gebhart/patrepeval huggingface dataset:
Selective epitaxial growth of i n situ carbon‐doped silicon on silicon substrates (2008)

Abstract The characteristics of i n situ carbon‐doped Si fabricated by selective epitaxial growth (SEG) were investigated. We confirmed the good selectivity, high crystalline quality, high strain and constant carbon profile of the film. The high ratio of the concentration of carbon atoms located at the substitutional sites to that of the total carbon atoms was achieved at low‐temperature SEG. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Quantitative Analysis of Peptides with NMR Spectroscopy (1997)

The determination of peptide concentration with 1 H nuclear magnetic resonance (NMR) spectroscopy using an internal standard or an external standard in a sealed glass capillary was investigated for three tyrosine-containing tripeptides. Trimethylsilylpropionic acid (TSP) and maleic acid were tested as external standards for quantitation by proton NMR. Although comparable results were obtained for either standard, the performance of maleic acid was found to be superior because of its better long-term stability in the sealed capillary. Loss of TSP from solution occurred over time due to adsorption onto the walls of the capillary, necessitating frequent recalibration against the primary standard, potassium acid phthalate (KHP). The peptide contents of solid peptides determined with 1 H NMR are compared with those obtained from ultraviolet (UV) absorbance measurements of the tyrosine chromophore. The versatility of NMR for the quantitative analysis of peptides that do not contain an appropriate UV chromophore make it well-suited for the determination of peptide concentration in aggregation studies or for the preparation of solutions for high-throughput screening of biological activity.
Unusual Intensities in the Resonance Raman Spectra and Excitation Profiles of an Intervalence Metal-to-Metal Charge Transfer Complex (1997)

The resonance Raman spectra of the metal-to-metal charge transfer (MMCT) mixed-valence complex [(OC)5Cr0−CN−OsIII(NH3)5](CF3SO3)2 are measured and analyzed. The excitation profiles (the Raman intensities as a function of excitation wavelength) are obtained using the SO3 stretch of the triflate ion as an internal standard. The ratios of the Raman intensities are not constant with different excitation wavelengths. This unusual observation is attributed to interference between two overlapping electronic states of the molecule. The electronic states are observed in the low-temperature polarized single crystal absorption spectrum. The resonance Raman intensities and excitation profiles are calculated with the time dependent theory of spectroscopy and include the interference between the electronic states. The origin of the unusual intensities is quantitatively explained in terms of the real and imaginary parts of the Raman cross sections from the two states.
Rotationplasty with Tibial Nerve Coaptation (2023)

Tibial nerve resection is not an absolute contraindication for rotationplasty, even in an adolescent. Nerve coaptation allows for well-functioning rotationplasty as an alternative to endoprosthetic reconstruction or above-knee amputation.
Automatic real-time guidance of laser machining with inline coherent imaging (2011)

Optical coherence imaging can measure hole depth in real-time (&amp;gt;20 kHz) during laser drilling without being blinded by intense machining light or incoherent plasma emissions. Rapid measurement of etch rate and stochastic melt relaxation makes these images useful for process development and quality control in a variety of materials including metals, semiconductors, and dielectrics. The ability to image through the ablation crater in materials transparent to imaging light allows the guidance of blind hole cutting even with limited a priori knowledge of the sample. Significant improvement in hole depth accuracy with the application of manual feedback from this imaging has been previously demonstrated [P. J. L. Webster et al., Opt. Lett. 35, 646 (2010)]. However, the large quantity of raw data and computing overhead are obstacles for the application of coherent imaging as a truly automatic feedback mechanism. Additionally, the high performance components of coherent imaging systems designed for their traditional application in biological imaging are costly and may be unnecessary for materials processing. In this work, we present a coherent imaging system design that costs less than a fifth of comparable commercial products. We also demonstrate streamlined image processing suited for automated feedback that increases processing speed by two orders of magnitude.
PARP inhibitors attenuate chemotherapy‐induced painful neuropathy (2012)

Chemotherapy-induced peripheral neuropathy (CIPN) is a major toxicity of chemotherapy treatment for which no therapy is approved. Poly(ADP-ribose) polymerase (PARP)1/2 are nuclear enzymes activated upon DNA damage, and PARP1/2 inhibition provides resistance against DNA damage. A role for PARP inhibition in sensory neurotransmission has also been established. PARP inhibitors attenuate pain-like behaviors and neuropathy-associated decreased peripheral nerve function in diabetic models. The hypothesis tested was that PARP inhibition protects against painful neuropathy. The objective of this study was to investigate whether the novel, selective PARP1/2 inhibitors (ABT-888 and related analogues) would attenuate development of mechanical allodynia in vincristine-treated rats. PARP inhibitors were dosed for 2 days, and then co-administered with vincristine for 12 days. Mechanical allodynia was observed in rats treated with vincristine. PARP1/2 inhibition significantly attenuated development of mechanical allodynia and reduced poly ADP-ribose (PAR) activation in rat skin. The data presented here show that PARP inhibition attenuates vincristine-induced mechanical allodynia in rats, and supports that PARP inhibition may represent a novel therapeutic approach for CIPN.
Application of Interferons in the Control of Infectious Diseases of Cattle (1991)

Recovery from infection involves a number of complex interactions between specific cells of the immune system. Many of these interactions are mediated by cytokines, which can activate these cells to kill or reduce the replication rate of the pathogen. Availability of large quantities of recombinant cytokines has provided the opportunity to investigate the mechanism or mechanisms of action of each cytokine in vitro and in vivo. In the present review, we describe the application of interferons to reduce morbidity and mortality of cattle suffering from bovine respiratory disease and mastitis. The potential application of interferons in disease modulation as well as the impediments to their use are discussed.
Temporally Consistent Relighting for Portrait Videos (2022)

Ensuring ideal lighting when recording videos of people can be a daunting task requiring a controlled environment and expensive equipment. Methods were recently proposed to perform portrait relighting for still images, enabling after-the-fact lighting enhancement. However, naively applying these methods on each frame independently yields videos plagued with flickering artifacts. In this work, we propose the first method to perform temporally consistent video portrait relighting. To achieve this, our method optimizes end-to-end both desired lighting and temporal consistency jointly. We do not require ground truth lighting annotations during training, allowing us to take advantage of the large corpus of portrait videos already available on the internet. We demonstrate that our method outperforms previous work in balancing accurate relighting and temporal consistency on a number of real-world portrait videos.
Targeting von gastroenterologischen Tumoren mittels magnetischer Nanopartikel zur hyperthermischen Therapie (2017)

Magnetische Nanopartikel (superparamagnetic iron oxides = SPION) können zur hyperthermischen Therapie von gastrointestinalen Tumoren verwendet werden. Hierfür werden sie in eine periphere Vene injiziert und am Tumor mithilfe von endoskopisch platzierten Magnetfeldfallen akkumuliert. Durch Applikation eines alternierenden magnetischen Feldes werden die Eisenoxidkerne kontrolliert aufgeheizt. Zunächst wurde die Machbarkeit am Großtiermodell Schwein überprüft, bevor die Auswirkungen der magnetischen Hyperthermie in vitro untersucht wurden.
Androgen receptor transcriptionally regulates semaphorin 3C in a GATA2-dependent manner (2016)

The androgen receptor (AR) is a member of the nuclear receptor superfamily of transcription factors and is central to prostate cancer (PCa) progression. Ligand-activated AR engages androgen response elements (AREs) at androgen-responsive genes to drive the expression of gene batteries involved in cell proliferation and cell fate. Understanding the transcriptional targets of the AR has become critical in apprehending the mechanisms driving treatment-resistant stages of PCa. Although AR transcription regulation has been extensively studied, the signaling networks downstream of AR are incompletely described. Semaphorin 3C (SEMA3C) is a secreted signaling protein with roles in nervous system and cardiac development but can also drive cellular growth and invasive characteristics in multiple cancers including PCa. Despite numerous findings that implicate SEMA3C in cancer progression, regulatory mechanisms governing its expression remain largely unknown. Here we identify and characterize an androgen response element within the SEMA3C locus. Using the AR-positive LNCaP PCa cell line, we show that SEMA3C expression is driven by AR through this element and that AR-mediated expression of SEMA3C is dependent on the transcription factor GATA2. SEMA3C has been shown to promote cellular growth in certain cell types so implicit to our findings is the discovery of direct regulation of a growth factor by AR. We also show that FOXA1 is a negative regulator of SEMA3C. These findings identify SEMA3C as a novel target of AR, GATA2, and FOXA1 and expand our understanding of semaphorin signaling and cancer biology.
Vascular fungi alter the apoplastic purinergic signaling in plants by deregulating the homeostasis of extracellular ATP and its metabolite adenosine (2022)

Abstract Purinergic signaling activated by extracellular nucleotides and their derivative nucleosides trigger sophisticated signaling networks. The outcome of these pathways determine the capacity of the organism to survive under challenging conditions. Both extracellular ATP (eATP) and Adenosine (eAdo) act as secondary messengers in mammals, essential for immunosuppressive responses. Despite the clear role of eATP as a plant damage-associated molecular pattern, the function of its nucleoside, eAdo, and of the eAdo/eATP balance in plant stress response remain to be fully elucidated. This is particularly relevant in the context of plant/microbe interaction, where the intruder manipulates the extracellular matrix. Here, we identify Ado as a main elicitor secreted by the vascular fungus Fusarium oxysporum . We show that eAdo modulates the plant’s susceptibility to fungal colonization by altering eATP-mediated physiological immune responses, such as apoplastic pH and calcium homeostasis. Our work indicates that plant pathogens actively imbalance the eAdo/eATP levels as a virulence mechanism. One Sentence Summary The apoplastic Adenosine/ATP balance is a messenger for plant defense and can be manipulated by the fungal pathogen F. oxysporum .
Generation of anti-GD2 CAR macrophages from human pluripotent stem cells for cancer immunotherapies (2023)

Macrophages armed with chimeric antigen receptors (CARs) provide a potent new option for treating solid tumors. However, genetic engineering and scalable production of somatic macrophages remains significant challenges. Here, we used CRISPR-Cas9 gene editing methods to integrate an anti-GD2 CAR into the AAVS1 locus of human pluripotent stem cells (hPSCs). We then established a serum- and feeder-free differentiation protocol for generating CAR macrophages (CAR-Ms) through arterial endothelial-to-hematopoietic transition (EHT). CAR-M produced by this method displayed a potent cytotoxic activity against GD2-expressing neuroblastoma and melanoma in vitro and neuroblastoma in vivo. This study provides a new platform for the efficient generation of off-the-shelf CAR-Ms for antitumor immunotherapy.
Frequency-Time Scheduling for streaming services in OFDMA systems (2008)

This paper proposes a novel Frequency Time scheduler, called Frequency Time Scheduler with Delay Constraints (FTSDC), in order to handle streaming traffic in OFDMA (Orthogonal Frequency Division Multiple Access) system. Streaming technique, widely developed and used in the internet to convey multimedia application (e.g., audio, video clip, etc.), is supposed to occupy a large share of bandwidth in future wireless systems (e.g. WiMAX, LTE ldquoLong Term Evolutionrdquo, etc.). The stringent QoS constraints of these services may be reached at the expense of the system capacity and therefore a trade off between Fairness and capacity should be achieved. The novel opportunistic scheduler proposed in this paper balances this trade off and allows thus OFDMA systems to handle streaming services without losing much cell capacity. Results afforded by this scheduler are promising and show that it outperforms the existing scheduling algorithms.
Engineers improve recycling system used in fracking to save water and energy (2013)

In the USA, chemical engineers at The University of Texas at Austin have developed high-efficiency, durable filters to improve mobile water-recycling systems used in hydraulic fracturing – the oil and gas drilling process known as fracking. According to the researchers, the filters may significantly reduce the amount of water and energy that fracking requires.
ENISI SDE: A novel web-based stochastic modeling tool for computational biology (2013)

Stochasticity is part of the nature of many biological processes and an important aspect in modeling and simulations of computational biology. Gillespie's algorithm was developed for modeling stochasticity of chemical reactions and has been broadly applied to stochastic modeling in computational biology. The Gillespie's algorithm accounts for the particle effect in chemical reactions. However, many biological processes including cellular and molecular immunological mechanisms have many other sources of stochasticity such as cell movement, ligand binding, or unaccounted variation in experimental settings. In this paper, we propose stochastic differential equations (SDE) being used as a generic stochastic modeling technique for systems immunology. SDE has been widely used in statistics and economics areas; but only a few isolated studies in computational biology are found using SDE to model stochastic behaviors of cells and molecules. In addition, to the best of our knowledge, there is no user-friendly SDE-based modeling tool available for computational biologists. This paper presents ENISI SDE, a web-based user-friendly stochastic modeling tool for computational biologists. This work provides three major contributions: (1) we discuss SDE and propose it as a generic approach for stochastic modeling in computational biology; (2) we develop ENISI SDE, a web-based user-friendly SDE modeling tool that only requires little extra effort beyond regular ODE-based modeling; (3) we use the model SDE modeling tool to study stochastic sources of cell heterogeneity in the context of a CD4+ T Cell differentiation process. The case study clearly shows the effectiveness of SDE as a stochastic modeling approach in biology in general and immunology in particular and the power of the SDE modeling tool we developed.
Aurein-Derived Antimicrobial Peptides Formulated with Pegylated Phospholipid Micelles to Target Methicillin-Resistant Staphylococcus aureus Skin Infections (2018)

Antimicrobial peptides have been the focus of considerable research; however, issues associated with toxicity and aggregation have the potential to limit clinical applications. Here, a derivative of a truncated version of aurein 2.2 (aurein 2.2Δ3), namely peptide 73, was investigated, along with its d-amino acid counterpart (D-73) and a retro-inverso version (RI-73). A version that incorporated a cysteine residue to the C-terminus (73c) was also generated, as this form is required to covalently attach antimicrobial peptides to polymers (e.g., polyethylene glycol (PEG) or hyperbranched polyglycerol (HPG)). The antimicrobial activity of the 73-derived peptides was enhanced 2- to 8-fold, and all the derivatives eradicated preformed Staphylococcus aureus biofilms. Formulation of the peptides with compatible polyethylene glycol (PEG)-modified phospholipid micelles alleviated toxicity toward human cells and reduced aggregation. When evaluated in vivo, the unformulated d-enantiomers aggregated when injected under the skin of mice, but micelle encapsulated peptides were well absorbed. Pegylated micelle formulated peptides were investigated for their potential as therapeutic agents for treating high-density infections in a murine cutaneous abscess model. Formulated peptide 73 reduced abscess size by 36% and bacterial loads by 2.2-fold compared to the parent peptide aurein 2.2Δ3. Micelle encapsulated peptides 73c and D-73 exhibited superior activity, further reducing abscess sizes by 85% and 63% and lowering bacterial loads by 510- and 9-fold compared to peptide 73.
Characterization of H9N2 Avian Influenza Viruses Isolated from Poultry Products in a Mouse Model (2022)

Low pathogenic H9N2 avian influenza viruses have spread in wild birds and poultry worldwide. Recently, the number of human cases of H9N2 virus infection has increased in China and other countries, heightening pandemic concerns. In Japan, H9N2 viruses are not yet enzootic; however, avian influenza viruses, including H5N1, H7N9, H5N6, and H9N2, have been repeatedly detected in raw poultry meat carried by international flight passengers from Asian countries to Japan. Although H9N2 virus-contaminated poultry products intercepted by the animal quarantine service at the Japan border have been characterized in chickens and ducks, the biological properties of those H9N2 viruses in mammals remain unclear. Here, we characterized the biological features of two H9N2 virus isolates [A/chicken/Japan/AQ-HE28-50/2016 (Ck/HE28-50) and A/chicken/Japan/AQ-HE28-57/2016 (Ck/HE28-57)] in a mouse model. We found that these H9N2 viruses replicate well in the respiratory tract of infected mice without adaptation, and that Ck/HE28-57 caused body weight loss in the infected mice. Our results indicate that H9N2 avian influenza viruses isolated from raw chicken meat products illegally brought to Japan can potentially infect and cause disease in mammals.
A novel approach for embedding communication symbols into physical radar waveforms (2017)

Due to constantly increasing demand from commercial communications, defense applications are losing spectrum while still striving to maintain legacy capabilities, not to mention the need for enhanced performance. Consequently, ongoing research is focused on developing multi-function methods to share spectrum between radar and military communication. One approach is to incorporate information-bearing communication symbols into the emitted radar waveforms. However, varying the radar waveform during a coherent processing interval (CPI) causes range sidelobe modulation (RSM) that results in increased residual clutter in the range-Doppler response, thus leading to reduced target visibility. Here a novel approach is proposed to embed information into radar emissions while preserving constant envelope waveforms with good spectral containment. Information sequences are implemented using continuous phase modulation (CPM) and phase-attached to a polyphase-coded frequency-modulated (PCFM) radar waveform, the implementation of which is also derived from CPM. The resulting communication-embedded radar waveforms therefore maintain high power and spectral efficiency. More importantly, the adjustable parameterization of the proposed approach enables direct control of the degree of RSM by trading off bit error rate (BER) and/or data throughput.
ChemInform Abstract: New Insights into the Palladium‐Catalyzed Synthesis of δ‐ Lactones from 1,3‐Dienes and Carbon Dioxide. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Multiplex CRISPR strategy targeting viral genome for agriculture and clinical use (2022)

Abstract African Swine Fever (ASF) is a viral disease with exceptionally high lethality in domestic pigs and wild boar worldwide, without any effective vaccine or drug to prevent its spread. In this study, we established a multiplexable CRISPR-Cas-gRNA system targeting 13 genomic loci in the ASF virus genome that could prevent viral replication by cutting its genome. Furthermore, we generated pig strains expressing the multiplexable CRISPR-Cas-gRNA via germline genome editing and demonstrated that the gene-edited pigs were more resistant to ASFV infection and less likely to spread the virus upon infection. As far as we know, our study presents the first living organism generated via germline editing to demonstrate resistance to viral infection via CRISPR-Cas. We anticipate our work to be helpful for both agricultural and biomedical applications, such as xenotransplantation.
Angiotensin-converting enzyme inhibitors predict acute kidney injury during chemoradiation for head and neck cancer (2014)

Head and neck cancer patients undergoing chemoradiation experience considerable toxicities including acute kidney injury (AKI). However, it remains unclear what factors predispose patients to renal toxicity during treatment. Here, we assessed the predictors and outcomes of patients experiencing AKI during chemoradiation. We carried out a retrospective cohort study to assess the maximum changes in serum creatinine (Cr) in 173 patients with stage III-IV head and neck cancer treated with chemoradiation between 1999 and 2012. We defined AKI as Cr increases 26.5 µmol/l or more over the pretreatment baseline. AKI was associated with angiotensin-converting enzyme inhibitor (ACEI) use (33.0 vs. 11.0%; P=0.0004), but no other medications or comorbidities. On multivariate analysis, ACEI use, weight loss 10% or more of body weight, and performance status 70 or more predicted for Cr increments 26.5 µmol/l or more, whereas only ACEI use predicted for Cr increments of 44.2 µmol/l or greater. Furthermore, on multivariate analysis, AKI predicted for more interventions during radiotherapy including intravenous fluid use (P=0.0005) and hospitalizations (P=0.007), as well as long-term renal dysfunction (P<0.0001). Renal toxicity was not associated with worse locoregional control, progression-free survival, or overall survival. Renal toxicity during chemoradiation was associated with ACEI use alone or coupled with weight loss 10% or more of body weight during therapy. Our results suggest that actively managing ACEI use and intravascular volume status during chemoradiation may avoid AKI, minimize subsequent interventions, and reduce the risk for long-term renal dysfunction.