gebhart/patrepeval huggingface dataset:
Early Field Detection of Bolting in Celery (2005)

Growers of early stalk celery ( Apium graveolens var. dulce ) often experience financial losses due to bolting (the premature and rapid elongation of the main celery stem) in temperate regions. A method was developed to provide early warning of bolting in field-grown celery, on the basis of two criteria, one visual and one microscopic, for inflorescence development. Bolting could be detected 40 days after transplanting using the visual criterion, and as early as 30 days after transplanting using the microscopic criterion. Early detection of bolting using the visual and microscopic criteria provided celery growers with periods of, respectively, 25 days and up to 35 days to consider harvesting earlier, before the length of the celery stems exceeded commercial standards. This method could be effective in minimizing financial losses due to bolting when coupled with agro-economic studies.
Polymer Layers through Self-Assembled Monolayers of Initiators (1998)

A novel concept for the generation of molecularly thin polymer layers attached to a solid surface is described. In contrast to commonly used techniques, where functional groups of the polymers are reacted with appropriate sites on the surfaces of a substrate the polymer layers are formed in situ by using self-assembled monolayers of an initiator. As an example, the formation of polystyrene monolayers terminally attached to silicon oxide surfaces through radical chain polymerization which has been started by a self-assembled monolayer of an azo initiator is described. The thickness of the attached polymer films can be adjusted over a wide range up to values of several hundred nanometers by variation of polymerization parameters such as temperature and azo conversion. When suitable conditions are chosen, monolayers with thicknesses inaccessible by other techniques of preparation can be obtained.
Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites (2006)

As a tool in directed genome manipulations, site-specific recombination is a double-edged sword. Exquisite specificity, while highly desirable, makes it imperative that the target site be first inserted at the desired genomic locale before it can be manipulated. We describe a combination of computational and experimental strategies, based on the tyrosine recombinase Flp and its target site FRT, to overcome this impediment. We document the systematic evolution of Flp variants that can utilize, in a bacterial assay, two sites from the human interleukin 10 gene, IL10, as recombination substrates. Recombination competence on an end target site is acquired via chimeric sites containing mixed sequences from FRT and the genomic locus. This is the first time that a tyrosine site-specific recombinase has been coaxed successfully to perform DNA exchange within naturally occurring sequences derived from a foreign genomic context. We demonstrate the ability of an Flp variant to mediate integration of a reporter cassette in Escherichia coli via recombination at one of the IL10-derived sites.
Cell Division in Escherichia coli : Analysis of Double Mutants for Filamentation and Abnormal Septation of Deoxyribonucleic Acid-Less Cells (1974)

The link between chromosome termination, initiation of cell division, and choice of division sites was studied in Escherichia coli by preparing double mutants. Hybrid mutants containing div52-ts, a cell division initiation mutation, and min, mutations which affect the choice of division sites resulting in the septation of minicells, were characterized. The mutants produced minicells and normal cells coordinately under all conditions studied, although the fraction of minicells is half that of the parental minicell strain. The mutant gradually stopped dividing at both the median and minicell septation sites when transferred from 30 to 41 C in rich medium. A synchronous cell division of filaments was induced 15 min after addition of chloramphenicol to the medium, even at 41 C. Divisions were observed at both normal and minicell sites. These results indicate that div52-ts and min functions share a common step in a cell division pathway. A double mutant containing div52-ts and div27-ts, a dnaB mutant which divides in the absence of DNA synthesis, was characterized. The mutant continues to divide after a shift to the high temperature, although at a reduced rate. The behavior of this hybrid mutant suggests a hypothesis that the chromosome termination signal and div52-ts division initiation signal act on a single membrane site which is altered in div27-ts strains.
Supramolecular shuttle and protective agent: a multiple role of methylated cyclodextrins in the chemoselective hydrogenation of benzene derivatives with ruthenium nanoparticles (2005)

Efficient chemoselectivities have been obtained in the hydrogenation of benzene derivatives under biphasic liquid-liquid conditions using Ru(0) nanoparticles stabilized and controlled by the relevant choice of cavity and methylation degree of cyclodextrins.
The Pairing of a Selective Estrogen Receptor Modulator, Bazedoxifene, with Conjugated Estrogens as a New Paradigm for the Treatment of Menopausal Symptoms and Osteoporosis Prevention (2008)

The menopausal transition is associated with decreased ovarian function and concomitant decline in estrogen production, which may result in physiological effects such as hot flashes, reduced bone mass, and altered lipid profile. It is well established that these unfavorable changes are effectively offset with estrogen therapy (ET) or, in women with a uterus, estrogens in combination with a progestin (hormone therapy). Selective estrogen receptor (ER) modulators (SERMs), which exhibit both ER agonist and antagonist activities depending on the target tissue, have been regarded as offering the potential to provide the benefits of ET and hormone therapy with an improved safety and tolerability profile. To date, no SERM alone has demonstrated an ideal benefit-risk profile for menopausal therapy. The tissue-selective estrogen complex, or the pairing of a SERM with estrogens, may provide an optimal blend of ER agonist and antagonist activities. We evaluated the physiological profile of this novel therapeutic paradigm by using various in vivo models to assess uterine, vasomotor, lipid, and skeletal responses to a tissue-selective estrogen complex partnering bazedoxifene with conjugated estrogens (CE). Bazedoxifene at 3.0 mg/kg effectively antagonized CE-induced uterine stimulation without reversing the positive effects of CE on vasomotor instability. When paired with CE, bazedoxifene at 3.0 mg/kg reduced total cholesterol levels by up to 20% compared with CE alone and significantly increased total bone density relative to control. These preclinical findings showed that the appropriate dose combination of bazedoxifene/CE exhibits positive vasomotor, lipid, and skeletal responses with minimal uterine stimulation.
ErbB-2 Induces the Cyclin D1 Gene in Prostate Epithelial Cells In vitro and In vivo (2007)

The receptor tyrosine kinase ErbB-2 plays an important role in the regulation of growth factor-induced signal transduction cascades in the epithelium, and ErbB-2 is frequently overexpressed in epithelial tumors. Our previous studies on clinical prostate cancer specimens indicated that ErbB-2 expression was increased in patients undergoing hormone ablation therapy. We had also shown that the critical cell cycle regulatory gene cyclin D1 and its promoter were targets of proliferative signaling in prostate cancer cell lines, and that cyclin D1 was required for ErbB-2-induced mammary tumorigenesis. In the current studies, we found that increased ErbB-2 membrane expression correlated with increased nuclear cyclin D1 staining in clinical prostate cancer specimens, and that expression of ErbB-2 was capable of inducing cell cycle progression in human prostate cancer cell lines. We further showed that ErbB-2 induced the cyclin D1 promoter in DU145 cells, and that small interfering RNA knockdown of cyclin D1 protein levels blocked a significant proportion of the heregulin-induced cell cycle progression in LNCaP cells. Probasin promoter-targeted expression of an activated ErbB-2 isoform induced cyclin D1 expression in the mouse prostate, commensurate with prostate intraepithelial neoplasia. Together, these in vitro and in vivo studies identify cyclin D1 as a critical downstream target of ErbB-2 in the prostate epithelium, both of which are possible therapeutic targets for cancer intervention. Furthermore, our novel mouse model provides a useful platform for ongoing in vivo investigations of ErbB-2 signaling in the prostate epithelium.
Techniques to Measure Nucleic Acid-Protein Binding and Specificity: Nuclear Extract Preparations, DNase I Footprinting, and Mobility Shift Assays (2003)

DNA-protein interactions are the basis for the molecular mechanisms responsible for nucleic-acid replication, gene transcription, recombination, viral integration, and gene regulation in both normal and pathophysiological conditions. Initially, deletional analysis coupled with reporter gene assays are used to roughly map the locations of regulatory regions involved in gene expression. Relevant cis-regulatory elements may also be detected as areas of DNase I hypersensitivity in native chromatin. DNase I footprinting analysis is subsequently used to precisely locate sites of DNA-protein interactions within the identified regulatory regions. The proteins that interact with these regulatory regions can be detected and isolated using various modifications of the mobility shift assay. The protocols described below have been successfully used in our laboratory to analyze the regulatory regions of several genes (, , , , , ).
Normalization of lactulose breath testing correlates with symptom improvement in irritable bowel syndrome: a double-blind, randomized, placebo-controlled study (2003)

An abnormal LBT is common in subjects with IBS. Normalization of LBT with neomycin leads to a significant reduction in IBS symptoms. The type of gas seen on LBT is also associated with IBS subgroup.
Estimating the Time of Last Cannabis Use from Plasma Δ9-Tetrahydrocannabinol and 11-nor-9-Carboxy-Δ9-Tetrahydrocannabinol Concentrations (2005)

This study extends the validation of the predictive models of time of last cannabis use to include multiple exposures and low THC concentrations. The models provide an objective and validated method for assessing the contribution of cannabis to accidents or clinical symptoms.
Novel IgE peptide‐based vaccine prevents the increase of IgE and down‐regulates elevated IgE in rodents (2007)

Antibodies against self-IgE can be induced by IgE peptide-based vaccines, which are effective in preventing the increase of IgE and in down-regulating IgE in sensitized animals.
RNAi targeting multiple cell adhesion molecules reduces immune cell recruitment and vascular inflammation after myocardial infarction (2016)

Nanoparticles deliver siRNA for multigene silencing of endothelial cell adhesion molecules, which dampens leukocyte recruitment in atherosclerosis and myocardial infarction in mice.
Three DNA sequencing methods using capillary gel electrophoresis and laser-induced fluorescence (1991)

Capillary gel electrophoresis is demonstrated for the four-spectral-channel sequencing technique of Smith, the two-spectral-channel sequencing technique of Prober, and the one-spectral-channel sequencing technique of Richardson and Tabor. Sequencing rates up to 1000 bases/h are obtained at electric field strengths of 465 V/cm. At lower electric field strengths, capillary electrophoresis produces useful data for fragments greater than 550 nucleotides in length with 2 times better resolution than slab gel electrophoresis. An on-column detector produces detection limits of 200 zmol (1 zmol = 10(-21) mol = 600 molecules) for the four-spectral-channel technique. A postcolumn detector, based on the sheath flow cuvette, produces detection limits of 20 and 2 zmol for the two- and one-spectral-channel techniques, respectively.
The Arabidopsis Basic/Helix-Loop-Helix Transcription Factor Family[W] (2003)

The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites and that have been well characterized in nonplant eukaryotes as important regulatory components in diverse biological processes. Based on evidence that the bHLH protein PIF3 is a direct phytochrome reaction partner in the photoreceptor's signaling network, we have undertaken a comprehensive computational analysis of the Arabidopsis genome sequence databases to define the scope and features of the bHLH family. Using a set of criteria derived from a previously defined consensus motif, we identified 147 bHLH protein-encoding genes, making this one of the largest transcription factor families in Arabidopsis. Phylogenetic analysis of the bHLH domain sequences permits classification of these genes into 21 subfamilies. The evolutionary and potential functional relationships implied by this analysis are supported by other criteria, including the chromosomal distribution of these genes relative to duplicated genome segments, the conservation of variant exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Considerable diversity in DNA binding site specificity among family members is predicted, and marked divergence in protein sequence outside of the conserved bHLH domain is observed. Together with the established propensity of bHLH factors to engage in varying degrees of homodimerization and heterodimerization, these observations suggest that the Arabidopsis bHLH proteins have the potential to participate in an extensive set of combinatorial interactions, endowing them with the capacity to be involved in the regulation of a multiplicity of transcriptional programs. We provide evidence from yeast two-hybrid and in vitro binding assays that two related phytochrome-interacting members in the Arabidopsis family, PIF3 and PIF4, can form both homodimers and heterodimers and that all three dimeric configurations can bind specifically to the G-box DNA sequence motif CACGTG. These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis.
Diversity in the Cow Ultralong CDR H3 Antibody Repertoire (2018)

Typical antibodies found in humans and mice usually have short CDR H3s and generally flat binding surfaces. However, cows possess a subset of antibodies with ultralong CDR H3s that can range up to 70 amino acids and form a unique "stalk and knob" structure, with the knob protruding far out of the antibody surface, where it has the potential to bind antigens with concave epitopes. Activation-induced cytidine deaminase (AID) has a proven role in diversifying antibody repertoires in humoral immunity, and it has been found to induce somatic hypermutation in bovine immunoglobulin genes both before and after contact with antigen. Due to limited use of variable and diversity genes in the V(D)J recombination events that produce ultralong CDR H3 antibodies in cows, the diversity in the bovine ultralong antibody repertoire has been proposed to rely on AID-induced mutations targeted to the IGHD8-2 gene that encodes the entire knob region. In this review, we discuss the genetics, structures, and diversity of bovine ultralong antibodies, as well as the role of AID in creating a diverse antibody repertoire.
The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge (2007)

PharmGKB is a knowledge base that captures the relationships between drugs, diseases/phenotypes and genes involved in pharmacokinetics (PK) and pharmacodynamics (PD). This information includes literature annotations, primary data sets, PK and PD pathways, and expert-generated summaries of PK/PD relationships between drugs, diseases/phenotypes and genes. PharmGKB's website is designed to effectively disseminate knowledge to meet the needs of our users. PharmGKB currently has literature annotations documenting the relationship of over 500 drugs, 450 diseases and 600 variant genes. In order to meet the needs of whole genome studies, PharmGKB has added new functionalities, including browsing the variant display by chromosome and cytogenetic locations, allowing the user to view variants not located within a gene. We have developed new infrastructure for handling whole genome data, including increased methods for quality control and tools for comparison across other data sources, such as dbSNP, JSNP and HapMap data. PharmGKB has also added functionality to accept, store, display and query high throughput SNP array data. These changes allow us to capture more structured information on phenotypes for better cataloging and comparison of data. PharmGKB is available at www.pharmgkb.org.
SLA calculus for end-to-end QoS of TCP-based applications in a multi-domain environment (2006)

Next-generation communication services will be offered over distributed information and communication infrastructures consisting of a multitude of administrative domains, owned by different parties. This raises the problem for service providers to provide satisfactory levels of end-to-end Quality of Service (QoS), as experienced by the paying end user, in a cost-effective manner. Motivated by this, we consider the problem of end-to-end QoS provisioning for TCP-based applications that cross multiple network domains. To this end, we construct an analytical model that provides a so-called SLA calculus, i.e. a mapping between per-domain network QoS parameters defined in the involved Service Level Agreements (SLAs) and end-to-end QoS metrics like response times and file download times that determine the QoS perceived by the end users. 1
Reliability and scaling issues in multicast communication (1992)

The efficiency with which multicast communication can take place is largely determined by the network level support available for such communication. Two factors contribute to the complexity of supporting current multicast applications: the lack of reliable multicast transport mechanisms at the network level and the lack of network support for large scale multicast communication. In this paper, we examine the issues pertinent to eliminating these shortcomings. We first show that internet multicasting algorithms based on reverse path forwarding are inherently unreliable and present a source-tree-based reliable multicasting scheme. The new scheme makes use of simple inter-gateway protocols and works on top of previously developed distance vector and link state internet routing schemes. Next, to support large scale applications, we present a scheme for partial multicasting and introduce a new network level operation, called gather. The partial multicasting mechanism allows messages to be delivered to subsets of multicast destinations, while the gather operation aids gateways in selectively suppressing redundant messages, thus reducing the message complexity. Using simulations, we investigate the efficacy of our schemes in supporting a sample application based on multicast communication.
Immunocytochemical analysis of the human osteoclast: phenotypic relationship to other marrow-derived cells. (1988)

The immunocytochemistry of the osteoclast, which is known to be derived from a circulating mononuclear precursor cell of bone marrow origin, is controversial. In this study, we have determined the antigenic phenotype of human osteoclasts in fetal and adult (Paget's disease, giant cell tumour of bone) specimens using a large number of monoclonal antibodies which react with granulocytes and mononuclear phagocytes. We have identified antibodies which reacted with human osteoclasts including CD13, CD15 and several groups of anti-macrophage antibodies. All the antibodies which reacted with osteoclasts are also known to react with monocytes or macrophages. Other marrow elements such as granulocytes, megakaryocytes and platelets were also commonly stained. Expression of myeloid and platelet antigens on osteoclasts shows that they are phenotypically related to these cells and is in keeping with the origin of osteoclast precursors from the pluripotential haemopoietic stem cell. Only a proportion of osteoclasts in fetal bone preparations were stained by CD15 antibodies, suggesting that subsets or different populations of osteoclasts, which can be identified by monoclonal antibodies, may be present in bone.
Understanding Non-compliance in the Marine Environment (2004)

A range of criminal activity takes place in marine environments. Combating this crime is a challenge for state, national and international regulators. The illicit activity can include illegal fishing, unauthorised hunting of protected species, causing damage to coral reefs, polluting, people smuggling, drug trafficking, and the commission of personal crimes (including violence). The Great Barrier Reef Marine Park (GBRMP) is renowned as the world’s largest living organism. Like other marine environments, it is at risk from each of these activities, although environmental crimes potentially have the greatest impact. This paper explores the type of criminal activity that occurs in marine environments, with a focus on the Great Barrier Reef, possible causes of that crime, and appropriate regulatory responses to it.
Functional analysis of the large periplasmic loop of the Escherichia coli K‐12 WaaL O‐antigen ligase (2008)

WaaL is a membrane enzyme implicated in ligating undecaprenyl-diphosphate (Und-PP)-linked O antigen to lipid A-core oligosaccharide. We determined the periplasmic location of a large (EL5) and small (EL4) adjacent loops in the Escherichia coli K-12 WaaL. Structural models of the EL5 from the K-12, R1 and R4 E. coli ligases were generated by molecular dynamics. Despite the poor amino acid sequence conservation among these proteins, the models afforded similar folds consisting of two pairs of almost perpendicular alpha-helices. One alpha-helix in each pair contributes a histidine and an arginine facing each other, which are highly conserved in WaaL homologues. Mutations in either residue rendered WaaL non-functional, since mutant proteins were unable to restore O antigen surface expression. Replacements of residues located away from the putative catalytic centre and non-conserved residues within the centre itself did not affect ligation. Furthermore, replacing a highly conserved arginine in EL4 with various amino acids inactivates WaaL function, but functionality reappears when the positive charge is restored by a replacement with lysine. These results lead us to propose that the conserved amino acids in the two adjacent periplasmic loops could interact with Und-PP, which is the common component in all WaaL substrates.