gebhart/patrepeval huggingface dataset:
Improved jellyfish gelatin quality through ultrasound-assisted salt removal and an extraction process (2022)

The use of by-products of salted jellyfish for gelatin production offers valuable gelatin products rather than animal feed. Several washes or washing machines have reported removing salt in salted jellyfish. However, the green ultrasound technique has never been reported for the desalination of salted jellyfish. The objectives were to determine how effectively the raw material's salt removal was done by combining the traditional wash and then subjected to the ultrasonic waves in a sonication bath for 20-100 min. For gelatin production, the ultrasonicated jellyfish by-products were pretreated with sodium hydroxide and hydrochloric acid, washed, and extracted with hot water for 4, 6, and 8 h. Results showed that the increased duration of ultrasound time increased the desalination rate. The highest desalination rate of 100% was achieved using 100 min ultrasonic time operated at a fixed frequency (40 kHz) and power (220 W). The jellyfish gelatin extracted for 4, 6, and 8 h showed gel strengths in 121-447, 120-278, and 91-248 g. The 80 min ultrasonicated sample and hot water extraction for 8 h (JFG80-8) showed the highest gel yield of 32.69%, with a gel strength of 114.92 g. Still, the 40 min ultrasonicated sample with 4 h of extraction delivered the highest gel strength of 447.01 g (JFG40-4) and the lower yield of 10.60%. The melting and gelling temperatures of jellyfish gelatin from ultrasonicated samples ranged from 15-25°C and 5-12°C, which are lower than bovine gelatin (BG) and fish gelatin (FG). Monitored by FITR, the synergistic effect of extended sonication time (from 20-100 min) with 4 h extraction time at 80 °C caused amide I, II, and III changes. Based on the proteomic results, the peptide similarity of JFG40-4, having the highest gel strength, was 17, 23, or 20 peptides compared to either BG, FG, or JFG100-8 having the lowest gel strength. The 14 peptides were similarly found in all JFG40-4, BG, and FG samples. In conclusion, for the first time in this report, the improved jellyfish gel can be achieved when combined with traditional wash and 40 min ultrasonication of desalted jellyfish and extraction time of 4 h at 80 °C.
Outside Front Cover: Biotechnology Journal 3/2020 (2020)

A label-free and enzyme-free uracil DNA glycosylase (UDG) activity assay is described. In the upper left bubble, detection duplex probe serving as substrate for UDG releases a catalyst strand (blue strand) due to the UDG-catalyzed degradation of uracil, which subsequently promotes the toehold-mediated strand displacement (TMSD) reaction in the upper right bubble. As a result, active split G-quadruplexes are produced leading to the colorimetric response in the bottom bubble. This is reported by Youna Kim, Yeonkyung Park, Chang Yeol Lee, Hyun Gyu Park in article 1900420.
An algorithm-architecture co-design framework for gridding reconstruction using FPGAs (2011)

Gridding is a method of interpolating irregularly sampled data on to a uniform grid and is a critical image reconstruction step in several applications which operate on non-Cartesian sampled data. In this paper, we present an algorithm architecture co-design framework for accelerating gridding using FPGAs. We present a parameterized hardware library for accelerating gridding to support both arbitrary and regular trajectories. We further describe our kernel automation framework which supports several kernel functions through look-up-table (LUT) based Taylor polynomial evaluation. This framework is integrated using an in-house multi-FPGA development platform which provides hardware infrastructure for integrating custom accelerators. Design-space exploration is enabled by an automation flow which allows system generation from an algorithm specification. We further provide several case studies by realizing systems for nonuniform fast Fourier transform (NuFFT) with different parameter sets and porting them on to the BEE3 platform. Results show speedups of more than 16X and 2X over existing CPU and FPGA implementations respectively, and up to 5.5 times higher performance-per-watt over a comparable GPU implementation.
Principles and Guidelines for Sharing Biomedical Data for Secondary Use: The University of Chicago Perspective (2023)

Academic medical centers are generating an increasing amount of biomedical data and there is an increasing demand for biomedical data for research purposes by research projects, research consortia, companies, and other third parties. At the same time, as the number of patients grows and the amount of data per patient grows, there is an increasing possibility that some information about some patients may become available if the data is shared with third parties and the third parties have a data breach or violate the terms of the data use agreement. Balancing the importance of research that may result in improved patient outcomes with the importance of protecting patient data is challenging. The article discusses the principles, considerations about risks and mitigating risks, and guidelines used at the University of Chicago used for making decisions about sharing biomedical data with third parties.
Triple Combination of Amantadine, Ribavirin, and Oseltamivir Is Highly Active and Synergistic against Drug Resistant Influenza Virus Strains In Vitro (2010)

The rapid emergence and subsequent spread of the novel 2009 Influenza A/H1N1 virus (2009 H1N1) has prompted the World Health Organization to declare the first pandemic of the 21st century, highlighting the threat of influenza to public health and healthcare systems. Widespread resistance to both classes of influenza antivirals (adamantanes and neuraminidase inhibitors) occurs in both pandemic and seasonal viruses, rendering these drugs to be of marginal utility in the treatment modality. Worldwide, virtually all 2009 H1N1 and seasonal H3N2 strains are resistant to the adamantanes (rimantadine and amantadine), and the majority of seasonal H1N1 strains are resistant to oseltamivir, the most widely prescribed neuraminidase inhibitor (NAI). To address the need for more effective therapy, we evaluated the in vitro activity of a triple combination antiviral drug (TCAD) regimen composed of drugs with different mechanisms of action against drug-resistant seasonal and 2009 H1N1 influenza viruses. Amantadine, ribavirin, and oseltamivir, alone and in combination, were tested against amantadine- and oseltamivir-resistant influenza A viruses using an in vitro infection model in MDCK cells. Our data show that the triple combination was highly synergistic against drug-resistant viruses, and the synergy of the triple combination was significantly greater than the synergy of any double combination tested (P<0.05), including the combination of two NAIs. Surprisingly, amantadine and oseltamivir contributed to the antiviral activity of the TCAD regimen against amantadine- and oseltamivir-resistant viruses, respectively, at concentrations where they had no activity as single agents, and at concentrations that were clinically achievable. Our data demonstrate that the TCAD regimen composed of amantadine, ribavirin, and oseltamivir is highly synergistic against resistant viruses, including 2009 H1N1. The TCAD regimen overcomes baseline drug resistance to both classes of approved influenza antivirals, and thus may represent a highly active antiviral therapy for seasonal and pandemic influenza.
Quantitative Analysis of Hexahydro-1,3,5-trinitro-1,3,5, Triazine/Pentaerythritol Tetranitrate (RDX–PETN) Mixtures by Terahertz Time Domain Spectroscopy (2015)

Absorption spectra of explosives such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), pentaerythritol tetranitrate (PETN), and mixtures of both were measured by terahertz time domain spectroscopy (THz-TDS). Chemometrics was applied to quantitative analysis of terahertz absorbance spectra obtained in transmission mode to predict the relative amounts of RDX and PETN in samples containing pure components or their mixtures. This analysis was challenging because significant spectral overlap prevented identification of each product fingerprint. Partial least squares (PLS) regression models were thus applied to the terahertz spectra. A comparison between the so-called PLS1 and PLS2 algorithms was performed to predict the PETN concentrations in mixture samples. PLS2 demonstrated better predictive ability than PLS1 with RMSE value lower than 3.5 mg for 400 mg total weight pellets. Moreover, the influence of the highly overlapping spectral frequency band was investigated by reducing the original 0.2-3 THz (6-100 cm(-1)) spectral band to 1.8-3 THz (60-100 cm(-1)). The predictive ability was quite similar in both cases, highlighting the excellent ability of chemometrics to perform quantitative analysis when applied to THz-TDS data, even in the case of highly overlapping spectra.
Quantitative analysis of aberrant protein glycosylation in liver cancer plasma by AAL-enrichment and MRM mass spectrometry (2013)

A lectin-coupled mass spectrometry (MS) approach was employed to quantitatively monitor aberrant protein glycosylation in liver cancer plasma. To do this, we compared the difference in the total protein abundance of a target glycoprotein between hepatocellular carcinoma (HCC) plasmas and hepatitis B virus (HBV) plasmas, as well as the difference in lectin-specific protein glycoform abundance of the target glycoprotein. Capturing the lectin-specific protein glycoforms from a plasma sample was accomplished by using a fucose-specific aleuria aurantia lectin (AAL) immobilized onto magnetic beads via a biotin-streptavidin conjugate. Following tryptic digestion of both the total plasma and its AAL-captured fraction of each HCC and HBV sample, targeted proteomic mass spectrometry was conducted quantitatively by a multiple reaction monitoring (MRM) technique. From the MRM-based analysis of the total plasmas and AAL-captured fractions, differences between HCC and HBV plasma groups in fucosylated glycoform levels of target glycoproteins were confirmed to arise from both the change in the total protein abundance of the target proteins and the change incurred by aberrant fucosylation on target glycoproteins in HCC plasma, even when no significant change occurs in the total protein abundance level. Combining the MRM-based analysis method with the lectin-capturing technique proved to be a successful means of quantitatively investigating aberrant protein glycosylation in cancer plasma samples. Additionally, it was elucidated that the differences between HCC and control groups in fucosylated biomarker candidates A1AT and FETUA mainly originated from an increase in fucosylation levels on these target glycoproteins, rather than an increase in the total protein abundance of the target glycoproteins.
The molecular biology of serotonin receptors. An overview. (1991)

Recently, the family of G protein-coupled serotonin (5-hydroxytryptamine[5-HT]) receptors has begun to yield to molecular analysis. The cloning of the 5-HT1C and 5-HT2 receptors has provided a structural basis for the similarities observed in their pharmacologic properties. Furthermore, pharmacologic characterization of the transfected human 5-HT2 receptor has answered two outstanding questions regarding this receptor. First, the few amino acid differences that exist between the human and the rat genes are sufficient to account for the species differences seen in their pharmacologic properties. Second, the single protein encoded by the human 5-HT2 receptor gene is capable of binding both [3H]DOB and [3H]ketanserin. Analysis of the effects of guanine nucleotides provides further evidence that this single protein binds both ligands, that this receptor has high- and low-affinity states, and that these states are partially interconvertible. Furthermore, the close relationship between the adrenergic receptors and the 5-HT1A receptor has been reaffirmed by the recent cloning of a new adrenergic receptor subtype, alpha 2B, by use of the 5-HT1A receptor sequence. Finally, the detailed level of structural information now available on serotonin receptors has yielded valuable information about the ligand binding site and about the possible functional significance of differing rates of evolutionary change in various parts of the gene.
A Phase I Trial of Ad.hIFN-β Gene Therapy for Glioma (2008)

Interferon-beta (IFN-beta) is a pleiotropic cytokine with antitumoral activity. In an effort to improve the therapeutic index of IFN-beta by providing local, sustained delivery of IFN-beta to gliomas, the safety and biological activity of a human IFN-beta (hIFN-beta)-expressing adenovirus vector (Ad.hIFN-beta) was evaluated in patients with malignant glioma by stereotactic injection, followed 4-8 days later by surgical removal of tumor with additional injections of Ad.hIFN-beta into the tumor bed. Eleven patients received Ad.hIFN-beta in cohorts of 2 x 10(10), 6 x 10(10), or 2 x 10(11) vector particles (vp). The most common adverse events were considered by the investigator as being unrelated to treatment. One patient, who was enrolled in the cohort with the highest dose levels, experienced dose-limiting, treatment-related Grade 4 confusion following the post-operative injection. Ad.hIFN-beta DNA was detected within the tumor, blood, and nasal swabs in a dose-dependent fashion and hIFN-beta protein was detectable within the tumor. At the highest doses tested, a reproducible increase in tumor cell apoptosis in post-treatment versus pre-treatment biopsies with associated tumor necrosis was observed. Direct Ad.hIFN-beta injection into the tumor and the surrounding normal brain areas after surgical removal was feasible and associated with apoptosis induction.
Increase in AC-Field Frequency and Recording Performance in Microwave-Assisted Magnetic Recording (2016)

Magnetic recording of a hard disk drive is negatively affected by a trilemma of noise, thermal fluctuation, and writability, which prevents high recording density. Microwave-assisted magnetic recording (MAMR) is a promising recording method for solving this trilemma. In this study, methods for increasing the AC-field frequency generated from a field generation layer (FGL) and recording performance were investigated using a micromagnetic simulator in consideration of magnetic interactions of an MAMR system. Firstly, we discuss methods for increasing the frequency of the AC-field by changing saturation magnetization (Ms) of the FGL. When the Ms of the FGL decreased, the AC-field amplitude decreased and its frequency increased. When the Ms of the FGL was lower than 1.4 T, the frequency was larger than 20 GHz. Secondly, we discuss the recording performances. As a result, to improve recording performance, high frequency of AC-field (> 20 GHz) is more important than the strength of STO field.
Ultracompact 4 × 3.4 Gbps optoelectronic package for an active optical HDMI cable (2012)

Refering to the increasing demand for extended transmission distances of high-definition video in consumer electronics we present a composite optoelectronic high-definition multimedia interface (HDMI) cable that replaces the four electrical transition-minimized differential signal video channels by a 4×3.4 Gb/s optical fiber link, the currently maximum specified bit rate. This improves the signal quality after 10 m transmission compared to a passive electrical cable significantly and enables even longer cable lengths or higher transmission rates. At the same time we developed a compact package of both the optical sub-assembly and its adjoining control ICs that fits inside the cable connector. We outline the package assembly and present basic transmission characteristics, as well as confirm 1080p video transmission over 10 m.
Interbed Removal: New Approaches for Modeling and Data Processing (2018)

Summary We introduce two methods for removing the scattering related to a single sub-horizontal reflector or a stack of layers. The first method combines full-waveform finite-difference (FD) solvers above and below the interface(s) of interest with one-way wavefield extrapolation across the interface(s). This removes the scattering associated with the interface(s), while preserving all other events with correct kinematics and dynamics. Furthermore, we show how scattering due to a single interface can be removed from surface reflection data using Marchenko redatuming. Reflection responses related to different depth intervals of the subsurface are isolated and combined such that scattering due to a certain depth interval is removed from the surface data. Both methods require the one-way transmission responses across the interface(s) of interest and we assume that we can intersect the medium above and below the reflector of interest. Potential applications include removing interbed multiples from surface data as well as the generation of FD reference data without interbed multiples.
Simulation of Molecular Motion under the Oscillation of Electromagnetic Field in the Microwave Band (2021)

Molecular dynamics calculations were performed to consider the peculiarities of microwave chemistry. The temperature rise curve obtained without using the parameters of permittivity and conductivity showed the rise due to the traveling energy in addition to the accumulation of thermal energy in the periodic application of the electric field. We showed that the non-thermal effects of microwave chemistry might be caused by this traveling energy.
Transplantation and beyond (2008)

Abstract The pathophysiology of diabetes, either type 1 or type 2, involves the loss of β cell mass to a point where there is insufficient insulin secretion to meet the body's needs. The overall loss of β cells results from β cell destruction in conjunction with a failure of physiological regulators to restore or regenerate the β cell population. Historically, therapy for diabetes has been limited to efforts to control hyperglycemia and to prevent and/or ameliorate the complications associated with diabetes. Multiple approaches to repopulate the diabetic pancreas with functional islets have been proposed, including whole pancreas transplantation with or without a kidney, direct islet transplantation from cadaveric donors, generation of artificial islets, and development of new islets from stem cells. Ex vivo differentiation of embryonic stem cells offers great attraction as an alternative islet source but, to date, fully functional islets have not been developed. An alternative approach is to target stem cells present in the adult pancreas. Stimulation of these cells with various factors offers the hope of promoting differentiation to functional islets. Islet neogenesis‐associated peptide (INGAP) is one such factor. INGAP treatment has reversed insulin‐dependent diabetes in a mouse model. INGAP treatment has elicited production of C‐peptide in insulin‐dependent diabetic patients. Future approaches may combine INGAP with immunosuppression in an attempt to reverse type 1 diabetes. Drug Dev Res 69:165–176, 2008 © 2008 Wiley‐Liss, Inc.
Sustained treatment with a stable long‐acting oxyntomodulin analogue improves metabolic control and islet morphology in an experimental model of type 1 diabetes (2015)

These studies emphasize the potential of stable Oxm-based peptides, such as (d-Ser(2) )Oxm[Lys(38) -γ-glu-PAL], as therapeutic agents for insulin-deficient type 1 diabetes.
Inside Cover: Furospinosulin‐1, Marine Spongean Furanosesterterpene, Suppresses the Growth of Hypoxia‐Adapted Cancer Cells by Binding to Transcriptional Regulators p54nrb and LEDGF/p75 (ChemBioChem 2/2016) (2016)

The inside cover picture shows the mode of action of marine spongean furanosesterterpene, furospinosulin-1, as an inhibitor for hypoxia-adapted cancer cells existing in the microenvironment of a tumor. Furospinosulin-1, directly binds to the transcriptional regulators, post-translationally modified p54nrb and LEDGF/p75, which have not been previously identified as mediators of hypoxia adaptation in cancer cells, under hypoxic conditions. Cancer cells lacking functions of p54nrb and LEDGF/p75 then fail the transcription of genes involved in the adaptation of cancer cells to hypoxic environments such as IGF-2. Therefore, furospinosulin-1 displays the hypoxia-selective growth inhibition and the anti-tumor effect. More information can be found in the full paper by M. Arai, M. Kobayashi et al. on page 181 in Issue 2, 2016 (DOI: 10.1002/cbic.201500519).
Multi-modal biometrics for mobile authentication (2014)

User authentication in the context of a secure transaction needs to be continuously evaluated for the risks associated with the transaction authorization. The situation becomes even more critical when there are regulatory compliance requirements. Need for such systems have grown dramatically with the introduction of smart mobile devices which make it far easier for the user to complete such transaction quickly but with a huge exposure to risk. Biometrics can play a very significant role in addressing such problems as a key indicator of the user identity and thus reducing the risk of fraud. While unimodal biometrics authentication systems are being increasingly experimented by mainstream mobile system manufacturers (e.g., fingerprint in iOS), we explore various opportunities of reducing risk in a multimodal biometrics system. The multimodal system is based on fusion of several biometrics combined with a policy manager. A new biometric modality: chirography which is based on user writing on multi-touch screens using their finger is introduced. Coupling with chirography, we also use two other biometrics: face and voice. Our fusion strategy is based on inter-modality score level fusion that takes into account a voice quality measure. The proposed system has been evaluated on an in-house database that reflects the latest smart mobile devices. On this database, we demonstrate a very high accuracy multi-modal authentication system reaching an EER of 0.1% in an office environment and an EER of 0.5% in challenging noisy environments.
Salmonella Secreted Factor L Deubiquitinase of Salmonella typhimurium Inhibits NF-κB, Suppresses IκBα Ubiquitination and Modulates Innate Immune Responses (2008)

Salmonella enterica translocates virulent factors into host cells using type III secretion systems to promote host colonization, intracellular bacterial replication and survival, and disease pathogenesis. Among many effectors, the type III secretion system encoded in Salmonella pathogenicity island 2 translocates a Salmonella-specific protein, designated Salmonella secreted factor L (SseL), a putative virulence factor possessing deubiquitinase activity. In this study, we attempt to elucidate the mechanism and the function of SseL in vitro, in primary host macrophages and in vivo in infected mice. Expression of SseL in mammalian cells suppresses NF-kappaB activation downstream of IkappaBalpha kinases and impairs IkappaBalpha ubiquitination and degradation, but not IkappaBalpha phosphorylation. Disruption of the gene encoding SseL in S. enterica serovar typhimurium increases IkappaBalpha degradation and ubiquitination, as well as NF-kappaB activation in infected macrophages, compared with wild-type bacteria. Mice infected with SseL-deficient bacteria mount stronger inflammatory responses, associated with increased production of NF-kappaB-dependent cytokines. Thus, SseL represents one of the first bacterial deubiquitinases demonstrated to modulate the host inflammatory response in vivo.