gebhart/patrepeval huggingface dataset:
Incremental Adoption of Information Security in Health-Care Organizations: Implications for Document Management (2005)

The incremental adoption of electronic media in U.S. health care has created increased risk of security and privacy violations in provider organizations. Protective regulatory efforts have been proposed to address ineffective security of patient information, with severe noncompliance penalties. Using data from a nationwide survey of health information managers, this study examines how industry-wide knowledge management trends may influence the degree of security program adoption in health-care organizations. Results suggest that significant nonadoption of mandated security measures continues to occur across the health-care industry. Paper-based systems still prevail, and computerized settings tend to have less security measures. Implications for document management and knowledge policy are discussed.
A Designed Phenylalanyl-tRNA Synthetase Variant Allows Efficient in Vivo Incorporation of Aryl Ketone Functionality into Proteins (2002)

Incorporation of non-natural amino acids into proteins in vivo expands the scope of protein synthesis and design. p-Acetylphenylalanine was incorporated into recombinant dihydrofolate reductase (DHFR) in Escherichia coli via a computationally designed mutant form of the phenylalanyl-tRNA synthetase of the host. DHFR outfitted with ketone functionality can be chemoselectively ligated with hydrazide reagents under mild conditions.
Hematopoietic Stem Cell Maintenance and Differentiation Are Supported by Embryonic Aorta-Gonad-Mesonephros Region–Derived Endothelium (1998)

Hematopoietic stem cells are capable of extensive self-renewal and expansion, particularly during embryonic growth. Although the molecular mechanisms involved with stem cell maintenance remain mysterious, it is now clear that an intraembryonic location, the aorta-gonad-mesonephros (AGM) region, is a site of residence and, potentially, amplification of the definitive hematopoietic stem cells that eventually seed the fetal liver and adult bone marrow. Because several studies suggested that morphologically defined hematopoietic stem/progenitor cells in the AGM region appeared to be attached in clusters to the ventrally located endothelium of the dorsal aorta, we derived cell lines from this intraembryonic site using an anti-CD34 antibody to select endothelial cells. Analysis of two different AGM-derived CD34(+) cell lines revealed that one, DAS 104-8, efficiently induced fetal-liver hematopoietic stem cells to differentiate down erythroid, myeloid, and B-lymphoid pathways, but it did not mediate self-renewal of these pluripotent cells. In contrast, a second cell line, DAS 104-4, was relatively inefficient at the induction of hematopoietic differentiation. Instead, this line provoked the expansion of early hematopoietic progenitor cells of the lin-CD34(+)Sca-1(+)c-Kit+ phenotype and was proficient at maintaining fetal liver-derived hematopoietic stem cells able to competitively repopulate the bone marrow of lethally irradiated mice. These data bolster the hypothesis that the endothelium of the AGM region acts to mediate the support and differentiation of hematopoietic stem cells in vivo.
Agent communication system for multimedia communication services (2002)

This paper proposes an agent communication system, in which many communication system's elements, such as communication services, charging and network operation functions, are expressed as agents and multimedia communication services are offered that multi-agents negotiate with each other. The agent communication system is the third communication system. The first communication model is circuit communication model for telephone services, and the second model is the packet communication model for data communication services. The agent communication model is based on the concept of distributed cooperative agent-oriented networking. The agent-oriented software architecture is introduced for supporting multimedia communication services in wide-area networks. Multimedia services are expressed as agents. The paper proposes an agent request broker for multimedia communication services in an agent communication wide-area network. The agent request broker, which is the platform for multi-agents, is based on the concept of agent-oriented software. Furthermore, a five-layer agent communication networking architecture is proposed. Finally, personal communication telephone services, video-mail services and video-on-demand services are presented by using the agent communication system's experimental setup of IP-over-ATM.
The Fidelity of Misinsertion and Mispair Extension Throughout DNA Synthesis Exhibited by Mutants of the Reverse Transcriptase of Human Immunodeficiency Virus Type 2 Resistant to Nucleoside Analogs (1997)

The AIDS‐causing retroviruses, human immunodeficiency virus types 1 and type 2 (HIV‐1 and HIV‐2, respectively) undergo extensive genetic variations, which effect their pathogenesis and resistance to drug therapy. It was postulated that this genetic hypervariability results from high rates of viral replication in conjugation with a relatively low fidelity of DNA synthesis [typical to the reverse transcriptases (RT) of these retroviruses]. As part of studying structure/function relationship in HIV RT, mutational analyses were conducted to identify amino acid residues which are involved in affecting the fidelity of DNA synthesis. The formation of 3′‐mispaired DNA due to nucleotide misinsertions, and the subsequent elongation of this mismatched DNA were shown to be major determinants in affecting those substitutions during DNA synthesis (exhibited in vitro by HIV RT). It was interesting to find a correlation between sensitivity to nucleoside analogs (due to the ability to incorporate or reject an incoming analog) and the fidelity of DNA synthesis (which depends on the capacity to incorporate and extend a wrong nucleotide). Such a connection has already been found for several drug‐resistant mutants of HIV‐1 RT, with an increased fidelity of DNA synthesis relative to the wild‐type RT. In the present study we have examined the fidelity of DNA synthesis using the same parameters of misinsertion and mispair extension for five novel drug‐resistant mutants of HIV‐2 RT; i.e. the single mutants [Val74]RT, [Gly89]RT and [Tyr215]RT and the double mutants [Val74, Tyr215]RT and [Gly89, Tyr215]RT. This comparative study suggests that unlike the Val74 mutant of HIV‐1 RT, which was shown earlier to display a substantially enhanced fidelity, the comparable mutant of HIV‐2 RT has fidelity similar to that of the wild‐type RT. Depending on the assay employed and the DNA sequences extended, most other mutants of HIV‐2 RT display moderate effects on the enzyme, leading to mild increases in fidelity of DNA synthesis. This implies a more complex and less distinctive correlation between drug‐resistance, misinsertion and mispair extension in HIV‐2 RT in contrast to HIV‐1 RT, providing evidence for potential biochemical differences between these two related RT.
Design of matching circuit controllers for radio-frequency heating (2003)

Electromagnetic energy in the microwave and radio-frequency (RF) portions of the spectrum can be used to heat or defrost (thaw) foodstuffs. This paper considers a fixed frequency RF oven, where a matching circuit is used to ensure that the combined impedance of the oven and the food (the load) matches the impedance of the generator and the transmission line. A controller measures the reflected RF signal and adjusts the settings of components in the matching circuit. The system is highly nonlinear and there are significant sources of uncertainty in the model of the process. A variable structure controller is designed and its stability is examined in the presence of uncertainties due to stray components. The switching lines are defined in terms of the real and imaginary parts of the reflected signal, which avoids the need to estimate the states. Conditions are derived for maintaining stability in the region close to the matching point. The performance of the controller is illustrated by results from an implementation on a prototype commercial RF oven.
Involvement of decidual Vα14 NKT cells in abortion (2000)

The immunological mechanisms that regulate abortion are largely unknown. Here, we found that a distinct subset of lymphocytes, Valpha14 NKT cells expressing an invariant antigen receptor encoded by Valpha14/Jalpha281 and Vbeta7 segments, accumulated in the decidua during pregnancy and provoked abortion upon stimulation with alpha-galactosylceramide (alpha-GalCer), a specific ligand for Valpha14 NKT cells. The alpha-GalCer-mediated abortion was not observed in Valpha14 NKT-, IFN-gamma-, tumor necrosis factor alpha-, or perforin-knock-out mice and appeared to be due to the degeneration of embryonic trophoblasts mediated by the activated Valpha14 NKT cells whose perforin-dependent killing and production of IFN-gamma and tumor necrosis factor alpha were essential. The possible role of the decidual Valpha14 NKT cells in the pathogenesis of abortion is discussed.
Thermal via placement in 3D ICs (2005)

As thermal problems become more evident, new physical design paradigms and tools are needed to alleviate them. Incorporating thermal vias into integrated circuits (ICs) is a promising way of mitigating thermal issues by lowering the thermal resistance of the chip itself. However, thermal vias take up valuable routing space, and therefore, algorithms are needed to minimize their usage while placing them in areas where they would make the greatest impact. With the developing technology of three-dimensional integrated circuits (3D ICs), thermal problems are expected to be more prominent, and thermal vias can have a larger impact on them than in traditional 2D ICs. In this paper, thermal vias are assigned to specific areas of a 3D IC and used to adjust their effective thermal conductivities. The thermal via placement method makes iterative adjustments to these thermal conductivities in order to achieve a desired maximum temperature objective. Finite element analysis (FEA) is used in formulating the method and in calculating temperatures quickly during each iteration. As a result, the method efficiently achieves its thermal objective while minimizing the thermal via utilization.
Anatomical Variation of Human Collector Channel Orifices (2016)

Collector channel orifice structure varied from simple ovals to complex tethered flaps and bridges. Collector channel orifices with complex flaps connect the inner and outer walls of Schlemm's canal, and may serve to enhance and regulate aqueous outflow in these regions.
Proteomics of the Chloroplast: Systematic Identification and Targeting Analysis of Lumenal and Peripheral Thylakoid Proteins (2000)

The soluble and peripheral proteins in the thylakoids of pea were systematically analyzed by using two-dimensional electrophoresis, mass spectrometry, and N-terminal Edman sequencing, followed by database searching. After correcting to eliminate possible isoforms and post-translational modifications, we estimated that there are at least 200 to 230 different lumenal and peripheral proteins. Sixty-one proteins were identified; for 33 of these proteins, a clear function or functional domain could be identified, whereas for 10 proteins, no function could be assigned. For 18 proteins, no expressed sequence tag or full-length gene could be identified in the databases, despite experimental determination of a significant amount of amino acid sequence. Nine previously unidentified proteins with lumenal transit peptides are presented along with their full-length genes; seven of these proteins possess the twin arginine motif that is characteristic for substrates of the TAT pathway. Logoplots were used to provide a detailed analysis of the lumenal targeting signals, and all nuclear-encoded proteins identified on the two-dimensional gels were used to test predictions for chloroplast localization and transit peptides made by the software programs ChloroP, PSORT, and SignalP. A combination of these three programs was found to provide a useful tool for evaluating chloroplast localization and transit peptides and also could reveal possible alternative processing sites and dual targeting. The potential of proteomics for plant biology and homology-based searching with mass spectrometry data is discussed.
Interaction of ‘toxic’ and ‘immunogenic’ A‐gliadin peptides with a membrane‐mimetic environment (2009)

Celiac disease (CD) is characterized by abnormally high concentrations of certain peptides in the small bowel. These peptides can be grouped in 'toxic' and 'immunogenic' classes, which elicit an innate immune response and an HLA-mediated adaptive response, respectively. It is not clear on which molecular mechanisms responses to these different classes are based, but the 31-43 (P31-43) and the 56-68 (P56-68) A-gliadin fragments are usually adopted as sequence representatives of toxic and immunogenic peptides, respectively. Here we report fluorescence experiments aiming to mimic the interaction of these peptides with the cell membrane surface by using sodium dodecyl sulphate (SDS) as a membrane-mimetic medium. We show that P31-43 is able to bind SDS micelles in a way that resembles mixed micelle formation. On the other hand, no binding at all could be detected for P56-68. This different behaviour could be related to the paracellular or transcellular route through which gluten peptides may cross the intestinal epithelium, and open new insights into the pathogenetic mechanisms of CD.
Novel Markers in the Acute Coronary Syndrome: BNP, IL-6, PAPP-A (2002)

Most patients (about 85%) seen in the ED to rule out an acute coronary event do not have acute coronary disease. In addition, the presenting ECG findings have been nondiagnostic in 50% of patients with acute MI. Our current knowledge of atherosclerosis as being a chronic low-grade inflammatory process triggered the search for reliable serum markers that have improved the diagnostic accuracy management and prognosis of this prevalent disease. Newer and potential inflammatory markers currently under investigation deserve watching in future reports. These among others include those markers produced by the arterial wall itself, that is, cell adhesion molecules (CAM), inter-cellular adhesion molecules (ICAM), and vascular adhesion molecules (VCAM). The expression of CAM is a marker of dysfunctional endothelial cells. It is likely that more cardiac markers will be reported in the future. Time will tell.
Increased Sensitivity of Fluorescence Detection Using Metallic Nanoparticles. (2003)

A new technique called radiative decay engineering can be used to modify fluorescence emissions by changing the free space conditions around the fluorophores.
Simultaneous Alternating and Direct Current Readout of Protein Ion Channel Blocking Events Using Glass Nanopore Membranes (2008)

Alternating current (ac) phase-sensitive detection is used to measure the conductance of the ion channel alpha-hemolysin (alphaHL), while simultaneously applying a direct current (dc) bias to electrostatically control the binding affinity and kinetics of charged molecules within the protein lumen. Ion channel conductance was recorded while applying a 10-20 mV rms, 1-2 kHz bias across a single alphaHL protein inserted in a 1,2-diphytanoyl-sn-glycero-3-phosphocholine lipid bilayer that is suspended across the orifice (100-500 nm radius) of a glass nanopore membrane. Step changes in the ac ion channel conductance with a temporal response (t(10-90)) of 1.5 ms and noise amplitude of approximately 2 pA were obtained using a low-noise potentiostat and a lock-in amplifier. These conditions were used to monitor the reversible and stochastic binding of heptakis-(6-O-sulfo)-beta-cyclodextrin and a nine base pair DNA hairpin molecule to the ion channel. Alternating current methodology allows the binding kinetics and affinity between the protein ion channel and analyte to be investigated as a function of the dc bias, including ion channel conductance measurements in the absence of a dc bias.
A Study of the Incidence and Significance of Intramammary Enterobacterial Infections Acquired During the Dry Period (2000)

We assessed the incidence of enterobacterial infection of the mammary glands of 629 cows, from six commercial herds in Somerset, during the nonlactating period; samples were collected from all clinical quarters of these cows during the subsequent lactation. A rise in the incidence of intramammary enterobacterial infection was detected between drying off and before calving. Quarters infected with an enterobacterial organism during the dry period were more likely to develop mastitis due to that pathogen than were uninfected quarters. Of all enterobacterial mastitis occurring in the first 100 d of lactation, 52.6% arose in quarters previously infected, during the dry period, with the same strain of bacteria, as identified by DNA fingerprinting using enterobacterial repetitive intergenic consensus primers. When compared with unsampled controls, quarters sampled during the dry period did not show a higher incidence of infection at calving or of subsequent clinical mastitis. These findings suggest that chronic infections are important in the epidemiology of enterobacterial mastitis and that environmental management during the dry period may greatly impact the incidence of enterobacterial mastitis in the subsequent lactation.
Bmpr encodes a type I bone morphogenetic protein receptor that is essential for gastrulation during mouse embryogenesis. (1995)

Bone morphogenetic proteins (BMPs) are secreted proteins that interact with cell-surface receptors and are believed to play a variety of important roles during vertebrate embryogenesis. Bmpr, also known as ALK-3 and Brk-1, encodes a type I transforming growth factor-beta (TGF-beta) family receptor for BMP-2 and BMP-4. Bmpr is expressed ubiquitously during early mouse embryogenesis and in most adult mouse tissues. To study the function of Bmpr during mammalian development, we generated Bmpr-mutant mice. After embryonic day 9.5 (E9.5), no homozygous mutants were recovered from heterozygote matings. Homozygous mutants with morphological defects were first detected at E7.0 and were smaller than normal. Morphological and molecular examination demonstrated that no mesoderm had formed in the mutant embryos. The growth characteristics of homozygous mutant blastocysts cultured in vitro were indistinguishable from those of controls; however, embryonic ectoderm (epiblast) cell proliferation was reduced in all homozygous mutants at E6.5 before morphological abnormalities had become prominent. Teratomas arising from E7.0 mutant embryos contained derivatives from all three germ layers but were smaller and gave rise to fewer mesodermal cell types, such as muscle and cartilage, than controls. These results suggest that signaling through this type I BMP-2/4 receptor is not necessary for preimplantation or for initial postimplantation development but may be essential for the inductive events that lead to the formation of mesoderm during gastrulation and later for the differentiation of a subset of mesodermal cell types.
Concurrent manipulation of binary search trees (1980)

The concurrent manipulation of a binary search tree is considered in this paper. The systems presented can support any number of concurrent processes which perform searching, insertion, deletion, and rotation (reorganization) on the tree, but allow any process to lock only a constant number of nodes at any time. Also, in the systems, searches are essentially never blocked. The concurrency control techniques introduced in the paper include the use of special nodes and pointers to redirect searches, and the use of copies of sections of the tree to introduce many changes simultaneously and therefore avoid unpredictable interleaving. Methods developed in this paper may provide new insights into other problems in the area of concurrent database manipulation.
Preventing β-Cell Loss and Diabetes With Calcium Channel Blockers (2012)

Although loss of functional β-cell mass is a hallmark of diabetes, no treatment approaches that halt this process are currently available. We recently identified thioredoxin-interacting protein (TXNIP) as an attractive target in this regard. Glucose and diabetes upregulate β-cell TXNIP expression, and TXNIP overexpression induces β-cell apoptosis. In contrast, genetic ablation of TXNIP promotes endogenous β-cell survival and prevents streptozotocin (STZ)- and obesity-induced diabetes. Finding an oral medication that could inhibit β-cell TXNIP expression would therefore represent a major breakthrough. We were surprised to discover that calcium channel blockers inhibited TXNIP expression in INS-1 cells and human islets and that orally administered verapamil reduced TXNIP expression and β-cell apoptosis, enhanced endogenous insulin levels, and rescued mice from STZ-induced diabetes. Verapamil also promoted β-cell survival and improved glucose homeostasis and insulin sensitivity in BTBR ob/ob mice. Our data further suggest that this verapamil-mediated TXNIP repression is conferred by reduction of intracellular calcium, inhibition of calcineurin signaling, and nuclear exclusion and decreased binding of carbohydrate response element-binding protein to the E-box repeat in the TXNIP promoter. Thus, for the first time, we have identified an oral medication that can inhibit proapoptotic β-cell TXNIP expression, enhance β-cell survival and function, and prevent and even improve overt diabetes.
Treatment of a Patient with b Cell Lymphoma by 1-131 Lym-1 Monoclonal Antibodies (1987)

A patient with Richter's syndrome, a malignant lymphomatous transformation of chronic lymphocytic leukemia, had become moribund with rapidly enlarging masses, granulocytopenia and thrombocytopenia despite the use of conventional chemotherapy and radiotherapy. Greater than ten percent of a test dose of I-131 Lym-1, a murine monoclonal antibody produced against Burkitt's African B cell lymphoma, was accumulated by her tumor. The patient was subsequently treated with a series of injections of I-131 Lym-1 with dramatic clinical response, reduction of tumor volume by x-ray computerized tomography and progression of circulating cellular elements toward normality. Her course over the next ten months was not like that to be expected for Richter's syndrome, which has an average survival of four months. This mode of treatment appears promising.
Human Tissue Inhibitor of Metalloproteinases 3 Interacts with Both the N- and C-terminal Domains of Gelatinases A and B (1999)

We compared the association constants of tissue inhibitor of metalloproteinases (TIMP)-3 with various matrix metalloproteinases with those for TIMP-1 and TIMP-2 using a continuous assay. TIMP-3 behaved more like TIMP-2 than TIMP-1, showing rapid association with gelatinases A and B. Experiments with the N-terminal domain of gelatinase A, the isolated C-terminal domain, or an inactive progelatinase A mutant showed that the hemopexin domain of gelatinase A makes an important contribution to the interaction with TIMP-3. The exchange of portions of the gelatinase A hemopexin domain with that of stromelysin revealed that residues 568-631 of gelatinase A were required for rapid association with TIMP-3. The N-terminal domain of gelatinase B alone also showed slower association with TIMP-3, again implying significant C-domain interactions. The isolation of complexes between TIMP-3 and progelatinases A and B on gelatin-agarose demonstrated that TIMP-3 binds to both proenzymes. We analyzed the effect of various polyanions on the inhibitory activity of TIMP-3 in our soluble assay. The association rate was increased by dextran sulfate, heparin, and heparan sulfate, but not by dermatan sulfate or hyaluronic acid. Because TIMP-3 is sequestered in the extracellular matrix, the presence of certain heparan sulfate proteoglycans could enhance its inhibitory capacity.