gebhart/patrepeval huggingface dataset:
Massively Parallel Haplotyping on Microscopic Beads for the High-Throughput Phase Analysis of Single Molecules (2012)

In spite of the many advances in haplotyping methods, it is still very difficult to characterize rare haplotypes in tissues and different environmental samples or to accurately assess the haplotype diversity in large mixtures. This would require a haplotyping method capable of analyzing the phase of single molecules with an unprecedented throughput. Here we describe such a haplotyping method capable of analyzing in parallel hundreds of thousands single molecules in one experiment. In this method, multiple PCR reactions amplify different polymorphic regions of a single DNA molecule on a magnetic bead compartmentalized in an emulsion drop. The allelic states of the amplified polymorphisms are identified with fluorescently labeled probes that are then decoded from images taken of the arrayed beads by a microscope. This method can evaluate the phase of up to 3 polymorphisms separated by up to 5 kilobases in hundreds of thousands single molecules. We tested the sensitivity of the method by measuring the number of mutant haplotypes synthesized by four different commercially available enzymes: Phusion, Platinum Taq, Titanium Taq, and Phire. The digital nature of the method makes it highly sensitive to detecting haplotype ratios of less than 1:10,000. We also accurately quantified chimera formation during the exponential phase of PCR by different DNA polymerases.
Versatile Functionalization of Polylysine:  Synthesis, Characterization, and Use of Neoglycoconjugates (1999)

Glycopolymers are useful macromolecules with a non-carbohydrate backbone for presenting saccharides in a multivalent form. Here, a new methodology is described which allows easy access to water-soluble, biodegradable glycopolymers with both predeterminable composition and molecular weight distribution. Thus, chloroacetylation of commercially available polylysine hydrobromide 3 gave the reactive homopolymer 4, whose chloroacetamide functions allowed subsequent coupling with thiol-containing components. Water-soluble homopolymers such as 8 and 13 were available by treatment with an excess of hydrophilic thiols. Heteroglycopolymers were obtained via quantitative incorporation of substoichiometric amounts of carbohydrates with a mercapto functionality linked to the reducing end; the remaining chloroacetamide groups were capped with an excess of thioglycerol. A variety of glycopolymers with up to four different components was prepared. The composition and purity of the products were reliably analyzed by 1H NMR. Generally, the quantitative incorporation of substoichiometric components was verified. The polymer backbone was not altered under the applied reaction conditions, as indicated by very similar polydispersities and degrees of polymerization of starting polylysine 3 and functionalized homo- and heteropolymers 8, 13, and 14. Glycopolymer 25, containing sialyl Lewisa and biotin as a functional group for enzyme-linked immuno sorbent assay, was used for developing cell-free selectin ligand binding assays. The inhibition of E-selectin by glycopolymers 16, containing sialyl Lewisx (sLex), was evaluated in a cell adhesion assay under flow conditions using activated human umbilical vein endothelial cells and polymorphonuclear neutrophils. The sLex polymers 16 showed no significant inhibition, whereas conjugates with additional charged groups (carboxylates 18, sulfonates 21) in addition to sLex gave 30−35% reduction of the number of interacting cells at the same concentration of 100 μM sLex.
Red blood cells inhibit activation-induced cell death and oxidative stress in human peripheral blood T lymphocytes (2001)

Red blood cells (RBCs) are known to perform one prominent function: to carry and deliver oxygen to the tissues. Earlier studies, however, suggested a role for RBCs in potentiating T-cell proliferation in vitro. Here it is shown that the presence of RBCs in cultures of stimulated human peripheral blood lymphocytes strengthens T-cell proliferation and survival. Analysis of phosphatidylserine externalization and DNA fragmentation showed that RBCs inhibit T-cell apoptosis. This inhibition correlated with a reduction in CD71 but not CD95 expression. RBCs enhanced T-cell proliferation and survival upon activation with phytohemagglutinin and with OKT3 antibodies. Studies aimed at characterizing the cellular and molecular basis of the protection afforded to T cells by RBCs showed that (1) optimal protection required intact RBCs and red cell/T-cell contact but not monocytes; (2) RBCs markedly reduced the level of intracellular reactive oxygen species; and (3) RBCs inhibited the formation of protein-bound acrolein, a peroxidation adduct in biologic systems. Overall, these data indicate that human RBCs protect T cells from activation-induced cell death, at least in part by reducing the pro-oxidant state, and suggest a role for RBCs as conceivable modulators of T-cell homeostasis.
Regularization of inverse planning for intensity-modulated radiotherapy (2005)

The performance of a variational regularization technique to improve robustness of inverse treatment planning for intensity modulated radiotherapy is analyzed and tested. Inverse treatment planning is based on the numerical solutions to the Fredholm integral equation of the first kind which is ill-posed. Therefore, a fundamental problem with inverse treatment planning is that it may exhibit instabilities manifested in nonphysical oscillations in the beam intensity functions. To control the instabilities, we consider a variational regularization technique which can be applied for the methods which minimize a quadratic objective function. In this technique, the quadratic objective function is modified by adding of a stabilizing functional that allows for arbitrary order regularization. An optimal form of stabilizing functional is selected which allows for both regularization and good approximation of beam intensity functions. The regularized optimization algorithm is shown, by comparison for a typical case of a head-and-neck cancer treatment, to be significantly more accurate and robust than the standard approach, particularly for the smaller beamlet sizes.
Inhibition of AAC(6′)-Ib-Mediated Resistance to Amikacin in Acinetobacter baumannii by an Antisense Peptide-Conjugated 2′,4′-Bridged Nucleic Acid-NC-DNA Hybrid Oligomer (2015)

Multiresistant Acinetobacter baumannii, a common etiologic agent of severe nosocomial infections in compromised hosts, usually harbors aac(6')-Ib. This gene specifies resistance to amikacin and other aminoglycosides, seriously limiting the effectiveness of these antibiotics. An antisense oligodeoxynucleotide (ODN4) that binds to a duplicated sequence on the aac(6')-Ib mRNA, one of the copies overlapping the initiation codon, efficiently inhibited translation in vitro. An isosequential nuclease-resistant hybrid oligomer composed of 2',4'-bridged nucleic acid-NC (BNA(NC)) residues and deoxynucleotides (BNA(NC)-DNA) conjugated to the permeabilizing peptide (RXR)4XB ("X" and "B" stand for 6-aminohexanoic acid and β-alanine, respectively) (CPPBD4) inhibited translation in vitro at the same levels observed in testing ODN4. Furthermore, CPPBD4 in combination with amikacin inhibited growth of a clinical A. baumannii strain harboring aac(6')-Ib in liquid cultures, and when both compounds were used as combination therapy to treat infected Galleria mellonella organisms, survival was comparable to that seen with uninfected controls.
Differential targeting of protein kinase CK2 to the nuclear matrix upon transient overexpression of its subunits (1999)

Modest dysregulation of CK2 has been shown to enhance the oncogenic potential in transgenic models of cancer. Since nuclear matrix serves as an anchor for CK2 and plays a key role in growth-related activities, we examined the effects of CK2 overexpression on its signaling to the nuclear matrix. Expression plasmids pCI-CK2α, pCI-CK2β, and the bicistronic pCI-CK2αβ containing full length cDNAs encoding the various subunits were employed to transiently transfect two cell lines, BPH-1 and COS-1. Cytosol from transfected BPH-1 cells containing α or β or α + β or αβ showed a modest increase in CK2 activity by 26%, 1%, 20%, and 17%, respectively, over that in the controls transfected with pCI vector. However, the corresponding increase in CK2 activity in the NM fraction was 156%, 8%, 147%, and 152%, respectively. Immunoblot analysis of the CK2 in the NM accorded with these data. Similar results were obtained with COS-1 cells or other expression vectors. The results suggest that moderate overexpression of CK2 in the cells evokes a differential several-fold enhancement in NM associated CK2 relative to that in the cytosol. This process may have a bearing on the functional signaling of this kinase in relation to its possible role in oncogenesis. J. Cell. Biochem. 74:127–134, 1999. © 1999 Wiley-Liss, Inc.
Pattern formation in Hamiltonian systems with continuous spectra; a normal-form single-wave model (2013)

Pattern formation in biological, chemical and physical problems has received considerable attention, with much attention paid to dissipative systems. For example, the Ginzburg--Landau equation is a normal form that describes pattern formation due to the appearance of a single mode of instability in a wide variety of dissipative problems. In a similar vein, a certain "single-wave model" arises in many physical contexts that share common pattern forming behavior. These systems have Hamiltonian structure, and the single-wave model is a kind of Hamiltonian mean-field theory describing the patterns that form in phase space. The single-wave model was originally derived in the context of nonlinear plasma theory, where it describes the behavior near threshold and subsequent nonlinear evolution of unstable plasma waves. However, the single-wave model also arises in fluid mechanics, specifically shear-flow and vortex dynamics, galactic dynamics, the XY and Potts models of condensed matter physics, and other Hamiltonian theories characterized by mean field interaction. We demonstrate, by a suitable asymptotic analysis, how the single-wave model emerges from a large class of nonlinear advection-transport theories. An essential ingredient for the reduction is that the Hamiltonian system has a continuous spectrum in the linear stability problem, arising not from an infinite spatial domain but from singular resonances along curves in phase space whereat wavespeeds match material speeds (wave-particle resonances in the plasma problem, or critical levels in fluid problems). The dynamics of the continuous spectrum is manifest as the phenomenon of Landau damping when the system is ... Such dynamical phenomena have been rediscovered in different contexts, which is unsurprising in view of the normal-form character of the single-wave model.
Identification of TIM3 2′-fluoro oligonucleotide aptamer by HT-SELEX for cancer immunotherapy (2015)

TIM3 belongs to a family of receptors that are involved in T-cell exhaustion and Treg functions. The development of new therapeutic agents to block this type of receptors is opening a new avenue in cancer immunotherapy. There are currently several clinical trials ongoing to combine different immune-checkpoint blockades to improve the outcome of cancer patients. Among these combinations we should underline PD1:PDL1 axis and TIM3 blockade, which have shown very promising results in preclinical settings. Most of these types of therapeutic agents are protein cell-derived products, which, although broadly used in clinical settings, are still subject to important limitations. In this work we identify by HT-SELEX TIM3 non-antigenic oligonucleotide aptamers (TIM3Apt) that bind with high affinity and specificity to the extracellular motives of TIM3 on the cell surface. The TIM3Apt1 in its monomeric form displays a potent antagonist capacity on TIM3-expressing lymphocytes, determining the increase of IFN-γ secretion. In colon carcinoma tumor-bearing mice, the combinatorial treatment of TIM3Apt1 and PDL1-antibody blockade is synergistic with a remarkable antitumor effect. Immunotherapeutic aptamers could represent an attractive alternative to monoclonal antibodies, as they exhibit important advantages; namely, lower antigenicity, being chemically synthesized agents with a lower price of manufacture, providing higher malleability, and antidote availability.
Recent Trends in Deep Learning Based Natural Language Processing (2017)

Deep learning methods employ multiple processing layers to learn hierarchical representations of data and have produced state-of-the-art results in many domains. Recently, a variety of model designs and methods have blossomed in the context of natural language processing (NLP). In this paper, we review significant deep learning related models and methods that have been employed for numerous NLP tasks and provide a walk-through of their evolution. We also summarize, compare and contrast the various models and put forward a detailed understanding of the past, present and future of deep learning in NLP.
Time course of the increase in the myocardial slow inward current after a photochemically generated concentration jump of intracellular cAMP. (1983)

Voltage-clamped atrial trabeculae from bullfrog hearts were exposed to membrane-permeant photolyzable o-nitrobenzyl esters of cAMP and cGMP. UV flashes produced intracellular concentration jumps of cAMP or cGMP. With the cAMP derivative, flashes resulted in an increased slow inward current (Isi), producing a broadened action potential. The Isi reached a maximum 10-30 sec after the flash and decreased over the next 60-300 sec. The first increases were observable within 150 msec; this value is an upper limit imposed by the instrumentation. Responses to flashes lasted longer at higher drug concentrations and in the presence of the phosphodiesterase inhibitor papaverine; effects of flashes developed and decreased faster at higher temperature. Although the amplitude of the Isi was increased, its waveform and voltage sensitivity were not affected. Intracellular concentration jumps of cAMP failed to affect the muscarinic K+ conductance. There were no observable effects of cGMP concentration jumps. The data confirm (i) that cAMP regulates the Isi and (ii) that the 5- to 10-sec delay between application of beta-agonists and the onset of positive inotropic effects, observed in previous studies, has been correctly ascribed to events prior to the interaction between cAMP and protein kinase.
Treatment of non-alcoholic fatty liver disease (2006)

Non-alcoholic fatty liver disease (NAFLD) is common and may progress to cirrhosis and its complications. The pathogenesis of steatosis and cellular injury is thought to be related mostly to insulin resistance and oxidative stress. Therefore, management entails identification and treatment of metabolic risk factors, improving insulin sensitivity, and increasing antioxidant defences in the liver. Weight loss and exercise improve insulin sensitivity. Bariatric surgery may improve liver histology in patients with morbid obesity. Insulin sensitising drugs showed promise in pilot trials as have a number of hepatoprotective agents. Further randomised, well controlled trials are required to determine the efficacy of these drugs.
Line coding for dispersion tolerance and spectral efficiency: duobinary and beyond (2003)

We propose and analyze a new class of transmission line codes that dramatically increase the dispersion tolerance and spectral efficiency of dense wavelength-division multiplexing transmission. These codes generalize and optimize duobinary signaling, yielding new binary and multibit data representations.
Peptide Microarrays for the Determination of Protease Substrate Specificity (2002)

A method is described for the preparation of substrate microarrays that allow for the rapid determination of protease substrate specificity. Peptidyl coumarin substrates, synthesized on solid support using standard techniques, are printed onto glass slides using DNA microarraying equipment. The linkage from the peptide to the slide is formed through a chemoselective reaction, resulting in an array of uniformly displayed fluorogenic substrates. The arrays can be treated with proteases to yield substrate specificity profiles. Standard instrumentation for visualization of microarrays can be used to obtain comparisons of the specificity constants for all of the prepared substrates. The utility of these arrays is demonstrated by the selective cleavage of preferred substrates with trypsin, thrombin, and granzyme B, and by assessing the extended substrate specificity of thrombin using a microarray of 361 different peptidyl coumarin substrates.
Population genetics of coagulant factor IX: frequencies of two DNA polymorphisms in five ethnic groups. (1987)

Two frequently used restriction-enzyme polymorphisms (RFLPs) of coagulant F.IX, TaqI and XmnI, have been examined in five ethnic groups: white Americans, black Americans, East Indians, Chinese, and Malays. There is a distinct "cline" in the frequencies of both polymorphisms, from white Americans to Malays. The rarer type 2 alleles of both polymorphisms, in which middle recognition sites are present--and which in our sample reach their highest frequencies in white Americans--are marginally higher in four groups of Europeans previously reported by others. The frequencies of the rarer alleles are significantly higher in Europeans than in black Americans and East Indians, and these alleles are essentially absent in Chinese and Malays. The frequency of heterozygosity diminishes in the same order, being zero in Malays for both polymorphisms. The polymorphisms are in strong linkage disequilibrium, and in all groups the type 1 allele for TaqI is disproportionately accompanied by the type 1 allele for XmnI. The paucity of type 2 alleles and the low rate of heterozygosity in four non-European groups suggest that the polymorphisms will be of little diagnostic value south of Gibraltar and east of Suez. This prediction is confirmed by the observed haplotype frequencies in the black American and the Oriental groups.
Enhancement of the antiproliferative activity of human interferon by polyamine depletion. (1985)

Recombinant leukocyte type A human interferon and human lymphoblastoid interferon in combination with alpha-difluoromethylornithine (DFMO), an inhibitor of polyamine biosynthesis, have synergistic antiproliferative activity against colony formation in vitro by human tumor cells differing greater than 1000-fold in their intrinsic sensitivity to inhibitory effects of interferon. Interferon and DFMO in combination with doxorubicin have greater antiproliferative activity than is expected on the basis of additive effects based on the activity of doxorubicin alone and the synergistic activity of interferon plus DFMO. The addition of the polyamine putrescine to the cell cultures eliminates the synergistic interactions of interferon and DFMO and does not inhibit the activity of interferon itself. Aspirin and indomethacin at concentrations in vitro greater than those required for anti-inflammatory activity in vivo did not inhibit the antiproliferative activity of interferon alone and did not inhibit the synergistic activity of the combination of interferon and DFMO. Combination regimens including interferon and DFMO merit clinical evaluation for therapeutic activity against advanced cancers. Nonsteroidal anti-inflammatory agents should be studied for their ability to ameliorate symptomatic toxicity from interferon.
Collagen-IV and laminin-1 regulate estrogen receptor α expression and function in mouse mammary epithelial cells (2003)

The expression level and functional activity of estrogen receptor alpha is an important determinant of breast physiology and breast cancer treatment. However, it has been difficult to identify the signals that regulate estrogen receptor because cultured mammary epithelial cells generally do not respond to estrogenic signals. Here, we use a combination of two- and three-dimensional culture systems to dissect the extracellular signals that control endogenous estrogen receptor alpha. Its expression was greatly reduced when primary mammary epithelial cells were placed on tissue culture plastic; however, the presence of a reconstituted basement membrane in combination with lactogenic hormones partially prevented this decrease. Estrogen receptor alpha expression in primary mammary fibroblasts was not altered by these culture conditions, indicating that its regulation is cell type specific. Moreover, estrogen receptor-dependent reporter gene expression, as well as estrogen receptor alpha levels, were increased threefold in a functionally normal mammary epithelial cell line when reconstituted basement membrane was added to the medium. This regulatory effect of reconstituted basement membrane was reproduced by two of its components, collagen-IV and laminin-1, and it was blocked by antibodies against alpha2, alpha6 and beta1 integrin subunits. Our results indicate that integrin-mediated response to specific basement membrane components, rather than cell rounding or cell growth arrest induced by reconstituted basement membrane, is critical in the regulation of estrogen receptor alpha expression and function in mammary epithelial cells.
Multi-laboratory comparison of three heparin-Mn2+ precipitation procedures for estimating cholesterol in high-density lipoprotein. (1978)

Plasma high-density lipoprotein is commonly estimated by measuring the cholesterol remaining in plasma supernatant solutions after other lipoproteins, which contain apolipoprotein B, are precipitated with heparin and Mn2+. The method (method I) now in use by the Lipid Research Clinics, in which Mn2+ is at 46 mmol/liter final concentration, is reasonably accurate, but precipitation and sedimentation of lipoproteins other than high-density lipoproteins is often incomplete. We evaluated two modifications of method I. In method II, the Mn2+ concentration was doubled; the second modification (method III) included the increased Mn2+ concentration in a combined heparin Mn2+ reagent, decreased sample volume (2 ml), and a shorter incubation time (10 min at room temperature). The percentages of samples with turbid supernates (i.e., incomplete sedimentation) by methods I, II, and III were 9, 3, and 2%, respectively. Among non-turbid supernates, the percentages of samples containing measurable apolipoprotein B (incomplete precipitation) were 79, 19, and 16%, respectively. We conclude that method III is the most convenient and accurate of the three procedures.
Curcumin Binding to Beta Amyloid: A Computational Study (2015)

Curcumin, a chemical constituent present in the spice turmeric, is known to prevent the aggregation of amyloid peptide implicated in the pathophysiology of Alzheimer's disease. While curcumin is known to bind directly to various amyloid aggregates, no systematic investigations have been carried out to understand its ability to bind to the amyloid aggregates including oligomers and fibrils. In this study, we constructed computational models of (i) Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper β-sheet assembly and (ii) full-length Aβ fibril β-sheet assembly. Curcumin binding in these models was evaluated by molecular docking and molecular dynamics (MD) simulation studies. In both the models, curcumin was oriented in a linear extended conformation parallel to fiber axis and exhibited better stability in the Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper model (Ebinding = -10.05 kcal/mol) compared to full-length Aβ fibril model (Ebinding = -3.47 kcal/mol). Analysis of MD trajectories of curcumin bound to full-length Aβ fibril shows good stability with minimum Cα-atom RMSD shifts. Interestingly, curcumin binding led to marked fluctuations in the (14) HQKLVFFA(21) region that constitute the fibril spine with RMSF values ranging from 1.4 to 3.6 Å. These results show that curcumin binding to Aβ shifts the equilibrium in the aggregation pathway by promoting the formation of non-toxic aggregates.
Dynamic Playlist Generation Based On Skipping Behavior. (2005)

[TODO] Add abstract here.