gebhart/patrepeval huggingface dataset:
Carbon−Sulfur Bond-Forming Reductive Elimination Involving sp-, sp2-, and sp3-Hybridized Carbon. Mechanism, Steric Effects, and Electronic Effects on Sulfide Formation (1998)

Palladium thiolato complexes [(L)Pd(R)(SR‘)], within which L is a chelating ligand such as DPPE, DPPP, DPPBz, DPPF, or TRANSPHOS, R is a methyl, alkenyl, aryl, or alkynyl ligand, and R‘ is an aryl or alkyl group, were synthesized by substitution or proton-transfer reactions. All of these thiolato complexes were found to undergo carbon−sulfur bond-forming reductive elimination in high yields to form dialkyl sulfides, diaryl sulfides, alkyl aryl sulfides, alkyl alkenyl sulfides, and alkyl alkynyl sulfides. Reductive eliminations forming alkenyl alkyl sulfides and aryl alkyl sulfides were the fastest. Eliminations of alkynyl alkyl sulfides were slower, and elimination of dialkyl sulfide was the slowest. Thus the relative rates for sulfide elimination as a function of the hybridization of the palladium-bound carbon follow the trend sp2 > sp ≫ sp3. Rates of reductive elimination were faster for cis-chelating phosphine ligands with larger bite angles. Kinetic studies, along with results from radical trapping reactions, analysis of solvent effects, and analysis of complexes with chelating phosphines of varying rigidity, were conducted with [Pd(L)(S-tert-butyl)(Ar)] and [Pd(L)(S-tert-butyl)(Me)]. Carbon−sulfur bond-forming reductive eliminations involving both saturated and unsaturated hydrocarbyl groups proceed by an intramolecular, concerted mechanism. Systematic changes in the electronic properties of the thiolate and aryl groups showed that reductive elimination is the fastest for electron deficient aryl groups and electron rich arenethiolates, suggesting that the reaction follows a mechanism in which the thiolate acts as a nucleophile and the aryl group an electrophile. Studies with thiolate ligands and hydrocarbyl ligands of varying steric demands favor a migration mechanism involving coordination of the hydrocarbyl ligand in the transition state.
The Difficult Leg Ulcer: A Case Review Illustrating the Problems and Difficulties Associated with Treatment (2005)

Through the vehicle of a case study, this paper illustrates the complexity associated with venous leg ulcerations. In order to be effective with treatment regimes, a comprehensive understanding of the pathophysiology of the lower leg venous system, the pathology of venous insufficiency and the pathology of venous leg ulcerations must be fully understood. Compression therapy is the cornerstone to treatment, however, this must only be applied after the patient has been thoroughly investigated to exclude other causes of the leg ulcer. Unlike the United Kingdom and Europe, Australia does not have national guidelines for the management of patients with venous leg ulcers. In view of the high costs associated with this condition, perhaps there may be better outcomes for patients if this approach were adopted in Australia.
A shortened adeno-associated virus expression cassette for CFTR gene transfer to cystic fibrosis airway epithelia (2005)

Adeno-associated viruses (AAVs) such as AAV5 that transduce airway epithelia from the apical surface are attractive vectors for gene transfer in cystic fibrosis (CF). However, their utility in CF has been limited because packaging of the insert becomes inefficient when its length exceeds approximately 4,900-5,000 bp. To partially circumvent this size constraint, we previously developed a CF transmembrane conductance regulator (CFTR) transgene that deleted a portion of the R domain (CFTRDeltaR). In this study, we focused on shortening the other elements in the AAV expression cassette. We found that portions of the CMV immediate/early (CMVie) enhancer/promoter could be deleted without abolishing activity. We also tested various intervening sequences, poly(A) signals, and an intron to develop an expression cassette that meets the size restrictions imposed by AAV. We then packaged these shortened elements with the CFTRDeltaR transgene into AAV5 and applied them to the apical surface of differentiated CF airway epithelia. Two to 4 weeks later, the AAV5 vectors partially corrected the CF Cl(-) transport defect. These results demonstrate that a single AAV vector can complement the CF defect in differentiated airway epithelia and thereby further the development of effective CF gene transfer.
A Unified Hypothesis of Early- and Late-Onset Alzheimer’s Disease Pathogenesis (2015)

Early-onset familial Alzheimer's disease (EOFAD) and late-onset sporadic AD (LOSAD) both follow a similar pathological and biochemical course that includes: neuron and synapse loss and dysfunction, microvascular damage, microgliosis, extracellular amyloid-β deposition, tau phosphorylation, formation of intracellular neurofibrillary tangles, endoreduplication and related cell cycle events in affected brain regions. Any mechanistic explanation of AD must accommodate these biochemical and neuropathological features for both forms of the disease. In this insight paper we provide a unifying hypothesis for EOFAD and LOSAD that proposes that the aberrant re-entry of terminally differentiated, post-mitotic neurons into the cell division cycle is a common pathway that explains both early and late-onset forms of AD. Cell cycle abnormalities appear very early in the disease process, prior to the appearance of plaques and tangles, and explain the biochemical (e.g. tau phosphorylation), neuropathological (e.g. neuron hypertrophy; polypoidy) and cognitive changes observed in EOFAD and LOSAD. Genetic mutations in AβPP, PSEN1, and PSEN2 that alter amyloid-β precursor protein and Notch processing drive reactivation of the cell cycle in EOFAD, while age-related reproductive endocrine dyscrasia that upregulates mitogenic TNF signaling and AβPP processing toward the amyloidogenic pathway drives reactivation of the cell cycle in LOSAD. In essence, AβPP and presenilin mutations initiate early, what endocrine dyscrasia initiates later: aberrant cell cycle re-entry of post-mitotic neurons leading to neurodegeneration and cognitive decline in AD. Inhibition of cell cycle re-entry in post-mitotic neurons may be a useful therapeutic strategy to prevent, slow or halt disease progression.
Hepatitis B and Delta in Adolescents. (1995)

Acute and chronic hepatitis B affect a large number of adolescents, and their complications are major causes of morbidity and mortality. The authors emphasize the importance of targeting adolescents for prevention and discuss the most recent diagnostic and therapeutic advances concerning both the hepatitis B and hepatitis delta viruses.
Therapeutic targets in osteoarthritis. (1995)

Osteoarthritis (OA) can be considered as a disease process, amenable to therapy, or as a consequence of evolution, resulting in special disadvantages to long lived humans. Possible therapeutic targets are considered for both models of the condition. Targets for a disease process might include inhibition of tissue destruction, or the stimulation of natural repair processes. Therapeutic targets for the disadvantages of OA include novel approaches to the treatment of pain and physical disability. The 2 approaches are not mutually exclusive, and both should be pursued.
Antibody microinjection reveals an essential role for human polo-like kinase 1 (Plk1) in the functional maturation of mitotic centrosomes. (1996)

Mammalian polo-like kinase 1 (Plk1) is structurally related to the polo gene product of Drosophila melanogaster, Cdc5p of Saccharomyces cerevisiae, and plo1+ of Schizosaccharomyces pombe, a newly emerging family of serine-threonine kinases implicated in cell cycle regulation. Based on data obtained for its putative homologues in invertebrates and yeasts, human Plk1 is suspected to regulate some fundamental aspect(s) of mitosis, but no direct experimental evidence in support of this hypothesis has previously been reported. In this study, we have used a cell duplication, microinjection assay to investigate the in vivo function of Plk1 in both immortalized (HeLa) and nonimmortalized (Hs68) human cells. Injection of anti-Plk1 antibodies (Plk1+) at various stages of the cell cycle had no effect on the kinetics of DNA replication but severely impaired the ability of cells to divide. Analysis of Plk1(+)-injected, mitotically arrested HeLa cells by fluorescence microscopy revealed abnormal distributions of condensed chromatin and monoastral microtubule arrays that were nucleated from duplicated but unseparated centrosomes. Most strikingly, centrosomes in Plk1(+)-injected cells were drastically reduced in size, and the accumulation of both gamma-tubulin and MPM-2 immunoreactivity was impaired. These data indicate that Plk1 activity is necessary for the functional maturation of centrosomes in late G2/early prophase and, consequently, for the establishment of a bipolar spindle. Additional roles for Plk1 at later stages of mitosis are not excluded, although injection of Plk1+ after the completion of spindle formation did not interfere with cytokinesis. Injection of Plk1+ into nonimmortalized Hs68 cells produced qualitatively similar phenotypes, but the vast majority of the injected Hs68 cells arrested as single, mononucleated cells in G2. This latter observation hints at the existence, in nonimmortalized cells, of a centrosome-maturation checkpoint sensitive to the impairment of Plk1 function.
Practical radio-frequency handbook (1997)

Preface Passive components and circuits RF transmission lines RF transformers Couplers, hybrids and directional couplers Active components for RF uses RF small-signal circuitry Modulation and demodulation Oscillators RF power amplifiers Transmitters and receivers Advanced architectures Propagation Antennas Attenuators and equalizers Measurements Appendices Index.
Failure to Demonstrate Antiviral Activity of Reticulose (1962)

Introduction A massive promotional campaign is currently under way in behalf of Reticulose,* a substance claimed to be an antiviral biotic (The first antiviral biotic with proven clinical results). The promotional material suggests that indications for use of Reticulose are the treatment of viral and over 600 cases are quoted in which material was said to have been used successfully in a number of virus infections including herpes simplex, infectious hepatitis, encephalitis, generalized vaccinia, mumps meningitis, influenza, infectious mononucleosis, upper respiratory infections, mumps orchitis, and others. It is claimed that Reticulose has demonstrated antiviral properties. A critical review of bibliography on this material is urged by all readers of this paper. 1-5 Therapeutic results claimed in these publications will be analyzed below. The mode of action claimed by manufacturers and authors of clinical articles appears obscure. On one hand immediate relief of symptoms
Multi-model similarity propagation and its application for web image retrieval (2004)

In this paper, we propose an iterative similarity propagation approach to explore the inter-relationships between Web images and their textual annotations for image retrieval. By considering Web images as one type of objects, their surrounding texts as another type, and constructing the links structure between them via webpage analysis, we can iteratively reinforce the similarities between images. The basic idea is that if two objects of the same type are both related to one object of another type, these two objects are similar; likewise, if two objects of the same type are related to two different, but similar objects of another type, then to some extent, these two objects are also similar. The goal of our method is to fully exploit the mutual reinforcement between images and their textual annotations. Our experiments based on 10,628 images crawled from the Web show that our proposed approach can significantly improve Web image retrieval performance.
Evidence for two distinct perceptual alterations in irritable bowel syndrome (1997)

Patients with IBS as a group have a greater propensity to label visceral sensations negatively and show a lower tolerance for rectal balloon distension. A subgroup of patients also have baseline rectal hypersensitivity, assessed by unbiased measures of discomfort threshold and stimulus intensity judgements.
Clinical Evaluation of an Automated Nucleic Acid Isolation System (2002)

Nucleic acid isolation is among the most technically demanding and labor-intensive procedures performed in molecular diagnostic laboratories. Although considerable progress has been made in automating the amplification and detection steps of nucleic acid amplification assays, sample preparation is still performed manually in many laboratories. Various automated systems have been developed to streamline these procedures, ranging from versatile robotic stations to systems dedicated to specific amplification platforms or formats.

The MagNA Pure LC system (Roche Applied Science, Indianapolis, IN) uses robotics, precision pipettors, and magnetic glass particles to purify DNA, RNA, mRNA, or total nucleic acid from various sample types. The samples are dissolved and simultaneously stabilized by incubation with a buffer containing denaturing agents and proteinase K. Nucleic acids are bound to the surface of the magnetic glass particles, and several washing steps remove the unbound substances. The purified nucleic acids are then eluted in a low-salt buffer, with elution volumes ranging from 50 to 100 μL. The instrument can process up to 32 samples in 1.5 h; it can also automate PCR set-up and transfer the purified nucleic acids directly into a wide variety of reaction vessels, including LightCycler capillary tubes (Roche Applied Science), 96-well microplates, standard PCR tubes, and COBAS AMPLICOR amplification rings (Roche Diagnostics).

We developed and verified MagNA Pure LC (software Ver. 2.1) protocols for use with a quantitative test for cytomegalovirus (CMV) DNA (COBAS AMPLICOR MONITOR CMV Test) (1) and a qualitative test for hepatitis C virus (HCV) RNA (AMPLICOR HCV Test version 2.0) (2). The MagNA Pure LC total nucleic acid reagent set was used to recover CMV DNA and HCV RNA from EDTA plasma. The starting sample volume in each case was 200 μL. The total nucleic acid isolation reagent set and instrument were used as recommended by the manufacturer with the following …
Adverse Events Associated With Testosterone Replacement in Middle-Aged and Older Men: A Meta-Analysis of Randomized, Placebo-Controlled Trials (2005)

Testosterone replacement in older men was associated with a significantly higher risk of detection of prostate events and of hematocrit >50% than was placebo; hematocrit increase was the most frequent adverse event associated with testosterone replacement. These data reaffirm the need to monitor hematocrit, PSA, and digital examination of the prostate during testosterone replacement in older men.
Activin is an essential early mesenchymal signal in tooth development that is required for patterning of the murine dentition (1998)

Development of the mammalian tooth has been intensively studied as a model system for epithelial/mesenchymal interactions during organogenesis, and progress has been made in identifying key molecules involved in this signaling. We show that activin betaA is expressed in presumptive tooth-germ mesenchyme and is thus a candidate for a signaling molecule in tooth development. Analysis of tooth development in activin betaA mutant embryos shows that incisor and mandibular molar teeth fail to develop beyond the bud stage. Activin betaA is thus an essential component of tooth development. Development of maxillary molars, however, is unaffected in the mutants. Using tissue recombination experiments we show that activin is required in the mesenchyme prior to bud formation and that although activin signaling from mesenchyme to epithelium takes place, mutant epithelium retains its ability to support tooth development. Implantation of beads soaked in activin A, into developing mandibles, is able to completely rescue tooth development from E11.5, but not E12.5 or E13.5, confirming that activin is an early, essential mesenchyme signal required before tooth bud formation. Normal development of maxillary molars in the absence of activin shows a position specific role for this pathway in development of dentition. Functional redundancy with activin B or other TGFbeta family members that bind to activin receptors cannot explain development of maxillary molars in the mutants since the activin-signaling pathway appears not to be active in these tooth germs. The early requirement for activin signaling in the mesenchyme in incisor and mandibular molar tooth germs must be carried-out in maxillary molar mesenchyme by other independent signaling pathways.
Efficient Grounding of Abstract Spatial Concepts for Natural Language Interaction with Robot Manipulators (2016)

Our goal is to develop models that allow a robot to understand natural language instructions in the context of its world representation. Contemporary models learn possible correspondences between parsed instructions and candidate groundings that include objects, regions and motion constraints. However, these models cannot reason about abstract concepts expressed in an instruction like, "pick up the middle block in the row of five blocks". In this work, we introduce a probabilistic model that incorporates an expressive space of abstract spatial concepts as well as notions of cardinality and ordinality. The graph is structured according to the parse structure of language and introduces a factorisation over abstract concepts correlated with concrete constituents. Inference in the model is posed as an approximate search procedure that leverages partitioning of the joint in terms of concrete and abstract factors. The algorithm first estimates a set of probable concrete constituents that constrains the search procedure to a reduced space of abstract concepts, pruning away improbable portions of the exponentiallylarge search space. Empirical evaluation demonstrates accurate grounding of abstract concepts embedded in complex natural language instructions commanding a robot manipulator. The proposed inference method leads to significant efficiency gains compared to the baseline, with minimal trade-off in accuracy.
Use of Polyclonal Avian Antibodies (2001)

for many years antibodies have been used for quantitation and detection of a lot of different substances. The specific recognition between antibodies and antigens has led to the development of diverse methods for basic research in the sciences as well as for diagnosis in human and veterinary medicine.
Differentiation-associated modulation of heparan sulfate structure and function in CaCo-2 colon carcinoma cells (1998)

Heparan sulfate species expressed by different cell and tissue types differ in their structural and functional properties. Limited information is available on differences in regulation of heparan sulfate biosynthesis within a single tissue or cell population under different conditions. We have approached this question by studying the effect of cell differentiation on the biosynthesis and function of heparan sulfate in human colon carcinoma cells (CaCo-2). These cells undergo spontaneous differentiation in culture when grown on semipermeable supports; the differentiated cells show phenotypic similarity to small intestine enterocytes. Metabolically labeled heparan sulfate was isolated from the apical and basolateral media from cultures of differentiated and undifferentiated cells. Compositional analysis of disaccharides, derived from the contiguous N-sulfated regions of heparan sulfate, indicated a greater proportion of 2-O-sulfated iduronic acid units and a smaller amount of 6-O-sulfated glucosamine units in differentiated than in undifferentiated cells. By contrast, the overall degree of sulfation, the chain length and the size distribution of the N-acetylated regions were similar regardless the differentiation status of the cells. The structural changes were found to affect the binding of heparan sulfate to the long isoform of platelet-derived growth factor A chain but not to fibroblast growth factor 2. These findings show that heparan sulfate structures change during cell differentiation and that heparan sulfate-growth factor interactions may be affected by such changes.
Altered Na+-K+pump activity and plasma lipids in salt-hypertensive Dahl rats: relationship toAtp1a1gene (2001)

A genetic variant of the gene for the alpha(1)-isoform of Na(+)-K(+)-ATPase (Atp1a1) was suggested to be involved in the pathogenesis of salt hypertension in Dahl rats through altered Na(+):K(+) coupling ratio. We studied Na(+)-K(+) pump activity in erythrocytes of Dahl salt-sensitive (SS/Jr) rats in relation to plasma lipids and blood pressure (BP) and the linkage of polymorphic microsatellite marker D2Arb18 (located within intron 1 and exon 2 of Atp1a1 gene) with various phenotypes in 130 SS/Jr x SR/Jr F(2) rats. Salt-hypertensive SS/Jr rats had higher erythrocyte Na(+) content, enhanced ouabain-sensitive (OS) Na(+) and Rb(+) transport, and higher Na(+):Rb(+) coupling ratio of the Na(+)-K(+) pump. BP of F(2) hybrids correlated with erythrocyte Na(+) content, OS Na(+) extrusion, and OS Na(+):Rb(+) coupling ratio, but not with OS Rb(+) uptake. In F(2) hybrids there was a significant association indicating suggestive linkage (P < 0.005, LOD score 2.5) of an intragenic marker D2Arb18 with pulse pressure but not with mean arterial pressure or any parameter of Na(+)-K(+) pump activity (including its Na(+):Rb(+) coupling ratio). In contrast, plasma cholesterol, which was elevated in salt-hypertensive Dahl rats and which correlated with BP in F(2) hybrids, was also positively associated with OS Na(+) extrusion. The abnormal Na(+):K(+) stoichiometry of the Na(+)-K(+) pump is a consequence of elevated erythrocyte Na(+) content and suppressed OS Rb(+):K(+) exchange. In conclusion, abnormal cholesterol metabolism but not the Atp1a1 gene locus might represent an important factor for both high BP and altered Na(+)-K(+) pump function in salt-hypertensive Dahl rats.
Non–antigen-contacting region of an asymmetric bispecific antibody to factors IXa/X significantly affects factor VIII-mimetic activity (2014)

While antibody engineering improves the properties of therapeutic antibodies, optimization of regions that do not contact antigens has been mainly focused on modifying the effector functions and pharmacokinetics of antibodies. We recently reported an asymmetric anti-FIXa/FX bispecific IgG4 antibody, ACE910, which mimics the cofactor function of FVIII by placing the two factors into spatial proximity for the treatment of hemophilia A. During the optimization process, we found that the activity was significantly affected by IgG subclass and by modifications to the inter-chain disulfide bonds, upper hinge region, elbow hinge region, and Fc glycan, even though these regions were unlikely to come into direct contact with the antigens. Of these non-antigen-contacting regions, the tertiary structure determined by the inter-chain disulfide bonds was found to strongly affect the FVIII-mimetic activity. Interestingly, IgG4-like disulfide bonds between Cys131 in the heavy chain and Cys114 in the light chain, and disulfide bonds between the two heavy chains at the hinge region were indispensable for the high FVIII-mimetic activity. Moreover, proline mutations in the upper hinge region and removal of the Fc glycan enhanced the FVIII-mimetic activity, suggesting that flexibility of the upper hinge region and the Fc portion structure are important for the FVIII-mimetic activity. This study suggests that these non-antigen-contacting regions can be engineered to improve the biological activity of IgG antibodies with functions similar to ACE910, such as placing two antigens into spatial proximity, retargeting effector cells to target cells, or co-ligating two identical or different antigens on the same cell.