gebhart/patrepeval huggingface dataset:
Sequence, assembly and analysis of pX01 and pX02 (1999)

Bacillus anthracis plasmids pX01 and pX02, harboured by the Sterne and Pasteur strains, respectively, have been sequenced by random 'shotgun' cloning and high throughout sequence analysis. These sequences have been assembled (Sequencher) to generate a circulate pX01 plasmid containing 181 656 bp and a single linear (gapped) pX02 contig containing at least 93.479 bp. Initial annotation suggests that the two plasmids combined contain at least 200 potential open reading frames (ORFs) with < 40% having significant similarity to sequences registered in open databases. Collectively, only 118 566 bp of the pX01 DNA (65%) represent predicted coding regions. This value is similar to published gene densities for other plasmids and is indicative of the larger intergenic spaces in plasmids vs those found in the chromosomes of the parental microbes (85-93% gene density). A 70 kbp region including the toxin genes (cya, lef and pag) is distinct from the remainder of the pX01 sequence: (1) it has a lower gene density (58 vs 70%) than the remaining 111 kbp; (2) it contains all but one of the co-regulated transcriptional fusions identified by transposon mutagenesis (Hoffmaster & Koehler 1997) and (3) it contains a significantly higher proportion of positive BLAST scores (62 vs 20%) for putative ORFs. These data suggest different origins for the two regions of pX01.
Microstructural evolution of a-plane GaN grown on a-plane SiC by metalorganic chemical vapor deposition (2004)

This letter describes the relationship between the morphological evolution of heteroepitaxial a-plane GaN films and the formation of the extended defect structure. The initial a-plane GaN growth on a-plane SiC substrates (via a high temperature AlN buffer layer) follows a Volmer–Weber growth mode. Consequently, the coalescence of three-dimensional (3D) islands generates threading dislocations which dominate the nonpolar GaN film’s microstructure (3×1010 cm−2). Exposed nitrogen-face surfaces, identified using x-ray diffraction measurements and convergent beam electron diffraction analysis, are present throughout the 3D growth and are the likely source of basal plane faulting (7×105 cm−1) within the film. Atomic force microscopy and scanning electron microscopy were used to image the morphological transition, which was correlated to changes in the a-GaN crystal tilt mosaic measured by x-ray rocking curves.
Medical information security: the evolving challenge (2002)

Electronic transfer is rapidly becoming the main means of medical information exchange. Because of the security related questions arising from the proliferation of electronic transfer or storage of sensitive medical data, the US government has begun an effort to set standards concerning levels of medical data sensitivity and to prescribe minimum safeguards for maintaining patient information. The "Health Insurance Portability and Accountability Act of 1996" (HIPAA), was signed into law as PL 104-191 on September 31, 1996. As the name implies, this law helps ensure that an individual can retain certain health insurance coverage when changing or losing employment. However, it also requires the Secretary of Health and Human Services (HHS) to adopt security standards and establish policies and procedures to prevent unauthorized access to health care information. The legislation further directs that those persons who maintain and transmit health information apply reasonable and appropriate administrative, technical and physical safeguards to ensure the integrity and confidentiality of such information and to "protect against any reasonably anticipated threats or hazards to the security or integrity of the information and unauthorized uses or disclosures..." This paper explores the existing problems relating to patient record confidentiality and the impact of the new legislation.
Studies of Plasma Properties in Rocket Plumes (1982)

Various factors which affect the gas density and electron density distribution in the exhaust plume from solid rocket engines were studied. The particulates affect the plume density distribution through their effects on the nozzle flow field. The two-body attachment reaction Hcl + e = H + cl- is the dominant reaction in determining the ionization level in the nozzle expansion. The chemical and physical phenomena required to accurately determine the plume plasma properties for subsequent radio frequency interaction analysis are identified. (Author)
The long‐term efficacy of sacral neuromodulation in the management of intractable cases of bladder pain syndrome: 14 years of experience in one centre (2010)

• SNM is an effective treatment to control the symptoms of BPS. It should be considered before any major invasive surgical intervention if conservative measures have failed. It is a minimally invasive, safe procedure with good long-term outcome. However, the revision rate is high and patients require lifelong follow-up.
The Accelerated Polyvinyl-Alcohol Method for GSR Collection—PVAL 2.0 (2000)

The polyvinyl-alcohol collection method (PVAL) is used in forensic practice to gather topographical information about gunshot residues (GSR) from the hands to decide if the subject has made use of firearms. The results allow a distinction between suicide and homicide. The only inconvenience of PVAL was that the procedure took about 60 min because three layers of liquid PVAL had to be applied and dried. Therefore, the collection method was only applied to corpses. The improved and accelerated PVAL 2.0 uses a sandwich technique. Cotton gauze for stabilization is moistened with a 10% PVAL solution. A solid film of PVAL (Solublon) is spread on the cotton mesh. The gauze is then modeled to the hand and dried with a hair dryer. After removing the cotton gauze, the traces are embedded in the water-soluble PVAL. The procedure does not take more than 15 min. The results demonstrate the qualities and advantages of PVAL: topographical distribution of GSR, highest gain of GSR, sampling of all other traces like blood, backspatter etc., and humidity does not reduce the gain. In addition, with the new PVAL 2.0 dislocation of GSR or contamination are excluded. PVAL 2.0 can also be applied on live suspects.
Hypnotism: A History (2001)

The discovery Mesmer in Paris year of crisis aftermath somnabulisam minor magnetists vision without eyes the spread of magnetism to Britain and the USA Elliotson and the Okey Sisters the Mesmeric campaign Braid and hypnotism Charcot at the Sapetriere the triumph of suggestion the 20th century.
T Cell CD3-ζη Heterodimer Expression and Coupling to Phosphoinositide Hydrolysis (1988)

The T cell antigen receptor consists of an antigen-binding heterodimer that is noncovalently associated with at least five CD3 subunits (gamma, delta, epsilon, zeta, and eta). The CD3-zeta chains are either disulfide-linked homodimers (CD3-zeta 2) or disulfide-linked heterodimers with eta (CD3-zeta eta). Variants of a murine antigen-specific T cell hybridoma that express normal amounts of CD3-zeta 2 but decreased amounts of CD3-zeta eta were isolated. When activated, the parental cell line increased both phosphatidylinositol hydrolysis and serine-specific protein kinase activity to a much greater extent than the variants. In contrast, the activation of a tyrosine-specific kinase after stimulation with a cross-linking antibody to CD3 was similar among these cells. There was a positive linear relation between the expression of CD3-zeta eta and phosphoinositide hydrolysis stimulated by the TCR, suggesting a differential coupling of the T cell alpha beta heterodimer to signal transduction mechanisms due to alpha beta association with either CD3-zeta 2 or CD3-zeta eta.
The role of gut hormones in glucose homeostasis (2007)

The gastrointestinal tract has a crucial role in the control of energy homeostasis through its role in the digestion, absorption, and assimilation of ingested nutrients. Furthermore, signals from the gastrointestinal tract are important regulators of gut motility and satiety, both of which have implications for the long-term control of body weight. Among the specialized cell types in the gastrointestinal mucosa, enteroendocrine cells have important roles in regulating energy intake and glucose homeostasis through their actions on peripheral target organs, including the endocrine pancreas. This article reviews the biological actions of gut hormones regulating glucose homeostasis, with an emphasis on mechanisms of action and the emerging therapeutic roles of gut hormones for the treatment of type 2 diabetes mellitus.
Compressed Sensing of Analog Signals in Shift-Invariant Spaces (2009)

A traditional assumption underlying most data converters is that the signal should be sampled at a rate exceeding twice the highest frequency. This statement is based on a worst-case scenario in which the signal occupies the entire available bandwidth. In practice, many signals are sparse so that only part of the bandwidth is used. In this paper, we develop methods for low-rate sampling of continuous-time sparse signals in shift-invariant (SI) spaces, generated by <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</i> kernels with period <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</i> . We model sparsity by treating the case in which only <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</i> out of the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</i> generators are active, however, we do not know which <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</i> are chosen. We show how to sample such signals at a rate much lower than <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</i> / <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</i> , which is the minimal sampling rate without exploiting sparsity. Our approach combines ideas from analog sampling in a subspace with a recently developed block diagram that converts an infinite set of sparse equations to a finite counterpart. Using these two components we formulate our problem within the framework of finite compressed sensing (CS) and then rely on algorithms developed in that context. The distinguishing feature of our results is that in contrast to standard CS, which treats finite-length vectors, we consider sampling of analog signals for which no underlying finite-dimensional model exists. The proposed framework allows to extend much of the recent literature on CS to the analog domain.
Plants as indicators of gold mineralization at Watson Bar, British Columbia, Canada (1979)

Shoot material of Phacelia sericca, Oxytropis campestris, and Sedum Lanceolatum collected at intervals across two mineralized areas were analyzed for gold and arsenic. Elevated values of gold were determined in plants from specific sites which were often accompanied by high arsenic concentrations. As determined by neutron activation analysis, the highest gold concentrations (as much as 55 ppb) were found in the cyanogenic species P. sericca. This gold was lost by dry ashing the plant at 550 degrees C. It was concluded that biogeochemical prospecting for gold is feasible.
Design of a processor bus interface ASIC for the stream memory controller (2002)

The Stream Memory Controller (SMC) is an experimental memory interface which allows hardware-assisted memory access reordering for vector computations in order to maximize the efficiency of the system memory bus. This paper describes the design and test strategies for the SMC Processor Bus Interface (PBI) and FIFO logic ASIC. This IC is designed as part of a daughter card attachment to a 40 MHz Intel i860 system. The entire integrated circuit design was completed in a top-down design environment using VHDL for synthesis and a target process of 0.75 /spl mu/m. The design includes SRAM elements, combinatorial logic, and state machine components. This ASIC is the first in a series of ICs intended as a proof-of-concept of the SMC based system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mobile packet data technology: an insight into MOBITEX architecture (1997)

Mobile data networks offer a cost-effective and efficient alternative for data communication. In order to present some aspects of mobile data technology, this article offers some insight into the basic networking layers of a popular and widely deployed network, MOBITEX. MOBITEX technology offers a versatile architecture to support wireless packet data service inside an extended geographical area with internetwork roaming and interoperability features. This technology has become quite popular, mainly due to its open architecture and its vast equipment/applications availability. The authors provide an overview of the MOBITEX architecture, services, and subscription types, and a detailed examination of the network, data link, and physical layers. The power-saving features of MOBITEX are also discussed.
A Robotic System for Real-Time Resin Flow Modification During Vacuum-Assisted Resin Transfer Molding (2006)

To complement existing resin flow control strategies currently under development for Vacuum-Assisted Resin Transfer Molding (VARTM), and to provide the ability to react to unexpected changes in resin behavior during injection, a new technique for resin flow manipulation has been investigated. This approach consists of a semi-cylindrical shaped vacuum chamber placed on a mold which, when evacuated, increases the permeability of the region under the chamber by lifting the bag atop the mold. A finite element model has been developed to predict the resin flow within the mold while using the external chamber. Laboratory testing has shown significant modification in resin flow with reduced injection time. Using the external chamber, a robotic system has been prototyped that identifies dry regions forming during injection via computer vision, deploys the vacuum chamber over the mold with a robotic arm, and actuates the chamber in order to modify and correct the resin flow within the mold. Test results using lab-scale molds with large variations in preform permeabilities indicate that the robotic system can correct and/or modify the resin flow within a mold in real time, thus eliminating dry, unimpregnated regions. This computer-based method has the potential to significantly enhance molded part quality and consistency by eliminating resin starved regions within a molded composite part.
Neonatal protection by an innate immune system of human milk consisting of oligosaccharides and glycans1 (2008)

This review discusses the role of human milk glycans in protecting infants, but the conclusion that the human milk glycans constitute an innate immune system whereby the mother protects her offspring may have general applicability in all mammals, including species of commercial importance. Infants that are not breastfed have a greater incidence of severe diarrhea and respiratory diseases than those who are breastfed. In the past, this had been attributed primarily to human milk secretory antibodies. However, the oligosaccharides are major components of human milk, and milk is also rich in other glycans, including glycoproteins, mucins, glycosaminoglycans, and glycolipids. These milk glycans, especially the oligosaccharides, are composed of thousands of components. The milk factor that promotes gut colonization by Bifidobacterium bifidum was found to be a glycan, and such prebiotic characteristics may contribute to protection against infectious agents. However, the ability of human milk glycans to protect the neonate seems primarily to be due to their inhibition of pathogen binding to their host cell target ligands. Many such examples include specific fucosylated oligosaccharides and glycans that inhibit specific pathogens. Most human milk oligosaccharides are fucosylated, and their production depends on fucosyltransferase enzymes; mutations in these fucosyltransferase genes are common and underlie the various Lewis blood types in humans. Variable expression of specific fucosylated oligosaccharides in milk, also a function of these genes (and maternal Lewis blood type), is significantly associated with the risk of infectious disease in breastfed infants. Human milk also contains major quantities and large numbers of sialylated oligosaccharides, many of which are also present in bovine colostrum. These could similarly inhibit several common viral pathogens. Moreover, human milk oligosaccharides strongly attenuate inflammatory processes in the intestinal mucosa. These results support the hypothesis that oligosaccharides and other glycans are the major constituents of an innate immune system of human milk whereby the mother protects her infant from enteric and other pathogens through breastfeeding. These protective glycans may prove useful as a basis for the development of novel prophylactic and therapeutic agents that inhibit disease by mucosal pathogens in many species.
Composable, distributed system to derive actionable mission information from intelligence, surveillance, and reconnaissance (ISR) data (2013)

Advances in sensor observation and collection technology, coupled with the use of multiple sensors distributed amongst multiple transport platforms to support a single mission; create the potentially crippling problem of data overload for DoD operators and imagery and video analysts as they strive to provide processing, exploitation, and dissemination (PED) to the end-user (i.e., warfighter). These operators and analysts depend on sensor data, specifically Intelligence, Surveillance and Reconnaissance (ISR) data, to perform time-critical mission functions such as target engagement. However, in many cases, the data they receive are not relevant to the mission, and they waste valuable time and resources sifting through thousands of still imagery and video footage gaining very little useful information that can be turned into actionable intelligence. The DoD seeks a solution to this problem that will reduce the vast amount of ISR data to actionable ISR information. The Multifactor Information Distributed Analytics Technology Aide (MiData) applies systems engineering and architectural principles to solve this challenge in a novel way. MiData is a composable system comprising independent factors integrated to perform critical processing functions that autonomously transform data to information. These factors may be distributed between mission segments located in the air, on the ground, or in the sea based on the mission requirements and PED resource availability. This distribution enables resource reduction, operator and analysts' productivity increases across the ISR mission segments, and response-time improvements to meet time-critical needs of end-users.
Arylation of Aldehyde Homoenolates with Aryl Bromides (2013)

A mild palladium catalyzed coupling of reactive aldehyde homoenolates with aryl bromides is described. Aldehyde homoenolates are generated by ring opening of cyclopropanols via a C-C cleavage step. The coupling generates aldehyde products at room temperature in 59-93% yield.
Detection of allergen-induced airway hyperresponsiveness in isolated mouse lungs (2006)

Airway hyperresponsiveness (AHR) is a hallmark of bronchial asthma. Important features of this exaggerated response to bronchoconstrictive stimuli have mostly been investigated in vivo in intact animals or in vitro in isolated tracheal or bronchial tissues. Both approaches have important advantages but also certain limitations. Therefore, the aim of our study was to develop an ex vivo model of isolated lungs from sensitized mice for the investigation of airway responsiveness (AR). BALB/c mice were sensitized by intraperitoneal ovalbumin (Ova) and subsequently challenged by Ova inhalation. In vivo AR was measured in unrestrained animals by whole body plethysmography after stimulation with aerosolized methacholine (MCh) with determination of enhanced pause (P(enh)). Twenty-four hours after each P(enh) measurement, airway resistance was continuously registered in isolated, perfused, and ventilated lungs on stimulation with inhaled or intravascular MCh or nebulized Ova. In a subset of experiments, in vivo AR was additionally measured in orotracheally intubated, spontaneously breathing mice 24 h after P(enh) measurement, and lungs were isolated further 24 h later. Isolated lungs of allergen-sensitized and -challenged mice showed increased AR after MCh inhalation or infusion as well as after specific provocation with aerosolized allergen. AR was increased on days 2 and 5 after Ova challenge and had returned to baseline on day 9. AHR in isolated lungs after aerosolized or intravascular MCh strongly correlated with in vivo AR. Pretreatment of isolated lungs with the beta(2)-agonist fenoterol diminished AR. In conclusion, this model provides new opportunities to investigate mechanisms of AHR as well as pharmacological interventions on an intact organ level.
Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade (2017)

The Cancer Genome Atlas revealed the genomic landscapes of human cancers. In parallel, immunotherapy is transforming the treatment of advanced cancers. Unfortunately, the majority of patients do not respond to immunotherapy, making the identification of predictive markers and the mechanisms of resistance an area of intense research. To increase our understanding of tumor-immune cell interactions, we characterized the intratumoral immune landscapes and the cancer antigenomes from 20 solid cancers and created The Cancer Immunome Atlas (https://tcia.at/). Cellular characterization of the immune infiltrates showed that tumor genotypes determine immunophenotypes and tumor escape mechanisms. Using machine learning, we identified determinants of tumor immunogenicity and developed a scoring scheme for the quantification termed immunophenoscore. The immunophenoscore was a superior predictor of response to anti-cytotoxic T lymphocyte antigen-4 (CTLA-4) and anti-programmed cell death protein 1 (anti-PD-1) antibodies in two independent validation cohorts. Our findings and this resource may help inform cancer immunotherapy and facilitate the development of precision immuno-oncology.
Human T-Cell Leukemia Virus Type 1 Envelope-Mediated Syncytium Formation Can Be Activated in Resistant Mammalian Cell Lines by a Carboxy-Terminal Truncation of the Envelope Cytoplasmic Domain (2002)

Human T-cell leukemia virus (HTLV) envelope (Env) glycoproteins induce fusion, leading to rampant syncytium formation in a broad range of cell lines. Here, we identified murine, hamster, canine, and porcine cell lines that are resistant to HTLV-1 Env-induced syncytium formation. This resistance was not due to the absence of functional receptors for HTLV Env, as these cells were susceptible to infection with HTLV Env-pseudotyped virions. As murine leukemia virus (MLV) Env and HTLV Env present close structural homologies (F. J. Kim, I. Seiliez, C. Denesvre, D. Lavillette, F. L. Cosset, and M. Sitbon, J. Biol. Chem. 275:23417-23420, 2000), and because activation of syncytium formation by MLV Env generally requires cleavage of the R peptide in the cytoplasmic domain of the Env transmembrane (TM) component, we assessed whether truncation of the cytoplasmic domain of HTLV Env would alleviate this resistance. Indeed, in all resistant cell lines, truncation of the last 8 amino acids of the HTLV Env cytoplasmic domain (HdC8) was sufficient to overcome resistance to HTLV Env-induced syncytium formation. Furthermore, HdC8-mediated cell-to-cell infection titers varied according to the target cell lines and could be significantly higher than that observed with HTLV Env on HeLa cells. These data indicate that a determinant located within the 8 carboxy-terminal cytoplasmic amino acids of TM plays a distinct role in HTLV Env-mediated cell-to-cell infection and syncytium formation.