gebhart/patrepeval huggingface dataset:
Amino acid analysis for peptide quantitation using reversed-phase liquid chromatography combined with multiple reaction monitoring mass spectrometry (2023)

Amino acid analysis (AAA) can be used for absolute quantitation of standard peptides after acid hydrolysis using 6 M HCl. Obtained individual amino acids can then be quantified by liquid chromatography-mass spectrometry (LC-MS). Achieving baseline separation of non-derivatized amino acids is challenging when reversed-phase (RP) chromatography is used. Several derivatization methods are commonly utilized to address this issue; however, derivatization has several drawbacks, such as derivative instability and lack of reproducibility. Currently, separation of non-derivatized amino acids is typically done using HILIC, but HILIC has problems of poor reproducibility and long column equilibration times. We developed a method to quantify non-derivatized amino acids, including methionine and cysteine, from peptide hydrolysates by RP-LC-MS without special pre-treatment of the samples. Samples were spiked with certified isotopically labeled (<sup>13</sup>C- and/or <sup>15</sup>N-) amino acids as internal standards. The amino acids released from acid hydrolysis were then analyzed by RP-UPLC-MRM-MS and quantified using the analyte/internal standard chromatographic peak area ratios. Peptide quantitation was based on the sum of the individual amino acid concentrations from the known peptide sequences. The resulting method did not require derivatization, used standard C18-based reversed-phase liquid chromatography, did not require external calibration, was robust, and was able to quantify all 17 amino acids for which we had internal standards, including the sulfur-containing amino acids, cysteine and methionine, in their respective oxidized forms. This simple and robust method enabled the absolute quantitation of standard peptides using only acid hydrolysis and a standard RP-UPLC-MRM-MS setup.
SATURATED ZONE FLOW AND TRANSPORT MODEL ABSTRACTION (2004)

The purpose of the saturated zone (SZ) flow and transport model abstraction task is to provide radionuclide-transport simulation results for use in the total system performance assessment (TSPA) for license application (LA) calculations. This task includes assessment of uncertainty in parameters that pertain to both groundwater flow and radionuclide transport in the models used for this purpose. This model report documents the following: (1) The SZ transport abstraction model, which consists of a set of radionuclide breakthrough curves at the accessible environment for use in the TSPA-LA simulations of radionuclide releases into the biosphere. These radionuclide breakthrough curves contain information on radionuclide-transport times through the SZ. (2) The SZ one-dimensional (I-D) transport model, which is incorporated in the TSPA-LA model to simulate the transport, decay, and ingrowth of radionuclide decay chains in the SZ. (3) The analysis of uncertainty in groundwater-flow and radionuclide-transport input parameters for the SZ transport abstraction model and the SZ 1-D transport model. (4) The analysis of the background concentration of alpha-emitting species in the groundwater of the SZ.
Enhancing the Antiaromaticity of <i>s</i>-Indacene through Naphthothiophene Fusion (2021)

Addressing the instability of antiaromatic compounds often involves protection with bulky groups and/or fusion of aromatic rings, thus decreasing paratropicity. We report four naphthothiophene-fused <i>s</i>-indacene isomers, one of which is more antiaromatic than parent <i>s</i>-indacene. This surprising result is examined computationally through nucleus-independent chemical shift XY calculations and experimentally via nuclear magnetic resonance spectroscopy, X-ray crystallography, ultraviolet-visible spectrophotometry, and cyclic voltammetry, with the latter two indicating that this molecule possesses the lowest highest occupied molecular orbital-lowest unoccupied molecular orbital energy gap observed for heterocycle-fused <i>s</i>-indacene.
On Lattice-Free Boosted MMI Training of HMM and CTC-Based Full-Context ASR Models (2021)

Hybrid automatic speech recognition (ASR) models are typically sequentially trained with CTC or LF-MMI criteria. However, they have vastly different legacies and are usually implemented in different frameworks. In this paper, by decoupling the concepts of modeling units and label topologies and building proper numerator/denominator graphs accordingly, we establish a generalized framework for hybrid acoustic modeling (AM). In this framework, we show that LF-MMI is a powerful training criterion applicable to both limited-context and full-context models, for wordpiece/mono-char/bi-char/chenone units, with both HMM/CTC topologies. From this framework, we propose three novel training schemes: chenone(ch)/wordpiece(wp)-CTC-bMMI, and wordpiece(wp)-HMM-bMMI with different advantages in training performance, decoding efficiency and decoding time-stamp accuracy. The advantages of different training schemes are evaluated comprehensively on Librispeech, and wp-CTC-bMMI and ch-CTC-bMMI are evaluated on two real world ASR tasks to show their effectiveness. Besides, we also show bi-char(bc) HMM-MMI models can serve as better alignment models than traditional non-neural GMM-HMMs.
Silver oxide coatings deposited on leathers to prevent diabetic foot infections (2022)

Diabetic foot is one of the most serious complications of diabetes, the appearance of foot ulcers is highly susceptible to the prevalence of infections. In this sense, thin films of silver (Ag) and silver oxide (AgOx) were deposited by the dc reactive magnetron sputtering technique on different leather substrates for application in insoles and/or footwear inside in order to functionalize them, thus promoting antibacterial properties. A detailed characterization is described to the uncoated and coated leathers. Cytotoxicity and antimicrobial activity were evaluated and, a silver antimicrobial mechanism was suggested. Among the uncoated and coated leathers, AgOx modified samples have higher CoF indicating that this coating can permit higher immobilization of the foot in relation to the skin. The AgOx coating has also impressive antibacterial and antifungal activity without causing any cytotoxic effect, suggesting the potential application of AgOx modified leathers to diabetic specialized footwear.
We need to talk (2011)

"In all the wonderful worlds that writing opens, the spoken word still resides and lives. Written texts all have to be related somehow, directly or indirectly, to the world of sound, the natural habitat of language, to yield their meanings."
Diazonium salt-based photoiniferter as a new efficient pathway to clay–polymer nanocomposites (2016)

Diazonium salts were used to prepare clay–polymer nanocomposites by living free radical photopolymerization of glycidyl methacrylate. The resulting intercalated nanocomposites have an organic mass loading of ∼41 wt% and a polymer-rich surface.
Supplementary Figure Legends from Cetuximab Resistance in Head and Neck Cancer Is Mediated by EGFR-K&lt;sub&gt;521&lt;/sub&gt; Polymorphism (2023)

&lt;p&gt;Supplementary Figure 1. Inhibitory effect of Cetuximab determined by western blot analysis of 12 HNSCC cell line lysates. Supplementary Figure 2. Time course of EGFR phosphorylation in HNSCC cell line UT-SCC 8. Supplementary Figure 3. Correlation of total and membrane exposed EGFR in HNSCC cell lines. Supplementary Figure 4. IL-3 dependent Ba/F3 cells can be transformed to EGF dependence by stable transduction with EGFR and EGFRK521 genes. Supplementary Figure 5. Far-UV CD spectra of Fc-EGFR and Fc-EGFRK521. Supplementary Figure 6. ADCC induction in EGFR-transduced Ba/F3 cells by Cetuximab and CetuGEX{trade mark, serif}.&lt;/p&gt;
Effect of Atomic Layer Epitaxy Growth Conditions on the Properties of ZnS Epilayers on (100)-Si Substrate (1996)

ZnS films have been grown on (100)-Si substrate in atomic layer epitaxy (ALE) mode using DMZn and H2S as source materials. The growth rate was 0.7 monolayer per cycle, independent of substrate temperature in the range 125° C to 225° C. Under optimum growth conditions, ZnS layers grown in ALE mode showed good surface morphology. In photoluminescence (PL) spectra, a sharp peak at 337 nm was observed at room temperature, which was attributed to band-to-band emission.
Tailoring the volatility and stability of oligopeptides (2017)

Amino acids are essential building blocks of life, and fluorinated derivatives have gained interest in chemistry and medicine. Modern mass spectrometry has enabled the study of oligo- and polypeptides as isolated entities in the gas phase, but predominantly as singly or even multiply charged species. While laser desorption of neutral peptides into adiabatically expanding supersonic noble gas jets is possible, UV-VIS spectroscopy, electric or magnetic deflectometry as well as quantum interferometry would profit from the possibility to prepare thermally slow molecular beams. This has typically been precluded by the fragility of the peptide bond and the fact that a peptide would rather 'fry', i.e. denature and fragment than 'fly'. Here, we explore how tailored perfluoroalkyl functionalization can reduce the intermolecular binding and thus increase the volatility of peptides and compare it to previously explored methylation, acylation and amidation of peptides. We show that this strategy is essential and enables the formation of thermal beams of intact neutral tripeptides, whereas only fragments were observed for an extensively fluoroalkyl-decorated nonapeptide. © 2017 The Authors. Journal of Mass Spectrometry Published by John Wiley & Sons Ltd.
Molecular Characterization of <i>Escherichia coli</i> Isolated from Chickens with Colibacillosis in Senegal (2018)

Avian pathogenic Escherichia coli (APEC), a subset of extraintestinal pathogenic E. coli (ExPEC), are the etiologic agent of avian colibacillosis, one of the main causes of economic losses in the poultry industry. The aim of this study was to characterize E. coli isolated from diseased chickens in Senegal to elucidate their virulence potential and antimicrobial resistance (AMR). A total of 58 isolates, each from a separate farm, were characterized for AMR, virulence, and AMR genes, phylogroup, serogroup, biofilm formation, and pulsed-field gel electrophoresis, and for two isolates, whole-genome sequencing (WGS). Fifty isolates (86.2%) were multidrug resistant. Many AMR genes were detected, including variants of bla<sub>CTX-M</sub> encoding resistance to third-generation cephalosporins (five isolates [8.6%]). Most fluoroquinolone-nonsusceptible isolates (21/26) were carriers of mutations in gyrA (Ser83Leu, Asp87Asn, and/or Asp87Tyr) and/or parC (Ser80Ile) genes. Forty-nine (84.5%) isolates exhibited at least one of the virulence markers of APEC, among which 23 (39.7%) were defined as potential virulent APEC. In addition, 10 isolates, of which 9 were defined as APEC, carried virulence profiles corresponding to ExPEC. Seven isolates, of which six were classified as ExPEC, belonged to phylo-serogroup F-O25, and following WGS of two of these isolates, were found to belong to the serotype O25:H1 and to the sequence type ST624. Some isolates classified as ExPEC, including F-O25, were found to strongly produce biofilm, suggesting their capability to persist for long time in the environment. F-O25-isolates, although found in different widely separated farms, formed a single cluster that included clones, suggesting that these isolates may have originated from a common source. Taken together, these results suggest that some E. coli involved in chicken colibacillosis in Senegal may pose a human health risk.
X-RAY ABSORPTION SPECTROSCOPY STUDY OF <font>Mn</font><sub>2</sub><font>O</font><sub>3</sub> AND <font>Mn</font><sub>3</sub><font>O</font><sub>4</sub> NANOPARTICLES SUPPORTED ON MESOPOROUS SILICA SBA-15 (2008)

Mn K-edge absorption measurements were carried out on α-Mn2O3 and Mn3O4 nanocrystals supported on a mesoporous silica, SBA-15. The X-ray absorption near edge structure (XANES) spectra demonstrate the existence of the oxidation states of Mn (2+ and 3+) in Mn3O4 and Mn (3+) in Mn2O3, those ions were present in different octahedral environments. Meanwhile, XANES data demonstrate that some Mn atoms that are bonding to the inner wall of the channels as isolated species, may exist as Mn4+ in Mn2O3/SBA-15. In addition, the structure, texture, and electronic properties of nanocomposites were also studied using various characterization techniques including X-ray diffraction (XRD) and laser Raman spectroscopy (LRS). The formation of the hausmannite Mn3O4 and bixbyite Mn2O3 structures has been confirmed clearly by XRD. The prepared nanocomposites of MnOx showed significant catalytic activity towards CO oxidation below 523 K.
Virtual reality-based therapy for the treatment of balance deficits in patients receiving inpatient rehabilitation for traumatic brain injury (2014)

This study provides a modest level of evidence to support using commercially available VR gaming systems for the treatment of balance deficits in patients with a primary diagnosis of TBI receiving inpatient rehabilitation. Additional research of these types of interventions for the treatment of balance deficits is warranted.
Nanoporous Metal - Combining Strength and Porosity (2006)

Recent nanomechanical tests on submicron metal columns and wires have revealed a dramatic increase in yield strength with decreasing sample size. This effect seems to be related to the increased strength observed in metals on decreasing grain size or film thickness, and has been explained by a dislocation nucleation/activation controlled plasticity regime in small sample volumes. The question arises whether one can utilize this new size effect to design materials with improved bulk properties. Here, we demonstrate that nanoporous metal foams can be envisioned as a three-dimensional network of ultrahigh-strength nanocolumns/wires, thus bringing together two seemingly conflicting properties: high strength and high porosity. Specifically, we studied the mechanical properties of nanoporous (np) Au using a combination of nanoindentation and column microcompression tests, as well as supplemental molecular dynamics simulations. We find that np-Au can be as strong as bulk Au, despite being a highly porous material, and that the ligaments in np-Au approach the theoretical yield strength of Au. The combination of high yield strength and high porosity can be used to design a new generation of energy absorbing materials for various engineering applications.
LiMn<sub>0.8</sub>Fe<sub>0.2</sub>PO<sub>4</sub>: An Advanced Cathode Material for Rechargeable Lithium Batteries (2009)

Capable and efficient: Carbon-coated nanoparticles of LiMn0.8Fe0.2PO4 (see TEM image) synthesized by a solid-state reaction were found to be an excellent cathode material for lithium-ion batteries: A stable reversible capacity of up to 165 mA h g−1 was observed, along with excellent cycling, very fast rate capabilities, excellent thermal stability, and very low surface reactivity in lithium-battery electrolyte solutions. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Nr3a-containing NMDA receptors promote neurotransmitter release and spike timing-dependent plasticity (2020)

Recent evidence suggests that presynaptic-acting NMDA receptors (preNMDARs) are important for neocortical synaptic transmission and plasticity. We found that unique properties of the Nr3a subunit enable preNMDARs to enhance spontaneous and evoked glutamate release and that Nr3a is required for spike timing–dependent long-term depression in the juvenile mouse visual cortex. In the mature cortex, Nr2b-containing preNMDARs enhanced neurotransmission in the absence of magnesium, indicating that presynaptic NMDARs may function under depolarizing conditions throughout life. Our findings indicate that Nr3a relieves preNMDARs from the dual-activation requirement of ligand-binding and depolarization; the developmental removal of Nr3a limits preNMDAR functionality by restoring this associative property.
Malaria Control, Elimination, and Prevention as Components of Health Security: A Review (2022)

International travel, a major risk factor for imported malaria, has emerged as an important challenge in sustaining malaria elimination and prevention of its reestablishment. To make travel and trade safe, the WHO adopted the International Health Regulations (IHR) which provides a legal framework for the prevention, detection, and containment of public health risks at source. We conducted a systematic review to assess the relevance and the extent of implementation of IHR practices that can play a role in reducing malaria transmission. Selected studies addressed control, elimination, and prevention of reestablishment of malaria. Study themes focused on appraisal of surveillance and response, updating national policies to facilitate malaria control and elimination, travel as a risk factor for malaria and risk mitigation methods, vector control, transfusion malaria, competing interests, malaria in border areas, and other challenges posed by emerging communicable diseases on malaria control and elimination efforts. Review results indicate that malaria has not been prioritized as part of the IHR nor has the IHR focused on vector-borne diseases such as malaria. The IHR framework in its current format can be applied to malaria and other vector-borne diseases to strengthen surveillance and response, overcome challenges at borders, and improve data sharing-especially among countries moving toward elimination-but additional guidelines are required. Application of the IHR in countries in the malaria control phase may not be effective until the disease burden is brought down to elimination levels. Considering existing global elimination goals, the application of IHR for malaria should be urgently reviewed and included as part of the IHR.
INDIUM BUMPS SHAPING AND TREATMENT FOR MATRIX PHOTODETECTOR ASSEMBLY BY FLIP CHIP TECHNOLOGY (2007)

Indium bumps properties for flip chip assembly of CdHgTe and InAs infrared detector arrays and silicon multiplexer have been investigated. It is shown that the indium bumps fabricated by a vacuum indium deposition and a photolithography, contain a surface layer more rigid in comparison with the bulk indium and having a poor adhesive ability. This layer prevents bumps from the good adhesive contact during assembly and leads to bumps disconnection under a temperature cycling because of the difference in the thermal-expansion coefficients of the infrared detector material and the silicon multiplexer. Designed in this work method of precise removal this layer and subsequent reflow increase the adhesion strength between indium bumps more than order and, thereby, increase the hybrid detector reliability.
MP16-02 ROLE OF SIMULTANEOUS TRUS GUIDED RANDOM BIOPSY IN MEN WITH UNILATERAL CANCER SUSPICIOUS REGIONS UNDERGOING MRI-US FUSION TARGETED PROSTATE BIOPSY (2016)

using ex vivo 3 Tesla or 7 Tesla magnetic field strengths from fresh prostatectomy specimens (n15) obtained from either organ donor or PCa patients under Institutional Review Board approval. To achieve the closest correspondence between histopathological components and MRI images in terms of resolution and sectioning planes, multiple high resolution imaging protocols (ranging from few minutes to overnight) were tested. Ductograms were generated as part of image post-processing. Specimens were subsequently submitted for histopathological evaluation.
Synthesis and Evaluation of 7‐Substituted‐3‐cyclobutylamino‐4H‐1,2,4‐benzothiadiazine‐1,1‐dioxide Derivatives as K<sub>ATP</sub> Channel Agonists. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
TRAP-5′ stem–loop interaction increases the efficiency of transcription termination in the <i>Bacillus subtilis trpEDCFBA</i> operon leader region (2007)

TRAP regulates expression of the Bacillus subtilis trpEDCFBA operon by a transcription attenuation mechanism in which tryptophan-activated TRAP binds to 11 (G/U)AG repeats in the nascent trp leader transcript. Bound TRAP blocks formation of an antiterminator structure and allows formation of an overlapping intrinsic terminator upstream of the trp operon structural genes. A 5' stem-loop (5'SL) structure located upstream of the triplet repeat region also interacts with TRAP. TRAP-5'SL RNA interaction participates in the transcription attenuation mechanism by preferentially increasing the affinity of TRAP for the nascent trp leader transcript during the early stages of transcription, when only a few triplet repeats have been synthesized. Footprinting assays indicated that the 5'SL contacts TRAP through two discrete groups of single-stranded nucleotides that lie in the hairpin loop and in an internal loop. Filter binding and in vivo expression assays of 5'SL mutants established that G7, A8, and A9 from the internal loop, and A19 and G20 from the hairpin loop are critical for proper 5'SL function. These nucleotides are conserved among certain other 5'SL-containing organisms. Single-round transcription results indicated that the 5'SL increases the termination efficiency when transcription is fast; however, the influence of the 5'SL was lost when transcription was slowed by reducing the ribonucleoside triphosphate concentration. Since there is a limited amount of time for TRAP to bind to the nascent transcript and promote termination, our data suggest that the contribution of TRAP-5'SL interaction increases the rate of TRAP binding, which, in turn, increases the efficiency of transcription termination.
Chemical Modification of CRISPR gRNAs Eliminate type I Interferon Responses in Human Peripheral Blood Mononuclear Cells (2018)

The results of our structure-activity relationship study, therefore, suggest that chemical modifications commonly used to reduce the immunostimulation of traditional RNA therapeutics can also be used as effective tools to eliminate undesirable IFN responses to <i>gRNAs.</i>
Preparation of Potassium Azidoaryltrifluoroborates and Their Cross-Coupling with Aryl Halides (2009)

Potassium azidoaryltrifluoroborates have been prepared from the corresponding haloaryltrifluoroborates in 73-98% yields. Also, we successfully cross-coupled the azido-functionalized organotrifluoroborates and carried out a one-pot sequential cross-coupling/1,3-dipolar cycloaddition and a one-pot cross-coupling/azide reduction process.
Image stabilisation of the beating heart by local linear interpolation (2006)

The stabilisation of motion on the beating heart is investigated in the context of minimally invasive robotic surgery. Although reduced by mechanical stabilisers, residual tissue motion makes safe surgery still difficult and time consuming. Compensation for this movement is therefore highly desirable. Motion can be captured by tracking natural landmarks on the heart surface recorded by a video endoscope. Stabilisation is achieved by transforming the images using a motion field calculated from captured local motion. Since the surface of the beating heart is distorted nonlinearly, compensating the occurring motion with a constant image correction factor is not sufficient. Therefore, heart motion is captured by several landmarks, the motion between which is interpolated such that locally appropriate motion correction values are obtained. To estimate the motion between the landmark positions, a triangulation is built and motion information in each triangle is approximated by linear interpolation. Motion compensation is evaluated by calculating the optical flow remaining in the stabilised images. The proposed linear interpolation model is able to reduce motion significantly and can also be implemented efficiently to stabilise images of the beating heart in realtime.