gebhart/patrepeval huggingface dataset:
Fast algorithms for frequent itemset mining using FP-trees (2005)

Efficient algorithms for mining frequent itemsets are crucial for mining association rules as well as for many other data mining tasks. Methods for mining frequent itemsets have been implemented using a prefix-tree structure, known as an FP-tree, for storing compressed information about frequent itemsets. Numerous experimental results have demonstrated that these algorithms perform extremely well. In this paper, we present a novel FP-array technique that greatly reduces the need to traverse FP-trees, thus obtaining significantly improved performance for FP-tree-based algorithms. Our technique works especially well for sparse data sets. Furthermore, we present new algorithms for mining all, maximal, and closed frequent itemsets. Our algorithms use the FP-tree data structure in combination with the FP-array technique efficiently and incorporate various optimization techniques. We also present experimental results comparing our methods with existing algorithms. The results show that our methods are the fastest for many cases. Even though the algorithms consume much memory when the data sets are sparse, they are still the fastest ones when the minimum support is low. Moreover, they are always among the fastest algorithms and consume less memory than other methods when the data sets are dense.
Identification of Bioactive Compounds in Polar and Nonpolar Extracts of Araujia sericifera (2017)

Abstract Araujia sericifera is a native perennial, climbing laticiferous shrub from South America that is currently naturalized in many other countries. Previous data describe promising properties for A. sericifera, but no systematic study of its bioactive compounds and possible medicinal applications has been conducted to date. In the present study, aerial parts of A. sericifera (leaves, stems, and fruits) were explored by combining GC-MS and NMR spectroscopy analysis for both nonpolar (hexane) and polar (methanol) extracts. The hexanic extracts contained high amounts of pentacyclic triterpenes including two new metabolites, 3-tigloyl germanicol (18) and 3-tigloyl lupeol (19). The methanolic extracts revealed the presence of luteolin-7-glucoside (24), trigonelline (22), and conduritol F (23) as the main constituents. A multivariate study of a meaningful number of extracts allowed us to determine the distribution of compounds inside the plant. A cytotoxic evaluation in vitro showed that both leaf and fruit hexanic extracts presented a moderate activity against human breast carcinoma cell lines (MDA-MB-453 and MCF-7) and human colon carcinoma cell line (HCT-116) by the MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay.
Supplementary Figure 1 from Immunotargeting of Antigen xCT Attenuates Stem-like Cell Behavior and Metastatic Progression in Breast Cancer (2023)

&lt;p&gt;Cellular localization and correlation with breast cancer patient clinical outcome (CO) of genes differentially expressed in TUBO cells and tumorspheres&lt;/p&gt;
Device-Grade Amorphous Silicon Prepared by High-Pressure Plasma (2002)

The high-pressure plasma regime (∼5 Torr) was investigated in order to break through the growth rate limit for device-grade hydrogenated amorphous silicon (a-Si:H) without increasing the substrate temperature. The growth rate was successfully increased up to ∼7 Å/s while preserving quality. Controlling the electrode gap is important for utilizing high-pressure plasma, and the narrowest possible gap, below which plasma becomes unstable, is necessary to obtain high growth rates with the same high quality that is obtained at lower growth rates. The combination of high pressure and the narrowest possible electrode gap reduces the higher silane formation and enhances the generation of proper growth radicals such as SiH3. It is essential to suppress the influence of higher silane related radicals in the surface reactions for the film growth. This method allows device-grade a-Si:H to be produced at practical growth rates without increasing the substrate temperature, and contributes to the effective production of a-Si:H devices.
Multiple Site‐Specific Installations of Nε‐Monomethyl‐L‐Lysine into Histone Proteins by Cell‐Based and Cell‐Free Protein Synthesis (2014)

Lysine methylation is one of the important post-translational modifications of histones, and produces an N(ε) -mono-, di-, or trimethyllysine residues. Multiple and site-specific lysine methylations of histones are essential to define epigenetic statuses and control heterochromatin formation, DNA repair, and transcription regulation. A method was previously developed to build an analogue of N(ε)-monomethyllysine, with cysteine substituting for lysine. Here, we have developed a new method of preparing histones bearing multiple N(ε)-monomethyllysine residues at specified positions. Release factor 1-knockout (RFzero) Escherichia coli cells or a cell-free system based on the RFzero cell lysate was used for protein synthesis, as in RFzero cells UAG is redefined as a sense codon for non-canonical amino acids. During protein synthesis, a tert-butyloxycarbonyl-protected N(ε)-monomethyllysine analogue is ligated to Methanosarcina mazei pyrrolysine tRNA (tRNA(Pyl)) by M. mazei pyrrolysyl-tRNA synthetase mutants, and is translationally incorporated into one or more positions specified by the UAG codon. Protecting groups on the protein are then removed with trifluoroacetic acid to generate N(ε)-monomethyllysine residues. We installed N(ε)-monomethyllysine residues at positions 4, 9, 27, 36, and/or 79 of human histone H3. Each of the N(ε)-monomethyllysine residues within the produced histone H3 was recognized by its specific antibody. Furthermore, the antibody recognized the authentic N(ε)-monomethyllysine residue at position 27 better than the N(ε)-monomethyllysine analogue built with cysteine. Mass spectrometry analyses also confirmed the lysine modifications on the produced histone H3. Thus, our method enables the installation of authentic N(ε)-monomethyllysines at multiple positions within a protein for large-scale production.
The Stoichiometric Production of IL-2 and IFN-γ mRNA Defines Memory T Cells That Can Self-Renew After Adoptive Transfer in Humans (2012)

Adoptive immunotherapy using ex vivo-expanded tumor-reactive lymphocytes can mediate durable cancer regression in selected melanoma patients. Analyses of these trials have associated the in vivo engraftment ability of the transferred cells with their antitumor efficacy. Thus, there is intensive clinical interest in the prospective isolation of tumor-specific T cells that can reliably persist after transfer. Animal studies have suggested that central memory CD8(+) T cells (T(CM)) have divergent capabilities including effector differentiation to target antigen and stem cell-like self-renewal that enable long-term survival after adoptive transfer. We sought to isolate human melanoma-specific T(CM) to define their in vivo fate and function after autologous therapeutic transfer to metastatic patients. To facilitate the high-throughput identification of these rare cells from patients, we report that T(CM) have a defined stoichiometric production of interleukin-2 (IL-2) and interferon-γ (IFN-γ) mRNA after antigen stimulation. Melanoma-specific T cells screened for high relative IL-2 production had a T(CM) phenotype and superior in vitro proliferative capacity compared to cells with low IL-2 production. To investigate in vivo effector function and self-renewal capability, we allowed melanoma-specific T(CM) to undergo in vitro expansion and differentiation into lytic effector clones and then adoptively transferred them back into their hosts. These clones targeted skin melanocytes in all five patients and persisted long term and reacquired parental T(CM) attributes in four patients after transfer. These findings demonstrate the favorable engraftment fitness for human T(CM)-derived clones, but further efforts to improve their antitumor efficacy are still necessary.
Isolation of native EVs from primary biofluids—Free‐flow electrophoresis as a novel approach to purify ascites‐derived EVs (2022)

Although extracellular vesicles (EVs) have been extensively characterized, efficient purification methods, especially from primary biofluids, remain challenging. Here we introduce free-flow electrophoresis (FFE) as a novel approach for purifying EVs from primary biofluids, in particular from the peritoneal fluid (ascites) of ovarian cancer patients. FFE represents a versatile, fast, matrix-free approach for separating different analytes with inherent differences in charge density and/or isoelectric point (pI). Using a series of buffered media with different pH values allowed us to collect 96 fractions of ascites samples. To characterize the composition of the individual fractions, we used state-of-the-art methods such as nanoflow and imaging flow cytometry (nFCM and iFCM) in addition to classical approaches. Of note, tetraspanin-positive events measured using nFCM were enriched in a small number of distinct fractions. This observation was corroborated by Western blot analysis and electron microscopy, demonstrating only minor contamination with soluble proteins and lipid particles. In addition, these gently purified EVs remain functional. Thus, FFE represents a new, efficient and fast method for separating native and highly purified EVs from complicated primary samples.
LINGO-1 antagonists as therapy for multiple sclerosis:in vitroandin vivoevidence (2008)

LINGO-1 is a potential target for neuroprotective therapy in that antagonists may promote remyelination in diseases such as MS.
3D Fin Waveguide on 10nm Gate Oxide Bonded Double-SOI for Low VΠL Accumulation Modulator (2018)

We propose a new design for a low VπL accumulation optical modulator using 3-Dimensional (3D) Fin-waveguides on double Silicon-On-Insulator (SOI). We have introduced and demonstrated a novel, self-aligned patterning process to pattern the bottom SOI layer using anisotropic wet etching.
High‐resolution cell division tracking demonstrates the Flt3‐ligand‐dependence of human marrow CD34+CD38− cell production in vitro (1997)

Investigation of primitive human haemopoietic cell behaviour requires methodologies for monitoring asynchronously activated cells over several generations. We describe a high-resolution procedure for tracking 5- (and 6-) carboxyfluorescein diacetate succinimidyl ester (CFSE)- labelled human haemopoietic cells through six cell cycles based on the precise halving of their CFSE-fluorescence at each mitosis. Using this approach in combination with DNA or surface antigen staining, we show that the addition of Flt3-ligand (FL) to a cytokine cocktail consisting of Steel factor, IL-3, IL-6 and G-CSF increased the proportion of CD34+ (CD45RA/CD71)-, but not CD34+(CD45RA/CD71)+, human marrow cells initially recruited into division in vitro, shortened the overall cycle time of their progeny, and enhanced the production of a derivative CD34+CD38- population through several (up to four) cell generations. These studies also showed that during the first 4d there was no detectable apoptosis among the progeny of the CD34+(CD45RA/CD71)- cells generated in the presence of this four-cytokine cocktail, regardless of the presence of FL. The availability of a technique for monitoring changes in the properties of individual cells as a function of their mitotic history and under conditions where they are asynchronously recruited to divide provides a new and powerful approach for studies of the regulation of primitive human haemopoietic cell proliferation and differentiation.
Cell Surface Expression of the Bovine Leukemia Virus-Binding Receptor on B and T Lymphocytes Is Induced by Receptor Engagement (2008)

Bovine leukemia virus (BLV), one of the most common infectious viruses of cattle, is endemic in many herds. Approximately 30-40% of adult cows in the United States are infected by this oncogenic C-type retrovirus and 1-5% of animals will eventually develop a malignant lymphoma. BLV, like the human and simian T cell leukemia viruses, is a deltaretrovirus but, in contrast with the latter, the BLV receptor remains unidentified. In this study, we demonstrate that the amino-terminal 182 residues of the BLV envelope glycoprotein surface unit encompasses the receptor-binding domain. A bona fide interaction of this receptor-binding domain with the BLV receptor was demonstrated by specific interference with BLV, but not human T cell leukemia virus, envelope glycoprotein-mediated binding. We generated a rabbit Ig Fc-tagged BLV receptor-binding domain construct and ascertained that the ligand binds the BLV receptor on target cells from multiple species. Using this tool, we determined that the BLV-binding receptor is expressed on differentiating pro/pre-B cells in mouse bone marrow. However, the receptor was not detected on mature/quiescent B cells but was induced upon B cell activation. Activation of human B and T lymphocytes also induced surface BLV-binding receptor expression and required de novo protein synthesis. Receptor levels were down-regulated as activated lymphocytes returned to quiescence. In the human thymus, BLV-binding receptor expression was specifically detected on thymocytes responding to the IL-7 cytokine. Thus, expression of the BLV-binding receptor is a marker of enhanced metabolic activity in B cells, T cells, and thymocytes.
Ethanol Extract of Hizikia fusiforme Induces Apoptosis in B16F10 Mouse Melanoma Cells through ROS-Dependent Inhibition of the PI3K/Akt Signaling Pathway (2020)

These results indicate that EHF induces apoptosis through activation of extrinsic and intrinsic apoptotic pathways and ROS-dependent inactivation of PI3K/Akt signaling in B16F10 cells.<br />.
Mechanically Versatile Soft Machines through Laminar Jamming (2018)

Abstract There are two major structural paradigms in robotics: soft machines, which are conformable, durable, and safe; and traditional rigid robots, which are fast, precise, and capable of applying high forces. Here, the paradigms are bridged by enabling soft machines to behave like traditional rigid robots on command. This task is accomplished via laminar jamming, a structural phenomenon in which a laminate of compliant strips becomes strongly coupled through friction when a pressure gradient is applied, causing dramatic changes in mechanical properties. Rigorous analytical and finite element models of laminar jamming are developed, and jamming structures are experimentally characterized to show that the models are highly accurate. Then jamming structures are integrated into soft machines to enable them to selectively exhibit the stiffness, damping, and kinematics of traditional rigid robots. The models allow jamming structures to efficiently meet arbitrary performance specifications, and the physical demonstrations illustrate how to construct systems that can behave like either soft machines or traditional rigid robots at will, such as continuum manipulators that can rapidly have joints appear and disappear. This study aims to foster a new generation of mechanically versatile machines and structures that cannot simply be classified as “soft” or “rigid.”
Two mechanisms of blueshift of edge emission in InGaN-based epilayers and multiple quantum wells (2002)

We present the results of a comparative photoluminescence (PL) study of GaN and InGaN-based epilayers, and InGaN/GaN multiple quantum wells (MQWs). Room-temperature PL spectra were measured for a very broad range of optical excitation from 10 mW/cm2 up to 1 MW/cm2. In contrast to GaN epilayers, all In-containing samples exhibited an excitation-induced blueshift of the peak emission. In addition, the blueshift of the emission in the InGaN epilayers with the same composition as the quantum well was significantly smaller. The comparison of the blueshift in the “bulk” InGaN and in the MQWs allowed us to separate two different mechanisms responsible for this effect: (i) filling of the localized states in In-rich areas and (ii) screening of the polarization electric field in strained MQW structures.
Identification of arterial oxygen intermittency in oximetry data (2022)

In patients with kidney failure treated by hemodialysis, intradialytic arterial oxygen saturation (SaO<sub>2</sub>) time series present intermittent high-frequency high-amplitude oximetry patterns (IHHOP), which correlate with observed sleep-associated breathing disturbances. A new method for identifying such intermittent patterns is proposed. The method is based on the analysis of recurrence in the time series through the quantification of an optimal recurrence threshold ([Formula: see text]). New time series for the value of [Formula: see text] were constructed using a rolling window scheme, which allowed for real-time identification of the occurrence of IHHOPs. The results for the optimal recurrence threshold were confronted with standard metrics used in studies of obstructive sleep apnea, namely the oxygen desaturation index (ODI) and oxygen desaturation density (ODD). A high correlation between [Formula: see text] and the ODD was observed. Using the value of the ODI as a surrogate to the apnea-hypopnea index (AHI), it was shown that the value of [Formula: see text] distinguishes occurrences of sleep apnea with great accuracy. When subjected to binary classifiers, this newly proposed metric has great power for predicting the occurrences of sleep apnea-related events, as can be seen by the larger than 0.90 AUC observed in the ROC curve. Therefore, the optimal threshold [Formula: see text] from recurrence analysis can be used as a metric to quantify the occurrence of abnormal behaviors in the arterial oxygen saturation time series.
An Early Step in Pseudomonas Exotoxin Action Is Removal of the Terminal Lysine Residue, Which Allows Binding to the KDEL Receptor (1997)

During the intoxication process, Pseudomonas exotoxin (PE) and immunotoxins containing PE internalize into the target cell and become processed into two fragments, and the carboxyl fragment translocates into the cytosol where it inactivates elongation factor 2. We have proposed that after internalization into cells the carboxyl-terminal fragment of PE (amino acids 280-613), which ends in REDLK, binds to the KDEL receptor (ERD2) which carries it to the endoplasmic reticulum, from which the PE fragment translocates to the cytosol. Earlier experiments showing that REDL but not REDLK binds to the KDEL receptor suggested that the terminal lysine is removed sometime during the intoxication process. To determine if and where this occurs, we exposed a peptide ending in REDLK to malignant cells in culture and found that binding to the KDEL receptor was restored. Restoration of receptor binding also occurred if a peptide or toxin ending in REDLK at its carboxyl terminus was incubated with plasma, indicating that the terminal lysine is removed prior to entry of the toxin into the cell. We conclude that plasma carboxypeptidase(s) cleave(s) the lysine residue from the carboxyl terminus of PE and PE-containing immunotoxins as an early and essential step in their cellular intoxication pathway.
Hb encapsulation in vesicles retards the reaction with NO, but not CO, by intracellular diffusion barrier (2008)

NO‐binding of Hb is restricted by encapsulation in RBCs to prevent vasoconstriction. To clarify the mechanism, we analyzed Hb‐vesicles (HbV) with different intracellular Hb concentrations, [Hb] in , and different particle sizes using stopped‐flow spectrophotometry. The apparent NO‐binding rate constant, k′ NO , of HbV at [Hb] in = 1 g/dl was almost equal to k NO of molecular Hb, indicating that the lipid membrane is not a barrier. With increasing [Hb] in to 35 g/dl, k′ NO decreased to 1/3, which was further decreased to 1/5 with enlarging particle diameter (&lt;450 nm). For CO‐binding, which is intrinsically much slower than NO‐binding, k′ CO did not change greatly with [Hb] in and the particle diameter. Results obtained using diffusion simulations coupled with elementary reactions concur with these tendencies and clarify that NO is trapped rapidly by Hb from the interior surface area to the core of HbV at a high [Hb] in , retarding NO‐diffusion toward the core of HbV. In contrast, slow CO‐binding allows time for further CO diffusion to the core. Simulations extrapolated to a large particle (8 μm) showing retardation even for CO‐binding. The obtained k′ NO and k′ CO yield similar values to those reported for RBCs. In summary, the intracellular, not extracellular, diffusion barrier is predominant owing to the rapid NO‐binding that induces a sink of NO from the interior surface to the core, retarding further NO‐diffusion and binding.
Limits imposed by spatial hole burning on the single-mode operation of standing wave laser cavities (1990)

A simple formula is derived that gives the ratio of the maximum single-longitudinal-mode inversion density to the threshold inversion density for a standing-wave laser in terms of the cavity geometry and well-known material parameters. This formula can be used as a guideline in the design of single-frequency lasers.
Focal Arrhythmia Confined Within the Coronary Sinus and Maintaining Atrial Fibrillation (2007)

This study provides evidence that the CS may be a potential source of focal rapid activity maintaining AF.
Salmonella enterica Serovar Diversity, Distribution, and Prevalence in Public-Access Waters from a Central California Coastal Leafy Green-Growing Region from 2011 to 2016 (2021)

Prevalence and serovar diversity of Salmonella enterica were measured during a 5-year survey of surface waters in a 500-mi<sup>2</sup> agricultural region of the Central California Coast. Rivers, streams, lakes, and ponds were sampled bimonthly resulting in 2,979 samples. Overall prevalence was 56.4% with higher levels detected in spring than in fall. Small, but significant, differences in prevalence were detected based on sample locations. Detection of Salmonella was correlated positively with both significant rain events and, in some environments, levels of generic Escherichia coli. Analysis of 1,936 isolates revealed significant serovar diversity, with 91 different serovars detected. The most common isolated serovars were S. enterica subsp. <i>enterica</i> serovars I 6,8:d:- (406 isolates, 21.0%, and potentially monophasic Salmonella Muenchen), Give (334 isolates, 17.3%), Muenchen (158 isolates, 8.2%), Typhimurium (227 isolates, 11.7%), Oranienburg (106 isolates, 5.5%), and Montevideo (78 isolates, 4%). Sixteen of the 24 most common serovars detected in the region are among the serovars reported to cause the most human salmonellosis in the United States. Some of the serovars were associated with location and seasonal bias. Analysis of XbaI pulsed field gel electrophoresis (PFGE) patterns of strains of serovars Typhimurium, Oranienburg, and Montevideo showed significant intraserovar diversity. PFGE pulsotypes were identified in the region for multiple years of the survey, indicating persistence or regular reintroduction to the region. <b>IMPORTANCE</b> Nontyphoidal Salmonella is among the leading causes of bacterial foodborne illness, and increasing numbers of outbreaks and recalls are due to contaminated produce. High prevalence and 91 different serovars were detected in this leafy green growing region. Seventeen serovars that cause most of the human salmonellosis in the United States were detected, with 16 of those serovars detected in multiple locations and multiple years of the 5-year survey. Understanding the widespread prevalence and diversity of Salmonella in the region will assist in promoting food safety practices and intervention methods for growers and regulators.