gebhart/patrepeval huggingface dataset:
Antimicrobial Activity of Submerged Cultures of Chilean Basidiomycetes (2010)

This study is part of a screening program aimed at searching for bioactive metabolites from Chilean basidiomycetes. Submerged cultivation of fungal mycelia in liquid media was evaluated for antimicrobial activity. A total of 148 strains were obtained in vitro. The extracts produced from submerged cultures were evaluated against bacteria and fungi. In the primary antimicrobial assay, approximately 60% of the extracts presented positive biological activity. The highest frequencies of active strains were from the orders Agaricales (31.0%), Polyporales (20.6%), Sterales (18.3%), Boletales (11.4%), and Cortinariales (9.1%). Antifungal activity was more pronounced than antibacterial activity. Twelve extracts that exhibited strong antimicrobial activity showed minimum inhibitory concentration (MIC) values of 50 µL/mL against Bacillus brevis and 25∼50 µL/mL against Penicillium notatum and Paecilomyces variotii. The biological activity of some strains did not vary considerably, regardless of the substrate or collection site whereas, for others, it showed marked variations. Differences in antimicrobial activities observed in the different fungal genera suggested that the ability to produce bioactive compounds is not homogenously distributed among basidiomycetes. The information obtained from this study reveals that Chilean basidiomycetes are able to generate small and/or large variations in the normal pathway of compounds production. Thus, it is necessary to evaluate this biological and chemical wealth, which could be an unsuspected reservoir of new and potentially useful molecules.
Flash-forward CCN (2014)

Content-centric Networking (CCN) promises significant advantages over the current Internet architecture by replacing its host-centric design with a content-centric one, and enabling in-network caching and name-based forwarding. However, despite its advantages, wire-speed forwarding in CCN remains a challenge, as CCN uses stateful forwarding and requires lookups on packets carrying hierarchically structured and variable-length content names. As a result, storage and computing requirements to support name-based forwarding in CCN determines the forwarding capacity.
Activation loop phosphorylation of a non-RD receptor kinase initiates plant innate immune signaling (2021)

Receptor kinases (RKs) are fundamental for extracellular sensing and regulate development and stress responses across kingdoms. In plants, leucine-rich repeat receptor kinases (LRR-RKs) are primarily peptide receptors that regulate responses to myriad internal and external stimuli. Phosphorylation of LRR-RK cytoplasmic domains is among the earliest responses following ligand perception, and reciprocal transphosphorylation between a receptor and its coreceptor is thought to activate the receptor complex. Originally proposed based on characterization of the brassinosteroid receptor, the prevalence of complex activation via reciprocal transphosphorylation across the plant RK family has not been tested. Using the LRR-RK ELONGATION FACTOR TU RECEPTOR (EFR) as a model, we set out to understand the steps critical for activating RK complexes. While the EFR cytoplasmic domain is an active protein kinase in vitro and is phosphorylated in a ligand-dependent manner in vivo, catalytically deficient EFR variants are functional in antibacterial immunity. These results reveal a noncatalytic role for EFR in triggering immune signaling and indicate that reciprocal transphoshorylation is not a ubiquitous requirement for LRR-RK complex activation. Rather, our analysis of EFR along with a detailed survey of the literature suggests a distinction between LRR-RKs with RD- versus non-RD protein kinase domains. Based on newly identified phosphorylation sites that regulate the activation state of the EFR complex in vivo, we propose that LRR-RK complexes containing a non-RD protein kinase may be regulated by phosphorylation-dependent conformational changes of the ligand-binding receptor, which could initiate signaling either allosterically or through driving the dissociation of negative regulators of the complex.
An operon encoding a novel ABC-type transport system in Bacillus subtilis (1995)

Downstream from the surfactin synthetase operon in Bacillus subtilis a new operon-type structure has been localized which, on the basis of sequence determination, potentially encodes an ABC-type transport system. The 268 amino acid protein, the product of orf1, represents the solute-binding component of the system whereas the orf2 product, a 234 amino acid protein, is the transmembrane component. Finally orf3 potentially encodes a typical 241 amino acid ATP-binding protein involved in energy supply. Comparison of the three proteins with the subunits of other ABC-type systems suggests that this new system is involved in amino acid transport.
Full-bridge MMC DC fault ride-through and STATCOM operation in multi-terminal HVDC grids (2017)

Abstract This paper investigates a control structure to enhance the DC fault ride-through capability of a full-bridge modular multilevel converter (MMC) station, while ensuring a stable controlled operation as a STATCOM during DC faults without the need for fault isolation. Taking advantage of the switching states of a full-bridge submodule, a DC current controller is proposed, which provides the DC voltage reference for the modulation when a DC fault is detected. By changing the outer controllers strategy from DC voltage or active power control to converter energy control during a fault, the decoupling of the converter operation from the DC side dynamics is realized. In this paper, the focus is on the control methodology at all times of operation and the evaluation of the STATCOM control during a fault. To this end, extensive simulations were performed on a three-terminal high voltage direct current (HVDC) grid in radial configuration and a pole-to-pole DC fault case was investigated. The results showed that the AC voltage and current were controlled within limits at all times, while the full-bridge MMC was able to provide reactive power support to the AC grid. Moreover, using the proposed control methodology, the transients at the operation transition points between STATCOM and inverter/rectifier operation were minimized and the stations were able to safely ride through the fault.
Grating-coupled surface emitting quantum cascade ring lasers (2008)

We report on the fabrication and operation of quantum cascade ring lasers providing grating-coupled surface emission. The devices exhibit tunable far fields, ranging from spot- to ring-shaped symmetric beam cross sections, depending on the grating period. This—along with threshold current densities as low as for comparable Fabry–Pérot lasers—demonstrates the compatibility of reduced beam divergence and two-dimensional integrability, resulting in an attractive light source for applications in midinfrared spectroscopy and imaging.
Interrogation of the cell wall integrity pathway in Aspergillus niger identifies a putative negative regulator of transcription involved in chitin deposition (2020)

Post-fermentation fungal biomass waste provides a viable source for chitin. Cell wall chitin of filamentous fungi, and in particular its de-<i>N-</i>acetylated derivative chitosan, has a wide range of commercial applications. Although the cell wall of filamentous fungi comprises 10-30% chitin, these yields are too low for cost-effective production. Therefore, we aimed to identify the genes involved in increased chitin deposition by screening a collection of UV-derived cell wall mutants in <i>Aspergillus niger</i>. This screen revealed a mutant strain (RD15.4#55) that showed a 30-40% increase in cell wall chitin compared to the wild type. In addition to the cell wall chitin phenotype, this strain also exhibited sensitivity to SDS and produces an unknown yellow pigment. Genome sequencing combined with classical genetic linkage analysis identified two mutated genes on chromosome VII that were linked with the mutant phenotype. Single gene knockouts and subsequent complementation analysis revealed that an 8 bp deletion in NRRL3_09595 is solely responsible for the associated phenotypes of RD15.4#55. The mutated gene, which was named <i>cwcA</i> (<i>cell wall chitin A</i>), encodes an orthologue of <i>Saccharomyces cerevisiae</i> Bypass of <i>ESS1</i> (<i>BYE1</i>), a negative regulator of transcription elongation. We propose that this conserved fungal protein is involved in preventing cell wall integrity signaling under non-inducing conditions, where loss of function results in constitutive activation of the cell wall stress response pathway, and consequently leads to increased chitin content in the mutant cell wall.
Bound state eigenfunctions from wave packets: Time→energy resolution (1990)

We present a method to obtain bound-state eigenfunctions in any arbitrary range of energies, by a Fourier resolution (from time to energy) of a real-time wave packet. The resolution is done simultaneously at a number of energies within the sought range, and the resulting vectors yield, after diagonalization, all bound-state eigenvalues and eigenfunctions within that range. The method is exemplified on a Morse potential: eigenfunctions for 18 high-lying states (n∼200) are obtained from resolution at 25 energies.
D‐Amino Acid Homopiperazine Amides: Discovery of A‐320436, a Potent and Selective Non‐Imidazole Histamine H3‐Receptor Antagonist (2004)

Structure-activity relationships of homopiperazine-containing alkoxybiaryl nitriles employing various D-amino acid moieties and their N-furanoyl analogues were undertaken. This led to A-320436, a potent and selective non-imidazole H(3)-receptor antagonist possessing balanced affinity for both rat and human H(3)-receptors. This compound was shown to demonstrate in vitro and in vivo functional antagonism and is non-neurotoxic at doses (i.p.) up to 163 mg/kg in a general observation test.
Patterns of Emphysema Heterogeneity (2015)

Many LVR technologies for treatment of emphysema have focused on interlobar heterogeneity and target an entire lobe per procedure. Our observations suggest that a high proportion of patients with emphysema are affected by interlobar as well as intralobar heterogeneity. These findings prompt the need for a segmental approach to LVR in the majority of patients to treat only the most diseased segments and preserve healthier ones.
Konformationsanalyse an NiII‐Modellkomplexen für die Methyl‐Coenzym‐M‐Reduktase methanogener Bakterien: ein Vergleich von Strukturen im Kristall und in Lösung (1993)

Wie aussagekräftig sind Kristallstrukturdaten für die Konformationsverhältnisse in Lösung? Dieser Frage wurde an den Ni II ‐Modellkomplexen rac ‐ 1 ‐ rac ‐ 3 durch NMR‐Spektroskopie und Röntgenstrukturanalyse nachgegangen. Das Ergebnis ‐ stark differierende Konformerenverteilungen in Lösung und im kristallinen Zustand ‐ könnte zum Verständnis des Wirkmechanismus des Nickelenzyms Methyl‐Coenzym‐M‐Reduktase beitragen. magnified image
What we learn about bipolar disorder from large‐scale neuroimaging: Findings and future directions from the ENIGMA Bipolar Disorder Working Group (2020)

MRI-derived brain measures offer a link between genes, the environment and behavior and have been widely studied in bipolar disorder (BD). However, many neuroimaging studies of BD have been underpowered, leading to varied results and uncertainty regarding effects. The Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA) Bipolar Disorder Working Group was formed in 2012 to empower discoveries, generate consensus findings and inform future hypothesis-driven studies of BD. Through this effort, over 150 researchers from 20 countries and 55 institutions pool data and resources to produce the largest neuroimaging studies of BD ever conducted. The ENIGMA Bipolar Disorder Working Group applies standardized processing and analysis techniques to empower large-scale meta- and mega-analyses of multimodal brain MRI and improve the replicability of studies relating brain variation to clinical and genetic data. Initial BD Working Group studies reveal widespread patterns of lower cortical thickness, subcortical volume and disrupted white matter integrity associated with BD. Findings also include mapping brain alterations of common medications like lithium, symptom patterns and clinical risk profiles and have provided further insights into the pathophysiological mechanisms of BD. Here we discuss key findings from the BD working group, its ongoing projects and future directions for large-scale, collaborative studies of mental illness.
Colloid Properties and Their Effects on Radionuclide Transport through Soils and Groundwaters (2002)

The transport of colloids through soils and groundwaters has been well established through both laboratory and field studies; however, while the potential transport of contaminants by colloids has been the subject of much speculation, such transport in the field has not been unequivocally demonstrated. This chapter describes the conditions necessary for colloid-facilitated contaminant transport to exist, given that colloid transport, itself, is occurring. The focus of this chapter is on the colloid-facilitated transport of contaminants that are, at least in principle, capable of partitioning among phases (i.e., pseudocolloids vs. intrinsic colloids). The discussion in this chapter shows that the range of three-phase system (immobile, colloid, and aqueous phases) properties required to foster colloid-facilitated contaminant transport is quite narrow. Consequently, colloid-facilitated contaminant transport will occur only under relatively rare geochemical conditions.
Abstract state machine based next generation IPv6 network (2005)

In this paper, we show the design of a network processing system in an IPv6 based media gateway based on abstract state machine (ASM) logic and show how the design features may help in scalability realization for end-to-end QoS issues in next generation networks. The novelty of the approach lies in the formal algorithmic definition of the processing hardware and generation of physical design unit from the data-driven algorithm function computation at compile time. The design in this paper is used to build an implementation prototype of an IPv6 media gateway with a feature of MPEG4 BIFS-MPEG4 LASeR transcoding, standardization activities of which are being currently pursued at the ISO MPEG MDS.
Optical control of alignment and patterning in an azobenzene liquid crystal photoresist (2023)

This report describes a liquid crystalline material that can be cured and patterned with green light and photoaligned with blue light.
A class of adaptively regularised PNLMS algorithms (2007)

A class of algorithms. representing a robust variant of the proportionate normalised least-mean-square (PNLMS) algorithm is proposed. To achieve this, adaptive regularisation is introduced within the PNLMS update, with file analysis conducted for both individual and global regularisation factors. The Update of file adaptive regularisation parameter is also made robust, to improve steady state performance and reduce computational complexity. The proposed algorithms are better suited not only for Operation in nonstationary environments, but are also less sensitive to changes in the input dynamics and the choice of their parameters. Simulations in a sparse environment show the proposed class of algorithms, offer enhanced performance and increased stability over the standard PNLMS.
Gerador de Pulsos Monociclo para um Sistema Rádio UWB (2005)

Resumo-Este artigo apresenta aspectos do projeto e simulac ¸ão de um gerador de pulsos ultra-curtos
Immune signatures associated with response to neoadjuvant PD-1 blockade in oral cavity cancer. (2019)

6055 Background: PD-1 inhibition therapy has revolutionized clinical medicine as it can mediate durable responses in a small cohort of patients. Yet, it remains incompletely understood why these patients respond. To address this question, we studied patients with oral cavity squamous cell carcinoma (OCSCC) to elucidate immune phenotypes associated with response to nivolumab. Methods: We defined the immune profile from the blood and tumor of patients on neoadjuvant nivolumab. We tested if tumor-infiltrating lymphocytes (TIL) could be preferentially expanded ex vivo from nivolumab-responsive patients versus those who were either non-responsive or had never received nivolumab. During the course of therapy, we comprehensively profiled a number of surface markers on patients’ T cells to define their activation status, cytotoxic capacity and memory phenotype. Moreover, the immune profile of the peripheral blood was assessed pre- and post-nivolumab using high dimensional mass cytometry. Results: Regardless of PD-1 therapy, TIL were successfully expanded from 11 of the 12 patients. TIL were comprised of both CD4 + and CD8 + T cells. Additional investigation revealed that the frequency of CD4 + T cells and effector memory T cells in TIL correlated with disease progression (CD4: p = 0.04, r = 0.74, effector memory: p = 0.046, r = 0.74). TILs from responders expressed higher CD26 (p = 0.007, r = -0.88) and Tim3 (p = 0.045, r = -0.74) while PD-1, Lag3, and Ox40 were not differentially expressed based on response. Spearman correlation and Mann Whitney U test were used to assess phenotypic differences. Conclusions: We demonstrate, for the first time, that TIL can be reliably expanded from OCSCC patients on neoadjuvant nivolumab. Moreover, individuals who were responsive to PD-1 blockade had TIL expressing high levels of CD26 and Tim3. Future studies will explore if these markers are predictive of responses and if they contribute to treatment outcome.
An open label phase 1b/2 trial of TRC105 and sorafenib in patient with advanced/metastatic hepatocellular carcinoma (HCC) (NCT01806064). (2018)

301 Background: Endoglin plays a critical role in angiogenesis and is implicated in resistance to VEGF inhibition. TRC105, an endoglin antibody potentiates anti-tumor activity of sorafenib (S) in preclinical HCC models. The combination of TRC105 and S demonstrated encouraging evidence of activity, including a 33% partial response rate (5/15 pts) by RECIST, at RP2D doses of TRC105 in HCC ( Clin Can Res 2017). Adverse events characteristic of each drug were not increased in frequency or severity when the two drugs were administered concurrently, and most commonly included epistaxis, fatigue, headache and anemia. Methods: Following dose escalation, 21 pts will be enrolled at the RP2D. Four objective responses are required to reject the null hypothesis that the true response rate probability is &lt; 5% with an alpha level of 0.1 and 80% power. Secondary endpoints: DR, PFS, frequency and severity of AEs, PK, immunogenicity, angiogenic biomarkers. Key inclusion criteria: disease not amendable to surgical or local therapies, ECOG ≤ 1; Child-Pugh A or B (7 points) classification. Results: Four pts have been enrolled in phase 1b at TRC105 10 mg/kg (n=4) weekly for four doses and 15 mg/kg every other week thereafter + S 800 mg daily without DLT. One of 3 evaluable pts achieved PR (41% reduction), ongoing at month 4. Serum levels of TRC105 exceeded the target concentration following 4 weekly doses of TRC105 at 10 mg/kg (mean = 59 µg/ml, range 43-80). Mean trough concentration decreased following every other week dosing (mean = 21 µg/ml, range 17-31). Common TRC105 related AEs included ≤ G2 epistaxis and G1 headache. Common S related AEs included G3 hand foot syndrome, ≤G3 periodontal disease, G2 hypertension, ≤G2 increased lipase, ≤G2 fatigue and G1 epistaxis. Conclusions: TRC105 dosed by a hybrid schedule of 10 mg/kg weekly for four doses followed by every other week dosing at 15 mg/kg was tolerable and did not potentiate the toxicity of S. The combination of TRC105 + S demonstrated additional signs of activity, including a PR in 1/3 evaluable pts. 21 pts will be enrolled at the RP2D to assess the primary endpoint of ORR by RECIST. Clinical trial information: NCT01806064.
Dynamics of Backbone Chain and Side Groups in a Nematic Liquid Single Crystal Elastomer Studied by Combined Mechanical and Stress-Optical Measurements (2000)

Abstract Dynamic mechanical and stress-optical measurements on nematic liquid single elastomers have been carried out both in the nematic and in the isotropic phase. In case of shear stress and in case of tensile stress applied parallel to the director the compliances were not affected by the nematic-isotropic transition. For tensile stress oriented perpendicular an increased compliance was observed in the vicinity of the phase transition. The stress-optical coefficients for tensile stresses applied pararallel and perpendicular to the director both increase on approaching the nematic-isotropic transition. In the isotropic phase its temperature dependence is well described by the Landau-de Gennes theory. Far from the transition temperature in the nematic phase other mechanisms superpose this behavior, leading to negative stress-optical coeffients for stress parallel, and positive coefficients perpendicular to the director.
Clonal Evolution in t(14;18)-Positive Follicular Lymphoma, Evidence for Multiple Common Pathways, and Frequent Parallel Clonal Evolution (2008)

Our analysis suggested that +der(18)t(14;18) may be an entry point to a distinct pathway of genetic evolution in follicular lymphoma. The other common early events appeared to provide multiple entry points, and they might cooperate in the pathogenesis and progression of the follicular lymphoma. Cytogenetically abnormal clones from same patients often showed divergence of genetic alterations, suggesting that parallel evolution from precursor clones are frequent events. This study provides the framework for further analysis of genetic pathways of tumor progression.
An Evolutionary Genomic Approach to Identify Genes Involved in Human Birth Timing (2011)

Coordination of fetal maturation with birth timing is essential for mammalian reproduction. In humans, preterm birth is a disorder of profound global health significance. The signals initiating parturition in humans have remained elusive, due to divergence in physiological mechanisms between humans and model organisms typically studied. Because of relatively large human head size and narrow birth canal cross-sectional area compared to other primates, we hypothesized that genes involved in parturition would display accelerated evolution along the human and/or higher primate phylogenetic lineages to decrease the length of gestation and promote delivery of a smaller fetus that transits the birth canal more readily. Further, we tested whether current variation in such accelerated genes contributes to preterm birth risk. Evidence from allometric scaling of gestational age suggests human gestation has been shortened relative to other primates. Consistent with our hypothesis, many genes involved in reproduction show human acceleration in their coding or adjacent noncoding regions. We screened >8,400 SNPs in 150 human accelerated genes in 165 Finnish preterm and 163 control mothers for association with preterm birth. In this cohort, the most significant association was in FSHR, and 8 of the 10 most significant SNPs were in this gene. Further evidence for association of a linkage disequilibrium block of SNPs in FSHR, rs11686474, rs11680730, rs12473870, and rs1247381 was found in African Americans. By considering human acceleration, we identified a novel gene that may be associated with preterm birth, FSHR. We anticipate other human accelerated genes will similarly be associated with preterm birth risk and elucidate essential pathways for human parturition.