gebhart/patrepeval huggingface dataset:
Data from Profiling Microdissected Epithelium and Stroma to Model Genomic Signatures for Cervical Carcinogenesis Accommodating for Covariates (2023)

&lt;div&gt;Abstract&lt;p&gt;This study is the first comprehensive, integrated approach to examine grade-specific changes in gene expression along the entire neoplastic spectrum of cervical intraepithelial neoplasia (CIN) in the process of cervical carcinogenesis. This was accomplished by identifying gene expression signatures of disease progression using cDNA microarrays to analyze RNA from laser-captured microdissected epithelium and underlying stroma from normal cervix, graded CINs, cancer, and patient-matched normal cervical tissues. A separate set of samples were subsequently validated using a linear mixed model that is ideal to control for interpatient gene expression profile variation, such as age and race. These validated genes were ultimately used to propose a genomically based model of the early events in cervical neoplastic transformation. In this model, the CIN 1 transition coincides with a proproliferative/immunosuppression gene signature in the epithelium that probably represents the epithelial response to human papillomavirus infection. The CIN 2 transition coincides with a proangiogenic signature, suggesting a cooperative signaling interaction between stroma and tumor cells. Finally, the CIN 3 and squamous cell carcinoma antigen transition coincide with a proinvasive gene signature that may be a response to epithelial tumor cell overcrowding. This work strongly suggests that premalignant cells experience a series of microenvironmental stresses at the epithelium/stroma cell interface that must be overcome to progress into a transformed phenotype and identifies the order of these events &lt;i&gt;in vivo&lt;/i&gt; and their association with specific CIN transitions. [Cancer Res 2007;67(15):7113–23]&lt;/p&gt;&lt;/div&gt;
High quality SWCNT synthesis in the presence of NH3 using a vertical flow aerosol reactor (2009)

Abstract High quality single‐walled carbon nanotubes (SWCNTs) were synthesized in the presence of ammonia (NH 3 ) using a vertical flow aerosol reactor and collected directly from the gas phase in a simple continuous process. The morphology of the carbon network and the quality of the SWCNTs was investigated combining local and overall probes such as transmission electron microscopy (TEM), electron diffraction, scanning tunneling microscopy (STM), Raman, and optical absorption. magnified image Representative STM image of a SWCNT synthesized by aerosol CVD (8 × 2 nm 2 , measured at a bias of 1 V and a tunneling current of 0.2 nA).
Pentamethylcyclopentadienyl-, Acetylcyclopentadienyl- und Indenyl-dicarbonyl-AcetylenkompIexe des Vanadiums. Molekülstruktur von C9H7V(CO)2PhC2H / Pentamethylcyclopentadienyl, Acetylcyclopentadienyl and Indenyl Dicarbonyl Acetylene Complexes of Vanadium. Molecular Structure of C9H7V(CO)2PhC2H (1988)

Abstract The photo-induced reaction of C 5 Me 5 V(CO) 4 (1). (C 5 H 4 COMe)V(CO) 4 (2) and C 9 H 7 V(CO) 4 (3) with acetylenes R 1 C 2 R 2 (R 1 , R 2 = H. Me, Ph) yields the substitution products C 5 Me 5 V(CO) 2 R 1 C 2 R 2 (4), (C 5 H 4 COMe)V(CO) 2 R 1 C 2 R 2 (6) and C 9 H 7 V(CO) 2 R 1 C 2 R 2 (7). One CO ligand of complexes 4 can be substituted by PMe 3 affording complexes of the type C 5 Me 5 V(CO)(PMe 3 )R 1 C 2 R 2 (5). The acetylene complexes 4-7 are characterized by their IR. 1H, 13 C and 51 V NMR as well as their mass spectra. In these compounds the alkyne ligand shows a hindered rotation around the metal alkyne bond axis. The rotation barrier (ΔG ≠ = 40-50 kJ/mol) is higher than in the corresponding cyclopentadienyl complexes. An X-ray crystal structure analysis of C 9 H 7 V(CO) 2 PhC 2 H indicates an orientation of the alkyne-C-C-axis in the symmetry plane of the C 9 H 7 V(CO) 2 fragment. The phenyl substituent is pointing away from the metal and the indenyl ligand.
Two-Photon Interference with Bright Remote Quantum Dot Sources (2021)

Fabricating multiple identical bright single-photon sources is critical for scalable quantum technologies. We demonstrate Hong-Ou-Mandel interference of photons from two distinct quantum dot sources in micropillar cavities with a visibility of (67 ± 4) %.
Photon noise correlations in electrically coupled semiconductor lasers (2003)

Measurements of the correlation between the photon noise of two semiconductor lasers sharing a bias circuit are presented. The photon noise of the electrically coupled lasers is found to be correlated by as much as 70%. The photon noise correlations are measured at low frequencies as a function of the bias current for lasers connected in series and in parallel, and for high and low impedance biases. The magnitude and sign of the noise correlations are consistent with theoretical expectations.
Water-Soluble and Blue Luminescent Cationic Polyelectrolytes Based on Poly(p-phenylene) (1999)

Two new (dialkylamino)ethoxy-substituted poly(p-phenylene)s (PPP) have been prepared, poly[2,5-bis(3-{N,N-diethylamino}-1-oxapropyl)-1,4-phenylene-alt-1,4-phenylene] (P−NEt2) and poly[2,5-bis(3-{N,N-dimethylamino}-1-oxapropyl)-1,4-phenylene-alt-1,4-phenylene] (P−NMe2). These PPPs were synthesized via Pd-catalyzed Suzuki polymerization and are soluble in organic solvents (THF, chloroform) and dilute aqueous acid. Water-soluble quaternary ammonium functionalized PPPs, poly[2,5-bis(3-{N,N,N-triethylammonium}-1-oxapropyl)-1,4-phenylene-alt-1,4-phenylene] dibromide (P−NEt3+) and poly[2,5-bis(3-{N,N,N-trimethylammonium}-1-oxapropyl)-1,4-phenylene-alt-1,4-phenylene] dibromide (P−NMe3+), were easily prepared from the neutral polymers. Number-average molecular weights ranging from 5000 to 19 000 g mol-1 were measured by GPC (relative to PS standards), and these values were standardized to PPP's via universal calibration. The neutral polymer is stable to over 300 °C by TGA, while the alkylated polymers begin to dealkylate at 230 °C. The polymer's electronic absorption is dependent on quaternization with the neutral polymer having a λmax at 350 nm, while the triethyl quaternized polymer's λmax shifts to 330 nm. This corresponds to an electronic band gap (Eg) shift from 3.0 to 3.3 eV where Eg is defined as the onset of the π to π* transition. The polymers luminesce blue light with an intensity that is a function of ionic composition, allowing them to be used as emitting materials in LED's constructed by both layer-by-layer electrostatic deposition and hybrid ink jet printing methods.
An improved molecular inversion probe based targeted sequencing approach for low variant allele frequency (2022)

Deep targeted sequencing technologies are still not widely used in clinical practice due to the complexity of the methods and their cost. The Molecular Inversion Probes (MIP) technology is cost effective and scalable in the number of targets, however, suffers from low overall performance especially in GC rich regions. In order to improve the MIP performance, we sequenced a large cohort of healthy individuals (<i>n</i> = 4417), with a panel of 616 MIPs, at high depth in duplicates. To improve the previous state-of-the-art statistical model for low variant allele frequency, we selected 4635 potentially positive variants and validated them using amplicon sequencing. Using machine learning prediction tools, we significantly improved precision of 10-56.25% (<i>P</i> < 0.0004) to detect variants with VAF > 0.005. We further developed biochemically modified MIP protocol and improved its turn-around-time to ∼4 h. Our new biochemistry significantly improved uniformity, GC-Rich regions coverage, and enabled 95% on target reads in a large MIP panel of 8349 genomic targets. Overall, we demonstrate an enhancement of the MIP targeted sequencing approach in both detection of low frequency variants and in other key parameters, paving its way to become an ultrafast cost-effective research and clinical diagnostic tool.
A New Whole Genome Culture-Independent Diagnostic Test (WG-CIDT) for Rapid Detection of Salmonella in Lettuce (2020)

The rapid detection of foodborne microbial pathogens contaminating fresh fruits and vegetables during the intervening period between harvest and consumption could revolutionize microbial quality assurance of food usually consumed raw and those with a limited shelf life. We have developed a sensitive, shotgun whole genome sequencing protocol capable of detecting as few as 1 colony forming unit (cfu) of <i>Salmonella enterica</i> serovar Typhimurium spiked on 25 g of lettuce. The Ion Torrent sequencing platform was used to generate reads of globally amplified DNA from microbes recovered from the surface of lettuce followed by bioinformatic analyses of the nucleotide sequences to detect the presence of <i>Salmonella</i>. The test is rapid and sensitive, and appropriate for testing perishable foods, and those consumed raw, for <i>Salmonella</i> contamination. The test has the potential to be universally applicable to any microbial contaminant on lettuce as long as a suitable bioinformatics pipeline is available and validated. A universal test is expected to pave the way for preventive and precision food safety and the re-shaping of the entire spectrum of food safety investigations from the current disease-limiting, reactive procedure to a proactive, disease prevention process.
Impact of package design and materials on reliability for temperature cycling, bend, and drop loading conditions (2008)

This paper presents a collection of test data showing how the choice of package design and material can have a different effect on performance depending on the loading conditions. Board level temperature cycling, drop (JESD22-B111), and cyclic bend (JESD22-B113) tests were performed on 0.4mm ball pitch packages. Factors investigated for this evaluation include mold compound material, mold cap thickness (0.45 vs. 0.7mm), ball pad finish (NiAu vs. Cu OSP), solder ball composition (SAC305, SAC105, SAC125Ni, Sn3.5Ag), solder volume (ball vs. bump), package material (RoHS vs Green), and board material (RoHS vs Green). The data presented in this paper indicates that lower silver content solder balls perform better under drop conditions, while temperature cycling reliability suffers as silver content decreases. In addition, mold compound material and thickness, die size, and solder volume have the opposite effect depending on the loading condition. The Green material for test board also showed lower performance than RoHS compliant board material.
All-Solid-State Diode-Pumped C.W. Femtosecond Cr:LiSrAlF6 Laser (1994)

The widespread application of ultrafast technology will require the development of compact, versatile lasers. We aim to develop an all-solid-state diode-pumped tunable femtosecond laser system employing Cr:LiSAF as the gain medium in both amplifier and oscillator to yield ultrashort pulse energies up to a few μ J for only a few watts of diode pump power. The diode-pumping at ~670 nm of a c.w. Cr:LiSAF laser has been demonstrated [e.g. 1]. Here we report on picosecond and femtosecond pulse generation from the first c.w. mode-locked, diode-pumped tunable solid-state lasers based on Cr:LiSrAlF 6 (Cr:LiSAF).
Bivalent SARS-CoV-2 mRNA vaccines increase breadth of neutralization and protect against the BA.5 Omicron variant (2022)

The emergence of SARS-CoV-2 variants in the Omicron lineage with large numbers of substitutions in the spike protein that can evade antibody neutralization has resulted in diminished vaccine efficacy and persistent transmission. One strategy to broaden vaccine-induced immunity is to administer bivalent vaccines that encode for spike proteins from both historical and newly-emerged variant strains. Here, we evaluated the immunogenicity and protective efficacy of two bivalent vaccines that recently were authorized for use in Europe and the United States and contain two mRNAs encoding Wuhan-1 and either BA.1 (mRNA-1273.214) or BA.4/5 (mRNA-1273.222) spike proteins. As a primary immunization series in BALB/c mice, both bivalent vaccines induced broader neutralizing antibody responses than the constituent monovalent vaccines (mRNA-1273 [Wuhan-1], mRNA-1273.529 [BA.1], and mRNA-1273-045 [BA.4/5]). When administered to K18-hACE2 transgenic mice as a booster at 7 months after the primary vaccination series with mRNA-1273, the bivalent vaccines induced greater breadth and magnitude of neutralizing antibodies compared to an mRNA-1273 booster. Moreover, the response in bivalent vaccine-boosted mice was associated with increased protection against BA.5 infection and inflammation in the lung. Thus, boosting with bivalent Omicron-based mRNA-1273.214 or mRNA-1273.222 vaccines enhances immunogenicity and protection against currently circulating SARS-CoV-2 strains.
Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing (2018)

Cancer-associated fibroblasts (CAFs) are a major constituent of the tumor microenvironment, although their origin and roles in shaping disease initiation, progression and treatment response remain unclear due to significant heterogeneity. Here, following a negative selection strategy combined with single-cell RNA sequencing of 768 transcriptomes of mesenchymal cells from a genetically engineered mouse model of breast cancer, we define three distinct subpopulations of CAFs. Validation at the transcriptional and protein level in several experimental models of cancer and human tumors reveal spatial separation of the CAF subclasses attributable to different origins, including the peri-vascular niche, the mammary fat pad and the transformed epithelium. Gene profiles for each CAF subtype correlate to distinctive functional programs and hold independent prognostic capability in clinical cohorts by association to metastatic disease. In conclusion, the improved resolution of the widely defined CAF population opens the possibility for biomarker-driven development of drugs for precision targeting of CAFs.
30 Years of Pearls from Electrochemical Society Journals (2021)

To celebrate Interface’s 30th anniversary, we showcase 30 “pearls of the journals.” They are the two most highly cited papers in each of the 14 topical areas published in JES and JSS in the last 30 years. Because this gave us 28 papers, we then rounded up to 30 by including the two next-most-cited papers (giving us one for each year of Interface’s existence), both of which happened to be in the battery topical area.
Optical Properties of InAs Quantum Dots (2002)

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Thermally Stable RuOx–CeO2 Nanofiber Catalysts for Low-Temperature CO Oxidation (2020)

With the ever-growing concerns for sustainable energy production and clean air, developing highly efficient catalysts to eliminate exhaust emission pollutants is of vital importance. In this work, we report a class of thermally stable RuOx–CeO2 nanofiber catalysts derived from a facile one-pot electrospinning method. Ru–CeO2 nanofiber catalysts exhibit outstanding low-temperature activity (∼90% conversion of CO below 150 °C) and long-term durability. The as-prepared Ru–CeO2 nanofiber catalysts show a high Brunauer–Emmett–Teller (BET) surface area (>110 m2/g), demonstrating the effectiveness of electrospinning for fabricating high-surface-area catalysts. The Ru–CeO2 nanofiber catalysts have a hollow interior and porous exterior structure, particularly at the Ru–CeO2 nanofiber interfaces, providing plentiful accessible CO and oxygen adsorption sites, which are beneficial for CO catalytic oxidation. H2 temperature-programmed reduction (H2-TPR) was applied to probe the reducibility of the as-synthesized catalysts. The reduced Ru–CeO2 nanofiber catalysts exhibited hydrogen consumption near room temperature. The catalysts were further characterized by scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), and transmission electron microscopy (TEM) to explore the relationship between the microstructure and extraordinary low-temperature reducibility, as well as the CO oxidation activity. In addition, X-ray photoelectron spectroscopy (XPS), in situ CO-diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and density functional theory (DFT) calculation were employed to investigate the chemical states of the active surface species and identify the gas adsorption and reaction sites.
Production of a novel FK520 analog in Streptomyces hygroscopicus: Improving titer while minimizing impurities (2002)

FK520, also called ascomycin, is an immunosuppressive agent produced by Streptomyces hygroscopicus. Engineering the polyketide synthase genes of the parent strain generated novel FK520 analogs with the potential for improved in vivo stability. By replacing the acyl transferase (AT) domain in the polyketide synthase module 8 with an AT specific for methylmalonyl CoA (the rapamycin AT 3), the strain produced 13-desmethoxy-13-methyl-FK520 (13dmmFK520). Process development and scale-up studies of this recombinant S. hygroscopicus strain producing 13dmmFK520 are described here. Production kinetics and compound stability in fermentation broth were significantly different compared to the native FK520. Fermentation of the new strain resulted in the synthesis of a contaminating substance that co-purified with the 13dmmFK520. To optimize 13dmmFK520 production and to facilitate purification, growth parameters and media development were examined. Although a medium was identified that increased product titers by ca. 300%, the ratio of impurity to product was doubled. Lower dissolved oxygen (20% compared to 50% and 80%) increased titers by 20% with no appreciable effect on the concentration of impurity. Increasing the fermentation pH from 6.0 to 6.5 did not change the 13dmmFK520 titer, but reduced the impurity-to-product ratio by approximately 450%.
Effect of genotype and root colonization in biological control of fusarium wilts in pigeonpea and chickpea byPseudomonas aeruginosaPNA1 (2003)

Pseudomonas aeruginosa PNA1, an isolate from chickpea rhizosphere in India, protected pigeonpea and chickpea plants from fusarium wilt disease, which is caused by Fusarium oxysporum f.sp. ciceris and Fusarium udum. Inoculation with strain PNA1 significantly reduced the incidence of fusarium wilt in pigeonpea and chickpea on both susceptible and moderately tolerant genotypes. However, strain PNA1 protected the plants from fusarium wilt until maturity only in moderately tolerant genotypes of pigeonpea and chickpea. Root colonization of pigeonpea and chickpea, which was measured using a lacZ-marked strain of PNA1, showed tenfold lower root colonization of susceptible genotypes than that of moderately tolerant genotypes, indicating that this plant-bacteria interaction could be important for disease suppression in this plant. Strain PNA1 produced two phenazine antibiotics, phenazine-1-carboxylic acid and oxychlororaphin, in vitro. Its Tn5 mutants (FM29 and FM13), which were deficient in phenazine production, caused a reduction or loss of wilt disease suppression in vivo. Hence, phenazine production by PNA1 also contributed to the biocontrol of fusarium wilt diseases in pigeonpea and chickpea.
Interferometric microscopy of silicon photonic devices (2015)

Silicon photonics provides the ability to construct complex photonic circuits that act on the amplitude and phase of multiple optical channels. Many applications of silicon photonics depend on maintenance of optical coherence among the various waveguides and structures on the chip. Other applications can depend on the modal structures of the waveguides. All these application require the ability to characterize the amplitude and phase of individual optical channels. Fourier imaging with high numerical aperture microscope objectives has been used to image the intensity of individual channels of photonic structures in both real and Fourier space. In other work, holographic imaging of multimode fibers has allowed modal decomposition. In this work we use interferometric microscopy to image the amplitude and phase of a variety of silicon photonic structures. These include a multimode interference splitter and a multimode waveguide under various excitation conditions.
Essential pathogenic role of endogenous IL‐18 in murine diabetes induced by multiple low doses of streptozotocin. Prevention of hyperglycemia and insulitis by a recombinant IL‐18‐binding protein: Fc construct (2003)

IL-18 is a cytokine structurally and functionally related to IL-1 that, in synergy with IL-12, stimulates the synthesis of IFN-gamma from T lymphocytes and natural killer cells. Because IFN-gamma plays a key pathogenic role in the development of murine immunoinflammatory diabetes induced by multiple low doses of streptozotocin (STZ) we investigated the effect of negating the actions of endogenous IL-18 in this model by administering recombinant IL-18-binding protein:Fc (IL-18 bp:Fc). C57BL/6 mice were injected once daily with 40 mg/kg STZ for 5 consecutive days, day 0 being the first day of STZ challenge. Relative to control animals treated in parallel with either PBS or human IgG, mice treated from day -3 to day 7 with daily doses of 150 microg of IL-18 bp:Fc exhibited lower incidence of diabetes and milder insulitis. In contrast, mice that were treated with IL-18 bp:Fc from day 7 to day 14 exhibited clinical and histological signs of STZ-induced diabetes similar to those of control mice treated with IgG. The protective effect of IL-18 bp:Fc was accompanied by modified ex vivo immune responses, in that spleen cells and peritoneal macrophages contained fewer IFN-gamma secreting cells and released lower amounts of nitrite (an index of nitric oxide production) and IL-1beta. We conclude that intact IL-18 function is essential for the full diabetogenic effect of low dose STZ in C57BL/6 mice.
Domain Adaptation for Structured Output via Discriminative Patch Representations (2019)

Predicting structured outputs such as semantic segmentation relies on expensive per-pixel annotations to learn supervised models like convolutional neural networks. However, models trained on one data domain may not generalize well to other domains without annotations for model finetuning. To avoid the labor-intensive process of annotation, we develop a domain adaptation method to adapt the source data to the unlabeled target domain. We propose to learn discriminative feature representations of patches in the source domain by discovering multiple modes of patch-wise output distribution through the construction of a clustered space. With such representations as guidance, we use an adversarial learning scheme to push the feature representations of target patches in the clustered space closer to the distributions of source patches. In addition, we show that our framework is complementary to existing domain adaptation techniques and achieves consistent improvements on semantic segmentation. Extensive ablations and results are demonstrated on numerous benchmark datasets with various settings, such as synthetic-to-real and cross-city scenarios.
A Novel Endoscopic Approach to Brachytherapy in the Management of Hilar Cholangiocarcinoma (2006)

LDR biliary brachytherapy administration via endoscopically placed biliary stents is technically feasible and appears reasonably safe in select patients with unresectable perihilar CCA. Unlike NBTs, stents can potentially be placed in bilateral ductal systems to accommodate dual brachytherapy catheters when indicated.