gebhart/patrepeval huggingface dataset:
Molecular Phylogeny and Evolution of Monilinia (Sclerotiniaceae) based on coding and Noncoding rDNA Sequences (1997)

The nuclear internal transcribed spacers, the 5.8S subunit, ~560 bp of the small subunit, and ~320 bp of the large subunit of the nuclear ribosomal DNA repeat from 17 species of Monilinia and eight species of closely related genera were sequenced. Phylogenies were constructed using maximum parsimony. The results support the hypothesis that Monilinia is not monophyletic. A fundamental distinction was found between the section Junctoriae and the section Disjunctoriae. Four evolutionary lineages were identified within the Disjunctoriae: one species on Crataegus, one group of species on dry stone fruits of rosaceous hosts, one group of species on capsular fruits of ericaceous hosts, and one group of species on sweet berry fruits of ericaceous hosts. Comparisons between branching topologies of hosts and Monilinia species suggest that although cospeciation among hosts and parasites has been the rule, several host jumps have taken place. Sclerotinia pirolae was determined to be a true member of the Disjunctoriae. The closest taxon groups to the Junctoriae were found to be Botrytis and Sclerotinia, with Ciborinia being the closest taxon group to the Disjunctoriae. There is evidence of an increased rate of ssrRNA evolution in the lineage of species that attack ericaceous berries.
Magnetic resonance imaging of multiple sclerosis: a study of pulse-technique efficacy (1984)

Forty-two patients with the clinical diagnosis of multiple sclerosis were examined by proton magnetic resonance imaging (MRI) at 0.5 T. An extensive protocol was used to facilitate a comparison of the efficacy of different pulse techniques. Results were also compared in 39 cases with high-resolution x-ray computed tomography (CT). MRI revealed characteristic abnormalities in each case, whereas CT was positive in only 15 of 33 patients. Milder grades 1 and 2 disease were usually undetected by CT, and in all cases, the abnormalities noted on MRI were much more extensive than on CT. Cerebral abnormalities were best shown with the T2-weighted spin-echo sequence (TE/TR = 120/1000); brainstem lesions were best defined on the inversion-recovery sequence (TE/TI/TR = 30/400/1250). Increasing TE to 120 msec and TR to 2000 msec heightened the contrast between normal and abnormal white matter. However, the signal intensity of cerebrospinal fluid with this pulse technique obscured some abnormalities.
Effect of colour of drugs: systematic review of perceived effect of drugs and of their effectiveness (1996)

Colours affect the perceived action of a drug and seem to influence the effectiveness of a drug. Moreover, a relation exists between the colouring of drugs that affect the central nervous system and the indications for which they are used. Research contributing to a better understanding of the effect of the colour of drugs is warranted.
A New Route to Zero-Barrier Metal Source/Drain MOSFETs (2004)

A new method for dramatically lowering the Schottky barrier resistance at a metal/Si interface by interposing an ultrathin insulator is demonstrated for the first time, with thermionic barriers less than those reported to date with silicides. Results with Er and near-monolayer thermal SiN/sub x/ at the interface are consistent with simulations of effective metal Fermi level separations from the silicon conduction band of 0.15 V for n-type Si and 45 mV for p-type Si. Simulations of advanced metal source/drain (S/D) ultrathin-body CMOS devices in comparison with competitive doped S/D devices show a significant performance advantage with a barrier to the conduction band of up to 0.1 V.
Flexible policy-directed code safety (2003)

The article introduces a new approach to code safety. We present Naccio, a system architecture that allows a large class of safety policies to be expressed in a general and platform-independent way. Policies are defined in terms of abstract resource manipulations. We describe mechanisms that can be used to efficiently and conveniently enforce these safety policies by transforming programs. We are developing implementations of Naccio that enforce policies on JavaVM classes and Win32 executables. We report on results using the JavaVM prototype.
Rate-adaptable optics for next generation long-haul transport networks (2013)

We discuss the emerging rate-adaptable optical transmission technology and how this new technology may be employed to further reduce the transport network cost to meet ever growing bandwidth demand in the core network. Two different types of transponders are considered: those adjusting either the transported bit rate (i.e., client data rate) or the symbol rate (with a fixed bit rate). We propose a methodology for calculating the (normalized) cost to build out an entire long-haul transport network with several options for bit-rate-adaptable transponders. By using link-length demands from an exemplary distance-diverse network, we demonstrate that time-domain hybrid-QAM-enabled fine-grain rate-adaptable transponders can reduce network cost by more than 20 percent within a traditional, fixed-bandwidth, wavelength-division-multiplexed grid. We also argue that the total transponder expense using symbol-rate-adaptable technology will be greater than when using bit-rate-adaptable technology, as well as requiring more costly flex-grid ROADMs for channel routing.
A Scalable graph-cut algorithm for N-D grids (2008)

Global optimisation via s-t graph cuts is widely used in computer vision and graphics. To obtain high-resolution output, graph cut methods must construct massive N-D grid-graphs containing billions of vertices. We show that when these graphs do not fit into physical memory, current max-flow/min-cut algorithms-the workhorse of graph cut methods-are totally impractical. Others have resorted to banded or hierarchical approximation methods that get trapped in local minima, which loses the main benefit of global optimisation. We enhance the push-relabel algorithm for maximum flow [14] with two practical contributions. First, true global minima can now be computed on immense grid-like graphs too large for physical memory. These graphs are ubiquitous in computer vision, medical imaging and graphics. Second, for commodity multi-core platforms our algorithm attains near-linear speedup with respect to number of processors. To achieve these goals, we generalised the standard relabeling operations associated with push-relabel.
Cell-Based Therapies for Parkinson's Disease: Past, Present, and Future (2009)

Parkinson's disease (PD) researchers have pioneered the use of cell-based therapies (CBTs) in the central nervous system. CBTs for PD were originally envisioned as a way to replace the dopaminergic nigral neurons lost with the disease. Several sources of catecholaminergic cells, including autografts of adrenal medulla and allografts or xenografts of mesencephalic fetal tissue, were successfully assessed in animal models, but their clinical translation has yielded poor results and much controversy. Recent breakthroughs on cell biology are helping to develop novel cell lines that could be used for regenerative medicine. Their future successful clinical application depends on identifying and solving the problems encountered in previous CBTs trials. In this review, we critically analyze past CBTs' clinical translation, the impact of the host in graft survival, and the role of preclinical studies and emerging new cell lines. We propose that the prediction of clinical results from preclinical studies requires experimental designs that allow blind data acquisition and statistical analysis, assessment of the therapy in models that parallel clinical conditions, looking for sources of complications or side effects, and limiting optimism bias when reporting outcomes.
Integration of genetic algorithms and GIS for optimal location search (2005)

Optimal location search is frequently required in many urban applications for siting one or more facilities. However, the search may become very complex when it involves multiple sites, various constraints and multiple‐objectives. The exhaustive blind (brute‐force) search with high‐dimensional spatial data is infeasible in solving optimization problems because of a huge combinatorial solution space. Intelligent search algorithms can help to improve the performance of spatial search. This study will demonstrate that genetic algorithms can be used with Geographical Information systems (GIS) to effectively solve the spatial decision problems for optimally sitting n sites of a facility. Detailed population and transportation data from GIS are used to facilitate the calculation of fitness functions. Multiple planning objectives are also incorporated in the GA program. Experiments indicate that the proposed method has much better performance than simulated annealing and GIS neighborhood search methods. The GA method is very convenient in finding the solution with the highest utility value.
Recombinant interleukin-12 suppresses the synthesis of immunoglobulin E by interleukin-4 stimulated human lymphocytes. (1992)

Interleukin-12 is a recently discovered lymphokine displaying an array of in vitro activities suggesting a major role in protective immunity against infectious agents like viruses. This study provides evidence that IL-12 may also be implicated in the selection of the immunoglobulin isotypes. We show that picomolar concentrations of rIL-12 markedly inhibit the synthesis of IgE by IL-4-stimulated PBMC. The suppression of IgE is observed at the protein and at the mRNA levels, it is isotype specific, and it is abolished by neutralizing anti-IL-12 mAbs. IL-12 may suppress IgE synthesis by: (a) inducing the production of IFN-gamma, a known inhibitor of IgE synthesis and (b) by a novel mechanism which is IFN-gamma independent. The best evidence for this is from studies on IgE synthesis by IL-4-plus hydrocortisone-stimulated umbilical cord blood lymphocytes, which do not produce detectable amounts of IFN-gamma. In such cultures, rIL-12 inhibits IgE synthesis even in the presence of a large excess of neutralizing anti-IFN-gamma mAb.
Macrophage Inflammatory Protein 3α–CC chemokine receptor 6 interactions play an important role in CD4+T-cell accumulation in periodontal diseased tissu (2002)

The regulatory role of chemokines and chemokine receptors on specific lymphocyte recruitment into periodontal diseased tissue is poorly characterized. We observed that lymphocytes infiltrating inflamed gingival tissue expressed marked levels of CCR6. In periodontal diseased tissue, the expression of MIP-3alpha mRNA was detected by RT-PCR and further, MIP-3alpha was distributed in the basal layer of gingival epithelial cells, microvascular endothelial cells and the areas of inflammatory cells as shown by immunohistochemistry. Moreover, CCR6-expressing cells infiltrated into periodontal diseased tissue, and the proportion of CCR6-positive CD4+ T cells was significantly elevated in periodontal diseased tissue compared with peripheral blood in the same patients. Furthermore, gingival lymphocytes isolated from patients showed migration toward MIP-3alpha in an in vitro chemotaxis assay in which migration was abrogated by specific antibody to CCR6. Thus, these findings suggested that CCR6 and the corresponding chemokine, MIP-3alpha may have an important regulatory role in specific lymphocyte migration into inflamed periodontal tissue.
The use of K+-free buffers eliminates a common cause of premature chain termination in PCR and PCR sequencing (1995)

Journal Article The use of K + -free buffers eliminates a common cause of premature chain termination in PCR and PCR sequencing Get access K. Woodford, K. Woodford Section on Genomic Structure and Function, National Institute of Diabetes, Digestive and Kidney DiseasesBuilding 8, Room 202 , National Institutes of Health, 8 CENTER DR MSC 0830Bethesda, MD 20892-0830, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar M.N. Weitzmann, M.N. Weitzmann Section on Genomic Structure and Function, National Institute of Diabetes, Digestive and Kidney DiseasesBuilding 8, Room 202 , National Institutes of Health, 8 CENTER DR MSC 0830Bethesda, MD 20892-0830, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar K. Usdin K. Usdin * Section on Genomic Structure and Function, National Institute of Diabetes, Digestive and Kidney DiseasesBuilding 8, Room 202 , National Institutes of Health, 8 CENTER DR MSC 0830Bethesda, MD 20892-0830, USA * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 23, Issue 3, 11 February 1995, Page 539, https://doi.org/10.1093/nar/23.3.539 Published: 11 February 1995 Article history Received: 19 October 1994 Revision received: 05 January 1995 Accepted: 05 January 1995 Published: 11 February 1995
p21-Activated Kinase 1 Phosphorylates the Death Agonist Bad and Protects Cells from Apoptosis (2000)

Bad is a critical regulatory component of the intrinsic cell death machinery that exerts its death-promoting effect upon heterodimerization with the antiapoptotic proteins Bcl-2 and Bcl-x(L). Growth factors promote cell survival through phosphorylation of Bad, resulting in its dissociation from Bcl-2 and Bcl-x(L) and its association with 14-3-3tau. Survival of interleukin 3 (IL-3)-dependent FL5.12 lymphoid progenitor cells is attenuated upon treatment with the Rho GTPase-inactivating toxin B from Clostridium difficile. p21-activated kinase 1 (PAK1) is activated by IL-3 in FL5.12 cells, and this activation is reduced by the phosphatidylinositol 3-kinase inhibitor LY294002. Overexpression of a constitutively active PAK mutant (PAK1-T423E) promoted cell survival of FL5.12 and NIH 3T3 cells, while overexpression of the autoinhibitory domain of PAK (amino acids 83 to 149) enhanced apoptosis. PAK phosphorylates Bad in vitro and in vivo on Ser112 and Ser136, resulting in a markedly reduced interaction between Bad and Bcl-2 or Bcl-x(L) and the increased association of Bad with 14-3-3tau. Our findings indicate that PAK inhibits the proapoptotic effects of Bad by direct phosphorylation and that PAK may play an important role in cell survival pathways.
Differentiation of rat myocytes in single cell cultures with and without proliferating nonmyocardial cells. Cross-striations, ultrastructure, and chronotropic response to isoproterenol. (1982)

Proliferating nonmyocardial cells (NMCs) complicate primary heart cultures and may influence myocardial cell (MC) differentiation.In cultures from the day-old rat ventricle, we validated a method to arrest this proliferation; and we quantitated cross-striated cells and the chronotropic response to isoproterenol to assess MC differentiation.MCs were cultured at single cell density using an improved method.By 4 days, all cells could be identified as MCs or NMCs.In cultures treated for 3 days with bromodeoxyuridine (BrdU), 0.1 miw, serial cell counts were unchanged through 11 days.Among 50,000 cells from 110 cultures, 75-80% were MCs.In control cultures without BrdU, NMC density was 3-and 6-fold that in BrdU-treated cultures at days 5 and 8, respectively (P < 0.01), although the MCs were not overgrown.The MCs did not proliferate in either culture.The proportion of living MCs with cross-striations was similar in treated and control cultures at day 5 (72.6% vs. 69.9%,P > 0.05) but was lower in controls at day 8 (86.3% vs. 50.4%,P < 0.01).A sensitive (ED 50 10-100 pM), specific chronotropic response to L-isoproterenol was present in both treated and control cultures, but the maximum response was only 20-30% as great in controls on days 4 and 8 (P < 0.01).Baseline beating rates were the same.The MCs had well-differentiated ultrastructure, including a T system.By autoradiography, a maximum 18.4% of MCs had nuclear incorporation of 3 H-BrdU at day 8. Media conditioned by NMCs or by the control cultures did not change the cross-striations or isoproterenol response of BrdU-treated cultures.Thus, in a new culture preparation with few and stable NMCs, morphological and functional MC characteristics were different from those of MCs in cultures with proliferating NMCs.We suggest that an MC-NMC interaction can alter MC properties and that this effect should be considered in studies of primary rat heart cultures.The pure, stable, well-differentiated MCs in BrdUtreated cultures will be useful for studying MC growth, repair, and other time-dependent phenomena.CircRes 50: [101][102][103][104][105][106][107][108][109][110][111][112][113][114][115][116] 1982 PRIMARY cultures of cells from the hearts of neonatal rats and embryonic chicks are used by many investigators.(See reviews by Lieberman and Sano, 1976;Sperelakis, 1978; Auclair and Freyss-Beguin, 1980).A major, unresolved problem with these cultures is contamination by a population of rapidly proliferating nonmyocardial cells (NMCs), the precise identity of which is unclear (Balk, 1980).The initial proportion of these contaminating cells can be reduced by the differential attachment technique (Hyde et al., 1969); but they eventually overgrow the myocardial cells (MCs), which are said to divide much more slowly (Kasten, 1972).This progressive increase in cell number is not charac-
ChemInform Abstract: Oxo (Keto) Acids (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Comparison of Responses of Tattoos to Picosecond and Nanosecond Q-Switched Neodymium:YAG Lasers (1998)

Picosecond pulses are more efficient than nanosecond pulses in clearing black tattoos. Black tattoos clear principally by laser-induced changes in the intrinsic optical properties of the ink.
Subgenomic RNAs mediate expression of cistrons located internally on the genomic RNA of tobacco necrosis virus strain A (1992)

Upon infection of tobacco protoplasts, the genomic RNA of tobacco necrosis virus strain A (TNV-A) accumulates linearly in time. The accumulation patterns of the two subgenomic RNAs resemble those of endogenous mRNAs in that the peak levels are reached after several hours. The accumulation of the 1.3-kb subgenomic RNA is delayed by 1 h compared with that of the 1.6-kb subgenomic RNA, which illustrates the important role of the subgenomic RNAs in the regulation of TNV-A gene expression. The locations of the 5' nucleotides of the subgenomic RNAs reveal that the 5'-proximal cistrons of the 1.6- and 1.3-kb RNAs encode an 8-kDa protein from open reading frame (ORF) 3 and the coat protein from ORF 5, respectively. In a wheat germ translation system, a synthetic transcript resembling the 1.6-kb RNA expresses both ORFs 3 and 4. Moreover, the synthesis of the 6-kDa protein from ORF 4 depends on the translation efficiency of ORF 3, suggesting that in vivo, ORFs 3 and 4 are both expressed from the 1.6-kb RNA. The major in vitro translation product of TNV-A genomic RNA is the coat protein. We show that the region upstream of the coat protein promotes internal initiation of translation in vitro. However, this region is functionally inactive in vivo, suggesting that TNV-A genomic RNA is not important for coat protein synthesis in plants.
Instantly indexed multimedia databases of real world events (2002)

We introduce a new paradigm for real-time conversion of a real world event into a rich multimedia database by processing data from multiple sensors observing the event. A real-time analysis of the sensor data, tightly coupled with domain knowledge, results in instant indexing of multimedia data at capture time. This yields semantic information to answer complex queries about the content and the ability to extract portions of data that correspond to complex actions performed in the real world. The power of such an instantly indexed multimedia database system, in content-based retrieval of multimedia data or in semantic analysis and visualization of the data, far exceeds that of systems which index multimedia data only after it is produced. We present LucentVision, an instantly indexed multimedia database system developed for the sport of tennis. This system analyzes video from multiple cameras in real time and captures the activity of the players and the ball in the form of motion trajectories. The system stores these trajectories in a database along with video, 3D models of the environment, scores, and other domain-specific information. LucentVision has been used to enhance live television and Internet broadcasts with game analyses and virtual replays in more than 250 international tennis matches.
Guidelines for the diagnosis and treatment of chronic lymphocytic leukemia: a report from the International Workshop on Chronic Lymphocytic Leukemia updating the National Cancer Institute–Working Group 1996 guidelines (2008)

Standardized criteria for diagnosis and response assessment are needed to interpret and compare clinical trials and for approval of new therapeutic agents by regulatory agencies. Therefore, a National Cancer Institute-sponsored Working Group (NCI-WG) on chronic lymphocytic leukemia (CLL) published guidelines for the design and conduct of clinical trials for patients with CLL in 1988, which were updated in 1996. During the past decade, considerable progress has been achieved in defining new prognostic markers, diagnostic parameters, and treatment options. This prompted the International Workshop on Chronic Lymphocytic Leukemia (IWCLL) to provide updated recommendations for the management of CLL in clinical trials and general practice.
Altered Pulmonary Vasoreactivity in the Chronically Hypoxic Lung (2000)

Prolonged exposure to alveolar hypoxia induces physiological changes in the pulmonary vasculature that result in the development of pulmonary hypertension. A hallmark of hypoxic pulmonary hypertension is an increase in vasomotor tone. In vivo, pulmonary arterial smooth muscle cell contraction is influenced by vasoconstrictor and vasodilator factors secreted from the endothelium, lung parenchyma and in the circulation. During chronic hypoxia, production of vasoconstrictors such as endothelin-1 and angiotensin II is enhanced locally in the lung, while synthesis of vasodilators may be reduced. Altered reactivity to these vasoactive agonists is another physiological consequence of chronic exposure to hypoxia. Enhanced contraction in response to endothelin-1 and angiotensin II, as well as depressed vasodilation in response to endothelium-derived vasodilators, has been documented in models of hypoxic pulmonary hypertension. Chronic hypoxia may also have direct effects on pulmonary vascular smooth muscle cells, modulating receptor population, ion channel activity or signal transduction pathways. Following prolonged hypoxic exposure, pulmonary vascular smooth muscle exhibits alterations in K+ current, membrane depolarization, elevation in resting cytosolic calcium and changes in signal transduction pathways. These changes in the electrophysiological parameters of pulmonary vascular smooth muscle cells are likely associated with an increase in basal tone. Thus, hypoxia-induced modifications in pulmonary arterial myocyte function, changes in synthesis of vasoactive factors and altered vasoresponsiveness to these agents may shift the environment in the lung to one of contraction instead of relaxation, resulting in increased pulmonary vascular resistance and elevated pulmonary arterial pressure.