gebhart/patrepeval huggingface dataset:
Solvent and Linker Influences on AQ•-/dA•+Charge-Transfer State Energetics and Dynamics in Anthraquinonyl-Linker-Deoxyadenosine Conjugates (2006)

The goal of this work is to produce high yields of long-lived AQ(*-)/dA(*+) charge transfer (CT) excited states (or photoproducts). This goal fits within a larger context of trying generally to produce high yields of long-lived CT excited states within DNA nucleoside conjugates that can be incorporated into DNA duplexes. Depending upon the energetics of the anthraquinonyl (AQ) (3)(pi,pi) state as well as the reduction potentials of the subunits in particular anthraquinonyl-adenine conjugates, CT quenching of the AQ (3)(pi,pi*) state may or may not occur in polar organic solvents. In MeOH, bis(3',5'-O-acetyl)-N(6)-(anthraquinone-2-carbonyl)-2'-deoxyadenosine (AQCOdA) behaves as intended and forms a (3)(AQ(*-)/dA(*+)) CT state with a lifetime of 3 ns. However, in nonpolar THF the AQ(*-)/dA(*+) CT states of AQCOdA are too high in energy to be formed, and in DMSO a (1)(AQ(*-)/dA(*+)) CT state is formed but lives only 6 ps. Although the lowest energy excited state for AQCOdA in MeOH is a (3)(AQ(*-)/dA(*+)) CT state, for N(6)-(anthraquinone-2-methylenyl)-2'-deoxyadenosine (AQMedA) in the same solvent it is a (3)(pi,pi*) state. Changing the linking carbonyl in AQCOdA to methylene in AQMedA makes the anthraquinonyl subunit harder to reduce by 166 mV. This raises the energy of the (3)(AQ(*-)/dA(*+)) CT state above that of the (3)(pi,pi*) in AQMedA. The conclusion is that anthraquinonyl-dA conjugates will not have lowest energy AQ(*-)/dA(*+) CT states in polar organic solvents unless the anthraquinonyl subunit is also substituted with an electron-withdrawing group that raises the AQ-subunit's reduction potential above that of AQ. A key finding in this work is that the lifetime of the (3)(AQ(*-)/dA(*+)) CT excited state (ca. 3 ns) is ca. 500-times longer than that of the corresponding (1)(AQ(*-)/dA(*+)) CT excited state (ca. 6 ps).'
Microdissection Testicular Sperm Extraction: Effect of Prior Biopsy on Success of Sperm Retrieval (2007)

There is no threshold of prior negative biopsies that precludes the success of sperm retrieval using microdissection testicular sperm extraction. A limited number of testicular biopsies provide limited or no prognostic value for sperm retrieval with microdissection testicular sperm extraction.
Multi-Omic Approach to Identify Phenotypic Modifiers Underlying Cerebral Demyelination in X-Linked Adrenoleukodystrophy (2020)

X-linked adrenoleukodystrophy (ALD) is a peroxisomal metabolic disorder with a highly complex clinical presentation. ALD is caused by mutations in the <i>ABCD1</i> gene, and is characterized by the accumulation of very long-chain fatty acids in plasma and tissues. Disease-causing mutations are 'loss of function' mutations, with no prognostic value with respect to the clinical outcome of an individual. All male patients with ALD develop spinal cord disease and a peripheral neuropathy in adulthood, although age of onset is highly variable. However, the lifetime prevalence to develop progressive white matter lesions, termed cerebral ALD (CALD), is only about 60%. Early identification of transition to CALD is critical since it can be halted by allogeneic hematopoietic stem cell therapy only in an early stage. The primary goal of this study is to identify molecular markers which may be prognostic of cerebral demyelination from a simple blood sample, with the hope that blood-based assays can replace the current protocols for diagnosis. We collected six well-characterized brother pairs affected by ALD and discordant for the presence of CALD and performed multi-omic profiling of blood samples including genome, epigenome, transcriptome, metabolome/lipidome, and proteome profiling. In our analysis we identify discordant genomic alleles present across all families as well as differentially abundant molecular features across the omics technologies. The analysis was focused on univariate modeling to discriminate the two phenotypic groups, but was unable to identify statistically significant candidate molecular markers. Our study highlights the issues caused by a large amount of inter-individual variation, and supports the emerging hypothesis that cerebral demyelination is a complex mix of environmental factors and/or heterogeneous genomic alleles. We confirm previous observations about the role of immune response, specifically auto-immunity and the potential role of PFN1 protein overabundance in CALD in a subset of the families. We envision our methodology as well as dataset has utility to the field for reproducing previous or enabling future modifier investigations.
Chromosomal Gene Inactivation in the Green Sulfur Bacterium Chlorobium tepidum by Natural Transformation (2001)

Conditions for inactivating chromosomal genes of Chlorobium tepidum by natural transformation and homologous recombination were established. As a model, mutants unable to perform nitrogen fixation were constructed by interrupting nifD with various antibiotic resistance markers. Growth of wild-type C. tepidum at 40 degrees C on agar plates could be completely inhibited by 100 microg of gentamicin ml(-1), 2 microg of erythromycin ml(-1), 30 microg of chloramphenicol ml(-1), or 1 microg of tetracycline ml(-1) or a combination of 300 microg of streptomycin ml(-1) and 150 microg of spectinomycin ml(-1). Transformation was performed by spotting cells and DNA on an agar plate for 10 to 20 h. Transformation frequencies on the order of 10(-7) were observed with gentamicin and erythromycin markers, and transformation frequencies on the order of 10(-3) were observed with a streptomycin-spectinomycin marker. The frequency of spontaneous mutants resistant to gentamicin, erythromycin, or spectinomycin-streptomycin was undetectable or significantly lower than the transformation frequency. Transformation with the gentamicin marker was observed when the transforming DNA contained 1 or 3 kb of total homologous flanking sequence but not when the transforming DNA contained only 0.3 kb of homologous sequence. Linearized plasmids transformed at least an order of magnitude better than circular plasmids. This work forms a foundation for the systematic targeted inactivation of genes in C. tepidum, whose 2.15-Mb genome has recently been completely sequenced.
Butanol tolerance of Clostridium beijerinckii NCIMB 8052 associated with down-regulation of gldA by antisense RNA. (2000)

Strain BR54 of Clostridium beijerinckii was derived from the wild type strain, NCIMB 8052, by mutagenesis with Tn1545 and selection for butanol tolerance. It harbours a single copy of Tn 1545 in a 435 bp intergenic region separating two convergently transcribed genes, accC and gldA. The former encodes biotin carboxylase (E.C.6.3.4.14), a subunit of acetyl-CoA carboxylase and the latter encodes glycerol dehydrogenase (E.C.1.1.1.6). Since Tn1545 generates outwardly directed transcripts from its right end, we considered the possibility that the transposon inserted in strain BR54 might affect the expression of the adjacent gldA gene. RT-PCR experiments revealed that the mutant, but not the wild type, contains antisense RNA corresponding to the gldA gene. Correlated with this, the level of glycerol dehydrogenase activity in the mutant was only 25% of that in the wild type when bacteria were grown with either glucose or glycerol as the fermentable substrate. We conclude that transcripts emerging from the right end of the conjugative transposon, Tn1545, can reduce the expression of the adjacent gldA gene by the generation of antisense RNA and that this is associated with a butanol-tolerant phenotype.
Sendai Virus Infection Induces Apoptosis through Activation of Caspase-8 (FLICE) and Caspase-3 (CPP32) (1999)

Sendai virus (SV) infection and replication lead to a strong cytopathic effect with subsequent death of host cells. We now show that SV infection triggers an apoptotic program in target cells. Incubation of infected cells with the peptide inhibitor z-VAD-fmk abrogated SV-induced apoptosis, indicating that proteases of the caspase family were involved. Moreover, proteolytic activation of two distinct caspases, CPP32/caspase-3 and, as shown for the first time in virus-infected cells, FLICE/caspase-8, could be detected. So far, activation of FLICE/caspase-8 has been described in apoptosis triggered by death receptors, including CD95 and tumor necrosis factor (TNF)-R1. In contrast, we could show that SV-induced apoptosis did not require TNF or CD95 ligand. We further found that apoptosis of infected cells did not influence the maturation and budding of SV progeny. In conclusion, SV-induced cell injury is mediated by CD95- and TNF-R1-independent activation of caspases, leading to the death of host cells without impairment of the viral life cycle.
Reduction of Intraocular Pressure by Domperidone (1986)

Domperidone, a dopamine antagonist was found to delay the intraocular pressure (IOP) recovery in rabbit eyes after infusion with hypertonic saline and to lower the IOP of normal cat eyes, indicating that domperidone is an ocular hypotensive agent. It did not affect cardiac function significantly but produced potent inhibition of bronchial muscle tone. It improved the blood flow to eye tissues including choroid, ciliary body and retina. These results suggest that domperidone could be used to treat glaucoma without producing cardiovascular disturbances and/or asthmatic attacks.
Structure-activity assessment of flavonoids as modulators of copper transport (2022)

Flavonoids are polyphenolic small molecules that are abundant in plant products and are largely recognized for their beneficial health effects. Possessing both antioxidant and prooxidant properties, flavonoids have complex behavior in biological systems. The presented work investigates the intersection between the biological activity of flavonoids and their interactions with copper ions. Copper is required for the proper functioning of biological systems. As such, dysregulation of copper is associated with metabolic disease states such as diabetes and Wilson’s disease. There is evidence that flavonoids bind copper ions, but the biological implications of their interactions remain unclear. Better understanding these interactions will provide insight into the mechanisms of flavonoids’ biological behavior and can inform potential therapeutic targets. We employed a variety of spectroscopic techniques to study flavonoid-Cu(II) binding and radical scavenging activities. We identified structural moieties important in flavonoid-copper interactions which relate to ring substitution but not the traditional structural subclassifications. The biological effects of the investigated flavonoids specifically on copper trafficking were assessed in knockout yeast models as well as in human hepatocytes. The copper modulating abilities of strong copper-binding flavonoids were largely influenced by the relative hydrophobicities. Combined, these spectroscopic and biological data help elucidate the intricate nature of flavonoids in affecting copper transport and open avenues to inform dietary recommendations and therapeutic development.
A fuzzy expert organizer/robust control strategy for a moving base robotic part assembly (2002)

In this paper, three analytical tasks, stability analysis, robust control, and fuzzy intelligent organizer for a moving base robot are introduced. These tools are necessary for a mobile robot to perform complex assembly or manufacturing tasks in an unstructured environment. A stability envelope based on the relations between the system's mechanical energy and the stability relation is derived. A robust control algorithm is applied to the moving base robot that accounts for the dynamics of the composite system. A fuzzy intelligent organizing control strategy, based on a fuzzy rulebase and derived from measured force/moment data, for a robotic device performing quasi-static assembly tasks is presented. A modified distance metric is employed to measure the uncertainty (fuzziness) as it is related to specific control actions. A learning algorithm based on the probability of a fuzzy event is introduced. The top organizing level determines the most appropriate n-tuple control values with minimum fuzziness and downlinks them to the lower level of the system which carries out the specified task. Experimental results show the effectiveness of the proposed approach. Finally a hierarchical controller which consists of a higher level fuzzy expert organizer coordinating with a lower level robust controller is proposed. Experimental and simulation results are used to demonstrate the effectiveness of the algorithms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ovulation induction for polycystic ovary syndrome (2000)

Polycystic ovary syndrome (PCOS) is the commonest cause of anovulatory infertility. Various factors influence ovarian function, and fertility is adversely affected by an individual being overweight or having high serum concentrations of LH. Strategies to induce ovulation include weight loss, oral anti-oestrogens (principally clomiphene citrate), parenteral gonadotrophin therapy and laparoscopic ovarian surgery. There have been no adequately powered randomized studies to determine which of these therapies provides the best overall chance of an ongoing pregnancy. Women with PCOS are at risk of ovarian hyperstimulation syndrome (OHSS) and so ovulation induction has to be monitored carefully with serial ultrasound scans. The recognition of an association between hyperinsulinaemia and PCOS has resulted in the use of insulin sensitizing agents, such as metformin, which appear to ameliorate the biochemical profile and improve reproductive function.
Ichthyobodo hippoglossi n. sp. (Kinetoplastea: Prokinetoplastida: Ichthyobodonidae fam. nov.), an ectoparasitic flagellate infecting farmed Atlantic halibut Hippoglossus hippoglossus (2007)

Diseased Atlantic halibut Hippoglossus hippoglossus juveniles from a hatchery in western Norway showed gill and skin infections with an Ichthyobodo species. Genus Ichthyobodo contains a single valid species, I. necator, a parasite originally described from the skin and fins of a salmonid fish in freshwater. Many studies have identified this species from other hosts, but recent molecular evidence suggests that many Ichthyobodo spp. occur in both fresh- and seawater. We redescribe I. necator from Atlantic salmon Salmo salar skin infections in Norway and compare the morphology of I. necator with the form from halibut. A scheme to standardise the measurements of Ichthyobodo cells is presented. Morphologically, the Ichthyobodo species from the skin and gills of halibut differs from I. necator from salmon skin by shape (in air dried stained smears), by a low number of variably sized kinetoplasts and by a long flagellar pocket. There is also a clear increase in the number of kinetoplasts in L necator with increasing cell size (area), a pattern absent from Ichthyobodo sp. from halibut. The 2 forms are also clearly separated by their small subunit (ssu) rDNA sequences; alignments of partial ssu sequences showed 93.5 % similarity. Consequently, Ichthyobodo sp. from halibut is considered a new species, and is named I. hippoglossi n. sp. Its closest relative is Ichthyobodo sp. IV from another marine fish, the Atlantic cod Gadus morhua. A family, Ichthyobodonidae fam. nov. in the order Prokinetoplastida Vickerman, 2004, is erected to encompass Ichthyobodo spp.
Systematic Investigation of Insulator-Based Protein Dielectrophoresis Under DC Condition (2011)

The ability to rapidly separate and analyze proteins in small volumes and concentrations is of great interest in situations where time is critical and sample availability is low. Here, we report on the dielectrophoretic manipulation of the proteins immunoglobulin G (IgG) and bovine serum albumin (BSA) under DC conditions in a tailored insulator-based microfluidic device. Our results demonstrate that dielectrophoresis can be used to concentrate protein monomers along a streamline profile. These findings are in excellent agreement with numerical simulations and indicate positive dielectrophoresis of proteins. Moreover, parameters such as conductivity and pH influencing protein dielectrophoresis were analyzed experimentally.
ChemInform Abstract: The Coordination Chemistry of Macrocyclic Ligands (2000)

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.
Alpha-1 Antitrypsin Replacement in Patients With COPD. (2019)

Chronic obstructive pulmonary disease can be attributed to genetic conditions and predispositions, among other factors. Alpha-1 antitrypsin deficiency (AATD) is a significant risk factor for COPD development and progression, and aggressive screening for all patients with COPD or adult-onset asthma is encouraged.
Patient Preferences for Physician Attire in Ophthalmology Practices (2019)

Physician attire is important to patients receiving ophthalmic care. Policies aimed at physician attire in ophthalmology practices should be considered.
Transient atypical monocytosis mimic acute myelomonocytic leukemia in post-chemotherapy patients receiving G-CSF: report of two cases (2004)

Granulocyte colony-stimulating factor (G-CSF) is now widely used in patients with malignant disorders receiving intensive chemotherapy to increase leukocyte count and to upregulate phagocyte function during neutropenia. Monocytosis associated with G-CSF has been reported in anecdotal literature. We report two cases of pseudoleukemia secondary to G-CSF administration. Both patients initially presented with myelodysplastic syndrome with chromosome 7 abnormalities that evolved into acute myeloid leukemia. Case one had deletion 7q while case two initially had monosomy 7 and subsequently developed a balanced translocation between the short (p) arm of chromosome 1 and long (q) arm of chromosome 15. Following the induction chemotherapy and G-CSF administration, both of these patients developed pseudoleukemia. Patient 1 had white blood cell (WBC) count of 26 x 10(9)/l with 72% monocytes, while patient two had WBC of 14.1 x 10(9)/l with 30% monocytes. In both patients the monocytosis resolved after the discontinuation of G-CSF therapy. In summary, patients treated with G-CSF should be followed closely. In those cases with pseudoleukemia discontinuation of the drug with no supplemental chemotherapy is probably enough to control the atypical monocytosis.
Nucleotide base recognition: a macrocyclic receptor for adenine employing hydrogen bonding and aromatic stacking interactions (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleotide base recognition: a macrocyclic receptor for adenine employing hydrogen bonding and aromatic stacking interactionsShyamaprosad Goswami, Donna Van Engen, and Andrew D. HamiltonCite this: J. Am. Chem. Soc. 1989, 111, 9, 3425–3426Publication Date (Print):April 1, 1989Publication History Published online1 May 2002Published inissue 1 April 1989https://pubs.acs.org/doi/10.1021/ja00191a048https://doi.org/10.1021/ja00191a048research-articleACS PublicationsRequest reuse permissionsArticle Views526Altmetric-Citations92LEARN 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
Introduction to the Special Issue on Arabic Computational Linguistics (2011)

introduction Share on Introduction to the Special Issue on Arabic Computational Linguistics Editors: Graham Katz Georgetown University Georgetown UniversityView Profile , Mona Diab Columbia University Columbia UniversityView Profile Authors Info & Claims ACM Transactions on Asian Language Information ProcessingVolume 10Issue 1Article No.: 1pp 1–4https://doi.org/10.1145/1929908.1929909Published:01 March 2011Publication History 0citation297DownloadsMetricsTotal Citations0Total Downloads297Last 12 Months8Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Pathways from laboratory to full scale carbon capture—Technology demonstrations in plant settings (2009)

Abstract The Cooperative Research Centre for Greenhouse Gas Technologies (CO2CRC) was setup with distinct programs focusing on storage, capture, demonstration, education and international collaboration designed to address the many issues facing potential carbon capture and storage (CCS) projects. In particular the Capture Program aims to research, develop and deploy technologies that can achieve significant cuts in capture cost (75%–80%) and provide Australia with a research and education capability to support industries using these technologies. This paper provides details on the capture research activities within the centre, the major demonstration projects underway, including outlines of the equipment employed and how they are enabling the progression of separation technologies from laboratory through to eventual large scale commercial operation. Aided by recent initiatives of the Victorian State Government, under their Energy Technology Innovation Strategy (ETIS) program, CO2CRC is leading the research in two such research and development projects. These three year projects, one a $6 million post combustion demonstration incorporating a 10,000 tpa CO 2 capture plant, and the other a $5.5 million pre-combustion application, each designed to test the CO2CRC’s full range of capture technologies (solvents, membranes and adsorption systems), in purpose built rigs under actual power plant conditions. The ability to demonstrate both conventional and novel capture techniques in the one facility is, we believe, unique.