gebhart/patrepeval huggingface dataset:
TLR4/MD-2 and RP105/MD-1 differentially regulate LPS responsiveness in B cells (135.4) (2009)

Abstract [Aims] TLR4/MD-2 is an essential complex for LPS recognition. RP105/MD-1 is a homologue of TLR4/MD-2 and is expressed in mainly B cells. RP105 or MD-1-deficient B cells show impaired LPS responsiveness, suggesting that B cells require both TLR4/MD-2 and RP105/MD-1 signals for LPS responses. However, precise mechanisms that functionally couple with the two types of complex remain unclear. Furthermore, as LPS stimulation activates B cells through both receptors, it is difficult to analyze the signals via TLR4/MD-2 and RP105/MD-1 differentially. To resolve this, we used agonistic mAbs to TLR4 and RP105 to explore differential roles for TLR4/MD-2 and RP105/MD-1 in B cell responses to LPS. [Methods] Mouse splenic B cells were stimulated with αTLR4 mAb, αRP105 mAb, or LPS in combination with IL-4. Expression of CD86, BAFF receptors (TACI, BAFF-R, BMCA), and CD138 was analyzed by FACS. For proliferation analysis, the B cells were stimulated with vehicles for 3 days and pulsed with 0.5 μCi [3H]-TdR. The μ to γ1 class switch recombination (CSR) was examined by analyzing the proportion of surface IgG1+ cells by FACS. [Results and Discussion] The αTLR4 mAb and αRP105 mAb induced massive B cell proliferation like as LPS. Expression of CD86 and BAFF receptors was induced by low doses of αRP105 (10 ng/ml), whereas those expression was very low by αTLR4 stimulation even at high doses (1 μg/ml). Combination of αTLR4 + IL-4 as well as LPS + IL-4 forced B cells to induce sIgG1+ cells. In contrast, αRP105 + IL-4 never showed this activity. CD138 expression was induced on B cells stimulated with αTLR4 but not with αRP105. These findings suggest that TLR4 and RP105 differentially regulate B cell response to LPS.
Radioimaging of Primary (AL) Amyloidosis with an Amyloid-Reactive Monoclonal Antibody (2004)

In the USA, there are no means to visualize amyloid deposits radiographically in patients with primary (AL) amyloidosis. The specific interaction of the 11-1F4 mAb with AL amyloid fibrils presents a unique opportunity for its application as a non-invasive diagnostic and prognostic imaging tool for patients with this invariably fatal and devastating form of amyloid disease. MicroSPECT and Computerized tomography (CT) images were co-registered manually. Each mouse image carried fiducial markers supplied by capillaries filled with a solution of 125I which appeared in the SPECT and CT images and could be co-registered in the 3-D reconstructions. CT data were acquired using a MicroCAT™ II — this circular orbit conebeam system is equipped with a 20–80 kVp microfocus x-ray source.
HPLC and Synthesis Strategy in Nucleoside and (Oligo)Nucleotide Chemistry (1990)

Abstract A judicious use of HPLC allows to simplify the synthetic approach of an (oligo)nucleotide. As an example, is reported a preparation of an antiviral (3′-5′)dinucleotide with simultaneous isolation of its (3′-3′) isomer.
Module-level matching algorithms for MSM clos-network switches (2012)

In this paper, we propose a simple module-level matching scheme for memory-space-memory Clos-network switches to avoid complex path-allocation algorithms in bufferless Clos networks, as well as cell out-of-order and saturation-tree problems in buffered Clos networks. We show that the module-level matching scheme can achieve 100% throughput.We propose static and dynamic dispatching cell schemes in addition to the module-level matching to improve the delay performance. The static cell dispatching scheme requires no additional scheduling; while the dynamic cell dispatching scheme is more adaptive to the traffic than the static one, thus can achieve better delay performance under non-uniform traffic loads. However, the wiring complexity of the scheduler for dynamic cell dispatching is high. Thus, the grouped dynamic cell dispatching scheme is proposed as a trade-off between the complexity and performance. In practice, embedded memory size is restricted, thus the queue length limitation in each switch module is also considered in this paper. We propose an efficient scheme to prevent queues to overflow in this situation which makes our work more practical.
Broadband Fully Integrated GaN Power Amplifier With Embedded Minimum Inductor Bandpass Filter and AM–PM Compensation (2019)

In this letter, we present a design technique for broadband linearized fully integrated GaN power amplifiers (PAs). The minimum inductor bandpass filter structure is used as the output matching network to achieve low loss and high out-of-band attenuation. Two parallel transistors with unbalanced gate biases are used to mitigate nonlinearity of their transconductance and input capacitance, and consequently, compensate AM–PM distortion of the PA. A fully integrated GaN PA prototype provides 35.1–38.9-dBm output power and 40%–55% power-added efficiency (PAE) in 2.0–4.0 GHz. For a 64-QAM signal with 8-dB peak-to-average power ratio (PAPR) and 100-MHz bandwidth at 2.4 GHz, average output power of 32.7 dBm and average PAE of 31% are measured with −30.2-dB error vector magnitude (EVM).
Dual-mode filters with grooved dielectric resonators for cellular-radio base stations (2003)

Dual-mode filters for cellular-radio base-stations require resonators with high unloaded Q-factor, wide spurious-free operating window and possibility of high coupling values either to input or between resonators. These features are obtained by employing a new cavity resonator loaded by a grooved ceramic disk. The groove, which may increase up to a full air gap, allows the insertion of probes and tuning/coupling screws where the field is stronger. Experimental results of an eight-pole transmit filter show the suitability of the proposed resonator for realizing cellular-radio base stations filters.
Probing Chiral Recognition of Enzyme Active Sites with Octahedral Iridium(III) Propeller Complexes (2015)

Abstract Chiral bis ‐cyclometalated octahedral organoiridium(III) complexes were designed to target different classes of enzymes, namely carbonic anhydrases, histone deacetylases, and serine proteases. The stereoselective non‐racemic synthesis of selected complexes was used to study the chiral discrimination of enzyme active sites for enantiomers of propeller‐type octahedral metal complexes. Cases for negligible, modest, and significant chiral discrimination in the interaction of iridium propeller complexes with enzyme active sites were identified.
Scaffold‐fused riboregulators for enhanced gene activation in Synechocystis sp. PCC 6803 (2015)

Cyanobacteria are an attractive host for biofuel production because they can produce valuable chemical compounds from CO2 fixed by photosynthesis. However, the available genetic tools that enable precise gene regulation for the applications of synthetic biology are insufficient. Previously, we engineered an RNA-based posttranscriptional regulator, termed riboregulator, for the control of target gene expression in cyanobacterium Synechocystis sp. PCC 6803. Moreover, we enhanced the gene regulation ability of the riboregulators in Escherichia coli by fusing and engineering a scaffold sequence derived from naturally occurring E. coli noncoding small RNAs. Here, we demonstrated that the scaffold sequence fused to the riboregulators improved their gene regulation ability in Synechocystis sp. PCC 6803. To further improve gene regulation, we expressed an exogenous RNA chaperone protein that is responsible for noncoding small RNA-mediated gene regulation, which resulted in higher target gene expression. The scaffold sequence derived from natural E. coli noncoding small RNAs is effective for designing RNA-based genetic tools and scaffold-fused riboregulators are a strong RNA-tool to regulate gene expression in cyanobacteria.
StruAP: A Tool for Bundling Linguistic Trees through Structure-based Abstract Pattern (2017)

Kohsuke Yanai, Misa Sato, Toshihiko Yanase, Kenzo Kurotsuchi, Yuta Koreeda, Yoshiki Niwa. Proceedings of the 2017 Conference on Empirical Methods in Natural Language Processing: System Demonstrations. 2017.
Dynamics of Bleomycin Interaction with a Strongly Bound Hairpin DNA Substrate, and Implications for Cleavage of the Bound DNA (2012)

Recent studies involving DNAs bound strongly by bleomycins have documented that such DNAs are degraded by the antitumor antibiotic with characteristics different from those observed when studying the cleavage of randomly chosen DNAs in the presence of excess Fe·BLM. In the present study, surface plasmon resonance has been used to characterize the dynamics of BLM B(2) binding to a strongly bound hairpin DNA, to define the effects of Fe(3+), salt, and temperature on BLM-DNA interaction. One strong primary DNA binding site, and at least one much weaker site, were documented. In contrast, more than one strong cleavage site was found, an observation also made for two other hairpin DNAs. Evidence is presented for BLM equilibration between the stronger and weaker binding sites in a way that renders BLM unavailable to other, less strongly bound DNAs. Thus, enhanced binding to a given site does not necessarily result in increased DNA degradation at that site; i.e., for strongly bound DNAs, the facility of DNA cleavage must involve other parameters in addition to the intrinsic rate of C-4' H atom abstraction from DNA sugars.
A Monoterpene Glucoside and Three Megastigmane Glycosides from Juniperus communis var. depressa. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Non-Invasive Skin Sampling Detects Systemically Administered Drugs in Humans (2021)

Abstract Clinical testing typically relies on invasive blood draws and biopsies. Alternative methods of sample collection are continually being developed to improve patient experience; swabbing the skin is one of the least invasive sampling methods possible. To show that skin swabs in combination with untargeted mass spectrometry (metabolomics) can be used for non-invasive monitoring of an oral drug, we report the kinetics and metabolism of diphenhydramine in healthy volunteers (n=10) over the course of 24 hours in blood and three regions of the skin. Diphenhydramine and its metabolites were observed on the skin after peak plasma levels, varying by compound and skin location, and is an illustrative example of how systemically administered molecules can be detected on the skin surface. The observation of diphenhydramine directly from the skin supports the hypothesis that both parent drug and metabolites can be qualitatively measured from a simple non-invasive swab of the skin surface. The mechanism of the drug and metabolites pathway to the skin’s surface remains unknown.
Time-domain analysis of dispersive transmission lines (1993)

We present and compare three time domain algorithms for calculating the dispersion characteristics of transmission lines of arbitrary cross-section : the 2-DV FD-TD, the Complex SCN TLM and the 2-DV SCN TLM proposed in this work. All the algorithms prove efficient, as a result of reducing the numerical analysis to two space dimensions. Their accuracy is demonstrated by means of comparison with the results obtained by other methods, for a range of practical examples of microwave guiding structures. We also introduce a new type of excitation which further improves the efficiency and reliability of the time-domain approach.
Large-mode-area ytterbium-doped fiber amplifier with distributed narrow spectral filtering and reduced bend sensitivity (2009)

A large-mode area polarization maintaining single-mode ytterbium-doped fiber amplifier with distributed narrow passband filtering is demonstrated. The fiber passband is 40 nm wide and centered at 1070 nm for efficient filtering of both short- and long-wavelength amplified spontaneous emission as well as stimulated raman scattering and four-wave-mixing. The fiber shows reduced bend sensitivity, has a mode field diameter of 27 microm and exhibits a slope efficiency of more than 65%.
Expandable N-Legged Converter to Drive Closely Spaced Multitransmitter Wireless Power Transfer Systems for Dynamic Charging (2019)

Expandable and flexible wireless power transfer (WPT) systems have been in demand in numerous industry applications, especially for dynamic chargers in electric vehicles. Those systems, however, bring about certain technical issues such as modulation technique and topology of the transmitter side, and transferred power profile of the transmitters. In this article, a new converter topology to drive closely spaced segmented dynamic wireless power transfer (DWPT) systems is proposed. The proposed converter can be expanded to cater for different number of transmitters, and it can provide a uniform transferred power profile throughout the path of transmitter coils, known as track. Furthermore, this article focuses on analyzing the operation of the converter and the effect of closely spaced transmitters over its operation. To show the effectiveness of the proposed topology and its modulation technique, the converter is simulated and experimentally tested using a laboratory prototype. The results are compared and analyzed, and their close agreement shows the validity of the proposed technique.
Efficient recovery in Harp (replicated Unix file system) (2003)

Harp is a replicated Unix file system accessible via the VFS interface. It provides highly available and reliable storage for files and guarantees that file operations are executed atomically in spite of concurrency and failures. Replication enables Harp to safely trade disk accesses for network communication and thus to provide good performance both during normal operation and during recovery. The authors focus on the techniques Harp uses to achieve efficient recovery.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Low-Complexity Channel Allocation Scheme for URLLC Traffic (2020)

In this paper, we consider the downlink transmission of URLLC packets requiring very low latency and ultra-reliability. Because of the low latency constraint, the Base Station may not have enough time to acquire the instantaneous Channel State Information (CSI) of the corresponding device and has then to transmit urgent packets immediately in the absence of CSI. To enhance reliability, we explore frequency diversity where a packet can be simultaneously sent over multiple channels. Using a Markov Decision Process framework, we address the problem of dynamic channel allocation to the URLLC devices in absence of instantaneous CSI. More precisely, we define a multi-agent MDP wherein the state of each device is the packet loss rate experienced in the previous time slots and the decision variable is how to split the available orthogonal channels across the devices. We design a new low-complexity algorithm which avoids the exhaustive enumeration of all possible resource allocations and enables significant computational savings compared to the Value Iteration algorithm. We investigate the gap between our proposed low complexity algorithm and the Value Iteration policy. We provide numerical performance results and show that our algorithm can achieve more than 80% of the optimal reward with substantial computational complexity reduction.
Involvement of Phenolic Acids in Short-Term Adaptation to Salinity Stress is Species-Specific among Brassicaceae (2019)

Salinity is a major abiotic stress negatively affecting plant growth and consequently crop production. The effects of short-term salt stress were evaluated on seedlings of three globally important Brassica crops-Chinese cabbage (<i>Brassica rapa</i> ssp. <i>pekinensis</i>), white cabbage (<i>B</i><i>rassica</i> <i>oleracea</i> var. <i>capitata</i>), and kale (<i>B</i><i>rassica</i> <i>oleracea</i> var. <i>acephala</i>)-with particular focus on phenolic acids. The physiological and biochemical stress parameters in the seedlings and the levels of three main groups of metabolites (total glucosinolates, carotenoids, and phenolics) and individual phenolic acids were determined. The salt treatments caused a dose-dependent reduction in root growth and biomass and an increase in stress parameters (Na<sup>+</sup>/K<sup>+</sup> ratio, reactive oxygen species (ROS) and glutathione (GSH)) in all seedlings but most prominently in Chinese cabbage. Based on PCA, specific metabolites grouped close to the more tolerant species, white cabbage and kale. The highest levels of phenolic acids, particularly hydroxycinnamic acids, were determined in the more tolerant kale and white cabbage. A reduction in caffeic, salicylic, and 4-coumaric acid was found in Chinese cabbage and kale, and an increase in ferulic acid levels was found in kale upon salinity treatments. Phenolic acids are species-specific among Brassicaceae, and some may participate in stress tolerance. Salt-tolerant varieties have higher levels of some phenolic acids and suffer less from metabolic stress disorders under salinity stress.
A Cost, Time, and Demographic Analysis of Participant Recruitment and Urine Sample Collection Through Social Media Optimization (2022)

We conducted a nationwide, contactless, urine sample collection through online recruitment in the midst of the COVID-19 pandemic. Results were compared with the samples collected in the clinical setting. Online recruitment can be utilized to collect urine samples rapidly, efficiently, and at a cost per sample that was 20% of an in-person clinic, and without risk of COVID-19 exposure.
Reciprocal repulsions instruct the precise assembly of parallel hippocampal networks (2021)

Mammalian medial and lateral hippocampal networks preferentially process spatial- and object-related information, respectively. However, the mechanisms underlying the assembly of such parallel networks during development remain largely unknown. Our study shows that, in mice, complementary expression of cell surface molecules teneurin-3 (Ten3) and latrophilin-2 (Lphn2) in the medial and lateral hippocampal networks, respectively, guides the precise assembly of CA1-to-subiculum connections in both networks. In the medial network, Ten3-expressing (Ten3+) CA1 axons are repelled by target-derived Lphn2, revealing that Lphn2- and Ten3-mediated heterophilic repulsion and Ten3-mediated homophilic attraction cooperate to control precise target selection of CA1 axons. In the lateral network, Lphn2-expressing (Lphn2+) CA1 axons are confined to Lphn2+ targets via repulsion from Ten3+ targets. Our findings demonstrate that assembly of parallel hippocampal networks follows a "Ten3→Ten3, Lphn2→Lphn2" rule instructed by reciprocal repulsions.
Influence of buoyancy-driven flow on mass transfer in a two-stream microfluidic channel: Introduction of cryoprotective agents into cell suspensions (2012)

A variety of methods have been used to introduce chemicals into a stream or to mix two or more streams of different compositions using microfluidic devices. In the following paper, the introduction of cryoprotective agents (CPAs) used during cryopreservation of cells in order to protect them from freezing injuries and increase viability post thaw is described. Dimethylsulphoxide (DMSO) is the most commonly used CPA. We aim to optimize the operating conditions of a two-stream microfluidic device to introduce a 10% vol/vol solution of DMSO into a cell suspension. Transport behavior of DMSO between two streams in the device has been experimentally characterized for a spectrum of flow conditions (0.7 < Re < 10), varying initial donor stream concentrations, (1% vol/vol < C o < 15% vol/vol) and different flow rate fractions (0.23 < f q < 0.77). The outlet cell stream concentration is analyzed for two different flow configurations: one with the cell stream flowing on top of the DMSO-rich donor stream, and the other with the cell stream flowing beneath the heavy DMSO-laden stream. We establish a transition from a diffusive mode of mass transfer to gravity-influenced convective currents for Atwood numbers (A t ) in the range of (1.7 × 10(-3) < A t < 3.1 × 10(-3)) for the latter configuration. Flow visualization with cells further our understanding of the effect of A t on the nature of mass transport. Cell motion studies performed with Jurkat cells confirm a high cell recovery from the device while underscoring the need to collect both the streams at the outlet of the device and suggesting flow conditions that will help us achieve the target DMSO outlet concentration for clinical scale flow rates of the cell suspension.
Importance of Neuraminidase Active-Site Residues to the Neuraminidase Inhibitor Resistance of Influenza Viruses (2006)

Neuraminidase inhibitors (NAIs) are antivirals designed to target conserved residues at the neuraminidase (NA) enzyme active site in influenza A and B viruses. The conserved residues that interact with NAIs are under selective pressure, but only a few have been linked to resistance. In the A/Wuhan/359/95 (H3N2) recombinant virus background, we characterized seven charged, conserved NA residues (R118, R371, E227, R152, R224, E276, and D151) that directly interact with the NAIs but have not been reported to confer resistance to NAIs. These NA residues were replaced with amino acids that possess side chains having similar properties to maintain their original charge. The NA mutations we introduced significantly decreased NA activity compared to that of the A/Wuhan/359/95 recombinant wild-type and R292K (an NA mutation frequently reported to confer resistance) viruses, which were analyzed for comparison. However, the recombinant viruses differed in replication efficiency when we serially passaged them in vitro; the growth of the R118K and E227D viruses was most impaired. The R224K, E276D, and R371K mutations conferred resistance to both zanamivir and oseltamivir, while the D151E mutation reduced susceptibility to oseltamivir only (approximately 10-fold) and the R152K mutation did not alter susceptibility to either drug. Because the R224K mutation was genetically unstable and the emergence of the R371K mutation in the N2 subtype is statistically unlikely, our results suggest that only the E276D mutation is likely to emerge under selective pressure. The results of our study may help to optimize the design of NAIs.
Faculty Opinions recommendation of LeX/ssea-1 is expressed by adult mouse CNS stem cells, identifying them as nonependymal. (2002)

Adult neural stem cells are rare, and little is known about their unique characteristics, leaving their in vivo identity enigmatic. We show that Lewis X (LeX), a carbohydrate expressed by embryonic pluripotent stem cells, is made by adult mouse subventricular zone (SVZ) stem cells and shed into their environment. Only 4% of acutely isolated SVZ cells are LeX(+); this subpopulation, purified by FACS, contains the SVZ stem cells. Ependymal cells are LeX(-), and purified ependymal cells do not make neurospheres, resolving the controversial claim that these are stem cells. Thus, LeX expression by adult CNS stem cells aids their in vivo identification, allows their enrichment, and raises new questions about the role of this unusual carbohydrate in stem cell biology. PMID: 12372282 Funding information This work was supported by: NINDS NIH HHS, United States Grant ID: R01 NS33529