gebhart/patrepeval huggingface dataset:
Isolation and some characteristics of anaerobic oxalate-degrading bacteria from the rumen (1980)

Obligately anaerobic oxalate-degrading bacteria were isolated from an enriched population of rumen bacteria in an oxalate-containing medium that had been depleted of other readily metabolized substrates. These organisms, which are the first reported anaerobic oxalate degraders isolated from the rumen, were gram negative, nonmotile rods. They grew in a medium containing sodium oxalate, yeast extract, cysteine, and minerals. The only substrate that supported growth was oxalate. Growth was directly related to the concentration of oxalate in the medium (1 to 111 mM), and cell yields were approximately 1.1 g (dry weight)/mol of oxalate degraded. Oxalate was stoichiometrically degraded to CO2 and formate. These anaerobes occupy a unique ecological niche and are distinct from any previously described oxalate-degrading bacteria.
Two distinct HLA-A0201–presented epitopes of the Wilms tumor antigen 1 can function as targets for leukemia-reactive CTL (2002)

Using the allo-restricted T-cell approach to circumvent tolerance, we have previously identified a cytotoxic T-lymphocyte (CTL) epitope in the transcription factor Wilms tumor antigen 1 (WT1) presented by HLA-A0201 (A2) class I molecules. Here we describe an additional A2-presented epitope and show that CTLs against both epitopes kill WT1-expressing leukemia cell lines. Colony-forming assays demonstrated that both types of CTL killed CD34(+) progenitor cells from A2(+) leukemia patients, but not from A2(+) healthy individuals. The long-term culture-initiating cell (LTC-IC) assay was used to analyze the killing activity of WT1-specific CTLs against the more immature fraction of CD34(+) cells. The CTLs killed LTC-ICs of patients with chronic myelogenous leukemia (CML), whereas the function of normal CD34(+) progenitor/stem cells was not inhibited. Together, the data show that CTLs specific for 2 distinct peptide epitopes of WT1 can discriminate between normal and leukemia LTC-ICs, suggesting that such CTLs have the potential to selectively kill CML progenitor/stem cells.
Functional Consequences of Prejunctional Receptor Activation or Blockade in the Iris (1994)

The iris is innervated by nerves of the sympathetic, parasympathetic, and sensory nervous systems. The terminal nerve fibres are endowed with prejunctional receptors which modulate neurotransmitter release. Activation or blockade of prejunctional receptors by drugs may have an influence on iris smooth muscle tone. Several findings are in favour of the hypothesis that prejunctional receptors may be involved in regulation of iris smooth muscle tone and/or pathophysiological events. (i). Release of acetylcholine from parasympathetic nerves of guinea-pig iris sphincter evoked by electrical stimulation is subject to autoinhibition via prejunctional M2 muscarinic receptors, and the release can be enhanced by M2 selective antagonists such as methoctramine or gallamine. Concomitantly with the increased neurotransmitter release, the sphincter contraction is enhanced in the presence of M2 antagonists, since the postjunctional muscarinic receptors (presumably M3, or at least not M2) are not simultaneously blocked. Unlike the non-selective blocker atropine, M2 antagonists are not expected to cause mydriasis but rather miosis. (ii). Sensory nerves are involved in pathophysiological events following ocular irritation. Release of substance P and/or neurokinin A from sensory nerves of rabbit iris is followed by a non-adrenergic-non-cholinergic iris sphincter contraction (mediated by NK1 and NK3 receptors) which can be used to estimate sensory neurotransmitter release. Exocytotic release of the sensory neurotransmitters is inhibited by activation of alpha 2B-adrenoceptors and probably also via putative prejunctional imidazoline receptors. Alpha-adrenoceptors are stimulated by oxymetazoline and other imidazoline derivatives (which are agonists at imidazoline receptors) leading to a reduction of sensory neurotransmitter release, as evident from a decrease in evoked sphincter contraction. Imidazolines in eye drops may not only cause relief in ocular inflammation due to postjunctional vasoconstriction but also possibly due to a prejunctional effect, a reduction of sensory neurotransmitter release. Reinforcement of inflammation due to release of sensory neurotransmitters may thus be prevented.
The molecular structure of spider dragline silk: Folding and orientation of the protein backbone (2002)

The design principles of spider dragline silk, nature's high-performance fiber, are still largely unknown, in particular for the noncrystalline glycine-rich domains, which form the bulk of the material. Here we apply two-dimensional solid-state NMR to determine the distribution of the backbone torsion angles (phi,psi) as well as the orientation of the polypeptide backbone toward the fiber at both the glycine and alanine residues. Instead of an "amorphous matrix," suggested earlier for the glycine-rich domains, these new data indicate that all domains in dragline silk have a preferred secondary structure and are strongly oriented, with the chains predominantly parallel to the fiber. As proposed previously, the alanine residues are predominantly found in a beta sheet conformation. The glycine residues are partly incorporated into the beta sheets and otherwise form helical structures with an approximate 3-fold symmetry.
Fluorene Analogues of Prodan with Superior Fluorescence Brightness and Solvatochromism (2010)

In a search for environmentally sensitive (solvatochromic) dyes with superior properties, we extended the electronic conjugation of one of the best solvatochromic dyes, Prodan, by substituting its naphthalene core with fluorene. The newly synthesized fluorene derivatives bearing strong electron-donor (dialkylamino) and -acceptor (carbonyl) groups at the 2 and 7 positions showed red-shifted absorption (close to 400 nm), twice as large of a absorption coefficient (43 000 M−1 cm−1), and a manifold larger two-photon absorption cross section (∼400 GM) compared to Prodan. Studies in solvents revealed much stronger fluorescence solvatochromism of the new dyes, which is connected with their twice as large transition dipole moment (14.0 D). Similarly to Prodan, they exhibit high fluorescence quantum yields, while their photostability is largely improved. Thus, substitution of the naphthalene core in Prodan with fluorene resulted in new fluorophores with superior spectroscopic and solvatochromic properties. We expect them to find a variety of applications as environmentally sensitive probes and labels in biology.
The Enzymic and Chemically Induced Decomposition of Glucosinolates (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Fatal lymphoreticular disease in the scurfy (sf) mouse requires T cells that mature in a sf thymic environment: potential model for thymic education. (1991)

Characteristic lesions in mice hemi- or homozygous for the X-linked mutation scurfy (sf) include lymphohistiocytic proliferation in the skin and lymphoid organs, Coombs' test-positive anemia, hypergammaglobulinemia, and death by 24 days of age. The role of the thymus in the development of fatal lymphoreticular disease in the scurfy mouse was investigated. Neonatal thymectomy doubles the life span of scurfy mice, moderates the histologic lesions, and prevents anemia, despite the continued presence of high levels of serum IgG. Animals bred to be nude and scurfy (nu/nu; sf/Y) are viable, fertile, and free of scurfy lesions. Bone marrow from scurfy mice can reconstitute lethally irradiated, H-2-compatible animals but does not transmit scurfy disease. We conclude, from these data, that scurfy lesions are mediated by T lymphocytes that mature in an abnormal (sf) thymic environment.
Androgen Receptor Interacts with the Positive Elongation Factor P-TEFb and Enhances the Efficiency of Transcriptional Elongation (2001)

Androgen receptor (AR) may communicate with the general transcription machinery on the core promoter to exert its function as a transcriptional modulator. Our previous report demonstrated that the AR interacted with transcription factor IIH (TFIIH) under physiological conditions and that overexpression of Cdk-activating kinase, the kinase moiety of TFIIH, enhanced AR-mediated transcription in prostate cancer cells. In an effort to further dissect the mechanisms implicated in AR transactivation, we report here that AR interacts with PITALRE, a kinase subunit of positive elongation factor b (P-TEFb). Cotransfection of the plasmid encoding the mutant PITALRE (mtPITALRE), defective in its RNA polymerase II COOH-terminal domain (CTD)-kinase activity, resulted in preferential inhibition of AR-mediated transactivation. Indeed, AR transactivation in PC-3 cells was preferentially inhibited at the low concentration of 5,6-dichloro-1-beta-d-ribofuranosylbenzimidazole (DRB), a CTD kinase inhibitor. These results suggest that CTD phosphorylation may play an important role in AR-mediated transcription. Furthermore, a nuclear run-on transcription assay of the prostate-specific antigen gene, an androgen-inducible gene, showed that transcription efficiency of the distal region of the gene was enhanced upon androgen induction. Taken together, our reports suggest that AR interacts with TFIIH and P-TEFb and enhances the elongation stage of transcription.
Sepsis (2007)

The burden of sepsis on our health care system is significant, with approximately 750,000 cases per year in the United States, 215,000 resultant deaths, and annual costs of $16.7 billion nationally (1). Organ failure is a significant contributor to mortality, with renal failure occurring in approximately 15% of patients (2). In a large registry of critically ill patients with acute renal failure, in 19% of whom was sepsis identified as the presumed cause, in-hospital mortality was 37% with a combined outcome of death or dialysis dependence in 50% (3). Clinicians are challenged to manage this disease in an aging population with multiple comorbidities, immunosuppression, and a changing pattern of causative microorganisms (2,4).

The increasing incidence of sepsis and the unacceptably high mortality rates associated with the disease have led to global efforts to understand pathophysiology, improve early diagnosis, and standardize management (5). Understanding the spectrum of the disease is important for gauging severity, determining prognosis, and developing methods for standardization of care in sepsis. At an international consensus conference in 1991, sepsis was defined as the systemic inflammatory response syndrome (SIRS) with a suspected source of infection. SIRS is defined as two or more of the following perturbations: Temperature >38 or 90 beats per minute; respiratory rate >20 breaths per minute or Paco2 12,000/mm3, 10% immature band forms. Organ dysfunction and hypoperfusion abnormalities characterize severe sepsis, and septic shock includes sepsis-induced hypotension despite adequate fluid resuscitation (6). These definitions allowed for a more uniform approach to clinical trials, hypothesis generation, and the care of the patient with sepsis.

The use of SIRS criteria for the identification of sepsis have been believed by many to be arbitrary and nonspecific. In 2001, …
Increased Frequency of Cysteine, Tyrosine, and Phenylalanine Residues Since the Last Universal Ancestor (2002)

Analysis of extant proteomes has the potential of revealing how amino acid frequencies within proteins have evolved over biological time. Evidence is presented here that cysteine, tyrosine, and phenylalanine residues have substantially increased in frequency since the three primary lineages diverged more than three billion years ago. This inference was derived from a comparison of amino acid frequencies within conserved and non-conserved residues of a set of proteins dating to the last universal ancestor in the face of empirical knowledge of the relative mutability of these amino acids. The under-representation of these amino acids within last universal ancestor proteins relative to their modern descendants suggests their late introduction into the genetic code. Thus, it appears that extant ancient proteins contain evidence pertaining to early events in the formation of biological systems.
Superprism effect in a metal-clad terahertz photonic crystal slab (2007)

We report an experimental demonstration of the superprism effect in a photonic crystal slab at terahertz frequencies. For a 10% frequency variation around 0.28 THz, the refraction angle at the output facet of a wedge-shaped photonic crystal varies by about 15 degrees. A comparison with the predictions of a band structure calculation demonstrates that a three-dimensional treatment, accurately modeling the finite slab thickness and the metallic boundary conditions, is required for even a qualitative agreement with the experimental observations.
Short DNA sequences inserted for gene targeting can accidentally interfere with off‐target gene expression (2010)

Targeting of genes in mice, a key approach to study development and disease, often leaves a neo cassette, loxP, or FRT sites inserted in the mouse genome. Insertion of neo can influence the expression of neighboring genes, but similar effects have not been reported for loxP sites. We therefore performed microarray analyses of mice in which the Ncam or the Tnr gene were targeted either by insertion of neo or loxP/FRT sites. In the case of Ncam, neo, but not loxP/FRT insertion, led to a 2-fold reduction in mRNA levels of 3 genes located at distances between 0.2 and 3.1 Mb from the target. In contrast, after introduction of loxP/FRT sites into introns of Tnr, we observed a 2.5- to 4-fold reduction in the transcript level of the Gas5 gene, 1.1 Mb away from Tnr, most probably due to disruption of a conserved regulatory element in Tnr. Insertion of short DNA sequences such as loxP/FRT can thus influence off-target mRNA levels if these sites are accidentally placed into regulatory elements. Our results imply that conditional knockout mice should be analyzed for genomic positional side effects that may influence the animals' phenotypes.
Suppression of vascular endothelial growth factor expression at the transcriptional and post-transcriptional levels (2005)

Gene expression is regulated at the transcriptional and post-transcriptional levels. Therefore, in order to achieve a high level of silencing, which includes minimizing any residual expression of a target gene, suppression at both the transcriptional and post-transcriptional levels is required. In this study, we describe a new method for highly efficient gene silencing that combines zinc finger protein-mediated transcriptional repression and small interfering RNA (siRNA)-mediated inhibition of post-transcriptional events. To measure the amount of gene expression under various conditions, we used a luciferase reporter gene that was driven by a variety of promoters, including that of the human vascular endothelial growth factor-A (VEGF-A) gene. We also measured expression of the endogenous VEGF-A gene. Inhibition of gene expression by each of the two individual technologies was effective, but in-depth analyses revealed residual expression of the target gene. The combination of specific zinc finger transcription factors and siRNAs greatly enhanced the silencing of the human VEGF-A gene, not only when cells were grown in the presence of normal amounts of oxygen but also under conditions of hypoxic stimulation. These results suggest that a bi-level approach to the silencing of VEGF-A expression may be clinically beneficial as part of a cancer treatment protocol.
Microscopic Theory of Superconductivity (1957)

TOR momentum operators by applying projection operators and we form an orthogonal set. For the uniform solution, St=i+ (LkAtg kt+CC). k0 Noting that the method has a variational aspect, L need not be taken from the small-oscillation analysis but may be freely chosen to describe average largeamplitude effects. We obtain improved ground-state energy and single-and multiple-excitation spectra.
Cytokine expression in bronchial biopsies of cystic fibrosis patients with and without acute exacerbation (1999)

In patients with cystic fibrosis (CF), the progression of pulmonary disease differs considerably, even in identical cystic fibrosis transmembrane conductance regulator-genotypes which could reflect an additional influence of the host's immune response. This study therefore measured cytokine expression patterns in CF patients with different clinical presentation. Expression of interleukin (IL)-8, interferon gamma (IFN-gamma), IL-4, IL-10, and transforming growth factor (TGF)beta(I) was assessed in bronchial mucosal biopsies of eight CF patients with acute exacerbation (age 6.0-14.2 yrs), eight CF patients with chronic stable disease (age 7.3-17.4 yrs), and in five normal control subjects by semiquantitative and quantitative reverse transcriptase polymerase chain reaction combined with histopathological assessment and immunohistochemical staining. All CF patients expressed IL-8. In acute exacerbation, expression of TGF-beta1 and IFN-gamma was either absent or extremely low. In contrast, all patients with stable disease strongly expressed TGF-beta1. The highest expression of TGF-beta1 and IFN-gamma was found in CF patients with mild disease and a history of infrequent exacerbations. No correlation was found between the expression of IL-4 and IL-10 and patient history. In normal control subjects, only a weak expression of TGF-beta1 was observed. These results show a remarkable correlation between cytokine pattern and the clinical course of cystic fibrosis. High expression of transforming growth factor-beta1 and interferon gamma was associated with mild disease, whereas no or very weak expression of these cytokines was typical for patients with acute disease and frequent exacerbations suggesting a contribution of the immune response to the progression of pulmonary disease in cystic fibrosis.
Informedia - Search and Summarization in the Video Medium (2000)

The Informedia system provides &amp;quot;full-content&amp;quot; search and retrieval of current and past TV and radio news and documentary broadcasts. The system implements a fully automatic intelligent process to enable daily content capture, analysis and storage in on-line archives. The current library consists of approximately a 2,000 hours, 1.5 terabyte library of daily CNN News captured over the last 3 years and documentaries from public television and government agencies. This database allows for rapid retrieval of individual &amp;quot;video paragraphs&amp;quot; which satisfy an arbitrary spoken or typed subject area query based on a combination of the words in the soundtrack, images recognized in the video, plus closed-captioning when available and informational text overlaid on the screen images. There are also capabilities for matching of similar faces and images, generation of related map-based displays. The latest work attempts to produce a visualization and summarization of the content across all the stories ...
High performance thin film transistors with cosputtered amorphous indium gallium zinc oxide channel (2007)

The authors report the fabrication of high performance thin film transistors (TFTs) with an amorphous indium gallium zinc oxide (a-IGZO) channel, which was deposited by cosputtering using a dual IGZO and indium zinc oxide (IZO) target. The effect of the indium content on the device performance of the a-IGZO TFTs was investigated. At a relatively low IZO power of 400W, the field-effect mobility (μFE) and subthreshold gate swing (S) of the a-IGZO TFTs were dramatically improved to 19.3cm2∕Vs and 0.35V/decade, respectively, compared to those (11.2cm2∕Vs and 1.11V/decade) for the TFTs with the a-IGZO channel (reference sample) prepared using only the IGZO target. The enhancement in the subthreshold IDS-VGS characteristics at an IZO power of 400W compared to those of the reference sample was attributed to the reduction of the interface trap density rather than the reduction of the bulk defects of the a-IGZO channel.
Authentic Matrix Vesicles Contain Active Metalloproteases (MMP) (2001)

Matrix vesicles (MV) play a key role in the initiation of cartilage mineralization. Although many components in these microstructures have been identified, the specific function of each component is still poorly understood. In this study, we show that metalloproteases (MMP), MMP-2, -9, and -13 are associated with MV isolated from growth plate cartilage. In addition, we provide evidence that MV contain transforming growth factor-beta (TGF-beta) and that MV-associated MMP-13 is capable of activating latent TGF-beta. To determine whether MMPs are associated directly with MV, vesicles isolated from growth plate cartilage were sequentially treated with hyaluronidase, NaCl, and bacterial collagenase to remove matrix proteins and other components attached to their outer surface. Finally, the vesicles were incubated with detergent to rupture the MV membrane and expose components that are inside the vesicles. Each treated MV fraction was subjected to substrate zymography, immunoblotting, and substrate activity assay. Whereas active MMP-13 was lost after combined treatment with hyaluronidase and NaCl, MMP-2 and -9 activities were still retained in the pellet fraction even after detergent treatment, suggesting that the gelatinases, MMP-2 and -9, are integral components of MV. In addition, MV contain TGF-beta in the small latent complex, and MMP-13 associated with the MV surface was responsible for activation of TGF-beta. Since the amount of TGF-beta activated by hypertrophic chondrocytes increased with mineral appearance in serum-free chondrocyte cultures, a role for active MV-associated MMPs is suggested in activation of TGF-beta seen during late chondrocyte hypertrophy and mineralization of growth plate cartilage.
Merck molecular force field. IV. conformational energies and geometries for MMFF94 (1996)

This article describes the parameterization and performance of MMFF94 for conformational energies, rotational barriers, and equilibrium torsion angles. It describes the derivation of the torsion parameters from high-quality computational data and characterizes MMFF94's ability to reproduce both computational and experimental data, the latter particularly in relation to MM3. The computational data included: (i) ∼ 250 comparisons of conformational energy based on “MP4SDQ/TZP” calculations (triple-zeta plus polarization calculations at a defined approximation to the highly correlated MP4SDQ level) at MP2/6-31G* geometries; and (ii) ∼ 1200 MP2/TZP comparisons of “torsion profile” structures at geometries derived from MP2/6-31G* geometries. The torsion parameters were derived in restrained least-squares fits that used the complete set of available computational data, thereby ensuring that a fully optimal set of parameters would be obtained. The final parameters reproduce the “MP4SDQ/TZP” and MP2/TZP computational data with root mean square (rms) deviations of 0.31 and 0.50 kcal/mol, respectively. In addition, MMFF94 reproduces a set of 37 experimental gas-phase and solution conformational energies, enthalpies, and free energies with a rms deviation of 0.38 kcal/mol; for comparison, the “MP4SDQ/TZP” calculations and MM3 each gives a rms deviation of 0.37 kcal/mol. Furthermore, MMFF94 reproduces 28 experimentally determined rotational barriers with a rms deviation of 0.39 kcal/mol. Given the diverse nature of the experimental conformational energies and rotational barriers and the clear indications of experimental error in some cases, the MMFF94 results appear excellent. Nevertheless, MMFF94 encounters somewhat greater difficulty in handling multifunctional compounds that place highly polar functional groups in close proximity, probably because it, like other commonly used force fields, too greatly simplifies the description of electrostatic interactions. Some suggestions for enhancements to MMFF94's functional form are discussed. © 1996 John Wiley & Sons, Inc.