gebhart/patrepeval huggingface dataset:
Reliability testing of Cu-Sn intermetallic micro-bump interconnections for 3D-device stacking (2010)

In this work, two different reliability experiments, thermal cycling and electromigration, are performed on fully packaged Si-to-Si stacks bonded with Cu-Sn intermetallic (IMC) micro-bumps. These experiments investigate both the more critical thermo-mechanical behavior as well as the expected positive thermal-electrical behavior. The Cu-Sn IMC bumps survive thermal cycling for more than 3900 cycles between −40 and 125°C with 1 hour per cycle. The resistance to electromigration is strongly dependant on the used Sn thickness and shows an improved performance for thinner Sn samples (3.5µm) compared to thicker Sn (8µm). In either case, IMC bumps outperform standard solder flip chip bumps.
Direct laser writing of three-dimensional photonic crystals in high index of refraction chalcogenide glasses (2005)

We present a two-step method for the direct fabrication of functional three-dimensional photonic crystals in high index of refraction (n=2.45) arsenic-sulphur based thin films. Complete fabrication cycles can be as short as a few hours.
Saccharomyces cerevisiae Ebs1p is a putative ortholog of human Smg7 and promotes nonsense-mediated mRNA decay (2007)

The Smg proteins Smg5, Smg6 and Smg7 are involved in nonsense-mediated RNA decay (NMD) in metazoans, but no orthologs have been found in the budding yeast Saccharomyces cerevisiae. Sequence alignments reveal that yeast Ebs1p is similar in structure to the human Smg5-7, with highest homology to Smg7. We demonstrate here that Ebs1p is involved in NMD and behaves similarly to human Smg proteins. Indeed, both loss and overexpression of Ebs1p results in stabilization of NMD targets. However, Ebs1-loss in yeast or Smg7-depletion in human cells only partially disrupts NMD and in the latter, Smg7-depletion is partially compensated for by Smg6. Ebs1p physically interacts with the NMD helicase Upf1p and overexpressed Ebs1p leads to recruitment of Upf1p into cytoplasmic P-bodies. Furthermore, Ebs1p localizes to P-bodies upon glucose starvation along with Upf1p. Overall our findings suggest that NMD is more conserved in evolution than previously thought, and that at least one of the Smg5-7 proteins is conserved in budding yeast.
MoS2 AND WS2 NANOTUBES ALLOYED WITH GOLD AND SILVER (1999)

We report on the existence of MoS 2 and WS 2 micro- and nanotubes alloyed with gold and silver. The tubes have been grown by chemical transport reaction with iodine as a transport agent. While the undoped inorganic tubes grow by spiral rolling of the molecular layers, the presence of noble metals can partially or completely remove the chirality. The molecular layers grow in the form of coaxial cylinders. The noble metal is situated inside the walls of the tubes. It influences the longitudinal terminations of the tubes and increases the wall thickness. Distortion of every second van der Waals gap reveals that staging is present. Stop of chirality in alloyed inorganic tubes appears to be strongly coupled with the expansion of VdW gaps. The existence of M x MoS 2 and M x WS 2 ; (M: Au, Ag) ternary compounds, which are not known in the usual plane layered structures, gives evidence that the cylindrical geometry of crystals can stabilize new compounds and changes the chemistry as well as the physical properties of the materials.
Evaluation of Multiclass Model Observers in PET LROC Studies (2007)

A localization ROC (LROC) study was conducted to evaluate nonprewhitening matched-filter (NPW) and channelized NPW (CNPW) versions of a multiclass model observer as predictors of human tumor-detection performance with PET images. Target localization is explicitly performed by these model observers. Tumors were placed in the liver, lungs, and background soft tissue of a mathematical phantom, and the data simulation modeled a full-3D acquisition mode. Reconstructions were performed with the FORE+AWOSEM algorithm. The LROC study measured observer performance with 2D images consisting of either coronal, sagittal, or transverse views of the same set of cases. Versions of the CNPW observer based on two previously published difference-of-Gaussian channel models demonstrated good quantitative agreement with human observers. One interpretation of these results treats the CNPW observer as a channelized Hotelling observer with implicit internal noise.
Aging‐related cell type‐specific pathophysiologic immune responses that exacerbate disease severity in aged COVID‐19 patients (2022)

Coronavirus disease 2019 (COVID-19) is especially severe in aged patients, defined as 65 years or older, for reasons that are currently unknown. To investigate the underlying basis for this vulnerability, we performed multimodal data analyses on immunity, inflammation, and COVID-19 incidence and severity as a function of age. Our analysis leveraged age-specific COVID-19 mortality and laboratory testing from a large COVID-19 registry, along with epidemiological data of ~3.4 million individuals, large-scale deep immune cell profiling data, and single-cell RNA-sequencing data from aged COVID-19 patients across diverse populations. We found that decreased lymphocyte count and elevated inflammatory markers (C-reactive protein, D-dimer, and neutrophil-lymphocyte ratio) are significantly associated with age-specific COVID-19 severities. We identified the reduced abundance of naïve CD8 T cells with decreased expression of antiviral defense genes (i.e., IFITM3 and TRIM22) in aged severe COVID-19 patients. Older individuals with severe COVID-19 displayed type I and II interferon deficiencies, which is correlated with SARS-CoV-2 viral load. Elevated expression of SARS-CoV-2 entry factors and reduced expression of antiviral defense genes (LY6E and IFNAR1) in the secretory cells are associated with critical COVID-19 in aged individuals. Mechanistically, we identified strong TGF-beta-mediated immune-epithelial cell interactions (i.e., secretory-non-resident macrophages) in aged individuals with critical COVID-19. Taken together, our findings point to immuno-inflammatory factors that could be targeted therapeutically to reduce morbidity and mortality in aged COVID-19 patients.
Phosphorylation of Hepatitis C Virus RNA Polymerases Ser29 and Ser42 by Protein Kinase C-Related Kinase 2 Regulates Viral RNA Replication (2014)

While the role of RNA-dependent RNA polymerases (RdRps) in viral RNA replication is clear, little is known about their functional regulation by phosphorylation. In this study, we addressed several important questions about the function and structure of phosphorylated hepatitis C virus (HCV) nonstructural protein 5B (NS5B). Reverse-genetics studies with HCV replicons encoding phosphorylation-defective NS5B mutants and analysis of their RdRp activities revealed previously unidentified NS5B protein features related to HCV replication and NS5B phosphorylation. These attributes most likely reflect potential structural changes induced by phosphorylation in the Δ1 finger loop region of NS5B with two identified phosphate acceptor sites, Ser29 and Ser42, which may transiently affect the closed conformation of NS5B. Elucidating the effects of dynamic changes in NS5B phosphorylation status during viral replication and their impacts on RNA synthesis will improve our understanding of the molecular mechanisms of NS5B phosphorylation-mediated regulation of HCV replication.
Soft and Stretchable Thermoelectric Generators Enabled by Liquid Metal Elastomer Composites (2020)

Stretchable thermoelectric generators (TEGs) capable of harvesting electrical energy from body heat under cold weather conditions have the potential to make wearable electronic and robotic systems more lightweight and portable by reducing their dependency on on-board batteries. However, progress depends on the integration of soft conductive materials for robust electrical wiring and thermal management. The use of thermally conductive soft elastomers is especially important for conforming to the body, absorbing body heat, and maintaining a temperature gradient between the two sides of the TEGs in order to generate power. Here, we introduce a soft-matter TEG architecture composed of electrically and thermally conductive liquid metal embedded elastomer (LMEE) composites with integrated arrays of n-type and p-type Bi<sub>2</sub>Te<sub>3</sub> semiconductors. The incorporation of a LMEE as a multifunctional encapsulating material allows for the seamless integration of 100 thermoelectric semiconductor elements into a simplified material layup that has a dimension of 41.0 × 47.3 × 3.0 mm. These stretchable thermoelectric devices generate voltages of 59.96 mV at Δ10 °C, 130 mV at Δ30 °C, and 278.6 mV and a power of 86.6 μW/cm<sup>2</sup> at Δ60 °C. Moreover, they do not electrically or mechanically fail when stretched to strains above 50%, making them well-suited for energy harvesting in soft electronics and wearable computing applications.
Combination of Imatinib Mesylate with Autologous Leukocyte-Derived Heat Shock Protein and Chronic Myelogenous Leukemia (2005)

Autologous Hsp70PC vaccination is feasible and safe. When combined with imatinib mesylate, it is associated with immunologic and possible clinical responses against CML in chronic phase.
Rapid capillary electrophoresis time‐of‐flight mass spectrometry separations of peptides and proteins using a monoquaternarized piperazine compound (M7C4I) for capillary coatings (2008)

A monoquaternarized piperazine, 1-(4-iodobutyl) 4-aza-1-azoniabicyclo[2,2,2] octane iodide (M7C4I), has been evaluated as a surface derivatization reagent for CE in combination with TOF MS for the analysis of proteins, peptides, and protein digests. The M7C4I piperazine, at alkaline pH, forms a covalent bond via alkylation of the ionized silanols producing a cationic surface with a highly stable and reversed EOF. The obtained surface yields rapid separations (less than 5 min) of peptides and proteins at acidic pH with high separation efficiencies (up to 1.1 x 10(6) plates/m for peptides and up to 1.8 x 10(6) plates/m for proteins) and no observed bleeding of the coating reagent into the mass spectrometer. The simplicity of the coating procedure also enables fast (2 min) regeneration of the surface, if necessary. This is useful in the analysis of complex samples in order to prevent possible memory effects. The potential of using M7C4I-coated capillaries for MS analysis of complex samples is demonstrated by the separation of peptides, proteins, and protein digests. Even more, the spectacular thing in which large intact proteins with molecular masses over 0.5 MDa could be separated. The coating showed good ability to handle these large proteins with high efficiency and retained peak shape as demonstrated by separation of IgG(1) (150 kDa) and thyroglobulin (669 kDa).
Direct interaction between FcγRI (CD64) and periplakin controls receptor endocytosis and ligand binding capacity (2004)

FcgammaRI depends for its biological function on both the intracellular domain of the alpha-chain and associated Fc receptor (FcR) gamma-chains. However, functional protein effectors of FcgammaRI's intracellular domain have not been identified. In this study, we identified periplakin (PPL) as a selective interacting protein for the intracellular tail of FcgammaRI but no other activatory FcRs. The interaction was confirmed by coimmunoprecipitation and blot-overlay assays. PPL and FcgammaRI colocalized at the plasma membrane in monocytes and cell transfectants, and both were up-regulated by IFN-gamma. By expressing C-terminal PPL in transfectants, we established a pivotal role for this protein in FcgammaRI ligand binding, endocytosis, and antigen presentation. These data illustrate that intracellular protein interactions with a multisubunit FcR alpha-chain can confer unique properties to the receptor.
Ultrasound-guided access to the distal radial artery at the anatomical snuffbox for catheter-based vascular interventions: a technical guide (2021)

Conventional radial access has been shown to have many advantages over the transfemoral approach. The risk of potential radial artery occlusion and subsequent hand ischaemia can be reduced further by accessing the vessel distally at the anatomical snuffbox, allowing maintenance of antegrade flow to the hand by the superficial palmar arch branch. Additional potential advantages of distal radial access in comparison to the conventional radial approach at the wrist include fewer puncture-site complications and faster post-procedural haemostasis as the vessel is very superficial. Furthermore, it provides another safe, non-femoral option for vascular access. The use of ultrasound guidance enables the operator to identify important anatomical landmarks and avoid injuring adjacent structures. We provide a detailed step-by-step guide for performing distal radial access using sonographic and anatomical correlation, thereby facilitating safe access and optimising technical success.
Ang1 Reduces Ischemia-Reperfusion Injury-Induced Microvascular Dysfunction and Chronic Rejection in Rat Cardiac Allografts (2012)

Introduction: Ischemia-reperfusion injury (IRI) is an inevitable factor in current clinical solid organ transplantations resulting in microvascular dysfunction, innate immunity activation and correlating with the later development of chronic rejection. Angiopoietin-1 (Ang1) is endothelial cell-specific growth factor having essential role in vascular development and in endothelial cell maintenance. We investigated the effects of preoperative ex vivo intracoronary perfusion with recombinant variant of native Ang1 (COMP-Ang1) on IRI-associated vascular leakage, no-reflow phenomenon, cardiomyocyte damage, innate immune activation and subsequent development of cardiac fibrosis and allograft vasculopathy. Methods: We performed fully MHC-mismatched cardiac allograft transplantations between DA donor and WF recipient rats. We perfused the donor hearts intracoronarily with COMP-Ang1 or control-PBS perioperatively and preserved the graft was in +4 °C PBS for 4h before transplantation. We analyzed vascular permeability and perfusion at 30 mins, IRI induced myocardial damage and inflammation at 6 h and chronic rejection at 8 weeks after transplantation. Results: COMP-Ang1 reduced IRI-induced microvascular dysfunction by reducing vascular permeability measured by Evans Blue absorbance and increasing the number of perfused vessels 30 min after reperfusion. COMP-Ang1 also significantly reduced endothelial activation, measured by VCAM1 immunoreactivity, ED1+ macrophage and MPO+ neutrophil influx and innate immune activation 6h after reperfusion. Furthermore, periopreative COMP-Ang1 treatment reduced cardiac fibrosis and allograft vasculopathy analyzed 8 weeks after transplantation. (Figure 1)[Figure 1]Conclusion: Here, we show that COMP-Ang1 protects cardiac allografts from IRI-induced microvascular dysfunction and from subsequent chronic allograft rejection. Such results suggest COMP-Ang1 as clinically feasible method for early allograft protection.
Symmetry of the Conduction-band Minima in AlP (2007)

We investigate the properties of quasi‐two‐dimensional electrons in AlP quantum wells by measuring cyclotron resonance, quantum Hall effect, and Shubnikov de Haas oscillations in modulation‐doped AlP‐GaP type‐II quantum wells. We find that in wide AlP wells, the lowest conduction band states are in the Xt valleys transverse to the growth direction, that the valley degeneracy of this state is gν=2, and that the cyclotron effective mass mtml = (0.52 ± 0.01) × m0. These results indicate that the biaxial strain resulting from the lattice mismatch of AlP quantum well with respect to the GaP substrate and barrier layers causes the longitudinal Xl valley to be lifted above the transverse Xt valley. Further, the two‐fold degeneracy of the Xt valley indicates that the conduction band minimum in AlP is located exactly at the X‐point of the Brillouin zone.
Relaxation charge anomalies in the charge–voltage characteristics of alternating-current thin-film electroluminescent devices (1996)

Anomalous charge–voltage (Q–V) characteristics are observed for several types of alternating-current thin-film electroluminescent (ACTFEL) devices. These Q–V curves are anomalous because conduction charge flows in these devices exclusively during the portion of the wave form in which the applied voltage is constant, at its maximum value; this kind of conduction charge is denoted relaxation charge. In a normal ACTFEL device, most of the conduction charge flows during the portion of the wave form in which the applied voltage increases with time. The anomalous Q–V characteristics are attributed to insulator leakage for the devices tested. Simulation shows that such anomalous behavior may arise from either insulator or phosphor leakage.
Route bazaar: automatic interdomain contract negotiation (2015)

While it is widely acknowledged that the Border Gateway Protocol (BGP) has many flaws, most of the proposed fixes focus solely on improving the stability and security of its path computation. However, because interdomain routing involves contracts between Autonomous Systems (ASes), this paper argues that contractual and routing issues should be tackled jointly. We propose Route Bazaar, a backward-compatible system for flexible Internet connectivity. Inspired by the decentralized construction of trust in cryptocurrencies, Route Bazaar uses a decentralized public ledger and cryptography to provide ASes with automatic means to form, establish, and verify end-to-end connectivity agreements.
Cutting Edge: Expansion and Activation of A Population of Autoreactive Marginal Zone B Cells in a Model of Estrogen-Induced Lupus (2001)

Abstract We have demonstrated previously that 17 β-estradiol (E2) treatment of BALB/c mice transgenic for the heavy chain of a pathogenic anti-DNA Ab induces a lupus-like phenotype with expansion of anti-DNA B cells, elevation of anti-DNA Ab titers, and glomerular immunoglobulin deposition. To understand this loss of B cell tolerance, the effects of E2 on B cell development and activation were examined. A sustained increase in E2 resulted in an altered distribution of B cell subsets, with a diminished transitional population and an increase in marginal zone B cells. Depletion of CD4+ T cells did not abrogate these effects. Furthermore, the B cells that spontaneously secreted anti-DNA Abs displayed a marginal zone phenotype. Thus, a sustained increase in E2 alters B cell development, leading to the survival, expansion, and activation of a population of autoreactive marginal zone B cells implicating this B cell subset in autoimmunity.
Point-Contact Bonding of Integrated Three-Dimensional Manifold Microchannel Cooling Within Direct Bonded Copper Platform (2023)

Abstract A microchannel heat sink integrated with a three-dimensional manifold using direct bonded copper (DBC) is promising for high power density electronics due to the combination of low thermal resistance and reduced pressure drop. However, this requires much progress on the fabrication and high-quality point-contact bonding processes of the microchannel substrate and three-dimensional manifold DBCs. In this study, we have developed processing techniques for surface preparations and high-quality point-contact solder bonding between the two DBC substrates. We utilized chemical polishing followed by electroless plating to prevent excess solder from blocking the microchannels. We performed a parametric study to investigate the impact of bonding time and surface roughness on the tensile strength of the bonding interface. The bonding strength increased from 1.8 MPa to 2.3 MPa as the bonding time increased from 10 to 30 min while reducing the surface roughness from Rz = 0.21 to 0.05 μm, resulting in increasing the bonding strength from 0.16 MPa to 2.07 MPa. We successfully tested the microcooler up to the inlet pressure of 70 kPa and pressure drop of 30 kPa, which translates to the tensile strength at the bonding point contacts, which remains well below the 2.30 MPa. We achieved the junction-to-coolant thermal resistance of 0.2 cm2 K/W at chip heat flux of 590 W/cm2. Thus, our study provides an important proof-of-concept demonstration toward enabling high power density modules for power conversion applications.
Design concepts in absorbance optical systems for analytical ultracentrifugation (2018)

Analytical ultracentrifugation is a powerful technique for analyzing particles in solution, and has proved valuable for a wide range of applications in chemistry, biochemistry and material sciences for many years. The field is presently seeing a resurgence of instrument development from commercial and academic groups. To date, no modern optical modeling techniques have ever been applied to the basic imaging properties of the optical system in analytical ultracentrifugation. In this manuscript we provide a contextual framework for the application of such techniques, including an overview of the essential optical principles. The existing commercial and open source detection systems are evaluated for imaging performance, highlighting the limitations of chromatic aberration for broadband acquisitions. These results are the inspiration for a new mirror-based design, free of chromatic aberration. Our findings present a path forward for continued development in imaging and detector technology, where improved data quality will now push the limits of detection and resolution of analytical ultracentrifugation for years to come.
The purine derivative PI‐55 blocks cytokinin action via receptor inhibition (2008)

One of several potential approaches to study mechanisms of action of biologically active compounds is to develop their agonists and antagonists. In the present study, we report the identification of the first known molecule antagonizing the activity of the plant hormone cytokinin at the receptor level. This compound, 6-(2-hydroxy-3-methylbenzylamino)purine, designated PI-55 in the present study, is structurally closely related to cytokinin 6-benzylaminopurine, but substitutions at specific positions of the aromatic side chain strongly diminished its cytokinin activity and conferred antagonistic properties. PI-55 competitively inhibited the binding of the natural ligand trans-zeatin to the Arabidopsis cytokinin receptors cytokinin response 1 (CRE1)/Arabidopsis histidine kinase (AHK) 4 and AHK3 and repressed induction of the cytokinin response gene ARR5:GUS. Genetic analysis revealed that CRE1/AHK4 is the primary target of PI-55. Cytokinin bioassays also demonstrated the anticytokinin effect of PI-55 in several other species. Furthermore, we show that PI-55 accelerated the germination of Arabidopsis seeds and promoted the root growth and formation of lateral roots, thus phenocopying the known consequences of a lowered cytokinin status and demonstrating its potential to inhibit cytokinin perception in planta. PI-55 is the first example for the targeted development of a cytokinin antagonist and represents an initial step for the preparation of cytokinin antagonists with broad activity and reduced agonistic properties.
Correction: Corrigendum: Tuning the optical response of a dimer nanoantenna using plasmonic nanoring loads (2016)

Scientific Reports 5: Article number: 9813; published online: 11 May 2015; updated: 04 March 2016. The Acknowledgements section was omitted from the Article. It should read: Acknowledgements This work was supported by the Center for Nanoscale Science, an NSF Materials Research Science and Engineering Center, under the award DMR-1420620.
Low power optical bistability in 1550 nm VCSOAs (2007)

Clockwise and counterclockwise bistability are demonstrated in 1550 nm VCSOAs at input powers two orders of magnitude lower than previously. Butterfly bistability is also observed for the first time in VCSOAs.