gebhart/patrepeval huggingface dataset:
High-efficiency retroviral vector mediated gene transfer into human peripheral blood CD4+ T lymphocytes. (1996)

Genetic modification of peripheral blood T lymphocytes has been proposed as a therapeutic strategy for treating congenital disorders, cancer and viral diseases. Central to all T lymphocyte-based gene therapy strategies is the ability to efficiently and stably deliver genes into primary T lymphocytes. In this study, we sought to increase the gene transfer efficiency in CD4+ peripheral blood T lymphocytes using procedures which could be utilized in clinical applications. In order to quantity the gene transfer efficiency in primary CD4+ T cells, a high-titer retroviral vector which efficiently expresses a truncated version of the human low-affinity nerve growth factor receptor (delta LNGFR) was constructed. Transduced cells were then accurately enumerated with immunofluorescence staining and fluorescence activated cell sorting (FACS) analysis and rapidly isolated at high purity for further analysis. Using this system, a supernatant-based gene transfer procedure was developed which routinely yields gene transfer efficiencies of 25-40% into a wide repertoire of both freshly obtained and cryopreserved peripheral blood CD4+ T lymphocytes.
Isolation of Protein Subpopulations Undergoing Protein-Protein Interactions (2002)

A new method is described for isolating and identifying proteins participating in protein-protein interactions in a complex mixture. The method uses a cyanogen bromide-activated Sepharose matrix to isolate proteins that are non-covalently bound to other proteins. Because the proteins are accessible to chemical manipulation, mass spectrometric identification of the proteins can yield information on specific classes of interacting proteins, such as calcium-dependent or substrate-dependent protein interactions. This permits selection of a subpopulation of proteins from a complex mixture on the basis of specified interaction criteria. The new method has the advantage of screening the entire proteome simultaneously, unlike the two-hybrid system or phage display, which can only detect proteins binding to a single bait protein at a time. The method was tested by selecting rat brain extract for proteins exhibiting calcium-dependent protein interactions. Of 12 proteins identified by mass spectrometry, eight were either known calcium-binding proteins or proteins with known calcium-dependent protein interactions, indicating that the method is capable of enriching a subpopulation of proteins from a complex mixture on the basis of a specific class of protein interactions. Because only naturally occurring interactions of proteins in their native state are observed, this method will have wide applicability to studies of protein interactions in tissue samples and autopsy specimens, for screening for perturbations of protein-protein interactions by signaling molecules, pharmacological agents or toxins, and screening for differences between cancerous and untransformed cells.
Purification and partial characterization of a human hematopoietic precursor population (1991)

This study reports the development of an assay, the Pre-colony-forming unit (CFU) assay, which detects human hematopoietic precursors. The Pre- CFU assay is based on the observation that precursors to CFU- granulocyte-macrophage (CFU-GM) that are undetectable in clonogenic assays differentiate into CFU-GM preferentially following treatment in suspension culture with recombinant human interleukin-1 alpha (rhIL-1 alpha) combined with rhIL-3. Using the Pre-CFU assay, hematopoietic precursors were detected in human bone marrow depleted of CFU-GM progenitors and differentiated hematopoietic elements via 4- hydroperoxycyclophosphamide treatment coupled with selection for CD34+ cells (4-HCresistant/CD34+ marrow). Additionally, the Pre-CFU assay detected recovery of hematopoiesis substantially earlier than the CFU- GM assay in primates following myeloablation with 5-fluorouracil. The Pre-CFU assay was used to asses purification of a phenotypically defined hematopoietic precursor population, the lin-CD34+ population. The lin-CD34+ population lacks detectable surface markers for T-cell, B- cell, natural killer cell, and myeloid lineage, possesses the CD34 antigen, is devoid of CFU-GM progenitors, and yields Pre-CFU assay values comparable with 4-HCresistant/CD34+ marrow. Using a combination of phenotypic analysis and Pre-CFU assay analysis, the action of rhIL-1 alpha plus rhIL-3 treatment on lin-CD34+ cells was further characterized. The data indicate that rhIL-1 alpha plus rhIL-3 treatment induces proliferation and differentiation of early hematopoietic precursors into progenitors and terminally differentiated cells, without inducing a significant expansion of the precursor population itself.
Interface imprinting by a rippled shock using an intense laser (2001)

Perturbation imprinting at a flat interface by a rippled shock has been observed in a laser hydrodynamics experiment. A strong shock was driven through a three-layer target, with the first interface rippled, and the second flat. The chosen thickness of the second layer gave instability growth with opposite phases at the two interfaces, consistent with two-dimensional simulations and rippled shock theory.
Drug-induced Nonalcoholic Steatohepatitis (2016)

Nonalcoholic steatohepatitis (NASH) is a chronic progressive liver disease characterized by intense liver steatosis accompanied by hepatocyte destruction, inflammation and fibrous, despite little or no history of alcoholic consumption. There are also cases of drug-induced secondary steatohepatitis. Drug-induced steatohepatitis is a relatively rare type of drug-induced liver disease, but close attention to the possible onset of steatohepatitis is needed when drugs with the potential to induce fatty liver are prescribed for long term use. Estrogen is a factor indispensable to smooth fatty acid β-oxidation in hepatocytes. However, treatment with Tamoxifen markedly suppresses fatty acid β-oxidation in the liver. As free fatty acids are toxic, their accumulation results in the activation of alternative fatty acid oxidation pathways mediated by CYP2E1 in cytosol and lipid peroxidases in peroxisomes in hepatocytes. CYP2E1 enhances lipid peroxidation and dicarboxylic acid synthesis via the activation of fatty acid ω-oxidation that injures mitochondria and results in the emergence of ballooned hepatocytes. In such cases, the attenuation of alternative fatty acid oxidation pathways could have some beneficial effects on mitochondrial injury, since fibrates (PPAR-α ligands) are potent enough to stimulate neutral fat consumption through the activation of peroxisomal fatty acid β-oxidation. Fortunately, fibrates attenuate serum estrogen levels by affecting estrogen receptor expression, so the co-administration of fibrates with Tamoxifen is expected to exert higher efficacy in breast cancer patients with Tamoxifen-induced hepatic steatosis.
Prorenin is the endogenous agonist of the (pro)renin receptor. Binding kinetics of renin and prorenin in rat vascular smooth muscle cells overexpressing the human (pro)renin receptor (2007)

H(P)RRs preferentially bind prorenin, and such binding results in angiotensin generation, most likely because binding results in prorenin activation.
Alginate as immobilization material: I. Correlation between chemical and physical properties of alginate gel beads (1989)

Calcium alginate gel beads were prepared from a range of well characterized alginates. The physical properties of beads depended strongly on the composition, sequential structure, and molecular size of the polymers. Beads with the highest mechanical strength, lowest shrinkage, best stability towards monovalent cations, and highest porosity were made from alginate with a content of L-guluronic acid higher than 70% and an average length of the G-blocks higher than 15. For these "high G" alginates the critical overlap intrinsic viscosities have been determined, and for molecular weight higher than 2.4 x 10(5), the gel strength was independent of the molecular weight.
Novel therapies for meningiomas (2006)

Although advances in surgery, radiation therapy and stereotactic radiosurgery have significantly improved the treatment of meningiomas, there remains an important subset of patients who remain refractory to conventional therapy. Treatment with chemotherapeutic agents such as hydroxyurea and alpha-interferon has provided minimal benefit. In this review, the role of newly emerging novel therapies for meningiomas, with a focus on targeted molecular agents, will be discussed.
Expansion of a CD8+PD-1+ Replicative Senescence Phenotype in Early Stage CLL Patients Is Associated with Inverted CD4:CD8 Ratios and Disease Progression (2011)

Our data show that the emergence of CD8(+)PD-1(+) replicative senescence phenotype in early stage CLL patients is associated with more aggressive clinical disease. Importantly, these findings were independent of tumor cell prognostic markers and could not be accounted for by patient age, changes in regulatory T-cell frequency, or cytomegalovirus serostatus (n = 217).
Oligonucleotides Containing Novel 4′-C- or 3′-C-(Aminoalkyl)-Branched Thymidines (2000)

The synthesis of four novel 3′-C-branched and 4′-C-branched nucleosides and their transformation into the corresponding 3′-O-phosphoramidite building blocks for automated oligonucleotide synthesis is reported. The 4′-C-branched key intermediate 11 was synthesized by a convergent strategy and converted to its 2′-O-methyl and 2′-deoxy-2′-fluoro derivatives, leading to the preparation of novel oligonucleotide analogues containing 4′-C-(aminomethyl)-2′-O-methyl monomer X and 4′-C-(aminomethyl)-2′-deoxy-2′-fluoro monomer Y (Schemes 2 and 3). In general, increased binding affinity towards complementary single-stranded DNA and RNA was obtained with these analogues compared to the unmodified references (Table 1). The presence of monomer X or monomer Y in a 2′-O-methyl-RNA oligonucleotide had a negative effect on the binding affinity of the 2′-O-methyl-RNA oligonucleotide towards DNA and RNA. Starting from the 3′-C-allyl derivative 28, 3′-C-(3-aminopropyl)-protected nucleosides and 3′-O-phosphoramidite derivatives were synthesized, leading to novel oligonucleotide analogues containing 3′-C-(3-aminopropyl)thymidine monomer Z or the corresponding 3′-C-(3-aminopropyl)-2′-O,5-dimethyluridine monomer W (Schemes 4 and 5). Incorporation of the 2′-deoxy monomer Z induced no significant changes in the binding affinity towards DNA but decreased binding affinity towards RNA, while the 2′-O-methyl monomer Z induced decreased binding affinity towards DNA as well as RNA complements (Table 2).
Pharmacogenomics of codeine, morphine, and morphine-6-glucuronide: model-based analysis of the influence of CYP2D6 activity, UGT2B7 activity, renal impairment, and CYP3A4 inhibition. (2012)

Overall, the model-based analysis predicts a wide range of morphine levels after codeine administration and supports recent doubts about safe and efficacious use of codeine for analgesia in non-genotyped individuals.
Use of amino acid composition to predict epitope residues of individual antibodies (2010)

We identified specific amino acid propensities at the interfaces of antigen-antibody interactions in non-redundant qualified antigen-antibody complex structures from Protein Data Bank. Propensities were expressed by the frequency of each of the 20 x 20 standard amino acid pairs that appeared at the interfaces of the complexes and were named the antibody-specific epitope propensity (ASEP) index. Using this index, we developed a novel method of predicting epitope residues for individual antibodies by narrowing down candidate epitope residues which was predicted by the conventional method. The 74 benchmarked antigens were used in ASEP prediction. The efficiency of this method was assessed using the leave-one-out approach. On elimination of residues with ASEP indices in the lowest 10% of all measured, true positives were enriched for 49 antigens. On subsequent elimination of residues with ASEP indices in the lowest 50%, true positives were enriched for 40 of the 74 antigens assessed. The ASEP index is the first benchmark proposed to predict epitope residues for an individual antibody. Used in combination with mutation experiments, this index has the potential to markedly increase the success ratio of epitope analysis.
Consistent Depth Maps Recovery from a Video Sequence (2009)

This paper presents a novel method for recovering consistent depth maps from a video sequence. We propose a bundle optimization framework to address the major difficulties in stereo reconstruction, such as dealing with image noise, occlusions, and outliers. Different from the typical multi-view stereo methods, our approach not only imposes the photo-consistency constraint, but also explicitly associates the geometric coherence with multiple frames in a statistical way. It thus can naturally maintain the temporal coherence of the recovered dense depth maps without over-smoothing. To make the inference tractable, we introduce an iterative optimization scheme by first initializing the disparity maps using a segmentation prior and then refining the disparities by means of bundle optimization. Instead of defining the visibility parameters, our method implicitly models the reconstruction noise as well as the probabilistic visibility. After bundle optimization, we introduce an efficient space-time fusion algorithm to further reduce the reconstruction noise. Our automatic depth recovery is evaluated using a variety of challenging video examples.
Accuracy assessment protocols for electromagnetic tracking systems (2003)

Electromagnetic tracking systems have found increasing use in medical applications during the last few years. As with most non-trivial spatial measurement systems, the complex determination of positions and orientations from their underlying raw sensor measurements results in complicated, non-uniform error distributions over the specified measurement volume. This makes it difficult to unambiguously determine accuracy and performance assessments that allow users to judge the suitability of these systems for their particular needs. Various assessment protocols generally emphasize different measurement aspects that typically arise in clinical use. This can easily lead to inconclusive or even contradictory conclusions. We examine some of the major issues involved and discuss three useful calibration protocols. The measurement accuracy of a system can be described in terms of its 'trueness' and its 'precision'. Often, the two are strongly coupled and cannot be easily determined independently. We present a method that allows the two to be disentangled, so that the resultant trueness properly represents the systematic, non-reducible part of the measurement error, and the resultant precision (or repeatability) represents only the statistical, reducible part. Although the discussion is given largely within the context of electromagnetic tracking systems, many of the results are applicable to measurement systems in general.
Adrenergic alpha 1 and alpha 2 binding sites are present in bovine retinal blood vessels. (1987)

Bovine retinal vessels have sites that specifically bind 3H-p-aminoclonidine (3H-PAC) with an apparent dissociation constant of 0.12 nM and a capacity of binding of 0.15 pmol/g. In addition, these vessels have 3H-prazosin binding sites bearing a dissociation constant of 5 nM and a binding capacity of 5 pmol/g. To understand the implications for retina-optic nerve vascular physiology and pathophysiology, studies of the exact location of the binding sites, the bioavailability of the adrenergic agonists, and the physiological responses to receptor stimulation in both normal and pathological states are required. The neural elements of the retina also have binding sites for 3H-PAC with an apparent dissociation constant of 0.38 nM in larger quantities (6.7 pmol/g tissue) than in the vascular elements. There are also binding sites for 3H-prazosin in a lower amount than in the vascular fraction (3 pmol/g tissue) with a dissociation constant of 2.4 nM. These sites are presumably related to the use of norepinephrine and dopamine as neurotransmitters by retinal neurons.
Synthesis and Characterization of Multiresponsive Core−Shell Microgels (2000)

We report the synthesis and characterization of temperature and pH responsive hydrogel particles (microgels) with core−shell morphologies. Core particles composed of cross-linked poly(N-isopropylacrylamide) (p-NIPAm) or poly(NIPAm-co-acrylic acid) (p-NIPAm-AAc) were synthesized via precipitation polymerization and then used as nuclei for subsequent polymerization of p-NIPAm-AAc and p-NIPAm, respectively. The presence of a core−shell morphology was confirmed by transmission electron microscopy (TEM). Thermally initiated volume phase transitions were interrogated via temperature-programmed photon correlation spectroscopy (TP-PCS) as a function of solution pH. The p-NIPAm-AAc core hydrogel displays both a strong temperature and pH dependence on swelling. However, both p-NIPAm-AAc (core)/p-NIPAm (shell) and p-NIPAm (core)/p-NIPAm-AAc (shell) particles display a more complex pH dependence than the homogeneous particles. Specifically, a multistep volume phase transition appears when the AAc component becomes highly charged at a high pH. It is apparent from the measured deswelling curves that a portion of the particle swelling behavior is dominated by p-NIPAm, regardless of its location in the particle. However, deswelling behavior that is due to a mixture of p-NIPAm-AAc and p-NIPAm is evident, as well as a regime that is largely attributed to p-NIPAm-AAc alone. Small differences in the effect of pH on the two core−shell particles indicate that the influence of p-NIPAm is somewhat greater when it is localized in the shell.
Reagentless, Reusable, Ultrasensitive Electrochemical Molecular Beacon Aptasensor (2005)

A bifunctional derivative of the thrombin-binding aptamer with a redox-active Fc moiety and a thiol group at the termini of the aptamer strand was synthesized. The ferrocene-labeled aptamer thiol was self-assembled through S-Au bonding on a polycrystalline gold electrode surface and the surface was blocked with 2-mercaptoethanol to form a mixed monolayer. By use of a fluorescent molecular beacon, the effect of counterions on quadruplex formation was established. The aptamer-modified electrode was characterized electrochemically by cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). The modified electrode showed a voltammetric signal due to a one-step redox reaction of the surface-confined ferrocenyl moiety of the aptamer immobilized on the electrode surface in 10 mM N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid (HEPES) buffer of pH 8.0. An increase in the DPV current signal was evident after blocking with 2-mercaptoethanol, effectively removing aptamer nonspecifically absorbed rather than bound to electrode surface or due to the formation of the aptamer-thrombin affinity interaction. The impedance measurement, in agreement with the differential pulse voltammetry (DPV), showed decreased Faradaic resistances in the same sequence. The "signal-on" upon thrombin association could be attributed to a change in conformation from random coil-like configuration on the probe-modified film to the quadruplex structure. The DPV of the modified electrode showed a linear response of the Fc oxidation signal to the increase in the thrombin concentration in the range between 5.0 and 35.0 nM with a linear correlation of r = 0.9988 and a detection limit of 0.5 nM. The molecular beacon aptasensor was amenable to full regeneration by simply unfolding the aptamer in 1.0 M HCl, and could be regenerated 25 times with no loss in electrochemical signal upon subsequent thrombin binding.
Efficient targeted mutagenesis of rice and tobacco genomes using Cpf1 from Francisella novicida (2016)

CRISPR/Cas9 systems are nowadays applied extensively to effect genome editing in various organisms including plants. CRISPR from Prevotella and Francisella 1 (Cpf1) is a newly characterized RNA-guided endonuclease that has two distinct features as compared to Cas9. First, Cpf1 utilizes a thymidine-rich protospacer adjacent motif (PAM) while Cas9 prefers a guanidine-rich PAM. Cpf1 could be used as a sequence-specific nuclease to target AT-rich regions of a genome that Cas9 had difficulty accessing. Second, Cpf1 generates DNA ends with a 5' overhang, whereas Cas9 creates blunt DNA ends after cleavage. "Sticky" DNA ends should increase the efficiency of insertion of a desired DNA fragment into the Cpf1-cleaved site using complementary DNA ends. Therefore, Cpf1 could be a potent tool for precise genome engineering. To evaluate whether Cpf1 can be applied to plant genome editing, we selected Cpf1 from Francisella novicida (FnCpf1), which recognizes a shorter PAM (TTN) within known Cpf1 proteins, and applied it to targeted mutagenesis in tobacco and rice. Our results show that targeted mutagenesis had occurred in transgenic plants expressing FnCpf1 with crRNA. Deletions of the targeted region were the most frequently observed mutations. Our results demonstrate that FnCpf1 can be applied successfully to genome engineering in plants.
Correcting for the Sampling Bias Problem in Spike Train Information Measures (2007)

Information Theory enables the quantification of how much information a neuronal response carries about external stimuli and is hence a natural analytic framework for studying neural coding. The main difficulty in its practical application to spike train analysis is that estimates of neuronal information from experimental data are prone to a systematic error (called "bias"). This bias is an inevitable consequence of the limited number of stimulus-response samples that it is possible to record in a real experiment. In this paper, we first explain the origin and the implications of the bias problem in spike train analysis. We then review and evaluate some recent general-purpose methods to correct for sampling bias: the Panzeri-Treves, Quadratic Extrapolation, Best Universal Bound, Nemenman-Shafee-Bialek procedures, and a recently proposed shuffling bias reduction procedure. Finally, we make practical recommendations for the accurate computation of information from spike trains. Our main recommendation is to estimate information using the shuffling bias reduction procedure in combination with one of the other four general purpose bias reduction procedures mentioned in the preceding text. This provides information estimates with acceptable variance and which are unbiased even when the number of trials per stimulus is as small as the number of possible discrete neuronal responses.
Validation of reference genes for quantitative RT-PCR studies of gene expression in perennial ryegrass (Lolium perenne L.) (2010)

This study is unique in the magnitude of samples tested with the inclusion of numerous field-grown samples, helping pave the way to conduct gene expression studies in perennial biomass crops under field-conditions. From our study several stably expressed reference genes have been validated. This provides useful candidates for reference gene selection in perennial ryegrass under conditions other than those tested here.