gebhart/patrepeval huggingface dataset:
Understanding the Biological Chemistry of Mercury Using a de novo Protein Design Strategy (2009)

Hg(II) is a well known toxin that has a high affinity for protein thiolate functional groups. While an area of significance, a dearth of literature exists on the chemistry of Hg(II) with thiolate containing proteins. In this chapter we demonstrate the design of proteins that complex Hg(II) in linear, trigonal planar, and tetrahedral environments. Physical techniques such as 199Hg NMR, 199mHg PAC and UV-vis spectroscopy to characterize Hg(II) sites in proteins are also described along with the application of our understanding of Hg(II) interactions with designed proteins to address the binding of Hg(II) in protein sites such as MerA (2-coordinate), MerR (3-coordinate) and Hg substituted rubredoxin (4-coordinate). Finally, knowledge from this system is used to predict the chemistry of Hg(II) bound forms of Hahl at high pH.
Biomarkers of drug-induced kidney injury (2017)

There is compelling evidence to support the use of biomarkers for the early detection of DIKI. Ongoing research is required to delineate their role in prognostication and for the prediction of outcomes. The inclusion of biomarkers in more clinical studies of DIKI would be a welcome advance, which may accelerate their integration into clinical diagnostics.
miR-26a Inhibits Feline Herpesvirus 1 Replication by Targeting SOCS5 and Promoting Type I Interferon Signaling (2019)

In response to viral infection, host cells activate various antiviral responses to inhibit virus replication. While feline herpesvirus 1 (FHV-1) manipulates the host early innate immune response in many different ways, the host could activate the antiviral response to counteract it through some unknown mechanisms. MicroRNAs (miRNAs) which serve as a class of regulatory factors in the host, participate in the regulation of the host innate immune response against virus infection. In this study, we found that the expression levels of miR-26a were significantly upregulated upon FHV-1 infection. Furthermore, FHV-1 infection induced the expression of miR-26a via a cGAS-dependent pathway, and knockdown of cellular cGAS significantly blocked the expression of miR-26a induced by poly (dA:dT) or FHV-1 infection. Next, we investigated the biological function of miR-26a during viral infection. miR-26a was able to increase the phosphorylation of STAT1 and promote type I IFN signaling, thus inhibiting viral replication. The mechanism study showed that miR-26a directly targeted host SOCS5. Knockdown of SOCS5 increased the phosphorylation of STAT1 and enhanced the type I IFN-mediated antiviral response, and overexpression of suppressor of the cytokine signalling 5 (SOCS5) decreased the phosphorylation of STAT1 and inhibited the type I IFN-mediated antiviral response. Meanwhile, with the knockdown of SOCS5, the upregulated expression of phosphorylated STAT1 and the anti-virus effect induced by miR-26a were significantly inhibited. Taken together, our data demonstrated a new strategy of host miRNAs against FHV-1 infection by enhancing IFN antiviral signaling.
The gene for retinal rod 33-kDa protein is on mouse chromosome 1, near <i>Lamb2</i> (1991)

A water-soluble protein (called "33-kDa protein") that exhibits light-dependent phosphorylation has been shown to be a major protein of mammalian rod photoreceptors. Although the function of this protein is unknown, it has been implicated in the biochemical cascade mediating the rod visual response. Using a retinal cDNA from the rat and somatic cell hybrids, we have mapped the gene corresponding to this protein to mouse Chromosome 1 and, by analyzing the progeny of an intersubspecific backcross, have positioned it near Lamb2 (the beta 2 chain of laminin). We have designated the gene Rpr-1 (rod photoreceptor protein-1).
DocEmul: A Toolkit to Generate Structured Historical Documents (2017)

We propose a toolkit to generate structured synthetic documents emulating the actual document production process. Synthetic documents can be used to train systems to perform document analysis tasks. In our case we address the record counting task on handwritten structured collections containing a limited number of examples. Using the DocEmul toolkit we can generate a larger dataset to train a deep architecture to predict the number of records for each page. The toolkit is able to generate synthetic collections and also perform data augmentation to create a larger trainable dataset. It includes one method to extract the page background from real pages which can be used as a substrate where records can be written on the basis of variable structures and using cursive fonts. Moreover, it is possible to extend the synthetic collection by adding random noise, page rotations, and other visual variations. We performed some experiments on two different handwritten collections using the toolkit to generate synthetic data to train a Convolutional Neural Network able to count the number of records in the real collections.
Uncertainty Representation and Reasoning for Combat Models (2012)

Military missions in a net-centric environment require distributed, autonomous agents to share information and cooperatively assess unpredictable situations to support real-time decisions in a rapidly changing environment. Combat models replicate this environment at various levels of detail and for different purposes. This chapter focuses on the application of specific Bayesian methods to support information fusion in combat models with uncertainty. It presents the concepts of Bayesian networks (BNs) and multi-entity Bayesian networks (MEBNs). The chapter gives an example of BN modeling with a very simple military vehicle recognition. This simple model is then extended to capture some characteristics common to models at Joint Directors of Laboratories (JDL) level 2 and above. The chapter focuses on MEBNs, which address the representational limitations posed by BNs, and illustrates the details of the technique with an extended version of the use case model. Controlled Vocabulary Terms modeling
Post-translational regulation of the NKG2D ligand Mult1 in response to cell stess (134.2) (2009)

Abstract NKG2D is a major stimulatory receptor expressed by natural killer cells and some T cells. The receptor recognizes MHC class I-like cell surface ligands that are poorly expressed by normal tissues but often induced in transformed and infected cells. Induction of NKG2D ligands during transformation or infection leads to activation of NKG2D-expressing immune cells and elimination of the diseased target cells. The existence of several NKG2D ligands in each individual, some with strikingly divergent protein sequences, raises the possibility that different ligands are regulated by distinct disease-associated stresses. The transcripts for some ligands, including murine UL16-binding protein-like transcript 1 (Mult1), are abundant in certain normal tissues where cell surface expression is absent suggesting the existence of translational or post-translational regulation. We report that under normal conditions, Mult1 protein undergoes ubiquitination dependent on lysines in its cytoplasmic tail and is degraded by the lysosome. Mult1 degradation and ubiquitination is reduced in response to stress imparted by heat shock or ultraviolet (UV) irradiation, but not by other forms of genotoxicity, providing a novel mechanism for stress-mediated cellular control of NKG2D ligand expression.
Rabi spectroscopy and excitation inhomogeneity in a one-dimensional optical lattice clock (2009)

We investigate the influence of atomic motion on precision Rabi spectroscopy of ultracold fermionic atoms confined in a deep one-dimensional optical lattice. We analyze the spectral components of longitudinal sideband spectra and present a model to extract information about the transverse motion and sample temperature from their structure. Rabi spectroscopy of the clock transition itself is also influenced by atomic motion in the weakly confined transverse directions of the optical lattice. By deriving Rabi flopping and Rabi line shapes of the carrier transition, we obtain a model to quantify trap-state-dependent excitation inhomogeneities. The inhomogeneously excited ultracold fermions become distinguishable, which allows $s$-wave collisions. We derive a detailed model of this process and explain observed density shift data in terms of a dynamic mean-field shift of the clock transition.
Dominant role of internal rotation in the dissociation of polyatomic ligands from the binding site. The case of opiates (1995)

An analysis is presented of the dissociation of polyatomic ligands from the binding site, with the focus on the local bond breaking process. The approach is based on the dynamics of the ‘reaction coordinate’ for dissociation of the local bond which is defined on the grounds of previous studies of vibrational energy transfer in encounters of polyatomic molecules. The mass corresponding to the coordinate in question depends crucially on the properties of the internal rotation of the group involved in the local bond, as well as on the geometry of this bond. The model reproduces well the striking relative magnitudes of the experimental dissociation rates of several opiates.
A band-structure model of strained quantum-well wurtzite semiconductors (1997)

We present a theoretical model for calculating the band structures of strained quantum-well wurtzite semiconductors. The theory is based on the Hamiltonian for wurtzite semiconductors and includes the strain effects on the shifts of the band edges. We show new results that include the matrix elements of the Hamiltonian using the finite-difference method for the calculations of the valence electronic band structures of quantum-well wurtzite semiconductors based on the effective-mass theory.
REVIEWS (1988)

REVIEWS A Linguistic Atlas of Late Mediaeval English. By ANGUS MCINTOSH, M. L. SAMUELS, and MICHAEL BENSKIN, with the assistance of Margaret Laing and Keith Williamson. Vol. I, General Introduction, Index of Sources, Dot Maps, pp. x+570; Vol. II, Item Maps, pp. xxiv+388; Vol. III, Linguistic Profiles, pp. xxiv+700; Vol. IV, County Dictionary, pp. xxii+346. Aberdeen: Aberdeen University Press, 1986. £220 net (US $330) the set. EDWARD WILSON EDWARD WILSON Worcester CollegeOxford Search for other works by this author on: Oxford Academic Google Scholar The Review of English Studies, Volume XXXIX, Issue 153, February 1988, Pages 94–96, https://doi.org/10.1093/res/XXXIX.153.94 Published: 01 February 1988
Alterations in Lipid Composition and Fluidity of Liver Plasma Membranes in Copper-Deficient Rats (1988)

In view of the importance of membrane fluidity on cell functions, the influence of phospholipid acyl groups on membrane fluidity, and the changes in lipid metabolism induced by copper (Cu) deficiency, this study was designed to examine the influence of dietary Cu on the lipid composition and fluidity of liver plasma membranes. Male Sprague-Dawley rats were divided into two dietary treatments, namely Cu deficient and Cu adequate. After 8 weeks of treatment, liver plasma membranes were isolated by sucrose density gradient centrifugation. The lipid fluidity of plasma membranes, as assessed by the intramolecular eximer fluorescence of 1,3-di(1-pyrenyl) propane, was significantly depressed by Cu deficiency. In addition, Cu deficiency significantly reduced the content of arachidonic and palmitoleic acids but increased the docosatetraenoic and docosahexaenoic acids of membrane phospholipids. This alteration in unsaturated phospholipid fatty acid composition, especially the large reduction in arachidonic acid, may have contributed to the depressed membrane fluidity. Furthermore, Cu deficiency also markedly altered the fatty acid composition of the triacylglycerols associated with the plasma membranes. Thus, the lipid composition and fluidity of liver plasma membranes are responsive to the animal's Cu status.
NASA's In-Space Propulsion Technology Project Systems Analysis Overview (2008)

NASA In-Space Propulsion Technology (ISPT) Project Office is investing in propulsion technologies to meet future science missions’ needs. A strategic area of investment for the ISPT office is on systems analysis. Systems analysis serves to define requirements for new technology developments, establish figures of merit to prioritize return on investment, and develop tools to assist the evaluation and infusion of new propulsion technologies. Recent ISPT systems analysis activities include: an initiative to define an electric propulsion life qualification standard; analyses to identify propulsion system requirements for a range of radioisotope electric propulsion (REP) missions, evaluation of commercial electric propulsion systems to meet NASA science mission needs, mission benefits of active mixture ratio control for bipropellant systems, validation of the Advanced Chemical Propulsion System (ACPS) sizing tool, a rapid aerocapture design tool, an integrated aero-assist tool, and improvements to the low-thrust trajectory tool suite. Status and progress of recent, on-going and near-term tasks are presented.
Regulation of Bone Marrow Angiogenesis by Osteoblasts during Bone Development and Homeostasis (2013)

Bone marrow is a highly heterogeneous and vascularized tissue. The various cell types populating the bone marrow extensively communicate with each other, and cell-to-cell cross talk is likely to be essential for proper bone development and homeostasis. In particular, the existence of osteogenesis and angiogenesis coupling has been recently proposed. Despite its high degree of vascularization, a gradient of oxygenation is present in the bone marrow, and the endosteal surface of cortical bone appears to be among the most hypoxic areas in the body. Oxygen (O2) is both an essential metabolic substrate and a regulatory signal that is in charge of a specific genetic program. An important component of this program is the family of transcription factors known as hypoxia-inducible factors (HIFs). In this Perspective, we will summarize our current knowledge about the role of the HIF signaling pathway in controlling bone development and homeostasis, and especially in regulating the crosstalk between osteoblasts, progenitor cells, and bone marrow blood vessels.
解读亚洲金融危机：历史、文化和机构实况（上） (2000)

学者们对亚洲金融危机的起因一直持有各种不同的见解。在一个极端，美国式自由市场制度的拥护者指责该地区的政治权贵和企业巨头实行“裙带资本主义”。而亚洲发展经历特殊论的拥护者则反驳说，西方的政治金融阴谋集团破坏了亚洲的成就。然而，只有较为不偏不倚的社会学观点才能更加深入地洞察这次危机。可以认为，人们对亚洲金融危机的起因有三种政治社会学见解：(1)有关亚太地区国家发展经历的历史社会学：(2)有关政治权贵与政策分析家之间争论的政治社会学：(3)有关现有机构的表现与合理性的政治社会学。
In utero programming of chronic disease (1998)

1. Many human fetuses have to adapt to a limited supply of nutrients. In doing so they permanently change their structure and metabolism. 2. These 'programmed' changes may be the origins of a number of diseases in later life, including coronary heart disease and the related disorders stroke, diabetes and hypertension. 3. This review examines the evidence linking these diseases to fetal undernutrition and provides an overview of previous studies in this area.
Sunflower (Helianthus annuus L.) Pathogenesis-Related Proteins (Induction by Aspirin (Acetylsalicylic Acid) and Characterization) (1993)

Sunflower leaf discs floated on a solution containing aspirin (acetylsalicylic acid) produced a set of new proteins extractable at pH 5.2 and excreted into the intercellular space. More than 80% of the proteins found in the intercellular fluids of induced leaf discs have been identified as pathogenesis-related (PR) proteins by their immunological relationship with tobacco PR proteins. Members of the four major classes of PR proteins have been characterized. Sunflower PR proteins of type 1 (PR1) and of type 3 (PR3) were found to have acidic isoelectric points, whereas the induced PR protein of type 2 (PR2) had a basic isoelectric point. Members of the type 5 PR proteins (PR5), known in tobacco as thaumatin-like proteins, showed a more complex pattern. Multiple sunflower PR5 isomers of similar molecular weight but of different isoelectric points were excreted from the cells in response to the aspirin treatment. PR2 and PR3 proteins were found at very low basal levels in untreated leaves, whereas PR1 and PR5 proteins could not be detected at all in the same extracts. Glucanase and chitinase activities were always associated with PR2 and PR3 proteins in partially purified sunflower extracts. All of these data indicate that, in response to aspirin treatment, sunflower plants produce a complete set of PR proteins characterized by an apparently exclusively extracellular localization.
The γ-Carboxylation Recognition Site Is Sufficient to Direct Vitamin K-dependent Carboxylation on an Adjacent Glutamate-rich Region of Thrombin in a Propeptide-Thrombin Chimera (1997)

The propeptides of the vitamin K-dependent proteins contain a gamma-carboxylation recognition site that is required for gamma-glutamyl carboxylation. To determine whether the propeptide is sufficient to direct carboxylation, two mutant prothrombin species were expressed and characterized with regard to posttranslational gamma-carboxylation. A double point mutant, in which serine substituted for cysteines 17 and 22 disrupted a conserved loop formed by a disulfide bond, was fully carboxylated when expressed in Chinese hamster ovary cells. A propeptide/thrombin chimeric protein, constructed by deleting the Gla, aromatic amino acid stack, and kringle domains of prothrombin, has the signal peptide and propeptide juxtaposed to a glutamate-rich COOH-terminal region of prothrombin, residues 249-530. Of the 8 glutamic acid residues contained within the first 40 residues of the NH2 terminus adjacent to the propeptide, at least seven were fully carboxylated as demonstrated by direct gamma-carboxyglutamic acid analysis of the alkaline hydrolysate and by NH2-terminal sequence analysis. These results indicate that the gamma-carboxylation recognition site within the prothrombin propeptide in a prothrombin propeptide-thrombin chimeric protein is sufficient to direct gamma-carboxylase-catalyzed carboxylation of adjacent glutamic acid residues in a glutamate-rich region of thrombin that is not normally gamma-carboxylated. Furthermore, the disulfide loop in the Gla domain of prothrombin is not required for complete carboxylation.
An experimental evaluation of the curvature-strain relation in fault-related folds (2008)

Substantial effort has gone into predicting the characteristics of subsurface fracture systems in fault-related folds. Curvature analysis is a common method used to predict the location and characteristics of fracture networks in folded rock layers. In curvature analysis, it is assumed that layers of rock deform like elastic plates so that layer-parallel strains are directly related to the curvature of the folded surface. This article tests the underlying assumption of all curvature analyses: that curvature is a direct proxy for strain in folded rock layers. We test the assumption by analyzing the curvature and strain in a series of scaled physical models of contractional, basement-involved, fault-related folds. Our objective is to constrain the conditions that lead to a strong positive correlation between curvature and extensional strain. Of particular interest is whether curvature and strain correlate over a wide range of fault throws and dips. The analysis of our folds demonstrates that both the distribution and magnitude of a fold-axis normal extension in the surface of the overlying layer appear to vary as a function of fault dip. Our results indicate that the correlation between strain and curvature generally becomes worse with decreasing fault dip. Fault throw also exhibits an effect on the curvature-strain relationship. However, this effect is dependent on the dip of the fault as well and only exhibits an effect on the curvature-strain relationship for moderately dipping faults. A direct correlation between curvature and strain at all stages of fold development is observed only for steeply dipping basement faults. These results suggest that curvature may not be a consistently reliable strain proxy in basement-involved fault-related folds and that the accuracy of curvature-related strain predictions will be strongly dependent on the dip and throw of the underlying basement fault.
2P1-M04 Development of a Discharging Unit for a Planetary Subsurface Excavation Robot with Peristaltic Crawling Mechanism(Space Engineering and Robotics and Mechatronics) (2013)

It is important to investigate the underground of the planets in terms of the elucidation of the planet's origin and a development of the bases that human can work on the planets. Therefore, we have developed a planetary subsurface excavation robot with peristaltic crawling mechanism. This robot consists of two units; a propulsion unit and an excavation unit. The propulsion unit has three subunits using a peristaltic motion. The excavation unit has an earth auger. But, the existing robot can't excavate without a discharging unit because the soil isn't smoothly discharged from a spout when it reaches below surface. So, we develop a discharging unit to solve this problem. Then, we have an excavating experiment with the robot in order to check the capacity of the discharging unit. Thus, we confirmed that the robot could discharge the soil by the discharging unit.
Multi-Layer Memory Resiliency (2014)

With memories continuing to dominate the area, power, cost and performance of a design, there is a critical need to provision reliable, high-performance memory bandwidth for emerging applications. Memories are susceptible to degradation and failures from a wide range of manufacturing, operational and environmental effects, requiring a multi-layer hardware/software approach that can tolerate, adapt and even opportunistically exploit such effects. The overall memory hierarchy is also highly vulnerable to the adverse effects of variability and operational stress. After reviewing the major memory degradation and failure modes, this paper describes the challenges for dependability across the memory hierarchy, and outlines research efforts to achieve multi-layer memory resilience using a hardware/software approach. Two specific exemplars are used to illustrate multilayer memory resilience: first we describe static and dynamic policies to achieve energy savings in caches using aggressive voltage scaling combined with disabling faulty blocks; and second we show how software characteristics can be exposed to the architecture in order to mitigate the aging of large register files in GPGPUs. These approaches can further benefit from semantic retention of application intent to enhance memory dependability across multiple abstraction levels, including applications, compilers, run-time systems, and hardware platforms.
Synthesis of Podophyllotoxin and Related Compounds (1992)

Over 40 papers have so far been published dealing with the synthesis of podophyllotoxin and its isomers. The attention devoted to this relatively small group of compounds stems from the use of derivatives of 4′-demethylepipodophyllotoxin in cancer chemotherapy. At first glance it would appear that a wide variety of synthetic methods have been employed. However, closer scrutiny reveals that three, or at most four, common themes can be distinguished. The syntheses can therefore be classified, depending upon whether they involve either a γ-oxo ester or a dihydroxy acid as a key intermediate, or whether they involve a tandem conjugate addition or a Diels-Alder reaction as a key step. Since there is much ongoing activity in this area and a steady stream of papers being published, it is clear that no totally satisfactory solution has so far been found and that ingenuity has not been exhausted. The quest for improved therapeutic activity is an important stimulus for further work, and the need to produce compounds in enantiomerically pure form means that there is continued and indeed increasing interest in this area. 1. Introduction 2. The Oxo Ester Route 3. The Dihydroxy Ester Route 4. The Tandem Conjugate Addition Route 5. Use of the Diels-Alder Reaction 6. Synthesis of 2-Azapodophyllotoxins 7. Modifications of Podophyllotoxin Itself