gebhart/patrepeval huggingface dataset:
Bacterial Glycosyltransferases: Challenges and Opportunities of a Highly Diverse Enzyme Class Toward Tailoring Natural Products (2016)

The enzyme subclass of glycosyltransferases (GTs; EC 2.4) currently comprises 97 families as specified by CAZy classification. One of their important roles is in the biosynthesis of disaccharides, oligosaccharides, and polysaccharides by catalyzing the transfer of sugar moieties from activated donor molecules to other sugar molecules. In addition GTs also catalyze the transfer of sugar moieties onto aglycons, which is of great relevance for the synthesis of many high value natural products. Bacterial GTs show a higher sequence similarity in comparison to mammalian ones. Even when most GTs are poorly explored, state of the art technologies, such as protein engineering, domain swapping or computational analysis strongly enhance our understanding and utilization of these very promising classes of proteins. This perspective article will focus on bacterial GTs, especially on classification, screening and engineering strategies to alter substrate specificity. The future development in these fields as well as obstacles and challenges will be highlighted and discussed.
Design correction in extreme ultraviolet lithography (2010)

Extreme ultraviolet (EUV) lithography is currently the most promising technology for advanced manufacturing nodes. This study aims to assess in detail the quality of a full chip optical correction for a EUV design, as well to discuss the available approaches to compensate for EUV-specific effects. Extensive data sets have been collected on the ASML EUV Alpha-Demo Tool using the latest Interuniversity Microelectronics Center baseline resist Shin-Etsu SEVR59. In total ~1300 critical dimension (CD) measurements at wafer level and 700 at mask level were used as input for model calibration and validation. The smallest feature size in the data set was 32 nm. Both one-dimensional and two-dimensional structures through CD and pitch were measured. The reticle used in this calibration exercise allowed one to modulate flare by varying tiling densities. The shadowing effect was modeled by means of a single bias correction throughout the design. Horizontal and vertical features of different types through pitch and CD were used to calibrate the shadowing correction. The model calibration yielded an root-mean square of ~1 nm, which was observed to improve by including reticle CD data. An EUV mask fully corrected for optical proximity correction, flare and shadowing was fabricated and qualified, demonstrating the effectiveness of the implemented corrections.
Anti-<i>Trypanosoma cruzi</i>Immunoglobulin G1 Can Be a Useful Tool for Diagnosis and Prognosis of Human Chagas' Disease (2001)

Two functionally distinct antibodies, categorized as conventional serology antibodies (CSA) and lytic antibodies (LA) have been described in Chagas' disease, based on their ability to bind to fixed epimastigotes (EPI) or live trypomastigotes (TRYPO), respectively. In this study, the profile of immunoglobulin G (IgG) subclasses of CSA and LA were analyzed by flow cytometry using serum samples from chronic chagasic patients with the indeterminate (IND), cardiac (CARD), and digestive (DIG) clinical forms of the disease. The results were expressed as percentage of positive fluorescent parasites (PPFP) for each sample. CSA showed a higher PPFP than LA for all samples. At serum dilutions between 1:256 and 1:2,048, IgG1 anti-EPI was able to distinguish chagasic from nonchagasic individuals. Different profiles of IgG subclasses were observed for CSA and LA. IgG1 and IgG2 were the main subclasses in CSA, whereas IgG1 and IgG3 were the predominant ones in LA. The reactivity of IgG2 anti-EPI was greater in IND and CARD than in DIG patients. Furthermore, a low level of IgG1 and IgG3 LA was associated with most of the CARD patients. On the other hand, a high level of IgG1 LA was associated with most of the IND patients. In summary, our findings indicate the potential of IgG1 anti-EPI for serological diagnosis of Chagas' disease, providing further evidence for a protective role of LA, and show that IgG1 anti-live Trypanosoma cruzi TRYPO may be used to predict the risk of cardiac damage in Chagas' disease.
Human T cell activation through the activation-inducer molecule/CD69 enhances the activity of transcription factor AP-1 (1992)

The induction of the AP-1 transcription factor has been ascribed to the early events leading to T cell differentiation and activation. We have studied the regulation of AP-1 activity in human peripheral blood T lymphocytes stimulated through the activation inducer molecule (AIM)/CD69 activation pathway. Phorbol esters are required to induce AIM/CD69 cell-surface expression as well as for triggering the proliferation of T cells in conjunction with anti-AIM mAb. Mobility shift assays showed that addition of anti-AIM mAb to PMA-treated T lymphocytes markedly enhanced the binding activity of AP-1 to its cognate sequence, the phorbol ester response element. In contrast, anti-AIM mAb did not induce any change in the binding activity of NF-kappa B, a transcription factor whose activity is also regulated by protein kinase C. The increase in AP-1-binding activity was accompanied by the marked stimulation of the transcription of c-fos but not that of c-jun. Blockade of the DNA-binding complexes with an anti-Fos mAb demonstrated a direct participation of c-Fos in the AP-1 complexes induced by anti-AIM mAb. Most of the AP-1 activity could be eliminated when the anti-AIM mAb was added to the culture medium in the presence of cycloheximide, suggesting that de novo protein synthesis is crucial for the induction of AP-1-binding activity. These data provide the evidence that activation of human peripheral blood T cells through the AIM activation pathway regulate the activity of AP-1. Therefore, this pathway appears as a crucial step in the initiation of early T cell activation events.
Modulation of water exchange in Eu(III) DOTA–tetraamide complexes: considerations for <i>in vivo</i> imaging of PARACEST agents (2009)

Modulation of water exchange in lanthanide(III)-DOTA type complexes has drawn considerable attention over the past two decades, particularly because of their application as contrast agents for magnetic resonance imaging. LnDOTA-tetraamide complexes display unusually slow water exchange kinetics and this chemical property offers an opportunity to use these complexes as a new type of contrast agent based upon the chemical exchange saturation transfer (CEST) mechanism. Six new DOTA-tetraamide ligands having side-chain amide arms with varying hydrophobicity and polarity were prepared and the water exchange characteristic of complexes formed with europium(III) complexes were investigated. The results show that introduction of steric bulk into the amide side-chain arms of the europium(III) complexes not only favors formation of the mono-capped twisted square antiprism coordination isomers, the isomer that is generally less favourable for CEST, but also accelerates water exchange in the mono-capped square antiprism isomers. However, converting single methyl groups on these bulky arms to carboxyl or carboxyl ethyl esters results in a rather dramatic decrease in water exchange rates, about 50-fold. Thus, steric bulk, polarity and hydrophobicity of the amide side-chains each contribute to organization of water molecules in the second hydration sphere of the europium(III) ion and this in turn controls water exchange in these complexes.
Vulnerabilities through Usability Pitfalls in Cloud Services: Security Problems due to Unverified Email Addresses (2012)

Cloud storage services become increasingly interesting for users to easily backup or synchronize their data. On top of this basic functionality, these services offer functions for collaboration that allow users to share their files with selected other persons in a user-friendly way. We have identified that several cloud storage services do not verify whether the registrating customer is the real owner of the email address entered during the registration. Cloud providers omit the verification for reasons of usability. Here, user-friendliness goes too far at the cost of security. This vulnerability combined with collaboration functions allows attacks on cloud customers. In this paper, we explain which attacks are possible. Missing email verification and collaboration functions allow espionage and malware distribution attacks. Execution is very easy, i.e., they can be done without coding expertise or special tools.
Assembly of computers to command and control a robot (1969)

There is a growing consensus among predictors of science that the world is about to witness the evolution of what might be called a new species---the robot. Whereas, animal evolution was a trial-and-error process, robot evolution appears likely to be carefully contrived. Starting where animal evolution left off, that is, with man, robot evolution promises to excel man is some respects, and be excelled by him in others.
Experimental Realization of a Magnetic Cloak (2012)

Invisibility to electromagnetic fields has become an exciting theoretical possibility. However, the experimental realization of electromagnetic cloaks has only been achieved starting from simplified approaches (for instance, based on ray approximation, canceling only some terms of the scattering fields, or hiding a bulge in a plane instead of an object in free space). Here, we demonstrate, directly from Maxwell equations, that a specially designed cylindrical superconductor-ferromagnetic bilayer can exactly cloak uniform static magnetic fields, and we experimentally confirmed this effect in an actual setup.
[Experimental study on regeneration of bone in standardized defects of rabbits tibia after application of collagen grafts in comparison to transplantation of cancellous bone (author's transl)]. (1977)

This study demonstrates, that regeneration of bone in cortical layer defect is about as intensive after application of collagen grafts as after transplantation of autologous of homologous cancellous bone.
Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish (2011)

Zinc-finger nucleases (ZFNs) allow targeted gene inactivation in a wide range of model organisms. However, construction of target-specific ZFNs is technically challenging. Here, we evaluate a straightforward modular assembly-based approach for ZFN construction and gene inactivation in zebrafish. From an archive of 27 different zinc-finger modules, we assembled more than 70 different zinc-finger cassettes and evaluated their specificity using a bacterial one-hybrid assay. In parallel, we constructed ZFNs from these cassettes and tested their ability to induce lesions in zebrafish embryos. We found that the majority of zinc-finger proteins assembled from these modules have favorable specificities and nearly one-third of modular ZFNs generated lesions at their targets in the zebrafish genome. To facilitate the application of ZFNs within the zebrafish community we constructed a public database of sites in the zebrafish genome that can be targeted using this archive. Importantly, we generated new germline mutations in eight different genes, confirming that this is a viable platform for heritable gene inactivation in vertebrates. Characterization of one of these mutants, gata2a, revealed an unexpected role for this transcription factor in vascular development. This work provides a resource to allow targeted germline gene inactivation in zebrafish and highlights the benefit of a definitive reverse genetic strategy to reveal gene function.
Effect of Lanthana as a Stabilizing Agent in Titanium Dioxide Support (1996)

The thermal stability of between 1 and 5 wt % lanthana-doped TiO2 was investigated. Three methods of aging the titania support were studied: stagnant air heating for 12 h at temperatures ranging from 450 to 900 °C, flowing humid 450 °C air for up to 25 days, and flowing humid 650 °C air for up to 30 days. The thermal stability was assessed using BET surface area and XRD. Chlorodifluoromethane (HCFC22) oxidation was used as a probe reaction to determine the effects of thermal aging on the reactivity of the catalyst. The XRD results indicate that the decrease in surface area corresponds to the phase transformation from anatase to rutile. In the fixed time results, all doping levels achieved the same elevated stability, increasing the phase transition temperature from approximately 450 to about 650 °C. However, when the support was aged by exposure for an extended time, increasing the lanthana loading increased the thermal stability. This surface area thermal stability was shown to be related to the activity of the catalyst in oxidizing HCFC22.
Preparation of Furan Dimer-based Biopolyester Showing High Melting Points (2017)

Furan dimer diester was obtained by reductive or oxidative homocoupling of furan carboxylate derivatives in the presence of a nickel or palladium catalyst. Treatment of the obtained diester with 1,ω-diol in the presence of titanium alkoxide as a catalyst leads to the corresponding polyester in excellent yields. The obtained polymers show remarkably high melting points compared with the related polyesters composed of a single furan ring derived from furan-2,5-dicarboxylic acid (FDCA). Thermal properties of the furan dimer-derived polyesters are comparable with those of terephthalate polymers such as poly(ethylene terephthalate).
Low-voltage indium gallium zinc oxide thin film transistors on paper substrates (2010)

We have fabricated bottom-gate amorphous (α-) indium-gallium-zinc-oxide (InGaZnO4) thin film transistors (TFTs) on both paper and glass substrates at low processing temperature (≤100 °C). As a water and solvent barrier layer, cyclotene (BCB 3022–35 from Dow Chemical) was spin-coated on the entire paper substrate. TFTs on the paper substrates exhibited saturation mobility (μsat) of 1.2 cm2 V−1 s−1, threshold voltage (VTH) of 1.9 V, subthreshold gate-voltage swing (S) of 0.65 V decade−1, and drain current on-to-off ratio (ION/IOFF) of ∼104. These values were only slightly inferior to those obtained from devices on glass substrates (μsat∼2.1 cm2 V−1 s−1, VTH∼0 V, S∼0.74 V decade−1, and ION/IOFF=105–106). The uneven surface of the paper sheet led to relatively poor contact resistance between source-drain electrodes and channel layer. The ability to achieve InGaZnO TFTs on cyclotene-coated paper substrates demonstrates the enormous potential for applications such as low-cost and large area electronics.
Mining the human autoantibody repertoire: Isolation of potent IL17A-neutralizing monoclonal antibodies from a patient with thymoma (2014)

Anti-cytokine autoantibodies have been widely reported to be present in human plasma, both in healthy subjects and in patients with underlying autoimmune conditions, such as autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) or thymic epithelial neoplasms. While often asymptomatic, they can cause or facilitate a wide range of diseases including opportunistic infections. The potential therapeutic value of specific neutralizing anti-cytokine autoantibodies has not been thoroughly investigated. Here we used mammalian cell display to isolate IL17A-specific antibodies from a thymoma patient with proven high-titer autoantibodies against the same. We identified 3 distinct clonotypes that efficiently neutralized IL17A in a cell-based in vitro assay. Their potencies were comparable to those of known neutralizing antibodies, including 2, AIN457 (secukinumab) and ixekizumab that are currently in clinical development for the treatment of various inflammatory disorders. These data clearly demonstrate that the human autoantibody repertoire can be mined for antibodies with high therapeutic potential for clinical development.
Operating system support for small objects (2002)

Operating systems should support fine-grained objects in two important ways. One is the use of fairly small pages (e.g. 1 KB) and fast, flexible virtual memory primitives. Another is the use of a binary code format that supports precise identification of pointers in registers and stacks. These features can support many novel and efficient uses of conventional hardware. Pointer swizzling (address translation) at page fault time can efficiently support huge address spaces with modest word sizes. Compressed paging implements a new level in the memory hierarchy (compressed in-memory storage) to bridge the growing gap between RAM and disk. Adaptive prefetching promises to reduce page fault costs more effectively than increasing page sizes. Many other applications would also benefit, including garbage collection, checkpointing, distributed virtual memories, lazy evaluation, and memory striping to reduce cache conflicts.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Inhibition of Sindbis Virus Release by Media of Low Ionic Strength: an Electron Microscope Study (1972)

Release of Sindbis virus from infected cells is inhibited by lowering the ionic strength of the medium. To determine the nature of the inhibited step, we examined, by electron microscopy, both freeze-etched and thin-sectioned preparations which had been fixed with either glutaraldehyde or formaldehyde. Inhibitory medium had two different effects on Sindbis virus release: virus budding was partially inhibited, and those virions which did mature were precipitated on the surface of the cell. Freeze-etched, inhibited cells showed very few viral buds. After shift to normal medium, the number of budding virions increased dramatically, far exceeding the quantity found in normal controls. Thus, low ionic strength medium clearly inhibited an early stage of virus maturation. The results were the same regardless of the fixative. Thin sections of glutaraldehyde-fixed, inhibited cells contained large extracellular aggregates of mature virus which were not present in similar, formaldehyde-fixed preparations. Fixation of radioactively-labeled, inhibited cultures revealed that approximately half of the virus that could be released from inhibited cells by raising the ionic strength of the medium could also be released by formaldehyde, but not by glutaraldehyde. This fraction probably represents mature virus attached to the cell surface by the ionic conditions.
Molecular cloning of a member of the gene family that encodes pMGA, a hemagglutinin of Mycoplasma gallisepticum (1993)

A hemagglutinin with an M(r) of 67,000 (pMGA) from Mycoplasma gallisepticum S6 was purified by using monoclonal antibody affinity chromatography. Purified pMGA was treated with a number of enzymes, the resultant peptides were purified, and their amino acid sequence was determined by using an Applied Biosystems (model 471A) protein sequencer. The DNA sequence encoding two peptides was used to dictate the sequences of synthetic oligonucleotides which were used to screen a library of EcoRI-cut M. gallisepticum DNA in pUC18. A clone reactive to both probes was isolated and found to contain a recombinant insert of 10 kb. The clone was mapped by using restriction endonucleases and fragments subcloned into pUC18 for DNA sequencing. Analysis of part of the DNA sequence revealed an open reading frame containing 1,941 nucleotides which encoded 647 amino acids. The amino terminus was preceded by a putative leader sequence of 25 amino acids. A promoter region preceding the putative start codon GUG was also located. This gene would encode a mature protein of 67,660 Da. There were a number of differences between the predicted amino acid sequence and that determined by direct peptide sequencing. Also, two tryptic peptides of pMGA were not found in the DNA sequence. This suggested that the cloned gene did not encode pMGA but did encode a homolog (pMGA1.2). Furthermore, downstream of pMGA1.2 was a region of DNA encoding a leader sequence followed by an amino acid sequence with high homology to that encoded by the pMGA1.2 gene. The presence within M. gallisepticum of a family of pMGA genes is inferred from the DNA sequence and Southern transfer data. A possible role for this gene family in immune evasion is discussed.
An Analysis of Three Self-Balancing Phase Inverters (1946)

A self-balancing phase inverter is a circuit converting one driving voltage to two output voltages of opposite phase but of essentially equal magnitude by an inherent characteristic of the device and not by virtue of any critical adjustment. The algebraic solution of three self-balancing phase inverters is given, assuming all circuit elements are linear. Included in the solution are the conditions for self-balance, the balance ratio, and the voltage gain. From this information, the type of inverter for a particular service may be selected and designed.
Abdominal Image Segmentation Using Three-Dimensional Deformable Models (1998)

The deformable model-based segmentation scheme produces robust and acceptable outputs on abdominal CT images.
Topoisomerase I and II Inhibitors Control Caspase-2 Pre-Messenger RNA Splicing in Human Cells (2004)

Abstract We have recently shown that the topoisomerase II inhibitor, etoposide (VP16), could trigger caspase-2 pre-mRNA splicing in human leukemic cell lines. This leads to increased inclusion of exon 9, which is specifically inserted into the short caspase-2S isoform mRNA and absent from the long caspase-2L isoform mRNA. One of the consequences of this alternative splicing is a decrease in the total amount of the mature form of caspase-2L mRNA and protein. In this study, we analyzed the effects of several representative molecules of various classes of cytotoxic agents on caspase-2 pre-mRNA splicing in both U937 leukemic cells and in HeLa cervix carcinoma cells. Very strikingly, both topoisomerase I (camptothecin and homocamptothecin derivatives) and II (VP16, amsacrine, doxorubicin, mitoxantrone) inhibitors induced exon 9 inclusion. DNA intercalating glycosyl indolocarbazole derivatives as well as DNA alkylating agents, such as cisplatin and melphalan, antimetabolites like 5-fluorouracil, and mitotic spindle poisons like vinblastine had no effect. Therefore, both classes of DNA topoisomerases can control pre-mRNA splicing of the caspase-2 transcript. In addition, the splicing reaction brought about by camptothecin was hampered in human CEM/C2 and in murine P388-45R leukemic deficient in topoisomerase I activity. Conversely, VP16 did not trigger caspase-2 alternative splicing in human HL60/MX2 leukemic cells harboring a mutant topoisomerase II. Minigene transfection analysis revealed that topoisomerase inhibitors did not change the splicing profile when cis-acting elements in intron-9, reported to control exon 9 inclusion independently of drug treatment, were removed. Rather, our experiments suggest that exon 9 inclusion induced by topoisomerase inhibitors reflects the activity exerted by topoisomerase I or II on proteins that control splicing reactions, or their direct involvement in pre-mRNA splicing.
Semi-supervised learning for detecting human trafficking (2017)

Human trafficking is one of the most atrocious crimes and among the challenging problems facing law enforcement which demands attention of global magnitude. In this study, we leverage textual data from the website “Backpage”—used for classified advertisement—to discern potential patterns of human trafficking activities which manifest online and identify advertisements of high interest to law enforcement. Due to the lack of ground truth, we rely on a human analyst from law enforcement, for hand-labeling a small portion of the crawled data. We extend the existing Laplacian SVM and present $$S^3VM-R$$ , by adding a regularization term to exploit exogenous information embedded in our feature space in favor of the task at hand. We train the proposed method using labeled and unlabeled data and evaluate it on a fraction of the unlabeled data, herein referred to as unseen data, with our expert’s further verification. Results from comparisons between our method and other semi-supervised and supervised approaches on the labeled data demonstrate that our learner is effective in identifying advertisements of high interest to law enforcement.