gebhart/patrepeval huggingface dataset:
Faculty Opinions recommendation of Toll-like receptor 2 controls mucosal inflammation by regulating epithelial barrier function. (2007)

BACKGROUND & AIMS: Toll-like receptors (TLRs) represent a class of transmembrane pattern recognition receptors essential for microbial recognition and control of innate immune responses. Commensal bacteria play an important role in maintaining tolerance and active stability of the intestinal epithelial barrier by suppressing intestinal inflammation, yet the mechanisms of action are unknown. The aim of this study was to determine the functional relevance of TLR2 to control tight junction (TJ)-associated intestinal epithelial barrier integrity to balance mucosal homeostasis against inflammatory stress-induced damage.METHODS: TLR2 ligand (synthetic Pam(3)Cys-SK4 [PCSK])-induced activation of signaling cascades and TJ-associated distribution was assessed by using Western blotting and confocal microscopy combined with functional transfection and inhibitor studies in model intestinal epithelial cell (IEC) lines (IEC-6, Caco-2) or primary IEC cultured short-term ex vivo. DSS colitis was induced by standard protocol in wild-type, TLR2-/-, and MyD88-/- mice. Spontaneous apoptosis was assessed by terminal deoxinucleotidyl-transferase-mediated dUTP-biotin nick end-labeling.RESULTS: Data from in vitro and ex vivo models of intestinal epithelial cells revealed that TLR2 stimulation effectively preserves TJ-associated barrier assembly against stress-induced damage through promotion of PI3K/Akt-mediated cell survival via MyD88. Furthermore, in vivo studies underscored that TLR2-mediated TJ regulation critically determines susceptibility to intestinal injury and inflammation. Inflammatory stress in mice deficient of TLR2 or MyD88 induced early TJ-associated disruption interrelated with anti-apoptotic failure of the intestinal epithelial barrier. Oral treatment of colitis with the TLR2 ligand PCSK significantly suppressed mucosal inflammation and apoptosis by efficiently restoring TJ-associated integrity of the intestinal epithelium in vivo.CONCLUSION: TLR2 may provide a target to pharmacologically modulate mucosal injury and intestinal inflammation. PMID: 17408640 Funding information This work was supported by: NIDDK NIH HHS, United States Grant ID: DK60049 NIDDK NIH HHS, United States Grant ID: DK43351 NIDDK NIH HHS, United States Grant ID: DK41557 NIDDK NIH HHS, United States Grant ID: R01 DK060049
Application of mutant <i>JAK2</i>V617F for in vitro generation of red blood cells (2015)

This is the first trial to use a PV erythropoiesis model for RBC differentiation from stem cells. The transduction of HSCs with mJAK2 increased their proliferation capacity in EPO-free culture conditions. This model may also be useful for investigating the pathogenesis of PV.
Ligand-inducible, prostate stem cell antigen (PSCA)-directed GoCAR-T cells in advanced solid tumors: Preliminary results with cyclophosphamide (Cy) ± fludarabine (Flu) lymphodepletion (LD). (2019)

2536 Background: Cell-surface protein PSCA is upregulated in many solid tumors and correlates with disease stage. BPX-601, an autologous T-cell product expressing a PSCA-CD3ζ CAR and a rimiducid (Rim)-inducible MyD88/CD40 co-activation switch to augment T-cell proliferation and persistence, is designed to have enhanced efficacy in solid tumors vs traditional CARs. This ongoing first-in-human study assesses safety, biologic, and clinical activity of BPX-601+Rim in PSCA+ cancers. Updated results, including those from patients (pts) who underwent LD with Flu/Cy, are presented. Methods: BP-012 is a 2-part, open-label trial. Part 1 is a 3+3 dose escalation of BPX-601 (1.25–5.0x10 6 cells/kg; Day [D] 0) given prior to a single, fixed Rim dose (0.4 mg/kg; D7) in pts with previously treated PSCA+ metastatic pancreatic, gastric, or prostate cancers with measurable disease. Results: As of Jan-22-2019, 15 pts have received BPX-601±Rim. Two pts at the highest cell dose received Flu/Cy for LD on D−5 to D−3 before BPX-601; LD after Flu/Cy was 96.6% and 84.3%. Thirteen pts received Cy alone on D−3; in these pts, LD ranged from 0–68.6%. Rapid cell expansion by D4 was observed in all pts with peak vector copy number 8.3-fold higher with Flu/Cy (n = 2) vs Cy LD (n = 13). Serum IP-10, IL-6 and TNFα increased &gt; 2-fold from baseline in ≥1 pt in all Rim cohorts, with 3- to 20-fold Rim-dependent cell expansion in 6 pts. No CRS or DLTs were reported. After Rim, one Flu/Cy pt experienced a serious Grade 2 AE (encephalopathy) related to BPX-601+Rim that resolved with IV steroids; despite time-matched nonserious Grade 1 pyrexia, the pt had no other CRS symptoms. After BPX-601+Rim and ≥1 scan, best responses were 8 SD and 3 PD (1 non-evaluable). With a median follow-up of 9.8 wks, time to next treatment (tx) after BPX-601 ranged from 2.7–22.1 wks (n = 8) and ongoing tx-free intervals range from 9.1–30.1 wks (n = 4). Conclusions: BPX-601+Rim was well-tolerated with manageable safety and early evidence of enhanced CAR T-cell expansion and prolonged persistence after Flu/Cy vs Cy. Additional pts will undergo Flu/Cy LD prior to BPX-601 with single- and repeat-dose Rim. Clinical trial information: NCT02744287.
Prion protein/protein interactions: fusion with yeast Sup35p‐NM modulates cytosolic PrP aggregation in mammalian cells (2007)

In mammalian prion diseases, an abnormally folded, aggregated form of the prion protein (PrP(Sc)) appears to catalyze a conformational switch of its cellular isoform (PrP(C)) to an aggregated state. A similar prion-like phenomenon has been reported for the Saccharomyces cerevisiae translation termination factor Sup35p that can adopt a self-propagating conformation. We have compared aggregation propensities of chimeric proteins derived from the Sup35p prion domain NM and PrP in vitro and in the cytosol of mammalian cells. Sup35p-NM and PrP displayed strikingly different aggregation behaviors when expressed in mammalian cells, with NM remaining soluble and cytosolic PrP spontaneously aggregating due to the globular domain of PrP. When fused to PrP(90-230), Sup35p-M exhibited an inhibitory effect for nucleation but increased aggregate growth, potentially by facilitating recruitment of newly synthesized chimeric proteins into the growing aggregates. This effect, however, could, to some extent, be counteracted by the prion-forming region Sup35p-N, thereby increasing aggregate frequency. Interestingly, a lowered nucleation rate was also observed in the presence of the amino-terminal region of PrP, suggesting that Sup35p-M and PrP(23-90) share some biological function in prion protein assembly. Our results provide new insights into prion protein aggregation behaviors, demonstrating the impact of dynamic interactions between prion domains and suggesting that aggregation of yeast and mammalian prion proteins is strongly influenced by yet unidentified cellular conditions or factors.
Comparative analysis of single-cell RNA sequencing methods with and without sample multiplexing (2023)

Abstract Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating biological heterogeneity at the single-cell level in human systems and model organisms. Recent advances in scRNA-seq have enabled the pooling of cells from multiple samples into single libraries, thereby increasing sample throughput while reducing technical batch effects, library preparation time, and the overall cost. However, a comparative analysis of scRNA-seq methods with and without sample multiplexing is lacking. In this study, we benchmarked methods from two representative platforms: Parse Biosciences (Parse; with sample multiplexing) and 10X Genomics (10x; without sample multiplexing). By using peripheral blood mononuclear cells (PBMCs) obtained from two healthy individuals, we demonstrate that demultiplexed scRNA-seq data obtained from Parse showed similar cell type frequencies compared to 10X data where samples are not multiplexed. Despite a relatively lower library and cell capture efficiencies, Parse can detect rare cell types (e.g. plasmablasts and dendritic cells) which is likely due to its relatively higher sensitivity in gene detection. Moreover, comparative analysis of transcript quantification between the two platforms revealed platform-specific distributions of gene length and GC content. These results offer guidance for researchers in designing high-throughput scRNA-seq studies.
Statistics of Stokes variables for correlated Gaussian fields (1994)

The joint and marginal probability distribution functions of the Stokes variables are derived for correlated Gaussian fields [an extension of D. Eliyahu, Phys. Rev. E 47, 2881 (1993)]. The statistics depend only on the first moment (averaged) Stokes variables and have a universal form for ${\mathit{S}}_{1}$, ${\mathit{S}}_{2}$, and ${\mathit{S}}_{3}$. The statistics of the variables describing the Cartesian coordinates of the Poincar\'e sphere are given also.
Development of modules for multidimensional on-line processing of microliter volume samples. (2006)

Abstract not provided.
1018 (2015)

Copyright © by 2015 by the Society of Critical Care Medicine and Wolters Kluwer Health, Inc. All Rights Reserved.
A novel synthesis of 6′′‐[<sup>18</sup>F]‐fluoromaltotriose as a PET tracer for imaging bacterial infection (2018)

The aim of this study was to develop a positron emission tomography (PET) tracer to visualize and monitor therapeutic response to bacterial infections. In our continued efforts to find maltose based PET tracers that can image bacterial infections, we have designed and prepared 6′′‐[ 18 F]fluoromaltotriose as a second generation PET imaging tracer targeting the maltodextrin transporter of bacteria. We have developed methods to synthesize 6′′‐deoxy‐6′′‐[ 18 F]fluoro‐α‐D‐glucopyranosyl‐(1‐4)‐O‐α‐D‐glucopyranosyl‐(1‐4)‐O‐D‐glucopyranose (6′′‐[ 18 F]‐fluoromaltotriose) as a bacterial infection PET imaging agent. 6′′‐[ 18 F]fluoromaltotriose was prepared from precursor, 2′′,3′′,4′′‐tri‐O‐acetyl‐6′′‐O‐nosyl‐α‐D‐glucopyranosyl‐(1‐4)‐O‐2′,3′,6′‐tri‐O‐acetyl‐α‐D‐glucopyranosyl‐(1‐4)‐1,2,3,6‐tetra‐O‐acetyl‐D‐glucopyranose (per‐O‐acetyl‐6′′‐O‐nosyl‐maltotriose 4 ). This method utilizes the reaction between precursor 4 and anhydrous [ 18 F]KF/Kryptofix 2.2.2 in dimethylformamide (DMF) at 85°C for 10 minutes to yield per‐O‐acetyl‐6′′‐deoxy‐6‐′′ [ 18 F]‐fluoromaltotriose ( 7) . Successive acidic and basic hydrolysis of the acetyl protecting groups in 7 produced 6′′‐[ 18 F]fluoromaltotriose ( 8 ). Also, cold 6′′‐ [ 19 F]fluoromaltotriose was prepared from per‐O‐acetyl‐6′′‐hydroxymaltotriose via a diethylaminosulfur trifluoride reaction followed by a basic hydrolysis. A successful synthesis of 6′′‐[ 18 F]‐fluoromaltotriose has been accomplished in 8 ± 1.2% radiochemical yield (decay corrected). Total synthesis time was 120 minutes. Serum stability of 6′′‐[ 18 F]fluoromaltotriose at 37°C indicated that 6′′‐[ 18 F]‐fluoromaltotriose remained intact up to 2 hours. In conclusion, we have successfully synthesized 6′′‐[ 18 F]‐fluoromaltotriose via direct fluorination of an appropriate precursor of a protected maltotriose.
A Nonlinear Regression Method for Composite Protection Modeling of Induction Motor Loads (2020)

Protection equipment is used to prevent damage to induction motor loads by isolating them from power systems in the event of severe faults. Modeling the response of induction motor loads and their protection is vital for power system planning and operation, especially in understanding system's dynamic performance and stability after a fault occurs. Induction motors are usually equipped with several types of protection with different operation mechanisms, making it challenging to develop adequate yet not overly complex protection models and determine their parameters for aggregate induction motor models. This paper proposes an optimization-based nonlinear regression framework to determine protection model parameters for aggregate induction motor loads in commercial buildings. Using a mathematical abstraction, the task of determining a suitable set of parameters for the protection model in composite load models is formulated as a nonlinear regression problem. Numerical examples are provided to illustrate the application of the framework. Sensitivity studies are presented to demonstrate the impact of lack of available motor load information on the accuracy of the protection models.
Multi-band Bloch equations and gain spectra of highly excited II-VI semiconductor quantum wells (1997)

Quasi-equilibrium excitation dependent optical probe spectra of II-VI semiconductor quantum wells at room temperature are investigated within the framework of multi-band semiconductor Bloch equations. The calculations include correlation effects beyond the Hartree-Fock level which describe dephasing, interband Coulomb correlations and band-gap renormalization in second Born approximation. In addition to the carrier-Coulomb interaction, the influence of carrier-phonon scattering and inhomogeneous broadening is considered. The explicit calculation of single particle properties like band structure and dipole matrix elements using k {center_dot} p theory makes it possible to investigate various II-VI material combinations. Numerical results are presented for CdZnSe/ZnSe and CdZnSe/MnZnSSe semiconductor quantum-well systems.
M-mode ultrasonic detection of microbubbles following saturation diving: a case report and proposal for a new grading system. (1989)

An M-mode ultrasound system was used to obtain a reliable method for the evaluation of microbubbles caused by decompression. When the probe is focused in the outflow tract of the right ventricle it is easy to recognize a linear configuration of the echoes caused by the microbubbles. A quantitative study of microbubbles can be done by counting the number of linear echoes per second. Application of this method is reported following saturation diving decompression. We think the reported method is worthy of further use.
A linear algebraic approach to orthogonal arrays and Latin squares (2012)

To study orthogonal arrays and signed orthogonal arrays, Ray-Chaudhuri and Singhi (1988 and 1994) considered some module spaces. Here, using a linear algebraic approach we define an inclusion matrix and fi nd its rank. In the special case of Latin squares we show that there is a strai ghtforward algorithm for generating a basis for this matrix using the so-called intercalates. We also extend this last idea.
Protective Role for B-1b B Cells and IgM in Obesity-Associated Inflammation, Glucose Intolerance, and Insulin Resistance (2016)

NAb-producing B-1b B cells are increased in Id3(Bcell KO) mice and attenuate adipose tissue inflammation and glucose intolerance in diet-induced obese mice. Additional findings are the first to identify VAT as a reservoir for human B-1 cells and to link anti-inflammatory IgM antibodies with reduced inflammation and improved metabolic phenotype in obese humans.
Imaginary Ribozymes (2020)

Biocatalysis is dominated by protein enzymes, and only a few classes of ribozymes are known to contribute to the task of promoting biochemical transformations. The RNA World theory encompasses the notion that earlier forms of life made use of a much greater diversity of ribozymes and other functional RNAs to guide complex metabolic states long before proteins had emerged in evolution. In recent years, the discoveries of various classes of ribozymes, riboswitches, and other noncoding RNAs in bacteria have provided additional support for the hypothesis that RNA molecules indeed have the catalytic competence to promote diverse chemical reactions without the aid of protein enzymes. Herein, some of the most striking observations made from examinations of natural riboswitches that bind small ligands are highlighted and used as a basis to imagine the characteristics and functions of long-extinct ribozymes from the RNA World.
Alterations of the cerebroside fraction of human thyroid glycosphingolipids in Graves' disease. (1985)

The influence of Graves' disease in human thyroid neutral glycosphingolipids was investigated. The major alteration was in the cerebroside fraction. Although the total amount of cerebroside was not different, the relative proportion of the bands of glucosylceramide separated on borated thin-layer plates was greatly modified in the disease. The band of glucosylceramide containing phytosphingosine and hydroxylated fatty acids decreased strongly, whereas the band with C18 sphingosine and normal fatty acids increased simultaneously. No change was observed in the content of galabiosylceramide. A slight elevation was seen in the amount of globoside at the expense of globotriaosylceramide.
A Highly Efficient and Practical Method for Catalytic Asymmetric Vinylogous Mannich (AVM) Reactions (2006)

Sehr selektiv und dabei noch einfach sind die hier vorgestellten asymmetrischen vinylogen Mannich-Reaktionen, die im Gramm-Maßstab in nicht destilliertem THF an Luft gelingen (siehe Schema; TMS=SiMe3). Man braucht nur käufliches AgOAc, ein leicht zugängliches Phosphanderivat einer Aminosäure und ein kommerziell erhältliches oder in einem Schritt herstellbares Siloxyfuran.
A review of tinnitus symptoms beyond ‘ringing in the ears’: a call to action (2011)

Patients with tinnitus experience a spectrum of distressing symptoms that impact their quality of life and there is a clear need for action. Clinicians need to recognize and diagnose tinnitus that occurs with other wide-ranging symptoms to ensure that these symptoms are identified and patients receive effective treatment.
Modulation of mucus production by interleukin‐13 receptor α<sub>2</sub> in the human airway epithelium (2007)

The soluble form of IL-13Ralpha(2) may therefore modulate mucus overproduction by IL-13 through the pathway including IL-13Ralpha(1) in NHBECs.
Aberrant Fat Metabolism in Caenorhabditis elegans Mutants with Defects in the Defecation Motor Program (2015)

The molecular mechanisms by which dietary fatty acids are absorbed by the intestine, and the way in which the process is regulated are poorly understood. In a genetic screen for mutations affecting fat accumulation in the intestine of Caenorhabditis elegans, nematode worms, we have isolated mutations in the aex-5 gene, which encodes a Kex2/subtilisin-family, Ca2+-sensitive proprotein convertase known to be required for maturation of certain neuropeptides, and for a discrete step in an ultradian rhythmic phenomenon called the defecation motor program. We demonstrate that aex-5 mutants have markedly lower steady-state levels of fat in the intestine, and that this defect is associated with a significant reduction in the rate at which labeled fatty acid derivatives are taken up from the intestinal lumen. Other mutations affecting the defecation motor program also affect steady-state levels of triglycerides, suggesting that the program is required per se for the proper accumulation of neutral lipids. Our results suggest that an important function of the defecation motor program in C. elegans is to promote the uptake of an important class of dietary nutrients. They also imply that modulation of the program might be one way in which worms adjust nutrient uptake in response to altered metabolic status.
A new interband multiwavelet decomposition for exact coding of multicomponent images (2002)

In this paper, we are interested in using multiwavelet transforms in the context of progressive and lossless coding of multi component images. More precisely, multiwavelet decompositions that map integers to integers are considered since they guarantee a perfect reconstruction in the absence of quantizers. Generally, these decompositions are performed separately on each spectral component of a multicomponent image. Therefore, they fail to exploit the spectral redundancies. Our main contribution in this paper consists in modifying multiwavelet decompositions in order to take into account simultaneously the spatial and the spectral redundancies contained in a multicomponent image. Simulation tests carried out on natural multicomponent images show that the the generalized interband decomposition outperforms the state-of-art lossless coders.
Investigation of Phase Composition in Dense and Porous Gelcast Alumina Sintered under Argon Atmosphere (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
The dynamic landscape of fission yeast meiosis alternative-splice isoforms (2016)

Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here, we exploit a single-molecule long-read sequencing technique and develop an open-source software program called SpliceHunter to characterize the transcriptome in the meiosis of fission yeast. We reveal 14,353 alternative splicing events in 17,669 novel isoforms at different stages of meiosis, including antisense and read-through transcripts. Intron retention is the major type of alternative splicing, followed by alternate "intron in exon." Seven hundred seventy novel transcription units are detected; 53 of the predicted proteins show homology in other species and form theoretical stable structures. We report the complexity of alternative splicing along isoforms, including 683 intra-molecularly co-associated intron pairs. We compare the dynamics of novel isoforms based on the number of supporting full-length reads with those of annotated isoforms and explore the translational capacity and quality of novel isoforms. The evaluation of these factors indicates that the majority of novel isoforms are unlikely to be both condition-specific and translatable but consistent with the possibility of biologically functional novel isoforms. Moreover, the co-option of these unusual transcripts into newly born genes seems likely. Together, the results of this study highlight the diversity and dynamics at the isoform level in the sexual development of fission yeast.
Seizure detection using regression tree based feature selection and polynomial SVM classification (2015)

This paper presents a novel patient-specific algorithm for detection of seizures in epileptic patients with low hardware complexity and low power consumption. In the proposed approach, we first compute the spectrogram of the input fragmented EEG signals from three or four electrodes. Each fragmented data clip is one second in duration. Spectral powers and spectral ratios are then extracted as features. The features are then subjected to feature selection using regression tree. The selected features are then subjected to a polynomial support vector machine (SVM) classifier with degree of 2. The algorithm is tested using the intra-cranial EEG (iEEG) from the UPenn and Mayo Clinic's Seizure Detection Challenge database. It is shown that the proposed algorithm can achieve a sensitivity of 100.0%, an average area under curve (AUC) of 0.9818, a mean detection horizon of 5.8 seconds, and a specificity of 99.9% on using half of the training data for classification. The proposed approach also achieved a mean AUC of seizure detection and early seizure detection of 0.9136 on the testing data.