gebhart/patrepeval huggingface dataset:
Expression of Receptors for Luteinizing Hormone-Releasing Hormone (LH-RH) in Prostate Cancers following Therapy with LH-RH Agonists (2010)

LH-RH receptor expression persisted despite prolonged exposure to LH-RH agonists. These findings support the concept of targeting cytotoxic LH-RH analogs to prostatic LH-RH receptors, using these receptors to gain entry into cancer cells to deliver a hybridized cytotoxic moiety for the treatment of prostate cancer.
Evaluating the Role of STAT3 in CD4 + T Cells in Susceptibility to Invasive Aspergillosis (2021)

We aimed to determine whether T cell-specific STAT3 deletion influences the immune response to <i>Aspergillus</i> in the immunosuppressed context in CD4 <i><sup>Stat3</sup></i><sup>-/-</sup> mice. Immunosuppressed and nonimmunosuppressed CD4 <i><sup>Stat3</sup></i><sup>-/-</sup> mice and littermate Stat3<sup>flox/flox</sup> (Stat3<sup>fl/fl</sup>) mice were infected with <i>Aspergillus fumigatus</i> in an aerosol chamber, and the weight, activity, appearance, and respiratory rate of the mice were monitored daily for 21 days to evaluate their survival. <i>Aspergillus</i> infection was confirmed by lung fungal culture counts, histology, and a galactomannan test. Cytokines were measured at 3 days postinfection in bronchoalveolar lavage (BAL) fluid and serum. Immunosuppressed CD4 <i><sup>Stat3</sup></i><sup>-/-</sup> mice began succumbing to infection by day 4, and by day 7, only 30% of mice survived. Immunosuppressed Stat3<sup>fl/fl</sup> mice started to succumb to the disease on day 5, and 40% of mice remained by day 7. The nonimmunosuppressed control Stat3<sup>fl/fl</sup> and CD4 <i><sup>Stat3</sup></i><sup>-/-</sup> mice maintained their weight over the study period, without any evidence of infection by <i>A. fumigatus</i> by histology. In the BAL fluid, tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), interferon gamma (IFN-γ), IL-17A, and IL-22 levels were elevated in Stat3<sup>fl/fl</sup> immunosuppressed mice compared to immunosuppressed CD4 <i><sup>Stat3</sup></i><sup>-/-</sup> mice at 3 days postinfection. STAT3 in CD4<sup>+</sup> T cells modulates the production of cytokines in the IL-17 pathway in immunosuppressed mice. However, it has no meaningful effect on the clearance of <i>Aspergillus</i> or the concomitant increase in susceptibility to <i>Aspergillus</i> infection.
Activin A‐induced diffrentiation in K562 cells is associated with a transient hypophosphorylation of RB protein and the concomitant block of cell cycle at G1 phase (1992)

The human erythroleukemic cell line, K562, can be induced to differentiate by the addition of activin A, a newly purified protein belonging to the TGF-beta 1 family. The present studies used flow cytometric cell cycle analysis, indirect immunofluorescence staining of the proliferating cell nuclear antigen (PCNA), and thymidine incorporation assay of cell proliferation to study the effects of activin A on the cell cycle during differentiation in K562 cells. Activin A-treated K562 cells were found to undergo a transient block in cell cycle, temporarily halting progression from G1 to S phase. The latter can be observed after approximately 24 hr of incubation with activin A and then disappears after this early stage of induction of differentiation. Cell cycle kinetics analysis using synchronized K562 cells also confirms that in the presence of activin A, K562 cells progress normally through various phases of cell cycle, except that there is prolongation of the G1 phase between 10 to 24 hr of culture. Furthermore, this transient arrest in G1 is correlated with dephosphorylation of a nucleoprotein, the RB gene product, which occurs within 9-24 hr of incubation with activin A; and phosphorylation of RB protein then develops afterward. In addition, these cell cycle-related events are observed to occur earlier than the accumulation of hemoglobins in K562 cells. It is concluded that transient dephosphorylation of RB protein and prolongation of G1 phase of cell cycle precede and accompany erythroid differentiation caused by activin A and chemical inducers, thus constituting part of the mechanism for induction of differentiation in the erythroleukemia cells.
Gut–Liver Axis in Nonalcoholic Fatty Liver Disease: the Impact of the Metagenome, End Products, and the Epithelial and Vascular Barriers (2021)

Nonalcoholic fatty liver disease (NAFLD) is a systemic, dynamic, heterogeneous, and multiaxis entity, the pathogenesis of which is still uncertain. The gut-liver axis is regulated and stabilized by a complex network encompassing a metabolic, immune, and neuroendocrine cross-talk between the gut, the microbiota, and the liver. Changes in the gut-liver axis affect the metabolism of lipids and carbohydrates in the hepatocytes, and they impact the balance of inflammatory mediators and cause metabolic deregulation, promoting NAFLD and its progression to nonalcoholic steatohepatitis. Moreover, the microbiota and its metabolites can play direct and indirect roles in gut barrier function and fibrosis development. In this review, we will highlight findings from the recent literature focusing on the gut-liver axis and its relation to NAFLD. Finally, we will discuss the impact of technical issues, design bias, and other limitations on current knowledge of the gut microbiota in the context of NAFLD.
Sol-gel processing of PZT thin films: A review of the state-of-the-art and process optimization strategies (1995)

Abstract Sol-gel processing has been widely employed for the fabrication of lead zirconate titanate (PZT) thin films. To successfully optimize thin film material properties for different applications, we must develop a fundamental understanding of the processing-property relationships inherent in the sol-gel fabrication process. In the asprepared state, sol-gel thin films are amorphous, have large organic contents, and can possess significant porosity. The preparation of thin films with acceptable properties requires that we effectively control densification and crystallization of the as-deposited film. We have determined that this “structural evolution” into the dense, crystalline ceramic phase may be affected by many aspects of the preparation process. In this paper we review the effects that tailored solution precursor characteristics and heat-treatment ramp rate can have on structural evolution. Specific examples are presented for process variation effects on the densification of thin films in the model system, ZrO2, and for the effects of controlled nucleation behavior on the optical scattering losses of PZT 40/60 thin films. Optimization strategies for sol-gel synthesis are also considered.
Approximation methods for control of acoustic/structure models with piezoceramic actuators (1991)

The active control of acoustic pressure in a 2-D cavity with a flexible boundary (a beam) is considered. Specifically, this control is implemented via piezoceramic patches on the beam which produces pure bending moments. The incorporation of the feedback control in this manner leads to a system with an unbounded input term. Approximation methods in this manner leads to a system with an unbounded input term. Approximation methods in the context of linear quadratic regulator (LQR) state space control formulation are discussed and numerical results demonstrating the effectiveness of this approach in computing feedback controls for noise reduction are presented.
A HYBRID LANGUAGE MODEL BASED ON STATISTICS AND LINGUISTIC RULES (2005)

Language modeling is a current research topic in many domains including speech recognition, optical character recognition, handwriting recognition, machine translation and spelling correction. There are two main types of language models, the mathematical and the linguistic. The most widely used mathematical language model is the n-gram model inferred from statistics. This model has three problems: long distance restriction, recursive nature and partial language understanding. Language models based on linguistics present many difficulties when applied to large scale real texts. We present here a new hybrid language model that combines the advantages of the n-gram statistical language model with those of a linguistic language model which makes use of grammatical or semantic rules. Using suitable rules, this hybrid model can solve problems such as long distance restriction, recursive nature and partial language understanding. The new language model has been effective in experiments and has been incorporated in Chinese sentence input products for Windows and Macintosh OS.
Improved three-phase micro-inverter using dynamic dead time optimization and phase-skipping control techniques (2016)

This paper introduces two efficiency improvement techniques for a grid-tied micro-inverter with current mode control zero voltage switching (ZVS) output stages. The first technique is dynamic dead time optimization wherein PWM dead times are dynamically adjusted as a function of load current. The second method is advanced phase-skipping control which distributes power on individual phases depending on the available input power from PV source. Neither of the techniques require any additional components and both can be easily implemented in the digital controller firmware. The two techniques were designed and implemented in a 400W three-phase micro-inverter prototype and the experimental results confirm practical implementation of these techniques and demonstrate that significant efficiency improvement can be achieved.
Microfabricated Fountain Pens for High-Density DNA Arrays (2003)

We used photolithographic microfabrication techniques to create very small stainless steel fountain pens that were installed in place of conventional pens on a microarray spotter. Because of the small feature size produced by the microfabricated pens, we were able to print arrays with up to 25,000 spots/cm2, significantly higher than can be achieved by other deposition methods. This feature density is sufficiently large that a standard microscope slide can contain multiple replicates of every gene in a complex organism such as a mouse or human. We tested carryover during array printing with dye solution, labeled DNA, and hybridized DNA, and we found it to be indistinguishable from background. Hybridization also showed good sequence specificity to printed oligonucleotides. In addition to improved slide capacity, the microfabrication process offers the possibility of low-cost mass-produced pens and the flexibility to include novel pen features that cannot be machined with conventional techniques.
Dynamic Interrogation of Stochastic Transcriptome Trajectories (DIST2) (2020)

New methods in genomics allow the tracking of single cell transcriptome across tens of thousands of genes for hundreds of cells dynamically changing over time. These advancements open new computational problems and provide opportunity to explore new solutions to the interrogation of the transcriptome data in humans and in animal models. Common data analysis pipelines include a dimensionality reduction step to facilitate visualizing the data in two or three dimensions, (e.g. using t-distributed stochastic neighbor embedding (t-SNE)). Such methods reveal structure in high-dimensional data, while aiming at accurately representing global structure of the data. A potential pitfall of some methods is gross data loss when constraining the analyses to gene space data that is not asynchronously changing from day to day, or that express more stable variability of some genes relative to other genes.
Noninvasive Glucose Sensing with Raman Spectroscopy (2009)

This chapter contains sections titled: Introduction to Raman Spectroscopy Biological Considerations for Raman Spectroscopy Quantitative Considerations for Raman Spectroscopy Instrumentation Data Preprocessing In Vitro Studies In Vivo Studies Toward Prospective Application Conclusion References
Specific Antibody in IV Immunoglobulin for Postsplenectomy Sepsis (2013)

IV immunoglobulin showed a significantly protective effect on overwhelming postsplenectomy infection via enhancement of specific antibody-mediated phagocytosis in the liver. Specific antibody, more than immunological modulation, is crucial for effects of IV immunoglobulin on overwhelming postsplenectomy infection.
Impact of Specimen Heterogeneity on Biomarkers in Repository Samples from Patients with Acute Myeloid Leukemia: A SWOG Report (2017)

To our knowledge, this is the first study to provide evidence that using cryopreserved specimens can introduce uncontrollable variables that may impact biomarker results and enrichment for viable AML blasts may mitigate this impact.
Rescue of Misfolded Proteins and Stabilization by Small Molecules (2010)

Increasing stability of functional proteins by binding small compounds and ions has long been used to extend shelf-life of protein formulations in the pharmacological and biotechnological industry. Likewise, the therapeutic application of small molecules for in vivo recovery and maintenance of structure and function of proteins is steadily increasing. Compounds that can rescue misfolded proteins by stimulating their correct folding and/or the stabilization of native-like conformations in vivo are referred to as pharmacological chaperones. Here we present thermal-shift and isothermal methods for the high-throughput screening of stabilizing pharmacological chaperones for soluble and membrane proteins. The effect of selected hit compounds on the kinetics of protein synthesis is further evaluated by an in vitro transcription-translation rapid translation system. These procedures can be integrated in an interdisciplinary and translational approach for the search of personalized pharmacological chaperones in genetic misfolding diseases.
Interaction between chest wall motion and lung mechanics in normal infants and infants with bronchopulmonary dysplasia (1991)

Asynchronous or paradoxic motion between the rib cage and abdomen may be seen in infants with lung disease. We have recently shown that after bronchodilator administration, the degree of asynchrony decreases proportionately to the improvement in lung mechanics. However, whether such thoraco-abdominal asynchrony (TAA) is a useful indicator of lung function in a cross-sectional population, i.e., whether asynchrony correlates with baseline lung mechanics, is unknown. Therefore, we quantitated the degree of TAA using respiratory inductive plethysmography during quiet sleep in ten infants with bronchopulmonary dysplasia (BPD) and six weight-matched control infants. We displayed abdominal wall (AB) and rib cage (RC) motion on an X-Y recorder, and from the tidal breathing loop we calculated a phase angle phi, between 0 degrees and 180 degrees as an index of asynchrony (synchronous RC/AB motion = 0 degrees, paradox = 180 degrees). Lung resistance (RL) and compliance/kg (CL/kg) were calculated from esophageal and mouth pressure, tidal volume, and tidal flow. As expected, BPD infants had abnormally high RL, and low CL/kg when compared to controls. All infants with BPD displayed marked thoraco-abdominal asynchrony (phi = 102 +/- 16 degrees, mean +/- SEM; range 35 degrees-160 degrees) with controls displayed synchronous chest wall motion (phi = 8 +/- 3 degrees, range 0 degrees-15 degrees) (P less than 0.001). The degree of TAA was significantly correlated with RL (r = 0.773, P less than 0.001) and inversely correlated with CL/kg (r = -0.67, P less than 0.01). We conclude that in infants of similar weight, TAA may be used as a cross-sectional index reflecting both resistive and elastic properties of the lungs.
Neural network-based model of photoresist reflow (2019)

When polymers are heated above their glass transition temperature, they enter a viscous rubbery state that allows the polymer to be reshaped in a process called “reflow.” The final shape depends on the material, substrate, the initial dimensions of the structure, the reflow temperature, and time and is mostly governed by energy minimization. Most empirical models so far have used linear regression to predict scalar parameters like the thickness of the reflowed structure but do not account for intermediate shapes. In this work, the authors measure the profiles of photoresist patterns subjected to various reflow conditions, complementing results in the literature. Using shallow neural networks, they develop models to predict the type of shape produced after reflow and its full cross-sectional height profile. These models can serve as an aid for polymer engineering and fabrication and also demonstrate the usefulness of a neural network-based approach to physical optimization problems without analytical solutions.
The Pattern of Interleukin-1β (IL-1β) and Its Modulating Agents IL-1 Receptor Antagonist and IL-1 Soluble Receptor Type II in Acute Meningococcal Infections (1997)

Interleukin-1β (IL-1β) is considered an important mediator in the pathogenesis of septic shock or bacterial meningitis. Its activity is specifically modulated by IL-1 receptor antagonist (IL-1Ra) and IL-1 soluble receptor type II (IL-1sRII). We now describe the time-course of IL-1β and these modulating agents in 59 patients with acute meningococcal infections, the prototype human disease of acute endotoxin exposure. Plasma IL-1β was increased only in severe shock and normalized within 12 to 24 hours, indicating that patients were admitted in an early stage of cytokine activation. Increased IL-1β values in cerebrospinal fluid (CSF ) were confined to patients with meningitis. Plasma IL-1Ra was elevated in both shock and nonshock patients, extremely high values being measured in severe shock. High concentrations of IL-1Ra in CSF were found in meningitis. Plasma IL-1Ra peaked shortly after IL-1β and decreased steeply in 1 to 2 days, followed by sustained moderately elevated levels in shock patients. Interestingly, IL-1sRII showed a completely different pattern. At admission, both nonshock and shock patients manifested a similar moderate increase of plasma IL-1sRII. However, during recovery plasma IL-1sRII further increased reaching maximal concentrations 3 to 5 days after admission, 1 to 2 days after normalization of IL-1Ra. In shock patients this increase was more prominent than in nonshock patients. It is hypothesized that this increase in plasma IL-1sRII can be explained by a synergistic effect of dexamethasone and endotoxin. A second interesting observation was that, unlike the pattern in plasma, IL-1sRII levels in CSF paralleled those of IL-1β and IL-1Ra. This suggests different modulation of IL-1β activity in the subarachnoid space and the plasma compartment. We conclude that: (1) During the early stage of meningococcal infections IL-1Ra modulates IL-1 activity, whereas during recovery IL-1sRII may be more important. (2) Modulation in CSF and in the plasma compartment are differentially regulated.
Inside Back Cover: Light‐Driven C−H Oxygenation of Methane into Methanol and Formic Acid by Molecular Oxygen Using a Perfluorinated Solvent (Angew. Chem. Int. Ed. 8/2018) (2018)

Methane oxygenation by O2 occurred in a two-phase system comprising perfluorohexane and water under ambient conditions. In their Communication on page 2126 ff., K. Ohkubo and K. Hirose show that the chlorine dioxide radical (ClO2•) acts as an efficient oxidizing agent in the aerobic oxygenation of methane to methanol and formic acid under photoirradiation. The yields of methanol and formic acid were 14% and 85%, respectively.
Grammatical Error Generation Based on Translated Fragments (2021)

We perform neural machine translation of sentence fragments in order to create large amounts of training data for English grammatical error correction. Our method aims at simulating mistakes made by second language learners, and produces a wider range of non-native style language in comparison to state-of-the-art synthetic data creation methods. In addition to purely grammatical errors, our approach generates other types of errors, such as lexical errors. We perform grammatical error correction experiments using neural sequence-to-sequence models, and carry out quantitative and qualitative evaluation. A model trained on data created using our proposed method is shown to outperform a baseline model on test data with a high proportion of errors.
Covalent Triazine Framework Nanoparticles via Size‐Controllable Confinement Synthesis for Enhanced Visible‐Light Photoredox Catalysis (2020)

Abstract For metal‐free, organic conjugated polymer‐based photocatalysts, synthesis of defined nanostructures is still highly challenging. Here, we report the formation of covalent triazine framework (CTF) nanoparticles via a size‐controllable confined polymerization strategy. The uniform CTF nanoparticles exhibited significantly enhanced activity in the photocatalytic formation of dibenzofurans compared to the irregular bulk material. The optoelectronic properties of the nanometer‐sized CTFs could be easily tuned by copolymerizing small amounts of benzothiadiazole into the conjugated molecular network. This optimization of electronic properties led to a further increase in observed photocatalytic efficiency, resulting in total an 18‐fold enhancement compared to the bulk material. Full recyclability of the heterogeneous photocatalysts as well as catalytic activity in dehalogenation, hydroxylation and benzoimidazole formation reactions demonstrated the utility of the designed materials.
Stress migration in a copper - Aluminum hybrid technology (2014)

Stress migration (SM) time, temperature and process dependencies are investigated using a highly sensitive tungsten to copper interface combined with “plate-nose” and “mesh-nose” structures to accelerate the SM mechanism. Voids formed below the W via on the nose, and the resistance increases caused by these voids peaked at temperatures of 300-325°C. The effects of several copper line and tungsten via process steps are discussed. Process steps which modulated the Cu surface and Cu to via bottom interface had the largest effects.
Phenols as Diamagnetic T2‐Exchange Magnetic Resonance Imaging Contrast Agents (2017)

Although T<sub>2</sub> -exchange (T<sub>2ex</sub> ) NMR phenomena have been known for decades, there has been a resurgence of interest to develop T<sub>2ex</sub> MRI contrast agents. One indispensable advantage of T<sub>2ex</sub> MR agents is the possibility of using non-toxic and/or bio-compatible diamagnetic compounds with intermediate exchangeable protons. Herein a library of phenol-based compounds is screened and their T<sub>2ex</sub> contrast (exchange relaxivity, r<sub>2ex</sub> ) at 9.4 T determined. The T<sub>2ex</sub> contrast of phenol protons allows direct detection by MRI at a millimolar concentration level. The effect of chemical modification of the phenol on the T<sub>2ex</sub> MRI contrast through modulation of exchange rate and chemical shift was also studied and provides a guideline for use of endogenous and exogenous phenols for T<sub>2ex</sub> MRI contrast. As a proof-of-principle application, phenol T<sub>2ex</sub> contrast can be used to detect enzyme activity in a tyrosinase-catalyzed catechol oxidation reaction.