gebhart/patrepeval huggingface dataset:
Rhamnose Replacement Analogs of Spinosyn A (2001)

This chapter describes the syntheses and bioactivities against tobacco budworm (TBW) and two-spotted spider mite (TSSM) of a number of rhamnose replacement analogs of spinosyn A; compounds in which the rhamnose has been replaced by other sugars, methoxybenzoic acids, methanol and 2-methoxyethanol. The sugar replacements include α-and β-linked pyranoses and furanoses: D-rhamnose, 2-deoxy-L-rhamnose, L-lyxose, L-ribose, L-mannose, L-(3-O-L-rhamnosyl)rhamnose and N-demethyl-D-forosamine. The D-sugar-, β-anomeric sugar-, furanose sugar- α, α'-disaccharide, forosaminyl- and non-sugar analogs were inactive against both TBW and TSSM. The α,β'-disaccharide retained activity against TBW. Removal of the 6-methyl group (L-lyxose analog) did not significantly affect activity, while addition of a methoxyl to the 6-methyl group (L-mannose analog) led to an ~ 10-fold enhancement of TBW activity. The 2-deoxyrhamnose analogs showed somewhat enhanced TBW activity but no TSSM activity.
Porphyrin Arrays Responsive to Additives. Fluorescence Tuning (2009)

The application of low-flux sunlight begins with the synthesis of effective antenna systems. This requires the development of dye integrates with optimized dye orientation for effective energy transfer. We here report a series of peptide-linked porphyrin arrays, denoted by Boc-(Por(Zn,S))(n)-OBu(t) (n = 2, 4, and 8), that change their dye orientation to increase fluorescence responsively to additive reagents. The B-band absorption (AB) regions of the arrays show blue shifts (dimer, 407.6 nm; tetramer, 408.2 nm; octamer, 407.8 nm) in organic solvents as compared to that of Boc-Por(Zn,S)-OBu(t) (monomer, 422.6 nm) and the fluorescence yield Phi' of the arrays decreases with increasing n, obeying the relationship Phi' = 0.03/n(1.5); however, the arrays are tuned up in fluorescence emission by the addition of 1,2-diaminoethane (en). The addition of a sufficient amount of en increases the fluorescence of the porphyrins in monomer, dimer, tetramer, and octamer by approximately 5, approximately 12, approximately 12, and >730 times, respectively, when compared with that observed in the absence of en. This also causes asymptotic red shifts in absorption (AB) bands (B-band lambda(max): 410 to 429-430 nm), as well as changes in circular dichroism (CD) spectra, and makes porphyrins approach new mutual asymmetric orientations. Our results show the potentiality of the tunable dye polymers that are a posteriori optimized in dye orientation and fluorescence emission by additive reagents for the development of effective light-harvesting materials.
TRANSGENIC MAMMALS EXPRESSINGHUMAN COAGULATION FACTOR VIII (1999)

A non-human transgenic mammalian animal, as described above, contains an exogenous double Stranded DNA Sequence Stably integrated into the genome of the animal, which comprises cis-acting regulatory units operably linked to a DNA sequence encoding human Factor VIII protein and a signal peptide, where the cis-acting regulatory units are active in mammary gland cells and the Signal peptide is active in directing newly expressed Factor VIII into the milk of the animal. The promoter may be a milk protein promoter Such as for whey acidic protein, casein, lactalbumin, or beta-lactoglobulin promoter. The transgenic mammals are preferably farm animals, for example, cows, goats, sheep, rabbits and pigs. Concurrent expression of a gene for human von Willebrand's Factor into milk may be used to stabilize newly-secreted Factor VIII.
Supplementary Figure 2 from Dual-specific Chimeric Antigen Receptor T Cells and an Indirect Vaccine Eradicate a Variety of Large Solid Tumors in an Immunocompetent, Self-antigen Setting (2023)

&lt;p&gt;High dose IL-2 enables durable tumor regression and proliferation of T cells.&lt;/p&gt;
Functionalization of Oligonucleotides with Amino Groups and Attachment of Amino Specific Reporter Groups (1994)

The most common technique to label oligodeoxynucleotides is the enzymatic incorporation of the radioisotope 32Pat the 5′-end. Although this method affords high sensitivity of detection, the use of the radiolabeled probe is precluded in many clinical and diagnostic applications. In the last few years, several labeling procedures for the detection of specific nucleic acid sequences using nonradioactive labels such as biotin, digoxigenin, dinitrophenol, acetylaminofluorene, and certain enzymes or fluorophores have been developed. The labels are incorporated into synthetic oligonucleotides either enzymatically or chemically before hybridization of the probe.
B0 shimming at 9.4T with multicoil approach: numerical investigation of different coil geometries (2015)

Purpose/Introduction: B0 inhomogeneities are caused by susceptibility differences between air and neighboring tissue and lead to image artifacts such as distortions, blurring, and signal loss. Modern scanners are equipped with spherical harmonics (SH) shim coils, generally up to 2nd or 3rd order, but the latter allow mitigating the magnetic field offsets only to a certain degree. A new method based on a multicoil approach has been proposed recently and was shown to be more effective than SH shimming [1–4]. Subjects and Methods: For the simulations, a set of coils was mounted on a cylinder (ø 360 mm), which would be large enough to accommodate inside additional RF transmit and receive arrays. Different coil arrangements and shapes were evaluated by trying to homogenize B0 distributions typically encountered in case of human brain imaging at 9.4 T. The comparison of the different configurations was based on the standard deviation of the resulting magnetic field distributions. Figure 1 shows some of the examined structures. Results: Among all investigated configurations, the best results were obtained for the given B0 field distribution with the 12 channel design (Figs. 1a, 2). Discussion/Conclusion: The simulations of the different configurations demonstrated that the homogeneity of the B0 field can be increased by the use of multiple small shimming coils. Future work will include practical realization of the proposed structures, investigation of their influence on the transmission efficiency of the RF coil and experimental validation of their B0 shimming capabilities.
Asymmetric additions to chiral naphthyloxazolines. An entry into tetracyclic terpene ring systems related to aphidicolin, scopadulcic acid, and kauranes (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric additions to chiral naphthyloxazolines. An entry into tetracyclic terpene ring systems related to aphidicolin, scopadulcic acid, and kauranesAlbert J. Robichaud and A. I. MeyersCite this: J. Org. Chem. 1991, 56, 8, 2607–2609Publication Date (Print):April 1, 1991Publication History Published online1 May 2002Published inissue 1 April 1991https://pubs.acs.org/doi/10.1021/jo00008a003https://doi.org/10.1021/jo00008a003research-articleACS PublicationsRequest reuse permissionsArticle Views358Altmetric-Citations46LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein (2003)

The Xrcc3 protein, which is required for the homologous recombinational repair of damaged DNA, forms a complex with the Rad51C protein in human cells. Mutations in either the Xrcc3 or Rad51C gene cause extreme sensitivity to DNA-damaging agents and generate the genomic instability frequently found in tumors. In the present study, we found that the Xrcc3 segment containing amino acid residues 63-346, Xrcc3(63-346), is the Rad51C-binding region. Biochemical analyses revealed that Xrcc3(63-346) forms a complex with Rad51C, and the Xrcc3(63-346)- Rad51C complex possesses ssDNA and dsDNA binding abilities comparable to those of the full-length Xrcc3-Rad51C complex. Based on the structure of RecA, which is thought to be the ancestor of Xrcc3, six Xrcc3 point mutants were designed. Two-hybrid and biochemical analyses of the Xrcc3 point mutants revealed that Tyr139 and Phe249 are essential amino acid residues for Rad51C binding. Superposition of the Xrcc3 Tyr139 and Phe249 residues on the RecA structure suggested that Tyr139 may function to ensure proper folding and Phe249 may be important to constitute the Rad51C-binding interface in Xrcc3.
Human Microglial Cells Synthesize Albumin in Brain (2008)

Albumin, an abundant plasma protein with multifunctional properties, is mainly synthesized in the liver. Albumin has been implicated in Alzheimer's disease (AD) since it can bind to and transport amyloid beta (Abeta), the causative agent of AD; albumin is also a potent inhibitor of Abeta polymerization. Despite evidence of non-hepatic transcription of albumin in many tissues including kidney and pancreas, non-hepatic synthesis of albumin at the protein level has been rarely confirmed. In a pilot phase study of Human Brain Proteome Project, we found evidence that microglial cells in brain may synthesize albumin. Here we report, for the first time, the de novo synthesis of albumin in human microglial cells in brain. Furthermore, we demonstrate that the synthesis and secretion of albumin from microglial cells is enhanced upon microglial activation by Abeta(1-42)- or lipopolysaccharide (LPS)-treatment. These data indicate that microglial cells may play a beneficial role in AD by secreting albumin that not only inhibits Abeta polymerization but also increases its clearance.
Protein name tagging guidelines: lessons learned (2005)

Interest in information extraction from the biomedical literature is motivated by the need to speed up the creation of structured databases representing the latest scientific knowledge about specific objects, such as proteins and genes. This paper addresses the issue of a lack of standard definition of the problem of protein name tagging. We describe the lessons learned in developing a set of guidelines and present the first set of inter-coder results, viewed as an upper bound on system performance. Problems coders face include: (a) the ambiguity of names that can refer to either genes or proteins; (b) the difficulty of getting the exact extents of long protein names; and (c) the complexity of the guidelines. These problems have been addressed in two ways: (a) defining the tagging targets as protein named entities used in the literature to describe proteins or protein-associated or -related objects, such as domains, pathways, expression or genes, and (b) using two types of tags, protein tags and long-form tags, with the latter being used to optionally extend the boundaries of the protein tag when the name boundary is difficult to determine. Inter-coder consistency across three annotators on protein tags on 300 MEDLINE abstracts is 0.868 F-measure. The guidelines and annotated datasets, along with automatic tools, are available for research use.
Temperature dependence of the photoinduced micro-crystalline surface topography of a diarylethene (2013)

By alternate irradiation with UV and visible light, reversible topographical changes were observed. Step and valley formation while keeping the crystal confinement was observed below the glass transition temperature (Tg), while crystal growth via a softened state was observed above the Tg on the same diarylethene crystalline surface.
Characterizing Cognitive Deficits and Dementia in an Aging Urban Population in India (2012)

Rapid rise in the population of older adults in India will lead to the need for increased health care services related to diagnosis, management, and long-term care for those with dementia and cognitive impairment. A direct approach for service provision through memory clinics can be an effective, successful, and sustaining means of delivering specialized health care services. We have established a memory clinic in Mumbai, India by employing the diverse clinical skills available in Indian academic institutions, diagnostic and research expertise of clinicians and psychologists, and the support of the U.S. National Institutes of Health. Our project involved recruitment of patients, clinical and neuropsychological assessment, and standardized diagnostic procedures, demonstrating the feasibility of using research methods to develop a memory clinic. In this paper, we describe the development of a community-based memory clinic in urban India, including linguistic and cultural factors and present detailed results, including diagnostic characterization, on 194 subjects with various stages of cognitive deficits. Our findings support the feasibility of developing a memory clinic in a public hospital and successful use of research diagnostic criteria to categorize cognitive deficits observed in this population, which may be used to inform the development of other such clinics.
SLC1A2 variant associated with essential tremor but not Parkinson disease in Chinese subjects (2013)

Essential tremor (ET) is characterized by postural and action tremor.(1-3) A genome-wide association study (GWAS) identified a LINGO1 gene variant to be associated with ET.(4) Subsequent GWAS further identified an intronic variant (rs3794087) of the main glial glutamate transporter (SLC1A2) gene to be associated with ET with an odds ratio (OR) of approximately 1.4.(5) We conducted a case-control study to examine the SLC1A2 gene variant in an Asian cohort of ET. In addition, we also investigated the variant in patients with Parkinson disease (PD) because the GWAS LINGO1 variant has been implicated in both ET and PD and etiologic links between the conditions have been suggested.(6.)
Cytochrome P450 pathways of arachidonic acid metabolism (2002)

Cytochrome P450s metabolize arachidonic acid to hydroxyeicosatetraenoic acids and epoxyeicosatrienoic acids. These eicosanoids are formed in a tissue and cell-specific manner and have numerous biological functions. Of major interest are the opposing actions of hydroxyeicosatetraenoic and epoxyeicosatrienoic acids within the vasculature. Regio- and stereoisomeric epoxyeicosatrienoic acids have potent vasodilatory properties while 20-hydroxyeicosatetraenoic acid is a potent vasoconstrictor. Both effects are mediated through actions on large-conductance Ca2+-activated K+ channels. Cytochrome P450-derived eicosanoids are also important in the regulation of ion transport, and have recently been shown to influence a number of fundamental biological processes including cellular proliferation, apoptosis, inflammation, and hemostasis. The formation of these functionally relevant eicosanoids is tightly controlled by the expression and activity of the cytochrome P450 epoxygenases and hydroxylases. In addition, soluble epoxide hydrolase catalyzes the hydrolysis of epoxyeicosatrienoic acids to dihydroxyeicosatrienoic acids, and the activity of this enzyme is a critical determinant of tissue epoxyeicosatrienoic and dihydroxyeicosatrienoic acid levels. The intracellular balance between epoxyeicosatrienoic, dihydroxyeicosatrienoic and hydroxyeicosatetraenoic acids influences the biological response to these eicosanoids and alterations in their levels have recently been associated with certain pathological conditions. The involvement of the cytochrome P450-derived eicosanoids in a wide array of biological functions and the observation that levels are altered in pathological conditions suggest that the enzymes involved in the formation and degradation of these fatty acids may be novel therapeutic targets.
An Evolutionarily Conserved Transcriptional Activator-Repressor Module Controls Expression of Genes for D-Galacturonic Acid Utilization inAspergillus niger (2016)

The expression of genes encoding extracellular polymer-degrading enzymes and the metabolic pathways required for carbon utilization in fungi are tightly controlled. The control is mediated by transcription factors that are activated by the presence of specific inducers, which are often monomers or monomeric derivatives of the polymers. A D-galacturonic acid-specific transcription factor named GaaR was recently identified and shown to be an activator for the expression of genes involved in galacturonic acid utilization in Botrytis cinerea and Aspergillus niger Using a forward genetic screen, we isolated A. niger mutants that constitutively express GaaR-controlled genes. Reasoning that mutations in the gaaR gene would lead to a constitutively activated transcription factor, the gaaR gene in 11 of the constitutive mutants was sequenced, but no mutations in gaaR were found. Full genome sequencing of five constitutive mutants revealed allelic mutations in one particular gene encoding a previously uncharacterized protein (NRRL3_08194). The protein encoded by NRRL3_08194 shows homology to the repressor of the quinate utilization pathway identified previously in Neurospora crassa (qa-1S) and Aspergillus nidulans (QutR). Deletion of NRRL3_08194 in combination with RNA-seq analysis showed that the NRRL3_08194 deletion mutant constitutively expresses genes involved in galacturonic acid utilization. Interestingly, NRRL3_08194 is located next to gaaR (NRRL3_08195) in the genome. The homology to the quinate repressor, the chromosomal clustering, and the constitutive phenotype of the isolated mutants suggest that NRRL3_08194 is likely to encode a repressor, which we name GaaX. The GaaR-GaaX module and its chromosomal organization is conserved among ascomycetes filamentous fungi, resembling the quinate utilization activator-repressor module in amino acid sequence and chromosomal organization.
Localized algorithms in wireless ad-hoc networks (2001)

The development of practical, localization algorithms is probably the most needed and most challenging task in wireless ad-hoc sensor networks (WASNs). Localized algorithms are a special type of distributed algorithms where only a subset of nodes in the WASN participate in sensing, communication, and computation. We have developed a generic localized algorithm for solving optimization problems in wireless ad-hoc networks that has five components: (i) data acquisition mechanism, (ii) optimization mechanism, (iii) search expansion rules, (iv) bounding conditions and (v) termination rules. the main idea is to request and process data only locally and only from nodes who are likely to contribute to rapid formation of the final solution. The approach enables two types of optimization: The first, guarantees the fraction of nodes that are contacted while optimizing for solution quality. The second, provides guarantees on solution qualities while minimizing the number of nodes that are contacted and/or amount of communication. The localized optimization approach is applied to two fundamental problems in sensor networks: location discovery and exposure-based coverage. We demonstrate its effective-ness on a number of examples
Modeling of Shunt Current in Liquid Electrolyte Fuel Cells (2006)

A general electrolyte model for calculation of the liquid electrolyte transport in fuel cells is presented. A 2-D formulation is used to describe the transport in an alkaline fuel cell. Numerical results were obtained by using commercial CFD software, in conjunction with the user defined functions that calculate the source terms of the transport equations. An order of magnitude analysis is conducted of the energy transport in the separator and electrode regions. The numerical calculation also examines the local primary current at the anode and cathode electrodes. The calculated current flux showed a higher value near the separator entrance and it decreased along the stream-wise direction. The non-uniformity of the local primary current is caused mainly by the species transport resistance between the electrodes instead of the temperature difference. The effects of four different electrolytes were also studied. The results suggested that the cell voltage differences were due to the competing effects of electrolyte conductance and species diffusion. Numerical calculation also captured the presence of shunt current. A net shunt current as high as 0.1 A/cm2 is calculated at the separator inlet and exit. Provisions to reduce shunt currents seem to be warranted for AFC operated at a condition similar to that examined in this paper.
Optimal Spatial Signal Design for mmWave Positioning Under Imperfect Synchronization (2022)

We consider the problem of spatial signal design for multipath-assisted mmWave positioning under limited prior knowledge on the user&#x2019;s location and clock bias. We propose an optimal robust design and, based on the low-dimensional precoder structure under perfect prior knowledge, a codebook-based heuristic design with optimized beam power allocation. Through numerical results, we characterize different position-error-bound (PEB) regimes with respect to clock bias uncertainty and show that the proposed low-complexity codebook-based designs outperform the conventional directional beam codebook and achieve near-optimal PEB performance for both analog and digital architectures.
All agents are not created equal (1998)

As the technology advances, we can expect the development of specialized agents to be used as standardized building blocks for information systems. Two trends lend credence to such a prediction. First, software systems in general are being constructed with larger components, such as ActiveX and JavaBeans, which are becoming closer to being agents themselves. They have more functionality than simple objects, respond to events autonomously, and, most importantly, respond to system builders at development time, as well as to events at runtime. Moreover, there is a move toward more cooperative information systems, in which the architecture itself plays an important role in the effectiveness of the system, as opposed to traditional software systems where effectiveness depends on the quality of the individual components. These architectures are generating a set of standardized agents. Architectures based on standardized agent types should be easier to develop, understand, and use. Perhaps most important of all, these architectures will make it easier for separately developed information systems to interoperate.