gebhart/patrepeval huggingface dataset:
A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528. (2019)

Abstract Background Pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of P. syringae strains is dependent on the type III secretion system, which secretes a suite of up to about thirty virulence 'effector' proteins into the host cytoplasm where they subvert the eukaryotic cell physiology and disrupt host defences. P. syringae pathovar tabaci naturally causes disease on wild tobacco, the model member of the Solanaceae, a family that includes many crop species as well as on soybean. Results We used the 'next-generation' Illumina sequencing platform and the Velvet short-read assembly program to generate a 145X deep 6,077,921 nucleotide draft genome sequence for P. syringae pathovar tabaci strain 11528. From our draft assembly, we predicted 5,300 potential genes encoding proteins of at least 100 amino acids long, of which 303 (5.72%) had no significant sequence similarity to those encoded by the three previously fully sequenced P. syringae genomes. Of the core set of Hrp Outer Proteins that are conserved in three previously fully sequenced P. syringae strains, most were also conserved in strain 11528, including AvrE1, HopAH2, HopAJ2, HopAK1, HopAN1, HopI, HopJ1, HopX1, HrpK1 and HrpW1. However, the hrpZ1 gene is partially deleted and hopAF1 is completely absent in 11528. The draft genome of strain 11528 also encodes close homologues of HopO1, HopT1, HopAH1, HopR1, HopV1, HopAG1, HopAS1, HopAE1, HopAR1, HopF1, and HopW1 and a degenerate HopM1'. Using a functional screen, we confirmed that hopO1, hopT1, hopAH1, hopM1', hopAE1, hopAR1, and hopAI1' are part of the virulence-associated HrpL regulon, though the hopAI1' and hopM1' sequences were degenerate with premature stop codons. We also discovered two additional HrpL-regulated effector candidates and an HrpL-regulated distant homologue of avrPto1. Conclusion The draft genome sequence facilitates the continued development of P. syringae pathovar tabaci on wild tobacco as an attractive model system for studying bacterial disease on plants. The catalogue of effectors sheds further light on the evolution of pathogenicity and host-specificity as well as providing a set of molecular tools for the study of plant defence mechanisms. We also discovered several large genomic regions in Pta 11528 that do not share detectable nucleotide sequence similarity with previously sequenced Pseudomonas genomes. These regions may include horizontally acquired islands that possibly contribute to pathogenicity or epiphytic fitness of Pta 11528.
Optimization and Deep Learning Techniques for Nanophotonic Inverse-Design (2022)

Metamaterial and metasurface devices (i.e., meta-devices) have shown tremendous potential for disrupting conventional RF and optical system design due to their ability to tailor the propagation of electromagnetic radiation in a desired fashion. Meta-devices are generally synthesized from “meta-atom” building blocks which are optimized to meet a certain set of user-designed performance criteria. Meta-atom optimization often requires the use of full-wave electromagnetic solvers which can make the process computationally challenging, especially when a large number of design parameters are used to define the meta-atoms. To this end, inverse-design strategies based on multi-objective optimization and deep learning which seek to efficiently explore the vast space afforded by nanofabricated meta-devices are presented.
Supplementary Figure 5 from MicroRNA Alterations of Pancreatic Intraepithelial Neoplasias (2023)

&lt;p&gt;PDF file - 2.9MB&lt;/p&gt;
Invention of MK-8262, a Cholesteryl Ester Transfer Protein (CETP) Inhibitor Backup to Anacetrapib with Best-in-Class Properties (2021)

Cholesteryl ester transfer protein (CETP) represents one of the key regulators of the homeostasis of lipid particles, including high-density lipoprotein (HDL) and low-density lipoprotein (LDL) particles. Epidemiological evidence correlates increased HDL and decreased LDL to coronary heart disease (CHD) risk reduction. This relationship is consistent with a clinical outcomes trial of a CETP inhibitor (anacetrapib) combined with standard of care (statin), which led to a 9% additional risk reduction compared to standard of care alone. We discuss here the discovery of MK-8262, a CETP inhibitor with the potential for being the best-in-class molecule. Novel in vitro and in vivo paradigms were integrated to drug discovery to guide optimization informed by a critical understanding of key clinical adverse effect profiles. We present preclinical and clinical evidence of MK-8262 safety and efficacy by means of HDL increase and LDL reduction as biomarkers for reduced CHD risk.
Silicon integrated antenna developments up to 80 GHz for millimeter wave wireless links (2005)

Today, SiGe HBT cut-off frequencies are higher than 230 GHz (Chevalier et al., 2004) and this increase allows new millimeter wave (MMW) applications on silicon such as 60 GHz WLAN and 77 GHz automotive radar. One of the success keys is then the passive integration. This study focuses on a 52 GHz silicon integrated antenna and related feeding transmission line (TL) topics. Double slot antenna integrated in a standard BiCMOS process and 40 GHz coplanar patch antenna (2.3dB gain @ 40 GHz) with a coplanar waveguide (CPW) feed line are depicted and characterized. Integrated TL achieved on standard STMicroelectronics (ST) BiCMOS, CMOS and silicon on insulator (SOI) technologies are described, performances are given (<0.7 dB/mm losses @ 80 GHz for SOI CPW). A full modeling has been developed up to 80 GHz with new approach for CPW on silicon technology due to passivation layer.
Generation ofE’ centers and oxygen hole centers in synthetic silica glasses by γ irradiation (1993)

Generation of typical paramagnetic centers by \ensuremath{\gamma} irradiation was studied for various kinds of synthetic silica glasses. Growth behavior of E' centers and nonbridging oxygen hole centers (NBOHC's) with \ensuremath{\gamma}-ray dose depends on contained preexisting point defects. By irradiation at room temperature, E' centers grow linearly and show a saturating tendency in silicas that contain precursors for E' centers, such as oxygen-deficient centers (ODC's), Si-H bonds or Si-Cl bonds. In silicas that contain very few precursors for E' centers, the growth of E' centers with the dose substantially equals that of NBOHC's and both follow a sublinear growth law in which the concentration of the defects is proportional to the square root of the dose. These results lead to the conclusion that \ensuremath{\gamma} irradiation fundamentally creates defect pairs of an E' center and an oxygen hole center from an intrinsic Si-O network of amorphous silica; this is in addition to a large amount of E' centers induced from preexisting point defects as precursors. By irradiation at 77 K, E' centers and self-trapped holes are suggested to be formed as the defect pair from the Si-O network, while the conversion of the precursors into E' centers is probably lessened. Concentration of E' centers generated by \ensuremath{\gamma} irradiation is almost the same as that of irradiation of ultraviolet lasers and x rays if they are compared based on the absorbed energy. Thus, defect generation with \ensuremath{\gamma} rays is suggested to involve similar fundamental processes as those with photons, which have much smaller energy than \ensuremath{\gamma} rays.
RhIII‐Catalyzed CH Activation: A Versatile Route towards Various Polycyclic Pyridinium Salts (2013)

An efficient and convenient method for the synthesis of highly substituted polycyclic pyridinium salts from the reaction of various 2-aryl-pyridines and 2-aryl-sp(2) -nitrogen-atom-containing heterocycles with alkynes through rhodium(III)-catalyzed CH activation and annulation under an O2 atmosphere is described. A possible mechanism that involves the chelation-assisted CH activation of the 2-aryl-pyridine substrate, insertion of the alkyne, and reductive elimination is proposed. This mechanism was supported by the isolation of a five-membered rhodacycle (I'). In addition, kinetic isotope studies were performed to understand the intimate reaction mechanism.
The molecular and atomic states of oxygen adsorbed on Rh(100): Adsorption (1983)

The adsorption of oxygen at 100 K on Rh(100) has been studied with temperature-programmed desorption and photoelectron spectroscopy. Oxygen adsorbs with a sticking probability of about 0.8 up to a near saturation coverage of 1.1×1015 atoms/cm2 or three-fourths of a monolayer coverage on Rh(100). Initial adsorption is dissociative. However, for coverages above half a monolayer a low temperature molecular state, denoted α, which does not exhibit isotopic exchange, desorbs at 150 K. Dissociated oxygen recombines and desorbs in three high temperature or β states. At low coverages oxygen desorbs in a second order state, β3, between 1200 and 1325 K with an activation energy for desorption of 360 kJ/mole (85 kcal/mole). At coverages above half a monolayer, two first order states, β1 and β2, appear at 820 and 920 K, respectively. Their respective heats of desorption are 210 kJ/mole (50 kcal/mole) and 260 kJ/mole (62 kcal/mole). In contrast with previously reported results, no bulk diffusion of adsorbed oxygen atoms into Rh is observed for temperatures up to the onset of oxygen desorption.
Table S1 from The Pathognomonic FOXL2 C134W Mutation Alters DNA-Binding Specificity (2023)

&lt;p&gt;RNA-seq (polyA and ribodepleted) RPKM matrix for protein coding genes from primary AGCT and SVOG3e derived isogenic cell lines.&lt;/p&gt;
ChemInform Abstract: ROH Molecule Assisted Elimination of F‐ from (CF3)2CH‐ and (CF3)2CD‐ in Gas‐Phase E1cb‐Type Reactions. (1988)

Abstract The gas‐phase reactions of (CF 3 ) 2 CH‐ and (CF 3 ) 2 CD‐ with (CF 3 ) 2 CH‐OH, CF 3 ‐CH2‐OH, Me 3 C‐OH, MeOH, and H 2 O are studied.
224 Gb/s Transmission over 10 km of SMF at 1550 nm Enabled by a SiN Optical Dispersion Compensator and Stokes Vector Direct Detect Receiver (2020)

We demonstrate 224 Gb/s net rate dual-polarization PAM4 signal transmission over 10 km of SMF in the C-band below the HD-FEC threshold of 3.8×10 -3 , using Stokes vector receiver and an integrated ring resonator based optical dispersion compensator.
MR1-Independent Activation of Human Mucosal-Associated Invariant T Cells by Mycobacteria (2019)

Tuberculosis (TB) is the leading cause of mortality from a single infectious agent, <i>Mycobacterium tuberculosis</i> Relevant immune targets of the partially efficacious TB vaccine bacille Calmette-Guérin (BCG) remain poorly defined. Mucosal-associated invariant T (MAIT) cells are MHC-related protein 1 (MR1)-restricted T cells, which are reactive against <i>M. tuberculosis</i>, and underexplored as potential TB vaccine targets. We sought to determine whether BCG vaccination activated mycobacteria-specific MAIT cell responses in humans. We analyzed whole blood samples from <i>M. tuberculosis-</i>infected South African adults who were revaccinated with BCG after a six-month course of isoniazid preventative therapy. In vitro BCG stimulation potently induced IFN-γ expression by phenotypic (CD8<sup>+</sup>CD26<sup>+</sup>CD161<sup>+</sup>) MAIT cells, which constituted the majority (75%) of BCG-reactive IFN-γ-producing CD8<sup>+</sup> T cells. BCG revaccination transiently expanded peripheral blood frequencies of BCG-reactive IFN-γ<sup>+</sup> MAIT cells, which returned to baseline frequencies a year following vaccination. In another cohort of healthy adults who received BCG at birth, 53% of mycobacteria-reactive-activated CD8 T cells expressed CDR3α TCRs, previously reported as MAIT TCRs, expressing the canonical TRAV1-2-TRAJ33 MAIT TCRα rearrangement. CD26 and CD161 coexpression correlated with TRAV1-2<sup>+</sup>CD161<sup>+</sup> phenotype more accurately in CD8<sup>+</sup> than CD4<sup>-</sup>CD8<sup>-</sup> MAIT cells. Interestingly, BCG-induced IFN-γ expression by MAIT cells in vitro was mediated by the innate cytokines IL-12 and IL-18 more than MR1-induced TCR signaling, suggesting TCR-independent activation. Collectively, the data suggest that activation of blood MAIT cells by innate inflammatory cytokines is a major mechanism of responsiveness to vaccination with whole cell vaccines against TB or in vitro stimulation with mycobacteria (<i>Clinical trial registration:</i> NCT01119521).
Analysis and Performance Evaluation of Conditional Handover in 5G Beamformed Systems. (2019)

Higher frequencies that are introduced into 5G networks cause rapid signal degradations and challenge user mobility. In recent studies, a conditional handover procedure has been adopted for 5G networks to enhance user mobility robustness. In this paper, mobility performance of the conditional handover has been analyzed for 5G mm-Wave systems with beamforming. In addition, a random access procedure is proposed that increases the chance of performing contention-free random access during the handover, which reduces signaling and interruption time. Results show that the overall failure performance improves by conditional handover scheme and the contention-free random access rate increases for proposed random access scheme.
Coexisting YAP expression and TP53 missense mutations delineates a molecular scenario unexpectedly associated with better survival outcomes in advanced gastric cancer (2018)

We have previously reported that nuclear expression of the Hippo transducer TAZ in association with Wnt pathway mutations negatively impacts survival outcomes in advanced gastric cancer (GC) patients. Here, we extended these previous findings by investigating another oncogenic cooperation, namely, the interplay between YAP, the TAZ paralogue, and p53. The molecular output of the YAP-p53 cooperation is dependent on TP53 mutational status. In the absence of mutations, the YAP-p53 crosstalk elicits a pro-apoptotic response, whereas in the presence of TP53 mutations it activates a pro-proliferative transcriptional program. In order to study this phenomenon, we re-analyzed data from 83 advanced GC patients treated with chemotherapy whose tissue samples had been characterized for YAP expression (immunohistochemistry, IHC) and TP53 mutations (deep sequencing). In doing so, we generated a molecular model combining nuclear YAP expression in association with TP53 missense variants (YAP+/TP53mut(mv)). Surprisingly, this signature was associated with a decreased risk of disease progression (multivariate Cox for progression-free survival: HR 0.53, 95% CI 0.30–0.91, p = 0.022). The YAP+/TP53mut(mv) model was also associated with better OS in the subgroup of patients who received chemotherapy beyond the first-line setting (multivariate Cox: HR 0.36, 95% CI 0.16–0.81, p = 0.013). Collectively, our findings suggest that the oncogenic cooperation between YAP and mutant p53 may translate into better survival outcomes. This apparent paradox can be explained by the pro-proliferative program triggered by YAP and mutant p53, that supposedly renders cancer cells more vulnerable to cytotoxic therapies.
Reliability improvement of 90nm large flip chip low-k die via dicing and assembly process optimization (2006)

Increasing demand for higher processing speeds and enhanced electrical performance have made the use of low-k dielectric materials mandatory. For such low-k dielectric materials, enhanced dielectric properties are achieved via increased porosity of the low-k materials. These new low-k materials have different chemical, thermal, and mechanical properties than traditional dielectric materials used in older silicon technology, which in turn creates integration issues. The adhesion of the low-k layers in the silicon is also relatively weak. Due to their poor adhesion and brittle nature, low-k materials have a tendency to crack and chip during mechanical dicing with diamond blades, a widely used die singulation technique. In the case of field programmable gate array (FPGA) chips, as the demand for higher speeds and enhanced functionality increases, the size of the flip chip die grows accordingly to offer higher number of logic cells. Large flip chip die also requires a large package for efficient signal routing. Consequently, the stresses generated due to thermal expansion mismatch are severe, and even a small defect created on the edge of the chip during the dicing process can have a severe impact on the reliability of the flip chip device. To study the impact on flip chip reliability, two different laser dicing technologies were compared with the conventional mechanical dicing process. Other important variables tested during this study were dicing location in the saw street, lid attach dispense pattern, wafer lots, die size, and underfill. Reliability analysis indicated that for improvement of the reliability of the samples diced with mechanical dicing process, correct choice of underfill and lid attach material, optimization of the lid attach dispense pattern, and optimization of dicing location were required. In contrast, a wide reliability and process window was achieved by laser grooving process and none of the above factors tested during the study had any impact on the reliability.
Chiral‐at‐Iron Catalyst for Highly Enantioselective and Diastereoselective Hetero‐Diels‐Alder Reaction (2021)

This study demonstrates that chiral-at-iron complexes, in which all coordinated ligands are achiral and the overall chirality the consequence of a stereogenic iron center, are capable of catalyzing asymmetric transformations with very high enantioselectivities. The catalyst is based on a previously reported design (J. Am. Chem. Soc. 2017, 139, 4322), in which iron(II) is surrounded by two configurationally inert achiral bidentate N-(2-pyridyl)-substituted N-heterocyclic carbenes in a C<sub>2</sub> -symmetric fashion and complemented by two labile acetonitriles. By replacing mesityl with more bulky 2,6-diisopropylphenyl substituents at the NHC ligands, the steric hindrance at the catalytic site was increased, thereby providing a markedly improved asymmetric induction. The new chiral-at-iron catalyst was applied to the inverse electron demand hetero-Diels-Alder reaction between β,γ-unsaturated α-ketoester and enol ethers provide 3,4-dihydro-2H-pyrans in high yields with excellent diastereoselectivities (up to 99 : 1 dr) and excellent enantioselectivities (up to 98 % ee). Other electron rich dienophiles are also suitable as demonstrated for a reaction with a vinyl azide.
Supplementary Figure 2 from Circulating B-Cell Chronic Lymphocytic Leukemia Cells Display Impaired Migration to Lymph Nodes and Bone Marrow (2023)

Supplementary Figure 2 from Circulating B-Cell Chronic Lymphocytic Leukemia Cells Display Impaired Migration to Lymph Nodes and Bone Marrow
Optically Driven Surfactant Coated Aqueous Droplets: A New Method to Develop Micro-reactors (2007)

We demonstrate laser driven optical motion of surfactant coated water drops immersed in decanol using the thermal Marangoni effect. The method is a promising new approach to study emulsions at the micrometer length scale.
Improved protein labeling by stannous tartrate reduction of pertechnetate. (1980)

A procedure has been developed whereby small amounts of protein--specifically human serum albumin and immunoglobulin G--can be labeled with Tc-99m. Artifactual problems associated with electrolytic and stannous chloride labeling procedures are virtually eliminated. The procedure is satisfactory for labeling human serum albumin, normal goat immunoglobulin G, and goat anti-carcinoembryonic antigen immunoglobulin G.
Screen for Inhibitors of STK33 Kinase Activity (2014)

This Note explores the conflict over whether a prisoner must suffer more than de minimis injury to sustain an Eighth Amendment excessive force claim. It examines this conflict against the backdrop of the various standards the U.S. Supreme Court adopted in its Eighth Amendment prison conditions jurisprudence between 1976 and 1992, principally focusing on the 1992 Hudson v. McMillian decision. Moreover, this Note considers the intersection of "the evolving standards of decency," the "hands-off doctrine," and the Eighth Amendment injury requirement. Ultimately, this Note advocates that excessive force--when meted out as punishment--violates the Eighth Amendment's prohibition on cruel and unusual punishment regardless of whether a prisoner's injuries are more than de minimis.
Treatment patterns and disease course of previously untreated Primary Central Nervous System Lymphoma: Feasibility of MTX‐based regimens in clinical routine (2021)

Although a relevant proportion of patients are not eligible for clinical trials due to age, performance status, or comorbidities, these results prove feasibility of different MTX-based treatment strategies in clinical routine. Even elderly patients displayed surprisingly favorable outcomes. However, with compromising organ toxicities, reduction of intensity should be part of strategies in future clinical trials.
Self-supervised Learning from 100 Million Medical Images (2022)

Building accurate and robust artificial intelligence systems for medical image assessment requires not only the research and design of advanced deep learning models but also the creation of large and curated sets of annotated training examples. Constructing such datasets, however, is often very costly -- due to the complex nature of annotation tasks and the high level of expertise required for the interpretation of medical images (e.g., expert radiologists). To counter this limitation, we propose a method for self-supervised learning of rich image features based on contrastive learning and online feature clustering. For this purpose we leverage large training datasets of over 100,000,000 medical images of various modalities, including radiography, computed tomography (CT), magnetic resonance (MR) imaging and ultrasonography. We propose to use these features to guide model training in supervised and hybrid self-supervised/supervised regime on various downstream tasks. We highlight a number of advantages of this strategy on challenging image assessment problems in radiography, CT and MR: 1) Significant increase in accuracy compared to the state-of-the-art (e.g., AUC boost of 3-7% for detection of abnormalities from chest radiography scans and hemorrhage detection on brain CT); 2) Acceleration of model convergence during training by up to 85% compared to using no pretraining (e.g., 83% when training a model for detection of brain metastases in MR scans); 3) Increase in robustness to various image augmentations, such as intensity variations, rotations or scaling reflective of data variation seen in the field.