have become more accepted as sources of human nutrition, phylogenetic analysis can help resolve the taxonomy of taxa that have not been well studied. This can help establish algal evolutionary relationships. Here, we compare A uxenochlorella protothecoides and 23 strains of P rototheca based on their complete 16S and partial 23S plastid r DNA sequences along with nutrient utilization (auxanographic) profiles. These data demonstrate that some of the species groupings are not in agreement with the molecular phylogenetic analyses and that auxanographic profiles are poor predictors of phylogenetic relationships.
Monocular‐SLAM–based navigation for autonomous micro helicopters in GPS‐denied environments (2011)

Abstract Autonomous micro aerial vehicles (MAVs) will soon play a major role in tasks such as search and rescue, environment monitoring, surveillance, and inspection. They allow us to easily access environments to which no humans or other vehicles can get access. This reduces the risk for both the people and the environment. For the above applications, it is, however, a requirement that the vehicle is able to navigate without using GPS, or without relying on a preexisting map, or without specific assumptions about the environment. This will allow operations in unstructured, unknown, and GPS‐denied environments. We present a novel solution for the task of autonomous navigation of a micro helicopter through a completely unknown environment by using solely a single camera and inertial sensors onboard. Many existing solutions suffer from the problem of drift in the xy plane or from the dependency on a clean GPS signal. The novelty in the here‐presented approach is to use a monocular simultaneous localization and mapping (SLAM) framework to stabilize the vehicle in six degrees of freedom. This way, we overcome the problem of both the drift and the GPS dependency. The pose estimated by the visual SLAM algorithm is used in a linear optimal controller that allows us to perform all basic maneuvers such as hovering, set point and trajectory following, vertical takeoff, and landing. All calculations including SLAM and controller are running in real time and online while the helicopter is flying. No offline processing or preprocessing is done. We show real experiments that demonstrate that the vehicle can fly autonomously in an unknown and unstructured environment. To the best of our knowledge, the here‐presented work describes the first aerial vehicle that uses onboard monocular vision as a main sensor to navigate through an unknown GPS‐denied environment and independently of any external artificial aids. © 2011 Wiley Periodicals, Inc.
Targeting Low-Druggability Bromodomains: Fragment Based Screening and Inhibitor Design against the BAZ2B Bromodomain (2013)

Bromodomains are epigenetic reader domains that have recently become popular targets. In contrast to BET bromodomains, which have proven druggable, bromodomains from other regions of the phylogenetic tree have shallower pockets. We describe successful targeting of the challenging BAZ2B bromodomain using biophysical fragment screening and structure-based optimization of high ligand-efficiency fragments into a novel series of low-micromolar inhibitors. Our results provide attractive leads for development of BAZ2B chemical probes and indicate the whole family may be tractable.