gebhart/patrepeval huggingface dataset:
Kaposi's sarcoma-associated herpesvirus-infected primary effusion lymphoma has a plasma cell gene expression profile (2003)

Kaposi's sarcoma-associated herpesvirus is associated with three human tumors: Kaposi's sarcoma, and the B cell lymphomas, plasmablastic lymphoma associated with multicentric Castleman's disease, and primary effusion lymphoma (PEL). Epstein-Barr virus, the closest human relative of Kaposi's sarcoma-associated herpesvirus, mimics host B cell signaling pathways to direct B cell development toward a memory B cell phenotype. Epstein-Barr virus-associated B cell tumors are presumed to arise as a consequence of this virus-mediated B cell activation. The stage of B cell development represented by PEL, how this stage relates to tumor pathology, and how this information may be used to treat the disease are largely unknown. In this study we used gene expression profiling to order a range of B cell tumors by stage of development. PEL gene expression closely resembles that of malignant plasma cells, including the low expression of mature B cell genes. The unfolded protein response is partially activated in PEL, but is fully activated in plasma cell tumors, linking endoplasmic reticulum stress to plasma cell development through XBP-1. PEL cells can be defined by the overexpression of genes involved in inflammation, cell adhesion, and invasion, which may be responsible for their presentation in body cavities. Similar to malignant plasma cells, all PEL samples tested express the vitamin D receptor and are sensitive to the vitamin D analogue drug EB 1089 (Seocalcitol).
Reconstructing trees from traces (2021)

We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree being a path. For many classes of trees, including complete trees and spiders, we provide algorithms that reconstruct the labels using only a polynomial number of traces. This exhibits a stark contrast to known results on string trace reconstruction, which require exponentially many traces, and where a central open problem is to determine whether a polynomial number of traces suffice. Our techniques combine novel combinatorial and complex analytic methods.
The Influence of a Small Boron Addition on the Microstructure and Mechanical Properties of Ti‐6Al‐4V Fabricated by Metal Injection Moulding (2011)

Abstract The effect of boron additions on the sintering behavior, microstructural development, and mechanical properties of a Ti‐6Al‐4V alloy fabricated by metal injection moulding (MIM) was studied. The addition of boron promotes a significant refinement of the microstructure by changing the microstructure from the typical lamellar to a more equiaxed morphology. The presence of both features: α colonies and α grains were confirmed by electron backscatter diffraction (EBSD) experiments. Furthermore, the pinning effect of TiB particles on grain boundary motion enhances the densification process due to the fact that the separation of pores and grain boundaries is suppressed. As a result of the refinement of the microstructure achieved by adding 0.5 wt% boron to the Ti‐6Al‐4V alloy, excellent tensile (σ 0.2 = 787 MPa, UTS = 902 MPa and ε = 12%) and fatigue (endurance limit = 640 MPa) properties were obtained.
Transgenic<i>Leishmania</i>Model for Delta-Aminolevulinate-Inducible Monospecific Uroporphyria: Cytolytic Phototoxicity Initiated by Singlet Oxygen-Mediated Inactivation of Proteins and Its Ablation by Endosomal Mobilization of Cytosolic Uroporphyrin (2008)

Inherent deficiencies of Leishmania in heme biosynthesis were genetically complemented for delta-aminolevulinate-inducible biosynthesis and accumulation of light-excitable uroporphyrin. The phototoxic flagellar immobilization and cytolysis phenotypes and porphyrin mobilization noted previously were further analyzed biochemically and cytologically to delineate the mechanism of phototoxicity and detoxification in this monoporphyric model. Under optimal conditions of induction for approximately 3 days, cells remained viable but became increasingly uroporphyric, peaking at > or =90% of the population by approximately day 2; thereafter, a small population of less porphyric or aporphyric cells emerged. On exposure to light, the flagella of porphyric cells were immobilized in milliseconds, and singlet oxygen became detectable in their lysates. Both photosensitive phenotypes increased proportionally with the cellular uroporphyric levels and were susceptible to inhibition by azide, but not by D-mannitol. Brief irradiation of the uroporphyric cells produced no appreciable protein degradation but inactivated cytosolic neomycin phosphotransferase and significantly bleached cytosolic green fluorescent protein, which was azide reversible. These cells were irreparably photodamaged, as indicated by their subsequent loss of membrane permeability and viability. This is the first in situ demonstration that early inactivation of functional proteins by singlet oxygen initiates the cytolytic phototoxicity in uroporphyria. Detoxification appears to involve endocytic/exocytic mobilization of uroporphyrin from cytosol to "porphyrinosomes" for its eventual extracellular expulsion. This is proposed as the sole mechanism of detoxification, since it is attributable to the reversion of porphyric to aporphyric cells during uroporphyrinogenesis and repeated cycles of this event plus photolysis selected no resistant mutants, only aporphyric clones of the parental phenotypes. Further characterization of the transport system for uroporphyrin in this model is expected to benefit not only our understanding of the cellular mechanism for disposal of toxic soluble wastes but also potentially the effective management of human uroporphyria and the use of uroporphyric Leishmania for vaccine/drug delivery.
Terahertz electromagnetic radiation from intrinsic Josephson junctions at zero magnetic field via breather-type self-oscillations (2011)

I propose a new mechanism of intense high-frequency electromagnetic wave generation by spatially uniform stacked Josephson junctions at zero magnetic field. The ac-Josephson effect converts the dc-bias voltage into ac supercurrent; however, in the absence of spatial variation of the Josephson phase difference it does not provide dc-to-ac power conversion, needed for emission of electromagnetic waves. Here I demonstrate that at geometrical resonance conditions, spatial homogeneity of the phase can be spontaneously broken by the appearance of breathers (bound fluxon-antifluxon pairs), facilitating effective dc-to-ac power conversion. This leads to self-oscillations at cavity-mode frequencies, accompanied by the emission of radiation. The proposed mechanism explains all major features of recently observed THz radiation from large-area Bi${}_{2}$Sr${}_{2}$CaCu${}_{2}$O${}_{8+x}$ mesa structures.
Atomic Layer Deposition of Titanium Oxide on Self-Assembled-Monolayer-Coated Gold (2004)

We demonstrate an atomic layer deposition of TiO2 thin films on self-assembled monolayers of ω-functionalized alkanethiolates. The TiO2 thin films were grown on OH-terminated alkanethiolate monolayer-coated gold by atomic layer deposition at 100 °C. The atomic layer deposition of the TiO2 thin films is self-controlled and extremely linear relative to the number of cycles. Selective deposition of the TiO2 thin film using atomic layer deposition was accomplished with patterned self-assembled monolayers as templates. Microcontact printing was done to prepare the patterned monolayers of the alkanethiolates on gold substrates. The selective atomic layer deposition is based on the fact that the TiO2 thin film is selectively deposited only on the regions exposing OH-terminated alkanethiolate monolayers of the gold substrates, because the regions covered with CH3-terminated monolayers do not have any functional group to react with precursors.
Police leadership: the challenges for developing contemporary practice (2017)

Purpose In recent years, police leadership integrity and standards have been positioned as central to the professionalisation agenda of the police service England and Wales (College of Policing, 2015). The purpose of this paper is to explore the challenges for developing innovative, more people-oriented approaches to leadership in a command environment like the police. Design/methodology/approach A case study approach in one UK police constabulary was adopted. In all, 38 semi-structured interviews were conducted with senior police officers from chief constable to inspector rank. Interviews were audio recorded, transcribed verbatim and thematically analysed. Findings Police officers drew on managerial and command discourses in their understandings of leadership. Perceptions of the situation, particularly in terms of perceived risk and visibility, influenced leadership practices in the constabulary. Originality/value Current research and policy places emphasis on “what works” in police leadership; the meanings of leadership to police officers is overshadowed by a focus on effectiveness. Through the use of semi-structured interviews, this research captures police leaders’ understandings of themselves and their leadership. The findings reveal that, at a time when police leadership needs to become more innovative and people focussed, the pressures and complexities of contemporary policing mean that police officers retreat to leadership that is command-based and driven by the primacy of business needs.
Economic Evaluation of Enhanced Oil Recovery (2002)

The research for tomorrow's oil reserves has directed the efforts of the energy industry to frontiers beyond the conventional exploration and production strategies. These frontiers are defined not by geography or geology but rather by technology. They are a collection of technologies-involving the use of thermal, gas and chemical means for producing more oil-that fall under the broad umbrella called Enhanced Oil Recovery (EOR). The results of successful application of this new technology will have a decisive impact on the energy conservation program of any oil producing country. A comprehensive national energy program is complex and to plan it represents a challenge. A unified and complete national program must encompass the consideration of all possible options. The potential of each need to be explored. One such option in Libya is to produce more oil, that is, to effect the enhancement of oil recovery from the nation oil fields. The planning of an EOR project demands a meticulous attention to many problems, thus requiring considerable lead time for studies, evaluations, project design and, most of all, the economics of these high cost EOR projects. The objective of this study is to conduct an economic analysis on one of the most representative candidate major field in Libya (D field) for application of the technically approved enhanced oil recovery methods. By performing economic sensitivity analysis on key input variables such as oil prices, the price of injection solvent, capital expenditures, operating expenses, and oil recovery, the aim is to develop sensitivity analysis graphs for each variable to assess future engineering planning with regard to the EOR projects economics in Libya. Economic optimization is the ultimate goal of reservoir engineering management. With estimated production, capital, operating expenses, and financial data, project economics are evaluated. Project finding could be applied to any EOR candidate reservoir worldwide.
Multi‐layered stochasticity and paracrine signal propagation shape the type‐I interferon response (2012)

The cellular recognition of viruses evokes the secretion of type-I interferons (IFNs) that induce an antiviral protective state. By live-cell imaging, we show that key steps of virus-induced signal transduction, IFN-β expression, and induction of IFN-stimulated genes (ISGs) are stochastic events in individual cells. The heterogeneity in IFN production is of cellular-and not viral-origin, and temporal unpredictability of IFN-β expression is largely due to cell-intrinsic noise generated both upstream and downstream of the activation of nuclear factor-κB and IFN regulatory factor transcription factors. Subsequent ISG induction occurs as a stochastic all-or-nothing switch, where the responding cells are protected against virus replication. Mathematical modelling and experimental validation show that reliable antiviral protection in the face of multi-layered cellular stochasticity is achieved by paracrine response amplification. Achieving coherent responses through intercellular communication is likely to be a more widely used strategy by mammalian cells to cope with pervasive stochasticity in signalling and gene expression.
Characteristics of Open Data CSV Files (2016)

This work analyzes an Open Data corpus containing 200K tabular resources with a total file size of 413 GB from a data consumer perspective. Our study shows that ~10% of the resources in Open Data portals are labelled as a tabular data of which only 50% can be considered CSV files. The study inspects the general shape of these tabular data, reports on column and row distribution, analyses the availability of (multiple) header rows and if a file contains multiple tables. In addition, we inspect and analyze the table column types, detect missing values and report about the distribution of the values.
Development and Characterization of Treprostinil Palmitil Inhalation Aerosol for the Investigational Treatment of Pulmonary Arterial Hypertension (2021)

Treprostinil palmitil (TP) is a prodrug of treprostinil (TRE), a pulmonary vasodilator that has been previously formulated for inhaled administration via a nebulizer. TP demonstrates a sustained presence in the lungs with reduced systemic exposure and prolonged inhibition of hypoxia-induced pulmonary vasoconstriction in vivo. Here, we report on re-formulation efforts to develop a more convenient solution-based metered-dose inhaler (MDI) formulation of TP, a treprostinil palmitil inhalation aerosol (TPIA) that matches the pharmacokinetic (PK) and efficacy profile of a nebulized TP formulation, treprostinil palmitil inhalation suspension (TPIS). MDI canisters were manufactured using a two-stage filling method. Aerosol performance, formulation solubility, and chemical stability assays were utilized for in vitro evaluation. For in vivo studies, TPIA formulations were delivered to rodents using an inhalation tower modified for MDI delivery. Using an iterative process involving evaluation of formulation performance in vitro (TP and excipient solubility, chemical stability, physical stability, and aerosol properties) and confirmatory testing in vivo (rat PK and efficacy, guinea pig cough), a promising formulation was identified. The optimized formulation, TPIA-W, demonstrates uniform in vitro drug delivery, a PK profile suitable for a once-daily administration, efficacy lasting at least 12 h in a hypoxic challenge model, and a significantly higher cough threshold than the parent drug treprostinil.
Reduction in Vehicle Temperatures and Fuel Use from Cabin Ventilation, Solar-Reflective Paint, and a New Solar-Reflective Glazing (2007)

<div class="htmlview paragraph">A new type of solar-reflective glass that improves reflection of the near-infrared (NIR) portion of the solar spectrum has been developed. Also developed was a prototype solar-reflective paint that increases the NIR reflection of opaque vehicle surfaces while maintaining desired colors in the visible portion of the spectrum. Both of these technologies, as well as solar-powered parked car ventilation, were tested on a Cadillac STS as part of the Improved Mobile Air Conditioning Cooperative Research Program (I-MAC). Significant reductions in interior and vehicle skin temperatures were measured.</div> <div class="htmlview paragraph">The National Renewable Energy Laboratory (NREL) performed an analysis to determine the impact of reducing the thermal load on the vehicle. A simplified cabin thermal/fluid model was run to predict the potential reduction in A/C system capacity. The potential reduction in fuel use was calculated using a vehicle simulation tool developed by the U.S. Department of Energy (DOE).</div>
Alteromonas atlantica sp. nov. and Alteromonas carrageenovora sp. nov., Bacteria That Decompose Algal Polysaccharides (1992)

We studied seven strains of aerobic, marine, polarly flagellated bacteria which decompose alginate, agar, and carrageenan. The major respiratory quinone of these strains was ubiquinone-8. The G+C content of their DNA was 39.5 to 41.7 mol%. “Pseudomonas atlantica” IAM 12927 and the conspecific five isolates were concluded to constitute a single species distinguished from the other nonpigmented Alteromonas species by DNA-DNA hybridization (homology values of more than 82%) and phenotypic similarity (similarity coefficients, based on assimilation of 145 carbon compounds, were 79 to 96%). “Pseudomonas carrageenovora” IAM 12662, the sole extant strain, was distinct from “P. atlantica” and other Alteromonas species in DNA-DNA hybridization and phenotypic features. Taxonomic affinity to Alteromonas espejiana was indicated by DNA-DNA hybridization with “P. atlantica” IAM 12927 and the five conspecific isolates (39 to 55%) and with “P. carrageenovora” IAM 12662 (43 to 45%). Phenotypically, higher similarity values (79 to 89%) for assimilation of 145 carbon compounds were shared between A. espejiana IAM 12927T and the six conspecific strains, including “P. atlantica” IAM 12927. Alteromonas atlantica sp. nov. (type strain, IAM 12927, =ATCC 19262, =NCIMB 301) and Alteromonas carrageenovora (type strain, IAM 12662, =IFO 12985, =ATCC 43555, =NCIMB 302) are proposed for “P. atlantica” IAM 12927 and the conspecific five isolates and “P. carrageenovora” IAM 12662, respectively. A set of phenotypic features which differentiate the two Alteromonas species is described.
Transdermal Delivery of Dideoxynucleoside-Type Anti-HIV Drugs. 2. The Effect of Vehicle and Enhancer on Skin Permeation (1996)

The effects of vehicles and enhancers on the skin permeation of the dideoxynucleoside-type anti-HIV drugs Zalcitabine (DDC), Didanosine (DDI), and Zidovudine (AZT) were studied using hairless rat skin at 37 degrees C. After each drug was saturated in various volume fractions of ethanol (EtOH)/water or EtOH/tricaprylin (TCP) cosolvent system for 48 h at 37 degrees C, an in vitro skin permeation study was conducted using Valia-Chien permeation cells for 30 h. The skin permeation rates of DDC, DDI, and AZT from both EtOH/water and EtOH/TCP cosolvent systems increased as the volume fraction of ethanol was increased, reached maximum values at 50-60% (v/v) of ethanol, and then decreased with further increase of ethanol volume fraction. The EtOH/water cosolvent system seems to enhance the skin permeation of these drugs by increasing both the solubility of drug in the vehicles and partitioning of drug into the skin. The skin permeation enhancing effect of EtOH/TCP seems to be solely due to the increase in partitioning of drug into the skin. Addition of 1.0% (v/v) of permeation enhancers, such as oleic acid (OA) and N-methyl-2-pyrrolidone (NMP), in the EtOH/TCP (50:50) cosolvent system could not significantly increase the permeation rate of these drugs. Incorporation of viscous TCP into ethanol probably reduced the thermodynamic activity of enhancers to distribute from the vehicle to the skin. However, incorporation of 1.0% (v/v) of OA in the EtOH/water (60:40) cosolvent system dramatically enhanced the skin permeation of these drugs while reducing the lag time. The permeation rates of these drugs increased as OA concentration was increased up to 0.3% (v/v) in the EtOH/water (60:40) cosolvent system and reached a plateau with further addition of OA. Using a saturated solution in the EtOH/water (60:40) cosolvent system containing 1.0% (v/v) OA, DDC, and AZT reached the target permeation rate required to maintain a therapeutic system level across hairless rat skin. Although only DDC reached the target permeation rate across human cadaver skin, these results suggest that the mutual enhancement effect of ethanol and OA may make transdermal delivery of dideoxynucleoside-type anti-HIV drugs feasible.
Abstracting network characteristics and locality properties of parallel systems (2002)

Abstracting features of parallel systems is a technique that has been traditionally used in theoretical and analytical models for program development and performance evaluation. We explore the use of abstractions in execution-driven simulators in order to speed up simulation. In particular, we evaluate abstractions for the interconnection network and locality, properties of parallel systems in the context of simulating cache-coherent shared memory (CC-NUMA) multiprocessors. We use the recently proposed LogP model to abstract the network. We abstract locality by modeling a cache at each processing node in the system which is maintained coherent, without modeling the overheads associated with coherence maintenance. Such an abstraction tries to capture the true communication characteristics of the application without modeling any hardware induced artifacts. Using a suite of applications and three network topologies simulated on a novel simulation platform, we show that the latency overhead modeled by LogP is fairly accurate. On the other hand, the contention overhead can become pessimistic when the applications display sufficient communication locality. Our abstraction for data locality closely models the behavior of the target system over the chosen range of applications. The simulation model which incorporated these abstractions was around 250-300% faster than the simulation of the target machine.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The move towards research in the health professions: A comparison of Chiropractic and Physiotherapy. (1988)

This paper compares the efforts of physiotherapy and chiropractic to move towards the development of a scientific body of knowledge through research. The history of both professions is discussed with particular reference to the education of the clinical practitioners and the educational faculty. Four cited factors contributing to the paucity of research in chiropractic, namely anti-scientific elements in philosophy, lack of suitable role-models, lack of funds and a lack of understanding of research methodology are also seen as barriers to physiotherapy research. These obstacles are discussed in the light of the strategies being employed by both professions to deal with this issue and their success or otherwise. It is stressed that research by members of both professions is fundamental to ensure professional survival. Solutions are principally concerned with increasing the research output from those institutions which educate future professionals. This new generation will likely ensure that the professions are soundly based on scientific principles. The paper considers, therefore, the pre-professional curriculum primarily, although not exclusively, from a Canadian perspective.