gebhart/patrepeval huggingface dataset:
Cytokine-Regulated Phosphorylation and Activation of TET2 by JAK2 in Hematopoiesis (2019)

Even though the Ten-eleven translocation (TET) enzymes catalyze the generation of 5-hydroxymethylcytosines required for lineage commitment and subsequent differentiation of stem cells into erythroid cells, the mechanisms that link extracellular signals to TET activation and DNA hydroxymethylation are unknown. We demonstrate that hematopoietic cytokines phosphorylate TET2, leading to its activation in erythroid progenitors. Specifically, cytokine receptor-associated JAK2 phosphorylates TET2 at tyrosines 1939 and 1964. Phosphorylated TET2 interacts with the erythroid transcription factor KLF1, and this interaction with TET2 is increased upon exposure to erythropoietin. The activating JAK2<sup>V617F</sup> mutation seen in myeloproliferative disease patient samples and in mouse models is associated with increased TET activity and cytosine hydroxymethylation as well as genome-wide loss of cytosine methylation. These epigenetic and functional changes are also associated with increased expression of several oncogenic transcripts. Thus, we demonstrate that JAK2-mediated TET2 phosphorylation provides a mechanistic link between extracellular signals and epigenetic changes during hematopoiesis. SIGNIFICANCE: Identification of TET2 phosphorylation and activation by cytokine-stimulated JAK2 links extracellular signals to chromatin remodeling during hematopoietic differentiation. This provides potential avenues to regulate TET2 function in the context of myeloproliferative disorders and myelodysplastic syndromes associated with the JAK2<sup>V617F</sup>-activating mutation.<i>This article is highlighted in the In This Issue feature, p. 681</i>.
Improving data-flow analysis with path profiles (2004)

Data-flow analysis computes its solutions over the paths in a control-flow graph. These paths---whether feasible or infeasible, heavily or rarely executed---contribute equally to a solution. However, programs execute only a small fraction of their potential paths and, moreover, programs' execution time and cost is concentrated in a far smaller subset of hot paths. This paper describes a new approach to analyzing and optimizing programs, which improves the precision of data flow analysis along hot paths. Our technique identifies and duplicates hot paths, creating a hot path graph in which these paths are isolated. After flow analysis, the graph is reduced to eliminate unnecessary duplicates of unprofitable paths. In experiments on SPEC95 benchmarks, path qualification identified 2--112 times more non-local constants (weighted dynamically) than the Wegman-Zadek conditional constant algorithm, which translated into 1--7% more dynamic instructions with constant results.
International consensus statement on allergy and rhinology: Olfaction (2022)

This critical review of the existing clinical olfaction literature provides much needed insight and clarity into the evaluation, diagnosis, and treatment of patients with olfactory dysfunction, while also clearly delineating gaps in our knowledge and evidence base that we should investigate further.
Disrupting insulin signaling in Schwann cells impairs myelination and induces a sensory neuropathy (2019)

Although diabetic mice have been studied for decades, little is known about the cell type specific contributions to diabetic neuropathy (DN). Schwann cells (SCs) myelinate and provide trophic support to peripheral nervous system axons. Altered SC metabolism leads to myelin defects, which can be seen both in inherited and DNs. How SC metabolism is altered in DN is not fully understood, but it is clear that insulin resistance underlies impaired lipid metabolism in many cell types throughout the body via the phosphoinositide 3-kinase/protein kinase b (PKB)/mammalian target of rapamycin (PI3K/AKT/mTOR) pathway. Here, we created an insulin resistant SC by deleting both insulin receptor (INSR) and insulin-like growth factor receptor 1 (IGF1R), to determine the role of this signaling pathway in development and response to injury in order to understand SC defects in DN. We found that myelin is thinner throughout development and adulthood in INSR/IGF1R Schwann cell specific knock out mice. The nerves of these mutant mice had reduced expression of key genes that mediate fatty acid and cholesterol synthesis due to reduced mTOR-sterol regulatory element-binding protein signaling. In adulthood, these mice show sensory neuropathy phenotypes reminiscent of diabetic mice. Altogether, these data suggest that SCs may play an important role in DN and targeting their metabolism could lead to new therapies for DN.
A Novel Online Stator Ground-Wall Insulation Monitoring Scheme for Inverter-Fed AC Motors (2014)

Insulation failures are one of the most common failure modes of ac motors, particularly high-voltage motors. Online monitoring of insulation health of ac motors is important for preventing unexpected outages and minimizing the associated financial losses, particularly in critical applications. Previously, an online ground-wall insulation monitoring technique has already been proposed for six-lead ac motors. In this paper, a novel online ground-wall insulation monitoring scheme is proposed for inverter-fed ac motors. This approach is based on measurement of common-mode insulation leakage current for online capacitance and dissipation factor (C/DF) monitoring. The proposed technique can be applied to both three-lead and six-lead ac motors and can also be extended to monitor the insulation health of the cable connecting the inverter and the motor. The proposed technique is demonstrated in the lab environment and correlated with standard offline C/DF measurements.
Demonstration of segmentation with interactive graph cuts (2005)

We demonstrate a new technique for general purpose interactive segmentation of N-dimensional images. The method creates two segments: “object” and “background”. The technical details can be found in our paper [1] in this proceedings. Below we concentrate on the actual interface. The user can enter seeds via mouse-operated brush of red (for object) or blue (for background) color. The size of the brush can be changed depending on the size of the object. The user should paint some pixels in the object of interest and some in the background. The seeds provide some clues on what the user intends to segment. As soon as initial seeds are entered, the whole image/volume can be segmented automatically. Basically, the algorithm tries to “predict” how the user would want to paint the rest of the image. Segmentation results are presented by highlighting the object and background segments with red and blue colors. Thus, the object segment appears reddish while the background appears bluish. This gives an intuitive feeling that the algorithm completes the painting started by the user. An optimal segmentation can be very efficiently recomputed when the user adds or removes any seeds. This allows the user to correct any result imperfections quickly via very intuitive interactions. If the algorithm makes a mistake, the user can add a stroke of red paint in the bluish segment (or blue paint in the reddish segment). The new segmentation would very quickly repaint the whole image to comply with additional hints from the user. Our method is not sensitive to exact positioning of seeds. Normally, the results would not change in the seeds are moved within the same object in the image or volume. Our method applies to N-D images (volumes). In case of 3D data the seeds are entered in selected representative slices. The information is automatically propagated between the slices because we compute our optimal segmentation directly in the volume. Thus, the whole volume can be segmented based on seeds in a single slice. 2. Examples
Novel evidence that apolipoprotein A-I deficiency is implicated in the pathogenesis of osteoporosis in mice (2014)

Searchable abstracts of presentations at key conferences on calcified tissues ISSN 2052-1219 (online)
Grating-Coupling of Surface Plasmons onto Metallic Tips:  A Nanoconfined Light Source (2007)

We describe and demonstrate a new nanometer-scale broadband light source. It is based on the grating-coupled excitation of surface plasmon polaritons (SPPs) on the shaft of a sharp conical metal taper with a tip radius of few tens of nanometers. Far-field excitation of linear nanoslit gratings results in the resonant generation of SPPs traveling over more than 10 mum to the tip apex and converging to an intense radiative local light spot. Such nanofabricated tips are expected to find various applications in nanospectroscopy, overcoming problems with background illumination in apertureless microscopy.
Mitigating COTS obsolescence in military test (2002)

This paper seeks to identify the causes of obsolescence in military test equipment, specifically in automated test equipment, while offering potential alternatives to reduce the occurrence and impact of the changes required. The analysis and alternatives is at a system level to advocate a proactive approach rather than the reactive approach forced by individual occurrences. The use of automated tools for predictive analysis is emphasized. An approach to reduce the impact of obsolescence is detailed.
A Protein Engineering Approach Differentiates the Functional Importance of Carbohydrate Moieties of Interleukin-5 Receptor α (2011)

Human interleukin-5 receptor α (IL5Rα) is a glycoprotein that contains four N-glycosylation sites in the extracellular region. Previously, we found that enzymatic deglycosylation of IL5Rα resulted in complete loss of IL5 binding. To localize the functionally important carbohydrate moieties, we employed site-directed mutagenesis at the N-glycosylation sites (Asn(15), Asn(111), Asn(196), and Asn(224)). Because Asn-to-Gln mutagenesis caused a significant loss of structural integrity, we used diverse mutations to identify stability-preserving changes. We also rationally designed mutations at and around the N-glycosylation sites based on sequence alignment with mouse IL5Rα and other cytokine receptors. These approaches were most successful at Asn(15), Asn(111), and Asn(224). In contrast, any replacement at Asn(196) severely reduced stability, with the N196T mutant having a reduced binding affinity for IL5 and diminished biological activity because of the lack of cell surface expression. Lectin inhibition analysis suggested that the carbohydrate at Asn(196) is unlikely involved in direct ligand binding. Taking this into account, we constructed a stable variant, with triple mutational deglycosylation (N15D, I109V/V110T/N111D, and L223R/N224Q). The re-engineered protein retained Asn(196) while the other three glycosylation sites were eliminated. This mostly deglycosylated variant had the same ligand binding affinity and biological activity as fully glycosylated IL5Rα, thus demonstrating a unique role for Asn(196) glycosylation in IL5Rα function. The results suggest that unique carbohydrate groups in multiglycosylated receptors can be utilized asymmetrically for function.
Effect of image charges in the drain delay of AlGaN∕GaN high electron mobility transistors (2008)

The drain delay in AlGaN∕GaN submicron high electron mobility transistors (HEMTs) accounts for almost 25% of the total electron delay. This long delay significantly limits the maximum frequency performance and linearity of these devices. This paper studies the origin of this important delay assuming that it is inversely proportional to α, a parameter related to how injected channel electrons image at different contacts in the HEMT. Through analysis and two-dimensional simulations, we have found that α equals 3 in a standard HEMT. This value has been confirmed experimentally through the coupling of Monte Carlo simulations and drain delay measurements.
Decreasing Killed in Action and Died of Wounds Rates in Combat Wounded (2010)

Blackbourne, Lorne H. MD; Czarnik, James MD; Mabry, Robert MD; Eastridge, Brian MD; Baer, David PhD; Butler, Frank MD; Pruitt, Basil Jr MD Author Information
A noise-power-area optimized novel programmable gain and bandwidth instrumentation amplifier for biomedical applications (2017)

In this paper, we are presenting a novel programmable gain and bandwidth instrumentation amplifier (PGB-INA) for biomedical applications. By virtue of its programmable gain and bandwidth, it can measure various bio-potentials such as ECG, EMG, EOG, etc. The proposed PGB-INA also features an extremely low input referred noise (1.34 μVrms within the integration bandwidth of 50 mHz to 11 kHz) and high CMRR (84 dB). The design is fabricated in 180 nm mixed-mode CMOS technology. The PgB-INA provides a measured programmable gain and bandwidth of 30 to 40 dB and 100 Hz to 2.7 kHz, respectively. The PGB-INA occupies die area of only 150 μm × 200 μm and consumes 18.3 μΑ current from 1.8 V supply. Various bio-potentials are measured using the proposed PGB-INA such as ECG, EMG and EOG which are also presented in the paper.
Asymmetric Synthesis of 1,2,3‐Trisubstituted Cyclopentanes and Cyclohexanes as Key Components of Substance P Antagonists. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Resting-State Network Alterations Differ between Alzheimer’s Disease Atrophy Subtypes (2021)

Several Alzheimer's disease (AD) atrophy subtypes were identified, but their brain network properties are unclear. We analyzed data from two independent datasets, including 166 participants (103 AD/63 controls) from the DZNE-longitudinal cognitive impairment and dementia study and 151 participants (121 AD/30 controls) from the AD neuroimaging initiative cohorts, aiming to identify differences between AD atrophy subtypes in resting-state functional magnetic resonance imaging intra-network connectivity (INC) and global and nodal network properties. Using a data-driven clustering approach, we identified four AD atrophy subtypes with differences in functional connectivity, accompanied by clinical and biomarker alterations, including a medio-temporal-predominant (S-MT), a limbic-predominant (S-L), a diffuse (S-D), and a mild-atrophy (S-MA) subtype. S-MT and S-D showed INC reduction in the default mode, dorsal attention, visual and limbic network, and a pronounced reduction of "global efficiency" and decrease of the "clustering coefficient" in parietal and temporal lobes. Despite severe atrophy in limbic areas, the S-L exhibited only marginal global network but substantial nodal network failure. S-MA, in contrast, showed limited impairment in clinical and cognitive scores but pronounced global network failure. Our results contribute toward a better understanding of heterogeneity in AD with the detection of distinct differences in functional connectivity networks accompanied by CSF biomarker and cognitive differences in AD subtypes.
ChemInform Abstract: A Model Study for the Synthesis of the Hexahydrobenzofuran Fragment of the Milbemycins and Avermectins. (1986)

Abstract Das ungesättigte Sulfon (I) liefert über (III) und (IV) die Oxime (V), die bei der Oxidation mit Hypochlorit zu den isomeren kondensierten Oxazolinen (VI)‐(IX) führen.
Compact Fabry-Perot Cavities in x-band with PEC and PMC Boundary Conditions (2007)

Resonator antennas based on Fabry-Perot (FP) cavities are low-profile directive antennas widely studied for moderate or high-gain applications. In contrast to previous studies, we investigate here their capabilities when employed as primary sources of Focal-Array Fed Reflector antennas (FAFR) for space applications in X-band. In addition to standard specifications in terms of bandwidth, return loss and radiation efficiency, one of the main requirements not addressed in prior works consists of the optimization of their aperture efficiency. To this end, we first investigate numerically the radiation performance of pure metallic (PEC) compact FP antennas whose size is in the order of a few wavelengths. Their key features are discussed and compared with the well-known characteristics of electrically large FP antennas. In particular, it is shown that there exists an optimum value for the grid reflectivity in order to maximize the antenna aperture efficiency. Then, a new TEM-mode FP antenna with PMC walls (closely-coupled printed dipoles on a grounded substrate) in H-plane is proposed. This configuration enables one to enhance significantly the aperture efficiency of the antenna as well as to produce an axis-symmetric beam, which is not possible with compact FP cavities with PEC walls.
A low-complexity beamforming algorithm for 3G macro-cellular system to reduce interference from high data rate users (2003)

A beamforming algorithm for a macro cell base station (BS) is proposed. The method has the following three features. Firstly, each direction of arrival (DOA) of waves from mobile terminals to the BS is calculated by the modified Fourier beamformer using a real number correlation vector (RV-Fourier), which greatly reduces complexity. Secondly each DOA is estimated accurately even if there are high power interference waves, applying the technique to subtract the other user's correlation vector. Lastly, nulls in interference directions are formed using the modified directionally constrained minimization of power (DCMP) method, which does not need the derivation of the inverse correlation matrix. In comparison with the conventional recursive least-squares (RLS) method, the proposed method requires a much smaller computational load (about 10-20%). Simulation results show that the tracking performance of the proposed method excels RLS when the terminals are moving fast.
Stem Cell Research & Therapy in 2012 (2012)

Stem Cell Research & Th erapy was launched just over two years ago, with the aim of its becoming the major forum for basic and translational stem cell research and the development of stem cell-based therapies Stem Cell Research & Th erapy is particularly interested in articles that bridge the gap between laboratory and clinic. Th ere are many challenges in bringing stem cell therapies to the clinic in comparison to the translational pathway for traditional pharmaceutical products.
Low-Capacitance and Fast Turn-on SCR for RF ESD Protection (2008)

With the smaller layout area and parasitic capacitance under the same electrostatic discharge (ESD) robustness, silicon-controlled rectifier (SCR) has been used as an effective on-chip ESD protection device in radio-frequency (RF) IC. In this paper, SCR's with the waffle layout structures are studied to minimize the parasitic capacitance and the variation of the parasitic capacitance within ultra-wide band (UWB) frequencies. With the reduced parasitic capacitance and capacitance variation, the degradation on UWB RF circuit performance can be minimized. Besides, the fast turn-on design on the low-capacitance SCR without increasing the I/O loading capacitance is investigated and applied to an UWB RF power amplifier (PA). The PA co-designed with SCR in the waffle layout structure has been fabricated. Before ESD stress, the RF performances of the ESD-protected PA are as well as that of the unprotected PA. After ESD stress, the unprotected PA is seriously degraded, whereas the ESD-protected PA still keeps the performances well.
Development of Peptide Vaccines in Dengue (2018)

Dengue is one of the most important arboviral infections worldwide, infecting up to 390 million people and causing 25,000 deaths annually. Although a licensed dengue vaccine is available, it is not efficacious against dengue serotypes that infect people living in South East Asia, where dengue is an endemic disease. Hence, there is an urgent need to develop an efficient dengue vaccine for this region. Data from different clinical trials indicate that a successful dengue vaccine must elicit both neutralizing antibodies and cell mediated immunity. This can be achieved by designing a multi-epitope peptide vaccine comprising B, CD8+ and CD4+ T cell epitopes. As recognition of T cell epitopes are restricted by human leukocyte antigens (HLA), T cell epitopes which are able to recognize several major HLAs will be preferentially included in the vaccine design. While peptide vaccines are safe, biocompatible and cost-effective, it is poorly immunogenic. Strategies to improve its immunogenicity by the use of long peptides, adjuvants and nanoparticle delivery mechanisms are discussed.
Next-generation multi-fiber ferrule using 165 micron pitch optical fiber (2021)

The continued acceleration of switching capacity and link transmission bandwidth is driving the need for new connectors in next generation optical networks. With 25.6Tb switch ASICs available in 2020 [1], only two years after the introduction of 12.8Tb switching, the industry is now looking to radical new architectures to achieve 51.2Tb switching, including the advent of optics integrated or co-packaged with ASIC technology. The standard 250μm pitch used in multi-fiber ferrules with 125μm cladding diameter optical fiber is physically too large to support the quantity of optical lanes that will be coupled inside the coming switching platforms. This paper describes a next generation MT-style ferrule designed for fibers with 80μm cladding diameter on a pitch of 165μm. By decreasing the pitch from 250μm to 165μm, up to 24 fibers can be placed in a single row between the pins of the MT-16 alignment structure. This tighter pitch enables higher fiber densities coupled directly to or in the proximity optical Tx/Rx photonic tiles. Endface geometry models combined with connector mating normal forces are based on the traditional 250μm pitch of MT-style ferrules. Fiber tip radii, fiber tip coplanarity, ferrule surface endface angles relative to alignment pin bores were measured empirically and documented on the new design. Varied topologies were combined with different mating forces demonstrating effective physical contact for the new ferrule. Mated pairs were monitored for attenuation changes during exposure to industry standard uncontrolled environment temperature cycling. Subsequent specifications for future end face geometry and mating spring force requirements are proposed.
The Effects of Waste Loading on the Durability of Nuclear Waste Glasses (2008)

The durability of Savannah River Plant (SRP) waste forms was assessed for glass containing up to 32 wt% simulated waste oxides. Leach tests included standard MCC-1 static tests and PCT experiments. Leachate solution analysis combined with bulk and surface studies were performed to study low-level waste- glass corrosion as a function of waste loading. Results of this study showed that the durability of the SRP low-level waste glass decreased as waste loading was increased, due to the presence of alkali in the waste. The formation of surface layers may have acted as a barrier to corrosion in glasses of lower waste loading.
Partially Oxidized Graphene/Metallic Single‐Walled Carbon Nanotubes Film‐Coated Electrode for Nanomolar Detection of Dopamine (2015)

Abstract Enriched metallic single‐walled carbon nanotubes (mSWCNTs) were dispersed in aqueous solution of partially oxidized graphene (po‐Gr). As‐prepared po‐Gr/mSWCNTs suspension was used to modify glassy carbon electrode (GCE) surface, which showed high electrocatalytic activity for dopamine (DA) oxidation in pH 7.0 phosphate buffered saline (PBS) solution. Using po‐Gr/mSWCNTs/GCE we could detect DA from 350 to 3600 nM, with a detection limit down to 25 nM in physiological condition (in pH 7.0 PBS); whereas, po‐Gr/GCE (without mSWCNTs) and bare GCE produced measurable signals only at or above 200 nM DA. Thus, the po‐Gr/mSWCNTs film we fabricated is a promising nanomaterial for fabrication of biosensors for nanomolar detection of DA.