gebhart/patrepeval huggingface dataset:
Lexical selection with competing distractors: Evidence from left temporal lobe lesions (2017)

According to the competition account of lexical selection in word production, conceptually driven word retrieval involves the activation of a set of candidate words in left temporal cortex and competitive selection of the intended word from this set, regulated by frontal cortical mechanisms. However, the relative contribution of these brain regions to competitive lexical selection is uncertain. In the present study, five patients with left prefrontal cortex lesions (overlapping in ventral and dorsal lateral cortex), eight patients with left lateral temporal cortex lesions (overlapping in middle temporal gyrus), and 13 matched controls performed a picture-word interference task. Distractor words were semantically related or unrelated to the picture, or the name of the picture (congruent condition). Semantic interference (related vs. unrelated), tapping into competitive lexical selection, was examined. An overall semantic interference effect was observed for the control and left-temporal groups separately. The left-frontal patients did not show a reliable semantic interference effect as a group. The left-temporal patients had increased semantic interference in the error rates relative to controls. Error distribution analyses indicated that these patients had more hesitant responses for the related than for the unrelated condition. We propose that left middle temporal lesions affect the lexical activation component, making lexical selection more susceptible to errors.
Study of the Magnetic Properties of a Lieb Core-Shell Nano-Structure: Monte Carlo Simulations (2019)

The object of this work is to study the magnetic properties of the Lieb structure based on magnetic particles with core-shell nano-structure. This system is consisting of a ferromagnetic 2D Ising model formed with spins: sigma=1/2, S=1 and q=3/2. Firstly, we examine the magnetic properties of this nanostructure. On the other hand, we study the effect of the coupling exchange interactions and the crystal field. We use the Monte Carlo simulations to investigate also the behavior of the Lieb nano-structure. Finally, we study the influence of the temperature on the critical and compensation behaviors of the studied system. The obtained results are summarized in the phase diagrams.
Selective reciprocity in antimicrobial activity versus cytotoxicity of hBD-2 and crotamine (2009)

Recent discoveries suggest cysteine-stabilized toxins and antimicrobial peptides have structure-activity parallels derived by common ancestry. Here, human antimicrobial peptide hBD-2 and rattlesnake venom-toxin crotamine were compared in phylogeny, 3D structure, target cell specificity, and mechanisms of action. Results indicate a striking degree of structural and phylogenetic congruence. Importantly, these polypeptides also exhibited functional reciprocity: (i) they exerted highly similar antimicrobial pH optima and spectra; (ii) both altered membrane potential consistent with ion channel-perturbing activities; and (iii) both peptides induced phosphatidylserine accessibility in eukaryotic cells. However, the Na(v) channel-inhibitor tetrodotoxin antagonized hBD-2 mechanisms, but not those of crotamine. As crotamine targets eukaryotic ion channels, computational docking was used to compare hBD-2 versus crotamine interactions with prototypic bacterial, fungal, or mammalian Kv channels. Models support direct interactions of each peptide with Kv channels. However, while crotamine localized to occlude Kv channels in eukaryotic but not prokaryotic cells, hBD-2 interacted with prokaryotic and eukaryotic Kv channels but did not occlude either. Together, these results support the hypothesis that antimicrobial and cytotoxic polypeptides have ancestral structure-function homology, but evolved to preferentially target respective microbial versus mammalian ion channels via residue-specific interactions. These insights may accelerate development of anti-infective or therapeutic peptides that selectively target microbial or abnormal host cells.
Fungal Infections in Left Ventricular Assist Device Recipients (1995)

The authors reviewed the charts of 26 recipients of a left ventricular assist device to determine the incidence of fungal infections and the clinical course of these patients. Nine patients (35%) had positive fungal cultures. Of these, six had clinical infections and three were colonized asymptomatically. Three of the six infected patients (including one with mediastinal sepsis and another requiring left ventricular assist device replacement for intractable fungemia) underwent orthotopic heart transplantation after successful therapy. Of the remaining three, one died of a thromboembolic stroke (probably septic in nature), one died secondary to driveline rupture, and the third succumbed to culturenegative sepsis. Two of the colonized patients underwent transplantation, and the third succumbed to perioperative right sided circulatory failure and hypoxia. Positive fungal cultures were a common finding in our series. Because of a significant incidence of fungal infection-related morbidity, the authors revised their pre operative and post operative protocol to include: 1) 2 weeks of fluconazole therapy (200 mg intravenously daily) for patients receiving broad spectrum antibiotics and for those with evidence of preoperative fungal colonization; 2) daily dressing changes around drivelines; 3) daily nystatin swish and swallow; and 4) empiric fluconazole treatment for culture-negative sepsis. Using this protocol, three left ventricular assist device recipients received prophylactic fluconazole and had no evidence of fungal morbidity or mortality on short-term follow-up.
Combined Low Frequency and Third Harmonic Injection in Power Amplifier Linearization (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Simultaneous injection of the difference frequency and triple frequency signals into the main RF amplifier (alongside the fundamental frequency signals) offers an independent improvement of IM3 and IM5. This advantage is not achievable by other reported techniques. </para>
Optical frequency discriminator with ultrahigh-amplitude-and-phase linearity for frequency-modulated microwave photonic links (2016)

A new linear optical frequency discriminator filter is proposed and analyzed. It offers high field-response linearity (e.g., >99%) and constant group delay for a wide selectable spectral range. Its structure is simple and compact which is based on mature MZI technology.
Cell–collagen interactions: the use of peptide Toolkits to investigate collagen–receptor interactions (2008)

Fibrillar collagens provide the most fundamental platform in the vertebrate organism for the attachment of cells and matrix molecules. We have identified specific sites in collagens to which cells can attach, either directly or through protein intermediaries. Using Toolkits of triple-helical peptides, each peptide comprising 27 residues of collagen primary sequence and overlapping with its neighbours by nine amino acids, we have mapped the binding of receptors and other proteins on to collagens II or III. Integrin alpha2beta1 binds to several GXX'GER motifs within the collagens, the affinities of which differ sufficiently to control cell adhesion and migration independently of the cellular regulation of the integrin. The platelet receptor, Gp (glycoprotein) VI binds well to GPO (where O is hydroxyproline)-containing model peptides, but to very few Toolkit peptides, suggesting that sequence in addition to GPO triplets is important in defining GpVI binding. The Toolkits have been applied to the plasma protein vWF (von Willebrand factor), which binds to only a single sequence, identified by truncation and amino acid substitution within Toolkit peptides, as GXRGQOGVMGFO in collagens II and III. Intriguingly, the receptor tyrosine kinase, DDR2 (discoidin domain receptor 2) recognizes three sites in collagen II, including its vWF-binding site, although the amino acids that support the interaction differ slightly within this motif. Furthermore, the secreted protein BM-40 (basement membrane protein 40) also binds well to this same region. Thus the availability of extracellular collagen-binding proteins may be important in regulating and facilitating direct collagen-receptor interaction.
Multi-process control software for HUBO2 Plus robot (2013)

Humanoid robots require greater software reliability than traditional mechatronic systems if they are to perform useful tasks in typical human-oriented environments. This paper covers a software architecture which distributes the load of computation and control tasks over multiple processes, enabling fail-safes within the software. These fail-safes ensure that unexpected crashes or latency do not produce damaging behavior in the robot. The distribution also offers benefits for future software development by making the architecture modular and extensible. Utilizing a low-latency inter-process communication protocol (Ach), processes are able to communicate with high control frequencies. The key motivation of this software architecture is to provide a practical framework for safe and reliable humanoid robot software development. The authors test and verify this framework on a HUBO2 Plus humanoid robot.
Oxidation of Amorphous Silicon for Superior Thin Film Transistors (1997)

The effects of low-pressure chemical vapor deposition (LPCVD) conditions of silicon films on polycrystalline silicon (polysilicon) thin film transistors (TFTs) fabricated through a high temperature process are studied. An LPCVD amorphous film is not uniformly flat, but has its own structure consisting of many amorphous grains. The size of these amorphous grains changes in accordance with the deposition conditions, because the conditions change the film nucleation and growth rates. An amorphous film composed of large amorphous grains is converted into a polycrystalline film of large crystalline grains after crystallization in the solid phase during thermal oxidation. It is also found that an LPCVD amorphous film has two different phases, i.e., amorphous-I and amorphous-II. The amorphous-I is a well-known phase in which the amorphous grains grow in size as the deposition temperature falls. The amorphous-II is a newly found phase in which the amorphous grains decrease in size as the deposition temperature falls. The best amorphous film is obtained in the amorphous-I phase, being deposited under a condition of large mass transfer and slow surface reaction.
Visible light modulator by sputter-deposited lithium niobate (2022)

Thin-film lithium niobate (LN) modulators have significant potential for ultra-high-speed optical communications. Although a significant cost reduction of the modulator is needed to satisfy the growing demands of huge data communications, all the existing studies of thin-film LN modulators were fabricated using the adhesion process of bulk LN to a substrate, and it severely constrains the use case of LN modulators. In order to overcome this critical issue, we have deposited thin-film LN (006) directly on a Al2O3 sapphire (001) substrate and fabricated LN modulators by using the wafer process. Furthermore, previous studies have been largely limited to the use of infrared light (typical wavelengths λ = 1550 nm), which also constrains half-wave voltage and interaction electrode length (Vπ · L) required for modulation. Small Vπ · L is essentially important not only for small die size with lower cost but also for small voltage operation by using a complementary metal oxide semiconductor. Here, we demonstrate the modulation of red (λ = 637 nm), green (λ = 520 nm), and blue (λ = 473 nm) visible light using sputter-deposited thin-film LN; the product of the half-wave voltage and interaction electrode length (Vπ · L) was 1.9, 1.4, and 1.2 V cm, respectively: it decreased with the decreasing wavelength. Thus, LN modulators can be adopted for emerging applications of visible light communications, and wafer-level fabrication using sputter-deposited thin-film LN provides opportunities for future mass production with a much lower fabrication cost.
Strongly Cavity-Enhanced Spontaneous Emission from Silicon-Vacancy Centers in Diamond (2018)

Quantum emitters are an integral component for a broad range of quantum technologies, including quantum communication, quantum repeaters, and linear optical quantum computation. Solid-state color centers are promising candidates for scalable quantum optics due to their long coherence time and small inhomogeneous broadening. However, once excited, color centers often decay through phonon-assisted processes, limiting the efficiency of single-photon generation and photon-mediated entanglement generation. Herein, we demonstrate strong enhancement of spontaneous emission rate of a single silicon-vacancy center in diamond embedded within a monolithic optical cavity, reaching a regime in which the excited-state lifetime is dominated by spontaneous emission into the cavity mode. We observe 10-fold lifetime reduction and 42-fold enhancement in emission intensity when the cavity is tuned into resonance with the optical transition of a single silicon-vacancy center, corresponding to 90% of the excited-state energy decay occurring through spontaneous emission into the cavity mode. We also demonstrate the largest coupling strength (g/2π = 4.9 ± 0.3 GHz) and cooperativity (C = 1.4) to date for color-center-based cavity quantum electrodynamics systems, bringing the system closer to the strong coupling regime.
Supplementary Figures 1-11 from Genomic and Functional Fidelity of Small Cell Lung Cancer Patient-Derived Xenografts (2023)

&lt;p&gt;Supplementary Figures 1-11&lt;/p&gt;
Synthesis and characterization of polycarbonate/polydimethylsiloxane multiblock copolymer prepared from dimethylsiloxane and various aromatic dihydroxyl monomers (2000)

This study utilizes different types of bisphenol monomers instead of bisphenol-A to synthesize phenol terminated polydimethylsiloxane-polycarbonate block copolymers. The copolymers were synthesized by interfacial phosgenation of α, ω-phenol-organofunctional polydimethylsiloxane oligomer with various aromatic dihydroxyl monomers. In addition,the thermal properties, flammability, and mechanical properties of the synthesized copolymers after extrusion and injection molding were investigated. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 75: 545–552, 2000
Characterization and regulation of H-K ATPase in intercalated cells of rabbit cortical collecting duct (1997)

K-dependent H+ extrusion was investigated using fluorescence techniques in rabbit cortical collecting tubules (CCTs). Experiments were performed in split-open tubules from normal animals exposed to the intracellular pH indicator 2',7'-bis(carboxyethyl)-5(6)-carboxyfluorescein (BCECF). This preparation permitted the study of individual intercalated cells (ICs). In the ICs, partial recovery of pH(i) was observed in response to an acute acid load upon readdition of 5 mM K to the superfusate. This recovery was SCH 28080-inhibitable (10(-5) M) and ouabain-insensitive suggesting the process is mediated by a gastric-type H-K ATPase. To see if H-K ATPase plays a role in acid secretion its function was evaluated under chronic metabolic acidosis (CMA) conditions. CMA was induced by replacing drinking water with 75 mM NH4Cl in 5% sucrose for 10-14 days. The SCH 28080-inhibitable K-dependent pH(i) recovery rate was three-fold higher in CMA ICs compared to controls. To determine the location of the H-K ATPase, CCTs were microperfused and individual peanut lectin binding (PNA) ICs studied. K-dependent pH(i) recovery was measured in response to an NH4Cl pulse. An apical SCH 28080-inhibited K-dependent pH(i) recovery process was observed in control and CMA ICs. Taken together these data confirm the existence of a gastric-type H-K ATPase in ICs of rabbit CCT. Based on our findings the H-K ATPase is found on the apical side of the cell and is stimulated under conditions of CMA.
EXTH-08. STAT3 AT THE CROSSROADS OF INNATE IMMUNE ACTIVATION IN GLIOBLASTOMA (2021)

Abstract BACKGROUND Innate immune cells comprise the majority of the immune microenvironment in glioblastoma (GBM) tumors where they are chiefly thought to foster a hospitable environment for cancer cells by regulating immune suppression and driving resistance to immunotherapy. Of these, myeloid-derived suppressor cells (MDSCs) are regarded as one of the most potent contributors to immune suppression in GBM and thus have become a focus of targeted therapy. Signal transducer and activator of transcription 3 (STAT3) is a key phenotypic regulator of MDSCs. Therefore, we sought to examine if targeted STAT3 inhibition may augment the immunogenicity of these tumors. HYPOTHESIS: Targeted STAT3 inhibition reduces GBM tumor infiltration by MDSCs. METHODS Using syngeneic murine models of GBM, we performed pharmacological inhibition analyses using a specific small molecule inhibitor of STAT3, LLL12B. Circulating numbers of immune cells were assessed in tumor bearing animals with or without concomitant focal radiation. Treated tumors were examined for immune infiltrates, and additional phenotyping analyses were performed. Therapeutic responses to LLL12B alone and in combination with immune checkpoint blockade were evaluated. RESULTS STAT3 is activated in the bone marrow of tumor-bearing animals, preferentially by Gr-1 positive granulocytic myeloid cells. Increased circulating numbers of these cells were also detected. These observations were markedly enhanced in tumor-bearing animals following cranial irradiation. Therapeutic inhibition with LLL12B could mitigate these effects, indicating a dependency on STAT3. Within the tumor compartment, granulocytic myeloid cells that successfully infiltrated following treatment demonstrated a pro-inflammatory phenotype denoted by interferon-gamma expression. Improved survival was also observed following combination treatment with LLL12B and radiation or immune checkpoint blockade. CONCLUSIONS These findings advocate a critically important role for STAT3 in regulating granulocytic myeloid cell mobilization and trafficking to GBM tumors. It further illustrates the plasticity of these cells within these tumors, which may be useful in designing successful immunotherapeutic strategies.
Array Platforms and Bioinformatics Tools for the Analysis of Plant Transcriptome in Response to Abiotic Stress (2010)

Current microarray technologies allow high-density in situ synthesis of oligonucleotides or ex situ spotting of target molecules (cDNA) for conducting genome-wide comparative gene expression profiling studies. The avalanche of available microarray gene expression data from model plant species covering cell-related, tissue-specific, and developmental events, as well as perturbations to a variety of environmental stimuli has triggered many activities regarding the development of adequate bioinformatics tools for the analysis of these complex data sets. In this chapter we summarize the technical issues of different microarray technologies, discuss the availability of bioinformatics tools, and present approaches to extract biologically meaningful knowledge. For case studies of abiotic stress transcriptome analysis we highlight the unprecedented opportunities provided by these high-throughput technologies to understand networks of regulatory and metabolic pathway responses of plant cells to the application of abiotic stress stimuli.
Scalable Enantioseparation of Amino Acid Derivatives Using Continuous Liquid−Liquid Extraction in a Cascade of Centrifugal Contactor Separators (2009)

Using a cascade of six centrifugal contactor separators in a countercurrent liquid−liquid extraction mode allowed the separation of one of the enantiomers of 3,5-dinitrobenzoyl-leucine in 55% yield and 98% ee using a catalytic amount of a chiral host compound based on a cinchona alkaloid. This method allows the preparation of kilograms of enantiopure material in table-top-sized equipment that can be operated in a fume cupboard. The methodology can be easily scaled up to ton amounts as large-volume centrifugal contactor separators are commercially available as well.
Biomolecular optoelectronic devices and their application to artificial sight (2003)

Using the technique of Kelvin force microscopy, we have performed the first measurements of photovoltages from single photosynthetic reaction centers. The measured values, typically 1 V or more, are sufficiently large to trigger a neural response. The goal of the project is insertion of purified Photosystem I (PSI) reaction centers or other photoactive agents into retinal cells where they will restore photoreceptor function to people who suffer from age-related macular degeneration (AMD) or retinitis pigmentosa (RP), diseases that are the leading causes of blindness world-wide. Although the neural wiring from eye to brain is intact, these patients lack photoreceptor activity. It is the ultimate goal of this proposal to restore photoreceptor activity to these patients using PSI as the optical trigger. In principle, the approach should work. PSI is a robust integral membrane molecular photovoltaic device. Depending on orientation, it can depolarize or hyperpolarize the cell membrane with sufficient voltage to trigger an action potential.
Risk of Thromboembolism in Heart Failure (2007)

In the SCD-HeFT patient cohort, which reflects contemporary treatment of patients with moderately symptomatic systolic heart failure, patients experienced thromboembolism events at a rate of 1.7% per year without antiarrhythmic therapy. Those treated with amiodarone or ICDs had lower risk of thromboembolism than those given placebo. Hypertension at baseline and lower ejection fraction were independent predictors of risk.
Singularities in three-legged platform-type parallel mechanisms (2003)

Parallel mechanisms frequently contain an unstable type of singularity that has no counterpart in serial mechanisms. When the mechanism is at or near this type of singularity, it loses the ability to counteract external forces in certain directions. The determination of unstable singular configurations in parallel robots is challenging in general, and is usually tackled via an exhaustive search of the workspace using an accurate analytical model of the mechanism kinematics. This paper considers the singularity determination problem from a geometric perspective for planar and spatial three-legged parallel mechanisms. By using the constraints on the passive joint velocities, we derive a necessary condition for the unstable singularities. Using this condition, certain singularities can be found for certain type of platforms. As an example, new singular poses are discovered using this approach for a six-degree-of-freedom machining center.
On the large-signal modeling of AlGaN/GaN HEMTs for RF switching-mode power amplifiers design (2009)

A large-signal model for GaN HEMT transistor suitable for designing switching-mode power amplifiers (SMPAs) is presented along with its parameters extraction procedure. This model is relatively easy to construct and implement in CAD software since it requires only DC and S-parameter measurements. The modeling procedure was applied to a 4-W packaged GaN-on-Si HEMT and the developed model is validated by comparing its small- and large-signal simulation to measured data. The model has been employed for designing a switching-mode inverse class-F power amplifier. Very good agreement between the amplifier simulation and measurement shows the validity of the model.