gebhart/patrepeval huggingface dataset:
beta-Endorphin: characteristics of binding sites in a neuroblastoma--glioma hybrid cell. (1981)

Specific binding of human beta-endorphin to NG108-15 cells is described; human beta-[Tyr27-3H2] endorphin was used as the ligand. The binding is time dependent and saturable; Kd = 0.3 nM and ka = 1.8 x 10(8) M-1 min-1. Under the conditions optimal for beta-endorphin binding, leucine-enkephalin has one-fourth to one-third as many binding sites as beta-endorphin and its affinity is 7--10% that of beta-endorphin. Monovalent and divalent cations potently inhibit binding. Trypsin, phospholipase A, and N-ethylmaleimide reduce the ability of NG108-15 cells to bind beta-endorphin. beta-Endorphin analogs are able to fully inhibit the binding of beta-[Tyr27-3H2]endorphin, although enkephalins, morphine, and naloxone inhibit only 50--80%.
Wireless service provision in TV white space with cognitive radio technology: A telecom operator's perspective and experience (2011)

Currently there is a very fundamental change happening in spectrum regulation, possibly the most fundamental ever in its history. This is the enabling of spectrum sharing, where primary (licensed) users of the spectrum, are forced to allow sharing with secondary users, who use license-exempt equipment. Such sharing is free for the secondary users, subject to the condition that they do not cause harmful interference to the primary users. The first instance of such sharing is occurring with the UHF digital TV spectrum, in what is commonly called TV white space. Regulators such as the FCC in the United States and Ofcom in the United Kingdom have indicated that other spectrum will follow suit. Cognitive radio is an enabling technology that allows such sharing. Following recent rulings by FCC and Ofcom and the emergence of a series of related industry standards, CR operation in TVWS is moving from the research domain towards implementation and commercialization, with use-cases that are of interest to telecom operators. In this article we describe three such use cases: future home networks, coverage of the street from inside buildings, and broadband access to rural and underserved premises. We present results of modeling and trials of technical feasibility, undertaken by the Innovate and Design team at BT. Based on our experience we draw conclusions regarding the feasibility and commercial importance of these use cases, and identify some of the remaining technical and commercial challenges.
Enabling Optical Devices for Scalable Networks: Introduction to the Feature Issue (2012)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Pascal Besnard, Liam Barry, and Dan Kilper, "Enabling Optical Devices for Scalable Networks: Introduction to the Feature Issue," J. Opt. Commun. Netw. 4, EOD1-EOD1 (2012) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Analysis of Degradation in Graphene-Based Spin Valves (2009)

The degradation mechanisms of multilayer graphene spin valves are investigated. The spin injection signals in graphene spin valves have been reported to be linearly dependent on the drain bias voltage, which indicates that the spin polarization of injected spins in graphene is robust against the bias voltage. We present that the disappearance of this robustness is due to two different degradation mechanisms of the spin valves. Our findings indicate that the disappearance of the robustness is due to degradation rather than an intrinsic characteristic of graphene. Thus, the robustness can be greatly enhanced if degradation can be prevented.
FIGURE 4 from A Novel Class of Ribosome Modulating Agents Exploits Cancer Ribosome Heterogeneity to Selectively Target the CMS2 Subtype of Colorectal Cancer (2023)

&lt;p&gt;Sensitivity to ZKN-157 enriched in CMS2 subtype and is associated with a distinct molecular signature. &lt;b&gt;A,&lt;/b&gt; Scatter plot displaying drug sensitivity metrics for ZKN-157 across 33 colorectal cancer cell lines with colors indicating sensitive, intermediate, and insensitive cell lines. Dotted lines indicate response percent (%) = 25 μmol/L (horizontal) and GI&lt;sub&gt;50&lt;/sub&gt; = 15 μmol/L (vertical). &lt;b&gt;B,&lt;/b&gt; Heat map of gene expression data for CMS subtype genes across colorectal cancer cell lines shows an enrichment of sensitive cell lines in the CMS2 subtype. Row annotations show drug sensitivity, MSI/MSS status, CMS subtypes and average CNV ratios for Chr20q11–13. “+” used to annotate cell lines with WT TP53, unannotated cell lines harbor mutations in TP53. &lt;b&gt;C,&lt;/b&gt; Bar graph plotting Chr20 CNV ratios for colorectal cancer cell lines, split by CMS2 subtype shows a further enrichment of sensitive cell lines in the CMS2 subtype with Chr20q11-13 CNV gain. &lt;b&gt;D,&lt;/b&gt; Bar graph plotting IC&lt;sub&gt;50&lt;/sub&gt; values for ZKN-157 across colorectal cancer–derived CMS2 (light blue bars) and normal (black bar) organoids. Dotted line indicates IC&lt;sub&gt;50&lt;/sub&gt; = 30 μmol/L.&lt;/p&gt;
A Markov Network Model for Natural Language Semantic Matching (2019)

We address the problem of designing practical methods for natural language semantic matching. While current deep neural networks can achieve high accuracy on benchmark datasets, their model structures are typically rigidly defined and as a result often encounter generalization issues and cannot easily adapt to various training data limitations. In this paper, we propose a Markov Network Model that leverages linguistic independence assumptions to decompose the problem into subproblems that can be solved independently for both generalization and the ability to adapt to various amounts of training data. The proposed framework is orthogonal to deep neural networks, since they can be integrated to the framework in the form of potential functions on the cliques corresponding to smaller sub-problems. Experiments on diverse real-world datasets show our method outperforms current state-of-the-art both in terms of accuracy, generalization and the ability to perform under various training data limitations.
The clinical impact of copy number variants in inherited bone marrow failure syndromes (2017)

Inherited bone marrow failure syndromes (IBMFSs) comprise a genetically heterogeneous group of diseases with hematopoietic failure and a wide array of physical malformations. Copy number variants (CNVs) were reported in some IBMFSs. It is unclear what impact CNVs play in patients evaluated for a suspected diagnosis of IBMFS. Clinical and genetic data of 323 patients from the Canadian Inherited Marrow Failure Registry from 2001 to 2014, who had a documented genetic work-up, were analyzed. Cases with pathogenic CNVs (at least 1 kilobasepairs) were compared to cases with other mutations. Genotype-phenotype correlations were performed to assess the impact of CNVs. Pathogenic nucleotide-level mutations were found in 157 of 303 tested patients (51.8%). Genome-wide CNV analysis by single nucleotide polymorphism arrays or comparative genomic hybridization arrays revealed pathogenic CNVs in 11 of 67 patients tested (16.4%). In four of these patients, identification of CNV was crucial for establishing the correct diagnosis as their clinical presentation was ambiguous. Eight additional patients were identified to harbor pathogenic CNVs by other methods. Of the 19 patients with pathogenic CNVs, four had compound-heterozygosity of a CNV with a nucleotide-level mutation. Pathogenic CNVs were associated with more extensive non-hematological organ system involvement (<i>p</i>=0.0006), developmental delay (<i>p</i>=0.006) and short stature (<i>p</i>=0.04) compared to nucleotide-level mutations. In conclusion, a significant proportion of patients with IBMFSs harbor pathogenic CNVs which were associated with a more extensive non-hematological phenotype in this cohort. Patients with a phenotype suggestive of IBMFSs but without identification of pathogenic nucleotide-level mutations should undergo specific testing for CNVs.
Long‐Term Generation of Longitudinal Spin Order Controlled by Ammonia Ligation Enables Rapid SABRE Hyperpolarized 2D NMR (2021)

Abstract The front cover artwork front cover artwork is provided by NMRCoRe, the Flemish NMR/X‐Ray platform for Convergence Research and was designed by Ir. Ewoud Vaneeckhaute and Dr. Eric Breynaert. The image shows the reciprocity between parahydrogen, deuterated ammonia and iridium allowing for hyperpolarized 2D NMR via long‐term availability of longitudinal spin order. Read the full text of the Article at 10.1002/cphc.202100079 .
Following the electrons (2012)

Commercial buildings are significant consumers of electricity. The first step towards better energy management in commercial buildings is monitoring consumption. However, instrumenting every electrical panel in a large commercial building is expensive and wasteful. In this paper, we propose a greedy meter (sensor) placement algorithm based on maximization of information gained, subject to a cost constraint. The algorithm provides a near-optimal solution guarantee. Furthermore, to identify power saving opportunities, we use an unsupervised anomaly detection technique based on a low-dimensional embedding. Further, to better manage resources such as lighting and HVAC, we propose a semi-supervised approach combining hidden Markov models (HMM) and a standard classifier to model occupancy based on readily available port-level network statistics.
Relationship between clinical and instrumental balance assessments in chronic post-stroke hemiparesis subjects (2013)

Correlation was found only among some of the clinical and instrumental balance outcomes, indicating that they might measure different aspects of balance control. Consistently with previous findings in healthy and pathological subjects, our results suggest that instrumented posturography should be recommended for use in clinical practice in addition to clinical functional tests.
Synthesis of &#946;-Nitroamines via Classical Mannich and Aza-Henry Reactions (2013)

Chemistry and pharmacological activity of various types of Mannich bases and their derivatives were well documented. A survey of the literature revealed extensive studies on the synthesis and reactivity of Mannich bases derived from ketones, amides, enamines, phenols and indoles of widely different structures, while comparatively little attention has been given to Mannich bases derived from nitroalkanes and related nitrocompounds. Mannich reactions using nitroalkanes and related compounds as substrates are of synthetic relevance and the products are promising as biologically active substances. It is known that the nitro group is an important constituent of many biologically significant heterocycles such as antibiotic drugs (nitrofurantoin and nitrofurazone). A number of nitro-heterocycles of pharmacological interest were also synthesized by Mannich reactions with suitable nitro-substrates. In view of this, and because of the widespread and increasing interest in the chemistry of Mannich bases, the present work is concerned with attempts to extend the scope of Mannich reactions with nitroalkanes to include the synthesis of a variety of nitro N- and S-heterocycles. Keywords: Asymmetric catalysis, Aza-Henry reaction, Nitroalkane, nitro-Mannich reaction, Reduction reaction, Vicinal diamines.
Polymerization of Aminophenols by Oxidative Coupling in Aqueous Solution of Iron Chelate (1969)

アミノフェノールは水溶液中で鉄キレートにより速やかに酸化重合し,常磁性の黒色重合体を与える。生成重合体は遊離のアミノ基および水酸基を有するほか,一部キノンイミン構造を有し,可逆的な酸化還元性を顕著に示す。すなわち亜ニチオン酸ナトリウム水溶液により直ちに還元脱色して淡黄色溶液となるが,空気中で速かに酸化されて元の黒色重合体となる。重合は酸素の存在下で進行するが,pHの高い領域ではアルカリによる副反応が生起する。pH7では酸素吸収量と重合収率は比例する。Fe(III)EDTAによる場合の重合収率はpH9で極大に達する。用いた鉄キレートの安定度定数と重合速度の間には明瞭な相関関係は認められない。重合系の電位は重合初期に速やかに変化し,平衡電位を保ったまま重合が進行することから,系中では鉄キレートと単量体の関与する平衡が成立しており,かつ2価の鉄キレートの酸化速度は遅いことがわかる。
Polymerization ofN‐vinylcarbazole with ziegler‐type catalyst systems (1963)

Abstract The polymerization of N ‐vinylcarbazole with the TiCl 4 –Al( i ‐Bu) 3 , TiCl 4 –AlEt 3 , TiCl 3 –Al( i ‐Bu) 3 , and the TiCl 4 – n ‐BuLi systems was studied. It was found that N ‐vinylcarbazole undergoes a very facile cationic polymerization with TiCl 4 , or TiCl 3 , and that catalyst complexes which contain a low metal alkyl/transition metal halide ratio promote a very rapid cationic polymerization. When the catalyst components are mixed in the presence of monomer, considerable cationic polymerization due to the transition metal halide alone takes place before the reaction between the titanium halide and metal alkyl is complete. Experiments with catalyst components mixed in the absence of monomer have shown that the rate of the reaction is markedly dependent on the ratio of the catalyst components and that each system studied had a characteristic ratio at which the catalytic activity suffered a marked drop. With TiCl 3 –Al( i ‐Bu) 3 this drop occurred at an Al/Ti ratio of 0.8, with TiCl 4 –Al( i ‐Bu) 3 at an Al/Ti ratio of 3, and with TiCl 4 – n ‐BuLi at a Li/Ti ratio of 1.5. This was interpreted as indicating that at these ratios the surface of the titanium halide becomes completely modified by the metal alkyl so that no N ‐vinylcarbazole–titanium halide interaction could take place. The per cent reduction of TiCl 4 to lower valence states was studied with the n ‐BuLi–TiCl 4 system as a function of the Li/Ti ratio and it was found that the maximum per cent reduction takes place at a Li/Ti ratio of 2. The per cent reduction rapidly decreased to zero at higher Li/Ti ratios. The polymers of N ‐vinylcarbazole formed with Ziegler‐type catalyst systems were examined by x‐ray diffraction, by their appearance under a polarizing microscope, by infrared spectroscopy, and by nuclear magnetic resonance. These measurements indicated that only amorphous, atactic polymers were formed.
Improved Enzyme Dosing Protocol to Increase Islet Yield in Chronic Pancreatitis Pancreas Intended for Clinical Islet Auto-Transplantation (2012)

Introduction: Chronic pancreatitis (CP) is characterized by irreversible changes to the pancreas. When associated with intractable abdominal pain refractory to medical or endoscopic treatment, total pancreatectomy (TP) may be required for pain relief, as well as an islet auto-transplantation (IAT) to minimize or prevent the resulting labile diabetes mellitus. At our institution, over 450 IATs have been performed and the islet isolation process has been continuously optimized to achieve the desired results. However, obtaining comparative results from each pancreas is complicated by the fact that the long standing injury and inflammation damages the normal architecture of the pancreas through fibrosis, duct obstruction, intra-ductal calcifications, and cysts. As enzymatic digestion is a multi-component, stoichiometric process, these changes make it difficult to produce consistent results each time and require revision of enzyme strategies to avoid incomplete or over digestion. In this study, we retrospectively analyzed the significant changes in enzyme dosing of CP pancreases in 231 cases (2007-2012). Methods: Three different enzyme dosing protocols in the cohort were identified and compared using (ANOVA, SPSS 19). Protocol-A (A) was the use of one full vial of collagenase and neutral protease (NP) on every pancreas. Protocol-B (B) was the use of fixed dose of collagenase and NP while protocol-C (C) is our current standard and is based on dosing enzymatic activity Units per gm of estimated pancreas weight (for both Collagenase and NP). A range is allowed based on severity of fibrosis of pancreas as determined on gross morphological evaluation. Factors affecting the yields (islet equivalents, IEQ) were compared with respect to digest IEQ/g pancreas, post-purification IEQ/g and transplant IEQ/kg to highlight significant improvements of each successive protocol. In our current protocol (C), we have started using intact C1 collagenase when compared to protocols A&B in which truncated collagenase was used. Results: There were no significant differences in age (p=0.987) and BMI (p=0.684) among the patient profiles for the three different approaches. Significant differences were noted with our current approach (Protocol-C) with respect to digested pancreas weight (gm), collagenase unit/gm pancreas, NP U/gm pancreas and superior isolation results obtained with significantly greater digest IEQ, (p=0.003), post purification IEQ, (p=0.002) and total transplanted IEQ/kg (p=0.015) compared to protocol B and A (table). All data are presented as Mean ± SD Conclusion: With our current standard procedure of careful dosing of each individual pancreas with intact C1 collagenase we have been able to improve the islet yield. It is thus important to select the dose of the digestive enzymes according to the weight of the pancreas and adjust their ratios for achieving maximal yields from fibrotic cases of chronic pancreatitis.Table: [Isolation result with different enzyme protocols]
A Bayesian Model for Supervised Clustering with the Dirichlet Process Prior (2009)

We develop a Bayesian framework for tackling the supervised clustering problem, the generic problem encountered in tasks such as reference matching, coreference resolution, identity uncertainty and record linkage. Our clustering model is based on the Dirichlet process prior, which enables us to define distributions over the countably infinite sets that naturally arise in this problem. We add supervision to our model by positing the existence of a set of unobserved random variables (we call these “reference types”) that are generic across all clusters. Inference in our framework, which requires integrating over infinitely many parameters, is solved using Markov chain Monte Carlo techniques. We present algorithms for both conjugate and non-conjugate priors. We present a simple—but general—parameterization of our model based on a Gaussian assumption. We evaluate this model on one artificial task and three real-world tasks, comparing it against both unsupervised and state-of-the-art supervised algorithms. Our results show that our model is able to outperform other models across a variety of tasks and performance metrics.
Differences in the composition of the immune infiltrate in breast cancer, colorectal carcinoma, melanoma and non-small cell lung cancer: A microarray-based meta-analysis (2015)

Recently, we interrogated public microarray databases with regard to the expression patterns of metagenes corresponding to major immune cell subtypes present in malignant tumors. This analysis, which involved approximately 3,500 tumor samples, revealed organ-specific differences in the composition of the immune infiltrate as well as in the correlation among distinct cell-type specific metagenes, reflecting changes in the functional organization of the anticancer immune response.
Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns (2016)

Phenotypic screening is in a renaissance phase and is expected by many academic and industry leaders to accelerate the discovery of new drugs for new biology. Given that phenotypic screening is per definition target agnostic, the emphasis of <i>in silico</i> and <i>in vitro</i> follow-up work is on the exploration of possible molecular mechanisms and efficacy targets underlying the biological processes interrogated by the phenotypic screening experiments. Herein, we present six exemplar computational protocols for the interpretation of cellular phenotypic screens based on the integration of compound, target, pathway, and disease data established by the IMI Open PHACTS project. The protocols annotate phenotypic hit lists and allow follow-up experiments and mechanistic conclusions. The annotations included are from ChEMBL, ChEBI, GO, WikiPathways and DisGeNET. Also provided are protocols which select from the IUPHAR/BPS Guide to PHARMACOLOGY interaction file selective compounds to probe potential targets and a correlation robot which systematically aims to identify an overlap of active compounds in both the phenotypic as well as any kinase assay. The protocols are applied to a phenotypic pre-lamin A/C splicing assay selected from the ChEMBL database to illustrate the process. The computational protocols make use of the Open PHACTS API and data and are built within the Pipeline Pilot and KNIME workflow tools.
Utilization of rye as energy source affects bacterial translocation, intestinal viscosity, microbiota composition, and bone mineralization in broiler chickens (2014)

Two independent trials were conducted to evaluate the utilization of rye as energy source on bacterial translocation (BT), intestinal viscosity, gut integrity, gut microbiota composition, and bone mineralization, when compared with a traditional cereal (corn) in broiler chickens. In each experiment, day-of-hatch, broiler chickens were randomly assigned to either a corn or a rye diet (n = 20 chickens/group). At 10 d of age, in both experiments, 12 chickens/group were randomly selected, and given an oral gavage dose of fluorescein isothiocyanate dextran (FITC-d). After 2.5 h of oral gavage, blood samples were collected to determine the passage of FITC-d. The liver was collected from each bird to evaluate BT. Duodenum, ileum, and cecum gut sections were collected to evaluate intestinal viscosity and to enumerate gut microbiota. Tibias were collected for observation of bone parameters. Broilers fed with rye showed increased (p < 0.05) intestinal viscosity, BT, and serum FITC-d. Bacterial enumeration revealed that chickens fed with rye had increased the number of total lactic acid bacteria in all three sections of the gastrointestinal tract evaluated when compared to chickens fed with corn. Chickens fed with rye also had significantly higher coliforms in duodenum and ileum, whereas the total number of anaerobes increased only in duodenum. A significant reduction in bone strength and bone mineralization was observed in chickens fed with rye when compared with corn fed chickens. In conclusion, rye evoked mucosal damage in chickens that alter the intestinal viscosity, increased leakage through the intestinal tract, and altered the microbiota composition as well as bone mineralization. Studies to evaluate dietary inclusion of selected DFM candidates that produce exogenous enzymes in rye fed chickens are currently being evaluated.
Characteristics of patients with pituitary gigantism: results of an international study (2013)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Telomerase Unplugged (2007)

The control of telomerase activity at chromosome ends by telomere-binding proteins is critical for telomere length homeostasis. Two recent papers identify TPP1 as a critical mediator of this control. TPP1 forms part of the telomeric shelterin complex while also associating with telomerase, stimulating its activity and processivity.
4-Oxo-4,7-dihydrothieno[2,3-b]pyridines as Non-Nucleoside Inhibitors of Human Cytomegalovirus and Related Herpesvirus Polymerases (2005)

A novel series of 4-oxo-4,7-dihydrothieno[2,3-b]pyridine-5-carboxamides have been identified as potential antivirals against human herpesvirus infections resulting from human cytomegalovirus (HCMV), herpes simplex virus type 1 (HSV-1), and varicella-zoster virus (VZV). Compounds 10c and 14 demonstrated broad-spectrum inhibition of the herpesvirus polymerases HCMV, HSV-1, and VZV. High specificity for the viral polymerases was observed compared to human alpha polymerase. The antiviral activity of 10c and 14, as determined by plaque reduction assay, was comparable or superior to that of existing antiherpes drugs, ganciclovir (for HCMV) and acyclovir (for HSV-1 and VZV). Drug resistance to compound 14 correlated to point mutations in conserved domain III of the herpesvirus DNA polymerase, but these mutations do not confer resistance to existing nucleoside therapy. In addition, compound 14 maintained potent antiviral activity against acyclovir-resistant HSV-1 strains. Substitution to the pyridone nitrogen (N7) was found to be critical for enhanced in vitro antiviral activity.