gebhart/patrepeval huggingface dataset:
Single-Molecule Dynamics of Lysozyme Processing Distinguishes Linear and Cross-Linked Peptidoglycan Substrates (2012)

The dynamic processivity of individual T4 lysozyme molecules was monitored in the presence of either linear or cross-linked peptidoglycan substrates. Single-molecule monitoring was accomplished using a novel electronic technique in which lysozyme molecules were tethered to single-walled carbon nanotube field-effect transistors through pyrene linker molecules. The substrate-driven hinge-bending motions of lysozyme induced dynamic electronic signals in the underlying transistor, allowing long-term monitoring of the same molecule without the limitations of optical quenching or bleaching. For both substrates, lysozyme exhibited processive low turnover rates of 20-50 s(-1) and rapid (200-400 s(-1)) nonproductive motions. The latter nonproductive binding events occupied 43% of the enzyme's time in the presence of the cross-linked peptidoglycan but only 7% with the linear substrate. Furthermore, lysozyme catalyzed the hydrolysis of glycosidic bonds to the end of the linear substrate but appeared to sidestep the peptide cross-links to zigzag through the wild-type substrate.
The Design of Large-Scale, Do-It-Yourself RAIDs (1995)

In this paper we explore the design of &amp;quot;Do-It-Yourself&amp;quot; RAIDs: RAID systems that can assembled by the end user from commercially available disks, enclosures, cables, racks, computers, and networks. We quantitatively evaluate the tradeoffs in cost, performance, and reliability of these DIY-RAID systems. Our principal result is an architecture that scales from 10s to 1000s of disks; we demonstrate that a 1995 implementation would have much lower cost, better and more scalable performance, and roughly the same reliability as commercially available hardware RAID systems. Furthermore, if current trends continue, these DIY-RAIDs will replace near-line tape libraries within a few years. 1. Introduction Recently, a number of applications have emerged that require active use of very large storage systems. Examples include multimedia digital libraries, video on demand, and enterprise-wide decision support. To address this opportunity, a number of researchers are designing systems software to t...
Picosecond time-resolved plasma and temperature-induced changes of reflectivity and transmission in silicon (1982)

A pump-and-probe technique is used to perform picosecond time-resolved measurements of reflectivity and transmission changes in silicon. The results provide direct evidence that lattice heating, melting, or boiling can occur on a picosecond time scale. Detailed analysis of the data provides information about the dynamics of the electron-hole plasma prior to melting and the kinetics of ultrafast phase transitions and crystal regrowth.
Synthetic models of DNA complexes with antimalarial compounds. 2. The problem of guanine specificity in chloroquine binding (1977)

Stacking interactions between the aminoquinoline ring of the antimalarial chloroquine and the purine bases have been studied by preparing and examining models in which the quinoline is linked to the base by a trimethylene chain. The degree of stacking of the models which reflects the strength of the interaction was quantitatively determined in water at different temperatures by hypochromism measurement in the uv. Adenine and guanine exhibit equal affinity for the quinoline nucleus as reflected by very close hypochromism values observed for the two models at all temperatures studied.
Role of C‐afferent fibres in the mechanism of action of sacral nerve root neuromodulation in chronic spinal cord injury (2000)

In spinally transected rats, sacral root neurostimulation abolished bladder hyper-reflexia and attenuated the rise in neuropeptide content of the L6 DRG. These results suggest that the blockade of C-afferent fibre activity is one of the mechanisms of action of sacral root neuromodulation.
Spectroscopic Properties, Electrochemistry, and Reactivity of Mo0, MoI, and MoII Complexes with the [Mo(bpa)(CO)3] Unit [bpa = bis(2-picolyl)amine] and Their Application for the Labelling of Peptides (2002)

The synthesis of the complexes [Mo(bpa)(CO)3] (1) and [Mo(Bz-bpa)(CO)3] (2) [bpa = bis(2-picolyl)amine; Bz-bpa = N-benzylbis(2-picolyl)amine] is described. These compounds have been characterized by spectroscopic techniques including multinuclear NMR spectroscopy (1H, 13C, and 95Mo), and also by X-ray crystallography. Complexes 1 and 2 underwent reversible one-electron oxidations in acetonitrile and dichloromethane with Bu4NPF6 as supporting electrolyte to yield the 17-electron organometallic compounds 1+ and 2+. With Bu4NBr as supporting electrolyte in dichloromethane, on the other hand, 1 and 2 underwent electrochemically irreversible two-electron oxidations, resulting in the formation of [Mo(bpa)(CO)3Br]+ and [Mo(Bz-bpa)(CO)3Br]+. Infrared spectra and electronic spectra of these oxidized species were recorded in spectro-electrochemical studies. The electrochemical behaviour and the infrared spectroscopic data of 1, 2, and their oxidized derivatives are compared in detail with those of analogous tricarbonylmolybdenum complexes with the ligands 1,4,7-triazacyclononane and hydridotris(pyrazolyl)borate. The complex [Mo(bpa)(CO)Br]Br3 (3) could be prepared by oxidation of 1 with elemental bromine. Under aerobic aqueous conditions, 3 reacted further to yield the dinuclear diamagnetic MoV complex [Mo2(bpa)2(O)2(μ-O)2](Br,PF6) (4). The identity of 4 was confirmed by a single-crystal X-ray crystallographic study. Finally, the syntheses of two bioconjugates of [Mo(bpa)(CO)3], in which bpa ligands are covalently linked to the N-termini of an amino acid (Phe-OMe, 8a) and of a dipeptide (Ala-Phe-OMe, 8b), are described. These bioconjugates were comprehensively characterized (including elemental analysis, 1H, 13C, and 95Mo NMR, IR, MS, and electrochemistry). All analytical data supported the proposed constitution and underscore the potential of the Mo(bpa)(CO)3 group as a robust marker group in bioorganometallic chemistry. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)
In vivo administration of insulin-like growth factor-I stimulates primary B lymphopoiesis and enhances lymphocyte recovery after bone marrow transplantation. (1994)

Recombinant human insulin-like growth factor-I (IGF-I) (100 micrograms/day) was infused by osmotic minipumps into mice to evaluate its effects on bone marrow B lymphopoiesis. IGF-I treatment resulted in a significant increase in the total number of bone marrow B lineage cells by 2 wk post-treatment in both normal, adult mice and animals that had been lethally irradiated and reconstituted with syngeneic bone marrow. Effects were still apparent at wk 3, even though pumps delivered IGF-I for only 14 days. In addition, the results confirm previous observations that IGF-I treatment results in an increase in numbers of splenic B cells and suggest that this is in part the result of stimulation of B cell proliferation in that organ.
Adaptation of a support vector machine algorithm for segmentation and visualization of retinal structures in volumetric optical coherence tomography data sets (2007)

Recent developments in Fourier domain-optical coherence tomography (Fd-OCT) have increased the acquisition speed of current ophthalmic Fd-OCT instruments sufficiently to allow the acquisition of volumetric data sets of human retinas in a clinical setting. The large size and three-dimensional (3D) nature of these data sets require that intelligent data processing, visualization, and analysis tools are used to take full advantage of the available information. Therefore, we have combined methods from volume visualization, and data analysis in support of better visualization and diagnosis of Fd-OCT retinal volumes. Custom-designed 3D visualization and analysis software is used to view retinal volumes reconstructed from registered B-scans. We use a support vector machine (SVM) to perform semiautomatic segmentation of retinal layers and structures for subsequent analysis including a comparison of measured layer thicknesses. We have modified the SVM to gracefully handle OCT speckle noise by treating it as a characteristic of the volumetric data. Our software has been tested successfully in clinical settings for its efficacy in assessing 3D retinal structures in healthy as well as diseased cases. Our tool facilitates diagnosis and treatment monitoring of retinal diseases.
Hyaluronidase Inhibitors: A Biological and Therapeutic Perspective (2009)

The hyaluronidases (HAases) are a group of less extensively studied glycosidases distributed throughout the animal kingdom and are popularly known as 'spreading factors'. In recent years, HAases received much attention due to their ability to abruptly alter the hyaluronic acid (HA) homeostasis. HAases preferentially degrade HA, which is a megadalton acidic structural polysaccharide found exclusively in the extracellular matrix (ECM) of animals. The HA-HAase system has been suggested to participate in many pathophysiological conditions. The HA degradation in ECM, crack down the structural integrity with an eventual increased tissue permeability that is attributed for the spreading property. The spreading property has been widely accepted in functions including envenomation, acrosomal reaction/ovum fertilization, cancer progression, microbial pathogenesis such as wound infections, pneumonia, and other sepses like, bacteremia and meningitis. HA fragmentation has dual effects; generation of a wide molecular range bioactive oligosaccharides of angiogenic, pro-inflammatory, and immunostimulatory properties; and impairment in the reservoir capacity of ECM that holds metal ions, growth factors, cytokines and various enzymes for signal transduction. Hence, inhibition of HA degradation appears critical and imperative in HAase mediated pathological conditions. HAase inhibitors are thus potent regulators that maintain HA homeostasis and they might serve as anti-inflammatory, anti-aging, anti-microbial, anticancer and anti-venom/toxin and contraceptive agents. In addition, HAase inhibitors may serve as tools to understand several unexplained and complex functions of HAases in HA metabolism. Therefore, this review is expected to provide an integrated update as of 2008 on the HAase inhibitors and their possible role as therapeutics in the management of a wide range of pathological conditions.
Predicting the reactivity of proteins from their sequence alone: Kazal family of protein inhibitors of serine proteinases (2001)

An additivity-based sequence to reactivity algorithm for the interaction of members of the Kazal family of protein inhibitors with six selected serine proteinases is described. Ten consensus variable contact positions in the inhibitor were identified, and the 19 possible variants at each of these positions were expressed. The free energies of interaction of these variants and the wild type were measured. For an additive system, this data set allows for the calculation of all possible sequences, subject to some restrictions. The algorithm was extensively tested. It is exceptionally fast so that all possible sequences can be predicted. The strongest, the most specific possible, and the least specific inhibitors were designed, and an evolutionary problem was solved.
Phthalonimides (1,3,4‐trioxo‐1,2,3,4‐tetrahydroisoquinolines) of potential biological interest (1968)

Abstract A new simple method for the preparation of phthalonimides (1,3,4‐trioxo‐1,2,3,4‐tetrahydroisoquinolines), consisting of the selenium dioxide‐oxidation of the appropriate homophthalimides, has been devised; the thiosemicarbazones and other derivatives of phthalonimides of possible biological interest (as potential antibacterial, antiviral, or immunosuppressive agents) have been synthesized.
Evaluation of epidermal growth factor receptor (EGFR) as a predictive marker in patients with non-small-cell lung cancer (NSCLC) receiving first-line gefitinib combined with platinum-based chemotherapy (2004)

7013 Background: In two Phase III trials (INTACT 1 & 2), gefitinib (‘Iressa’, ZD1839) in combination with first-line platinum-based chemotherapy regimens failed to show benefit in terms of survival when compared with chemotherapy alone in patients (pts) with NSCLC. The primary objective of this analysis was to evaluate if EGFR staining was predictive of survival. Methods: Pretreatment tumor biopsies were assessed by immunohistochemistry for EGFR using the DakoCytomation pharmDx assay™. The percentage of tumor cells was assessed using 4 levels of intensity: no staining, 0; weak, 1+; moderate, 2+; strong, 3+; as well as the presence of complete membrane staining. 516 pts (INTACT 1/2, 219/297) with tumor samples fully evaluable for EGFR were analyzed in the per protocol population of the combined trials. The analysis was stratified by trial and performed independently for pts randomized to placebo or gefitinib. A restricted backwards elimination Cox regression analysis was conducted to identify independent EGFR factors. Variables found to be significant (p<0.1) were also tested for treatment interaction to determine if they served as predictive factors. Results: The demographics of the analysis population were representative of the overall population in each trial as were common disease characteristics. The analysis showed that two EGFR-based variables are independent strong prognostic factors for both placebo- and gefitinib-treated patients. However, no interactions with treatment (ie no value for predicting benefit of gefitinib treatment) were indicated for either of these two variables (p=0.8688 and 0.4967) or for any other EGFR-based variables. Conclusion: Given the overall trial results for INTACT 1 & 2 showing no survival benefit between gefitinib and placebo, it was highly unlikely that EGFR variables would identify a subset of pts who receive survival benefit. The data presented support this hypothesis. 'Iressa' is a trademark of the AstraZeneca group of companies 'PharmDx assay' is a trademark of DakoCytomation Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration AstraZeneca Pharmaceuticals; DakoCytomation AstraZeneca; DakoCytomation; Genentech AstraZeneca AstraZeneca AstraZeneca Pharmaceuticals
Effects of drying on flavour compounds in Australian-grown ginger (Zingiber officinale) (2000)

The volatile compounds responsible for the flavour of Australian-grown ginger have been extracted using supercritical carbon dioxide. Both fresh and dried ginger samples have been examined and the major effects of the drying process are a reduction in gingerol content, an increase in terpene hydrocarbons and the conversion of some monoterpene alcohols to their corresponding acetates. © 2000 Society of Chemical Industry
Germline VH/VL pairing in antibodies (2012)

Antibodies are key molecules of the adaptive immune response and are now a major class of biopharmaceuticals. Pairing of heavy and light chains is one of the ways of generating antibody diversity and, while little is known about mechanisms governing V(H)/V(L) pairing, previous studies have suggested that the germline source from which chains are paired is random. By selecting paired antibody protein sequences from human and mouse antibodies from the KabatMan database and mapping them onto their corresponding germline sequences, we find that pairing preferences do exist in the germline, but only for a small proportion of germline gene segments; others are much more promiscuous showing no preferences. The closest equivalent human and mouse gene families were identified and pairing preferences compared. This work may impact on the ability to generate more stable antibodies for use as biopharmaceuticals.
Tissue-engineered bone formation using human bone marrow stromal cells and novel β-tricalcium phosphate (2007)

In this study we investigated not only the cellular proliferation and osteogenic differentiation of human bone marrow stromal cells (hBMSCs) on the novel beta-tricalcium phosphate (beta-TCP) scaffolds in vitro but also bone formation by ectopic implantation in athymic mice in vivo. The interconnected porous beta-TCP scaffolds with pores of 300-500 microm in size were prepared by the polymeric sponge method. beta-TCP scaffolds with the dimension of 3 mm x 3 mm x 3 mm were combined with hBMSCs, and incubated with (+) or without (-) osteogenic medium in vitro. Cell proliferation and osteogenic differentiation on the scaffolds were evaluated by scanning electron microscopy (SEM) observation, MTT assay, alkaline phosphatase (ALP) activity and osteocalcin (OCN) content measurement. SEM observation showed that hBMSCs attached well on the scaffolds and proliferated rapidly. No significant difference in the MTT assay could be detected between the two groups, but the ALP activity and OCN content of scaffolds (+) were much higher than those of the scaffolds (-) (p < 0.05). These results indicated that the novel porous beta-TCP scaffolds can support the proliferation and subsequent osteogenic differentiation of hBMSCs in vitro. After being cultured in vitro for 14 days, the scaffolds (+) and (-) were implanted into subcutaneous sites of athymic mice. In beta-TCP scaffolds (+), woven bone formed after 4 weeks of implantation and osteogenesis progressed with time. Furthermore, tissue-engineered bone could be found at 8 weeks, and remodeled lamellar bone was also observed at 12 weeks. However, no bone formation could be found in beta-TCP scaffolds (-) at each time point checked. The above findings illustrate that the novel porous beta-TCP scaffolds developed in this work have prominent osteoconductive activity and the potential for applications in bone tissue engineering.
Application of Shaping Technique to Multi-level Turbo-coded Modulation (2002)

This article presents a method for the combined Turbo-code and QAM modulation using coset coding. A Turbo-code (acting on nonbinary symbols) is used to select a coset along each one-D co-ordinate using a one-D lattice partition (Ungerboeck partition). The proposed method satisfies the conditions for the separability of shaping and coding, and consequently, can be easily integrated with a shaping algorithm. Numerical results are presented which show that the proposed configuration outperforms the best known techniques in terms of the complexity, delay and BER performance (even ignoring the extra gain achievable through shaping). Furthermore, we are able to achieve an additional gain of about 1 dB through integration with shaping. The proposed method also demonstrates an excellent performance near the error floor region.
Effects of Pirenzepine on Pupil Size and Accommodation in Rhesus Monkeys (2004)

Subconjunctival injections of 0.02% or greater pirenzepine result in a significant decrease in accommodation and are probably acting through nonselective muscarinic antagonism. Subconjunctival injections of 0.002% or less pirenzepine do not decrease EW-stimulated accommodation.
INFORMATION-SEEKING BEHAVIOUR OF INTERNATIONAL ISLAMIC UNIVERSITY MALAYSIA LAW FACULTY MEMBERS (2000)

Adequate knowledge about the information needs and seeking behaviour of users is vital for developing library collections, services and facilities to meet their information needs effectively. The purpose of this study is to identify the information channels used by the International Islamic University Malaysia (IIUM) law faculty members, information sources preferred by them, methods employed for getting the needed information and their library use pattern. A questionnaire was distributed to 80 IIUM law faculty members and 66 filledin questionnaires were returned, giving an overall response rate of 82.5 percent. It was found that respondents used various sources for acquiring the needed information. Books were ranked as the most important source for teaching and research purposes, followed by law reports and statutes. Respondents preferred to first consult their personal collection before resorting to other information providing sources and agencies. The Online Public Access Catalogue (OPAC) and CD-ROM were the most frequently used IT-based sources and facilities. E-mail was the most popular among the Internet-based services and applications. On the whole, respondents perceived IIUM library collections, services and facilities as adequate to meet their information needs effectively.
Development, implantation, in vivo elution, and retrieval of a biocompatible, sustained release subretinal drug delivery system (2005)

A biocompatible, sustained-release subretinal drug-delivery platform was developed to overcome the therapeutic accessibility limitations of current retinal disease treatments. The prototype implants were fabricated by coating nitinol, poly(methyl methacrylate) or chromic gut core filaments, with a drug-eluting polymer matrix. The polymer coatings are manufactured and coated by SurModics. The coating is a mixture of poly(butyl methacrylate) and poly(ethylene-co-vinyl acetate). The drug is either triamcinolone acetonide or sirolimus. The rods were successfully implanted into the subretinal space of 20/24 rabbits. Four rabbits were lost to early surgery from a dysfunctional infusion line and hemorrhage. No serious complications were observed during the 4-week follow-up period. Slight conjunctival redness was reported in all rabbits by 1-day follow-up, but the redness had subsided by the following week. Intraocular lens touch occurred in six rabbits during the implantations; of these, four had a lensectomy at the time of surgery, and the remaining two developed cataract. Corneal edema developed in three rabbits by 1-week follow-up, but subsided within 2 weeks. Initial observations of the implantation and elution characteristics revealed that the implants are well tolerated by the retinal tissue and that the implant can elute triamcinolone acetonide for a period of at least 4 weeks without eliciting an inflammatory response or complications. There were adverse clinical indications with the sirolimus-loaded implants at the delivered dose. Device retrieval required an uncomplicated surgical procedure, and revealed no associated or adherent tissue. Implant drug content analysis and opacity changes to the polymer matrix coating following retrieval demonstrated the sustained elution of the drug.
A Bicyclic Autotrophic CO2 Fixation Pathway in Chloroflexus aurantiacus (2002)

Phototrophic CO(2) assimilation by the primitive, green eubacterium Chloroflexus aurantiacus has been shown earlier to proceed in a cyclic mode via 3-hydroxypropionate, propionyl-CoA, succinyl-CoA, and malyl-CoA. The metabolic cycle could be closed by cleavage of malyl-CoA affording glyoxylate (the primary CO(2) fixation product) with regeneration of acetyl-CoA serving as the starter unit of the cycle. The pathway of glyoxylate assimilation to form gluconeogenic precursors has not been elucidated to date. We could now show that the incubation of cell extract with a mixture of glyoxylate and [1,2,3-(13)C(3)]propionyl-CoA afforded erythro-beta-[1,2,2'-(13)C(3)]methylmalate and [1,2,2'-(13)C(3)]citramalate. Similar experiments using a partially purified protein fraction afforded erythro-beta-[1,2,2'-(13)C(3)]methylmalyl-CoA and [1,2,2'-(13)C(3)]mesaconyl-CoA. Cell extracts of C. aurantiacus were also shown to catalyze the conversion of citramalate into pyruvate and acetyl-CoA in a succinyl-CoA-dependent reaction. The data suggest that glyoxylate obtained by the cleavage of malyl-CoA can be utilized by condensation with propionyl-CoA affording erythro-beta-methylmalyl-CoA, which is converted to acetyl-CoA and pyruvate. This reaction sequence regenerates acetyl-CoA, which serves as the precursor of propionyl-CoA in the 3-hydroxypropionate cycle. Autotrophic CO(2) fixation proceeds by combination of the 3-hydroxypropionate cycle with the methylmalyl-CoA cycle. The net product of that bicyclic autotrophic CO(2) fixation pathway is pyruvate serving as an universal building block for anabolic reactions.