gebhart/patrepeval huggingface dataset:
Nanopillar Polymer Films as Antibacterial Packaging Materials (2022)

This work presents a comprehensive analytical survey of the antibacterial and antibiofouling properties of sub-100-nanometer scale nanopatterned polymers fabricated using scalable industrial processes that are directly applicable for commercial use. Regular nanopillar arrays of 60 nm height and 60 nm pitch were fabricated on polyethylene terephthalate (PET), polypropylene (PP), acrylic, and nylon polymer films using nanoimprint lithography. Analyses of the influence of material type on antibacterial performance revealed that the nanoscale patterns produced using acrylic and nylon polymers were most suitable as anti-infective nanostructured materials. Further assessment of the influence of the nanopattern geometric parameters on the antibacterial efficacy of acrylic and nylon materials revealed the superlative pattern for inactivating and repelling both Gram-positive and Gram-negative bacteria. Acrylic nanostructured films consisting of nanopillars with a height of 60 nm and pitch of 30 nm, respectively, demonstrated distinctly superior antimicrobial and antibiofouling behavior toward both Gram-negative Pseudomonas aeruginosa and Gram-positive Staphylococcus aureus bacterial species.
Distinct Roles of JNKs/p38 MAP Kinase and ERKs in Apoptosis and Survival of HCD-57 Cells Induced by Withdrawal or Addition of Erythropoietin (1999)

Erythropoietin (EPO), a major regulator of erythroid progenitor cells, is essential for the survival, proliferation, and differentiation of immature erythroid cells. To gain insight into the molecular mechanism by which EPO functions, we analyzed the activation of Jun N-terminal kinases (JNKs) and extracellular signal-regulated kinases (ERKs) in HCD-57 cells, a murine erythroid progenitor cell line that requires EPO for survival and proliferation. Withdrawal of EPO from the cell culture medium resulted in sustained activation of JNKs plus p38 MAP kinase, and inactivation of ERKs, preceding apoptosis of the cells. Addition of EPO to the EPO-deprived cells caused activation of ERKs accompanied by inactivation of JNKs and p38 MAP kinase and rescued the cells from apoptosis. Phorbol 12-myristate 13-acetate, which activated ERKs by a different mechanism, also suppressed the activation of JNKs and significantly retarded apoptosis of the cells caused by withdrawal of EPO. Furthermore, MEK inhibitor PD98059, which inhibited activation of ERKs, caused activation of JNKs, whereas suppression of JNK expression by antisense oligonucleotides and inhibition of p38 MAP kinase by SB203580 caused attenuation of the apoptosis that occurs upon withdrawal of EPO. Finally, the activation of JNKs and p38 MAP kinase and concurrent inactivation of ERKs upon withdrawal of EPO were also observed in primary human erythroid colony-forming cells. Taken together, the data suggest that activation of ERKs promotes cell survival, whereas activation of JNKs and p38 MAP kinase leads to apoptosis and EPO functions by controlling the dynamic balance between ERKs and JNKs.
VEGF-C signaling pathways through VEGFR-2 and VEGFR-3 in vasculoangiogenesis and hematopoiesis (2000)

Signaling by vascular endothelial growth factors (VEGFs) through VEGF receptors (VEGFRs) plays important roles in vascular development and hematopoiesis. The authors analyzed the function of VEGF-C signaling through both VEGFR-2 and VEGFR-3 in vasculoangiogenesis and hematopoiesis using a coculture of para-aortic splanchnopleural mesoderm (P-Sp) explants from mouse embryos with stromal cells (OP9). Vasculogenesis and angiogenesis were evaluated by the extent of vascular bed and network formation, respectively. Addition of VEGF-C to the P-Sp culture enhanced vascular bed formation and suppressed definitive hematopoiesis. Both vascular bed and network formations were completely suppressed by addition of soluble VEGFR-1–Fc competitor protein. Formation of vascular beds but not networks could be rescued by VEGF-C in the presence of the competitor, while both were rescued by VEGF-A. VEGFR-3–deficient embryos show the abnormal vasculature and severe anemia. Consistent with these in vivo findings, vascular bed formation in the P-Sp from the VEGFR-3–deficient embryos was enhanced to that in wild-type or heterozygous embryos, and hematopoiesis was severely suppressed. When VEGFR-3–Fc chimeric protein was added to trap endogenous VEGF-C in the P-Sp culture of the VEGFR-3–deficient embryos, vascular bed formation was suppressed and hematopoiesis was partially rescued. These results demonstrate that because VEGF-C signaling through VEGFR-2 works synergistically with VEGF-A, the binding of VEGF-C to VEGFR-3 consequently regulates VEGFR-2 signaling. In VEGFR-3–deficient embryos, an excess of VEGF-C signals through VEGFR-2 induced the disturbance of vasculogenesis and hematopoiesis during embryogenesis. This indicates that elaborated control through VEGFR-3 signaling is critical in vasculoangiogenesis and hematopoiesis.
Efficient Synthesis of DNA Containing the Guanine Oxidation-Nitration Product 5-Guanidino-4-nitroimidazole:  Generation by a Postsynthetic Substitution Reaction (2003)

[reaction: see text] A convertible nucleoside was synthesized and used to prepare the 2'-deoxynucleoside of 5-guanidino-4-nitroimidazole, a putative in vivo product of the reaction of peroxynitrite with guanine. The convertible nucleoside was incorporated into an oligodeoxynucleotide by the phosphoramidite method and converted postsynthetically to yield an oligodeoxynucleotide containing 5-guanidino-4-nitroimidazole at a specific site. The oligodeoxynucleotide was inserted into a viral genome. Melting temperature analysis revealed that duplexes containing 5-guanidino-4-nitroimidazole were greatly destabilized relative to unmodified duplexes.
High performance 32nm SOI CMOS with high-k/metal gate and 0.149µm 2 SRAM and ultra low-k back end with eleven levels of copper (2006)

This work presents a 32 nm SOI CMOS technology featuring high-k/metal gate and an SRAM cell size of 0.149 µm2. V min operation down to 0.6 V in a 16Mb SRAM array test vehicle has been demonstrated. Aggressive ground rules are achieved with 193 nm immersion lithography. High performance is enabled by hig-hk/metal gate plus innovation on strained silicon elements including embedded SiGe and dual stress liner (DSL). Gate lengths down to 25 nm have been demonstrated enabling performance without the power penalty from gate capacitance. AC drive currents of 1.55 mA/um and 1.22 mA/um have been achieved at an off-state of 100 nA/µm and V DD of 1 V for NFET and PFET, respectively. For the first time, we have also demonstrated that SOI maintains performance benefit over bulk silicon in high-k/metal gate and 32 nm ground rules.
The Role of Humoral Immunity in the Defense Against Pneumocystis (2004)

I. Introduction The immune system comprises a complex organization of innate and adaptive host defenses involving multiple organs. These include organ systems with mucosal surfaces, such as the respiratory and alimentary tracts, that encounter the bulk of the microbes to which we are exposed. The circulatory and lymphatic systems are classically thought of as contributing cellular and humoral adaptive immune mechanisms against infection. Nontraditional ‘‘immune’’ organ systems such as the central nervous and endocrine systems also participate in immunity against infection. As our understanding of immune defense mechanisms deepens, we come to see that the defense against most microorganisms is usually multifactorial. Thus, while it may be somewhat artificial to focus on a single aspect of the immune response in the defense against an infectious agent, such an approach may be useful in helping us to understand how various elements of host immunity can bring about control of an infection. In this chapter, we summarize the evidence that antibody-mediated immunity is critical in protecting against the development of Pneumocystis pneumonia (PcP), knowing full well that many components of the immune system interact to control disease produced by Pneumocystis. We also briefly describe examples of antibody-mediated immunity against other fungi as models that may provide a guide for future studies on Pneumocystis.
Genetic Algorithms for the Optimization of Diffusion Parameters in Content-Based Image Retrieval (2019)

Several computer vision and artificial intelligence projects are nowadays exploiting the manifold data distribution using, e.g., the diffusion process. This approach has produced dramatic improvements on the final performance thanks to the application of such algorithms to the kNN graph. Unfortunately, this recent technique needs a manual configuration of several parameters, thus it is not straightforward to find the best configuration for each dataset. Moreover, the brute-force approach is computationally very demanding when used to optimally set the parameters of the diffusion approach. We propose to use genetic algorithms to find the optimal setting of all the diffusion parameters with respect to retrieval performance for each different dataset. Our approach is faster than others used as references (brute-force, random-search and PSO). A comparison with these methods has been made on three public image datasets: Oxford5k, Paris6k and Oxford105k.
Development of Liposomal Gemcitabine with High Drug Loading Capacity (2019)

Liposomes are widely used for systemic delivery of chemotherapeutic agents to reduce their nonspecific side effects. Gemcitabine (Gem) makes a great candidate for liposomal encapsulation due to the short half-life and nonspecific side effects; however, it has been difficult to achieve liposomal Gem with high drug loading capacity. Remote loading, which uses a transmembrane pH gradient to induce an influx of drug and locks the drug in the core as a sulfate complex, does not serve Gem as efficiently as doxorubicin (Dox) due to the low p K<sub>a</sub> value of Gem. Existing studies have attempted to improve Gem loading capacity in liposomes by employing lipophilic Gem derivatives or creating a high-concentration gradient for active loading into the hydrophilic cores (small volume loading). In this study, we combine the remote loading approach and small volume loading or hypertonic loading, a new approach to induce the influx of Gem into the preformed liposomes by high osmotic pressure, to achieve a Gem loading capacity of 9.4-10.3 wt % in contrast to 0.14-3.8 wt % of the conventional methods. Liposomal Gem showed a good stability during storage, sustained-release over 120 h in vitro, enhanced cellular uptake, and improved cytotoxicity as compared to free Gem. Liposomal Gem showed a synergistic effect with liposomal Dox on Huh7 hepatocellular carcinoma cells. A mixture of liposomal Gem and liposomal Dox delivered both drugs to the tumor more efficiently than a free drug mixture and showed a relatively good anti-tumor effect in a xenograft model of hepatocellular carcinoma. This study shows that bioactive liposomal Gem with high drug loading capacity can be produced by remote loading combined with additional approaches to increase drug influx into the liposomes.
Experimental Validation of Numerical Simulation for An Acoustic Liner in Grazing Flow (2013)

A coordinated experimental and numerical simulation effort is carried out to improve our understanding of the physics of acoustic liners in a grazing flow as well our computational aeroacoustics (CAA) method prediction capability. A numerical simulation code based on advanced CAA methods is developed. In a parallel effort, experiments are performed using the Grazing Flow Impedance Tube at the NASA Langley Research Center. In the experiment, a liner is installed in the upper wall of a rectangular flow duct with a 2 inch by 2.5 inch cross section. Spatial distribution of sound pressure levels and relative phases are measured on the wall opposite the liner in the presence of a Mach 0.3 grazing flow. The computer code is validated by comparing computed results with experimental measurements. Good agreements are found. The numerical simulation code is then used to investigate the physical properties of the acoustic liner. It is shown that an acoustic liner can produce self-noise in the presence of a grazing flow and that a feedback acoustic resonance mechanism is responsible for the generation of this liner self-noise. In addition, the same mechanism also creates additional liner drag. An estimate, based on numerical simulation data, indicates that for a resonant liner with a 10% open area ratio, the drag increase would be about 4% of the turbulent boundary layer drag over a flat wall.
1700V Bi-Mode Insulated Gate Transistor (BIGT) on Thin Wafer Technology (2010)

An advanced Reverse Conducting (RC) IGBT concept referred to as the Bi-mode Insulated Gate Transistor (BIGT) has been previously documented mainly for high voltage devices rated at 3300V. In this paper, we report on the progress made to implement the new technology for lower voltage classes rated below 2000V which would require complex thin wafer processing for the design realization. The paper covers mainly the process challenges met to introduce the BIGT into the lower voltage class and present the latest test results of the first thin wafer 1700V/150A prototype BIGT in both IGBT and diode mode of operation.
Early‐onset Parkinson's disease caused by a compound heterozygous DJ‐1 mutation (2003)

Mutations in DJ-1 have been linked to an autosomal recessive form of early-onset parkinsonism. To identify mutations causing Parkinson's disease (PD), we sequenced exons 1 through 7 of DJ-1 in 107 early-onset (age at diagnosis up to 50 years) PD subjects. One subject had a frameshift mutation in the first coding exon and an exon 7 splice mutation both predicted to result in a loss of functional protein. This subject was diagnosed with probable PD at age 24 years with asymmetric onset and an excellent response to levodopa therapy. Our observations suggest that sequence alterations in DJ-1 are a rare cause of early-onset PD.
PAWP, a Sperm-specific WW Domain-binding Protein, Promotes Meiotic Resumption and Pronuclear Development during Fertilization (2007)

We report a novel alkaline extractable protein of the sperm head that exclusively resides in the post-acrosomal sheath region of the perinuclear theca (PT) and is expressed and assembled in elongating spermatids. It is a protein that shares sequence homology to the N-terminal half of WW domain-binding protein 2, while the C-terminal half is unique and rich in proline. A functional PPXY consensus binding site for group-I WW domain-containing proteins, and numerous unique repeating motifs, YGXPPXG, are identified in the proline-rich region. Considering these molecular characteristics, we designated this protein PAWP for postacrosomal sheath WW domain-binding protein. Microinjection of recombinant PAWP or alkaline PT extract into metaphase II-arrested porcine, bovine, macaque, and Xenopus oocytes induced a high rate of pronuclear formation, which was prevented by co-injection of a competitive PPXY motif containing peptide derived from PAWP but not by co-injection of the point-mutated peptide. Intracytoplasmic sperm injection (ICSI) of porcine oocytes combined with co-injection of the competitive PPXY peptide or an anti-recombinant PAWP antiserum prevented pronuclear formation and arrested fertilization. Conversely, co-injection of the modified PPXY peptide, when the tyrosine residue of PPXY was either phosphorylated or substituted with phenylalanine, did not prevent ICSI-induced fertilization. This study uncovers a group I WW domain module signal transduction event within the fertilized egg that appears compulsory for meiotic resumption and pronuclear development during egg activation and provides compelling evidence that a PPXY motif of sperm-contributed PAWP can trigger these events.
Supplementary Figures and Tables from Clonal Spreading of Tumor-Infiltrating T Cells Underlies the Robust Antitumor Immune Responses (2023)

&lt;p&gt;Supplementary Figure S1-S5, Table S1-S12&lt;/p&gt;
Digestion Performance of Various Combinations of Thermophilic and Mesophilic Sludge Digestion Systems (2010)

Various combinations of single- and multi-stage anaerobic and aerobic-anaerobic digestion systems were studied to evaluate their solids reduction potential with capabilities to control sulfur-based biosolids odor compounds. All the multi-stage digestion systems removed more volatile solids than the single-stage anaerobic digestion systems, even at the same overall retention time. However, digestion systems with mesophilic digestion as the final stage showed a much lower headspace organic sulfur content in the dewatered biosolids than the systems with thermophilic digestion as the final stage. This observation leads to the conclusion that placing a mesophilic anaerobic digestion system at the end of multi-stage digestion systems will enable greater sulfur-based odor reduction from dewatered biosolids with greater solid reduction than single-stage mesophilic or thermophilic digestion systems.
Increased Production of Tumor Necrosis Factor- α Induces Apoptosis after Traumatic Spinal Cord Injury in Rats (2003)

We showed previously that, after spinal cord injury (SCI), tumor necrosis factor-alpha (TNF-alpha) may serve as an external signal, initiating apoptosis in neurons and oligodendrocytes. To further characterize the apoptotic cascade initiated by TNF-alpha after SCI, we examined the expression of TNF-alpha, inducible nitric oxide (NO) synthase (iNOS), and the level of NO after SCI. Western blots and reverse transcription polymerase chain reactions showed an early upregulation of TNF-alpha after injury. A peak TNF-alpha expression was observed within 1 h of injury. By 4 h after injury, the expression of iNOS and the level of NO were markedly increased in the injured spinal cord. Terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate-biotin nick end labeling (TUNEL)-positive cells were also first observed in the lesioned area 4 h after SCI. The largest number of TUNEL-positive cells was observed between 24-48 h after SCI. Injecting a neutralizing antibody against TNF-alpha into the lesion site after injury significantly reduced the expression of iNOS, the level of NO and the number of TUNEL-positive cells in the injured spinal cord. Injecting the NOS inhibitors, N(G)-monomethyl-L-arginine monoacetate and S-methylisothiourea sulfate, or an NO scavenger, carboxy-PTIO, into the lesion site also significantly reduced the level of NO and the degree of DNA laddering in the injured spinal cord. These data suggest that after SCI, apoptosis induced by TNF-alpha may be mediated in part by NO via upregulation of iNOS, induced in response to TNF-alpha.
Materials characterization for process integration of multi-channel gate all around (GAA) devices (2017)

Multi-channel gate all around (GAA) semiconductor devices march closer to becoming a reality in production as their maturity in development continues. From this development, an understanding of what physical parameters affecting the device has emerged. The importance of material property characterization relative to that of other physical parameters has continued to increase for GAA architecture when compared to its relative importance in earlier architectures. Among these materials properties are the concentration of Ge in SiGe channels and the strain in these channels and related films. But because these properties can be altered by many different process steps, each one adding its own variation to these parameters, their characterization and control at multiple steps in the process flow is crucial. This paper investigates the characterization of strain and Ge concentration, and the relationships between these properties, in the PFET SiGe channel material at the earliest stages of processing for GAA devices. Grown on a bulk Si substrate, multiple pairs of thin SiGe/Si layers that eventually form the basis of the PFET channel are measured and characterized in this study. Multiple measurement techniques are used to measure the material properties. In-line X-Ray Photoelectron Spectroscopy (XPS) and Low Energy X-Ray Fluorescence (LE-XRF) are used to characterize Ge content, while in-line High Resolution X-Ray Diffraction (HRXRD) is used to characterize strain. Because both patterned and un-patterned structures were investigated, scatterometry (also called optical critical dimension, or OCD) is used to provide valuable geometrical metrology.
Esophageal Dysmotility in Patients following Total Laryngectomy (2017)

Objectives Dysphagia is common in total laryngectomees, with some symptoms suggesting esophageal dysmotility. Tracheoesophageal (TE) phonation requires effective esophagopharyngeal air passage. Hence, esophageal dysmotility may affect deglutition or TE phonation. This study aimed to determine (1) the characteristics of esophageal dysmotility in laryngectomees, (2) whether clinical history is sensitive in detecting esophageal dysmotility, and (3) the relationship between esophageal dysmotility and TE prosthesis dysfunction. Study Design Multidisciplinary cross-sectional study. Setting Tertiary academic hospital. Subjects and Methods For 31 participants undergone total laryngectomy 1 to 12 years prior, clinical histories were taken by a gastroenterologist and a speech pathologist experienced in managing dysphagia. Esophageal high-resolution manometry was performed and analyzed using Chicago Classification v3.0. Results Interpretable manometric studies were obtained in 23 (1 normal manometry). Esophageal dysmotility patterns included achalasia, esophagogastric junction outflow obstruction, diffuse esophageal spasm, and other major (30%) and minor (50%) peristaltic disorders. The sensitivity of predicting any esophageal dysmotility was 28%, but it is noteworthy that patients with achalasia and diffuse esophageal spasm (DES) were predicted. Two of 4 participants with TE puncture leakage had poor esophageal clearance. Of 20 TE speakers, 12 had voice problems, no correlation between poor voice, and any dysmotility pattern. Conclusions Peristaltic and lower esophageal sphincter dysfunction are common in laryngectomees. Clinical history, while not predictive of minor motor abnormalities, predicted correctly cases with treatable spastic motor disorders. Dysmotility was not associated with poor phonation, although TE puncture leakage might be linked to poor esophageal clearance. Esophageal dysmotility should be considered in the laryngectomees with persisting dysphagia or leaking TE puncture.
Force Relationships for an XYZ Micromanipulator With Three Translational Degrees of Freedom (2004)

This paper introduces the force analysis of the XYZ Micromanipulator (XYZM). The XYZM has three independent linear inputs and a positioning platform. The positioning platform remains horizontal throughout its motion and has translation in the x, y, and z directions. The design and displacement analysis for the XYZM was reported previously. This paper concentrates on the input-output force relationships and the derivation of the XYZM kinematic coefficients. Equations for the three versions of the XYZM are reported and sample results provided. Slider displacements of 45 micrometers result in a predicted out-of-plane displacement of 188 micrometers for the rigid-body XYZM and 262 micrometers for the compliant XYZM. This correlates to output force of 286 micronewtons with an input force of 150 micronewtons for the rigid-body XYZM and 261 micronewton output force with an input force of 150 micronewtons for the compliant XYZM.