gebhart/patrepeval huggingface dataset:
Biotin production under limiting growth conditions by Agrobacterium/Rhizobium HK4 transformed with a modified Escherichia coli bio operon (1999)

The E. coli biotin (bio) operon was modified to improve biotin production by host cells: (a) the divergently transcribed wild-type bio operon was re-organized into one transcriptional unit; (b) the wild-type bio promoter was replaced with a strong artificial (tac) promoter; (c) a potential stem loop structure between bioD and bioA was removed; and (d) the wild-type bioB ribosomal binding site (RBS) was replaced with an artificial RBS that resulted in improved bioB expression. The effects of the modifications on the bio operon were studied in E. coli by measuring biotin and dethiobiotin production, and bio gene expression with mini-cells and two-dimensional polyacrylamide gel electrophoresis. The modified E. coli bio operon was introduced into a broad host-range plasmid and used to transform Agrobacterium/Rhizobium HK4, which then produced 110 mg L-1 of biotin in a 2-L fermenter, growing on a defined medium with diaminononanoic acid as the starting material. Biotin production was not growth-phase dependent in this strain, and the rate of production remained high under limiting (maintenance) and zero growth conditions.
High-sensitivity multi-channel single-interferometer DPSK receiver (2006)

A high-sensitivity method of demodulating wavelength-division-multiplexed optical DPSK channels using a single interferometer is described and demonstrated. We show that this technique can operate within existing standards and achieve near-quantum-limited receiver performance. The resulting hardware simplification has potential to reduce the cost of deploying and scaling future wide-band optical-communication networks employing WDM-DPSK.
Preparation of Mutants Resistant to Catabolite Repression of<i>Trichoderma reesei</i> (1985)

Journal Article Preparation of Mutants Resistant to Catabolite Repression of Trichoderma reesei Get access Mikio Kawamori, Mikio Kawamori Tokyo Research Laboratories, Kyowa Hakko Kogyo Co., Ltd., Asahimachi, Machida-shi, Tokyo 194, Japan Search for other works by this author on: Oxford Academic Google Scholar Yasushi Morikawa, Yasushi Morikawa Research and Development Division, Kyowa Hakko Kogyo Co., Ltd., Otemachi, Chiyoda-ku, Tokyo 100, Japan Search for other works by this author on: Oxford Academic Google Scholar Yoriko Shinsha, Yoriko Shinsha Tokyo Research Laboratories, Kyowa Hakko Kogyo Co., Ltd., Asahimachi, Machida-shi, Tokyo 194, Japan Search for other works by this author on: Oxford Academic Google Scholar Kenichiro Takayama, Kenichiro Takayama Tokyo Research Laboratories, Kyowa Hakko Kogyo Co., Ltd., Asahimachi, Machida-shi, Tokyo 194, Japan Search for other works by this author on: Oxford Academic Google Scholar Seigo Takasawa Seigo Takasawa Tokyo Research Laboratories, Kyowa Hakko Kogyo Co., Ltd., Asahimachi, Machida-shi, Tokyo 194, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 49, Issue 10, 1 October 1985, Pages 2875–2879, https://doi.org/10.1080/00021369.1985.10867203 Published: 01 October 1985 Article history Received: 19 February 1985 Published: 01 October 1985
Prevention of deadlocks and livelocks in lossless, backpressured packet networks (2002)

When congestion builds up in a packet network, two general approaches are possible to cope with the shortage of buffer space. One approach is to drop incoming packets for the buffer that is not available and to rely on the end-to-end protocols for the recovery of lost packets. The alternative approach is to insist that no packets should be dropped inside a packet network, even when congestion builds up. One way to accomplish this goal is to have the congested nodes send backpressure feedback to neighboring nodes, informing them of unavailability of buffering capacity and in effect stopping them from forwarding packets until enough buffer becomes available. While there are potential advantages in backpressured networks that do not allow packet dropping, such networks are susceptible to a condition known as deadlock in which throughput of the network or part of the network goes to zero (i.e., no packets are transmitted). In this paper, we describe a simple, lossless method of preventing deadlocks and livelocks in backpressured packet networks. In contrast with prior approaches, our proposed technique does not introduce any packet losses, does not corrupt the packet sequence, and does not require any changes to packet headers. In addition to presenting the new congestion control protocol in a general context, we describe an important application of the technique to Gigabit Ethernet (IEEE 802.3z).
A novel explicit rate congestion control algorithm (2002)

In this paper, we introduce a novel explicit rate algorithm to support available bit rate service in asynchronous transfer mode (ATM) networks. Our algorithm is based on observing the maximum bandwidth usage of different connections and incorporating both rate and queue length information to achieve a stable operation. Zero steady state queue length is achieved. We separate congestion control and fairness issues in our design, which allows us to have a common framework to support multiple fairness criteria. In our algorithm, we estimate the number of locally bottlenecked active connections. This number is used to normalize control and to redistribute spare bandwidth during transients and does not affect the steady state fair rate used by each connection. As such, our algorithm is relatively insensitive to the accuracy of this number. The issue of supporting both UBR and ABR is addressed. The performance of our algorithm is evaluated through simulations.
Design and Synthesis of Novel α<sub>1</sub><sub>a</sub> Adrenoceptor-Selective Antagonists. 4. Structure−Activity Relationship in the Dihydropyrimidine Series (1999)

We have previously disclosed dihydropyridines such as 1a,b as selective alpha(1a) antagonists as a potential treatment for benign prostatic hyperplasia (BPH). The propensity of dihydropyridines toward an oxidation led us to find suitable replacements of the core unit. The accompanying papers describe the structure-activity relationship (SAR) of dihydropyrimidinones 2a,b as selective alpha(1a) antagonists. We report herein the SAR of dihydropyrimidines such as 4 and highlight the similarities and differences between the dihydropyrimidine and dihydropyrimidinone series of compounds.
Real-time jitter correction in a photonic analog-to-digital converter (2020)

A real-time jitter meter is used to measure and digitally sample the pulse-to-pulse timing error in a laser pulse train. The jitter meter is self-referenced using a single-pulse delay line interferometer and measures timing jitter using optical heterodyne detection between two frequency channels of the pulse train. Jitter sensitivity down to 3×10<sup>-10</sup><i>f</i><i>s</i><sup>2</sup>/<i>H</i><i>z</i> at 500 MHz has been demonstrated with a pulse-to-pulse noise floor of 1.6 fs. As a proof of principle, the digital correction of the output of a high-frequency photonic analog-to-digital converter (PADC) is demonstrated with an emulated jitter signal. Up to 23 dB of jitter correction, down to the noise floor of the PADC, is accomplished with radio-frequency modulation up to 40 GHz.
ChemInform Abstract: Chemical Biology of Anticancer Gold(III) and Gold(I) Complexes (2016)

Abstract Review: 108 refs.
New variants of a method of MRI scale standardization (2000)

One of the major drawbacks of magnetic resonance imaging (MRI) has been the lack of a standard and quantifiable interpretation of image intensities. Unlike in other modalities, such as X-ray computerized tomography, MR images taken for the same patient on the same scanner at different times may appear different from each other due to a variety of scanner-dependent variations and, therefore, the absolute intensity values do not have a fixed meaning. We have devised a two-step method wherein all images (independent of patients and the specific brand of the MR scanner used) can be transformed in such a way that for the same protocol and body region, in the transformed images similar intensities will have similar tissue meaning. Standardized images can be displayed with fixed windows without the need of per-case adjustment. More importantly, extraction of quantitative information about healthy organs or about abnormalities can be considerably simplified. This paper introduces and compares new variants of this standardizing method that can help to overcome some of the problems with the original method.
Properties of Engineered Cementitious Composites with Raw Sugarcane Bagasse Ash Used as Sand Replacement (2021)

This study investigates the effects of raw sugarcane bagasse ash (SCBA) used as a partial or complete replacement for silica sand in engineered cementitious composites (ECCs). ECC mixtures with five different replacement levels of sand with SCBA were produced (i.e., 0%, 25%, 50%, 75%, and 100% by volume). The SCBA utilized in this study was comprehensively characterized. Furthermore, the fresh and hardened properties of the produced ECC materials were thoroughly evaluated. The characterization of SCBA revealed that raw SCBA consisted mainly of small (i.e., 256 μm average particle size), porous, and irregularly shaped particles with carbon and silica as the main constituents. Furthermore, the SCBA met the pozzolanic component requirement for Class C pozzolans; however, it did not meet the minimum strength activity index requirement to be classified as a pozzolan; however, it did not meet the minimum strength activity index requirement to be classified as a pozzolan. In terms of ECC fresh properties, the incorporation of SCBA produced an important loss in workability, which was mitigated with increasing dosages of high-range water reducer for increasing amounts of SCBA, which also resulted in a substantial increase in the air content. In the case of hardened material properties, the incorporation of SCBA as sand replacement produced a slight decrease (up to 11%) of the compressive strength of ECCs. However, the tensile strength and especially the tensile ductility of the composites were substantially enhanced (up to 22.3% and 311%, respectively). The tensile strength improvements were credited to the pozzolanic and/or filler effect of SCBA. On the other hand, enhancements in the tensile ductility were associated to the combined effect of the reduction of crack-tip matrix toughness (credited to the decrease in aggregate particle size), reduction in ECC cracking strength (due to increase in air content), and increase in the complementary energy (attributed to the potential decrease in the chemical bond of the fiber/matrix interface and an enhanced fiber dispersion). The surface resistivity of ECC materials was negatively affected by the addition of SCBA. Furthermore, the length change of all SCBA-ECC materials, at all ages of curing, was higher in comparison with that of the control mixture, except for the mixture with 25% replacement at 28 days of curing.
The P-selectin glycoprotein ligand from human neutrophils displays sialylated, fucosylated, O-linked poly-N-acetyllactosamine. (1994)

We previously demonstrated that P-selectin binds with high affinity to a trace, homodimeric glycoprotein ligand on human myeloid cells. The ligand carries the sialyl Lewis x (sLe(x)) epitope, a limited number of N-linked glycans, and clustered, sialylated O-linked glycans. In this study we demonstrate that the polypeptide component of this ligand is identical to that of P-selectin glycoprotein ligand-1 (PSGL-1), a molecule recently identified by expression cloning from a human myeloid cell cDNA library. We have examined the effects of glycosidases on purified, radioiodinated PSGL-1 from human neutrophils to further characterize the structure and function of the attached oligosaccharides. We found that PSGL-1 had poly-N-acetyllactosamine, only some of which could be removed with endo-beta-galactosidase. The majority of the Le(x) and sLe(x) structures were on endo-beta-galactosidase-sensitive chains. Peptide:N-glycosidase F (PNGaseF) treatment removed at least two of the three possible N-linked oligosaccharides from PSGL-1. Expression of Le(x) and sLe(x) was not detectably altered by PNGaseF digestion, indicating that these structures were primarily on O-linked poly-N-acetyllactosamine. Endo-beta-galactosidase-treated PSGL-1 retained the ability to bind to P-selectin, suggesting that some of the oligosaccharides recognized by P-selectin were either on enzyme-resistant poly-N-acetyllactosamine or on chains which lack poly-N-acetyllactosamine. PNGaseF treatment did not affect the ability of PSGL-1 to bind to P-selectin, demonstrating that the oligosaccharides required for P-selectin recognition are O-linked. PSGL-1 also bound to E-selectin, but with at least 50-fold lower affinity than to P-selectin. These data suggest that PSGL-1 from human neutrophils displays complex, sialylated, and fucosylated O-linked poly-N-acetyllactosamine that promote high affinity binding to P-selectin, but not to E-selectin.
High-speed reduced-state sequence estimation (2002)

Reduced-state sequence estimation (RSSE) is a suboptimal modification of the Viterbi algorithm (VA) which reduces the computational complexity of maximum likelihood sequence estimation. However, the maximum achievable throughput of RSSE may be significantly lower than the VA, as in addition to the add-compare-select function the critical path comprises branch metric computation, survivor memory operations, and decision-feedback calculation, This paper shows that precomputation of branch metrics can shorten the critical path of RSSE such that its delay becomes of the same order as the VA.
ACTION PATTERN OF BACILLUS LICHENIFORMIS ALPHA-AMYLASE ON ORDINARY, WAXY, AND HIGH-AMYLOSE CORN STARCHES AND THEIR HYDROXYPROPYL DERIVATIVES (1987)

The action of thermally stable alpha-amylase from Bacillus licheniformis on ordinary, waxy and high-amylose corn starches and their hydroxypropyl derivatives gave distinctive patterns of malto-oligosaccharide products that were dependent on conversion time. These alpha-amylolysis patterns of the various starches were derived from high performance liquid chromatographic analyses of the oligosaccharide compositions produced at various levels of hydrolysis. The products from amylolysis at high substrate concentrations (20–30%) and elevated temperature (95°C) suggest an endo-specific hydrolysis of the amylose and amylopectin chains to give a trio product-specificity for the formation of DP5, DP3, and DP2 oligosaccharides. These results confirm and expand the studies by Saito (1973) and Nakakuki et al. (1984), who found that B. licheniformis amylase degraded a 1% solution of short-chain amylose at 40° to give mainly DP5 and DP3 oligomers. The hydroxypropyl groups on ordinary, waxy and high-amylose starch derivatives greatly hindered alpha-amylolysis, but the action patterns were essentially the same.
ChemInform Abstract: 3‐FLUOROBENZODIAZEPINES (1984)

Abstract Eine Serie von 3‐Fluorbenzdiazepinen (IV) wird durch die Reaktion von Diethylaminoschwefeltrifluorid (DAST) (III) mit den 3‐Hydroxybenzdiazepinen (II) synthetisiert.
Lanthanide-based luminescent probes for selective time-gated detection of hydrogen peroxide in water and in living cells (2010)

Lanthanide-based luminescent probes TPR1 and TPR2 were developed for the detection of hydrogen peroxide (H(2)O(2)) in living systems. The chemoselective reaction of these boronate-protected probes with H(2)O(2) resulted in an enhanced lanthanide sensitization and a 6-fold increase in luminescent intensity. TPR2 was utilized to measure the endogenous production of H(2)O(2) in RAW 264.7 macrophages using time-gated luminescent spectroscopy.
A Practical Algorithm for Realizing GDFE Precoder for Multiuser MIMO Systems (2010)

It is well known that multiuser multiple-input multiple-output (MU-MIMO) systems can achieve superior data rates compared to single user MIMO links. The improvement in data rates offered by the MU-MIMO systems is dependent on the design of precoding scheme for the broadcast channel (BC). A precoding scheme based on generalized decision feedback equalizer (GDFE) is known to achieve MIMO BC capacity. However, GDFE precoder suffers from huge computational complexity and is not suitable for practical systems. Much of computational cost of implementing a GDFE precoder can be attributed to its reliance on the covariance matrix corresponding to the ``least favorable noise'', which has prohibitive computational complexity. In this paper, we provide an alternative framework for realizing a GDFE precoder, which avoids the need to compute ``least favorable noise''. While maintaining capacity optimality of the GDFE precoder, the proposed algorithm has significantly lower complexity that is comparable to other MU-MIMO precoding schemes. Additionally, the proposed algorithm provides a useful tradeoff between desired complexity and performance.
Emission Spectral Properties of Cadmium Sulfide Nanoparticles with Multiphoton Excitation (2002)

We describe the luminescence spectral properties of CdS nanoparticles with multiphoton excitation. Three types of CdS nanoparticles were examined which were a CdS/dendrimer composite which displays high anisotropy, Cd<sup>2+</sup>-enriched nanoparticles which display two emission maxima, and polyphosphate-stabilized nanoparticles which display long wavelength emission. Illumination with long wavelengths near 700-790 nm resulted in two-photon excitation. Essentially the same emission spectra and intensity decays were observed with one-photon and two-photon excitation. Comparison with fluorescein indicates the NPs display large two-photon cross sections near 100 GM. The CdS/dendrimer and Cd<sup>2+</sup>-enriched CdS nanoparticles displayed large anisotropy values with two-photon excitation, substantially larger than with one-photon excitation. It appears that semiconductor nanoparticles are comparable to organic fluorophores which display the same spectral properties with one-photon and two-photon excitation.
Interferon-Responsive Regulatory Elements in the Promoter of the Human 2′,5′-Oligo(A) Synthetase Gene (1987)

The interferon (IFN)-activated human 2',5'-oligo(A) synthetase E gene contains 11 RNA starts and lacks TATA and CAAT signals. DNA sequences around the promoter make the expression of the chloramphenicol acetyltransferase gene (CAT) inducible over 20-fold by IFN. A 72-base-pair segment (E-IRS) immediately upstream of the RNA starts was defined as being required for IFN-activated expression of the E-gene promoter-CAT constructs and acts in a position-independent manner. It also confers IFN-activated enhancement to the herpes simplex virus thymidine kinase promoter. On this promoter, the 5' part of the E-IRS functions as a constitutive enhancer, while the last 16 base pairs of the E-IRS is sufficient to give IFN-induced expression. On the E-gene promoter, the constitutive enhancer and the IFN-activated sequence are both needed but can be separated. In addition, promoter competition experiments indicate a third regulatory region which helps to repress expression of the E gene in uninduced cells.
Optical oximetry of volume-oscillating vascular compartments: contributions from oscillatory blood flow (2016)

We present a quantitative analysis of dynamic diffuse optical measurements to obtain oxygen saturation of hemoglobin in volume oscillating compartments. We used a phasor representation of oscillatory hemodynamics at the heart rate and respiration frequency to separate the oscillations of tissue concentrations of oxyhemoglobin (O) and deoxyhemoglobin (D) into components due to blood volume (subscript V V ) and blood flow (subscript F F ): O=O V +O F O=OV+OF , D=D V +D F D=DV+DF . This is achieved by setting the phase angle Arg(O F )−Arg(O) Arg(OF)−Arg(O) , which can be estimated by a hemodynamic model that we recently developed. We found this angle to be −72 deg −72 deg for the cardiac pulsation at 1 Hz, and −7 deg −7 deg for paced breathing at 0.1 Hz. Setting this angle, we can obtain the oxygen saturation of hemoglobin of the volume-oscillating vascular compartment, S V =|O V |/(|O V |+|D V |) SV=|OV|/(|OV|+|DV|) . We demonstrate this approach with cerebral near-infrared spectroscopy measurements on healthy volunteers at rest (n=4 n=4 ) and during 0.1 Hz paced breathing (n=3 n=3 ) with a 24-channel system. Rest data at the cardiac frequency were used to calculate the arterial saturation, S (a) S(a) ; over all subjects and channels, we found ⟨S V ⟩=⟨S (a) ⟩=0.96±0.02 ⟨SV⟩=⟨S(a)⟩=0.96±0.02 . In the case of paced breathing, we found ⟨S V ⟩=0.66±0.14 ⟨SV⟩=0.66±0.14 , which reflects venous-dominated hemodynamics at the respiratory frequency.
Shear Stress Activates p60src-Ras-MAPK Signaling Pathways in Vascular Endothelial Cells (1998)

The aim of this study was to elucidate the upstream signaling mechanism that mediates the fluid shear stress activation of mitogen-activated protein kinases (MAPKs), including c-Jun NH2-terminal kinase (JNK) and extracellular signal-regulated kinases (ERKs), in vascular endothelial cells (ECs). Our results indicate that p60src is rapidly activated by fluid shear stress in bovine aortic endothelial cells (BAECs). Shear stress induction of the hemagglutinin (HA) epitope-tagged HA-JNK1 and the Myc epitope-tagged Myc-ERK2 was significantly attenuated by v-src(K295R) and c-src(K295R), the kinase-defective mutants ofv-src and c-src, respectively. HA-JNK1 and Myc-ERK2 were activated by c-src(F527), a constitutively activated form of p60src, and the activation was abolished by RasN17, a dominant-negative mutant of p2lras. In contrast, although HA-JNK1 and Myc-ERK2 were also activated by RasL61, an activated form of p21ras, the activation was not affected by v-src(K295R). These results indicate that p60src is upstream to the Ras-JNK and Ras-ERK pathways in response to shear stress. The shear stress inductions of the promoters of monocyte chemotactic protein-1 (MCP-1) and c-fos, driven by TPA-responsive element (TRE) and serum-responsive element (SRE), respectively, were attenuated by v-src(K295R). This attenuation is associated with decreased transcriptional activities of c-Jun and Elk-1, the transcription factors targeting TRE and SRE, respectively. Thus, p60src plays a critical role in the shear stress activation of MAPK pathways and induction of Activating Protein-1 (AP- 1)/TRE and Elk-1/SRE-mediated transcription in ECs.
Hypermethylated promoter region of <i>DR3</i>, the death receptor 3 gene, in rheumatoid arthritis synovial cells (2006)

The CpG island in the DR3 gene promoter was specifically methylated to down-modulate the expression of DR-3 protein in rheumatoid synovial cells, which may provide resistance to apoptosis in RA synovial cells.
Sparse functional stores for imperative programs (1995)

In recent years, the trend in program representations for imperative programs has been to make them more functional, or to make them more sparse. However, new sparse representations have been non-functional, and new functional representations have not been sparse in the presence of pointer operations. In this paper, we present a functional representation that is sparse even in the presence of pointer operations.
Hyperthermia‐Induced Drug Delivery from Thermosensitive Liposomes Encapsulated in an Injectable Hydrogel for Local Chemotherapy (2014)

A novel drug delivery system, enabling an in situ, thermally triggered drug release is described, consisting of an injectable thermoresponsive chitosan hydrogel containing doxorubicin-loaded thermosensitive liposomes. The design, fabrication, characterization, and an assessment of in vitro bioactivity of this formulation is detailed. Combining on-demand drug delivery with in situ gelation results in a promising candidate for local chemotherapy.