gebhart/patrepeval huggingface dataset:
The Free Energy Landscape of Internucleosome Interactions and Its Relation to Chromatin Fiber Structure (2019)

The supramolecular chromatin fiber is governed by molecular scale energetics and interactions. Such energetics originate from the fiber's building block, the nucleosome core particle (NCP). In recent years, the chromatin fiber has been examined through perturbative methods in attempts to extract the energetics of nucleosome association in the fiber. This body of work has led to different results from experiments and simulations concerning the nucleosome-nucleosome energetics. Here, we expand on previous experiments and use coarse-grained simulations to evaluate the energetics inherent to nucleosomes across a variety of parameters in configurational and environmental space. Through this effort, we are able to uncover molecular processes that are critical to understanding the 30 nm chromatin fiber structure. In particular, we describe the NCP-NCP interactions by relying on an anisotropic energetic landscape, rather than a single potential energy value. The attractions in that landscape arise predominantly from the highly anisotropic interactions provided by the NCP histone N-terminal domain (NTD) tails. Our results are found to be in good agreement with recent nucleosome interaction experiments that suggest a maximum interaction energy of 2.69<i>k</i> <sub>B</sub> <i>T</i>. Furthermore, we examine the influence of crucial epigenetic modifications, such as acetylation of the H4 tail, and how they modify the underlying landscape. Our results for acetylated NCP interactions are also in agreement with experiment. We additionally find an induced chirality in NCP-NCP interactions upon acetylation that reduces interactions which would correspond to a left-handed superhelical chromatin fiber.
Identification of multiple informative genomic mutations by deep sequencing of circulating cell-free tumor DNA in plasma of metastatic melanoma patients. (2014)

9018 Background: We have been assesseing the prognostic utility of genomic changes in circulating cell-free DNA(cfDNA) in melanoma patients. The limitation has been assessing a few selected genomic targets and sensitivity. The approach of cfDNA analysis in melanoma patients offers detection of potential targeted tumor-related genes mutation(mt) without tumor biopsy. Methods: AJCC stage IV melanoma patients (n=18; different metastasis sites) plasma and paired metastatic tumor tissues resected after blood draw were assessed. The assay was performed on 2 ml filtered plasma. We employed Guardant360, a single-molecule digital sequencing assay that enables detection of rare genomic abnormalities with ultra high-specificity and sensitivity. Using bioinformatics and single molecule sensitivity, rare variants could be detected in cfDNA. Results: In an initial 8 patients, BRAF and TP53 in tumor genomic DNA were sequenced. We found ctDNA with somatic mt in 6/8 matched tumor and plasma specimens(mt allele frequency of 0.2-23.1%) with an overall concordance of 86% for the status of BRAF and TP53 mt in a single bleed. To note known BRAFmt at multiple exons were detectable. Subsequently, matched tumor and plasma from 10 patients were analyzed. We found ctDNA mt in 8/10 cases (mt allele frequency of 0.1-19.1%). Well known frequent melanoma-related mt were detected in patients cfDNA(BRAF, TP53). Other known tumor mt were also detected(CDKN2A, NRAS, PTEN, NOTCH1, EGFR, JAK2) that have not been reported. We established the overall concordance of cfDNA mt with metastatic melanomas across all 54 genes and 80kbps to be 49% whereby, individual single gene concordance were significantly much higher. Conclusions: This ongoing study demonstrates that using Guardant360, cfDNA mt can be detected that match with paired melanomas. The approach offers a more comprehensive approach of monitoring metastatic melanoma patients’ blood for multiple mt during tumor progression. This unique approach will allow for much more comprehensive blood tumor genetic profiling to provide better treatment decision and monitoring for multiple drugable targeted genes without tissue biopsies.
Antimicrobial Fibers Created via Polycarboxylic Acid Durable Press Finishing (2007)

An N-halamine precursor, m-aminophenyl hydantoin ( m-APH), which was rendered antimicrobial through exposure to chlorine bleach, was synthesized and was applied on cotton fabric using polycarboxylic acids as crosslinking agents. Particularly, 1,2,3,4-butanetetracarboxylic acid (BTCA) with m-APH treated cotton fabric resulted in the highest increased wrinkle recovery angle and chlorine content simultaneously. Durability and rechargeability were measured through an AATCC test method and antimicrobial efficacy of BTCA/ m-APH treated cotton fabric against Gram-positive and Gram-negative bacteria showed a 6 log reduction within 1 min of contact time.
Immunological cross-reactivity of a Mycoplasma pneumoniae membrane-associated protein antigen with Mycoplasma genitalium and Acholeplasma laidlawii (1987)

A murine monoclonal antibody, OC2F5, reacts with a Mycoplasma pneumoniae antigen with an approximate Mr of 43,000. This antigen is trypsin and proteinase K sensitive and partitions in the detergent phase of a Triton X-114 solution. The monoclonal antibody cross-reacts with an antigen from both Mycoplasma genitalium and Acholeplasma laidlawii with a similar molecular weight. This cross-reactivity should be considered in the development of M. pneumoniae antigen detection systems based on the use of antibodies directed to this protein antigen.
Dietary Pulverized Konjac Glucomannan Prevents the Development of Allergic Rhinitis-Like Symptoms and IgE Response in Mice (2007)

Konjac is a traditional Japanese food with a peculiar texture, and it has been suggested that its main ingredient, konjac glucomannan (KGM), ameliorates metabolic disorders such as diabetes and hypercholesteremia. We have found that feeding with pulverized KGM (PKGM) prevents skin inflammation in a murine model of atopic dermatitis. Here, we show that dietary PKGM suppresses allergic rhinitis-like symptoms in mice upon immunization and nasal sensitization with ovalbumin (OVA). The PKGM-fed mice showed a much lower frequency of sneezing than in control animals. We also found that PKGM supplementation exclusively suppressed OVA-specific IgE response without affecting IgG1/IgG2a responses as well as systemic Th1/Th2 cytokine production. These results suggest that PKGM can be a beneficial foodstuff in preventing nasal allergy such as seasonal pollinosis.
Hierarchical Market Competition in a Duopoly Super Wi-Fi Spectrum Market (2013)

Super Wi-Fi refers to Wi-Fi-like Internet access via spectrum white spaces (WS), which is expected to enhance today's Wi-Fi thanks to the superior propagation characteristics of the WS compared to ISM/UNII bands. A Super Wi-Fi wireless service provider (WSP) dynamically leases and opportunistically utilizes a licensed band while it is temporarily unoccupied by its (licensed) primary users (PUs). The PUs' spectrum usage pattern presents time-varying spectrum availability, thus necessitating eviction of in-service customers upon return of PUs where the evicted customers are compensated with partial reimbursement of their service charge. This paper investigates the dynamics of a duopoly Super Wi-Fi market where two co-located WSPs compete for leasing better quality channels and for setting competitive service price to entice more customers. The channel quality is measured by the PUs' utilization factor (smaller the better). Since higher quality channels possess more WS incurring larger channel leasing cost, a WSP should strike a balance between channel quality and service tariff in maximizing its profit. The market competition is modeled as hierarchical noncooperative price- and quality-games, and their Nash Equilibria (NE) are derived. In addition, we investigate the impact of differentiated reimbursement rates and limited channel availability. Finally, we demonstrate the tradeoffs among leasing cost, customer arrival rate, and channel characteristics via numerical analyses.
Molecular Profiling Reveals Prognostically Significant Subtypes of Canine Lymphoma (2012)

We performed genomewide gene expression analysis of 35 samples representing 6 common histologic subtypes of canine lymphoma and bioinformatics analyses to define their molecular characteristics. Three major groups were defined on the basis of gene expression profiles: (1) low-grade T-cell lymphoma, composed entirely by T-zone lymphoma; (2) high-grade T-cell lymphoma, consisting of lymphoblastic T-cell lymphoma and peripheral T-cell lymphoma not otherwise specified; and (3) B-cell lymphoma, consisting of marginal B-cell lymphoma, diffuse large B-cell lymphoma, and Burkitt lymphoma. Interspecies comparative analyses of gene expression profiles also showed that marginal B-cell lymphoma and diffuse large B-cell lymphoma in dogs and humans might represent a continuum of disease with similar drivers. The classification of these diverse tumors into 3 subgroups was prognostically significant, as the groups were directly correlated with event-free survival. Finally, we developed a benchtop diagnostic test based on expression of 4 genes that can robustly classify canine lymphomas into one of these 3 subgroups, enabling a direct clinical application for our results.
Threshold voltage of excimer-laser-annealed polycrystalline silicon thin-film transistors (2000)

Based on experimental studies of n-channel excimer-laser-annealed polycrystalline silicon thin-film transistors with gate ratio width/length varying from 0.5 to 2.5, we propose a reliable method to determine the threshold voltage Vt from linear extrapolation of the transconductance to zero. The results reveal that the determined values of Vt are independent of the device geometry and the applied drain voltage in the linear region, in contrast with the drain current linear extrapolation method. The values of Vt are correlated with the density of the total trap states derived from the subthreshold gate swing voltage.
Validation of radiographic response evaluation criteria of preoperative chemotherapy for bone and soft tissue sarcomas: Japanese Orthopaedic Association Committee on Musculoskeletal Tumors Cooperative Study (2008)

The JOA criteria, based on the change in primary tumor size, is valid for malignant bone tumors but invalid for soft tissue sarcomas. Other new evaluation modalities of the response to preoperative chemotherapy using innovative functional imaging techniques are needed for soft tissue sarcomas.
A simple model for deep tissue attenuation correction and large organ analysis of Cerenkov luminescence imaging (2014)

Cerenkov luminescence imaging (CLI) is an emerging cost effective modality that uses conventional small animal optical imaging systems and clinically available radionuclide probes for light emission. CLI has shown good correlation with PET for organs of high uptake such as kidney, spleen, thymus and subcutaneous tumors in mouse models. However, CLI has limitations for deep tissue quantitative imaging since the blue-weighted spectral characteristics of Cerenkov radiation attenuates highly by mammalian tissue. Large organs such as the liver have also shown higher signal due to the contribution of emission of light from a greater thickness of tissue. In this study, we developed a simple model that estimates the effective tissue attenuation coefficient in order to correct the CLI signal intensity with a priori estimated depth and thickness of specific organs. We used several thin slices of ham to build a phantom with realistic attenuation. We placed radionuclide sources inside the phantom at different tissue depths and imaged it using an IVIS Spectrum (Perkin-Elmer, Waltham, MA, USA) and Inveon microPET (Preclinical Solutions Siemens, Knoxville, TN). We also performed CLI and PET of mouse models and applied the proposed attenuation model to correct CLI measurements. Using calibration factors obtained from phantom study that converts the corrected CLI measurements to %ID/g, we obtained an average difference of less that 10% for spleen and less than 35% for liver compared to conventional PET measurements. Hence, the proposed model has a capability of correcting the CLI signal to provide comparable measurements with PET data.
1H, 13C and 17O NMR study of substituent effects in 4-substituted phenylthiol esters (1998)

The 1H and 13C NMR spectra of 4-substituted phenylthiol acetates, benzoates and cinnamates and the 17O NMR spectra of a few thiol acetates were measured. The 13C chemical shifts of C-1 of the thiol esters when correlated with appropriate substituent-induced chemical shifts (SCS) of monosubstituted benzenes reveal an enhancement of substituent effect at C-1. Several good dual substituent parameter (DSP) correlations of 13C chemical shifts with σ1 and σR parameters were obtained for the carbons para to the substituent and the carbonyl carbons of all the three series of thiol esters display inverse substituent effects, indicating π-polarization of the thiol ester functionality by the dipole of the substituent. © John Wiley & Sons Ltd.
Mass spectrometry-based steroid profiling in primary bilateral macronodular adrenocortical hyperplasia (2020)

Biochemical characterization of primary bilateral macronodular adrenocortical hyperplasia (PBMAH) by distinct plasma steroid profiles and its putative correlation to disease has not been previously studied. LC-MS/MS-based steroid profiling of 16 plasma steroids was applied to 36 subjects (22 females, 14 males) with PBMAH, 19 subjects (16 females, 3 males) with other forms of adrenal Cushing's syndrome (ACS), and an age and sex-matched control group. Germline ARMC5 sequencing was performed in all PBMAH cases. Compared to controls, PBMAH showed increased plasma 11-deoxycortisol, corticosterone, 11-deoxycorticosterone, 18-hydroxycortisol, and aldosterone, but lower progesterone, DHEA, and DHEA-S with distinct differences in subjects with and without pathogenic variants in ARMC5. Steroids that showed isolated differences included cortisol and 18-oxocortisol with higher (P < 0.05) concentrations in ACS than in controls and aldosterone with higher concentrations in PBMAH when compared to controls. Larger differences in PBMAH than with ACS were most clear for corticosterone, but there were also trends in this direction for 18-hydroxycortisol and aldosterone. Logistic regression analysis indicated four steroids - DHEA, 11-deoxycortisol, 18-oxocortisol, and corticosterone - with the most power for distinguishing the groups. Discriminant analyses with step-wise variable selection indicated correct classification of 95.2% of all subjects of the four groups using a panel of nine steroids; correct classification of subjects with and without germline variants in ARMC5 was achieved in 91.7% of subjects with PBMAH. Subjects with PBMAH show distinctive plasma steroid profiles that may offer a supplementary single-test alternative for screening purposes.
Clinical Outcomes and Fusion Success at 2 Years of Single-Level Instrumented Posterolateral Fusions With Recombinant Human Bone Morphogenetic Protein-2/Compression Resistant Matrix Versus Iliac Crest Bone Graft (2006)

There was significant improvement of Short Form 36 (physical component score and pain), Oswestry Low Back Pain Disability Index, and leg and back pain scores in both groups over all time intervals. Surgical time and blood loss were significantly less in the BMP/compression resistant matrix group. The fusion rate in the BMP/compression resistant matrix group was significantly higher than the iliac crest bone graft group.
1,8-Naphthalenediylbis(dichloroborane) chloride: the first bis boron chloride chelate (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1,8-Naphthalenediylbis(dichloroborane) chloride: the first bis boron chloride chelateHoward Edan KatzCite this: Organometallics 1987, 6, 5, 1134–1136Publication Date (Print):May 1, 1987Publication History Published online1 May 2002Published inissue 1 May 1987https://pubs.acs.org/doi/10.1021/om00148a038https://doi.org/10.1021/om00148a038research-articleACS PublicationsRequest reuse permissionsArticle Views433Altmetric-Citations96LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
IMMUNOHISTOCHEMICAL ANALYSIS OF T CELL PHENOTYPES IN PATIENTS WITH GRAFT-VERSUS-HOST DISEASE FOLLOWING ALLOGENEIC BONE MARROW TRANSPLANTATION (1995)

Allogeneic bone marrow transplantation has become the therapy of choice in many cases of hematologic malignancy. In both matched related donor transplants--and, to a greater degree, in unrelated donor transplant situations--a major complication of the procedure is GVHD. This problem is caused by mature T cells in the graft, which also facilitate engraftment, and mediate an antitumor effect to reduce relapse. In order to further characterize the T cells that are present at the GVHD site of injury, we have studied 134 fresh tissue biopsies using immunohistochemical methods from 50 consecutive ABMT recipients clinically suspected of having acute GVHD. Antibodies specific for T cells, T cell receptor subsets, B cells, and NK cells were used to characterize the lymphocytic infiltrate in the biopsy tissue from GVHD patients. The data showed that the majority of lymphocytes that had infiltrated the epithelium or epidermis were CD3+ T cells. Using antibodies that distinguished the alpha/beta (beta F1) from the gamma/delta TCR (TCR delta 1)-expressing T cells, we observed that the lymphocytic infiltrates from involved tissues of the gastrointestinal tract, skin, and liver are almost exclusively derived from the alpha/beta expressing T cell subset, and are of the memory cell subset of T cells (CD45RO). This is in contrast to some examples from other disease states, in which a significant proportion of the lymphocytes that infiltrate the epidermal layers are of the gamma/delta type.
Fast algorithm for visibility enhancement of the images with low local contrast (2015)

In the paper, we propose new fast and effective approach for automatic visibility enhancement of images with poor global and local contrast. Initially, we developed the technique for scanned images with dark and light background regions and low visibility of foreground objects in both types of regions. Newly proposed algorithm carries out locally adaptive tone mapping by means of variable S-shaped curve. We use cubic Hermit spline. Starting and ending points of the spline depend on global brightness contrast, whereas tangents depend on local distribution of background and foreground pixels. Alteration of the tangents for adjacent areas is smoothed in order to avoid forming of visible artifacts. The description of several optimization tricks, which allow realization of high-speed algorithm, is given. We compare proposed method with several well-known image enhancement techniques by means of estimation of Michelson contrast (also known as visibility metric) for a number of test patterns. Disclosed algorithm outperforms tested alternatives. Finally, we extend application of proposed method for photo enhancement and correction of images with haze.
Regularized mre method for blind multichannel image deconvolution (2005)

In this paper we deal with blind image restoration in a multi-channel framework. We use the mutually referenced equalizers (MRE) in order to perform exact image restoration in the noiseless case and under some identifiability conditions. In presence of noise, this method fails to restore correctly the original image. So, we introduce a regularization term to improve the restored image quality. We introduce two regularization techniques: a norm minimization scheme and an eigen value truncation scheme in order to perform the regularization and reduce the noise amplification assigned to image restoration. We compare the performance gain of our method for different number of observed images with the mono-channel case. We evaluate the performance of our method using an image similarity index.
An improved intermolecular potential function for simulations of liquid hydrogen fluoride (1984)

A simple, intermolecular potential function has been derived empirically to yield good thermodynamic and structural results for liquid hydrogen fluoride. The function was tested in Monte Carlo statistical mechanics simulations for the liquid at temperatures of 0°C and -70°C at 1 atm. The average errors in the computed densities and energies are 1 and 5 per cent, respectively. The temperature dependence of the structural results is also analysed by means of radial distribution functions and hydrogen bond distributions. As expected, hydrogen bonded chains dominate the liquid's structure. Enhanced structure and hydrogen bonding are evident as the temperature is lowered. In view of the simplicity of the potential function and the quality of the results, the potential is well suited for simulations of dilute solutions including studies of the solvation of carbonium ions in a model superacid solvent.
Polysiloxane Nanofibers via Surface Initiated Polymerization of Vapor Phase Reagents: A Mechanism of Formation and Variable Wettability of Fiber-Bearing Substrates (2008)

A detailed study of polysiloxane nanofiber formation by surface initiated polymerization of vapor phase organotrichlorosilane reagents is presented. Substrate composition, substrate activation, reagent quantity, reaction pressure, and reaction time are parameters shown to influence nanofiber synthesis. Stepwise variation of the parameters isolates the role of each on polysiloxane nanofiber growth, and a mechanism for fiber formation is proposed based on these findings. Tunable aqueous wettability of the fibers is also demonstrated in this report, with contact angles varying from 85 degrees to 130 degrees +/- 2 degrees depending upon fiber surface density and length. Aqueous contact angles are further increased to >150 degrees by either solution functionalization of calcined fibers or copolymerization with an organofluorosilane
ChemInform Abstract: Synthesis and Photochemical Rearrangement of (1R,7aS)‐1‐(tert‐Butyldipheylsiloxy)‐7a‐methyl‐5(7aH)‐indanone. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.