gebhart/patrepeval huggingface dataset:
A Mutation in the Lactose Permease of Escherichia coli That Decreases Conformational Flexibility and Increases Protein Stability (2003)

Lactose permease with Cys154 --> Gly (helix V) binds substrate with high affinity but catalyzes little or no transport. The purified, detergent-solubilized mutant protein exhibits much greater thermal stability than the wild type and little tendency to aggregate. Stabilization is also observed in vivo with an unstable mutant that is expressed at significantly higher levels when the Cys154 --> Gly mutation is introduced. In addition, ligand-induced conformational changes are markedly reduced or abolished by the Cys154 --> Gly mutation: (i) Although the fluorescence of purified single Trp33 (helix I) permease is enhanced by ligand binding, introduction of the Cys154 --> Gly mutation abolishes the effect. (ii) The rate of 2-(4'-maleimidylanilino)naphthalene-6-sulfonic acid (MIANS) labeling of permease with a single Cys residue in place of Val331 (helix X) is increased in the presence of ligand but reduced when the Cys154 --> Gly mutation is present. (iii) Fluorescence emission intensity of MIANS-labeled single Cys331 permease is enhanced and blue shifted in the Cys154 --> Gly mutant background, indicating that the latter mutation causes position 331 to become exposed to a less polar environment. The results indicate that the Cys154 --> Gly mutation causes a more compact structure and decreased conformational flexibility, an alteration that specifically blocks the structural changes necessary for substrate translocation with little or no effect on ligand binding.
The effects of intramolecular H‐bond formation on the stability constant and water exchange rate of the Gd(III)‐diethylenetriamine‐N′‐(3‐amino‐1,1‐propylenephosphonic)‐N, N,N″,N″‐tetraacetate complex (2007)

The binding interaction of metal chelates to biological macromolecules, though driven by properly devoted recognition synthons, may cause dramatic changes in some property associated with the coordination cage such as the thermodynamic stability or the exchange rate of the metal coordinated water. Such changes are due to electrostatic and H-bonding interactions involving atoms of the coordination cage and atoms of the biological molecule at the binding site. To mimic this type of H-bonding interactions, lanthanide(III) complexes with a DTPA-monophosphonate ligand bearing a propylamino moiety (H6NP-DTPA) were synthesized. Their thermodynamic stabilities and the exchange lifetime of the coordinated water molecule (for the Gd-complex) were compared with those of the analog complexes with DTPA and the parent DTPA-monophosphonate derivative (H6P-DTPA). It was found that the intramolecular H-bond between the epsilon-amino group and the phosphonate moiety in NP-DTPA complexes causes displacements of electric charges in their coordination cage that are markedly pH dependent. In turn, this affects the characteristic properties of the coordination cage. In particular it results in a marked elongation of the exchange lifetime of the coordinated water molecule.
Interference rejection in impulsive noise for VLF communications (2003)

The use of frequency-shift (FRESH) filtering for the rejection of adjacent channel interference (ACI) in GMSK modulated VLF communications is investigated in the presence of impulsive noise. The effects of such filtering in conjunction with a simple "hole-punching" technique for removing impulses from the signal are characterised. A range of realistic scenarios based on a high powered GMSK interferer (10 to 30 dB greater than the signal of interest (SOI)) in an adjacent channel are described. It is known that in the presence of interference and Gaussian noise a simple FRESH filter, which exploits the cyclostationarity of the interferer, is highly effective at removing the interference. We show that when non-Gaussian impulsive noise is present, the FRESH filter is still effective against interference, even when the two signals have cyclic frequencies in common. However if hole-punching is used to remove the larger impulses of the noise, this adversely affects the performance of the FRESH filter.
Evidence for Fast Electron Transfer between the High-Spin Haems in Cytochrome bd-I from Escherichia coli (2016)

Cytochrome bd-I is one of the three proton motive force-generating quinol oxidases in the O2-dependent respiratory chain of Escherichia coli. It contains one low-spin haem (b558) and the two high-spin haems (b595 and d) as the redox-active cofactors. In order to examine the flash-induced intraprotein reverse electron transfer (the so-called ''electron backflow''), CO was photolyzed from the ferrous haem d in one-electron reduced (b5583+b5953+d2+-CO) cytochrome bd-I, and the fully reduced (b5582+b5952+d2+-CO) oxidase as a control. In contrast to the fully reduced cytochrome bd-I, the transient spectrum of one-electron reduced oxidase at a delay time of 1.5 μs is clearly different from that at a delay time of 200 ns. The difference between the two spectra can be modeled as the electron transfer from haem d to haem b595 in 3-4% of the cytochrome bd-I population. Thus, the interhaem electron backflow reaction induced by photodissociation of CO from haem d in one-electron reduced cytochrome bd-I comprises two kinetically different phases: the previously unnoticed fast electron transfer from haem d to haem b595 within 0.2-1.5 μs and the slower well-defined electron equilibration with τ ~16 μs. The major new finding of this work is the lack of electron transfer at 200 ns.
pH localization: a case study during electrophoretic deposition of ternary MAX phase carbide-Ti<sub>3</sub>SiC<sub>2</sub> (2013)

The pH localization phenomenon during electrophoretic deposition (EPD) of the MAX phase-Titanium silicon carbide (Ti3SiC2), from suspension in aqueous and mixed (water-ethanol) solvent was experimentally verified in presence of a cationic dispersant, polyethyleneimine (PEI). The local pHs at the electrodes were dependent on solid loadings of the suspensions; pH localization was pronounced at lower solid loading. Higher solid loading resulted in thicker deposits, shielding the electrode surface and hindering direct interaction of the electrode with the particles, thereby suppressing the change in local pH. Comparison of local pH at cathode during EPD from aqueous and mixed solvent revealed a delay in the attainment of isoelectric point (IEP) at the vicinity of electrode and slower deposition rate for mixed solvent. A necessity of concurrence between the IEP of the material and the local pH at the deposition electrode for a given system was established for the formation of good deposits.
Curriculum Design for Machine Learners in Sequential Decision Tasks (2018)

Existing work in machine learning has shown that algorithms can benefit from the use of curricula-learning first on simple examples before moving to more difficult problems. This work studies the curriculum-design problem in the context of sequential decision tasks, analyzing how different curricula affect learning in a Sokoban-like domain, and presenting the results of a user study that explores whether nonexperts generate effective curricula. Our results show that 1) the way in which evaluative feedback is given to the agent as it learns individual tasks does not affect the relative quality of different curricula, 2) nonexpert users can successfully design curricula that result in better overall performance than having the agent learn from scratch, and 3) nonexpert users can discover and follow salient principles when selecting tasks in a curriculum. We also demonstrate that our curriculum-learning algorithm can be improved by incorporating the principles people use when designing curricula. This work gives us insights into the development of new machine-learning algorithms and interfaces that can better accommodate machineor human-created curricula.
Twi-difference algorithm for video's abrupt shot change detection (2003)

The first step of video retrieval is the shot change detection, which segments a video into temporal shots and makes the retrieval possible. A new effective algorithm for video's abrupt shot change detection, called twi-difference algorithm, is proposed in the paper. This method eliminates the influence of video movement on the abrupt shot change detection and improves the detecting performance greatly without additional computational cost. And it is based on the property of the inter-frame difference of the frames at the video movement, and is sequence-independent. Experiments show that the twi-difference algorithm outperforms the inter-frame difference algorithm greatly, and the pixel-matching twi-difference algorithm realizes the no-missing detection with close-to-zero or few false detection for the abrupt shot change.
Mapping accessible chromatin regions using Sono-Seq (2009)

Disruptions in local chromatin structure often indicate features of biological interest such as regulatory regions. We find that sonication of cross-linked chromatin, when combined with a size-selection step and massively parallel short-read sequencing, can be used as a method (Sono-Seq) to map locations of high chromatin accessibility in promoter regions. Sono-Seq sites frequently correspond to actively transcribed promoter regions, as evidenced by their co-association with RNA Polymerase II ChIP regions, transcription start sites, histone H3 lysine 4 trimethylation (H3K4me3) marks, and CpG islands; signals over other sites, such as those bound by the CTCF insulator, are also observed. The pattern of breakage by Sono-Seq overlaps with, but is distinct from, that observed for FAIRE and DNase I hypersensitive sites. Our results demonstrate that Sono-Seq can be a useful and simple method by which to map many local alterations in chromatin structure. Furthermore, our results provide insights into the mapping of binding sites by using ChIP-Seq experiments and the value of reference samples that should be used in such experiments.
Cholesterol crystals rupture biological membranes and human plaques during acute cardiovascular events‐a novel insight into plaque rupture by scanning electron microscopy (2006)

Plaque rupture and/or erosion are considered the leading cause of cardiovascular events. To elucidate this process, we demonstrated that during cholesterol crystallization the occupied volume increases rapidly and sharp-tipped crystals cut through thin biological membranes in their path. The amount of cholesterol correlated directly with both peak level and rate of crystal growth (r = 0.98; r = 0.99; p < 0.01, respectively). These observations suggest that crystallization of cholesterol in atherosclerotic plaques can induce cap rupture and/or erosion. Observations by scanning electron microscopy confirmed similar findings of cholesterol crystals perforating the lumen surface in human coronary artery segments with ruptured plaque.
The plasmid profile of Edwardsiellaictaluri* (1987)

Abstract. The plasmid content of 18 isolates of Edwardsiella ictaluri found in channel catfish was analysed by agarose gel electrophoresis. Each isolate contained an identical set of plasmids. This set consisted of two prominent plasmids of 5.2 and 4.4 kilobase pairs, and three smaller and less apparent plasmids. One plasmid (the 5.2 kilobase plasmid) was radiolabelled and used to probe a blot of DNA from all isolates. All plasmids were hybridized but no chromosomal DNA was labelled. These plasmids must share some homologous regions. DNAs from other bacteria, including the related Edwardsiella tarda , were also probed and no hybridization was seen. It is suggested that a plasmid probe may be a sensitive, specific probe for detection of E. ictaluri in channel catfish
Biological Effects and Antitumor Activity Induced by Benzocaine Conjugated Anionic Polymers (2002)

Three maleic anhydride copolymers [poly(maleic anhydride-vinyl acetate), poly(maleic anhydride-styrene) and poly(maleic anhydride-methyl methacrylate)] were prepared as well as the corresponding benzocaine conjugates. The maleic anhydride moiety was hydrolyzed to the corresponding polycarboxylate anions and then biologically evaluated using pyran copolymer as the standard. All of the polymers showed internal organ toxicity of the liver, kidneys and spleen which increased with increasing molecular weight, however, the benzocaine derivatives decreased this effect in most cases. The biological evaluations included hemoglobin levels, hematocrit levels, red blood indices and mean cell volumes which were increased on an average of 50%. The blood protein profiles were not changes significantly; on average they were changed about ±50%. The unmodified copolymers decreased the major serum and cholesterol levels by ∼75%. The copolymers (with or without) benzocaine decreased both the blood sugar and enzyme profiles. The antitumour activity was evaluated against Walker carcinosarconoma; although the benzocaine enhanced these effects, only pyran and the 18,000 Mw benzocaine-modified poly(maleic anhydride-vinyl acetate) produced significant effects.
Using an Ensemble of Incrementally Fine-Tuned CNNs for Cross-Domain Object Category Recognition (2019)

When the training data is inadequate, it is difficult to train a deep Convolutional Neural Network (CNN) from scratch with randomized initial weights. Instead, it is common to train a source CNN model on a very large data set beforehand, and then use the learned source CNN model as an initialization to train a target CNN model. In deep learning realm, this procedure is called fine-tuning a CNN. This paper presents an experimental study on how to combine a collection of incrementally fine-tuned CNN models for cross-domain and multi-class object category recognition tasks. A group of fine-tuned CNN models is trained on the target data set by incrementally transferring parameters from a source CNN model trained on a large data set initially. The last two fully-connected (FC) layers of the source CNN model are eliminated, and two New FC layers are added to make the learned new CNN model suitable for the target task. Based on Caltech-101 and Office data sets, the experimental results demonstrate the effectiveness and good performance of the proposed methods. The proposed method is more suitable for the object recognition task when there is inadequate target training data.
Mouse acute leukemia develops independent of self-renewal and differentiation potentials in hematopoietic stem and progenitor cells (2019)

The cell of origin, defined as the normal cell in which the transformation event first occurs, is poorly identified in leukemia, despite its importance in understanding of leukemogenesis and improving leukemia therapy. Although hematopoietic stem cells (HSCs) and hematopoietic progenitor cells (HPCs) were used for leukemia models, whether their self-renewal and differentiation potentials influence the initiation and development of leukemia is largely unknown. In this study, the self-renewal and differentiation potentials in 2 distinct types of HSCs (HSC1 [CD150<sup>+</sup>CD41<sup>-</sup>CD34<sup>-</sup>Lineage<sup>-</sup>Sca-1<sup>+</sup>c-Kit<sup>+</sup> cells] and HSC2 [CD150<sup>-</sup>CD41<sup>-</sup>CD34<sup>-</sup>Lineage<sup>-</sup>Sca-1<sup>+</sup>c-Kit<sup>+</sup> cells]) and 3 distinct types of HPCs (HPC1 [CD150<sup>+</sup>CD41<sup>+</sup>CD34<sup>-</sup>Lineage<sup>-</sup>Sca-1<sup>+</sup>c-Kit<sup>+</sup> cells], HPC2 [CD150<sup>+</sup>CD41<sup>+</sup>CD34<sup>+</sup>Lineage<sup>-</sup>Sca-1<sup>+</sup>c-Kit<sup>+</sup> cells], and HPC3 [CD150<sup>-</sup>CD41<sup>-</sup>CD34<sup>+</sup>Lineage<sup>-</sup>Sca-1<sup>+</sup>c-Kit<sup>+</sup> cells]) were isolated from adult mouse bone marrow, and examined by competitive repopulation assay. Then, cells from each population were retrovirally transduced to initiate MLL-AF9 acute myelogenous leukemia (AML) and the intracellular domain of NOTCH-1 T-cell acute lymphoblastic leukemia (T-ALL). AML and T-ALL similarly developed from all HSC and HPC populations, suggesting multiple cellular origins of leukemia. New leukemic stem cells (LSCs) were also identified in these AML and T-ALL models. Notably, switching between immunophenotypical immature and mature LSCs was observed, suggesting that heterogeneous LSCs play a role in the expansion and maintenance of leukemia. Based on this mouse model study, we propose that acute leukemia arises from multiple cells of origin independent of the self-renewal and differentiation potentials in hematopoietic stem and progenitor cells and is amplified by LSC switchover.
Supplementary Figure 1B from A Systematic Review of p53 as a Prognostic Factor of Survival in Squamous Cell Carcinoma of the Four Main Anatomical Subsites of the Head and Neck (2023)

Supplementary Figure 1B from A Systematic Review of p53 as a Prognostic Factor of Survival in Squamous Cell Carcinoma of the Four Main Anatomical Subsites of the Head and Neck
Novel fibre optic sensors for monitoring corrosion-related properties of concrete (2006)

The monitoring of a number of parameters which are indicative of the corrosion of concrete structures is very important to ensure the structural health of the major civil engineering infrastructure. This paper reports on a suite of novel sensors developed to improve monitoring through determining temperature, pH, strain and moisture level, demonstrated through laboratory tests and extensive evaluations of the durability and sensitivity of the sensors themselves.
Distinct patient responses to activation of T-cells by free HER-2, G89 (777-789) and protected LRMK-linked HER-2, {AE-39 [p776 (Ava-774-788)], AE-47 [(Ava-776-788)] and AE-37[p776 (774-788)]} peptides could lead to development of personalized cancer vaccines. (2009)

The objective of this study was to find whether the peptide LRMK linked to the N-terminus of HER-2, 774-788 and shorter peptides create a T helper antigen, which can replace all functional HER-2 peptides in a cancer vaccine. Of the 6 LRMK-HER-2 peptides tested in the presence of IL-12, AE-37, AE-38 and AE-39 induced higher IFN-gamma in PBMCs from 4 healthy donors than the other peptides. AE-37 and AE-39 contained the immunogenic HER-2 peptide, p776 (774-788), while AE-38 contained the truncated HER-2 peptide G89 (777-788). The free, unprotected HER-2 peptide G89 (777-789) activated IFN-gamma production in PBMCs from another BRC patient. Responses to free p776 and F7 could not be tested. Three out of 11 patients responded strongly only to AE-37, while 3 of 10 patients responded strongly only to G89. One responded only to AE-39. All 3 patients diagnosed with DICS of mixed HER(hi), ER+ PR+ type responded to AE-37. Three out of 4 patients diagnosed with luminal cancer and one HERhi, ER- PR- BRC patient responded only to G89. AE-37, at low concentration, helped to expand more E75-TCR(Hi+Med) cells than the negative control AE-47, for IFN-gamma induction AE-47, but was a weaker helper than AE-47 at higher concentrations, and eliminated E75-TCR(Hi) cells. The strongest and most consistent effect of AE-37 was the elimination of CD4(Hi) CD25(Hi) cells. When LRMK is linked to AE-37, the side-chains of L(P-10) and R(P-9) are positioned away from MHC; LRMK forms a bi-strophynx (rotating-double-hook-like) structure when attached to AE-37 and the minimum HER-2 peptide in the peptide-binding groove (PBG). K(P-8) anchors the bi-strophynx to HLA-DR outside the PBG in a novel site DRalpha, 49-52. The HER-2 amino acids, Y(P-1) and R(P3) point towards TCR; R(P-9) and M(P-8) can contact the TCRValpha1. The positions of K(P-8) in AE-37 and Ava (epsilonV)(P-8) in AE-39 modulated immunogenicity of p776. It is unknown whether LRMK adds TCR contact points to the minimal HLA-DR-bound HER-2 peptide (780-788) or activates T-cells of other specificities to produce cytokines and die. Preferential activation of Th1 cells in distinct individuals by AE-37, G89 and AE-39 indicates that cancer vaccines will benefit from correct individual and disease-associated help. Emergence of distinct daughters of luminal and myoepithelial BRC stem cells during metastasis through "de-differentiation" and "reverse differentiation" of drug-resistant cancer requires personalized vaccines, which use an optimal-helper antigen.
Front2Back: Single View 3D Shape Reconstruction via Front to Back Prediction (2020)

Reconstruction of a 3D shape from a single 2D image is a classical computer vision problem, whose difficulty stems from the inherent ambiguity of recovering occluded or only partially observed surfaces. Recent methods address this challenge through the use of largely unstructured neural networks that effectively distill conditional mapping and priors over 3D shape. In this work, we induce structure and geometric constraints by leveraging three core observations: (1) the surface of most everyday objects is often almost entirely exposed from pairs of typical opposite views; (2) everyday objects often exhibit global reflective symmetries which can be accurately predicted from single views; (3) opposite orthographic views of a 3D shape share consistent silhouettes. Following these observations, we first predict orthographic 2.5D visible surface maps (depth, normal and silhouette) from perspective 2D images, and detect global reflective symmetries in this data; second, we predict the back facing depth and normal maps using as input the front maps and, when available, the symmetric reflections of these maps; and finally, we reconstruct a 3D mesh from the union of these maps using a surface reconstruction method best suited for this data. Our experiments demonstrate that our framework outperforms state-of-the art approaches for 3D shape reconstructions from 2D and 2.5D data in terms of input fidelity and details preservation. Specifically, we achieve 12% better performance on average in ShapeNet benchmark dataset, and up to 19% for certain classes of objects (e.g., chairs and vessels).
Haptoglobin Phenotyping of Bloodstains by Nongradient Polyacrylamide Electrophoresis (1977)

Abstract Haptoglobin is a plasma glycoprotein with α2: electrophoretic mobility which plays a role in hemoglobin catabolism. It is of interest to the forensic scientist because it exhibits polymorphism. The three most common phenotypes are designated Hp 2-1 (the heterozygous state), Hp 2-2, and Hp 1-1.
Patients with Rheumatoid Arthritis in Clinical Remission Manifest Persistent Joint Inflammation on Histology and Imaging Studies (2014)

Despite clinical remission, histology and imaging studies documented a persistently active disease state that may explain the mechanism for radiographic progression.
Another Example of the Novel Conversion of a Phosphonate to a Phosphate (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnother Example of the Novel Conversion of a Phosphonate to a PhosphateB. H. Alexander, L. S. Hafner, M. V. Garrison, and J. E. BrownCite this: J. Org. Chem. 1963, 28, 12, 3499–3501Publication Date (Print):December 1, 1963Publication History Published online1 May 2002Published inissue 1 December 1963https://pubs.acs.org/doi/10.1021/jo01047a055https://doi.org/10.1021/jo01047a055research-articleACS PublicationsRequest reuse permissionsArticle Views132Altmetric-Citations3LEARN 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