gebhart/patrepeval huggingface dataset:
Enhanced ubiquitin-dependent degradation by Nedd4 protects against α-synuclein accumulation and toxicity in animal models of Parkinson's disease (2014)

Parkinson's disease is a neurodegenerative disorder, characterized by accumulation and misfolding of α-synuclein. Although the level of α-synuclein in neurons is fundamentally linked to the onset of neurodegeneration, multiple pathways have been implicated in its degradation, and it remains unclear which are the critical ubiquitination enzymes that protect against α-synuclein accumulation in vivo. The ubiquitin ligase Nedd4 targets α-synuclein to the endosomal-lysosomal pathway in cultured cells. Here we asked whether Nedd4-mediated degradation protects against α-synuclein-induced toxicity in the Drosophila and rodent models of Parkinson's disease. We show that overexpression of Nedd4 can rescue the degenerative phenotype from ectopic expression of α-synuclein in the Drosophila eye. Overexpressed Nedd4 in the Drosophila brain prevented the α-synuclein-induced locomotor defect whereas reduction in endogenous Nedd4 by RNAi led to worsening motor function and increased loss of dopaminergic neurons. Accordingly, AAV-mediated expression of wild-type but not the catalytically inactive Nedd4 decreased the α-synuclein-induced dopaminergic cell loss in the rat substantia nigra and reduced α-synuclein accumulation. Collectively, our data in two evolutionarily distant model organisms strongly suggest that Nedd4 is a modifier of α-synuclein pathobiology and thus a potential target for neuroprotective therapies.
The role of FPGAs in a converged future with heterogeneous programmable processors (2011)

The battle of fixed function devices vs. programmable devices has been won by the programmables. The question facing us now is to determine what kinds of programmability to place on next generation systems/devices. Research and development on many applications has shown that different kinds of hardware and software programmability succeed for different application classes: powerful, singlethread-optimized CPUs continue to do very well for many applications; the General Purpose GPU is carving a niche in high throughput, parallel floating point codes in addition to its home turf of graphics; the FPGA is particularly good at variable bit-size computations and data steering, as well as parallel distributed control of networks. Future systems may well need all three types of these types of engines, and perhaps interesting mixtures of them. This is particularly true when we deal with the combined goals of optimizing cost, performance and energy.
Community guidelines for GPCR ligand bias: IUPHAR review 32 (2022)

GPCRs modulate a plethora of physiological processes and mediate the effects of one-third of FDA-approved drugs. Depending on which ligand activates a receptor, it can engage different intracellular transducers. This 'biased signalling' paradigm requires that we now characterize physiological signalling not just by receptors but by ligand-receptor pairs. Ligands eliciting biased signalling may constitute better drugs with higher efficacy and fewer adverse effects. However, ligand bias is very complex, making reproducibility and description challenging. Here, we provide guidelines and terminology for any scientists to design and report ligand bias experiments. The guidelines will aid consistency and clarity, as the basic receptor research and drug discovery communities continue to advance our understanding and exploitation of ligand bias. Scientific insight, biosensors, and analytical methods are still evolving and should benefit from and contribute to the implementation of the guidelines, together improving translation from in vitro to disease-relevant in vivo models.
Label-Aware Ranked Loss for robust People Counting using Automotive in-cabin Radar (2021)

In this paper, we introduce the Label-Aware Ranked loss, a novel metric loss function. Compared to the state-of-the-art Deep Metric Learning losses, this function takes advantage of the ranked ordering of the labels in regression problems. To this end, we first show that the loss minimises when datapoints of different labels are ranked and laid at uniform angles between each other in the embedding space. Then, to measure its performance, we apply the proposed loss on a regression task of people counting with a short-range radar in a challenging scenario, namely a vehicle cabin. The introduced approach improves the accuracy as well as the neighboring labels accuracy up to 83.0% and 99.9%: An increase of 6.7%and 2.1% on state-of-the-art methods, respectively.
Vascular Endothelial Growth Factor Receptor 2 Blockade Disrupts Postnatal Lung Development (2005)

Abstract Vascular endothelial growth factor (VEGF) is necessary for normal postnatal lung development and may underlie the structural lung damage that follows hyperoxic exposure. To determine the individual roles of VEGF receptors (VEGFR) 2 and 1 on postnatal lung growth, neonatal mice were treated with neutralizing antibodies to VEGFR-2 (DC101) or VEGFR-1 (MF1) in the perinatal period. At 1 wk of age, mice treated with DC101 on Days 2 and 4 of life had significantly larger mean alveolar diameters consistent with impaired alveolization. By 2 wk of age, however, perinatally treated DC101 mice had normal-appearing alveolar structure. Mice exposed to perinatal hyperoxia (O2) also had larger mean alveolar diameters at 1 wk of age, but unlike DC101-treated mice, their mitotic index was decreased at 1 wk of age and they had persistent alveolar enlargement beyond the first 2 wk of life. The O2-treated lung also had an increase in caspase 3 at 1 wk of age and significantly greater expression of nitrotyrosine at 2 wk of age. Therefore, VEGFR-2 blockade in the perinatal period disrupts early alveolar development, but the effect is reversible with time, whereas hyperoxic lung injury is associated with ongoing lung structural impairment.
A 3.3V CMOS 10.7MHz 6th–order bandpass ΣΔ modulator with 78dB dynamic range (1999)

A 3.3 V bandpass ΣΔ modulator for IF sampling at 10.7MHz to be used in radio application has been developed. The modulator presents a 6th-order single-loop architecture and features a 78dB DR with a 200kHz signal bandwidth (FM signal), while for a 9kHz signal bandwidth (AM signal) the DR raises to 93dB. The modulator has been implemented in a standard 0.35µm CMOS technology using SC technique and consumes 80mW from a single 3.3V supply.
Figures S1 - S6 from Preclinical Development and First-in-Human Study of KA2507, a Selective and Potent Inhibitor of Histone Deacetylase 6, for Patients with Refractory Solid Tumors (2023)

&lt;p&gt;Supplementary Figures&lt;/p&gt;
A novel fine pitch TSV interconnection method using NCF with Zn nano-particles (2014)

Non-conductive film (NCF) with Zn nano-particles is an effective solution for fine-pitch Cu-pillar/Sn-Ag hybrid bump interconnection in terms of manufacturing process and interfacial reliability. In this study, NCFs with Zn nano-particles of different acidity, viscosity, and curing speed were formulated, and diffused Zn contents in the Cu pillar/Sn-Ag hybrid bumps were measured after 3D TSV chip-stack bonding. Amount of Zn diffusion into the Cu pillar/Sn-Ag bumps increased as the acidity of resin increased, as the viscosity of resin decreased, as the curing speed of resin decreased, and as the bonding temperature increased. Diffusion of Zn nano-particles into the Cu pillar/Sn-Ag bumps are maximized when the resin viscosity became lowered and the solder oxide layer was removed. To analyze the effect of Zn on IMC reduction, NCFs with 0 wt%, 1 wt%, 5 wt%, and 10 wt% of Zn nano-particles were bonded on the test vehicles, and aged at 150°C up to 500 hours. NCF with 10wt% Zn nano-particle showed remarkable suppression in Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> Sn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> and (Cu, Ni) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> Sn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> IMC compared to NCFs with 0 wt%, 1 wt%, and 5 wt% of Zn nano-particles. However, in terms of Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> Sn IMC suppression, which is the most critical goal of this experiment NCFs with 1 wt%, 5wt%, and 10wt% showed an equal amount of IMC suppression. As a result, it was successfully demonstrated that the suppression of Cu-Sn IMCs was achieved by the addition of Zn nano-particles in the NCFs resulting an enhanced reliability performance in the Cu/Sn-Ag hybrid bumps bonding in 3D TSV interconnection.
High Speed Communication Circuits and Systems (PDF) (2006)

6.976 covers circuit and system level design issues of high speed communication systems, with primary focus being placed on wireless and broadband data link applications. Specific circuit topics include transmission lines, high speed and low noise amplifiers, VCO's, and high speed digital circuits. Specific system topics include frequency synthesizers, clock and data recovery circuits, and GMSK transceivers. In addition to learning analysis skills for the above items, students will gain a significant amount of experience in simulating circuits in SPICE and systems in CppSim (a custom C++ simulator).
Enhanced immunotherapeutic profile of oncolytic virus-based cancer vaccination using cyclophosphamide preconditioning (2020)

Despite a sizeable body of research, the efficacy of therapeutic cancer vaccines remains limited when applied as sole agents. By using a prime:boost approach involving two viral cancer vaccines, we were able to generate large tumor-specific CD8<sup>+</sup> T-cell responses in a murine model of disseminated pulmonary melanoma. Significant increases in the number and quality of circulating effector T-cells were documented when low-dose cyclophosphamide (CTX) was administered pre-vaccination to tumor-bearing but not tumor-free hosts. Interestingly, tumor-bearing mice receiving CTX and co-primed with a melanoma differentiation antigen together with an irrelevant control antigen exhibited significantly enhanced immunity against the tumor, but not the control antigen, in secondary lymphoid organs. This result highlighted an increased cancer-specific reactivity of vaccine-induced T-cell responses following CTX preconditioning. Additionally, an acute reduction of the frequency of peripheral regulatory T-cells (Tregs) was noticeable, particularly in the proliferating, presumably tumour-reactive, subset. Enhanced infiltration of lungs with multifunctional T-cells resulted in overt reduction in metastatic burden in mice pretreated with CTX. Despite doubling the median survival in comparison to untreated controls, most vaccinated mice ultimately succumbed to cancer progression. However, preconditioning of the virus-based vaccination with CTX resulted in a remarkable improvement of the therapeutic activity leading to complete remission in the majority of the animals. Collectively, these data reveal how CTX can potentiate specific cellular immunity in an antigen-restricted manner that is only observed in vaccinated tumor-bearing hosts while depleting replicating Tregs. A single low dose of CTX enhances antitumor immunity and the efficacy of this potent prime:boost platform by modulating the kinetics of the vaccine-specific responses. Clinical assessment of CTX combined with next-generation cancer vaccines is indicated.
Saturated Two-Photon Resonance Ionization ofHe(2S1) (1975)

We have developed a photoionization method for complete conversion of a quantum-selected population to ionization, making possible sensitive and absolute measurement of the selected populations in a gas. Each photoionization involves the absorption of two photons (from a pulsed dye laser), one of which is resonant with an intermediate state. In this demonstration we measured the absolute number of $\mathrm{He}(2^{1}S)$ states per ion pair following interaction of pulses of 2-MeV protons with He.
Deformability of ascending thoracic aorta aneurysms assessed using ultrafast ultrasound and a principal strain estimator: In vitro evaluation and in vivo feasibility (2022)

The proposed principal strain estimator showed an ability to potentially assess TAA deformability, which may provide an individualized and reliable evaluation method for TAA rupture risk assessment.
Oscillating Pulse Generator Based on a Nonlinear Inductive Line (2013)

A chain of cascading LC sections consisting of series nonlinear inductors and parallel linear capacitors can be used to generate oscillating pulses. When a rectangular pulse is injected into the input of such a nonlinear inductive line (NLIL), the pulse undergoes modulation and exits at the output with oscillations in the waveform. This paper describes the implementation of high-voltage NLILs using commercial-off-the-shelf components. A pulser comprising of a storage capacitor and a fast semiconductor switch is used to provide the input pulse with approximate rectangular pulse shape. The design of the NLIL, which is a type of nonlinear lumped element transmission line (NLETL), is based on a NLETL circuit model developed earlier in-house. The nonlinear inductors made of ferrites are modeled using a simplified form of the Landau-Lifshitz-Gilbert (LLG) equation. A simple novel approach is proposed to determine the characteristic parameters in the LLG equation. Simulation results from the NLETL model are compared to the experimental results, and analyses on the voltage modulation and frequency content of the output pulses are performed. The use of crosslink capacitors in the line to modify the dispersive characteristics to enhance the performance is also investigated. With the results, the conditions and trends for producing oscillating pulses in NLILs are discussed.
Cambits (2017)

Multiple computational cameras can be assembled from a common set of imaging components.
22.4: Synthesis of Host Materials for Blue Phosphorescent Organic Light Emitting Diodes (OLEDs) with High Efficiency and Low Driving Voltage (2015)

Blue host materials for phosphorescent organic light‐emitting diodes (PHOLEDs) were synthesized with carbazole as a donor moiety and a‐carboline as an accepter moiety to assign bipolar property. Synthesized carbazole‐carboline core was modified with benzonitrile, phenyl and carbazole to control charge transport property. The host materials showed high triplet energy above 2.85 eV, and their highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital energy levels (LUMO) were −5.90/−2.79, −5.90/−2.72 and −5.89/−2.67 eV, respectively, depending on the substituent of the core structure. Maximum quantum efficiencies of 23.4%, 19.6% and 17.4% were obtained with low driving voltage in blue PHOLEDs using the new host materials.
The Microbiota Promotes Skin Allograft Rejection. (2014)

The kinetics of transplant rejection are determined both by genetic and environmental factors. One potential environmental factor that is gaining wide attention as modulating immune responses is the microbiota, the collection of microbes that inhabit body surfaces; but whether the microbiota influences alloresponses is not known. Moreover, commensal bacteria have been shown to promote both effector and regulatory T cell responses locally and systemically such that whether the microbiota would exacerbate or dampen alloreactivity cannot be anticipated. To address this question, we transplanted minor mismatched skin grafts bearing H-Y antigens into female mice, using donors and recipients that were either both germ-free (GF) or both conventional mice treated with broad spectrum antibiotics prior to transplantation. Whereas GF mice lacked microbial colonization, antibiotic-treated mice showed a marked reduction in bacterial diversity of their intestinal and cutaneous flora, with relative expansion of Lactobacillales, but no decrease in bacterial load. Mean skin allograft survival more than doubled in either GF or antibiotic-treated conventional mice compared to controls. Colonization of GF mice with the microbiota of conventional mice through gavage of fecal material restored faster rejection kinetics, confirming the causal role of the commensal flora in promoting graft rejection. Adoptive transfer of CFSE-labeled CD4+ anti-HY Marilyn T cells into antibiotic- and control-treated mice revealed reduced proliferation of graft-specific T cells in the draining lymph nodes and graft of antibiotic-treated animals. In addition, the proportion of IFN-g producing T cells in the graft was also reduced. Together, these data suggest decreased priming of allogeneic T cells when the diversity of resident bacterial communities is diminished. This effect is not due to a reduction in bacterial load and associated reduction in microbe-associated molecular pattern signaling; rather, the effect is caused by loss of taxon-specific host-microbe interactions. This study illustrates the profound systemic effects of the microbial environment in transplant recipients and points to the microbiota as a potential therapeutic target for enhancing graft acceptance.
Deep Learning for the Degraded Broadcast Channel (2019)

Machine learning has shown promising results for communications system problems. We present results for using deep auto-encoders for the multiuser degraded broadcast channel. The auto encoder is able to learn to communicate on this channel using superposition coding. Additionally, the deep neural net is also able to determine a bit labeling and optimize the per user power allocation that depends on the per user SNR.
Two-phase concurrent sensing and transmission scheme for full duplex cognitive radio (2016)

Among several potential applications of Full- Duplex (FD) technology, FD Cognitive Radio (CR) communication is one important area where FD can provide several advantages and possibilities such as concurrent sensing and transmission, improved sensing efficiency and the secondary throughput. However, the main challenge is to mitigate the harmful effects of the residual Self-Interference (SI) which depends on the SI mitigation capability of the employed technique. One way to mitigate this effect is to control the transmit power of the CR node, however, this power control over the entire frame duration results in a power- throughput tradeoff. In this context, we propose a novel Two-Phase Concurrent Sensing and Transmission (2P-CST) framework in which a CR performs concurrent sensing and transmission for a certain fraction of the frame duration by employing a power control mechanism and for the remaining fraction of the frame duration, the CR only transmits with the full power. The proposed framework allows the flexibility to optimize the sensing time and the transmit power in order to maximize the achievable throughput of the FD-CR system. Our results demonstrate that the proposed 2P-CST FD transmission strategy provides better performance in terms of the achievable throughput than the conventional Periodic Sensing and Transmission (PST) and CST techniques.
Improving the Figure-of-Merit of Integrated Solid-State Diodes through the Use of Nanostructured Porous Silicon (2018)

Here, we report on the use of nanostructured porous-silicon (PS) technology as an alternative to standard technologies to increase the breakdown voltage VBR of silicon-based integrated solid-state diodes, while leaving the on-state resistance Ron unaltered. Specifically, we show that integration of nanostructured porous silicon in the high-field regions of a standard diode allows a significant increase of the breakdown voltage (VBR > 65 V) to be achieved with respect to a reference diode (VBR = 25 V) under reverse-bias operation. On the other hand, the electrical characteristics of the diode under forward-bias operation are not affected by the presence of nanostructured PS, with Ron changing of only a few percent. If we define as figure-of-merit (FoM) the ratio VBR/RON, the presence of PS allows the FoM to be improved of a factor of 3. We argue that the nanostructured nature of PS reduces the mean-free path of charge carriers accelerated in high-field regions of the diode reducing, in turn, carrier velocity developed for a given applied voltage under reverse-bias operation.
Quantitative selection of media benchmarks (2002)

Over the last decade, significant advances have been made in compilation technology and microprocessor architectures for capitalizing on instruction-level parallelism (ILP). While most of the processors containing superscalar, VLIW and SIMD structures that are well matched to the needs and capabilities of the ILP compilers are targeted at embedded applications, the majority of all ILP compilation work has been conducted in the context of general-purpose computing. As a consequence, there currently exists a gap between the compiler community and embedded application developers. We present a quantitative benchmark selection and validation technique to close the gap. It is based on more quantitatively rigorous metrics to accurately measure usefulness and effectiveness of benchmarks. We assemble a collection of DSP and communication applications written in a high-level language. An experimental selection of benchmarks from the collected applications is conducted and its applicability and usefulness are verified through an application specific system synthesis.
Cell type–specific channelrhodopsin-2 transgenic mice for optogenetic dissection of neural circuitry function (2011)

Available in PMC 2011 October 12.
Proton implantation for electrical insulation of the InGaAs/InAlAs superlattice material used in 8–15 μm-emitting quantum cascade lasers (2017)

We demonstrate the conversion of lattice-matched InGaAs/InAlAs quantum-cascade-laser (QCL) active-region material into an effective current-blocking layer via proton implantation. A 35-period active region of an 8.4 μm-emitting QCL structure was implanted with a dose of 5 × 1014 cm−2 protons at 450 keV to produce a vacancy concentration of ∼1019 cm−3. At room temperature, the sheet resistance, extracted from the Hall measurements, increases by a factor of ∼240 with respect to that of an unimplanted material. Over the 160–320 K temperature range, the activation energy of the implanted-material Hall sheet-carrier density is 270 meV. The significant increase in room-temperature sheet resistance indicates that upon implantation deep carrier traps have been formed in the InAlAs layers of the superlattice. Fabricated mesas show effective current blocking, at voltages ≥10 V, up to at least 350 K. Thus, the implanted InGaAs/InAlAs superlattices are highly resistive to at least 350 K heat sink temperature. Such implanted material should prove useful for effective current confinement in 8–15 μm-emitting InP-based single-emitter QCL structures as well as in resonant leaky-wave coupled phase-locked arrays of QCLs.