gebhart/patrepeval huggingface dataset:
Influence of metal salts on the hydrogelation properties of ultrashort aliphatic peptides (2013)

Over the last decade, a variety of peptides have been designed and studied for their ability to form hydrogels for potential use as functional biomaterials. Peptide hydrogels have been employed as tissue-engineering scaffolds, drug delivery systems, and platforms for biosensors. We have recently added to the existing peptide systems a new class of ultrashort self-assembling peptides containing 3–7 aliphatic amino acids, which are able to easily form solid hydrogels in plain water. These hydrogels can entrap up to 99.9% of water in scaffolds that are made of long helical fibers. Although the aliphatic peptides do not need ionic conditions to form hydrogels, we were interested to investigate if physiological metal salts interfere with hydrogelation. This is particularly important for future in vivo application in biomedicine and biotechnology. Thus, we have studied the effect of multivalent metal salts on the hydrogelation properties of two members of this peptide class, the hexapeptide Ac-LIVAGD and tripeptide Ac-IVD. The majority of the metal salts did not disrupt the hydrogelation process, whereas the trivalent salts could initiate precipitation of the peptides. The characteristic fibrillar network of the hydrogels was still observable by field emission scanning electron microscopy in the presence of moderate and high concentrations of metal salts. Rheological studies of the hexapeptide hydrogel in the presence of monovalent metal salts demonstrated the ability of the salts to reduce the viscoelasticity of the hydrogel. Rheology, together with Fourier transform infrared spectroscopy, confirmed that the ionic strength of the peptide solution affects the bonding interaction between peptide fibers/sheets and the water molecules during hydrogelation. Overall, our results demonstrate that metal salts in general do not significantly affect the self-assembly process of two aliphatic peptides, but exert an influence on their viscoelastic properties, presumably via disruption of the ordered water layer around the peptide fibers. Given that common physiological metal salts have minimal effect on the integrity/morphology of the studied hydrogels, but only slightly influence the mechanical properties, biomedical applications seem to be feasible.
The Development of a Magnesium Biodegradable Stent: Design, Analysis, Fabrication, and In-vivo Test (2020)

Stents are widely used as scaffolding to open up blood vessel stenosis. A stent can provide early stage scaffolding, increase blood flow, and optimize hemodynamics. Stainless steel is the most popular material for conventional stents, and it has excellent mechanical behavior during deformation. On the downside, stents made of stainless steel remain in the body permanently and may cause complications or lead to occlusion of the vessel. Biodegradable stents that eventually dissolve and disappear in the body are being developed to overcome these shortcomings. However, biodegradable materials such as magnesium alloys are relatively brittle and cannot deform as much as stainless steel. A proper geometry for the stent that allows large displacement and plastic deformation is necessary and required. In this paper, a balloon-expandable design of magnesium AZ31 alloy venous stent is proposed and evaluated. Computational analysis using finite element analysis (FEA) tools simulated the expansion and recoiling process. The stent was expanded from 6.0 mm to 10.0 mm in the radial direction with the expansion ratio of 1.67. Strain and stress distributions, structural stiffness, and radial strength were studied. The maximum stress did not exceed the ultimate tensile strength (in the plastic region) of the stent material, and the maximum strain was 64% of the elongation. The stent design was then fabricated with methods of electro-discharge machining (EDM), laser machining, and electro-polishing. Lastly, these prototyped stents were prepared for future in-vivo experiment in animal models.
Characterization of a Peptide Inhibitor of Janus Kinase 2 That Mimics Suppressor of Cytokine Signaling 1 Function (2004)

Positive and negative regulation of cytokines such as IFN-gamma are key to normal homeostatic function. Negative regulation of IFN-gamma in cells occurs via proteins called suppressors of cytokine signaling (SOCS)1 and -3. SOCS-1 inhibits IFN-gamma function by binding to the autophosphorylation site of the tyrosine kinase Janus kinase (JAK)2. We have developed a short 12-mer peptide, WLVFFVIFYFFR, that binds to the autophosphorylation site of JAK2, resulting in inhibition of its autophosphorylation as well as its phosphorylation of IFN-gamma receptor subunit IFNGR-1. The JAK2 tyrosine kinase inhibitor peptide (Tkip) did not bind to or inhibit tyrosine autophosphorylation of vascular endothelial growth factor receptor or phosphorylation of a substrate peptide by the protooncogene tyrosine kinase c-src. Tkip also inhibited epidermal growth factor receptor autophosphorylation, consistent with the fact that epidermal growth factor receptor is regulated by SOCS-1 and SOCS-3, similar to JAK2. Although Tkip binds to unphosphorylated JAK2 autophosphorylation site peptide, it binds significantly better to tyrosine-1007 phosphorylated JAK2 autophosphorylation site peptide. SOCS-1 only recognizes the JAK2 site in its phosphorylated state. Thus, Tkip recognizes the JAK2 autophosphorylation site similar to SOCS-1, but not precisely the same way. Consistent with inhibition of JAK2, Tkip inhibited the ability of IFN-gamma to induce an antiviral state as well as up-regulate MHC class I molecules on cells at a concentration of approximately 10 microM. This is similar to the K(d) of SOCS-3 for the erythropoietin receptor. These data represent a proof-of-concept demonstration of a peptide mimetic of SOCS-1 that regulates JAK2 tyrosine kinase function.
Irreversible Inhibition of DNA Polymerase β by Small-Molecule Mimics of a DNA Lesion (2014)

Abasic sites are ubiquitous DNA lesions that are mutagenic and cytotoxic but are removed by the base excision repair pathway. DNA polymerase β carries out two of the four steps during base excision repair, including a lyase reaction that removes the abasic site from DNA following incision of its 5'-phosphate. DNA polymerase β is overexpressed in cancer cells and is a potential anticancer target. Recently, DNA oxidized abasic sites that are produced by potent antitumor agents were shown to inactivate DNA polymerase β. A library of small molecules whose structures were inspired by the oxidized abasic sites was synthesized and screened for the ability to irreversibly inhibit DNA polymerase β. One candidate (3a) was examined more thoroughly, and modification of its phosphate backbone led to a molecule that irreversibly inactivates DNA polymerase β in solution (IC50 ≈ 21 μM), and inhibits the enzyme's lyase activity in cell lysates. A bisacetate analogue is converted in cell lysates to 3a. The bisacetate is more effective in cell lysates, more cytotoxic in prostate cancer cells than 3a and potentiates the cytotoxicity of methyl methanesulfonate between 2- and 5-fold. This is the first example of an irreversible inhibitor of the lyase activity of DNA polymerase β that works synergistically with a DNA damaging agent.
Site-Specific Protein Modification with a Dirhodium Metallopeptide Catalyst (2011)

A new method for chemical protein modification is presented utilizing a dirhodium metallopeptide catalyst. The combination of peptide-based molecular recognition and a dirhodium catalyst with broad side-chain scope enables site-specific protein functionalization. The scope and utility of dirhodium-catalyzed biomolecule modification is expanded to allow reaction at physiological pH and in biologically relevant buffer solutions. Specific protein modification is possible directly in E. coli lysate, demonstrating the remarkable activity and specificity of the designed metallopeptide catalyst. Furthermore, a new biotin-diazo conjugate 1b is presented that allows affinity tagging of target proteins.
Design and Synthesis of Highly Potent and Specific ABHD6 Inhibitors (2021)

Abstract Fine‐tuning than complete disruption of 2‐arachidonoylglycerol (2‐AG) metabolism in the brain represents a promising pharmacological approach to limit potential untoward effects associated with complete blockade of monoacylglycerol lipase (MGL), the primary hydrolase of 2‐AG. This could be achieved through a/b‐hydrolase domain containing 6 (ABHD6) inhibition, which will provide a smaller and safer contribution to 2‐AG regulation in the brain. Pharmacological studies with ABHD6 inhibitors have recently been reported, where modulation of ABHD6 activity either through CB1R‐dependent or CB1R‐independent processes showed promise in preclinical models of epilepsy, neuropathic pain and inflammation. Furthermore in the periphery, ABHD6 modulates 2‐AG and other fatty acid monoacylglycerols (MAGs) and is implicated in Type‐2 diabetes, metabolic syndrome and potentially other diseases. Herein, we report the discovery of single‐digit nanomolar potent and highly specific ABHD6 inhibitors with >1000‐fold selectivity against MGL and FAAH. The new ABHD6 inhibitors provide early leads to develop therapeutics for neuroprotection and the treatment of inflammation and diabetes.
Exploiting Frame Preamble Waveforms to Support New Physical-Layer Functions in OFDM-Based 802.11 Systems (2017)

The frame preamble in current WiFi systems is designed to facilitate various PHY-layer functions, including frequency offset estimation and frame detection. However, this preamble is typically fixed and is never used to convey any user-specific bits. Embedding information into the preamble opens the door for several new PHY-layer applications. For example, the PHY header no longer needs to be transmitted at a known (lowest) rate if this rate can be announced earlier in the preamble. A full-duplex transmitter can use the embedded information to inform other devices of its current operation mode (e.g., transmit/receive versus transmit/sense), obviating the need for additional control packets. In security applications, a PHY-layer sender identifier can be embedded in the preamble to facilitate PHY-level encryption. However, modifying the standard preamble to embed user information may disrupt the operation of 802.11a/n/ac devices. In this paper, we propose P-modulation, a method that enables an OFDM-based 802.11 transmitter to embed up to 19 user-specific bits in the frame preamble while maintaining the highest reliability required by the system. The proposed P-modulation is also backward-compatible with legacy receivers. Our analysis and USRP-based experimental results confirm the practicality of the scheme. Our scheme further provides insights into designing time-varying preambles for future wireless systems.
Multi-biomarker panel prediction model for diagnosis of pancreatic cancer (2021)

Doo-Ho LEE, Woongchang YOON, Areum LEE, Youngmin HAN, Yoonhyeong BYUN, Jae Seung KANG, Hongbeom KIM, Wooil KWON, Young-Ah SUH, Yonghwan CHOI, Junghyun NAMKUNG, Sangjo HAN, Sung Gon YI, Jin Seok HEO, In Woong HAN, Joon Oh PARK, Joo Kyung PARK, Song Cheol KIM, Eunsung JUN, Chang Moo KANG, Woo Jin LEE, Hyeon Kook LEE, Huisong LEE, Seungyeoun LEE, Seung-Yong JEONG, Kyu Eun LEE, Wonshik HAN, Taesung PARK, Jin-Young JANG*. Ann Hepatobiliary Pancreat Surg 2021;25:S42. https://doi.org/10.14701/ahbps.BP-BEST-OP-2
InGaAs/GaAs interdigitated metal-semiconductor-metal (IMSM) photodetectors operational at 1.3 um grown by molecular beam epitaxy (1991)

The paper reports on InGaAs interdigitated metal-semiconductor-metal (IMSM) photodetectors operational at 13 micron fabricated on GaAs substrates. Different Schottky barrier enhancement cap layers were used in order to study the thermal stability and device performance characteristics. Dark current, dc responsivity, and high frequency response results are reported. Relationship between the responsivity and the cap structure is discussed. Using oxygen plasma passivation, photodetectors with low dark current and high frequency performance were obtained.
Pay-Per-Action Model for On-line Advertising (2008)

The on-line advertising industry is based on two dominant business models: pay-per-impression and pay-per-click. The growth of sponsored search has fostered a move to the pay-per-click model because it is less risky for small advertisers. An alternative model, discussed but not widely used in the advertising industry, is pay-per-conversion, or more generally, pay-per-action. This paper discusses the challenges of designing mechanisms for the pay-per-action model and approaches to tackle some of them.
Assessment and Clinical Relevance of Serum IL-19 Levels in Psoriasis and Atopic Dermatitis Using a Sensitive and Specific Novel Immunoassay (2019)

Because development of reliable biomarkers in psoriasis and atopic dermatitis has lagged behind therapeutic progress, we created a blood-based test to fill the void in objective methods available for dermatological assessments. Our novel interleukin-19 (IL-19) immunoassay was initially tested to determine concentrations of IL-19 serum levels, then correlated with the psoriasis activity and severity index (PASI) in psoriasis, and the eczema area and severity index (EASI) in atopic dermatitis. Not only was IL-19 increased in psoriasis and correlated to PASI, but ixekizumab administration led to rapid, sustained IL-19 decreases to normal levels, with decreases at 2-weeks correlating with PASI improvement at 16-weeks. IL-19 increased upon ixekizumab withdraw, prior to relapse, and decreased following re-treatment. In baricitinib- and etanercept-treated psoriasis patients, IL-19 decreases also correlated with improvement. Many patients with limited skin disease, including genital psoriasis and psoriatic arthritis patients, also had increased IL-19, which was reduced to normal levels upon ixekizumab treatment, correlating with PASI improvement. We also measured IL-19 in baricitinib-treated atopic dermatitis patients. In atopic dermatitis, IL-19 was significantly elevated, correlated with EASI scores, and decreased with skin improvement. Therefore, measurement of serum IL-19 provides clinicians with an objective disease-activity assessment tool for psoriasis and atopic dermatitis patients.
Functional Enhancement of a Partially Active Single-Chain Variable Fragment Antibody to Venezuelan Equine Encephalitis Virus (2003)

Previously cloned recombinant A116 single chain fragment variable (scFv) antibody gene has been re-engineered for enhanced reactivity to Venezuelan equine encephalitis virus (VEE) successfully. A PCR-based site-directed mutagenesis approach was adopted to re-introduce the three single-base deletions in the 5' region of the V(L) gene of A116, corresponding to the framework-1 region. The mutagenized A116 was designated as MA116. The introduction of these three bases corrected a localized frame-shift to a consensus framework-1 amino acid sequence. Four MA116 clones (MA116-4, MA116-14, MA116-15, and MA116-16) have been analysed in detail for their reactivity to VEE antigen, and all showed varying degrees of reactivity to VEE antigen. ScFv antibody expressed by MA116-14, MA116-15, and MA116-16 clones showed three to five-fold enhanced enzyme-linked immunosorbant assay reactivity to VEE antigen over the parental A116 clone, while scFv antibody from MA116-4 was less reactive than A116 clone. MA116-15 purified scFv protein showed comparable reactivity to the parental 1A4A-1 monoclonal antibody in recognizing VEE antigen. Sequence analysis revealed that only MA116-15 had incorporated the three intended base insertions. The varying degrees of reactivity of MA116 clones are discussed in light of their molecular changes.
Four genes from Pseudomonas fluorescens that encode the biosynthesis of pyrrolnitrin (1997)

Pyrrolnitrin is a secondary metabolite of Pseudomonas and Burkholderia sp. strains with strong antifungal activity. Production of pyrrolnitrin has been correlated with the ability of some bacteria to control plant diseases caused by fungal pathogens, including the damping-off pathogen Rhizoctonia solani. Pseudomonas fluorescens BL915 has been reported to produce pyrrolnitrin and to be an effective biocontrol agent for this pathogen. We have isolated a 32-kb genomic DNA fragment from this strain that contains genes involved in the biosynthesis of pyrrolnitrin. Marker-exchange mutagenesis of this DNA with Tn5 revealed the presence of a 6.2-kb region that contains genes required for the synthesis of pyrrolnitrin. The nucleotide sequence of the 6.2-kb region was determined and found to contain a cluster of four genes that are required for the production of pyrrolnitrin. Deletion mutations in any of the four genes resulted in a pyrrolnitrin-nonproducing phenotype. The putative coding sequences of the four individual genes were cloned by PCR and fused to the tac promoter from Escherichia coli. In each case, the appropriate tac promoter-pyrrolnitrin gene fusion was shown to complement the pyrrolnitrin-negative phenotype of the corresponding deletion mutant. Transfer of the four gene cluster to E. coli resulted in the production of pyrrolnitrin by this organism, thereby demonstrating that the four genes are sufficient for the production of this metabolite and represent all of the genes required to encode the pathway for pyrrolnitrin biosynthesis.
Hardware Designs for Decimal Floating-Point Addition and Related Operations (2008)

Decimal arithmetic is often used in commercial, financial, and Internet-based applications. Due to the growing importance of decimal floating-point (DFP) arithmetic, the IEEE 754-2008 Standard for Floating-Point Arithmetic (IEEE 754-2008) includes specifications for DFP arithmetic. IBM recently announced adding DFP instructions to their POWER6, z9, and z10 microprocessor architectures. As processor support for DFP arithmetic emerges, it is important to investigate efficient arithmetic algorithms and hardware designs for common DFP arithmetic operations. This paper gives an overview of DFP arithmetic in IEEE 754-2008 and discusses previous research on decimal fixed-point and floating-point addition. It also presents novel designs for a DFP adder and a DFP multifunction unit (DFP MFU) that comply with IEEE 754-2008. To reduce their delay, the DFP adder and MFU use decimal injection-based rounding, a new form of decimal operand alignment, and a fast flag-based method for rounding and overflow detection. Synthesis results indicate that the proposed DFP adder is roughly 21 percent faster and 1.6 percent smaller than a previous DFP adder design, when implemented in the same technology. Compared to the DFP adder, the DFP MFU provides six additional operations, yet only has 2.8 percent more delay and 9.7 percent more area. A pipelined version of the DFP MFU has a latency of six cycles, a throughput of one result per cycle, an estimated critical path delay of 12.9 fanout-of-four (F04) inverter delays, and an estimated area of 45, 681 NAND2 equivalent gates.
Reducing Offset and Bias Instability in Lorentz Force Magnetic Sensors Through Bias Chopping (2016)

In this paper, we describe a method for reducing offset and offset-related 1/f (flicker) noise in micromechanical resonator-based Lorentz force magnetometers by chopping the dc bias voltage applied to the resonator. This 1/f noise is shown to determine the stability of the sensor's output at long averaging times. The magnetometer is operated at a 40-Hz frequency offset from its 62.88-kHz resonant frequency. At 4.6-mA bias current, the input referred noise is 70 nT/√Hz limited by white electronic noise. Using the proposed bias chopping method, the sensor's offset is reduced from 310 to 15 μT, and the bias instability is reduced from 27 to 7 nT. The averaging time to reach the bias instability increases from 18 to 290 s as a result of chopping. The root cause of 1/f noise is demonstrated to be 1/f noise on the ac and dc bias voltages applied to the sensor. While the sensor's readout is modulated at the 62.92-kHz excitation frequency and could therefore be expected to be free from 1/f noise, the baseband 1/f noise on these voltage sources is shown to be up-converted to the excitation frequency. Up-conversion occurs through the existence of fabrication imperfections that lead to mismatches in the sensing capacitances, resistances, and parasitic feedthrough capacitances of the sensor. By chopping the bias voltage, the Lorentz force signal is separated from the offset and 1/f noise produced by these error sources. This technique is a generic method to reduce 1/f noise and bias instability in sensors based on micromechanical resonators. [2016-0184].
Three-dimensional ultrasound-guided minimally invasive therapy of the prostate (2003)

Prostate cancer is the most commonly diagnosed cancer in men in North America. Although 2D transrectal ultrasound imaging is widely used for the evaluation of prostate disease it suffers from limitations that limit its use in diagnosis and therapy of prostate cancer. The outcome of a 2D-ultrasound guided minimally invasive procedure depends on the skill and expertise of the operator in manipulating the transducer and in forming a correct mental impression of the 3D anatomy and pathology. In addition, the process of quantifying and monitoring small changes during the therapeutic procedure is also severely limited by using a spatially variable 2D imaging technique. We have developed a 3D ultrasound imaging approach that overcomes these problems. In this paper, we describe a 3D ultrasound imaging system for use in prostate imaging and report on its performance. The system consists of a conventional ultrasound machine, a microcomputer with an video frame grabber, and a custom-built assembly for rotating the ultrasound transducer. A typical scan of 100 2D B-mode images takes 7 seconds. These images can then be reconstructed into a 3D image, which can be displayed and interactively manipulated using 3D visualization software. We also show that the process of reconstruction does not distort the geometry, and that the 3D system can be used to localize brachytherapy seeds in phantoms with a precision (SEM) of better than 0.4 mm. We also show that the 3D system can be used to image brachytherapy seeds in patients post-implantation.