gebhart/patrepeval huggingface dataset:
Molecular Cloning and Expression of the Novel Fungal  -Glucosidase Genes from Humicola grisea and Trichoderma reesei (1999)

A novel fungal beta-glucosidase gene (bgl4) and its homologue (bgl2) were cloned from the cellulolytic fungi Humicola grisea and Trichoderma reesei, respectively. The deduced amino acid sequences of H. grisea BGL4 and T. reesei BGL2 comprise 476 and 466 amino acids, respectively, and share 73.1% identity. These beta-glucosidases show significant homology to plant beta-glucosidases belonging to the beta-glucosidase A (BGA) family. Both genes were expressed in Aspergillus oryzae, and the recombinant beta-glucosidases were purified. Recombinant H. grisea BGL4 is a thermostable enzyme compared with recombinant T. reesei BGL2. In addition to beta-glucosidase activity, recombinant H. grisea BGL4 showed a significant level of beta-galactosidase activity, while recombinant T. reesei BGL2 showed weak beta-galactosidase activity. Cellulose saccharification by Trichoderma cellulases was improved by the addition of recombinant H. grisea BGL4.
A Transformation System for Developing Recursive Programs (1977)

A system of rules for transforming programs is described, with the programs in the form of recursion equations. An initially very simple, lucid, and hopefully correct program is transformed into a more efficient one by altering the recursion structure. Illustrative examples of program transformations are given, and a tentative implementation is described. Alternative structures for programs are shown, and a possible initial phase for an automatic or semiautomatic program-manipulation system is indicated.
Variable attenuator for use in single-mode fiber transmission systems (1980)

A novel compact optical variable-attenuator with a wide dynamic range for use in single-mode fiber transmission systems has been developed. Attenuation rate can be continuously adjusted by changing the distance between the end faces of the two fibers in the V-channel on a concave surface. The calculated insertion loss is <0.5 dB; the dynamic range of 30 dB is attained by <2.5 mm end separation. The calculated losses were verified experimentally. Reproducibility of the attenuation is within 0.5 dB.
Structure of the TDP- <i>epi</i> -vancosaminyltransferase GtfA from the chloroeremomycin biosynthetic pathway (2003)

During the biosynthesis of the vancomycin-class antibiotic chloroeremomycin, TDP-epi-vancosaminyltransferase GtfA catalyzes the attachment of 4-epi-vancosamine from a TDP donor to the beta-OHTyr-6 of the aglycone cosubstrate. Glycosyltransferases from this pathway are potential tools for the combinatorial design of new antibiotics that are effective against vancomycin-resistant bacterial strains. These enzymes are members of the GT-B glycosyltransferase superfamily, which share a homologous bidomain topology. We present the 2.8-A crystal structures of GtfA complexes with vancomycin and the natural monoglycosylated peptide substrate, representing the first direct observation of acceptor substrate binding among closely related glycosyltransferases. The acceptor substrates bind to the N-terminal domain such that the aglycone substrate's reactive hydroxyl group hydrogen bonds to the side chains of Ser-10 and Asp-13, thus identifying these as residues of potential catalytic importance. As well as an open form of the enzyme, the crystal structures have revealed a closed form in which a TDP ligand is bound at a donor substrate site in the interdomain cleft, thereby illustrating not only binding interactions, but the conformational changes in the enzyme that accompany substrate binding.
Detection of hypotension during hemodialysis using the ECG (2005)

There is today a lack of clinical techniques for detecting acute hypotension during conventional hemodialysis treatment, despite the fact that hypotension remains the - most common acute complication during hemodialysis. Hypotension is often followed by nausea, vomiting, and even fainting, not only strenuous for the patient but requires considerable attention from the nursing staf. The problem of detecting hypotension was studied by means of a multimodal database. The database consists of 30 treatments in which each treatment includes several simultaneously acquired signals. Acute .symptomatic hypotension occurred in 2 of the 30 treatments. An ECG-based method for detecting hypotension has been developed. n e method involves information on heart rate variability (HRV) and ectopic beat patterns. The proposed method does not only detect the two cases of acute hypotension but also provides information of the patient's propensity to hypotension at an early stage of hemodialysis.
Automatic recovery from disk failure in continuous-media servers (2002)

Continuous-media (CM) servers have been around for some years. Apart from server capacity, another important issue in the deployment of CM servers is reliability. This study investigates rebuild algorithms for automatically rebuilding data stored in a failed disk into a spare disk. Specifically, a block-based rebuild algorithm is studied with the rebuild time and buffer requirement modeled. A buffer-sharing scheme is then proposed to eliminate the additional buffers needed by the rebuild process. To further improve rebuild performance, a track-based rebuild algorithm that rebuilds lost data in tracks is proposed and analyzed. Results show that track-based rebuild, while it substantially outperforms block-based rebuild, requires significantly more buffers (17-135 percent more) even with buffer sharing. To tackle this problem, a novel pipelined rebuild algorithm is proposed to take advantage of the sequential property of track retrievals to pipeline the reading and writing processes. This pipelined rebuild algorithm achieves the same rebuild performance as track-based rebuild, but reduces the extra buffer requirement to insignificant levels (0.7-1.9 percent). Numerical results computed using models of five commercial disk drives demonstrate that automatic rebuild of a failed disk can be done in a reasonable amount of time, even at relatively high server utilization (e.g., less than 1.5 hours at 90 percent utilization).
Optimization of a flow injection analysis system for multiple solvent extraction (1982)

The performance of a multistage flow Injection analysis solvent extraction system has been optimized. The effect of solvent segmentation devices, extraction colls, and phase separators on performance characteristics is discussed. Theoretical consideration Is given to the effects and determination of dispersion and the extraction dynamics within both glass and Teflon extraction coils. The optimized system has a sample recovery similar to an Identical manual procedure and a 1.5% relative standard deviation between Injections. Sample throughput time is under 5 min. These characteristics represent significant Improvements over the performance of the same system before optimization. © 1982, American Chemical Society. All rights reserved.
Accurate Cancer Classification Using Expressions of Very Few Genes (2007)

We aim at finding the smallest set of genes that can ensure highly accurate classification of cancers from microarray data by using supervised machine learning algorithms. The significance of finding the minimum gene subsets is three-fold: 1) It greatly reduces the computational burden and "noise" arising from irrelevant genes. In the examples studied in this paper, finding the minimum gene subsets even allows for extraction of simple diagnostic rules which lead to accurate diagnosis without the need for any classifiers. 2) It simplifies gene expression tests to include only a very small number of genes rather than thousands of genes, which can bring down the cost for cancer testing significantly. 3) It calls for further investigation into the possible biological relationship between these small numbers of genes and cancer development and treatment. Our simple yet very effective method involves two steps. In the first step, we choose some important genes using a feature importance ranking scheme. In the second step, we test the classification capability of all simple combinations of those important genes by using a good classifier. For three "small" and "simple" data sets with two, three, and four cancer (sub)types, our approach obtained very high accuracy with only two or three genes. For a "large" and "complex" data set with 14 cancer types, we divided the whole problem into a group of binary classification problems and applied the 2-step approach to each of these binary classification problems. Through this "divide-and-conquer" approach, we obtained accuracy comparable to previously reported results but with only 28 genes rather than 16,063 genes. In general, our method can significantly reduce the number of genes required for highly reliable diagnosis.
Analysis of the <i>Drosophila melanogaster</i> anti‐ovarian response to honey bee queen mandibular pheromone (2018)

Queen mandibular pheromone (QMP) is a potent reproductive signal to which honey bee workers respond by suppressing their ovaries and adopting alloparental roles within the colony. This anti-ovarian effect of QMP on workers can, surprisingly, be induced in other insects, including fruit flies, in which females exposed to synthetic QMP develop smaller ovaries with fewer eggs. In this study, we use the Drosophila melanogaster model to identify the components of synthetic QMP required for the anti-ovarian effect. We found that virgin females respond strongly to 9-oxo-2-decenoic acid and 10-hydroxy-2-decenoic acid (10HDA), suggesting that the decenoic acid components of QMP are essential for the anti-ovarian response. Further, a nuclear factor of activated T-cells reporter system revealed neurones expressing the olfactory receptors Or-56a, Or-49b and Or-98a are activated by QMP in the antenna. In addition, we used olfactory receptor GAL4 drivers and a neuronal activator (a neuronal activating bacterial sodium channel) to test whether the candidate neurones are potential labelled lines for a decenoic acid response. We identified Or-49b as a potential candidate receiver of the 10HDA signal. Finally, the anti-ovarian response to synthetic QMP is not mediated by decreasing the titre of the reproductive hormones ecdysone and juvenile hormone.
<i>In vitro</i> assessment of strength, fatigue durability, and disassembly of Ti6Al4V and CoCrMo necks in modular total hip replacements (2011)

Abstract Modularity in total hip replacement offers advantages with regard to biomechanical adjustments and leg lengths. Recently, modular femoral necks were introduced as an added advantage to head modularity permitting further adjustments in femoral version as well as offset and ease of revision. Currently, most necks are made of Ti6Al4V for which cases of in vivo fractures and inseparable neck‐stem junctions have been reported. Therefore, we investigated CoCrMo head–Ti6Al4V stem hip replacements with necks made of CoCrMo as an alternative to Ti6Al4V. We compared the two materials with respect to (1) compressive load bearing capacity; (2) fatigue durability; and (3) component distraction. We performed in vitro fatigue‐pull‐off, microscopy, fatigue durability and compression investigations. The CoCrMo neck showed a load bearing capacity of 18 kN, 38% higher than 13 kN for the Ti6Al4V neck. A fatigue load of 11.2 kN for 1 million cycle failure was achieved with CoCrMo translating into nearly 1000 times longer fatigue life compared to Ti6Al4V necks. The neck‐stem distraction force showed large statistical variation and was similar for both neck materials. Overall, the results suggest a superiority of CoCrMo over Ti6Al4V as neck material with regard to mechanical behavior. However, the corrosion behavior was not appropriately assessed and necessitates additional investigations. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2011.
Potent siRNA Inhibitors of Ribonucleotide Reductase Subunit RRM2 Reduce Cell Proliferation <i>In vitro</i> and <i>In vivo</i> (2007)

An anti-RRM2 siRNA duplex is identified that exhibits significant antiproliferative activity in cancer cells of varying human type and species (mouse, rat, monkey); these findings suggest that this duplex is a promising candidate for therapeutic development.
Results of a phase I/II trial of recombinant human granulocyte- macrophage colony-stimulating factor in very low birthweight neonates: significant induction of circulatory neutrophils, monocytes, platelets, and bone marrow neutrophils (1995)

Neonates, especially those of very low birthweight (VLBW), have an increased risk of nosocomial infections secondary to deficiencies in development. We previously demonstrated that granulocyte-macrophage colony-stimulating factor (GM-CSF) production and mRNA expression from stimulated neonatal mononuclear cells are significantly less than that from adult cells. Recombinant murine GM-CSF administration to neonatal rats has resulted in neutrophilia, increased neutrophil production, and increased survival of pups during experimental Staphylococcus aureus sepsis. In the present study, we sought to determine the safety and biologic response of recombinant human (rhu) GM-CSF in VLBW neonates. Twenty VLBW neonates (500 to 1,500 g), aged < 72 hours, were randomized to receive either placebo (n = 5) or rhuGM-CSF at 5.0 micrograms/kg once per day (n = 5), 5.0 micrograms/kg twice per day (n = 5), or 10 micrograms/kg once per day (n = 5) given via 2-hour intravenous infusion for 7 days. Complete blood counts, differential, and platelet counts were obtained, and tibial bone marrow aspirate was performed on day 8. Neutrophil C3bi receptor expression was measured at 0 and 24 hours. GM-CSF levels were measured by a sandwich enzyme-linked immunosorbent assay at 2, 4, 6, 12, and 24 hours after the first dose of rhuGM-CSF. At all doses, rhuGM-CSF was well tolerated, and there was no evidence of grade III or IV toxicity. Within 48 hours of administration, there was a significant increase in the circulating absolute neutrophil count (ANC) at 5.0 micrograms/kg twice per day and 10.0 micrograms/kg once per day, which continued for at least 24 hours after discontinuation of rhuGM-CSF. When the ANC was normalized for each patient's first ANC, there was a significant increase in the ANC on days 6 and 7 at each dose level. By day 7, all tested doses of rhuGM-CSF resulted in an increase in the absolute monocyte count (AMC) compared with placebo-treated neonates. In those receiving rhuGM-CSF 5.0 micrograms/kg twice per day, there was additionally a significant increase in the day 7 and 8 platelet count. Tibial bone marrow aspirates demonstrated a significant increase in the bone marrow neutrophil storage pool (BM NSP) at 5.0 micrograms/kg twice per day and 10.0 micrograms/kg once per day. Neutrophil C3bi receptor expression was significantly increased 24 hours after the first dose of rhuGM-CSF at 5.0 micrograms/kg once per day. The elimination half-life (T1/2) of rhuGM-CSF was 1.4 +/- 0.8 to 3.9 +/- 2.8 hours.(ABSTRACT TRUNCATED AT 400 WORDS)
Accurate Waypoint Navigation using Non-Differential GPS (2002)

Abstract : Land-based waypoint navigation usually requires accurate position informafion to effectively function in either natural or n%an-n%ade terrain. Most systems solve this problem by using differential GPS and/or high-quality, expensive inertial navigation systems. In an effort to make waypoint navigation available to smaller tactical platforms, a tightly packaged, portable and inexpensive waypoint navigation system was developed. This system was implemented on the Man Portable Robotic System (MPRS) Urban Robot (URBOT)'. The package uses inexpensive sensors and a combination of standard Kalman Filter and waypoint following techniques along with some novel approaches to compensate for the deficiencies of the GPS and gyroscope sensors. The algorithms run on a low-cost embedded processor. A control unit was also developed that allows the operator to specify path waypoints on ortho-rectified aerial photographs.
The tpl promoter of Citrobacter freundii is activated by the TyrR protein (1997)

The ability of microorganisms to degrade L-tyrosine to phenol, pyruvate, and ammonia is catalyzed by the inducible enzyme L-tyrosine phenol lyase (EC 4.1.99.2). To investigate possible mechanisms for how the synthesis of this enzyme is regulated, a variety of biochemical and genetic procedures was used to analyze transcription from the tpl promoter of Citrobacter freundii ATCC 29063 (C. braakii). By computer analysis of the region upstream of the tpl structural gene, two segments of DNA bearing strong homology to the known operator targets of the TyrR protein of Escherichia coli were detected. A DNA fragment of 509 bp carrying these operator targets plus the presumptive tpl promoter was synthesized by PCR and used to construct a single-copy tpl-lacZ reporter system. The formation of beta-galactosidase in strains carrying this reporter system, which was measured in E. coli strains of various genotypes, was strongly dependent on the presence of a functional TyrR protein. In strains bearing deletions of the tyrR gene, the formation of beta-galactosidase was reduced by a factor of 10. Several mutationally altered forms of TyrR were deficient in their abilities to activate the tpl promoter. The pattern of loss of activation function was exactly parallel to the effects of the same tyrR mutations on the mtr promoter, which is known to be activated by the TyrR protein. When cells carrying the tpl-lacZ reporter system were grown on glycerol, the levels of beta-galactosidase were 10- to 20-fold higher than those observed in glucose-grown cells. The effect was the same whether or not TyrR-mediated stimulation of the tpl promoter was in effect. By deleting the cya gene, it was shown that the glycerol effect was attributable to stimulation of the tpl promoter by the cyclic AMP (cAMP)-cAMP reporter protein system. A presumptive binding site for this transcription factor was detected just upstream of the -35 recognition hexamer of the tpl promoter. The transcriptional start point of the tpl promoter was determined by chemical procedures. The precise locations of the TyrR binding sites, which were established by DNase I footprinting, agreed with the computer-predicted positions of these regulatory sites. The two TyrR operators, which were centered at coordinates -272.5 and -158.5 with respect to the transcriptional start point, were independently disabled by site-directed mutagenesis. When the upstream operator was altered, activation was completely abolished. When the downstream operator was altered, there was a fourfold reduction in reporter enzyme levels. The tpl system presents a number of intriguing features not previously encountered in TyrR-activated promoters. First among these is the question of how the TyrR protein, bound to widely separated operators, activates the tpl promoter which is also widely separated from the operators.
A new interoperable management model for IP and OSI architectures (2002)

This paper presents a new architecture for combining OSI management protocol (CMIP) and the Internet management protocol (SNMP) in order to manage both OSI networks and IP networks. A comparison between both management protocols is presented also shows how CMIP can run over the TCP/UDP/IP stack (CMOT), and how SNMP can run over the OSI stack. Finally a new layer between the management protocols and the underlying stacks (Internet and OSI) is presented to provide CMIP and SNMP, with the availability to run over either OSI or TCP/UDP/IP stacks.
Determination of the prognostic value of cyclin D1 overexpression in breast cancer. (1995)

Cyclin D1 plays a critical role in the timing of the initiation of DNA synthesis in the normal cell cycle of mammalian cells. Deregulated expression of this protein has been seen in a variety of tumours either as a result of gene amplification or chromosomal translocation, in breast cancer and B cell malignancies respectively. In order to determine the role this putative oncoprotein plays in breast cancer, we have applied a new monoclonal antibody, recently produced in our laboratory, in an immunohistochemical study of 93 primary breast carcinomas. We show that approximately 28% of the cases displayed enhanced expression of the cyclin D1 protein. Furthermore, either cyclin D1, cyclin D3, or both, were expressed in 69% of cases, suggesting that overexpression of any one member of this family may relieve cancer cells of their mitogenic stimulatory requirement. In addition, we show that those patients whose breast cancers co-express cyclin D1 with either epidermal growth factor receptor (EGFR) or the retinoblastoma protein (pRB) have a significantly poorer prognosis in comparison to those expressing cyclin D1 alone. Our observations indicate that, in a subset of breast cancers, aberrant cyclin D1 expression is a contributory factor to tumorigenesis and in association with EGFR or pRB expression, identify those tumours which may require more aggressive therapy.
The Effect of Myopia and Loss Aversion on Risk Taking: An Experimental Test (1997)

Myopic loss aversion is the combination of a greater sensitivity to losses than to gains and a tendency to evaluate outcomes frequently. Two implications of myopic loss aversion are tested experimentally. 1. Investors who display myopic loss aversion will be more willing to accept risks if they evaluate their investments less often. 2. If all payoffs are increased enough to eliminate losses, investors will accept more risk. In a task in which investors learn from experience, both predictions are supported. The investors who got the most frequent feedback (and thus the most information) took the least risk and earned the least money.
Tunable and Sensitive Biophotonic Waveguides Based on Photonic-Bandgap Microcavities (2006)

This paper presents a theoretical study of the single-mode and birefriengence condition of the silicon photonic wires using the imaginary distance beam propagation method. The photonic wires are suitable for integration with active one-dimensional silicon photonic bandgap waveguides. This inherently will reduce the propagation loss caused by the scattering factors within the photonic bandgap structure itself. To the best of our knowledge, we provide for the first time, a systematic study of the various physical parameters that can affect the Q-factor and transmission properties in such waveguides. In order to make this technology viable, the waveguides must be tunable, have low attenuation, possess high Q-factor, and can be switched. Can these be achieved simultaneously without changing the device width and height dimensions? Furthermore, can we meet these aims without placing unrealistic demands in fabrication? The electrical switching of this device is implemented using a p-i-n optical diode. The diode is predicted to require an on state power of 81 nW with rise and fall times of 0.2 and 0.043 ns, respectively. The length of the microcavity and the diameter of the air holes are finely tuned with reference to the Q-factor and transmission. It will be shown that for certain desired resonant wavelength, the Q-factor and transmission properties can be optimized by tuning the length of the cavity and the diameter of the two inner most air holes. This method allows ease of fabrication by not having to vary the waveguide width and height to obtain the tuning effects. Optical simulation was performed using the three-dimensional finite-difference time-domain simulation method