gebhart/patrepeval huggingface dataset:
Prediction of three dimensional structure of bispecific antibodies linked by flexible peptide (2009)

Objective To construct the gene of a bispecific antibodies against red blood cells (RBCs) and HIV-1p24 antigen with different length peptides and simulate the tertiary structure of the bispecific antibodies for confirming the proper formulation of the protein expression. Methods The variable region genes of monoclonal antibodies were respectively amplified using RT-PCR from 3D7 hybridoma cells which secrets monoclonal antibodies against HIV-1p24 antigen. The variable region genes of heavy and light chains were spliced by overlap extension (SOE) PCR to assemble ScFv (ScFv3D7) gene encoding the anti-HIV-1p24 antigen. Based on the sequence,the physical and chemical characteristics and the secondary structure of ScFv3D7 were analyzed by the software of ANTHEPROT5.0. Meanwhile,the tertiary structure prediction of ScFv3D7 was performed by SWISS-MODLE software. On the basis of sequence from ScFv3D7 and ScFv2E8 gene encoding the anti-RBC (red blood cell),which was prepared before,the gene of bispecific antibodies against RBC and HIV-1p24 antigen was constructed by different length peptides to simulate the tertiary structure with SWISS-MODLE software. Results The assembled ScFv3D7 gene consisted of 729 bp,including the sequence of linker peptide (G4S)3. The isoelectric point (pI) and the relative molecular masses of ScFv3D7 encoded 243 amino acids were 5.665 and 26 147.937 Da respectively. The secondary structure analysis of ScFv3D7 showed the different ratio of helix,sheet and turn structures by ANTHEPROT5.0 software. The predicting tertiary structure of ScFv3D7 indicated that it met the antibody structure of immunoglobulin family by SWISS-MODLE. Finally,the bispecific antibodies against RBC and HIV-1p24 antigen was simulated to construct tertiary structure as a integrity molecule by SWISS-MODLE with 75 peptide (G4S)15. Conclusion The bispecific antibodies against RBC and HIV-1p24 antigen linked by flexible peptides with 75 amino acids are confirmed as the proper formulation for the protein expression.
From Visual Attributes to Adjectives through Decompositional Distributional Semantics (2015)

As automated image analysis progresses, there is increasing interest in richer linguistic annotation of pictures, with attributes of objects (e.g., furry, brown…) attracting most attention. By building on the recent “zero-shot learning” approach, and paying attention to the linguistic nature of attributes as noun modifiers, and specifically adjectives, we show that it is possible to tag images with attribute-denoting adjectives even when no training data containing the relevant annotation are available. Our approach relies on two key observations. First, objects can be seen as bundles of attributes, typically expressed as adjectival modifiers (a dog is something furry, brown, etc.), and thus a function trained to map visual representations of objects to nominal labels can implicitly learn to map attributes to adjectives. Second, objects and attributes come together in pictures (the same thing is a dog and it is brown). We can thus achieve better attribute (and object) label retrieval by treating images as “visual phrases”, and decomposing their linguistic representation into an attribute-denoting adjective and an object-denoting noun. Our approach performs comparably to a method exploiting manual attribute annotation, it out-performs various competitive alternatives in both attribute and object annotation, and it automatically constructs attribute-centric representations that significantly improve performance in supervised object recognition.
Resolution analysis in computational imaging with patterned illumination and single-pixel detection (2014)

In computational imaging by pattern projection a sequence of microstructured light patterns codified onto a programmable spatial light modulator is used to sample an object. The patterns are used as generalized measurement modes where the object information is expressed. Our paper makes two specific contributions within the field of single-pixel imaging through patterned illumination. First, we perform an analysis of the optical resolution of the computational image. This resolution is shown not to be limited at all by the optical quality of the collection optics. This result is proved by using a low NA microscope objective for imaging at a CCD camera. Spatial frequencies that are not transmitted through this low quality optics are demonstrated to be present in the retrieved image through patterned illumination. Second, we experimentally demonstrate the capability of our technique to properly recover an image even when an optical diffuser is located in between the sample and the single-pixel detector.
Systematics and distribution of spruce species in the North-West of Russia (2020)

Norway spruce (Picea abies) and Siberian spruce (P. obovata) are among the most important forest-forming coniferous species in the boreal part of Eurasia. Despite numerous publications on the taxonomy of Norway spruce and closely related taxa (P. obovata Ledeb. and P. fennica (Regel) Kom.), the problem of their identification, as well as clarification of their taxonomic status, has not been solved so far. Species delimitation is particularly challenging when P. abies, P. obovata and P. fennica occur in sympatry. Our study aims to assess taxonomic value of proposed earlier and search for stable diagnostic characters of cones and their scales to distinguish Picea abies and its sympatric in the North-West of Russia P. fennica and P. obovata. In addition, we analyzed and updated information on geographical distribution and phytocenotic characteristics of the above-mentioned species in the North-West of the European part of Russia. We examined herbarium specimens and cones sampled from 88 trees from 22 Picea stands located throughout the study region. Each tree was represented on average by 5 cones, in total 415 cones were analyzed. Morphometric analyses included 16 morphological characters of cones and their scales selected based on our own observations and published data. Multivariate comparison had shown a large overlap between P. obovata and P. fennica, while individuals of P. abies formed a separate and less overlapping cluster. Among the six qualitative (discrete) characters, shape of seed scale and shape of its upper margin have non-overlapping frequency distributions and can separate P. abies and P. obovata. Several new diagnostic characters are proposed: morphology and size of bract scales and ratio of the size of seed scales and bract scales. Phytocenotic analysis showed that different spruce taxa occupy specific habitats, which in their turn connected with the latitudinal gradient: in normally drained habitats, Picea obovata is found mainly in poor shrubby-green-mossy forests, which are typical of the northern and middle parts of the Northern taiga; Picea abies – in richer green-mossy habitats (Vaccinioso-hylocomiosum, Oxalidoso-hylocomiosum, Hylocomiosum), which begin to occur already from the middle part of the Northern taiga. Picea fennica occupies both habitats.
Carrier Trapping and Recombination at Point Defects and Dislocations in MOCVD n-GaN (2001)

We present the results of an approach that allows the analysis of grown-in defects in n-GaN grown by metal organic vapor phase epitaxy by relating the presence of various structural defects to the concentration and properties of distinct deep levels. Transmission electron microscopy and electron beam induced current (EBIC) microscopy together with post-growth hydrogenation are used to determine the threading dislocation density (TDD) and observe their local electrical activity. In conjunction, deep level optical and transient spectroscopies (DLOS and DLTS, respectively) are used to detect deep levels, determine their concentration and analyze their carrier trapping kinetics for these films. The comparison of EBIC analysis with trap spectra prior and after hydrogenation establishes a strong correlation between two specific levels, at Ec — Et = 0.58 and 1.35 eV, and recombination centers distributed in the field of the GaN films. Further, EBIC analysis shows that, independent of hydrogenation, TDs behave as strong recombination centers, and indicates that there must be a deep level associated with these regions. A level observed at Ec — 2.64/Ev + 0.87 eV is a good candidate to account for the electrical activity of the TDs because it captures both electrons and holes, which is characteristic of recombination centers. This is supported by DLTS analysis of the trapping kinetics for this level that reveals a behavior characteristic of a linear arrangement of point defects likely found along the TDs.
The Odyssey of Hsp60 from Tumor Cells to Other Destinations Includes Plasma Membrane-Associated Stages and Golgi and Exosomal Protein-Trafficking Modalities (2012)

We propose a multistage process for the translocation of Hsp60 from the inside to the outside of the cell that includes a combination of protein traffic pathways and, ultimately, presence of the chaperonin in the circulating blood. The new information presented should help in designing future strategies for research and for developing diagnostic-monitoring means useful in clinical oncology.
Tightly synchronized two-color femtosecond source based on low-noise SPM-enabled spectral selection (2018)

We demonstrate that SPM-enabled spectral selection generates low noise high-energy wavelength tunable femtosecond pulses that exhibit sub-fs relative timing jitter and therefore are tightly synchronized to the source laser pulse.
Speed-up keypoint mapping technique by multi-resolution and global information (2015)

This work deals with the problem of high computation complexity in image registration. A hierarchical multiresolution strategy is utilized to speed up the processing of SIFT by starting on a low resolution octave. The initial affine transformation model will be achieved. In subsequent multiresolution octaves, we apply the transformation affine model getting from upper octave to current octave, then, combined with geometrical distribution of matched keypoints to further remove incorrect mappings and update affine transformation model. The strategy ends with the best affine transformation model on the bottom octave(full-size image). Experimental results show that the proposed method can achieve comparative accuracy with less computational than original SIFT
The Structure of the Pteridine Glycoside from Aspergillus oryzae (1972)

Abstract The structures of two blue-fluorescent substances, asperopterfn-A and -B, isolated from Aspergillus oryzae were investigated. Asperopterin-B was identified as 2-amino-3,4,7,8-tetrahydro-6-hydroxymethyl-8-methyl-4,7-dioxopteridine (7) by studying its chemical degradation, pKα values, and UV spectra; the structure was confirmed by synthesis. Asperopterin-A was shown to be the β-d-ribofuranoside of 7, 2-amino-3,4,7,8-tetrahydro-8-methyl-4,7-dioxo-6-pteridinylmethyl β-d-ribofuranoside (10).
Connecting Biomass and Petroleum Processing with a Chemical Bridge (2010)

Biomass-derived sugars can be converted to fuels via conventional petrochemical processing.
An Interactive Simulation to Change Outcome Expectancies and Intentions in Adults With Type 2 Diabetes: Within-Subjects Experiment (2018)

A novel interactive simulation is efficacious in changing the outcome expectancies and behavioral intentions of adults with T2DM. We discuss applications of our results to the design of mobile health (mHealth) interventions.
The role of ezrin-associated protein network in human sperm capacitation (2010)

在精子房间的膜修正在精子 capacitation 代表关键步；然而，这些修正的分子的基础充分没被理解。Ezrin 是 ezrin/radixin/merlin 家庭的学习最好的成员。作为在外皮的细胞骨架和血浆膜蛋白质之间的 cross-linker， ezrin 贡献膜表面结构改变。而且，激活 ezrin 和 Rho 分离禁止者， RhoGDI，通过 Rho 激活支持外皮的 cytoskeleton-polymerized 肌动朊的形成。因此， ezrin，肌动朊， RhoGDI， Rho 和血浆膜蛋白质在 vivo 形成一个复杂网络，它贡献膜表面的结构的集会。以前，我们证明 ezrin 和 RhoGDI1 在人的睾丸被表示。因此，我们寻求了决定 ezrin 鈥揜h oGDI1 鈥揳c 听鈥搈e mbrane 蛋白质网络是否在人的精子 capacitation 有一个角色。我们由西方的污点的结果显示 ezrin 被 threonine567 残余的 phosphorylation 在 capacitation 期间激活。Co-immunoprecipitation 研究表明在精子 capacitation 期间，在 ezrin 和 RhoGDI1 之间的相互作用增加，并且二维的电气泳动胶化的 phosphostaining 证明 RhoGDI1 是 phosphorylated，建议 RhoGDI1 从 RhoA 分裂并且导致精子头上的肌动朊聚合。我们推测那激活的 ezrin 在 capacitation 以后与 polymerized 肌动朊和 glycosylated 膜蛋白质 cd44 交往。用 ezrin 特定或肌动朊特定的 monoclonal 抗体堵住精子 capacitation 减少他们的 acrosome 反应(AR ) 率，但是没独自在 AR 上有效果。一起拿，我们的结果证明由 ezrin， RhoGDI1， RhoA， F 肌动朊和膜蛋白质组成的一个网络工作影响在人的精子 capacitation 期间发生在精子头的膜上的修正。
Fluorimetric Assay of Enzymes (1969)

This chapter contains sections titled: Introduction Instrumentation Principles of Assay Assay of Coenzymes Assay of Oxidoreductases Assay of Transferases Assay of Hydrolases Lyases Miscellaneous Enzymes
Wheat Rusts: An Atlas of Resistance Genes (1995)

We determined whether the participation rate for a brush-based cervicovaginal self-sampling device is noninferior to the participation rate for a lavage-based one for testing for hrHPV (high-risk human papillomavirus). Additionally, positivity rates for hrHPV, the detection rates for cervical intraepithelial neoplasia grades 2 and 3 or worse (CIN2+/3+), and user comfort were compared. A total of 35,477 non-responders of the regular cervical screening program aged 33-63 years were invited to participate. Eligible women (n = 30,130) were randomly assigned to receive either a brush-based or a lavage-based device, and a questionnaire for reporting user convenience. Self-sampling responders testing hrHPV-positive were invited for a physician-taken sample for cytology; triage-positive women were referred for colposcopy. A total of 5,218 women participated in the brush-based sampling group (34.6%) and 4809 women in the lavage-based group (31.9%), i.e. an absolute difference of 2.7% (95%CI 1.8-4.2). The hrHPV-positivity rates in the two groups were identical (8.3%, relative risk (RR) 0.99, 95%CI 0.87-1.13). The detection of CIN2+ and CIN3+ in the brush group (2.0% for CIN2+; 1.3% for CIN3+) was similar to that in the lavage group (1.9% for CIN2+; 1.0% for CIN3+) with a cumulative RR of 1.01, 95%CI 0.83-1.24 for CIN2+ and 1.25, 95%CI 0.92-1.70 for CIN3+. The two self-sampling devices performed similarly in user comfort. In conclusion, offering a brush-based device to non-responders is noninferior to offering a lavage-based device in terms of participation. The two self-sampling methods are equally effective in detecting hrHPV, CIN2+/CIN3+ and are both well accepted.
A Newly Described, Highly Prevalent Arterial Pedicle Perfuses Both Gracilis and Profunda Artery Perforator Flap Tissues: An Angiographic Study of the Medial Thigh (2019)

Existence of a single-arterial pedicle to both the gracilis muscle and PAP flap tissues is frequently present in most patients in at least one lower extremity. This chimeric flap configuration could serve as a reconstructive avenue for patients, particularly those who have exhausted other more common flap options. Screening angiography is warranted in patients looking for this anatomic variation to establish its presence.
Response to: Causes of visual disability among Central Africans with diabetes mellitus (2013)

Dear Editor,

I read with great interest the article by Mvitu and Longo-Mbenza that appeared in a recent issue of African Heath Sciences.1 In that paper, the authors were interested in determining whether diabetes is an independent and significant determinant of visual disability. I commend them for performing this study. However a closer look at Figure 1 indicates a steady increase in the rate of visual disability by more than 10% per decade. On the contrary Figure 2 shows that the rate of disability sharply decreases by more than 20% and remains unchanged over time after the disease has lasted 5 years. While Figure 1 is understandable, the message conveyed by Figure 2 is surprising and questionable. Indeed, visual impairment has repeatedly been shown to be associated with longer duration of diabetes, which together with poor diet, uncontrolled diabetes, and other factors increases the risk of diabetic retinopathy. Since this was a hospital-based study, it would have been informative to provide the readers with the number of subjects who had access to laser, subjects who were taking insulin or other drugs vs. untreated, subjects who had controlled glycemia vs. uncontrolled. Additionally, age-related macular degeneration is underreported in sub-Saharan Africa partly due to the lack of imaging modalities that may assist clinicians in the diagnosis. Assuming that long-lasting diabetes did not increase the rate of visual disability over time, once would expect Figure 2 to display a trend toward increase in the rate of disability as a result of other factors such as age-related macular degeneration, cataract, and glaucoma. Not including these age-related causes of visual loss in the multivariate analysis may have affected the outcome. I am pondering the clinical implications of this finding and seek further clarification from the authors.

Sincerely,


Dr. Mwanza Jean Claude
Gas chromatographic/mass spectroscopy analysis of mutagenic extracts of aqueous chlorinated humic acid. A comparison of the byproducts to drinking water contaminants (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGas chromatographic/mass spectroscopy analysis of mutagenic extracts of aqueous chlorinated humic acid. A comparison of the byproducts to drinking water contaminantsW. Emile. Coleman, Jean W. Munch, William H. Kaylor, Robert P. Streicher, H. Paul. Ringhand, and John R. MeierCite this: Environ. Sci. Technol. 1984, 18, 9, 674–681Publication Date (Print):September 1, 1984Publication History Published online1 May 2002Published inissue 1 September 1984https://pubs.acs.org/doi/10.1021/es00127a008https://doi.org/10.1021/es00127a008research-articleACS PublicationsRequest reuse permissionsArticle Views376Altmetric-Citations104LEARN 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
A novel assembly process of the multicomponent xenobiotic efflux pump in Pseudomonas aeruginosa (2002)

The nfxC-type cells of Pseudomonas aeruginosa show resistance to a wide range of structurally and functionally diverse antibiotics, which is a phenomenon that is mainly attributable to the expression of the MexEF-OprN xenobiotic transporter. The MexF, MexE and OprN subunits of this transporter are located on the inner membrane, the periplasm and the outer membrane, respectively, and are assumed to function as an energy-dependent transporter, a bridge connecting the inner and outer membranes and outer membrane channel respectively. The nfxC-type cells showed a single protein band of MexF and OprN, whereas MexE appeared as three distinct bands in an SDS-polyacrylamide gel electrophoretogram. The mutant cells lacking MexF produced undetectable OprN and only a full-size of MexE even though the cells had unimpaired oprN and mexE. Expression of the plasmid-borne MexF in this mutant fully restored OprN and three MexE bands. Another class of mutants producing a full amount of MexF yielded undetectable OprN and two MexE bands lacking the smallest protein species suggesting that the presence of the smallest MexE subunit is required for stabilization of OprN. To identify which part of MexE was needed for stabilization and assembly of OprN, the carboxyl-terminal-truncated MexE tagged with polyhistidine was constructed and protein bands were visualized in the presence of MexF with an antibody raised against polyhistidine or MexE. The results revealed that the proteolytic processing of MexE would occur at carboxyl terminal amino acids between 11 and 16, thereby suggesting that the presence of the C-terminal truncated MexE is essential for stabilization and the proper assembly of OprN. Nucleotide sequencing of mutant mexFs, which produce a wild-type level of MexF but are unable to support the production of the smallest MexE, thereby destabilizing OprN, revealed that all the mutations were located within two large periplasmic domains of MexF between transmembrane segments 1-2 and 7-8. Taking these findings together, we concluded that two large periplasmic domains of MexF interact with MexE thereby promoting programmed processing of MexE, and this complex eventually assists the correct assembly and sorting of OprN.
Design considerations and effects of class-AB polarization in active filters realized by means of active inductors (2017)

Class-AB polarization is usually missing in active filters. An innovative design solution is here described with circuitry details and deeply analyzed. It is based on the use of an active inductor realized with a single active device in class-AB polarization, allowing to achieve at the same time a minimum power consumption and a wide dynamic range. The performance that have been obtained with a hybrid prototype are fully investigated, showing the capability of the proposed solution to be adopted as integrated solution and commercial applications. The match between simulations and measurements is also promising.
Radiosynthesis and initial evaluation of [18F]FSPTAD as new tyrosine-specific prosthetic group for radiofluorination of biomolecules (2014)

158 Objectives The aim of this study was to develop a new F-18 prostatic group for rapid and efficient method specific for tyrosine containing peptides and proteins. A novel fluoride-18 prosthetic ligand, 4-(p-([18F]fluorosulfonyl)phenyl)-1,2,4-triazoline-3,5-dione ([18F]FSPTAD), for site-specific labeling of tyrosine residue in small molecules, peptides and proteins was developed. [18F]FSPTAD reacts efficiently and selectively with phenol derivatives such as tyrosine side chain through an ene-like reaction for radiolabeling of proteins for use in positron emission tomography (PET). Methods An innovative simple procedure to obtain radiofluorinated sulfonyl fluoride by avoiding time-consuming azeotropic drying was applied. The radiosynthesis of [18F]FSPTAD was performed in two steps at room temperature using different solvent (i-PrOH, THF, and MeCN). N-Acetyl-L-tyrosine ethyl ester and small peptide (Tyr-CO-Glu, TUG) were used as model compounds for coupling. [18F]FSPTAD was conjugated with the model compounds under mild aqueous reaction at room temperature and the obtained radiopharmaceuticals were tested for their affinity in human cancer cell lines. Results [18F]FSPTAD was obtained in 85±2.7% RCY using MeCN at room temperature and a reaction time of 15 min. DBDMH was used as oxidant to yield [18F]FSPTAD in 5 min in quantitative yield. The coupling of [18F]FSPTAD with N-acetyl-L-tyrosine ethyl ester and TUG was achieved in a buffered aqueous solution at room temperature for 5-10 min to give 45±5.6% and 62±4.3% radiochemical yield, respectively. In addition, [18F]FSTPAD-Ty-OH and [18F]FSTPAD-TUG presented tumour affinity. Conclusions An efficient method for the preparation of new fluoride-18 prosthetic ligand ([18F]FSPTAD) was developed. Moreover, the mild aqueous reaction shows promising radio-conjugation of broad tyrosine containing biomolecules such as small molecules, peptides and proteins.