gebhart/patrepeval huggingface dataset:
Proteomic Identification of a Stress Protein, Mortalin/mthsp70/GRP75 (2006)

Functional impairment of mitochondria and proteasomes and increased oxidative damage comprise the main pathological phenotypes of Parkinson disease (PD). Using an unbiased quantitative proteomic approach, we compared nigral mitochondrial proteins of PD patients with those from age-matched controls. 119 of 842 identified proteins displayed significant differences in their relative abundance (increase/decrease) between the two groups. We confirmed that one of these, mortalin (mthsp70/GRP75, a mitochondrial stress protein), is substantially decreased in PD brains as well as in a cellular model of PD. In addition, nine candidate mortalin-binding partners were identified as potential mediators of PD pathology. Manipulations of mortalin level in dopaminergic neurons resulted in significant changes in sensitivity to PD phenotypes via pathways involving mitochondrial and proteasomal function as well as oxidative stress.
Studies on peptides. CI. Synthesis of a wasp venom, mastoparan M. (1981)

A tetradecapeptide amide, H-Ile-Asn-Leu-Lys-Ala-Ile-Ala-Ala-Leu-Ala-Lys-Lys-Leu-Leu-NH2, corresponding to the entire amino acid sequence of a wasp venom, mastoparan M, was synthesized using the thioanisole-mediated trifluoroacetic acid deprotecting procedure.
Correction to “On-Demand and Location Selective Particle Assembly via Electrophoretic Deposition for Fabricating Structures with Particleto-Particle Precision” (2021)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to "On-Demand and Location Selective Particle Assembly via Electrophoretic Deposition for Fabricating Structures with Particleto-Particle Precision"Fang QianFang QianMore by Fang Qian, Andrew J. PascallAndrew J. PascallMore by Andrew J. Pascall, Mihail BoraMihail BoraMore by Mihail Bora, T. Yong-Jin HanT. Yong-Jin HanMore by T. Yong-Jin Han, Shirui GuoShirui GuoMore by Shirui Guo, Sonny S. LySonny S. LyMore by Sonny S. Ly, Marcus A. WorsleyMarcus A. WorsleyMore by Marcus A. Worsley, Joshua D. KuntzJoshua D. KuntzMore by Joshua D. Kuntz, and Tammy Y. OlsonTammy Y. OlsonMore by Tammy Y. OlsonCite this: Langmuir 2021, 37, 24, 7625Publication Date (Web):June 8, 2021Publication History Published online8 June 2021Published inissue 22 June 2021https://pubs.acs.org/doi/10.1021/acs.langmuir.1c01202https://doi.org/10.1021/acs.langmuir.1c01202correctionACS PublicationsCopyright © 2021 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views413Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (462 KB) Get e-Alertsclose Get e-Alerts
S3140 Does Age Influence How Gastroenterology Patients View Adverse Effects of Proton Pump Inhibitors? (2020)

INTRODUCTION: Proton Pump Inhibitors (PPIs) are generally considered to be safe. Recently, observational studies have associated PPI use with new adverse drug reactions (ADRs) including chronic kidney disease, dementia, and hypomagnesemia. Few studies have addressed patient awareness of potential PPI-related ADRs and its effect on continued use of PPIs. In 2019, our group reported that most gastroenterology patients on PPIs were unaware of ADRs, but when alerted to potential ADRs, 60% expressed some degree of concern. We now report new findings on the influence of age on knowledge and concern about PPI-related ARDs and likelihood of discontinuing PPIs. METHODS: An anonymous survey with 15 multiple choice questions regarding PPI use was distributed to adults from our community outpatient endoscopy center at Advocate Lutheran General Hospital from June 2019 to January 2020. The survey included demographic information, indication and duration of PPI use, awareness of PPI ADRs, level of concern for ADRs, and drug discontinuation. RESULTS: 537 patients (14%) indicated current PPI use and are the subject of this analysis. 52 individuals were between the ages of 18-39 years (Group A = A), 276 were between the age of 40-65 years (Group B= B), and 209 individuals were > age 65 (Group C= C). The most common patient identified ADRs related to PPI use in all age groups were osteoporosis and Vitamin B12 deficiency (Figure 1). Most patients (55%) reported that they were unaware of any ADRs from PPIs. For patients aware of ADRs, the most common source of this information was from healthcare providers (A n = 10, B n = 60, C n = 42), and the Internet (A n = 9, B n = 41, C n = 16) (Figure 2). 377 patients (70%) expressed concern regarding ADRs. 21% expressed extreme concern (A n = 5, B n = 18, C n = 19), 23% moderate concern (A = 4, B = 24, C = 15), 41% were somewhat concerned (A n = 9, B n = 47, C n = 32), and 15% were hardly concerned (A n = 5, B n = 15, C n = 11). Patients over the age of 39 comprised 93% of patients (B n = 28, C n = 10) who discontinued PPIs due to concern about ADRs, compared to only 4 patients in A. CONCLUSION: The majority of patients on PPIs surveyed are unaware of PPI-related ADRs. Older patient populations are more likely to express concern for PPI-related ADRs and more likely to discontinue PPIs as a result.Figure 1.: The graph depicts the most common patient identified potential ADRs by age group.Figure 2.: The graph demonstrates where patients received their information regarding PPI ADRs by age group. Most patients surveyed regardless of age had learned of PPI ADRs from a physician.Figure 3.: The graph depicts the overall concern of patients by age related to PPI ADRs. The majority from all age groups are all somewhat concerned regarding PPI related ADRs.
Distribution of the gyromitrin mycotoxin in the lorchel family assessed by a pre-column-derivatization and ultra high-performance liquid chromatography method (2022)

ABSTRACT Gyromitrin (acetaldehyde N -methyl- N -formylhydrazone) and its homologs are deadly mycotoxins produced most infamously by the lorchel (also known as false morel) Gyromitra esculenta , which is paradoxically consumed as a delicacy in some parts of the world. There is much speculation about the presence of gyromitrin in other species of the lorchel family (Discinaceae), but no studies have broadly assessed its distribution. Given the history of poisonings associated with the consumption of G. esculenta and G. ambigua , we hypothesized that gyromitrin evolved in the last common ancestor of these taxa and would be present in their descendants with adaptive loss of function in the nested truffle clade, Hydnotrya . To investigate this hypothesis, we developed a sensitive analytical derivatization method for the detection of gyromitrin using 2,4-dinotrobenzaldehyde as the derivatization reagent. In total, we analyzed 66 specimens for the presence of gyromitrin over 105 tests. Moreover, we sequenced the nuc rDNA ITS1-5.8S-ITS2 region (ITS barcode) and nuc 28S rDNA to assist in species identification and to infer a supporting phylogenetic tree. We detected gyromitrin in all tested specimens from the G. esculenta group as well as G. leucoxantha . This distribution is consistent with a model of rapid evolution coupled with horizontal transfer, which is typical for secondary metabolites. We clarified that gyromitrin production in Discinaceae is both discontinuous and more limited than previously thought. Further research is required to elucidate the gyromitrin biosynthesis gene cluster and its evolutionary history in lorchels. KEYWORDS: 2,4-dinitrobenzaldehyde, Gyromitra spp., Hydnotrya spp., Discinaceae, Pezizales, Schiff bases, UHPLC-DAD analysis
COFFE 2 (2019)

FPGAs are becoming more heteregeneous to better adapt to different markets, motivating rapid exploration of different blocks/tiles for FPGAs. To evaluate a new FPGA architectural idea, one should be able to accurately obtain the area, delay, and energy consumption of the block of interest. However, current FPGA circuit design tools can only model simple, homogeneous FPGA architectures with basic logic blocks and also lack DSP and other heterogeneous block support. Modern FPGAs are instead composed of many different tiles, some of which are designed in a full custom style and some of which mix standard cell and full custom styles. To fill this modelling gap, we introduce COFFE 2, an open-source FPGA design toolset for automatic FPGA circuit design. COFFE 2 uses a mix of full custom and standard cell flows and supports not only complex logic blocks with fracturable lookup tables and hard arithmetic but also arbitrary heterogeneous blocks. To validate COFFE 2 and demonstrate its features, we design and evaluate a multi-mode Stratix III-like DSP block and several logic tiles with fracturable LUTs and hard arithmetic. We also demonstrate how COFFE 2’s interface to VTR allows full evaluation of block-routing interfaces and various fracturable 6-LUT architectures.
Phase chaos in coupled oscillators (2005)

A complex high-dimensional chaotic behavior, phase chaos, is found in the finite-dimensional Kuramoto model of coupled phase oscillators. This type of chaos is characterized by half of the spectrum of Lyapunov exponents being positive and the Lyapunov dimension equaling almost the total system dimension. Intriguingly, the strongest phase chaos occurs for intermediate-size ensembles. Phase chaos is a common property of networks of oscillators of very different natures, such as phase oscillators, limit-cycle oscillators, and chaotic oscillators, e.g., Rössler systems.
Multiple Dirac cones at the surface of the topological metal LaBi (2017)

The rare-earth monopnictide LaBi exhibits exotic magneto-transport properties, including an extremely large and anisotropic magnetoresistance. Experimental evidence for topological surface states is still missing although band inversions have been postulated to induce a topological phase in LaBi. In this work, we have revealed the existence of surface states of LaBi through the observation of three Dirac cones: two coexist at the corners and one appears at the centre of the Brillouin zone, by employing angle-resolved photoemission spectroscopy in conjunction with ab initio calculations. The odd number of surface Dirac cones is a direct consequence of the odd number of band inversions in the bulk band structure, thereby proving that LaBi is a topological, compensated semimetal, which is equivalent to a time-reversal invariant topological insulator. Our findings provide insight into the topological surface states of LaBi's semi-metallicity and related magneto-transport properties.
A Tunable Hybrid Waveguide-Coupled Cavity Design for Improved Spin-Photon Interfaces (2017)

We describe a hybrid cavity design for enhancing quantum emitters that achieves an unloaded quality factor Q > 1 × 106 and loaded Q of 5.5 × 104 with >75% of the emission coupled to a waveguide mode. The cavity resonance can be spectrally tuned by microelectromechanical actuation.
Secondary Reactive Oxygen Species Extend the Range of Photosensitization Effects in Cells: DNA Damage Produced Via Initial Membrane Photosensitization¶† (2003)

The type-II photosensitization process is mediated by the formation of singlet oxygen (O2[1deltag]). The short lifetime of this species dictates that chemical reactions with biological substrates can only occur when O2(1deltag) is in very close proximity to the photosensitizer itself. In this study, deuteroporphyrin, a type-II, membrane-localized photosensitizer, was used to generate O2(1deltag) in human lymphoblast WTK-1 cells, and the range of influence was determined by a variety of biological assays. Surprisingly, the initial membrane-confined events were shown, by comet assay, to induce DNA damage in these cells. DNA damage was inhibited both by membrane-localized (alpha-tocopherol acetate) and by cytoplasmic (trolox) free radical scavengers. Comet formation also was inhibited by treatment at low temperature. DNA fragmentation was not influenced by treatment with the pan-caspase inhibitor, benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone, showing that apoptosis was not responsible for fragmentation. Taken together, these results show that primary photosensitization reactions involving O2(1deltag), even when tightly confined in extranuclear locations, leads to the production of secondary reactive oxygen species, probably as a result of lipid peroxidation, that can act at greater distances from the photosensitizer itself. These experiments were carried out under conditions where cell survival was significant and raise questions regarding DNA damage and mutagenesis pathways, even when extranuclear O2(1deltag)-generating compounds are used.
Rank and Tenure Requirements at Teaching-Based University (2020)

Abstract Rank and Tenure Requirements at Teaching-Based UniversityThe requirements for attaining tenure and advancement in rank are vastly different atresearch-oriented universities vs. teaching-based universities. In general, mostuniversities require a faculty member to satisfy university-defined requirements onteaching, scholarship, professional development, community service, service to theprofession, and service to the university for attaining tenure and advancement in rank.Even though requirements for rank and tenure at teaching-based universities havechanged over the years, the focus still remains on teaching and service. Requirements forteaching and service may vary from university to university but they are very similar inmost of the aspects. This paper presents the typical requirements at Gannon University,Erie, PA in each of the above mentioned areas. A comparison will also be made withother teaching-based institutions. Requirements at Gannon University have changed overthe years from no scholarship requirements before the 1980s to significant scholarlyactivity requirements today. Faculty members rely on student evaluations conducted atthe end of each semester and once a year peer evaluation to satisfy teaching requirements.At Gannon University, the Boyer’s model of scholarship was adopted around 2000 tosatisfy scholarship requirements.Key Words: Tenure, advancement in rank, teaching-based university, research-orienteduniversity
Inhibitory KIR/HLA incompatibility between sexual partners confers protection against HIV-1 transmission (2012)

Killer immunoglobulin-like receptors (KIRs) regulate natural killer (NK) cells in a human leukocyte antigen (HLA)-dependent manner. KIR/HLA mismatched hematopoietic stem cell transplants induce alloreactive NK cells, which prevent leukemia relapse. Certain KIR/HLA combinations protect against HIV-1 infection, but the effect of KIR/HLA mismatches between sexual partners has never been investigated. In this study, we analyzed the effect of allogeneic KIR/HLA combinations on HIV-1 transmission in a West African population of HIV-1-discordant and concordant couples. HIV-1-discordant couples were characterized by recipient partners with homozygous KIR2DL2, and by a mismatched recipient partner KIR2DL1/HLA-C2 with index partner HLA-C1/C1 combination expected to allow licensed missing self NK cell killing of index partners' cells. HIV-1-concordant couples on the other hand were characterized by KIR2DL3 homozygous recipient partners with HLA-C1/C2 bearing index partners, resulting in a matched KIR/HLA combination expected to inhibit NK cell killing. In vitro cocultures of healthy donor-derived NK cells and HIV-1 patient-derived CD4(+) T cells confirmed the involvement of these allogeneic KIR/HLA combinations in NK cell-mediated CD4(+) T-cell killing. Our data suggest that KIR/HLA incompatibility between sexual partners confers protection against HIV-1 transmission and that this may be due to alloreactive NK cell killing of the HIV-1-infected partner's cells.
All-digital impulse radio for MUI/ISI-resilient multiuser communications over frequency-selective multipath channels (2002)

Impulse radio (IR) is an ultra-wideband system with attractive features for baseband asynchronous multiple access (MA), multimedia services, and tactical wireless communications. Implemented with analog components, the continuous-time IRMA model utilizes pulse-position modulation (PPM) and random time-hopping codes to alleviate multipath effects and suppress multiuser interference (MUI). We introduce a novel continuous-time multiple input multiple output (MIMO) PPM-IRMA scheme, and derive its discrete-time equivalent model. Relying on a time-division-duplex access protocol and orthogonal user codes, we design composite linear and non-linear receivers for the downlink. The linear step eliminates MUI deterministically and accounts for frequency-selective multipath, while a maximum likelihood (ML) receiver performs symbol detection.
Development of a SRM-based multiplexed quantitation of protein biomarkers in Gammarus fossarum (2016)

Biomarkers are recognized as relevant tools for diagnostic and hazard assessment of aquatic systems. However, few are used in invertebrate species studies. It mainly results from the lack of genomic and/or proteomic data, preventing the development of specific and direct method for the quantification of biomarkers. Recently, a novel proteogenomics approach has emerged for a straightforward strategy to discover proteins in non-model organisms. This approach was applied in the amphipod Gammarus fossarum, generating a large proteome dataset and offering the opportunity to develop direct and specific analytical mass spectrometry methods. Selected reaction monitoring (SRM) is a liquid chromatography mass spectrometry based technique for the quantitation of a specific protein of interest. SRM has the ability to detect low amounts (to the picograms per milliliter range) of a targeted analyte, with tryptic peptides as multi-indicators of proteins. Absolute quantification can be performed by the addition of an isotopically internal standard. Targeted proteomics can be performed to quantify simultaneously multiple peptides per protein from the same biological sample. Multiplexing analyses by mass spectrometry is in this case straightforward and offers innovative perspectives in ecotoxicology. Using less biological material, resource investments in terms of organism and experimental maintenance are reduced and yield indicators on each biological sample. Herein, we described a highlymultiplexed MRM-based assay for the determination of proteins biomarkers in Gammarus fossarum an ecotoxicological model. The assay uses 71 stable isotope-labeled peptide standards for the quantitation of 40 putative biomarkers of candidate proteins related to essential physiological functions including reproductive cycle or defence mechanism. A good linearity was observed for the spiked peptides in extracted individual and, for the proof of concept, the assays precision and accuracy were determined between 0 and 20 % and between 80 and 120% respectively. The assay presented in this study is easy to use, robust and sensitive. High-throughput capabilities will be established to quantify protein biomarkers in Gammarus fossarum. Validation of assay was performed with protein changes assessment throughout contrasted physiological process (sex, reproductive status).
The design of a laser range imaging device (1992)

In this thesis, a methodology and techniques for the design of a laser range imaging device (LRID) for robotic applications are presented. Furthermore, a prototype incorporating the concepts presented has been successfully tested in the laboratory. In this LRID, the range is determined by the shift in phase in the return of a modulated laser beam illuminating an object. The device is designed using a low power and visible (for laboratory safety reasons) diode laser and an APD detector. The device is also equipped with a fully programmable X-Y galvonometric scanning unit. The scene, which can be dark as well as brightly lit, is scanned in either a vector or raster mode and both range and reflected intensity data are collected. In addition to typical range data applications, the range and intensity images can be combined to provide useful data sets to aid in object recognition and scene understanding.
Codebook-Based SDMA for Coexistence with Fixed Wireless Service (2010)

A portion of frequency band for International Mobile Telecommunications (IMT)-Advanced is currently allocated to Fixed Wireless Service (FWS) such as Fixed Service (FS), Fixed Satellite Service (FSS), or Fixed Wireless Access (FWA), which requires frequency sharing between both the systems. SDMA, due to its high throughput nature, is candidate for IMT-Advanced. This paper proposes a systematic design of a precoder codebook for SDMA sharing spectrum with existing FWS. Based on an estimated direction angle of a victim FWS system, an interfering transmitter adaptively constructs a codebook forming a transmit null in the direction angle while satisfying orthogonal beamforming constraint. We derive not only asymptotic throughput scaling laws, but also an upperbound on throughput loss to analyze performance loss of the proposed SDMA relative to the popular SDMA called per-user unitary rate control (PU2RC). Furthermore, we develop a method of evaluating protection distance in order to analyze the spectrum sharing performance of the proposed approach. The simulation results of protection distance confirm that the proposed SDMA efficiently shares spectrum with FWS systems by reducing protection distance to more than 66%. Although our proposed SDMA always has lower throughput compared to PU2RC in non-coexistence scenario, it offers an intriguing opportunity to reuse spectrum already allocated to FWS.
Testing and debugging delay faults in dynamic circuits (2006)

We propose novel design for test and debug techniques to apply two patterns for delay fault test and debug in dynamic circuits. Dynamic circuits, which have traditionally been difficult to test, pose new challenges for AC tests due to the presence of a reset phase between applications of any two patterns, which impedes delay fault testing of such circuits. We present two sets of design for test and debug techniques. The first set facilitates application of two patterns to dynamic circuits in general, overcoming the issue of reset phase, and reduces the problem of test generation for dynamic circuits to test generation for pull down paths of static CMOS circuits. The second set enables application of two patterns to scan based dynamic circuits. The proposed techniques reduce the problem of delay test generation for scan based dynamic circuits to that of delay test generation for static CMOS circuits with complete accessibility to all primary inputs. The techniques have minimal area overhead and also provide significant reduction in power during scan operation