gebhart/patrepeval huggingface dataset:
DNA Transcription and tRNA Ligase: the Work of John Abelson (2009)

Saccharomyces cerevisiae tRNA Ligase. Purification of the Protein and Isolation of the Structural Gene (Phizicky, E. M., Schwartz, R. C., and Abelson, J. (1986) <i>J. Biol. Chem.</i> 261, 2978–2986) Yeast RNA Ligase Mutants Are Nonviable and Accumulate tRNA Splicing Intermediates (Phizicky, E. M., Consaul, S. A., Nehrke, K. W., and Abelson, J. (1992) <i>J. Biol. Chem.</i> 267, 4577–4582)
Syntaxin-6 delays prion protein fibril formation and prolongs presence of toxic aggregation intermediates (2022)

Abstract Prions replicate via the autocatalytic conversion of cellular prion protein (PrPC) into fibrillar assemblies of misfolded PrP. While this process has been extensively studied in vivo and in vitro, non-physiological reaction conditions of fibril formation in vitro have precluded the identification and mechanistic analysis of cellular proteins, which may alter PrP self-assembly and prion replication. Here, we have developed a fibril formation assay for recombinant murine and human PrP (23-231) under near-native conditions (NAA) to study the effect of cellular proteins, which may be risk factors or potential therapeutic targets in prion disease. Genetic screening suggests that variants that increase syntaxin-6 expression in the brain (gene: STX6) are risk factors for sporadic Creutzfeldt-Jakob disease (CJD). Analysis of the protein in NAA revealed counterintuitively that syntaxin-6 is a potent inhibitor of PrP fibril formation. It significantly delayed the lag phase of fibril formation at highly sub-stoichiometric molar ratios. However, when assessing toxicity of different aggregation time points to primary neurons, syntaxin-6 prolonged the presence of neurotoxic PrP species. Electron microscopy and super-resolution fluorescence microscopy revealed that, instead of highly ordered fibrils, in the presence of syntaxin-6 PrP formed less-ordered aggregates containing syntaxin-6. These data strongly suggest that the protein can directly alter the initial phase of PrP self-assembly and, uniquely, can act as an ‘anti-chaperone’, which promotes toxic aggregation intermediates by inhibiting fibril formation.
On the nature of trapping and desorption at high surface temperatures. Theory and experiments for the Ar–Pt(111) system (1991)

We report molecular dynamics calculations and molecular beam experiments on trapping and desorption as a function of surface temperature and initial gas conditions for the Ar–Pt(111) system. The trapping process involves very rapid equilibration of the normal component of incidence velocity but extremely slow accommodation of the parallel component. At high surface temperatures for which the residence time of Ar is sufficiently short (e.g., roughly 40 ps at 273 K), trapped atoms desorb before their incident parallel velocity is thermalized. Thus trapping in the usual sense of complete equilibration with the surface does not occur; instead these quasitrapped atoms are characterized by full accommodation of only the normal velocity component. In both simulations and experiments there is a range of temperatures for which the desorbing flux associated with quasitrapping is distinguishable from the flux due to direct inelastic scattering. These results are qualitatively reproduced by a simple model for the time-varying velocity distribution of quasitrapped atoms, which treats the different components of velocity independently.
Rastronole A, B, C, D, E, F, G und H; eine Gruppe multioxygenierter Diterpenbitterstoffe der ent‐Kauran‐Reihe aus Englerastrum scandens ALSTON (1976)

Rastronols A, B, C, D, E, F, G, and H, a group of multioxygenated bitter principles with ent ‐kaur‐16‐en‐15‐one structure from Englerastrum scandens ALSTON ( Labiatae ) We have isolated from the leaves of Englerastrum scandens from Kenya eight new, highly oxygenated ent ‐kaur‐16‐en‐15‐ones named rastronol A, B, C, D, E, F, G, and H, and determined their structures mainly by spectroscopic techniques as 1, 8, 14, 17, 20, 29, 39 , and 51 respectively.
Sialylation of Thomsen–Friedenreich Antigen is a Noninvasive Blood-Based Biomarker for GNE Myopathy (2014)

Plasma T/ST ratios are a robust blood-based biomarker for GNE myopathy, and may also help explain the pathology and course of the disease.
Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a (2020)

Pluripotent embryonic stem cells (ESCs) self-renew or differentiate into all tissues of the developing embryo and cell-specification factors are necessary to balance gene expression. Here we delineate the function of the PHD-finger protein 5a (Phf5a) in ESC self-renewal and ascribe its role in regulating pluripotency, cellular reprogramming, and myoblast specification. We demonstrate that Phf5a is essential for maintaining pluripotency, since depleted ESCs exhibit hallmarks of differentiation. Mechanistically, we attribute Phf5a function to the stabilization of the Paf1 transcriptional complex and control of RNA polymerase II elongation on pluripotency loci. Apart from an ESC-specific factor, we demonstrate that Phf5a controls differentiation of adult myoblasts. Our findings suggest a potent mode of regulation by the Phf5a in stem cells, which directs their transcriptional program ultimately regulating maintenance of pluripotency and cellular reprogramming.
Dynamic Clustering and Cooperative Scheduling for Vehicle-to-Vehicle Communication in Bidirectional Road Scenarios (2017)

Efficient data dissemination is critical for enabling emerging applications in vehicular ad hoc networks. As a typical traffic scenario, the bidirectional road scenario of highways bring unique challenges on well exploiting the benefit of vehicle-to-vehicle (V2V) communication for data sharing among vehicles driving in opposite directions. This paper is dedicated to investigating the characteristics of data services in such a scenario and exploring new opportunities for enhancing overall system performance. Specifically, we present a system architecture to enable the road-side unit assisted data scheduling via vehicle-to-infrastructure communication. Then, we give a theoretical analysis on the opportunity of successful data sharing among vehicles driving in opposite directions based on the analysis of signal-to-interference-noise-ratio of V2V communication. On this basis, we propose a clustering mechanism based on the design of a time division policy and the derivation of the optimal cluster length. In addition, a cluster association strategy is designed to enable vehicles to dynamically join or leave a cluster based on their real-time velocities. Furthermore, a two-phase backoff mechanism is designed for distributed data sharing based on V2V communication, and a cooperative scheduling algorithm is proposed for selecting sender vehicles as well as the corresponding data items for broadcasting. Finally, we build the simulation model and give a comprehensive simulation study, which demonstrates that the proposed solutions can effectively improve the overall system performance.
Tip-induced flipping of droplets on Janus pillars: From local reconfiguration to global transport (2020)

Despite their simplicity, water droplets manifest a wide spectrum of forms and dynamics, which can be actuated using special texture at solid surfaces to achieve desired functions. Along this vein, natural or synthetic materials can be rendered water repellent, oleophobic, antifogging, anisotropic, etc.-all properties arising from an original design of the substrate and/or from the use of special materials promoting capillary or elastic forces at the droplet scale. Here, we report an original phenomenon occurring at the tip of asymmetric (half-flat, half-curved) pillars: Droplets reconfigure and get oriented on the curved side of these Janus tips. This local, geometry-driven effect, namely, tip-induced flipping of droplets, is found to be generic and have spectacular global consequences: Vast assemblies of Janus pillars enable a continuous, long-range, and fast self-transport of water harvested from fogs, which makes it possible to collect and concentrate droplets at different scales.
Quantitating dendritic cell clustering in the lymph node. (2016)

Abstract The efficiency of the T cell search for antigen presented by dendritic cells (DCs) in lymph nodes (LNs) is a determinant of the overall timing of the T cell immune response to infection. While there is suggestion that DCs are clustered in LNs, there has been little quantitative analysis done to precisely analyze DC positioning in LNs. We present the quantitation of murine DC motility, surface area, and volume in the lymph node. We also use computational analysis of 2 photon microscopy images of explanted murine lymph nodes from CD11c-YFP mice to determine the degree of clustered-ness of DCs. Our analysis indicates a degree of DC clustering within the lymph node. Previously our lab identified sites in the lymph node visited with greater frequency by T cells than would be expected by random motility. We hypothesize such sites demonstrate that DC clusters may actively attract T cells. Elucidating whether T cell motility around DC clusters is distinctive from T cell motility in areas where DCs are non-clustered will help decipher T cell search strategy and the timing of the adaptive immune response.
Geranylgeranyl transferase regulates CXC chemokine formation in alveolar macrophages and neutrophil recruitment in septic lung injury (2012)

Overwhelming accumulation of neutrophils is a significant component in septic lung damage, although the signaling mechanisms behind neutrophil infiltration in the lung remain elusive. In the present study, we hypothesized that geranylgeranylation might regulate the inflammatory response in abdominal sepsis. Male C57BL/6 mice received the geranylgeranyl transferase inhibitor, GGTI-2133, before cecal ligation and puncture (CLP). Bronchoalveolar lavage fluid and lung tissue were harvested for analysis of neutrophil infiltration, as well as edema and CXC chemokine formation. Blood was collected for analysis of Mac-1 on neutrophils and CD40L on platelets. Gene expression of CXC chemokines, tumor necrosis factor-α (TNF-α), and CCL2 chemokine was determined by quantitative RT-PCR in isolated alveolar macrophages. Administration of GGTI-2133 markedly decreased CLP-induced infiltration of neutrophils, edema, and tissue injury in the lung. CLP triggered clear-cut upregulation of Mac-1 on neutrophils. Inhibition of geranylgeranyl transferase reduced CLP-evoked upregulation of Mac-1 on neutrophils in vivo but had no effect on chemokine-induced expression of Mac-1 on isolated neutrophils in vitro. Notably, GGTI-2133 abolished CLP-induced formation of CXC chemokines, TNF-α, and CCL2 in alveolar macrophages in the lung. Geranylgeranyl transferase inhibition had no effect on sepsis-induced platelet shedding of CD40L. In addition, inhibition of geranylgeranyl transferase markedly decreased CXC chemokine-triggered neutrophil chemotaxis in vitro. Taken together, our findings suggest that geranylgeranyl transferase is an important regulator of CXC chemokine production and neutrophil recruitment in the lung. We conclude that inhibition of geranylgeranyl transferase might be a potent way to attenuate acute lung injury in abdominal sepsis.
High efficiency GHz laser processing with long bursts (2022)

Abstract Bursts of GHz repetition rate pulses involve more ablation mechanisms than single femtosecond pulses. Efficient ablation by GHz laser pulses is a multi-step process, consisting of a first thermal incubation phase, followed by a highly efficient ablation phase. GHz ablation therefore combines thermal and non-thermal ablation mechanisms. With an optimal choice of the burst duration, the ablation efficiency can be highly enhanced. Long bursts, comprising tens of pulses to hundreds of pulses, are needed to take full advantage of the increase in ablation efficiency.
Color atlas of dermatoscopy (2002)

History of skin-surface microscopy basis of dermatoscopy and skin-surface microscopy dermatoscopic criteria differential diagnosis of pigmented skin lesions benign melanocytic lesions and dysplastic nevi malignant melanoma pigmented skin lesions on hands and feet nonmelanocytic pigmented skin lesions computer-aided digital dermascopy dermatoscopical differential diagnosis conclusions. Appendix: synopsis of dermatoscopical differential diagnosis hints for dermatoscopic criteria within figures hints for diagnosis in the figures addresses of manufacturers.
Economic Predictions for Heat Mining: A Review and Analysis of Hot Dry Rock (HDR) Geothermal Energy Technology (1990)

The main objectives of this study were first, to review and analyze several economic assessments of Hot Dry Rock (HDR) geothermal energy systems, and second, to reformulate an economic model for HDR with revised cost components. The economic models reviewed include the following studies sponsored by Electric Power Research Institute (EPRI)-Cummings and Morris (1979), Los Alamos National Laboratory (LANL)-Murphy, et al. (1982), United Kingdom (UK)-Shock (1986), Japan-Hori, et al. (1986), Meridian-Entingh (1987) and Bechtel (1988). A general evaluation of the technical feasibility of HDR technology components was also conducted in view of their importance in establishing drilling and reservoir performance parameters required for any economic assessment. In this review, only economic projections for base load electricity produced from HDR systems were considered. Bases of 1989 collars ($) were selected to normalize costs. Following the evaluation of drilling and reservoir performance, power plant choices and cost estimates are discussed in section 6 of the report. In Section 7, the six economics studies cited above are reviewed and compared in terms of their key resource, reservoir and plant performance, and cost assumptions. Based on these comparisons, the report estimates parameters for three composite cases. Important parameters include: (1) resource quality-average geothermal gradient (C/km) and well depth, (2) reservoir performance-effective productivity, flow impedance, and lifetime (thermal drawdown rate), (3) cost components-drilling, reservoir formation, and power plant costs and (4) economic factors-discount and interest rates, taxes, etc. In Section 8, composite case conditions were used to reassess economic projections for HDR-produced electricity. In Section 9, a generalized economic model for HDR-produced electricity is presented to show the effects of resource grade, reservoir performance parameters, and other important factors on projected costs. A sensitivity and uncertainty analysis using this model is given in Section 10. Section 11 treats a modification of the economic model for predicting costs for direct, non-electric applications. HDR economic projections for the U.S. are broken down by region in Section 12. In Section 13, the report provides recommendations for continued research and development to reduce technical and economic uncertainties relevant to the commercialization of HDR. [DJE-2005]
Multicenter Study of the Clinical Efficacy of Imipenem/Cilastatin (1985)

logic efficacy of therapy could be evaluated. Toxicity data were analyzed for all 79 infections. Overall, 35 of 49 infections were cured or improved: 10 of 11 cases of pneumonia; 8 of 15 cases of pyelonephritis; 4 of 5 cases of osteomyelitis; 3 of 4 intravascular infections; 6 of 9 soft tissue infections; and 4 of 5 miscellaneous infections. There were 13 bacteriologic failures; superinfections with resistant organisms (i.e., Candida albicans, methicillin-resistant Staphylococcus epidermidis, and Pseudomonas maltophilia) occurred in three patients; reinfection with sensitive pathogens complicated one urinary tract infection; relapses developed of five urinary tract infections and of one case of endarteritis; and bacteriologic persistence occurred in three soft tissue infections. Infections with Pseudomonas aeruginosa were the most difficult to treat. In only six of 11 R aeruginosa infections was both bacteriologic and clinical cure achieved. Adverse effects were minimal; no serious hematologic or hepatic toxicity and no adverse renal effects were noted.
Theoretical and computational concepts for periodic optical waveguides (2007)

We present a general, rigorous, modal formalism for modeling light propagation and light emission in three-dimensional (3D) periodic waveguides and in aggregates of them. In essence, the formalism is a generalization of well-known modal concepts for translation-invariant waveguides to situations involving stacks of periodic waveguides. By surrounding the actual stack by perfectly-matched layers (PMLs) in the transverse directions, reciprocity considerations lead to the derivation of Bloch-mode orthogonality relations in the sense of E x H products, to the normalization of these modes, and to the proof of the symmetrical property of the scattering matrix linking the Bloch modes. The general formalism, which rigorously takes into account radiation losses resulting from the excitation of radiation Bloch modes, is implemented with a Fourier numerical approach. Basic examples of light scattering like reflection, transmission and emission in periodic-waveguides are accurately resolved.
Histone deacetylase inhibitors suppress IL-2–mediated gene expression prior to induction of apoptosis (2000)

Histone deacetylase (HDAC) inhibitors can induce transcriptional activation of a number of genes and induce cellular differentiation as histone acetylation levels increase. Although these inhibitors induce apoptosis in several cell lines, the precise mechanism by which they do so remains obscure. This study shows that HDAC inhibitors, sodium butyrate and trichostatin A (TSA), abrogate interleukin (IL)-2–mediated gene expression in IL-2–dependent cells. The HDAC inhibitors readily induced apoptosis in IL-2–dependent ILT-Mat cells and BAF-B03 transfectants expressing the IL-2 receptor βc chain, whereas they induced far less apoptosis in cytokine-independent K562 cells. However, these inhibitors similarly increased acetylation levels of histones in both cells. Although histone hyperacetylation is believed to lead to transcriptional activation, the results showed an abrogation of IL-2–mediated induction of c-myc,bag-1, and LC-PTP gene expression. This observed abrogation of gene expression occurred prior to phosphatidylserine externalization, a process that occurs in early apoptotic cells. Considering the biologic role played by IL-2–mediated gene expression in cell survival, these data suggest that its abrogation may contribute to the apoptotic process induced by HDAC inhibitors.
Dysfunctional cytokine receptor signaling in severe combined immunodeficiency. (1996)

I have reviewed the data demonstrating that XSCID results from mutations in gamma c and that an autosomal recessive form of SCID results from mutations in Jak3, a kinase that interacts with gamma c and is responsible for transducing gamma c-dependent signals. These findings underscore the dysfunctional cytokine receptor signaling that occurs in at least two forms of SCID. Features of the biology of Jak-STAT pathways have been discussed, as have the potential roles of overactive Jak-STAT pathways in cellular transformation. Implicit in these findings are the exciting possibilities of gene therapy for XSCID and Jak3-deficient SCID, as well as the possibility that new immunosuppressive drugs might be based on the ability to disrupt Jak-STAT pathways.
Advances Toward Lsd1 Inhibitors for Cancer Therapy (2017)

LSD1 has become an important biologically validated epigenetic target for cancer therapy since its identification in 2004. LSD1 mediates many cellular signaling pathways and is involved in the initiation and development of cancers. Aberrant overexpression of LSD1 has been observed in different types of cancers, and inactivation by small molecules suppresses cancer cell differentiation, proliferation, invasion and migration. To date, a large number of LSD1 inhibitors have been reported, RG6016, GSK-2879552, INCB059872, IMG-7289 and CC-90011 are currently undergoing clinical assessment for the treatment of acute myeloid leukemia, small-cell lung cancer, etc. In this review, we briefly highlight recent advances of LSD1 inhibitors mainly covering the literatures from 2015 to 2017 and tentatively propose our perspectives on the design of new LSD1 inhibitors for cancer therapy.
Neuronal circuitry underlying female aggression in Drosophila (2020)

Abstract Aggressive social interactions are used to compete for limited resources and are regulated by complex sensory cues and the organism’s internal state. While both sexes exhibit aggression, its neuronal underpinnings are understudied in females. Here, we describe a set of connected neurons in the adult Drosophila melanogaster central brain that drive female aggression. We identified a population of sexually dimorphic aIPg neurons whose optogenetic activation increased, and genetic inactivation reduced, female aggression. Analysis of GAL4 lines identified in an unbiased screen for increased female chasing behavior revealed the involvement of another sexually dimorphic neuron, pC1d, and implicated pC1d and aIPg neurons as core nodes regulating female aggression. pC1d activation increased female aggression and electron microscopy (EM) connectomic analysis demonstrated that aIPg neurons and pC1d have strong reciprocal connections. Our work reveals important regulatory components of the neuronal circuitry that underlies female aggressive social interactions and provides tools for their manipulation.
<title>User modeling for distributed virtual environment intelligent agents</title> (1999)

This paper emphasizes the requirement for user modeling by presenting the necessary information to motivate the need for and use of user modeling for intelligent agent development. The paper will present information on our current intelligent agent development program, the Symbiotic Information Reasoning and Decision Support (SIRDS) project. We then discuss the areas of intelligent agents and user modeling, which form the foundation of the SIRDS project. Included in the discussion of user modeling are its major components, which are cognitive modeling and behavioral modeling. We next motivate the need for and user of a methodology to develop user models to encompass work within cognitive task analysis. We close the paper by drawing conclusions from our current intelligent agent research project and discuss avenues of future research in the utilization of user modeling for the development of intelligent agents for virtual environments.
Protective Effects of Propranolol on the Exercise-Induced Reduction of Blood Flow in Arteriopathic Patients (1979)

The vascular steal phenomenow, that is, the shunting of blood from ischemic to normally perfused areas, is commonly observed during exercise in the affected limbs of patients with peripheral arterial insufficiency. Propranolol was administered to 18 arteriopathic patients before the exercise to ascertain whether the reverse situation can be induced. The results indicate that before propranolol administration, Jantsch's index (used to quantify the plethysmographic waves) decreased from 0.53 +/- 0.05 to 0.33 +/- 0.04 (P less than 0.001) at 1 minute, and to 0.38 +/- 0.04 (P less than 0.001) at 5 minutes after the end of the exercise. When the exercise was repeated after propranolol, Jantsch's index did not change. These findings indicate that propranolol can inhibit exercise-induced vascular steal.