gebhart/patrepeval huggingface dataset:
Phosphoproteomic Analysis of Dopamine D2 Receptor Signaling Reveals Interplay of G Protein- and β-Arrestin-Mediated Effects (2022)

Leveraging biased signaling of G protein-coupled receptors has been proposed as a promising strategy for the development of drugs with higher specificity. However, the consequences of selectively targeting G protein- or β-arrestin-mediated signaling on cellular functions are not comprehensively understood. In this study, we utilized phosphoproteomics to gain a systematic overview of signaling induced by the four biased and balanced dopamine D2 receptor (D<sub>2</sub>R) ligands MS308, BM138, quinpirole, and sulpiride in an in vitro D<sub>2</sub>R transfection model. Quantification of 14,160 phosphosites revealed a low impact of the partial G protein agonist MS308 on cellular protein phosphorylation, as well as surprising similarities between the balanced agonist quinpirole and the inverse agonist sulpiride. Analysis of the temporal profiles of ligand-induced phosphorylation events showed a transient impact of the G protein-selective agonist MS308, whereas the β-arrestin-preferring agonist BM138 elicited a delayed, but more pronounced response. Functional enrichment analysis of ligand-impacted phosphoproteins and treatment-linked kinases confirmed multiple known functions of D<sub>2</sub>R signaling while also revealing novel effects, for example of MS308 on sterol regulatory element-binding protein-related gene expression. All raw data were deposited in MassIVE (MSV000089457).
<title>Characterizing electroactive polymers for use in robotic surgical instruments</title> (2002)

The popularity of minimally invasive surgical procedures over traditional open procedures motivates us to develop new instruments that address the limits of existing technology and enable more widespread use of minimally invasive approaches. Robotic surgical instruments have the potential to provide improved dexterity and range of motion within the confines of the human body when compared with manually actuated instruments. The high strain response and elastic energy density of electron-irradiated P(VDF-TrFE) make it a candidate actuator material for robotic instruments that provide electronic mediation and multiple degrees of freedom of tip movement. We are currently studying both active and passive properties of P(VDF-TrFE) with the goal of constructing a mathematical model of the material's behavior. Studies have been conducted on 15 micron thick film samples in rolled and rolled-flattened configurations. Passive properties can be represented by a 5 parameter viscoelastic model with two time constants on the order of ten and 200 seconds. Active responses were found to have strong dependence upon field and modest dependence upon load. We suggest means by which the active and passive responses can be combined in a model of steady-state response that would be of value in positioning tasks. The time course of the active response appears to contain components on two time scales, but further studies are required to characterized it in more detail.
Broadband absorption enhancement in ultra-thin crystalline Si solar\n cells by incorporating metallic and dielectric nanostructures in the back\n reflector (2013)

We propose a back-reflecting scheme in order to enhance the maximum\nachievable current in one micron thick crystalline silicon solar cells. We\nperform 3-dimensional numerical investigations of the scattering properties of\nmetallic nanostructures located at the back side, and optimize them for\nenhancing absorption in the silicon layer. We validate our numerical results\nexperimentally and also compare the absorption enhancement in the solar cell\nstructure, both with quasi-periodic and random metallic nanostructures. We have\nlooked at the interplay between the metallic nanostructures and an integrated\nback-reflector. We show that the combination of metallic nanoparticles and a\nmetallic reflector results in significant parasitic absorption. We compared\nthis to another implementation based on titanium dioxide nanoparticles which\nact as a lambertian reflector of light. Our simulation and experimental results\nshow that this proposed configuration results in reduced absorption losses and\nin broadband enhancement of absorption for ultra-thin solar cells, paving the\nway to an optimal back reflector for thin film photovoltaics.\n
Supplementary Table 2 from A <i>Survivin</i> Gene Signature Predicts Aggressive Tumor Behavior (2023)

Supplementary Table 2 from A &lt;i&gt;Survivin&lt;/i&gt; Gene Signature Predicts Aggressive Tumor Behavior
A Recovery Conscious Framework for Fault Resilient Storage Systems (2007)

In this paper we present a recovery-conscious framework for&#13;\nimproving the fault resiliency and recovery efficiency of highly&#13;\nconcurrent embedded storage software systems. Our framework&#13;\nconsists of a three-tier architecture and a suite of recovery&#13;\nconscious techniques. In the top tier, we promote fine-grained&#13;\nrecovery at the task level by introducing recovery groups to&#13;\nmodel recovery dependencies between tasks. At the middle tier&#13;\nwe develop highly effective mappings of dependent tasks to processor&#13;\nresources through careful tuning of recovery efficiency&#13;\nsensitive parameters. At the bottom tier, we advocate the use of&#13;\nrecovery-conscious scheduling by careful serialization of dependent&#13;\ntasks, which provides high recovery efficiency without&#13;\nsacrificing system performance. We develop a formal model&#13;\nto guide the understanding and the development of techniques&#13;\nfor effectively mapping fine-grained tasks to system resources,&#13;\naiming at reducing the ripple effect of software failures while&#13;\nsustaining high performance even during system recovery. Our&#13;\ntechniques have been implemented on a real industry-standard&#13;\nstorage system. Experimental results show that our techniques&#13;\nare effective, non-intrusive and can significantly boost system&#13;\nresilience while delivering high performance.
Nanotechnological approaches for pentamidine delivery (2022)

Pentamidine (PTM), which is a diamine that is widely known for its antimicrobial activity, is a very interesting drug whose mechanism of action is not fully understood. In recent years, PTM has been proposed as a novel potential drug candidate for the treatment of mental illnesses, myotonic dystrophy, diabetes, and tumors. Nevertheless, the systemic administration of PTM causes severe side effects, especially nephrotoxicity. In order to efficiently deliver PTM and reduce its side effects, several nanosystems that take advantage of the chemical characteristics of PTM, such as the presence of two positively charged amidine groups at physiological pH, have been proposed as useful delivery tools. Polymeric, lipidic, inorganic, and other types of nanocarriers have been reported in the literature for PTM delivery, and they are all in different development phases. The available approaches for the design of PTM nanoparticulate delivery systems are reported in this review, with a particular emphasis on formulation strategies and in vitro/in vivo applications. Furthermore, a critical view of the future developments of nanomedicine for PTM applications, based on recent repurposing studies, is provided. Created with BioRender.com.
Transmit beamforming (2008)

The capability to perform adaptive transmit beamforming is provided in the 802.11n standard. With transmit beamforming (TxBF), we apply weights to the transmitted signal to improve reception. The weights are adapted from knowledge of the propagation environment or channel state information (CSI). Since by definition transmit beamforming weights are derived from channel information, spatial expansion as defined in Section 6.2 is not considered transmit beamforming.
Successive bit loading scheme (2009)

A new bit loading procedure with a successive loading structure is presented. The optimisation criterion of this scheme is to minimise the bit error rate (BER). This bit loading scheme is applied to an orthogonal frequency division multiplexing (OFDM) transmission system. Based on the measured signal-to-noise ratio (SNRn) values per subcarrier a successive loading structure is developed where the next bit is always loaded onto that subcarrier i which has the lowest BER and maximum remaining SNRi value.
S3352 Gut Microbiome 6 Months After Fecal Microbiota Transplant (FMT) in an Adolescent With Autism Using Familial Donor (2022)

Introduction: Autism affects 1/40 to 1/100 children in America and worldwide. Autism Spectrum disorder (ASD) is a varied set of neurobehavioral changes characterized by distinct, repetitive behaviors along with impaired socialization and communication. Several studies point to gut dysbiosis present in these children, leading to intestinal microbiota transplant as a therapeutic option. Studies by Kang, Adams, and Borody et al. showed a 50% regression of neurological symptoms in children 2 years post-transplant. Cases show more improvement in younger patients, suggesting early treatment with a better donor, such as a family member, especially in the older ASD patients. Case Description/Methods: Fecal matter from a healthy sibling (15 year old sister as donor) was infused via colonoscopy into the subject’s gastrointestinal tract following a protocol approved by FDA as an Investigational New Drug. This study was IRB approved. Fecal samples were collected at baseline (patient and donor) and then from the patient at week 5, and month 3 and 6. Metagenomic Next Generation Sequencing was performed on fecal samples, where DNA samples were extracted and normalized for library downstream fabrication using Shotgun methodology. There were marked improvements in the patients’ gut microbiome post-transplant. Compared to baseline, there was a decrease in relative abundance of phylum Proteobacteria from 49% to 1.3%. Over the 6 months a significant increase was noted post-transplant in phylum Actinobacteria (0.012% to 2.5%) and specifically genus bifidobacteria ( 0.0% to 1.9%). Species Lactobacillus animalis, absent in the donor, disappeared in the recipient (from 58% to 0.0%) after transplant. Shannon Index of bacterial diversity significantly improved (2.2 to 6.2) almost matching donor who was 6.7. Clinically, the patient progressed from aggressive to calm and said his first 2 words “mama” and “baba” after 1 month. Childhood Autism Rating Scale (CARS) testing is underway, but given recent nature of the implant and subject’s age (19 yrs.) substantial changes are not yet expected. Discussion: This is the first case demonstrating implantation of microbes from a familial donor (sister) to an adolescent patient (brother) with Autism. Although early in clinical assessment, this case demonstrates disappearance of an overabundant microbe (L. Animalis) and restoration of phyla and species missing or in low numbers in the autistic patient when compared to his sister.
Demonstration of inverse acoustic band gap structures in AlN and integration with piezoelectric contour mode transducers (2009)

This paper presents the first design and demonstration of a novel inverse acoustic band gap (IABG) structure in aluminum nitride (AlN) and its direct integration with piezoelectric contour-mode transducers. The experimental results indicate that the IABG structure has a stop band from 185 MHz to 240 MHz and is centered around 219 MHz with maximum rejection of 30 dB. The ABG-induced phonon scattering causes a frequency band gap that prohibits the propagation of certain acoustic wavelengths. In this work, the IABG unit cell consists of a high acoustic velocity (V) center material, which is formed by 2-mum-thick AlN sandwiched by 200-nm-thick platinum (Pt) and is held by four thin tethers and surrounded by a low acoustic velocity material (air). This cell arrangement enlarges the frequency band gap and eases the requirements on the thickness (d) to lattice constant (a) ratio, which was imposed by previous ABG demonstration in the very high frequency range. The finite element method (FEM) analysis indicates that the IABG can produce a gap-to-midgap ratio of 13.5% even when the d/a ratio is as small as 0.23. This advantage further allows the direct integration of the IABG with high frequency bulk acoustic wave (BAW) transducers.
Central scars in primary liver tumors: MR features, specificity, and pathologic correlation. (1989)

Tumor scars were identified at pathologic study and magnetic resonance (MR) imaging in ten of 17 (59%) primary liver tumors (nine hepatocellular carcinomas, four giant hemangiomas, two hepatic adenomas, and two cases of focal nodular hyperplasia). Histopathologic examination revealed three types of scar tissue. Inflammatory scars (n = 4), with edema, necrosis, hypercellularity, and loose fibrous tissue, appeared hypointense relative to liver on T1-weighted images and hyperintense on T2-weighted images. Vascular scars (n = 3), predominantly composed of vascular channels traversing collagenous tissue, showed MR features similar to those of inflammatory scars. Collagenous scars (n = 3) appeared hypointense relative to liver on both T1-weighted and T2-weighted images. Central tumor scars are a frequent but nonspecific feature of both benign and malignant primary liver tumors.
Comparison of a branched spike wheat with the cultivars Neepawa and HY320 for grain yield and yield components (1992)

Branched-spike spring wheat (Triticum turgidum L.) genotypes are periodically promoted in western Canada as having very high grain yield capacity. These "Miracle" wheats tend to have a low tillering capacity and may require higher plant populations in order to achieve maximum grain yield. This study was conducted to critically evaluate the high-yield claims of a branched-spike wheat (BSW) and to determine whether this cultivar has a higher optimum seeding rate requirement than the spring wheat (Triticum aestivum L.) cultivars Neepawa and HY320. The three cultivars were seeded at rates of 150, 250, 350, 450, and 550 seeds m −2 in each of three experiments: two dryland and one irrigated. Averaged over experiments and seeding rates the BSW yielded 45% less than the conventional cultivars. Significant (P &lt; 0.05) cultivar × experiment cross-overs were detected for spikes m −2 , spikelets spike −1 , and kernels spike −1 . BSW and HY320 switched ranks for spikes m −2 , spikelets spike −1 and kernels spike −1 in 1988 and 1989. In 1988, on average, BSW produced 230% as many fertile spikelets as the other cultivars, but 40% fewer spikelets in 1989. Similarly, BSW produced more kernels spike −1 than Neepawa and HY320 in 1988 while the reverse was observed in 1989. The three cultivars responded differently to seeding rate, as indicated by significant (P &lt; 0.01) cultivar × seeding rate interaction for spikelets spike −1 and kernel weight. Neither of these interactions involved significant changes in cultivar rank from one seeding rate to the next. BSW yielded less grain than either Neepawa or HY320, regardless of seeding rate. Attempts to increase the grain yield of a BSW cultivar by manipulating yield components via increased seeding rates were not successful.Key words: Branched-spike, spring wheat, seeding rate, Triticum turgidum L.
New technology in immunology (PP-063) (2010)

Metabolic syndrome is a major risk factor of cardiovascular events. Obese visceral adipose tissue remodeling and malfunctioning based on chronic inflammation and local immunological changes plays a central role. To assess dynamic interplay between multiple cell-types in obese adipose, a visualization technique in vivo was therefore developed to reveal the underlying multi-cellular and molecular mechanisms of obesity. In vivo imaging revealed close spatial and temporal interrelationships between angiogenesis and adipogenesis in obese adipose in inflammatory cell clusters including inflammatory "M1" macrophages (2007 Diabetes). Increased leukocyte-platelet-endothelial cell interactions in the microcirculation of obese adipose were observed, a hallmark of inflammation (2008 J Clin Invest). We also found that large numbers of CD8+ effector T cells infiltrated into obese adipose. The infiltration by CD8+ Tcells preceded the accumulation of macrophages, and immunological and genetic depletion of CD8+ Tcells reduced macrophage infiltration and adipose tissue inflammation, and ameliorated systemic insulin resistance. Coculture and other in vitro experiments revealed the vicious interactions between CD8+ T cells, macrophages and adipose tissue. Our findings suggest that obese adipose tissue activates CD8+ T cells, which in turn promote the recruitment and activation of macrophages, thereby initiating and maintaining inflammatory cascades in obese adipose tissue. Infiltration by CD8+ T cells is, thus, essential for the initiation and development of adipose inflammation (2009 Nat Med). Our results clearly demonstrated the power of our imaging technique to analyze complex immunological cellular interplays in vivo and to evaluate new therapeutic interventions against them.
Transition from Long-Range to Short-Range Energy Transfer through Donor Migration in Garnet Hosts (2011)

We demonstrate that the mechanism for nonradiative energy transfer, a critical aspect in many optical systems, can switch from a longer-range dipole−dipole mechanism to a short-range exchange mechanism through energy migration between donors. This transition significantly increases energy transfer rates and is analyzed using measurements of Tb3+(5D4)→Ce3+(5d1) energy transfer as a function of Tb3+ concentration in (Lu,Tb)3Al5O12:Ce3+ garnet phosphors. The additional short-range energy transfer is assigned to exchange by the analysis of the migration and trapping rates as well as estimates of the relevant exchange integrals.
Occlusion Boundary Detection via Deep Exploration of Context (2016)

Occlusion boundaries contain rich perceptual information about the underlying scene structure. They also provide important cues in many visual perception tasks such as scene understanding, object recognition, and segmentation. In this paper, we improve occlusion boundary detection via enhanced exploration of contextual information (e.g., local structural boundary patterns, observations from surrounding regions, and temporal context), and in doing so develop a novel approach based on convolutional neural networks (CNNs) and conditional random fields (CRFs). Experimental results demonstrate that our detector significantly outperforms the state-of-the-art (e.g., improving the F-measure from 0.62 to 0.71 on the commonly used CMU benchmark). Last but not least, we empirically assess the roles of several important components of the proposed detector, so as to validate the rationale behind this approach.
The mechanism of interaction between natural laminar hydrosilicates and friction surfaces (2009)

Analytical results are presented regarding how powder-like laminar hydrosilicates of the serpentinite type interact with the surfaces of components in tribointerfaces. The greatest amount of attention is paid to the processes of the formation of protective cermet layers on friction surfaces due to the atomic and molecular structure of laminar hydrosilicates.
Immunohistochemical localization of adenosine 5`-triphosphate-gated ion channel P2X2 receptor subunits in adult and developing rat cochlea (2000)

Substantial in vitro and in vivo data support a role for extracellular adenosine 5;-triphosphate (ATP) and associated P2 receptors in cochlear function. However, the precise spatiotemporal distribution of the involved receptor protein(s) has not been determined. By using a specific antiserum and immunoperoxidase labeling, the tissue distribution of the P2X(2) subunit of the ATP-gated ion channel was investigated. Here, we describe the first extensive immunohistochemical mapping of P2X(2) receptor subunits in the adult and developing rat cochlea. In the adult, immunoreactivity was observed in most cells bordering on the endolymphatic compartment (scala media), particularly in the supporting cells. Hair cells were not immunostained by the P2X(2) antiserum, except for outer hair cell stereocilia. In addition, weak immunolabeling was observed in some spiral ganglion neurons. P2X(2) receptor subunit protein expression during labyrinthine ontogeny was detected first on embryonic day 19 in the spiral ganglion and in associated nerve fibers extending to the inner hair cells. Immunostaining also was observed underneath outer hair cells, and, by postnatal day 6 (P6), intense immunolabeling was seen in the synaptic regions of both types of hair cell. Supporting cells of the sensory epithelium were labeled at P0. This labeling became most prominent from the onset of cochlear function (P8-P12). Conversely, expression in the vascular stria declined from this time. By P21, the pattern of immunolabeling was similar to that found in the adult. The localization and timing of P2X(2) immunoreactivity suggest involvement of extracellular ATP and associated ATP-gated ion channels in important physiological events, such as inner ear ontogeny, sound transduction, cochlear micromechanics, electrochemical homeostasis, and auditory neurotransmission.
Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization (2017)

A novel data-independent acquisition (DIA) method incorporating a scanning quadrupole in front of a collision cell and orthogonal acceleration time-of-flight mass analyzer is described. The method has been characterized for the qualitative and quantitative label-free proteomic analysis of complex biological samples. The principle of the scanning quadrupole DIA method is discussed, and analytical instrument characteristics, such as the quadrupole transmission width, scan/integration time, and chromatographic separation, have been optimized in relation to sample complexity for a number of different model proteomes of varying complexity and dynamic range including human plasma, cell lines, and bacteria. In addition, the technological merits over existing DIA approaches are described and contrasted. The qualitative and semiquantitative performance of the method is illustrated for the analysis of relatively simple protein digest mixtures and a well-characterized human cell line sample using untargeted and targeted search strategies. Finally, the results from a human cell line were compared against publicly available data that used similar chromatographic conditions but were acquired with DDA technology and alternative mass analyzer systems. Qualitative comparison showed excellent concordance of results with >90% overlap of the detected proteins.
Architectural implications of bit-level computation in communication applications (2002)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.