gebhart/patrepeval huggingface dataset:
Structure and Temporal Dynamics of Populations within Wheat Streak Mosaic Virus Isolates (2001)

Variation within the Type and Sidney 81 strains of wheat streak mosaic virus was assessed by single-strand conformation polymorphism (SSCP) analysis and confirmed by nucleotide sequencing. Limiting-dilution subisolates (LDSIs) of each strain were evaluated for polymorphism in the P1, P3, NIa, and CP cistrons. Different SSCP patterns among LDSIs of a strain were associated with single-nucleotide substitutions. Sidney 81 LDSI-S10 was used as founding inoculum to establish three lineages each in wheat, corn, and barley. The P1, HC-Pro, P3, CI, NIa, NIb, and CP cistrons of LDSI-S10 and each lineage at passages 1, 3, 6, and 9 were evaluated for polymorphism. By passage 9, each lineage differed in consensus sequence from LDSI-S10. The majority of substitutions occurred within NIa and CP, although at least one change occurred in each cistron except HC-Pro and P3. Most consensus sequence changes among lineages were independent, with substitutions accumulating over time. However, LDSI-S10 bore a variant nucleotide (G(6016)) in NIa that was restored to A(6016) in eight of nine lineages by passage 6. This near-global reversion is most easily explained by selection. Examination of nonconsensus variation revealed a pool of unique substitutions (singletons) that remained constant in frequency during passage, regardless of the host species examined. These results suggest that mutations arising by viral polymerase error are generated at a constant rate but that most newly generated mutants are sequestered in virions and do not serve as replication templates. Thus, a substantial fraction of variation generated is static and has yet to be tested for relative fitness. In contrast, nonsingleton variation increased upon passage, suggesting that some mutants do serve as replication templates and may become established in a population. Replicated mutants may or may not rise to prominence to become the consensus sequence in a lineage, with the fate of any particular mutant subject to selection and stochastic processes such as genetic drift and population growth factors.
Adoption of the Octal Number System (1971)

The possible adoption of the metric system in the United States makes it logical that any other major changes be considered at the same time. Therefore, it is proposed to adopt the octal number system in place of the decimal. The importance of computers in our lives makes it reasonable that we adopt a number system with a base 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> . The advantages and disadvantages of the various values of n are given. The octal (n=3) number system is found to be the best one. The feasibility and some ramifications of octal adoption are presented.
An Introduction to Bioinformatics for Glycomics Research (2008)

Carbohydrates are considered the thirdclass of information-encoding biologicalmacromolecules. ‘‘Glycomics,’’ the scientificattempt to characterize and study carbohy-drates, is a rapidly emerging branch ofscience, for which informatics is just begin-ning. Glycomics requires sophisticated algo-rithmic approaches. Several algorithms andmodels have been developed for glycobiol-ogy research in the past several years. Thistutorial will provide a brief introduction tothe field of glycome informatics, which willinclude a primer on glycobiology as well asdescriptions of the algorithms and modelsthat have been developed in this field.The four essential molecular buildingblocks of cells are nucleic acids, proteins,lipids, and carbohydrates, often referred toas glycans. Nucleotide and protein sequenc-es are at the heart of nearly all bioinfor-matics applications and research, whereasglycan and lipid structures have been widelyneglected in bioinformatics. However, gly-cans are the most abundant and structurallydiverse biopolymers formed in nature.Bound to proteins, as glycoproteins, theyare known to affectthefunctions of proteins.More than half of all protein sequencesdeposited in the SWISS-PROT databankinclude potential glycosylation sites and thusmay be glycoproteins. Based on an analysisof well-annotated and characterized glyco-proteins inSWISS-PROT,itwas concludedthat more than half of all proteins areglycosylated [1].The development and use of informaticstools and databases for glycobiology andglycomics research has increased consider-ably in recent years. However, the generaldevelopment in this field can still beconsidered as being in its infancy whencompared to the genomics and proteomicsareas. In terms of bioinformatics in glyco-biology, there are several paths of researchthat are currently in progress. The develop-ment of algorithms to reliably support thecharacterization of glycan structures forhigh-throughput applications is the mostimmediate demand of the glycomics com-munity. Additionally, several major glyco-related projects (Consortium for FunctionalGlycomics [2], KEGG Glycan [3], GLY-COSCIENCES.de [4]) are maturing andprovide well-structured glyco-related datathat are awaiting data mining and analysis.With the exciting new developments incarbohydrate arrays and automated MSannotation, the analysis of the glycome hasreached a new level of sophistication, whichrequires broader informatics support. Thistutorial aims to give an overview of thecurrent status of carbohydrate databases, thenewest analytical techniques, as well as theinformatics needed for rapid progress inglycomics research.
ChemInform Abstract: Convenient Synthesis of 3H‐Pyrrolo[2,3‐c]isoquinolines and 3‐H‐Pyrrolo[2,3‐c][1,7]‐, 3,4‐Benzo[c][1,7]‐ and Dihydropyrido[4,3‐c][1,8]naphthyridines via Palladium‐Assisted Nucleophilic Amination. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Integrins in mammary-stem-cell biology and breast-cancer progression – a role in cancer stem cells? (2008)

Cancer cells with stem cell-like properties (cancer stem cells) are believed to drive cancer and are associated with poor prognosis. Data from mouse models have demonstrated that integrins, the major cellular receptors for extracellular-matrix components, have essential roles both during cancer initiation and progression, and during cell differentiation in normal development. By presenting an overview of the role of integrins in stem-cell biology and in cancer progression, this Commentary aims to present evidence for a role of integrins in the biology of cancer stem cells. Given the recent interest in the role of integrins in breast-cancer initiation and progression, we focus on the role of the members of the integrin family and their coupled signaling pathways in mammary-gland development and tumorigenesis.
Mass spectrometry-based quantitative proteomic profiling (2005)

Quantitative proteomics involves the identification and quantitation of protein components in various biological systems. Stable isotope labelling technology, by both metabolic and chemical methods, has been the most commonly used approach for global proteome-wide profiling. Recently, its capability has been extended from labelled pairs to multiple labels, allowing for the simultaneous quantification of multiplex samples. The ion intensity-based quantitative approach has progressively gained more popularity as mass spectrometry performance has improved significantly. Although some success has been reported, it remains difficult comprehensively to characterise the global proteome, due to its enormous complexity and dynamic range. The use of sub-proteome fractionation techniques permits a simplification of the proteome and provides a practical step towards the ultimate dissection of the entire proteome. Further development of the technology for targeting sub-proteomes on a functional basis - such as selecting proteins with differential expression profiles from mass spectrometric analyses, for further mass spectrometric sequencing in an intelligent manner--is expected in the near future.
Absence of Mutations in the Human <i>OB</i> Gene in Obese/Diabetic Subjects (1996)

The product of the obese (ob) gene, leptin, is a secreted protein that is important in the regulation of body weight. Mice with mutations in the ob gene are obese and diabetic and manifest reduced physical as well as metabolic activity. In this study, we tested the possibility that mutations in the OB gene may contribute to human obesity. We report the isolation and partial sequence of the human OB gene and the screening of 105 obese patients for mutations in the protein coding sequence using the technique of single-strand conformational polymorphism. No coding sequence polymorphism was found, suggesting that mutations in the coding sequence of the OB gene do not constitute a common cause of increased body weight in humans. We also identified a highly polymorphic simple dinucleotide repeat DNA polymorphism in this gene that will be useful for genetic studies.
The fate of surface roots of citrus seedlings in dry soil (1994)

The top portions of the root system of deeply rooted plants are frequently in dry soil while deeper roots still have access to water. We expected that many surface roots would be shed when subject to localized soil drying. We further hypothesized that the cost of fine root construction per unit root length would be negatively correlated with the rate at which root length is shed. Seedlings of four citrus root- stocks that varied widely in specific root length (cm g−1 root) were used to test these hypotheses. Plants were grown for 4 months in a split-pot system divided into a top and bottom pot. After roots were well established in the bottom pot, water was withheld from the top pots of half of the plants; plants were harvested every 2 weeks thereafter. Sufficient water was supplied to the bottom pot to prevent shoots of droughted seedlings from experiencing significant water stress. All plants were labelled with 14CO2 48 h before harvesting, and autoradiographs made of the fine roots harvested from the droughted compartment. Comparisons of the autoradiographs with digitized images of the root system allowed us to assess root mortality and root sink activity. As expected, the proportion of 14C-labelled photosyrithate allocated to fine roots in the top pot declined with soil drying in all four genotypes; however, there was no genotypic effect on this decline. Contrary to our expectations, extensive root mortality was not apparent for any genotype, even after 60 d of localized soil drying. Apparently, selection for rapid shedding of roots in response to soil drying has not occurred in these Citrus species.
Optimizing signal constellations for the output of a quantizer (2003)

A technique is presented for optimizing signal constellations for the output of a quantizer. The quantizer outputs are assumed to occur with unequal probabilities, and the mean-square error introduced by the channel is used as the performance criterion. A memoryless Gaussian channel and a peak power constraint are assumed. Transmitter power gains of 1 dB-2 dB were demonstrated when the technique was used to optimize signal constellations for the output of a DPCM (differential pulse code modulation) image coder.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Proposal for the reclassification of Thiobacillus novellus as Starkeya novella gen. nov., comb. nov., in the alpha-subclass of the Proteobacteria. (2000)

Thiobacillus novellus is a facultatively chemolithoautotrophic and methylotrophic, Gram-negative, rod-shaped sulfur bacterium, shown by 16S rRNA gene sequence analysis to be a member of the alpha-2 subclass of the Proteobacteria. As such, it must be excluded from the genus Thiobacillus, whose species are members of the beta-Proteobacteria. It closest phylogenetic neighbour appears to be Ancylobacter, from which it is distinct morphologically and in some physiological characteristics. It is distinct physiologically and biochemically in a number of diagnostic features from Paracoccus versutus, in the alpha-3 subclass of the Proteobacteria and does not appear to be sufficiently closely related to any other genus of the alpha-Proteobacteria to be reassigned to a known genus. The new genus and species name Starkeya novella is proposed for T. novellus. The type strain is ATCC 8093T (= NCIMB 10456T = NCIMB 9113T = DSM 506T = IAM 12100T = IFO 12443T = CCM 1077T).
Efficient Organic Solar Cells with Helical Perylene Diimide Electron Acceptors (2014)

We report an efficiency of 6.1% for a solution-processed non-fullerene solar cell using a helical perylene diimide (PDI) dimer as the electron acceptor. Femtosecond transient absorption spectroscopy revealed both electron and hole transfer processes at the donor-acceptor interfaces, indicating that charge carriers are created from photogenerated excitons in both the electron donor and acceptor phases. Light-intensity-dependent current-voltage measurements suggested different recombination rates under short-circuit and open-circuit conditions.
Catalyst Deactivation and Regeneration Processes in Biogas Tri-Reforming Process. The Effect of Hydrogen Sulfide Addition (2018)

This work studies Ni-based catalyst deactivation and regeneration processes in the presence of H2S under a biogas tri-reforming process for hydrogen production, which is an energy vector of great interest. 25 ppm of hydrogen sulfide were continuously added to the system in order to provoke an observable catalyst deactivation, and once fully deactivated two different regeneration processes were studied: a self-regeneration and a regeneration by low temperature oxidation. For that purpose, several Ni-based catalysts and a bimetallic Rh-Ni catalyst supported on alumina modified with CeO2 and ZrO2 were used as well as a commercial Katalco 57-5 for comparison purposes. Ni/Ce-Al2O3 and Ni/Ce-Zr-Al2O3 catalysts almost recovered their initial activity. For these catalysts, after the regeneration under oxidative conditions at low temperature, the CO2 conversions achieved—79.5% and 86.9%, respectively—were significantly higher than the ones obtained before sulfur poisoning—66.7% and 45.2%, respectively. This effect could be attributed to the support modification with CeO2 and the higher selectivity achieved for the Reverse Water-Gas-Shift (rWGS) reaction after catalysts deactivation. As expected, the bimetallic Rh-Ni/Ce-Al2O3 catalyst showed higher resistance to deactivation and its sulfur poisoning seems to be reversible. In the case of the commercial and Ni/Zr-Al2O3 catalysts, they did not recover their activity.
The Collaborative ORDnance Data Repository (CORD): 2018 Upgrades (2017)

The Collaborative ORDnance Data Repository (CORD) has been in existence since 2015. It is a database of over 5,000 entries detailing a wide range of explosive ordnance. The database is used extensively as a means of identifying munitions by those working in the field of humanitarian mine action, but also by others. Users range from mine clearance operators in Sri Lanka, police bomb disposal teams in Florida or Abu Dhabi, human rights advocates in Washington, D.C., to journalists in London. CORD is not intended as a detailed database. It is intended as a simple online ordnance identification guide with limited detail, accessible to all.
Improved targeting device and computer navigation for accurate placement of brachytherapy needles (2005)

Successful treatment of skull base tumors with interstitial brachytherapy requires high targeting accuracy for the brachytherapy needles to avoid harming vital anatomical structures. To enable safe placement of the needles in this area, we developed an image-based planning and navigation system for brachytherapy, which includes a custom-made mechanical positioning arm that allows rough and fine adjustment of the needle position. The fine-adjustment mechanism consists of an XYZ microstage at the base of the arm and a needle holder with two fine-adjustable inclinations. The rotation axes of the inclinations cross at the tip of the needle so that the inclinational adjustments do not interfere with the translational adjustments. A vacuum cushion and a noninvasive fixation frame are used for the head immobilization. To avoid mechanical bending of the needles due to the weight of attached tracking markers, which would be detrimental for targeting accuracy, only a single LED marker on the tail of the needle is used. An experimental phantom-based targeting study with this setup demonstrated that a positioning accuracy of 1.4 mm (rms) can be achieved. The study showed that the proposed setup allows brachytherapy needles to be easily aligned and inserted with high targeting accuracy according to a preliminary plan. The achievable accuracy is higher than if the needles are inserted manually. The proposed system can be linked to a standard afterloader and standard dosimetry planning module. The associated additional effort is reasonable for the clinical practice and therefore the proposed procedure provides a promising tool for the safe treatment of tumors in the skull base area.
An Enhancement of LSSD to Reduce Test Pattern Generation Effort and Increase Fault Coverage (1982)

In this paper we propose designs of latches which can be used in Level Sensitive Scan Design (LSSD). These new designs can use the existing software support for design rule checks but result into a reduction of effort in test pattern generation and provide a better fault coverage. The system performance is not degraded with the use of latches proposed in this paper.
A Humanized Anti-CD30 Monoclonal Antibody, XmAb™2513, with Enhanced In Vitro Potency Against CD30-Positive Lymphomas Mediated by High Affinity Fc-Receptor Binding. (2005)

Abstract CD30 (also known as Ki-1), a member of the TNF-receptor superfamily, is normally expressed at low levels on activated lymphocytes and has been implicated in cell death and T-cell proliferation. CD30 is highly expressed in Hodgkin’s disease, (HD) and in Anaplastic Large Cell Lymphoma (ALCL). Unmodified CD30 antibodies as well as anti-CD30 based bi-specific antibodies, antibody-toxin conjugates, and radioimmuno-therapeutics have examined CD30 as a therapeutic target in preclinical and clinical studies. Unmodified antibodies have met with limited success and a lack of engagement of immune effector cells may be one of the major short-comings. Although bispecific antibodies proved among the most clinically effective through the recruiting of host effector functions to tumor cells, they pose significant manufacturing challenges. Similarly, toxin- and radio-conjugates require complicated manufacture and handling. Recent advances in antibody engineering have led to the development of “naked” antibodies with greatly enhanced effector function through mutagenesis at the Fc-receptor binding interface. This approach has been applied to a humanized antibody specific for CD30 to produce an antibody with enhanced potency and efficacy coupled with the ease of manufacture and handling of a traditional IgG antibody. The murine:human chimeric antibody cAC10 was humanized using the novel method of human string content optimization. The humanized antibody (hAC10) has an affinity for antigen 4-fold higher than that of the corresponding chimeric antibody. The humanized variable domain was then combined with a modified Fc region and exhibited an approximately 20 fold increase in affinity for the FcγRIIIA receptor resulting in the therapeutic lead XmAb2513. Expression levels from a stable cell-line were close to 1 gm/L in preliminary development. The cytotoxic activity of XmAb2513 was measured by Antibody Dependent Cell-mediated Cytotoxicity (ADCC) assay. ADCC assays used PBMC’s isolated from peripheral blood as effector cells and the human Hodgkin’s cell line L540 which expresses high levels of CD30 as the target at an effector:target ratio of 25:1; cytotoxicity was measured by release of LDH or preloaded TDA. The activity of XmAb2513 was compared to that of cAC10 with no Fc-receptor binding enhancement (IgG1) as well as to the antibody 5F11 (also human IgG1). Significant improvements were observed in both potency (concentration of antibody required to effect 50% of maximal lysis) and efficacy (maximal percent lysis at saturating antibody concentration). The potency of XmAb2513 is ~3 fold higher than that of cAC10-IgG1 and 10-fold higher than 5F11 with an increase in efficacy of 4-fold relative to cAC10-IgG1. XmAb2513 has advantageous properties for a therapeutic compound against CD30-positive lymphomas including high levels of cytotoxicity and ease of manufacture and handling. The promising results reported herein clearly warrant further investigation.
A transparent online memory test for simultaneous detection of functional faults and soft errors in memories (2003)

The Transparent Online Memory Test (TOMT) introduced here has been specifically developed for online testing of word-oriented memories with parity or Hamming protection. Careful interleaving of a word-oriented and a bit-oriented test facilitates a fault coverage and a test duration comparable to the widely used March C- algorithm. Unlike similar methods TOMT actively exercises all bit cells in memory within one test period. Hence it not only detects soft errors but also functional faults and reliably prevents fault accumulation. Different variants of the basic TOMT algorithm are investigated in terms of fault coverage and test time. A prototype implementation for SRAM is introduced which-integrated into a standard processor/memory interface-autonomously performs the transparent online memory test. The trade-offs in terms of hardware overhead and memory access delay caused by this system integration are explored.
Radical Cascade Transformations of Tris(<i>o</i>-aryleneethynylenes) into Substituted Benzo[<i>a</i>]indeno[2,1-<i>c</i>]fluorenes (2008)

Oligomeric o-aryleneethynylenes with three triple bonds undergo cascade radical transformations in reaction with a Bu 3SnH/AIBN system. These cascades involve three consecutive cycle closures with the formation of substituted benzo[ a]indeno[2,1- c]fluorene or benzo[1,2]fluoreno[4,3- b]silole derivatives. The success of this sequence depends on regioselectivity of the initial attack of the Bu 3Sn radical at the central triple bond of the o-aryleneethynylene moiety. The cascade is propagated through the sequence of 5-exo-dig and 6-exo-dig cyclizations which is followed by either a radical attack at the terminal Ar substituent or radical transposition which involves H-abstraction from the terminal TMS group and 5-endo-trig cyclization. Overall, the transformation has potential to be developed into an approach to a new type of graphite ribbons.
Markovian analysis of cervical cell images. (1976)

Markovian analysis is a method to measure optical texture based on gray-level transition probabilities in digitized images. Experiments are described that investigate that classification performance of parameters generated by Markovian analysis. Results using Markov texture parameters show that the selection of a Markov step size strongly affects classification error rates and the number of parameters required to achieve the maximum correct classification rates. Markov texture parameters are shown to achieve high rates of correct classification in discriminating images of normal from abnormal cervical cell nuclei.