gebhart/patrepeval huggingface dataset:
Odor Coding in a Model Olfactory Organ: The<i>Drosophila</i>Maxillary Palp (1999)

Odor coding relies on the activity of different classes of receptor neurons, each with distinct response characteristics. We have examined odor coding in a model olfactory organ, the maxillary palp of Drosophila. This organ contains only 120 olfactory receptor neurons, compartmentalized in sensory hairs called sensilla, and provides an opportunity to characterize all neurons in an entire olfactory organ. Extensive extracellular recordings from single sensilla reveal that the neurons fall into six functional classes. Each of the 60 sensilla houses two neurons, which observe a pairing rule: each sensillum combines neurons of two particular classes, thereby yielding three sensillum types. The sensillum types are intermingled on the surface of the palp, but their distribution is not random. The neurons exhibit diverse response characteristics, providing the basis for an olfactory code. A particular odor can excite one neuron and inhibit another, and a particular neuron can be excited by one odor and inhibited by another. Some excitatory responses continue beyond the end of odor delivery, but responses to most odors terminate abruptly after the end of odor delivery, with some followed by a period of poststimulus quiescence. The specificity of odor response is examined in detail for the neurons of one sensillum, which were found to differ in their relative responses to a homologous series of esters. Adaptation and cross-adaptation are documented, and cross-adaptation experiments demonstrate that the two neurons within one type of sensillum can function independently. The analysis of all neuronal types in this model olfactory organ is discussed in terms of its functional organization and the mechanisms by which it encodes olfactory information.
Abstract LB-058: Linker variation and structure-activity relationship analyses of salicylic, benzoic and hydroxamic acid-based small molecule Stat3 inhibitors (2016)

Abstract Benzoic acid, salicylic acid and hydroxamic acid-based small molecules have been reported that inhibit Stat3 activation. However, the structural basis for their Stat3-inhibitory activities are not clearly defined. To investigate the molecular determinants for activity and to derive structurally optimized analogs of improved pharmacokinetic parameters and potency, we conducted a computer-aided molecule optimization program and synthesized new analogs of the previously reported lead Stat3 inhibitors, BP-1-102 (IC50, 6.8 ± 2.5), SH4-54 (IC50 4.4 ± 0.3), and SH5-07 (IC50 3.9 ± 0.6). All three leads are based on N-methylglycinamide scaffold with its two amine moieties condensed with three different functionalities. The three functionalities or the CH2 group of the glycolamide scaffold were separately modified to generate a series of compounds, some of which show improved potency compared to the corresponding parental compounds. Specifically, H012, H070 and H072 had improved inhibitory activity against Stat3 DNA-binding activity in vitro, with IC50 of 3.0 ± 0.9, 2.4 ± 0.4, and 2.2 ± 0.9 μM, respectively. The replacement of the pentafluorobenzene or the cyclohexylbenzene with other components was detrimental to activity and led to decreased potency of the new analogues, as did the substitution of the benzene of the pTyr-mimetic moiety with heterocyclic components containing nitrogen and oxygen elements. Pharmacokinetic study showed that analog H058 has improved permeability in Caco-2 bidirectional permeability studies, compared to the lower relative permeability of the lead agents. Ala-based analogs, such as H048 and H058, were low in microsomal stability, presumably due to the labile methyl groups of the Ala. Select active analogs inhibited constitutive Stat3 activation and the DNA-binding activity of Stat3 in cancer cells, and they further decreased the growth, colony formation, and migration of human cancer cells harboring persistently active Stat3. Studies together demonstrate a significant progress towards developing a more suitable Stat3 inhibitor with drug-like features. Additional efforts are focused on refining the physicochemical properties to further improve the activity and efficacy and ultimately furnish suitable Stat3-inhibiting candidates for clinical application. Citation Format: Peibin Yue, Francisco Lopez-Tapia, Christine Brotherton-Pleiss, Marcus Tius, James Turkson. Linker variation and structure-activity relationship analyses of salicylic, benzoic and hydroxamic acid-based small molecule Stat3 inhibitors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-058.
Noise considerations in circuit optimization (1998)

Noise can cause digital circuits to switch incorrectly and thus produce spurious results. Noise can also have adverse power, timing and reliability effects. Dynamic logic is particularly susceptible to charge-sharing and coupling noise. Thus, the design and optimization of a circuit should take noise considerations into account. Such considerations are typically stated as semi-infinite constraints. In addition, the number of signals to be checked and the number of sub-intervals of time during which the checking must be performed can potentially be very large. Thus, the practical incorporation of noise constraints during circuit optimization is a hitherto unsolved problem. This paper describes a novel method for incorporating noise considerations during automatic circuit optimization. Semi-infinite constraints representing noise considerations are first converted to ordinary equality constraints involving time integrals, which are readily computed in the context of circuit optimization based on time-domain simulation. Next, the gradients of these integrals are computed by the adjoint method. By using an augmented Lagrangian optimization merit function, the adjoint method is applied to compute all the necessary gradients required for optimization in a single adjoint analysis, no matter how many noise measurements are considered, and irrespective of the dimensionality of the problem. Numerical results are presented.
Fluorescent Probes Based on Nucleophilic Substitution–Cyclization for Hydrogen Sulfide Detection and Bioimaging (2013)

The design, synthesis, properties, and cell imaging applications of a series of 2-pyridyl disulfide based fluorescent probes (WSP1, WSP2, WSP3, WSP4 and WSP5) for hydrogen sulfide detection are reported. The strategy is based on the dual-nucleophilicity of hydrogen sulfide. A hydrogen sulfide mediated tandem nucleophilic substitution-cyclization reaction is used to release the fluorophores and turn on the fluorescence. The probes showed high sensitivity and selectivity for hydrogen sulfide over other reactive sulfur species, including cysteine and glutathione.
Design and Testing of the CubeSat Form Factor Thermal Control Louvers (2019)

As CubeSat and SmallSat missions increase in complexity and power consumption they present innate thermal challenges. Science instruments may require thermal stability while a variety of factors such as high-powered components, sunlight and shadow on orbit, or tight spacecraft layout may produce a wide range of temperatures. The CubeSat Form Factor Thermal Control Louvers are a passive method of stabilizing the thermal environment inside of small spacecraft via miniature thermal louvers. These louvers are a patented design, with a technology demonstration version of the louvers operating correctly in flight on the Dellingr CubeSat in 2018. This paper will describe the methods used to develop and test this technology, as well as the results obtained and how this technology may be used in CubeSat and SmallSat missions.
Gene Therapy Using Muscle-Derived Stem Cells (2004)

Novel molecular techniques such as ex vivo gene therapy and tissue engineering have only recently been introduced to the field of urology. Stem cell-based tissue engineering can be a platform for ex vivo gene therapy, the aim of which is to replace, repair, or enhance the function of damaged tissues or organs. The ex vivo process involves harvesting cells from donors, manipulating the cells in vitro to express genes that would enhance the therapeutic potential of the harvested cells, and injecting the cells back into the donor.
Theoretical overview of the large-area plasma processing system (LAPPS) (2000)

A large-area plasma processing system (LAPPS) is under development at the Naval Research Laboratory. In the LAPPS, the plasma is generated by a sheet electron beam with voltages and current densities of the order of kilovolts and tens of milliamps per cm2. The plasma dimensions are a metre square by a few centimetres thick. The beam is guided by a magnetic field of 50-300 G. Since an electron beam of this type efficiently ionizes any gas, high electron densities of n~1012-1013 cm-3 are easily generated at 30-100 mTorr background pressure. In addition to large area and high electron density, the LAPPS has advantages for plasma processing. These include independent control of ion and free radical fluxes to the surface, very high uniformity, very low electron temperature (Te, {<}1 eV, but can be controllably increased to a desired value) and a geometry that is well suited for many applications. This paper sketches an initial theoretical overview of issues in the LAPPS and compares aspects of the theory to a preliminary experiment.
Electrical Tissue Property Imaging at Low Frequency Using MREIT (2014)

The tomographic imaging of tissue's electrical properties (e.g., conductivity and permittivity) has been greatly improved by recent developments in magnetic resonance (MR) imaging techniques, which include MR electrical impedance tomography (MREIT) and electrical property tomography. When the biological material is subjected to an external electric field, local changes in its electrical properties become sources of magnetic field perturbations, which are detectable by the MR signals. Controlling the external excitation and measuring the responses using an MRI scanner, we can formulate the imaging problem as an inverse problem in which unknown tissue properties are recovered from the acquired MR signals. This inverse problem is nonlinear; it involves the incorporation of Maxwell's equations and Bloch equations during data acquisition. Each method for visualizing internal conductivity and permittivity distributions has its own methodological limitations, and is restricted to imaging only a part of the ensemble or mean tissue structures or states. Therefore, imaging methods can be improved by developing complementary methods that can employ the beneficial aspects of various existing techniques. This paper focuses on recent progress in MREIT and discusses its distinct features in comparison with other imaging methods.
Frame Rate Converter With Pixel-Based Motion Vectors Selection and Halo Reduction Using Preliminary Interpolation (2010)

A new two-image-based method for frame rate conversion is proposed to reduce blocking, halo, and flickering artifacts. For blocking effects, a pixel-based motion vector (MV) selection is suggested based on neighboring block-based motion vectors. For halo reduction, after a preliminary image interpolation, MV at each pixel is re-estimated using the interpolated intensities and the MV of the current pixel and its neighbors constrained in adaptive sliding windows. Experimental results showed that the proposed method outperforms objectively and subjectively in comparison with some existing interpolation techniques.
A three-dimensional electron spin resonance microscope (2004)

An electron spin resonance (ESR) imaging system, capable of acquiring three-dimensional (3D) images with a resolution of ∼10×10×30 μm in a few minutes of acquisition, is presented. This ESR microscope employs a commercial continuous wave ESR spectrometer, working at 9.1 GHz, in conjunction with a miniature imaging probe (resonator+gradient coils), gradient current drivers, and control software. The system can acquire the image of a small (∼1.5×1.5×0.25 mm) sample either by the modulated field gradient method, the projection reconstruction method, or by a combination of the two. A short discussion regarding the resolution of the modulated field gradient method in two-dimensional (2D) and 3D imaging is given. Detailed descriptions of the various system components are provided, along with several examples of 2D and 3D images that demonstrate the capabilities of the system.
Gene probes for the detection of 6-deoxyhexose metabolism in secondary metabolite-producing streptomycetes (1992)

DNA probes were designed from the streptomycin production genes strDELM of Streptomyces griseus involved in the biosynthesis of the 6-deoxyhexose (6DOH) dihydrostreptose which could detect the genomic fragments coding for 6DOH formation in other actinomycetes strains. In about 70% of the 43 strains tested at least one signal could be detected with strD-, strE- or strLM-specific probes. Evidence is presented that the hybridizing genes are mostly clustered and probably engaged in the formation of secondary metabolites. Because of the wide-spread use of 6DOH constituents in natural products these probes should allow to detect a vast array of different secondary metabolic gene clusters in actinomycetes.
Development of an Internally Controlled Real-Time Reverse Transcriptase PCR Assay for Pan-Dengue Virus Detection and Comparison of Four Molecular Dengue Virus Detection Assays (2013)

A number of diagnostic tests are available for dengue virus (DENV) detection, including a variety of nucleic acid amplification tests (NAATs). However, reports describing a direct comparison of different NAATs have been limited. In this study, we report the design of an internally controlled real-time reverse transcriptase PCR (rRT-PCR) that detects all four DENV serotypes but does not distinguish between them (the pan-DENV assay). Two hundred clinical samples were then tested using four different DENV RT-PCR assays: the pan-DENV assay, a commercially produced, internally controlled DENV rRT-PCR (the Altona assay), a widely used heminested RT-PCR, and a serotype-specific multiplex rRT-PCR assay. The pan-DENV assay had a linear range extending from 1.0 to 7.0 log10 cDNA equivalents/μl and a lower limit of 95% detection ranging from 1.7 to 7.6 cDNA equivalents/μl, depending on the serotype. When measured against a composite reference standard, the pan-DENV assay proved to be more clinically sensitive than either the Altona or heminested assays, with a sensitivity of 98.0% compared to 72.3% and 78.8%, respectively (P ≤ 0.0001 for both comparisons). The pan-DENV assay detected DENV in significantly more samples collected on or after day 5 of illness and in a subgroup of patients with detectable anti-DENV IgM at presentation. No significant difference in sensitivity was observed between the pan-DENV assay and the multiplex rRT-PCR, despite the presence of an internal control in the former. The detection of DENV RNA late in the course of clinical illness should serve to lengthen the period during which a confirmed molecular diagnosis of DENV infection can be provided.
Advanced metal-gate/high-&#x03BA; CMOS with small EOT and better high field mobility (2012)

Continuously down-scaling the operation voltage, saving energy, and maintaining high performance are the major challenge for CMOS device. Small 0.95∼1.4 nm equivalent-oxide thickness (EOT) and 1.4∼2.5X better mobility than universal SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> /Si data are achieved in metal-gate/high-κ/Ge CMOS at 1 MV/cm effective field (E <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</inf> ). These excellent performances were achieved by using interface engineering and novel process, to overcome the poor high-κ/Ge interface reaction, low source-drain dopant activation, and n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> /p ohmic contact. The all-Ge CMOS with measured higher electron and hole mobility has irreplaceable merits of much simpler process, lower cost, and potentially higher yield than the InGaAs-nMOS/Ge-pMOS platform for IC manufacture.
Color halftone document segmentation and descreening (2002)

The advent of electronic publishing creates strong interest in converting existing printed documents into electronic formats. During this process, image reproduction problems can occur due to the formation of moire patterns in the screened halftone areas. A wavelet packet based color halftone segmentation algorithm is first designed to locate possible halftone regions based on a decision function. A color halftone descreening technique based on the color sigma filter is proposed which does not assume any a priori knowledge about the halftoning process, making it applicable to any color halftone image. Combined with color halftone segmentation techniques, a complete document processing algorithm for color documents is proposed. Experimental results are offered to illustrate the performance of our algorithm.
Human immunodeficiency virus type 1 replication is blocked prior to reverse transcription and integration in freshly isolated peripheral blood monocytes (1996)

Peripheral blood monocytes are resistant to productive human immunodeficiency virus type 1 (HIV-1) infection in vitro immediately after isolation. No viral cDNA (either early or late transcripts) was detected by PCR in monocytes exposed to virus on the day of isolation. In contrast, in monocytes cultured for as little as 1 day, initiated and completed reverse transcripts were readily detectable within 24 h of infection with both HIV-1(Ba-L) and primary isolates. The levels of initiated, partially completed, and completed viral DNA copies found 24 h after infection increased progressively with time in culture before infection. Unlike quiescent T lymphocytes, there appeared to be no block or delay in the integration of viral DNA into the genome of susceptible cultured monocytes. With an Alu-PCR method designed to specifically detect proviral DNA being used, integration events were found within 24 h of infection in monocytes cultured for a day or more after isolation. No integration signal was found in freshly isolated monocytes up to 7 days following exposure to the virus. Cloning and sequencing of Alu-PCR-amplified DNA confirmed integration in HIV-1-infected cultured monocytes. Our finding that in vitro replication of HIV-1 is clearly blocked prior to the initiation of reverse transcription in freshly isolated peripheral blood monocytes suggests that these cells may not be susceptible to infection in vivo. Further studies to clarify this possibility and the nature of the block to infection should provide useful information for treatment strategies against HIV-1.
An observer based sample detection scheme for atomic force microscopy (2004)

In dynamic mode operation of atomic force microscopes steady state signals like amplitude and phase are typically used for the detection and imaging of sample. Due to the high quality factor of the micro-cantilever probe the corresponding methods are inherently slow. In this paper we present a novel methodology for fast interrogation of sample that exploits the transient signals. A novel method is introduced for the detection of small time scale tip-sample interactions. Simulations and experiments show that the method results in significant increase in bandwidth and resolution as compared to the steady state data based methods.
Multibeam satellites performance analysis in non-uniform traffic conditions (2013)

Multibeam satellite systems are typically designed assuming a uniform traffic demand. However, in reality, the uncertainty of real traffic (i.e. non-spatially-uniform) creates load imbalances among different beams so that some beams work at their maximum, but are still not able to fully meet the traffic demand (overloaded), while others beams use only a fraction of their potential capacity (underloaded). This translates into a situation in which part of the system capacity is left unused, while there is still some demand to be met elsewhere. The overall effect is a serious limitation to the usability of the total system resources. The most intuitive way to address this issue is allocating the available resources (bandwidth, time and power) on demand, depending on the specific traffic conditions.
Ibrutinib Monotherapy in Symptomatic, Treatment-Naïve Patients With Waldenström Macroglobulinemia (2018)

Purpose Ibrutinib is active in previously treated Waldenström macroglobulinemia (WM). MYD88 mutations ( MYD88<sup>MUT</sup>) and CXCR4 mutations ( CXCR4<sup>MUT</sup>) affect ibrutinib response. We report on a prospective study of ibrutinib monotherapy in symptomatic, untreated patients with WM, and the effect of CXCR4<sup>MUT</sup> status on outcome. Patients and Methods Symptomatic, treatment-naïve patients with WM were eligible. Ibrutinib (420 mg) was administered daily until progression or unacceptable toxicity. All tumors were genotyped for MYD88<sup>MUT</sup> and CXCR4<sup>MUT</sup>. Results A total of 30 patients with WM received ibrutinib. All carried MYD88<sup>MUT</sup>, and 14 (47%) carried a CXCR4<sup>MUT</sup>. After ibrutinib treatment, median serum IgM levels declined from 4,370 to 1,513 mg/dL, bone marrow involvement declined from 65% to 20%, and hemoglobin level rose from 10.3 to 13.9 g/dL ( P < .001 for all comparisons). Overall (minor or more than minor) and major (partial or greater than partial) responses for all patients were 100% and 83%, respectively. Rates of major (94% v 71%) and very good partial (31 v 7%) responses were higher and time to major responses more rapid (1.8 v 7.3 months; P = 0.01) in patients with wild-type CXCR4 versus those with CXCR4<sup>MUT</sup>, respectively. With a median follow-up of 14.6 months, disease in two patients (both with CXCR4<sup>MUT</sup>) progressed. The 18-month, estimated progression-free survival is 92% (95% CI, 73% to 98%). All patients are alive. Grade 2/3 treatment-related toxicities in > 5% of patients included arthralgia (7%), bruising (7%), neutropenia (7%), upper respiratory tract infection (7%), urinary tract infection (7%), atrial fibrillation (10%), and hypertension (13%). There were no grade 4 or unexpected toxicities. Conclusion Ibrutinib is highly active, produces durable responses, and is safe as primary therapy in patients with symptomatic WM. CXCR4<sup>MUT</sup> status affects responses to ibrutinib.
Research on a New Type Magnetic Puffer Gas Circuit Breaker (1974)

The magnetic repulsive force which arises between a secondary short circuit ring and a primary coil through which short circuit current flows was used for a new magnetic puffer gas circuit breaker. A floating piston type magnetic puffer circuit breaker showed much success in experiments and the examples of theoretically calculated results together with a fixed piston type magnetic puffer circuit breaker are shown by the authors for the first time. It is proved that the interrupting performance of SF6 gas circuit breakers is much improved with the addition of a simple magnetic drive mechanism as shown in the following.