gebhart/patrepeval huggingface dataset:
Design and Characterization of an Intramolecular Antiparallel Coiled Coil Peptide (1994)

A 56-residue polypeptide was designed to fold into a stable intramolecular antiparallel coiled coil, referred to as a coiled coil stem loop. The antiparallel orientation of the alpha-helices was dictated by the alignment of hydrophobic and ionic residues in the heptad repeat sequence (a, b, c, d, e, f, g)n. The hydrophobic core at the coiled coil interface was occupied by leucine and valine residues in heptad positions d and a' and positions a and d', respectively. The interface border positions e and g were occupied by glutamic acid in the amino-terminal helix and lysine residues in the carboxy-terminal helix. A loop segment connecting the alpha-helices began and ended with the helix-breaking residues glycine and proline. Alanine and serine residues were placed on the exposed b, c, and f positions of both helices to increase the helical propensity and solubility of the peptide, respectively. Several lines of evidence argued that the synthetic peptide made with this design folded into a stable monomeric coiled coil stem loop conformation: (1) the peptide was highly soluble in 150 mM sodium chloride and 50 mM sodium phosphate, pH 7.4; (2) the circular dichroism spectrum was alpha-helical but with relative ellipticity minima at 222 and 208 nm characteristic of a coiled coil structure: (3) the peptide exhibited an alpha-helical content near 80%, which was independent of peptide concentration and unchanged in the presence of trifluoroethanol; (4) size exclusion chromatography and sedimentation equilibrium ultracentrifuge measurements confirmed that the peptide was monomeric in aqueous solution; (5) the peptide exhibited high helical content over a wide pH range; (6) the apparent Tm for unfolding the alpha-helical structure was greater than 65 degrees C, and 3.0 M urea was required to reduce the helical structure by 50%; (7) a disulfide bond was readily formed in the monomer between the amino- and carboxy-terminal cysteine residues, confirming the antiparallel orientation of the helices; and (8) the peptide competed with fibrinogen for the GPIIbIIIa receptor indicating that the RGD residues present in the loop sequence were available for binding. This work establishes that an antiparallel alignment of alpha-helices can be achieved by designing specific hydrophobic and ionic interactions within the coiled coil. The prototype coiled coil peptide represents a sequence-simplified scaffold into which residues from alpha-helices and loops of native proteins can be inserted to form conformationally constrained mimetic recognition molecules.
Novel wideband bandpass filter using open-ended stub loaded parallel coupled short-circuited three-line unit (2009)

Open-ended stub loaded parallel coupled short-circuited three-line structure is proposed to realize a new wideband bandpass filter. The characteristics of the new coupling unit were firstly investigated based on simulation, followed by proposing a two-step design scheme: 1. A Chebyshev filter is synthesized on the desired passband, using symmetric three-line coupling units. 2. The transmission zeros are then introduced to improve the skirt and stopband characteristics by properly designing the stubs. Then, a UWB bandpass filter covering the lower UWB band (BW: 3.1-4.8 GHz, FBW: 43%) is designed to explain the proposed design procedure. The filter was then simulated, fabricated and measured to compare with the theoretical predictions. A good agreement validates the effectiveness of the proposed new coupling structure and corresponding filter design technique.
Tilt and decentration of intraocular lenses in vivo from Purkinje and Scheimpflug imaging (2007)

Both systems showed high reproducibility. Validation experiments on physical model eyes showed slightly higher accuracy with the Purkinje method than the Scheimpflug imaging method. Horizontal measurements of patients with both techniques were highly correlated. The IOLs tended to be tilted and decentered nasally in most patients.
Combinatorial image analysis of DNA microarray features (2003)

Fortran90 subroutines implementing these methods are available from the authors, or at http://www.bioss.ac.uk/~chris.
Changes in the composition of milk from healthy and mastitic dairy cows during the lactation cycle (1995)

Variations in milk composition during lactation were studied in normal and mastitic dairy cows from 2 seasonally calving herds in northern Victoria. Milk yields, somatic cell counts (SCC), and concentrations of lactose, fat, total protein (TP), casein protein (CP), non-casein protein (NCP), sodium, potassium, and calcium varied considerably as lactation progressed. The basic patterns of change over lactation were similar whether cows were healthy or mastitic (SCC >3 x 105 cells/mL milk). Milk from mastitic cows had higher concentrations of TP, NCP, and sodium, but lower concentrations of fat, lactose, CP, and potassium, than milk from healthy cows, although differences were not consistently significant. The activity of the milk protease, plasmin, was positively correlated with log10SCC in both herds.
Mitochondria as a Therapeutic Target for Aging and Neurodegenerative Diseases (2011)

Mitochondria are cytoplasmic organelles responsible for life and death. Extensive evidence from animal models, postmortem brain studies of and clinical studies of aging and neurodegenerative diseases suggests that mitochondrial function is defective in aging and neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. Several lines of research suggest that mitochondrial abnormalities, including defects in oxidative phosphorylation, increased accumulation of mitochondrial DNA defects, impaired calcium influx, accumulation of mutant proteins in mitochondria, and mitochondrial membrane potential dissipation are important cellular changes in both early and late-onset neurodegenerative diseases. Further, emerging evidence suggests that structural changes in mitochondria, including increased mitochondrial fragmentation and decreased mitochondrial fusion, are critical factors associated with mitochondrial dysfunction and cell death in aging and neurodegenerative diseases. This paper discusses research that elucidates features of mitochondria that are associated with cellular dysfunction in aging and neurodegenerative diseases and discusses mitochondrial structural and functional changes, and abnormal mitochondrial dynamics in neurodegenerative diseases. It also outlines mitochondria-targeted therapeutics in neurodegenerative diseases.
Pharmacokinetics and pharmacology of terbinafine and itraconazole (1998)

The low MFCs exhibited by terbinafine for dermatophytes may be important in its clinical efficacy and low relapse rates. The safety profile of terbinafine directly reflects its mechanism of action.
A user friendly password authenticated key agreement for multi server environment (2009)

Two Factor authentication mechanisms are considered to be secure for authenticating a user in Internet based environment. As the number of services provided online is day by day increasing, users intending to use various online services are also increasing. With each service requiring the user to register separately, the overhead of remembering many ID/password pairs has lead to the problem of memorability. To address this, researchers have proposed mechanisms for multi-server environment where in the user needs to register with a single registration centre using one ID/password pair and thereby access all the services registered through that server. But, as these mechanisms employ textual passwords, they suffer from many inherent drawbacks. In this paper we propose a two factor password authenticated key agreement mechanism using graphical password where in the user needs to recognize his secret image presented to him as challenge. The protocol is designed such that there is no need of maintaining a password table at server for verification. In addition, the protocol provides secure low computation mutual authentication and session key agreement. The proposed protocol is computationally efficient and is expected to be secure against ID theft, Insider attack, Replay attack, Shoulder surfing attack, Reconnaissance attack, Server spoofing attack and guessing attack.
A New Carborane, B<sub>9</sub>C<sub>2</sub>H<sub>11</sub>, and Its Derivatives (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA New Carborane, B9C2H11, and Its DerivativesFred. Tebbe, Philip M. Garrett, and M. Frederick. HawthorneCite this: J. Am. Chem. Soc. 1964, 86, 19, 4222–4223Publication Date (Print):October 1, 1964Publication History Published online1 May 2002Published inissue 1 October 1964https://pubs.acs.org/doi/10.1021/ja01073a082https://doi.org/10.1021/ja01073a082research-articleACS PublicationsRequest reuse permissionsArticle Views200Altmetric-Citations30LEARN 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-Alertsclose Get e-Alerts
ARISER: A randomized double blind phase III study to evaluate adjuvant cG250 treatment versus placebo in patients with high-risk ccRCC—Results and implications for adjuvant clinical trials. (2013)

4507^ Background: cG250 (Rencarex) is a chimeric monoclonal antibody that binds to the CAIX cell-surface antigen present on 95% of ccRCC. Its safety and activity in phase II studies provided the rationale to investigate its use as an adjuvant monotherapy in subjects with clinically localized high-risk ccRCC—50% of whom progress to metastatic disease. Methods: We performed an international, prospective, multicenter, phase III trial of the efficacy and safety of adjuvant cG250 vs placebo (randomized 1:1) by assessing disease-free (DFS) and overall survival (OS) in 864 RCC patients after nephrectomy. Inclusion criteria were: 1) T3/T4 N0/M0; 2) any T stage and N+/M0; or 3) T1b/T2 N0/M0 high-grade ccRCC. Treatment consisted of a 50 mg loading dose followed by 23-weekly infusions of 20 mg. DFS and CAIX antigen expression were quantified by an independent radiological review and a central pathologist. CAIX score was derived by multiplying the intensity of staining (1–3) by the fraction of positive of cells (0–1), yielding a range of 0.0–3.0. Results: Baseline demographics were well balanced across groups. Treatment demonstrated an excellent safety profile. There were 360 confirmed recurrences and 181 deaths during follow up. When compared with the placebo group, cG250-treated subjects did not enjoy a statistically significant DFS (HR=0.99, p=0.74) or OS advantage (HR=1.01, p=0.94). Median DFS and OS were over 6 years and never reached irrespective of treatment, respectively. However, on subset analysis, subjects with high CAIX expression (>2.0) who received cG250 experienced a statistically significant treatment effect with improved DFS (HR=0.55; p=0.01). Conclusions: While cG250 appears not to have clinical benefit in the adjuvant treatment for all high-risk patients, cG250-treated patients with a high CAIX score appeared to have a significantly improved DFS. The CAIX score may help in stratifying patients who may benefit from cG250 adjuvant therapy. Notwithstanding this benefit, the surprising median DFS of over 6 years and outstanding OS in high-risk patients represent a significant challenge to adjuvant ccRCC drug development. Clinical trial information: NCT00087022.
Dielectrophoresis based‐cell patterning for tissue engineering (2006)

Engineering functional tissues and organs in vitro is considered integral to regenerative medicine. Many recent cell patterning technique developments position cells at a pre-designated pattern to improve tissue engineering efficiency and quality and to facilitate 3-D cell-cell interaction exploration. Among these techniques, dielectrophoresis (DEP)-based cell patterning advantageously offers speed, ease of operation, low degree of cell damage, and precision. This article reviews recent advances in DEP-based patterning techniques, including electrode design, suitable buffer and hydrogel, effects of the electric current to cells, combination potential with other techniques, as well as efforts to generate 3-D tissues.
Glomerular Endothelial Cell Injury and Focal Segmental Glomerulosclerosis Lesion in Idiopathic Membranous Nephropathy (2015)

Glomerular capillary injury was seen in all MN cases. Furthermore, the prominent injuries of glomerular capillaries may be associated with the deterioration of eGFR and the formation of FSGS lesions in MN.
Evaluation of solubilized herpes simplex virus membrane antigen by enzyme-linked immunosorbent assay (1983)

An antigen prepared by solubilization of membranes from herpes simplex virus (HSV)-infected cells with deoxycholate was evaluated by enzyme-linked immunosorbent assay. The deoxycholate-solubilized antigen, previously shown to contain all major HSV glycoproteins, was noninfectious and adsorbed easily and reproducibly to a polystyrene surface at pH 9.6. The deoxycholate-solubilized antigen provided an enzyme-linked immunosorbent assay of high sensitivity and reproducibility with complete correlation with complement fixation for the diagnosis of acute HSV infection. The correlation with neutralization and immunofluorescence for the presence or absence of anti-HSV activity was very good. Comparison with an HSV envelope preparation yielded results slightly in favor of the deoxycholate-solubilized antigen. The assay seems to be useful for demonstration of intrathecal production of antibody activity in HSV encephalitis.
Flow Cytometry of Bacteria: a Promising Tool in Experimental and Clinical Microbiology (1983)

The DNA and protein content of individual Escherichia coli cells were measured at a rate of 10(4) cells per second with a sensitive microscope-based flow cytometer. DNA and protein were quantified by measuring the fluorescence from cells stained with a combination of the DNA-binding drugs Mithramycin and ethidium bromide and by scattered light, respectively. Separate experiments demonstrated that the light scatter signal was proportional to protein content. Dual parameter histograms (fluorescence/scattered light) of bacterial cultures gave detailed pictures of changes dependent upon the growth conditions and of the cell cycle kinetics. Effects of antibiotics could be readily detected and characterized after a few hours. The results demonstrate that flow cytometry is a promising method for application in experimental and clinical microbiology.
Experimental study on improved parametric stereo for bit rate scalable audio coding (2014)

This paper presents an experimental study on generalizing Parametric Stereo (PS) technique in an attempt to make it scalable for low and high bit rate implementations which are very useful for various internet services. As specified in the MPEG standard, PS is only intended for applications at a stereo bit rate of 24 kb/s. If operated at higher bit rates, PS would have much worse performance than other audio codecs such as MPEG-1/2 Layer 3 (MP3) and MPEG Advanced Audio Coding (AAC). To improve performance at higher bit rates, the proposed Improved PS transmits residual signal. However, the bit rates of the down-mix and residual signals have to be selected properly to achieve optimal performance. The results of the experiments show that performance of the Improved PS, in terms of objective difference grade (ODG), significantly improves as the bit rate increases. Testing objectively using 5 different critical audio materials, Improved PS consistently outperforms AAC Stereo at a bit rate of 128 kb/s.
Antibody Response To Transfusion With Pyridoxalated Polymerized Hemoglobin Solution (1987)

We evaluated the antigenicity of pyridoxalated polymerized stroma-free human hemoglobin (SFHS-PP) under condition of anticipated emergency use (hemorrhagic shock). SFHS-PP was administered intravenously to two groups of dogs. One group was subjected to hemorrhagic shock (mean arterial pressure 40 torr for 30 min) prior to resuscitation with a volume of SFHS-PP equal to their blood loss. A second group of dogs was infused with 100 ml of SFHS-PP without prior bleeding. Six weeks after the initial infusion, both groups were drawn for antibody assay and reinfused with 100 ml of SFHS-PP. A final bleeding was performed at 10 weeks after primary infusion. Four of five dogs infused after hemorrhagic shock mounted an antibody response which was significantly greater (p < 0.02) than that observed in only two of four dogs in the non-shock group. SFHS-PP is antigenic when infused into normal animals and into animals under conditions which could impair the immune system (hypoperfusion and tissue hypoxia).
Effects of Structural and Energetic Disorders on Charge Transports in Crystal and Amorphous Organic Layers (2018)

Understanding charge transports in organic films is important for both fundamental science and practical applications. Here, contributions of off-diagonal (structural) and diagonal (energetic) disorders to charge transports were clarified using molecular-based multiscale simulation. These disorders, important for understanding charge transport in organic systems, are investigated by comparing crystal and amorphous aggregates of N,N'-diphenyl-N,N'-bis(1-naphthyl)-1,1'-biphenyl-4,4'-diamine (NPD). Although NPD has been used as a hole transport material, it also exhibits comparable electron mobility experimentally. The experimental mobility and its electric field dependence in amorphous layers were reasonably reproduced by the multiscale simulation, confirming the electron transport properties of NPD. We assumed that the structural disorder would lower mobilities; however, the mobilities were found to be independent of the degree of structural disorder. Energetic disorder markedly lowered charge mobility instead. Charge migration in crystals was dominated by maximum electronic coupling pairs, whereas small electronic coupling pairs significantly contributed to charge transport in amorphous aggregate.
Dielectric barrier discharge technique in improving the wettability and adhesion properties of polymer surfaces (2005)

A dielectric barrier discharge (DBD) in helium at atmospheric pressure was used to improve the polymer surface wettability as a first condition for ensuring a good adhesivity in particular for a subsequent immobilization of selected biological macromolecules (heparin, drugs, enzymes, etc.) on these surfaces. The DBD was analyzed by electrical measurements and optical emission spectroscopy. The polymer surface was characterized by thermodynamic parameters which may predict the adhesion properties, the adhesion work and the surface polarity, and also by its morphology. The results show that the DBD treatments improve the wettability and thus the adhesive properties due to the creation of functional groups and less due to a physical adsorption induced by an expected larger area of the treated surfaces. Dimensions of grains/crystallites are decreased on the treated surface, but a significant and systematic modification of the surface roughness was not observed.
The role of α-methylacyl-CoA racemase in bile acid synthesis (2002)

According to current views, the second peroxisomal β-oxidation pathway is responsible for the degradation of the side chain of bile acid intermediates. Peroxisomal multifunctional enzyme type 2 [peroxisomal multifunctional 2-enoyl-CoA hydratase/(R)-3-hydroxyacyl-CoA dehydrogenase; MFE-2] catalyses the second (hydration) and third (dehydrogenation) reactions of the pathway. Deficiency of MFE-2 leads to accumulation of very-long-chain fatty acids, 2-methyl-branched fatty acids and C27 bile acid intermediates in plasma, but bile acid synthesis is not blocked completely. In this study we describe an alternative pathway, which allows MFE-2 deficiency to be overcome. The alternative pathway consists of α-methylacyl-CoA racemase and peroxisomal multifunctional enzyme type 1 [peroxisomal multifunctional 2-enoyl-CoA hydratase/(S)-3-hydroxyacyl-CoA dehydrogenase; MFE-1]. (24E)-3α,7α,12α-Trihydroxy-5β-cholest-24-enoyl-CoA, the presumed physiological isomer, is hydrated by MFE-1 with the formation of (24S,25S)-3α,7α,12α,24-tetrahydroxy-5β-cholestanoyl-CoA [(24S,25S)-24-OH-THCA-CoA], which after conversion by a α-methylacyl-CoA racemase into the (24S,25R) isomer can again be dehydrogenated by MFE-1 to 24-keto-3α,7α,12α-trihydroxycholestanoyl-CoA, a physiological intermediate in cholic acid synthesis. The discovery of the alternative pathway of cholesterol side-chain oxidation will improve diagnosis of peroxisomal deficiencies by identification of serum 24-OH-THCA-CoA diastereomer profiles.