gebhart/patrepeval huggingface dataset:
Crystal structure of 4-hydroxybutyryl-CoA dehydratase: Radical catalysis involving a [4Fe–4S] cluster and flavin (2004)

Dehydratases catalyze the breakage of a carbon-oxygen bond leading to unsaturated products via the elimination of water. The 1.6-A resolution crystal structure of 4-hydroxybutyryl-CoA dehydratase from the gamma-aminobutyrate-fermenting Clostridium aminobutyricum represents a new class of dehydratases with an unprecedented active site architecture. A [4Fe-4S](2+) cluster, coordinated by three cysteine and one histidine residues, is located 7 A from the Re-side of a flavin adenine dinucleotide (FAD) moiety. The structure provides insight into the function of these ubiquitous prosthetic groups in the chemically nonfacile, radical-mediated dehydration of 4-hydroxybutyryl-CoA. The substrate can be bound between the [4Fe-4S](2+) cluster and the FAD with both cofactors contributing to its radical activation and catalytic conversion. Our results raise interesting questions regarding the mechanism of acyl-CoA dehydrogenases, which are involved in fatty acid oxidation, and address the divergent evolution of the ancestral common gene.
Maize Kernel Set at Low Water Potential: II. Sensitivity to Reduced Assimilates at Pollination (1991)

Plant water deficits at pollination decrease kernel set in maize. An important component of this kernel loss is developmental failure after fertilization. This study was undertaken to determine if zygotic abortion in water‐deficient plants results primarily from a decrease in assimilate supply daring the critical period around pollination. Plants were grown in soil/sand media in a controlled environment, and photosynthesis was inhibited by water‐deficit or low‐light treatments. Plants were hand‐pollinated when silk water potential of control, low‐light, and water‐deficient plants was −0.4, −0.4, and −1.0 MPa, respectively. Corresponding leaf water potentials were −0.3, −0.3, and −1.7 MPa. The water deficit decreased ovary water potential, osmotic potential, and turgor by 0.6, 0.3, and 0.3 MPa, respectively, compared with values in well‐watered plants. Treatments were terminated 2 d after pollination, and leaf photosynthesis recovered to control values within 24 h. Kernel numbers per ear were 598 ± 17 for control, 222 ± 72 for low light, and 15 ± 6 for water‐deficit treatments. The brief inhibition of photosynthesis had little impact on C and N accumulation in vegetative sinks, but severely reduced assimilate movement to reproductive sinks. At pollination, concentrations (mg g −1 dry wt.) of fructose, glucose, and sucrose in ovaries were similar for all treatments. The high levels of these soluble sugars in both setting and aborting ovaries suggests that kernel set depends on the rate of movement of assimilates into the ovaries, rather than the concentration of soluble sugars per se. Sucrose uptake by isolated ovaries was inhibited at low water potential, suggesting a direct effect of ovary water status on kernel development. The nearly complete kernel loss observed in the water‐deficit plants indicates that low ovary water potential at pollination decreased kernel set beyond that which can be attributed to reduced assimilate supplies alone.
Percutaneous Radiofrequency Gangliotomy in the Treatment of Trigeminal Neuralgia and Other Facial Pain (1975)

Thirty-eight patients with facial pain in the trigeminal distribution have been treated by percutaneous coagulation of the trigeminal ganglion. Although use has been made of radiological criteria, it has been found from the physiological data obtained from stimulation that motor and sensory phenomena provide more information of electrode placement and that good pain relief results when these criteria are met. The advantages of the method are: (i) minimal operative risk; (ii) control of the extent of the lesion created; (iii) small sensibility deficit; (iv) minimal complication rate; (v) short hospitalization; (vi) satisfactory result in more than 90% of patients; (vii) no recurrence of pain to date.
Fast photoinduced electron transfer through DNA intercalation. (1994)

We report evidence for fast photoinduced electron transfer mediated by the DNA helix that requires metal complexes that are avid intercalators of DNA. Here the donor bis(phenanthroline)(dipyridophenazine)ruthenium(II) [Ru(phen)2dppz2+] and acceptor bis(9,10-phenanthrenequinone diimine)(phenanthroline)rhodium(III) [Rh(phi)2phen3+] intercalate into DNA with Kb > 10(6) M-1. Luminescence quenching experiments in the presence of two different lengths of DNA yield upward-curving Stern-Volmer plots and the loss of luminescence intensity far exceeds the change in emission lifetimes. In the presence of a nonintercalative electron acceptor, Ru(NH3)3+(6), Ru(phen)2dppz2+ luminescence is quenched much less efficiently compared to that found for the intercalative Rh(phi)2phen3+ quencher and follows linear Stern-Volmer kinetics; steady-state and time-resolved Stern-Volmer plots are comparable in scale. These experiments are consistent with a model involving fast long-range electron transfer between intercalators through the DNA helix.
Effects of Cooling Rate on Seeds Exposed to Liquid Nitrogen Temperatures (1989)

The effect of cooling rate on seeds was studied by hydrating pea (Pisum sativum), soybean (Glycine max), and sunflower (Helianthus annuus) seeds to different levels and then cooling them to - 190 degrees C at rates ranging from 1 degrees C/minute to 700 degrees C/minute. When seeds were moist enough to have freezable water (> 0.25 gram H(2)O/gram dry weight), rapid cooling rates were optimal for maintaining seed vigor. If the seeds were cooled while at intermediate moisture levels (0.12 to 0.20 gram H(2)O per gram dry weight), there appeared to be no effect of cooling rate on seedling vigor. When seeds were very dry (< 0.08 gram H(2)O per gram dry weight), cooling rate had no effect on pea, but rapid cooling rates had a marked detrimental effect on soybean and sunflower germination. Glass transitions, detected by differential scanning calorimetry, were observed at all moisture contents in sunflower and soybean cotyledons that were cooled rapidly. In pea, glasses were detectable when cotyledons with high moisture levels were cooled rapidly. The nature of the glasses changed with moisture content. It is suggested that, at high moisture contents, glasses were formed in the aqueous phase, as well as the lipid phase if tissues had high oil contents, and this had beneficial effects on the survival of seeds at low temperatures. At low moisture contents, glasses were observed to form in the lipid phase, and this was associated with detrimental effects on seed viability.
The Role of Mast Cells in Stroke (2019)

Mast cells (MCs) are densely granulated perivascular resident cells of hematopoietic origin. Through the release of preformed mediators stored in their granules and newly synthesized molecules, they are able to initiate, modulate, and prolong the immune response upon activation. Their presence in the central nervous system (CNS) has been documented for more than a century. Over the years, MCs have been associated with various neuroinflammatory conditions of CNS, including stroke. They can exacerbate CNS damage in models of ischemic and hemorrhagic stroke by amplifying the inflammatory responses and promoting brain-blood barrier disruption, brain edema, extravasation, and hemorrhage. Here, we review the role of these peculiar cells in the pathophysiology of stroke, in both immature and adult brain. Further, we discuss the role of MCs as potential targets for the treatment of stroke and the compounds potentially active as MCs modulators.
Dehydrated human amnion/chorion membrane allografts in patients with chronic diabetic foot ulcers: A long-term follow-up study (2013)

Diabetic foot ulcers (DFU) are notoriously slow to heal and even in cases where primary healing is achieved ulcers frequently recur. An optimal treatment for DFU would be one that supports both rapid and long-term healing. Our purpose is to evaluate recurrence rates of DFU healed with use of dehydrated human amnion/chorion membrane (dHACM). Twenty-two patients with chronic DFU that healed with the use of dHACM were eligible for inclusion. All eligible patients had completed a single-center randomized clinical trial comparing rates of primary healing over a 12 week period with dHACM versus a standard regimen of care [20] (Zelen et al., 2013). Follow-up examinations were scheduled for 9–12 months after primary healing with dHACM. Subsequent evaluation of clinical records was made with IRB approval and patient consent. Eighteen of 22 eligible patients (81.8%) returned for follow-up examination. Mean wound size prior to treatment with dHACM was 3.1 ± 3.8 cm2, median 1.7 cm2 (0.7, 13.5). Mean time to wound closure after dHACM initiation was 3.1 ± 2.8 weeks (median 2.0 weeks, range 1.0–9.0 weeks). At the 9–12 month follow-up visit 17 of 18 (94.4%) wounds treated with dHACM remained fully healed. These findings support the effectiveness of dHACM for treatment of DFU.
Hydrodynamic micro-encapsulation of aqueous fluids and cells via ‘on the fly’ photopolymerization (2006)

We report a new technique that, in contrast to conventional methods, uses a microfluidic platform for the fabrication of polymeric microcapsules that can contain sensitive biological materials. This encapsulation process is carried out through the use of hydrodynamic phenomena (e.g., multiphase laminar flow), and 'on the fly' photopolymerization. Our method allows for the generation of microcapsules whose size can be controlled by a regulation of flow rates, and the polymerized capsule can protect fragile materials, such as cells, DNA and enzymes from harsh environments. The proposed approach is extended to the fabrication of a microcontainer that can handle small volumes of liquid. The flexibility of the method across different materials and scales is a key advantage over many existing methods.
Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering (2008)

Homing endonucleases, also known as meganucleases, are sequence-specific enzymes with large DNA recognition sites. These enzymes can be used to induce efficient homologous gene targeting in cells and plants, opening perspectives for genome engineering with applications in a wide series of fields, ranging from biotechnology to gene therapy. Here, we report the crystal structures at 2.0 and 2.1 A resolution of the I-DmoI meganuclease in complex with its substrate DNA before and after cleavage, providing snapshots of the catalytic process. Our study suggests that I-DmoI requires only 2 cations instead of 3 for DNA cleavage. The structure sheds light onto the basis of DNA binding, indicating key residues responsible for nonpalindromic target DNA recognition. In silico and in vivo analysis of the I-DmoI DNA cleavage specificity suggests that despite the relatively few protein-base contacts, I-DmoI is highly specific when compared with other meganucleases. Our data open the door toward the generation of custom endonucleases for targeted genome engineering using the monomeric I-DmoI scaffold.
Promoters of Rice Seed Storage Protein Genes Direct Endosperm-Specific Gene Expression in Transgenic Rice (1998)

The promoters of genes encoding rice seed storage proteins (glutelin, prolamin, globulin and albumin) were analyzed for their ability to direct /7-gIucuronidase (GUS) gene expression in transgenic rice plants. All promoters tested could direct endosperm-specific expression of the GUS reporter gene irrespective of variable activities and patterns in the endosperm.
Propagation of dendritic cell progenitors from normal mouse liver using granulocyte/macrophage colony-stimulating factor and their maturational development in the presence of type-1 collagen. (1994)

Within 1 wk of liquid culture in granulocyte/macrophage colony-stimulating factor (GM-CSF), normal B10 BR (H-2k I-E+) mouse liver nonparenchymal cells (NPC) formed loosely adherent myeloid cell clusters that have been shown to contain dendritic cell (DC) progenitors in similar studies of mouse blood or bone marrow. Mononuclear cell progeny released from these clusters at and beyond 4 d exhibited distinct dendritic morphology and were actively phagocytic. After 6-10 d of culture, these cells strongly expressed CD45, CD11b, heat stable antigen, and CD44. However, the intensity of expression of the DC-restricted markers NLDC 145, 33D1, and N418, and the macrophage marker F4/80, intercellular adhesion molecule 1, and Fc gamma RII was low to moderate, whereas the cells were negative for CD3, CD45RA, and NK1.1. Splenocytes prepared in the same way also had a similar range and intensity of expression of these immunophenotypic markers. Unlike the splenic DC, however, most of the GM-CSF-propagated putative liver DC harvested at 6-10 d expressed only a low level of major histocompatibility complex (MHC) class II (I-Ek), and they failed to induce primary allogeneic responses in naive T cells, even when propagated additionally in GM-CSF and tumor necrosis alpha and/or interferon gamma-supplemented medium. However, when 7-d cultured GM-CSF-stimulated liver cells were maintained additionally for three or more days on type-1 collagen-coated plates in the continued presence of GM-CSF, they exhibited characteristics of mature DC: MHC class II expression was markedly upregulated, mixed leukocyte reaction stimulatory activity was increased, and phagocytic function was decreased. Similar observations were made when Ia+ cells were depleted from the GM-CSF-propagated cells before exposure to collagen. Further evidence that the GM-CSF-stimulated class IIdim or class II-depleted hepatic NPC were immature DC was obtained by injecting them into allogeneic B10 (H-2b I-E-) recipients. They "homed" to T cell-dependent areas of lymph nodes and spleen where they strongly expressed donor MHC class II antigen 1-5 d later. These observations provide insight into the regulation of DC maturation, and are congruent with the possibility that the migration of immature DC from normal liver and perhaps other organ allografts may help explain their inherent tolerogenicity.
Deadlock probability in unrestricted wormhole routing networks (2002)

To minimize latency in local area networks, the wormhole routing technique can be used. Drawbacks of this technique are the blocking of messages and, if backpressure flow control is used, the possibility of deadlock. Two principal mechanisms can be employed to deal with deadlocks, namely a deadlock-free routing scheme or a deadlock resolution mechanism. The relative performance of these two mechanisms depends mainly on the deadlock frequency. In this paper, we study analytically the probability of deadlock in an unrestricted wormhole routing network. We capture the topology of the system in two parameters with intuitive meaning, and we derive a closed form expression for an upper bound of the deadlock probability. Simulation runs with different topologies provide good confirmation for the analytical results.
Psychopathological and Cognitive Effects of Therapeutic Cannabinoids in Multiple Sclerosis (2008)

Cannabinoid treatment did not induce psychopathology and did not impair cognition in cannabis-naïve patients with MS. However, the positive correlation between blood levels of Delta-9-tetrahydrocannabinol and psychopathological scores suggests that at dosages higher than those used in therapeutic settings, interpersonal sensitivity, aggressiveness, and paranoiac features might arise, although greater statistical power would be necessary to confirm this finding.
Fundamental Differences of Excitation Spectrum between Malignant and Benign Breast Tissues (1997)

Differences observed in the UV excitation spectrum of malignant and benign breast tissues are used to distinguish between malignant and benign breast tissues. These changes are attributed to changes with specialized proteins.
Behaviour of several 'progression markers' during the HIV-Ab seroconversion period. Comparison with later stages. (1992)

Two acute phase reactants, four cytokines, five soluble factors and lymphocyte subpopulations have been simultaneously evaluated in 16 subjects before and closely after the HIV-Ab seroconversion time. The same variables have also been determined in 50 HIV-Ab-negative high risk subjects, in 36 CDC II-III and in 30 CDC IV patients, utilizing a mixed longitudinal epidemiological model. The results show significant variations of few parameters in the early phases (increase: sCD8, beta-2-Microglobulin, sIL-2R, sCD23, Neopterin, IFN-alpha; decrease: CD4+ lymphocytes). In the course of the disease, many others parameters progressively increase (IFN-tau, IL-4, IL-6, acid-alpha 1-glycoprotein, alpha 1-antitrypsin) or decrease (B- and T-lymphocytes). Ferritin, in particular, highly increases only in CDC IV stage. These data may be useful to monitor patients during the entire course of their disease and to suggest the time elapsed from seroconversion.
Code-pointer integrity (2014)

Systems code is often written in low-level languages like C/C++, which offer many benefits but also delegate memory management to programmers. This invites memory safety bugs that attackers can exploit to divert control flow and compromise the system. Deployed defense mechanisms (e.g., ASLR, DEP) are incomplete, and stronger defense mechanisms (e.g., CFI) often have high overhead and limited guarantees [19, 15, 9].We introduce code-pointer integrity (CPI), a new design point that guarantees the integrity of all code pointers in a program (e.g., function pointers, saved return addresses) and thereby prevents all control-flow hijack attacks, including return-oriented programming. We also introduce code-pointer separation (CPS), a relaxation of CPI with better performance properties. CPI and CPS offer substantially better security-to-overhead ratios than the state of the art, they are practical (we protect a complete FreeBSD system and over 100 packages like apache and postgresql), effective (prevent all attacks in the RIPE benchmark), and efficient: on SPEC CPU2006, CPS averages 1.2% overhead for C and 1.9% for C/C++, while CPI's overhead is 2.9% for C and 8.4% for C/C++.A prototype implementation of CPI and CPS can be obtained from http://levee.epfl.ch.
A Tactile Sensor Sheet Using Pressure Conductive Rubber With Electrical-Wires Stitched Method (2004)

A new type of tactile sensor using pressure-conductive rubber with stitched electrical wires is presented. The sensor is thin and flexible and can cover three-dimensional objects. Since the sensor adopts a single-layer composite structure, the sensor is durable with respect to external force. In order to verify the effectiveness of this tactile sensor, we performed an experiment in which a four-fingered robot hand equipped with tactile sensors grasped sphere and column. The sensor structure, electrical circuit, and characteristics are described. The sensor control system and experimental results are also described.
TET Family Proteins: Oxidation Activity, Interacting Molecules, and Functions in Diseases (2015)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTTET Family Proteins: Oxidation Activity, Interacting Molecules, and Functions in DiseasesXingyu Lu†‡, Boxuan Simen Zhao†‡, and Chuan He*†‡View Author Information† Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States‡ Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States*Phone: 773-702-5061. Fax: 773-702-0805. E-mail: [email protected]Cite this: Chem. Rev. 2015, 115, 6, 2225–2239Publication Date (Web):February 12, 2015Publication History Received25 August 2014Published online12 February 2015Published inissue 25 March 2015https://doi.org/10.1021/cr500470nCopyright © 2015 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views3214Altmetric-Citations75LEARN 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 InReddit Read OnlinePDF (6 MB) Get e-AlertsSUBJECTS:Cancer,Cytosine,Genetics,Oxidation,Peptides and proteins Get e-Alerts
Increased collagen-linked pentosidine levels and advanced glycosylation end products in early diabetic nephropathy. (1993)

Microalbuminuria is associated with elevated levels of pentosidine similar to those found in overt diabetic nephropathy suggesting that elevated AGE levels are already present during the earliest detectable phase of diabetic nephropathy.
Isomerization of (Z,Z) to (E,E)1-Bromo-2,5-bis-(3-hydroxycarbonyl-4-hydroxy)styrylbenzene in Strong Base:  Probes for Amyloid Plaques in the Brain (2001)

In developing probes for detecting β-amyloid (Aβ) plaques in the brain of Alzheimer's disease (AD), we have synthesized 1-bromo-2,5-bis-(3-hydroxycarbonyl-4-hydroxy)styrylbenzene (5, BSB). Due to the presence of two double bonds, formation of four different isomers is possible. Four isomers, E,E-5, E,Z-5, Z,E-5, and Z,Z-5, were prepared. Surprisingly, all showed strong fluorescent labeling of Aβ plaques in the brain of postmortem brain sections of patients with confirmed AD. In vitro binding assay also showed that all four isomers of BSB (E,E-5, E,Z-5, Z,E-5, and Z,Z-5) displayed a similar high binding affinity inhibiting the binding of [125I]E,E-6, 1-iodo-2,5-bis-(3-hydroxycarbonyl-4-methoxy)styrylbenzene (IMSB) to Aβ1-40 aggregates. The inhibition constants (Ki) of E,E-5, E,Z-5, Z,E-5, and Z,Z-5 were 0.11 ± 0.01, 0.19 ± 0.03, 0.27 ± 0.06, and 0.13 ± 0.02 nM, respectively. Due to the fact that geometric stability of these styrylbenzenes is unknown, and the conversion of Z,Z-5 to E,E-5 may occur automatically in the binding or labeling assaying conditions, we have investigated the kinetics of conversion of Z,Z-5 to E,E-5 by NMR in D2O/NaOD at elevated temperatures (70, 95, and 115 °C). The activation energy was determined to be 14.15 kcal/mol. The results strongly suggest that the isomeric conversion at room temperature in aqueous buffer solution is unlikely. All of the styrylbenzene isomers clearly showed potential as useful tools for studying Aβ aggregates in the brain. The data suggest that, despite the rigidity of this series of styrylbenzenes, the binding sites on Aβ aggregates may have certain flexibility and the binding pockets could be adaptable for binding to other smaller ligands. Such information could be exploited to develop new ligands for detecting amyloid plaques in AD.