gebhart/patrepeval huggingface dataset:
HLA haplotypes in a family with multiple cases of rheumatoid arthritis. (1982)

Population studies have identified the histocompatibility antigen HLA-DR4 to be a genetic marker of significantly increased risk for the development of rheumatoid arthritis (RA). Family studies are now beginning to elucidate the role of this and other genetic factors in the pathogenesis of RA. We have studied a large family in which the mother and 3 of the 6 children have seropositive RA. One maternal and 1 paternal HLA haplotype contain HLA-DR4. The mother and the 2 children with the maternal DR4 containing haplotype have RA. One sibling inherited neither of the DR4 haplotypes, yet developed RA at age 20. The inheritance of RA in this family illustrates the complexity of the genetic predisposition to this immunologically mediated disorder.
The Pol II preinitiation complex (PIC) influences Mediator binding but not promoter–enhancer looping (2021)

Knowledge of how Mediator and TFIID cross-talk contributes to promoter-enhancer (P-E) communication is important for elucidating the mechanism of enhancer function. We conducted an shRNA knockdown screen in murine embryonic stem cells to identify the functional overlap between Mediator and TFIID subunits on gene expression. Auxin-inducible degrons were constructed for TAF12 and MED4, the subunits eliciting the greatest overlap. Degradation of TAF12 led to a dramatic genome-wide decrease in gene expression accompanied by destruction of TFIID, loss of Pol II preinitiation complex (PIC) at promoters, and significantly decreased Mediator binding to promoters and enhancers. Interestingly, loss of the PIC elicited only a mild effect on P-E looping by promoter capture Hi-C (PCHi-C). Degradation of MED4 had a minor effect on Mediator integrity but led to a consistent twofold loss in gene expression, decreased binding of Pol II to Mediator, and decreased recruitment of Pol II to the promoters, but had no effect on the other PIC components. PCHi-C revealed no consistent effect of MED4 degradation on P-E looping. Collectively, our data show that TAF12 and MED4 contribute mechanistically in different ways to P-E communication but neither factor appears to directly control P-E looping, thereby dissociating P-E communication from physical looping.
Development of Potent Inhibitors of the Human Microsomal Epoxide Hydrolase (2020)

Microsomal epoxide hydrolase (mEH) hydrolyzes a wide range of epoxide containing molecules. Although involved in the metabolism of xenobiotics, recent studies associate mEH with the onset and development of some diseases. This phenomenon is partially attributed to the significant role mEH plays in hydrolyzing endogenous lipid mediators, suggesting more complex and extensive physiological functions. In order to obtain pharmacological tools to further study the biology and therapeutic potential of this enzyme target, we describe the development of highly potent inhibitors of the human mEH with IC 50 values in the low nanomolar range, around 2 orders of magnitude more potent than previously obtained mEH inhibitors. Rationalization of binding through docking calculations of the inhibitors to a mEH homology model revealed that an acetamide, with a bulky aliphatic substituent at the α‐position, as well as an aryl ring 3–4 bonds away function as key pharmacophore units. No interaction was observed with the thioether moiety, suggesting it can be replaced by more metabolically stable (e.g. methylene) groups in future studies. Support or Funding Information National Institute of Health (NIH) R35 ES030443 and R01 GM076324‐11 grants; National Institute of Environmental Health Sciences (NIEHS) Superfund Research Program P42 ES004699 grant; National Science Foundation Awards 1827246, 1805510 and 1627539; Computation support from Rosetta Commons and the US National Science Foundation’s XSEDE program Compound 62 : The most potent mEH inhibitor Figure 1 Modeling of key molecular interactions in one binding mode. Left: interactions between amide group of 62 with D226, Y299 and Y374 side chain. Right: π–π stacking between 62 and W227. Figure 2
Gated classifiers: Boosting under high intra-class variation (2011)

In this paper we address the problem of using boosting (e.g. AdaBoost [7]) to classify a target class with significant intra-class variation against a large background class. This situation occurs for example when we want to recognize a visual object class against all other image patches. The boosting algorithm produces a strong classifier, which is a linear combination of weak classifiers. We observe that we often have sets of weak classifiers that individually fire on many examples of the target class but never fire together on those examples (i.e. their outputs are anti-correlated on the target class). Motivated by this observation we suggest a family of derived weak classifiers, termed gated classifiers, that suppress such combinations of weak classifiers. Gated classifiers can be used on top of any original weak learner. We run experiments on two popular datasets, showing that our method reduces the required number of weak classifiers by almost an order of magnitude, which in turn yields faster detectors. We experiment on synthetic data showing that gated classifiers enables more complex distributions to be represented. We hope that gated classifiers will extend the usefulness of boosted classifier cascades [29].
Distal Radius Fracture (2002)

Department of Orthopaedic Surgery, Boston University School of Medicine, and the Department of Orthopaedic Trauma, Boston Medical Center, Boston, Massachusetts, U.S.A.
SPECIFIC PLASMA PROTEIN DETECTED ON PHYSICAL EDUCATION ATHLETIC STUDENTS (1986)

The purpose of this study is to analyze the plasma proteins of physical education athletic and general students (aged 19-22) before their breakfast by two-dimensional electrophoresis.The results of this study, a protein which has not been found in any original report yet is detcted from physical education athletic students before breakfast.This protein was not detected from general studenets before breakfast. This protein was detected at the position of pI5.0, molecular weight of about 70, 000 on two-dimensional polyacrylamide gel electrophosis under non-denaturing codition, but it showed a molecular weight of about 30, 000 on SDS-polyacrylamide gel electrophoresis.As far as this research is concerned, neither special physical education athletic students and nor general students were observed in changes of two-dimensional electrophoretic patterns of blood cell cytosol and blood cell membrane proteins.
Matrix Completion and Low-Rank SVD via Fast Alternating Least Squares. (2015)

The matrix-completion problem has attracted a lot of attention, largely as a result of the celebrated Netflix competition. Two popular approaches for solving the problem are nuclear-norm-regularized matrix approximation (Candès and Tao, 2009; Mazumder et al., 2010), and maximum-margin matrix factorization (Srebro et al., 2005). These two procedures are in some cases solving equivalent problems, but with quite different algorithms. In this article we bring the two approaches together, leading to an efficient algorithm for large matrix factorization and completion that outperforms both of these. We develop a software package softlmpute in R for implementing our approaches, and a distributed version for very large matrices using the Spark cluster programming environment.
Productivity and Suitability of Eucalyptus Provenances in Lateritic Soils of West Bengal (1998)

The growth, biomass production and productivity of Eucalyptus tereticornis and E. camaldulensis in a Provenance Trial under lateritic soil conditions of West Bengal have been studied. The suitability indices of the provenances of two species were also worked out. Consistently flteady performance of E. tereticornis than E. camaldulensis was observed. On sample tree basis few provenances of E. camaldulensis produced more organic matter than those of E. tereticornis . Kennedy River, 20 km N Mt. Molly and Mitchell River of E. tereticornis and Gilbert River, Emu Creek Nt Petford and Ferguson River of E. camaldulensis showed greatest potential for large scale plantation in lateritic belts.
Design and implementation of a VBR continuous media file server (2001)

We describe the design and implementation of a file server for variable bit rate continuous media. We address the problem of building a server where each stream may have a different bit rate and, more importantly, where the bit rate within a single stream may vary considerably. Such a server has been implemented within a high-speed network environment. The server is designed to be used in a heterogeneous environment and is linearly scalable. A significant aspect of the design of the system is the detailed consideration of the variable bit-rate profile of each data stream in performing admission control for the disk and for the network. This paper describes the system model, the user interface design, implementation details, and performance results based on initial experience with the server.
Functional NMDA receptors in rat erythrocytes (2010)

N-methyl-d-aspartate (NMDA) receptors are ligand-gated nonselective cation channels mediating fast neuronal transmission and long-term potentiation in the central nervous system. These channels have a 10-fold higher permeability for Ca(2+) compared with Na(+) or K(+) and binding of the agonists (glutamate, homocysteine, homocysteic acid, NMDA) triggers Ca(2+) uptake. The present study demonstrates the presence of NMDA receptors in rat erythrocytes. The receptors are most abundant in both erythroid precursor cells and immature red blood cells, reticulocytes. Treatment of erythrocytes with NMDA receptor agonists leads to a rapid increase in intracellular Ca(2+) resulting in a transient shrinkage via Gardos channel activation. Additionally, the exposure of erythrocytes to NMDA receptor agonists causes activation of the nitric oxide (NO) synthase facilitating either NO production in l-arginine-containing medium or superoxide anion (O(2)(.-)) generation in the absence of l-arginine. Conversely, treatment with an NMDA receptor antagonist MK-80, or the removal of Ca(2+) from the incubation medium causes suppression of Ca(2+) accumulation and prevents attendant changes in cell volume and NO/O(2)(.-) production. These results suggest that the NMDA receptor activity in circulating erythrocytes is regulated by the plasma concentrations of homocysteine and homocysteic acid. Moreover, receptor hyperactivation may contribute to an increased incidence of thrombosis during hyperhomocysteinemia.
Effects Of Wheelchair Tai Chi On Selected Physical Functional Abilities For Individuals With SCI (2011)

PURPOSE: The purpose of this study was to implement a 3-month pilot Wheelchair Tai Chi Modified 10- form (WTC10) intervention for individuals with Spinal Cord Injury (SCI) and examine the effects of the WTC10 intervention on selected physical functional abilities. METHODS: A convenience sample of 17 subjects with spinal cord injury between the ages of 49 and 78 were recruited from the Atlanta VA Medical Center to participate in this study; 12 subjects completed the study. The study was approved by the university and VA Medical Center IRBs. The subjects signed the informed consent forms and participated in the WTC10 intervention over a 3-month duration, consisting of 20 sessions each lasting an hour. Subjects were assessed before and immediately after the Tai Chi intervention using the following outcome measures: active joint range of motion of the upper extremities and trunk, vital capacity and respiratory function, and the Pain Self Efficacy Questionnaire (PSEQ). Paired t-tests were used to determine (p<.05) the change of the selected physical functional abilities before and after the intervention. RESULTS: After 20 sessions of the intervention, improvements were found in active range of motion at all joints tested with significant improvements in left shoulder flexion (pretest 118.420+28.00 vs posttest 132.200+25.22, p<.020), right elbow flexion (pre 131.920+11.29 vs post 141.360+10.06, p<.001), right elbow extension (pre -13.140+8.49 vs post-7.860+5.61, p<.001), and bilateral trunk rotation (right pre 20.420+10.79 vs right post 30.530+, p<.003) (left pre 22.530+8.31 vs left post 38.700+11.98, p<.001). Significant improvement was also found in expiratory vital capacity (EVC) (pre 1.39lit+1.34 vs post 2.45lit+0.80, p<.046). No significant changes were observed for the PSEQ. CONCLUSIONS: The modified WTC10 program is feasible for SCI participants to learn and practice and is effective for improving respiratory function and active range of motion in the upper extremity and trunk for individuals with SCI. This project was supported by Paralyzed Veterans of America (Grant #:592)
NASAL SINUSITIS PRODUCED BY DIETS DEFICIENT IN FAT-SOLUBLE A VITAMIN (1923)

In studying the effects on rats of diets low in the fat-soluble vitamin (vitamin A 1 ), it has been observed that these animals frequently suffer from what appears to be a nutritive disaster, manifested by stationary weight, or sudden loss in weight and death before the appearance of the characteristic eye infection, xerophthalmia. Similar results have been observed by a number of other workers. For example, Emmett 2 found that of 122 rats fed low fat-soluble A diets, 98.2 per cent, developed xerophthalmia, while out of 136 animals on vitamin A free diets in Osborne and Mendel's 3 group, only sixty-nine developed the disease. Walker, 4 who also observed that the lack of the fat-soluble A vitamin produced xerophthalmia in a variable percentage of experimental animals, suggests that hereditary predisposition may explain the dissimilar results obtained by the different investigators. With the exception of the specific pathologic changes in the
Proteomic analysis of protein S ‐nitrosylation (2008)

Nitric oxide (NO) produces covalent PTMs of specific cysteine residues, a process known as S-nitrosylation. This route is dynamically regulated and is one of the major NO signalling pathways known to have strong and dynamic interactions with redox signalling. In agreement with this scenario, binding of NO to key cysteine groups can be linked to a broad range of physiological and pathological cellular events, such as smooth muscle relaxation, neurotransmission and neurodegeneration. The characterization of S-nitrosylated residues and the functional relevance of this protein modification are both essential information needed to understand the action of NO in living organisms. In this review, we focus on recent advances in this field and on state-of-the-art proteomic approaches which are aimed at characterizing the S-nitrosylome in different biological backgrounds.
566: Comparative Genomic Hybridization of Chemotherapy Survived Wilms' Tumor Cells (2004)

You have accessJournal of UrologyDiscussed Poster, Sunday, May 9, 2004, 1:00 - 5:00 pm1 Apr 2004566: Comparative Genomic Hybridization of Chemotherapy Survived Wilms' Tumor Cells Thorsten Schlomm, Bastian Gunawan, Hans J. Schulten, Norbert Graf, Ivo Leuschner, Rolf H. Ringert, and Lazio Fuezesi Thorsten SchlommThorsten Schlomm More articles by this author , Bastian GunawanBastian Gunawan More articles by this author , Hans J. SchultenHans J. Schulten More articles by this author , Norbert GrafNorbert Graf More articles by this author , Ivo LeuschnerIvo Leuschner More articles by this author , Rolf H. RingertRolf H. Ringert More articles by this author , and Lazio FuezesiLazio Fuezesi More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)37828-5AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "566: Comparative Genomic Hybridization of Chemotherapy Survived Wilms' Tumor Cells." The Journal of Urology, 171(4S), pp. 150–151 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 171Issue 4SApril 2004Page: 150-151 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Thorsten Schlomm More articles by this author Bastian Gunawan More articles by this author Hans J. Schulten More articles by this author Norbert Graf More articles by this author Ivo Leuschner More articles by this author Rolf H. Ringert More articles by this author Lazio Fuezesi More articles by this author Expand All Advertisement PDF downloadLoading ...
In Situ Electron Paramagnetic Resonance and X-ray Diffraction Monitoring of Temperature-Induced Breathing and Related Structural Transformations in Activated V-Doped MIL-53(Al) (2016)

The metal–organic framework MIL-53(Al) is characterized by a distinct reversible structural transition between a narrow pore (NP) and a large pore (LP) state, resulting in expansion or contraction of this three-dimensional porous framework also called breathing. This transition is studied for vanadium-doped MIL-53(Al), induced by temperature (T) using in situ electron paramagnetic resonance (EPR) and X-ray diffraction (XRD) in air and in vacuum. The EPR active VIV═O molecular ions are used as local probes to detect the NP to LP transitions. The EPR spectra of VIV═O embedded in the NP and LP MIL-53(Al) states are clearly distinguishable. The temperature-dependent EPR and XRD data can consistently be interpreted in terms of T-ranges in the experiments where one of the states is predominantly present and a narrow T-range in which the two states coexist. In addition the XRD data indicate that the NP state undergoes a transition to a metastable state characterized by different lattice parameters than the NP state at room temperature, before the transition to the LP state occurs. The EPR spectra, however, show that only in the LP state the VIV═O ions can exhibit an interaction with paramagnetic O2 molecules from air.
Networks from Liquid Crystalline Segmented Chain Polymers (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNetworks from Liquid Crystalline Segmented Chain PolymersUgo Caruso, Barbara Panunzi, Antonio Roviello, and Augusto SiriguCite this: Macromolecules 1994, 27, 13, 3513–3519Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/ma00091a011https://doi.org/10.1021/ma00091a011research-articleACS PublicationsRequest reuse permissionsArticle Views77Altmetric-Citations15LEARN 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
Synthesis, Spectroscopic Characterization, and Determination of the Solution Association Energy of the Dimer [Co{N(SiMe3)2}2]2: Magnetic Studies of Low-Coordinate Co(II) Silylamides [Co{N(SiMe3)2}2L] (L = PMe3, Pyridine, and THF) and Related Species That Reveal Evidence of Very Large Zero-Field Splittings (2013)

The synthesis, magnetic, and spectroscopic characteristics of the synthetically useful dimeric cobalt(II) silylamide complex [Co{N(SiMe3)2}2]2 (1) and several of its Lewis base complexes have been investigated. Variable-temperature nuclear magnetic resonance (NMR) spectroscopy of 1 showed that it exists in a monomer-dimer equilibrium in benzene solution and has an association energy (ΔGreacn) of -0.30(20) kcal mol(-1) at 300 K. Magnetic data for the polycrystalline, red-brown [Co{N(SiMe3)2}2]2 (1) showed that it displays strong antiferromagnetic exchange coupling, expressed as -2JexS1S2, between the two S = (3)/2 cobalt(II) centers with a Jex value of -215(5) cm(-1), which is consistent with its bridged dimeric structure in the solid state. The electronic spectrum of 1 in solution is reported for the first time, and it is shown that earlier reports of the melting point, synthesis, electronic spectrum, and magnetic studies of the monomer "Co{N(SiMe3)2}2" are consistent with those of the bright green-colored tetrahydrofuran (THF) complex [Co{N(SiMe3)2}2(THF)] (4). Treatment of 1 with various Lewis bases yielded monomeric three-coordinated species-[Co{N(SiMe3)2}2(PMe3)] (2), and [Co{N(SiMe3)2}2(THF)] (4), as well as the previously reported [Co{N(SiMe3)2}2(py)] (3)-and the four-coordinated species [Co{N(SiMe3)2}2(py)2] (5) in good yields. The paramagnetic complexes 2-4 were characterized by electronic and (1)H NMR spectroscopy, and by X-ray crystallography in the case of 2 and 4. Magnetic studies of 2-5 and of the known three-coordinated cobalt(II) species [Na(12-crown-4)2][Co{N(SiMe3)2}3] (6) showed that they have considerably larger χMT products and, hence, magnetic moments, than the spin-only values of 1.875 emu K mol(-1) and 3.87 μB, which is indicative of a significant zero-field splitting and g-tensor anisotropy resulting from the pseudo-trigonal crystal field. A fit of χMT for 2-6 yields a large g-tensor anisotropy, large negative D-values (between -62 cm(-1) and -82 cm(-1)), and E-values between ±10 cm(-1) and ±21 cm(-1).
Monitoring of Magnetic Targeting to Tumor Vasculature Through MRI and Biodistribution (2010)

MR and biodistribution analysis clearly show the efficacy of MCLs as MRI contrast agents, prove the use of magnetic guidance, and demonstrate the potential of MCLs as agents for imaging, guidance and therapeutic delivery.
Lipidomic Comparison of 2D and 3D Colon Cancer Cell Culture Models (2022)

Altered lipid metabolism is one of the hallmarks of cancer. Cellular proliferation and de novo synthesis of lipids are related to cancer progression. In this study, we evaluated the lipidomic profile of two-dimensional (2D) monolayer and multicellular tumor spheroids from the HCT 116 colon carcinoma cell line. We utilized serial trypsinization on the spheroid samples to generate three cellular populations representing the proliferative, quiescent, and necrotic regions of the spheroid. This analysis enabled a comprehensive identification and quantification of lipids produced in each of the spheroid layer and 2D cultures. We show that lipid subclasses associated with lipid droplets form in oxygen-restricted and acidic regions of spheroids and are produced at higher levels than in 2D cultures. Additionally, sphingolipid production, which is implicated in cell death and survival pathways, is higher in spheroids relative to 2D cells. Finally, we show that increased numbers of lipids comprised of polyunsaturated fatty acids (PUFAs) are produced in the quiescent and necrotic regions of the spheroid. The lipidomic signature for each region and cell culture type highlights the importance of understanding the spatial aspects of cancer biology. These results provide additional lipid biomarkers in the tumor microenvironment that can be further studied to target pivotal lipid production pathways.