gebhart/patrepeval huggingface dataset:
Spatially Resolved Spectroscopy of Blue and Green InGaN Quantum Wells by Scanning Near‐Field Optical Microscopy (2017)

We investigated nanoscopic spectroscopy of blue and green InGaN multiple quantum wells (MQWs) by scanning near‐field optical microscopy (SNOM). The photoluminescence (PL) spectra showed emission peaks related to GaN and a main InGaN peak both in the blue and green MQWs. In addition, local emission peaks appeared on the higher‐energy side of the main InGaN peak (high‐E emission) in only the green InGaN MQW. The PL intensity map acquired from the high‐E emission in the green MQW was compared with the GaN emission intensity map, and there was no clear correlation between the high‐E emission regions and the dark spots in the GaN emission intensity map at room temperature (RT). The high‐E emissions are not due to potential barriers, but to other defects in the quantum wells. This may be because there is no high‐E emission related to the potential barrier at RT owing to the small V‐pit size, which reduces the suppression of carrier diffusion into dislocations especially at RT. Thus, the SNOM‐PL is measured for the green MQW at low temperature. In contrast to RT, there was a clear correlation between the high‐E emission regions and the dark spots in the GaN emission intensity map at 40 K, indicating that potential barriers formed around threading dislocations. The potential barrier height estimated from the SNOM‐PL spectra of the green MQW was sufficient to suppress carrier diffusion into threading dislocations.
Supplementary File 1 from Identifying Allelic Loss and Homozygous Deletions in Pancreatic Cancer without Matched Normals Using High-Density Single-Nucleotide Polymorphism Arrays (2023)

Supplementary File 1 from Identifying Allelic Loss and Homozygous Deletions in Pancreatic Cancer without Matched Normals Using High-Density Single-Nucleotide Polymorphism Arrays
A Method for Connecting Solution-Phase Enzyme Activity Assays with Immobilized Format Analysis by Mass Spectrometry (2004)

This paper reports an enzyme activity assay that combines the assets of both homogeneous and solid-phase formats. In this method, enzyme reactions are carried out in solution using substrates that are tagged with an immobilization reagent that allows the substrates to be selectively immobilized to self-assembled monolayers (SAMs), for direct analysis by matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). As a model enzyme reaction, this work examined the transfer of a methyl group from S-adenosyl-l-methionine (AdoMet) to an arginine side chain of a peptide substrate by the enzyme protein arginine methyltransferase 1 (RMT1). A cysteine-terminated peptide substrate was methylated by RMT1 in solution and then applied to a maleimide-presenting SAM to give selective immobilization of the peptide. Time-dependent analysis of methylation using MALDI-TOFMS clearly showed that both the presence and relative amount of the two reaction products-the mono- and dimethylated peptides-can be conveniently evaluated. This assay strategy is rapid, takes advantage of solution-phase assay conditions, avoids the use of labels and complicated purification steps, and is applicable to multianalyte analyses.
Characterization of SOI wafers by synchrotron X-ray topography (2004)

Synchrotron X-ray topographs were taken for bonded silicon-on-insulator wafers. Under the grazing incident condition, the topographs of the top Si layer and the substrate are similar, which represent the variation in incident angle due to surface undulation. Furthermore, a circular concentric pattern was observed in the topographs of the top Si layer both at the grazing and higher incident angles. This shows that the concentric pattern is not due to surface undulation, but due to lattice distortion.
Effects of Vacuum Hydration on the Incidence of Splits in Canned Kidney Beans (Phaseolus vulgaris) (1985)

ABSTRACT Dry red kidney beans were canned using two different pretreatments: soaking for 12 hr at 20°C, and vacuum hydration for 5 min followed by soaking for 2 hr at temperatures from 45‐59.1°C. Samples were then packed, processed to commercial sterility, and tested for percentage of split beans after processing. Vacuum hydration pretreatments greatly decreased the incidence and severity of splitting in the canned product and accelerated water uptake while retaining the same moisture content after soaking as the conventional soak treatment. Vacuum‐hydrated beans gained less moisture during retorting than conventionally treated samples.
Lipoxin A4 decreases human memory B cell antibody production via an ALX/FPR2-dependent mechanism: A link between resolution signals and adaptive immunity (P5151) (2013)

Abstract Specialized proresolving mediators (SPMs) are endogenous bioactive lipid molecules that play a fundamental role in the regulation of inflammation and its resolution. SPMs are classified into lipoxins, resolvins, protectins and maresins. Lipoxins and other SPM have been identified in immunological tissues including bone marrow, spleen and blood. Lipoxins regulate functions of the innate immune system such as monocyte recruitment and inhibition of neutrophil infiltration to the site of inflammation. A major knowledge gap is whether lipoxins influence adaptive immune cells. Here, we discovered that B cells express the lipoxin A4 (LXA4) receptor, ALX/FPR2, and upregulate its expression following mitogen activation. Furthermore, LXA4 decreased IgM and IgG production on activated B cells through an ALX/FPR2-dependent mechanism. This caused a reduction in NF-κB p65 nuclear translocation. We found that memory B cells express higher levels of ALX/FPR2 compared to naïve B cells. Interestingly, LXA4 inhibited human memory B cell antibody production and proliferation, but not naïve B cell function. LXA4 also decreased antigen-specific antibody production in vivo. To our knowledge, this is the first description of the effects of lipoxins on B cells, which provides a link between resolution signals and adaptive immunity. The ability of lipoxins to decrease memory B cell antibody production could be particularly beneficial to threat chronic inflammatory diseases and autoimmune disorders.
Tide versus storm in Epeiric coastal deposition: Two Proterozoic sequences, India (1990)

Abstract The relative importance of tides and storms in coastal sedimentation in ancient epeiric seas is frequently problematical. Here we appraise the depositional regimes in two Proterozoic Vindhyan formations in India with the aim of elucidating the records of each of these processes. The respective products of the two processes are not easily distinguished as both of them entail repeated fluctuations in water level and depositional energy. Two orders of fluctuation are recognized in both formations. The nature and scale of these two orders of fluctuation along with high‐resolution facies analysis make the distinction between the respective products of the two processes possible. Many of the features so long counted as characteristics of tidal rhythms, in the studied formations, exclusively or frequently manifest waxing and waning of storms or fairweather–storm cyclicity. This study highlights the need for reevaluation of ancient coastal sequences in epeiric setting.
γ-Aminobutyric Acid, a Neurotransmitter, Induces Planktonic Abalone Larvae to Settle and Begin Metamorphosis (1979)

gamma-Aminobutyric acid (a simple amino acid and potent neurotransmitter in human brain and other tissues of higher animals) and certain of its congeners rapidly and synchronously induce planktonic larvae of the red abalone, Haliotis rufescens, to settle and commence behavioral and developmental metamorphosis. These naturally occurring inducers of algal origin apparently are responsible, in part, for the substrate-specific recruitment, induction of settling, and the onset of metamorphosis of abalone and other planktonic larvae upon specific algae which provide naturally favorable habitats for the young of these species in coastal waters. These observations provide a convenient experimental model for further analysis of the basic molecular mechanisms by which environmental and endogenous factors control the recruitment and development of planktonic larvae. Halogenated organic pesticides significantly interfere with larval settling, as quantified in a new bioassay based upon these findings.
Infection by Human Herpesvirus 6 (HHV-6) of Human Lymphoid T Cells Occurs Through an Endocytic Pathway (1992)

We have analyzed by immunoelectron microscopy the early events of binding and internalization of human herpesvirus 6 (HHV-6, strain GS) on a susceptible T-lymphoblastoid cell line, HSB-2. The virions bound to the cell surface at 4 degrees C were tightly associated with the plasma membrane. Gold immunolabeling of the viral envelope proteins was strong and specific. Warming at 37 degrees C for different times showed viral internalization through smooth surfaced pits and vesicles. Fusion events of the virions with the cell plasma membrane were never observed. Gold immunolabeling performed in parallel experiments before or after viral internalization showed: (1) absence of viral envelope proteins on the cell plasma membranes at all times of internalization, again excluding fusion events; (2) entry of the virions with their envelopes. Treatment of the cells with chloroquine, a drug known to affect the endocytic pathway, led to an almost complete inhibition of viral infectivity, suggesting that the endocytosed virions are responsible for a successful infection. Comparable results were obtained using a second strain of HHV-6 (BA92), with biologic and molecular characteristics similar to the prototype strain Z29. The chloroquine inhibition was effective on two different T cell lines (HSB-2 and J-Jhan), as well as on phytohemagglutinin-stimulated peripheral blood mononuclear cells.
The Periplasmic Folding of a Cysteineless Autotransporter Passenger Domain Interferes with Its Outer Membrane Translocation (2006)

Autotransporters are single polypeptides consisting of an outer membrane translocation domain mediating the translocation of a passenger domain. The periplasmic folding state of the passenger domain is controversial. By comparisons of passenger domains differing in their folding properties, our results suggest that periplasmic folding of passenger domains interferes with translocation.
Effect of atomic layer deposition on the quality factor of silicon nanobeam cavities (2012)

In this work we study the effect of thin-film deposition on the quality factor (Q) of silicon nanobeam cavities. We observe an average increase in the Q of 38±31% in one sample and investigate the dependence of this increase on the initial nanobeam hole sizes. We note that this process can be used to modify cavities that have larger than optimal hole sizes following fabrication. Additionally, the technique allows the tuning of the cavity mode wavelength and the incorporation of new materials, without significantly degrading Q.
Kinetic modeling of the reaction and crystallization of acetylsalicylic acid using ATR UV-vis spectroscopy (2011)

In industry, spectroscopy is used to monitor batch chemical reactions and to maximize production of a material for a minimum cost. However, there are many challenges involved in using spectroscopic methods to characterize reaction systems that undergo crystallization. For instance, the crystallization of a product in solution creates a slurry mixture for which it is hard to measure light absorption due to the nature of the mixture. Some of these problems are less prominent when using attenuated total reflectance (ATR) techniques (provided the enhancement of solid particles is low), due to its ability to circumvent the problems of separating light absorption from light scattering encountered in diffuse reflectance measurements [1]. &lt;br&gt;&lt;br&gt; The aim of this work is to formulate a kinetic model [2] for the reaction of salicylic acid with acetic anhydride that leads to the formation of acetylsalicylic acid and to its subsequent crystallization. The experiment involves a solid addition of salicylic acid into acetic anhydride, followed by an addition of water to consume the excess reactant, and finally a cooling step to initiate nucleation and crystal growth. The kinetic model will be constructed based on changes in light absorption measured by attenuated total reflectance ultravioletâvisible (ATR UVâVis) spectroscopy. In addition, near infrared (NIR) diffuse reflectance spectroscopy will be used to determine the onset of nucleation and the degree of supersaturation which is the driving force for a power law based model describing the crystallization of the product. &lt;br&gt;&lt;br&gt; [1] Falconet et al. (2008). Estimation of optical properties of turbid media: experimental comparison of spatially and temporally resolved reflectance methods. Applied Optics, 1734â1739. &lt;br&gt; [2] Gemperline, P. (2006). Practical Guide to Chemometrics. Second Edition. Boca Raton: Taylor &amp; Francis.
High Prevalence of 16S rRNA methylase genes High Prevalence of 16S rRNA methylase genes Among Carbapenem-resistant Hypervirulent Klebsiella pneumoniae Isolates in China (2019)

Abstract Background : the existence of 16S rRNA methylase genes would increase treatment difficulty of patients infected with CR-hvKP strains, this study was aimed to testify the prevalence of the 16S rRNA methylase genes genes in the CR-hvKP strains in China.Methods : Thirty-nine carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) isolates collected from a Chinese hospital during the whole year of 2018 were evaluated to characterize the prevalence of 16S rRNA methylase genes. Results : In tatal 66.7% (26/39) of the CR-hvKP isolates were found to carry 16S rRNA methylase genes, and the most frequently detected gene was armA (11,42.3%), followed by rmtB (8,30.8%),and 7 CR-hvKP strains were found to carry both armA and rmtB (26.9%). All the clinical isolates were found to carry at least one carbapenemase gene,with KPC-2 (79.5%,31/39), NDM-1 (10.3%,4/39), and cocarrying KPC-2 and NDM-1 (10.3%,4/39). A total of 89.7% (35/39) isolates carried ESBL genes, including 61.5% (24/39) blaSHV-1 ,71.8% (28/39) blaTEM-1 and 89.7% (35/39) blaCTX-M-1 4. All except four isolates (89.7%,35/39) harbored PMQR genes,with qnrS (82.1%,32/39), aac(6’)-Ib-cr (79.5%,31/39), qnrB (2.6%,1/39).All the 16S rRNA methylase genes-positive CR-hvKP strains were firstly found to cocarry carbapenemase genes, ESBL genes and PMQR genes simultaneously. The most prevalent virulence genes were rmpA2 and entB (100%, 39/39),followed by silS (97.4%, 38/39), ybtS (94.9%, 37/39), iutA (92.3%, 36/39), kpn (92.3%, 36/39), rmpA (87.2%, 34/39), terW (84.6%, 33/39), aerobactin (23.1%, 9/39), repA (17.9%, 7/39), magA (10.3%, 4/39), kfuB C (10.3%, 4/39), w ca G (10.3%, 4/39), allS (10.3%, 4/39). Multilocus sequence typing (MLST) analysis assigned the 39 CR-hvKP isolates into 4 sequence types (STs), with ST11 encompassing 79.5% of the strains. Pulsed field gel electrophoresis (PFGE) typing showed that strains closely related by MLST clustered in major PFGE clusters, of which cluster A accounts for 31 ST11 isolates.The analysis of the transconjugants showed a high-level aminoglycoside resistance and a popular cotransfer of bla KPC-2 with the 16S rRNA methylase genes.Conclusions : 16S rRNA methylase genes are highly prevalent in CR-hvKP clinical isolates especially for ST11, it is therefore critical to continuously monitor the 16S rRNA methylase-producing CR-hvKP epidemiology and minimize potential risks from aminoglycoside -resistant CR-hvKP.
“Photobiomics”: Can Light, Including Photobiomodulation, Alter the Microbiome? (2019)

<b><i>Objective</i>:</b> The objective of this review is to consider the dual effects of microbiome and photobiomodulation (PBM) on human health and to suggest a relationship between these two as a novel mechanism. <b><i>Background</i>:</b> PBM describes the use of low levels of visible or near-infrared (NIR) light to heal and stimulate tissue, and to relieve pain and inflammation. In recent years, PBM has been applied to the head as an investigative approach to treat diverse brain diseases such as stroke, traumatic brain injury (TBI), Alzheimer's and Parkinson's diseases, and psychiatric disorders. Also, in recent years, increasing attention has been paid to the total microbial population that colonizes the human body, chiefly in the gut and the mouth, called the microbiome. It is known that the composition and health of the gut microbiome affects many diseases related to metabolism, obesity, cardiovascular disorders, autoimmunity, and even brain disorders. <b><i>Materials and methods</i>:</b> A literature search was conducted for published reports on the effect of light on the microbiome. <b><i>Results</i>:</b> Recent work by our research group has demonstrated that PBM (red and NIR light) delivered to the abdomen in mice, can alter the gut microbiome in a potentially beneficial way. This has also now been demonstrated in human subjects. <b><i>Conclusions</i>:</b> In consideration of the known effects of PBM on metabolomics, and the now demonstrated effects of PBM on the microbiome, as well as other effects of light on the microbiome, including modulating circadian rhythms, the present perspective introduces a new term "photobiomics" and looks forward to the application of PBM to influence the microbiome in humans. Some mechanisms by which this phenomenon might occur are considered.
Colonic formation of soft feces in rabbits: a role for endogenous prostaglandins (1986)

Rabbits produce hard and soft feces in a circadian rhythm. The motor activity of the haustrated proximal colon is inhibited during the formation of soft feces, whereas the spiking activity of the distal colon is stimulated. A potential role for endogenous prostaglandins (PG) in the control of the soft-feces elaboration by the rabbit colon was investigated in conscious animals by using PGE2 and PGF2 alpha and by inhibiting them with indomethacin. The infusion of both PGE2 and PGF2 alpha induced typical electromechanical events consisting of inhibition of the proximal and stimulation of the distal colon and was followed by soft-pellet defecation. Rabbits accustomed to be fed twice daily produced soft feces at fixed intervals of 252 +/- 32 min after the evening meal, with a soft-to-hard feces ratio of 1.45. After indomethacin treatment, this ratio was significantly (P less than 0.01) reduced to 0.92. These results are consistent with the concept that endogenous prostaglandins play a major role in the motor function involved in soft-feces formation by the rabbit.
Multi-Band Transmission Using Reconfigurable Complex Multi-Band Delta Sigma Polar Modulator (2021)

This brief presents a new reconfigurable complex multi-band delta sigma polar modulator (CMB-DSPM) architecture for multi-band transmission. In this brief, a <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$6^{\mathrm{ th}}$ </tex-math></inline-formula> order band-pass delta sigma modulator (DSM) is designed and implemented for reconfigurable triple-band transmission. The proposed DSM architecture utilizes the advantage of a complex DSM structure to reduce the required processing block and polar quantizer to reduce the quantization noise. The proposed CMB-DSPM architecture improves the in-band and out-of-band performance in terms of signal-to-noise distortion ratio (SNDR) and coding efficiency (CE), respectively. The proposed scheme is validated in MATLAB/SIMULINK-based digital signal processing platform using three 5 MHz long-term evolution (LTE) signals. The results show up to 12.4 dB improvement in SNDR and 12.3% improvement in CE compared to the standard cartesian DSM architecture. The measured EVM is below 3%, which shows the good in-band performance of the proposed scheme.
pH Regulation of Sterigmatocystin and Aflatoxin Biosynthesis inAspergillusspp. (1997)

ABSTRACT Aflatoxin (AF) and sterigmatocystin (ST) are toxic secondary metabolites produced by the same biochemical pathway found in several Aspergillus spp. The expression of the homologous ST/AF structural gene, stcU in A. nidulans and ver-1 in A. parasiticus, was affected by external pH of liquid growth media. Both stcU and ver-1 mRNAs appeared earlier and were expressed at higher levels in cultures grown in acidic media (pH 4 to 6) versus neutral (pH 7) and alkali (pH 8) media. Transcript levels correlated with ST/AF production. Visual and spectrophotometric analysis of production of the orange ST/AF intermediate, norsolorinic acid (NOR), also paralleled transcript patterns and indicated that the pH effects were operative in different nitrogen- and carbon-based solid growth media. Five- to 10-fold increases in ST, AF, and NOR were measured in cultures grown in pH 4 or 5 versus pH 8 media. An A. nidulans strain carrying a mutation resulting in constitutive activity of the pH regulatory factor, PacC, produced 10-fold less ST than did wild type. The stcU transcript was not noticeably affected by pH in this strain. The results suggest a general pattern of pH regulation of ST/AF biosynthesis that may override previously noted carbon and nitrogen effects.
Distribution of integrons and phylogenetic groups among highly virulent serotypes of Klebsiella pneumoniae in a Chinese tertiary hospital (2019)

In summary, a high prevalence of integrons (55.6%) was found among HVS K. pneumoniae isolates in a Chinese tertiary hospital. Class 1 integrons were the most predominant and their variable regions were polymorphic. The presence of integrons in HVS K. pneumoniae isolates results in increased antimicrobial resistance.
Targeted Identification of SUMOylation Sites in Human Proteins Using Affinity Enrichment and Paralog-specific Reporter Ions (2013)

Protein modification by small ubiquitin-like modifier (SUMO) modulates the activities of numerous proteins involved in different cellular functions such as gene transcription, cell cycle, and DNA repair. Comprehensive identification of SUMOylated sites is a prerequisite to determine how SUMOylation regulates protein function. However, mapping SUMOylated Lys residues by mass spectrometry (MS) is challenging because of the dynamic nature of this modification, the existence of three functionally distinct human SUMO paralogs, and the large SUMO chain remnant that remains attached to tryptic peptides. To overcome these problems, we created HEK293 cell lines that stably express functional SUMO paralogs with an N-terminal His6-tag and an Arg residue near the C terminus that leave a short five amino acid SUMO remnant upon tryptic digestion. We determined the fragmentation patterns of our short SUMO remnant peptides by collisional activation and electron transfer dissociation using synthetic peptide libraries. Activation using higher energy collisional dissociation on the LTQ-Orbitrap Elite identified SUMO paralog-specific fragment ions and neutral losses of the SUMO remnant with high mass accuracy (< 5 ppm). We exploited these features to detect SUMO modified tryptic peptides in complex cell extracts by correlating mass measurements of precursor and fragment ions using a data independent acquisition method. We also generated bioinformatics tools to retrieve MS/MS spectra containing characteristic fragment ions to the identification of SUMOylated peptide by conventional Mascot database searches. In HEK293 cell extracts, this MS approach uncovered low abundance SUMOylated peptides and 37 SUMO3-modified Lys residues in target proteins, most of which were previously unknown. Interestingly, we identified mixed SUMO-ubiquitin chains with ubiquitylated SUMO proteins (K20 and K32) and SUMOylated ubiquitin (K63), suggesting a complex crosstalk between these two modifications.