gebhart/patrepeval huggingface dataset:
Appropriate aglycone modification significantly expands the glycan substrate acceptability of α1,6-fucosyltransferase (FUT8) (2021)

The α1,6-fucosyltransferase, FUT8, is the sole enzyme catalyzing the core-fucosylation of N-glycoproteins in mammalian systems. Previous studies using free N-glycans as acceptor substrates indicated that a terminal β1,2-GlcNAc moiety on the Man-α1,3-Man arm of N-glycan substrates is required for efficient FUT8-catalyzed core-fucosylation. In contrast, we recently demonstrated that, in a proper protein context, FUT8 could also fucosylate Man5GlcNAc2 without a GlcNAc at the non-reducing end. We describe here a further study of the substrate specificity of FUT8 using a range of N-glycans containing different aglycones. We found that FUT8 could fucosylate most of high-mannose and complex-type N-glycans, including highly branched N-glycans from chicken ovalbumin, when the aglycone moiety is modified with a 9-fluorenylmethyloxycarbonyl (Fmoc) moiety or in a suitable peptide/protein context, even if they lack the terminal GlcNAc moiety on the Man-α1,3-Man arm. FUT8 could also fucosylate paucimannose structures when they are on glycoprotein substrates. Such core-fucosylated paucimannosylation is a prominent feature of lysosomal proteins of human neutrophils and several types of cancers. We also found that sialylation of N-glycans significantly reduced their activity as a substrate of FUT8. Kinetic analysis demonstrated that Fmoc aglycone modification could either improve the turnover rate or decrease the KM value depending on the nature of the substrates, thus significantly enhancing the overall efficiency of FUT8 catalyzed fucosylation. Our results indicate that an appropriate aglycone context of N-glycans could significantly broaden the acceptor substrate specificity of FUT8 beyond what has previously been thought.
The temperature dependence of ice-nucleating particle concentrations affects the radiative properties of tropical convective cloud systems (2021)

Abstract. Convective cloud systems in the maritime tropics play a critical role in global climate, but accurately representing aerosol interactions within these clouds persists as a major challenge for weather and climate modelling. We quantify the effect of ice-nucleating particles (INPs) on the radiative properties of a complex tropical Atlantic deep convective cloud field using a regional model with an advanced double-moment microphysics scheme. Our results show that the domain-mean daylight outgoing radiation varies by up to 18 W m−2 depending on the chosen INP parameterisation. The key distinction between different INP parameterisations is the temperature dependence of ice formation, which alters the vertical distribution of cloud microphysical processes. The controlling effect of the INP temperature dependence is substantial even in the presence of Hallett–Mossop secondary ice production, and the effects of secondary ice formation depend strongly on the chosen INP parameterisation. Our results have implications for climate model simulations of tropical clouds and radiation, which currently do not consider a link between INP particle type and ice water content. The results also provide a challenge to the INP measurement community, as we demonstrate that INP concentration measurements are required over the full mixed-phase temperature regime, which covers around 10 orders of magnitude.
Nutritive qualities of patties prepared with mixture of meat and oyster mushroom (2014)

Nutritive qualities of patties prepared from chicken, beef and oyster mushroom were determined. Three groups of rats were fed with patty diets prepared with either a combination of 75% chicken + 25% oyster mushroom (CMP) or 75% beef + 25% oyster mushroom (BMP) or 100% chicken patty + 0% oyster mushroom (CP). There was no significant difference (P < 0.05) in total tryglyceride (0.3-0.5 mmol/L), total cholesterol (1.7-1.9 mmol/L) LDL-cholesterol (0.30.4 mmol/L) and HDL-cholesterol (1.2-1.4 mmol/L) for all groups except for protein free. Protein effeciency ratio (PER) values of CMP and BMP groups were significantly lower than casein group but significantly higher than chicken patty (CP) group. Both CMP and BMP fed groups recorded PER values at 1.73 and 1.69 while CP had PER value at 1.52. The AD of rats fed with CMP, BMP and CP diets were closely ranged from 98.3-98.9% but not significant as compared to casein diet group (98.5%). The close AD values between CMP, BMP and CP indicated that the mixture of patty protein from either chicken or beef with protein of oyster mushroom did not affect digestibility aspect. In summary, addition of oyster mushroom into either chicken or beef patties did not changed AD but improved PER value, thus proving that oyster mushroom could be used as an alternative ingredient to replace meat partially in the making of patties.
Pyrosequence Analysis of the hsp65 Genes of Nontuberculous Mycobacterium Communities in Unchlorinated Drinking Water in the Netherlands (2013)

Studies have shown that certain opportunistic pathogenic species of nontuberculous mycobacteria (NTM) can be present in distributed drinking water. However, detailed information about NTM population composition in drinking water is lacking. Therefore, NTM communities in unchlorinated drinking water from the distribution system of five treatment plants in the Netherlands were characterized using 454 pyrosequencing of the hsp65 gene. Results showed high diversities in unchlorinated drinking water, with up to 28 different NTM operational taxonomic units (OTUs) in a single sample. Each drinking water sample had a unique NTM community, and most (81.1%) OTUs were observed only once. One OTU was observed in 14 of 16 drinking water samples, indicating that this NTM species is well adapted to unchlorinated drinking water conditions. A clear influence of season, source type (groundwater, surface water), easily assimilable organic carbon (AOC) concentration, biofilm formation rate, and active biomass in treated water on the establishment of an NTM community in drinking water was not observed. Apparently, local conditions are more important for the development of a specific NTM community in the drinking water distribution system. A low (4.2%) number of hsp65 gene sequences showed more than 97% similarity to sequences of the opportunistic pathogens M. avium, M. genavense, and M. gordonae. However, most (95.8%) NTM hsp65 gene sequences were related to not-yet-described NTM species that have not been linked to disease, indicating that most NTM species in unchlorinated drinking water from distribution systems in the Netherlands have a low public health significance.
Fetal Anomalies and Long-Term Effects Associated with Substance Abuse in Pregnancy: A Literature Review (2014)

The literature summarized in this review suggests that drug exposure during pregnancy may increase the risk of congenital anomalies and long-term adverse effects in exposed children and adolescents. These conclusions must be tempered by the many confounders associated with drug use. A multidisciplinary approach is paramount for appropriate counseling regarding the known immediate and long-term risks of substance abuse in pregnancy.
Diagnostics for the LCLS Photoinjector Beamline (2006)

Two spectrometers have been added to the LCLS photoinjector beamline. The first one will be located close to the exit of the Photoinjector RF gun. With this diagnostic, we will measure beam energy, energy spread (correlated and uncorrelated), possibly deleterious structure in the longitudinal phase space induced by longitudinal space charge force, and slice thermal emittance ... This extensive characterization of the 5MeV electron bunch will be made possible by combining this spectrometer with other diagnostics (YAG screens and Cerenkov Radiator). A second spectrometer located at the end of the beamline has been designed to characterize the 6-dimensional phase space of the 135MeV beam to be injected in the main accelerator. At that second spectrometer station, we will measure energy, energy spread (correlated and uncorrelated), longitudinal phase space, slice emittances ... Those last two measurements require using this spectrometer in combination with the transverse RF deflecting cavity and with the quadrupole scan emittance station. The designs of these two spectrometers have been supported by simulations from MAD and PARMELA.
Structure-Reconfiguring Robots: Autonomous Truss Reconfiguration and Manipulation (2013)

In this article, we present a robot capable of autonomously traversing and manipulating a three-dimensional (3-D) truss structure. The robot can approach and traverse multiple structural joints using a combination of translational and rotational motions. A key factor in allowing reliable motion and engagement is the use of specially designed structural building blocks comprised of bidirectional geared rods. A set of traversal plans, each comprised of basic motion primitives, were analyzed for speed, robustness, and repeatability. Paths covering eight joints are demonstrated, as well as automatic element assembly and disassembly. We suggest that the robot architecture and truss module design, such as the one presented here, could open the door to robotically assembled, maintained, and reconfigured structures that would ordinarily be difficult, risky, or time consuming for humans to construct.
Understanding driving situations using a network model (2002)

In the rear-end collision avoidance system (RCAS), which incorporates the functions of detecting and reporting distance headway as well as of collision avoidance through the use of automatic braking, the development of the technique to integrate the advanced characteristic of each sensors becomes important. In this paper, we propose the uniting processing technique which uses the network as a trial. We classify the recognition system into some modules from the software point of view, link these modules as the network and make the states of the network correspond to the driving environment. We referred to a immune network when making the network. The immune network is a technological model of the immune mechanism in the living body. We applied this network mechanism to fuse functions of the distance headway, the road lane position and the position of the preceding vehicle obtained by the laser radar and image processing. These three functions are transferred to modules, each module tests mutually, and each certainty degree is changed continuously. This paper describes this network technique and the experimental results.
Inhibitory effect of d-glucosamine and other sugar analogs on the viability and transplantability of ascites tumor cells. (1969)

Summary d-Glucosamine has been shown to have a powerful cytotoxic effect on various ascites tumor lines, resulting in a decrease in viability and transplantability of the neoplastic cells. The toxic effect of glucosamine was not significantly altered by addition of either glucose or pyruvate. The effects of d-glucosamine and other sugar analogs were evident histologically even before the cells became stainable by trypan blue. d-Galactosamine and d-mannosamine also reduced the viability and transplantability of ascites tumor cells similar to that of d-glucosamine. However, the N-acetylhexosamines caused only a minor decrease in cell viability, and these cells developed tumors when inoculated into mice. d-Mannose was the only neutral sugar showing a cytotoxic effect on ascites tumor cells.
Cannabidiol activates neuronal Kv7 channels (2022)

Cannabidiol (CBD), a chemical found in the <i>Cannabis sativa</i> plant, is a clinically effective antiepileptic drug whose mechanism of action is unknown. Using a fluorescence-based thallium flux assay, we performed a large-scale screen and found enhancement of flux through heterologously expressed human Kv7.2/7.3 channels by CBD. Patch-clamp recordings showed that CBD acts at submicromolar concentrations to shift the voltage dependence of Kv7.2/7.3 channels in the hyperpolarizing direction, producing a dramatic enhancement of current at voltages near -50 mV. CBD enhanced native M-current in mouse superior cervical ganglion starting at concentrations of 30 nM and also enhanced M-current in rat hippocampal neurons. The potent enhancement of Kv2/7.3 channels by CBD may contribute to its effectiveness as an antiepileptic drug by reducing neuronal hyperexcitability.
Fish Oil Is More Potent than Flaxseed Oil in Modulating Gut Microbiota and Reducing Trimethylamine-N-oxide-Exacerbated Atherogenesis (2019)

Trimethylamine-<i>N</i>-oxide (TMAO) is a risk factor for atherosclerosis. We compared the potency of fish oil with flaxseed oil in reducing TMAO-exacerbated atherogenesis. Five groups of ApoE<sup>-/-</sup> mice were given one of five diets, namely, a low-fat diet, a Western high fat diet (WD), a WD plus 0.2% TMAO, and two WDs containing 0.2% TMAO with 50% lard being replaced by flaxseed oil or fish oil. TMAO accelerated atherosclerosis and disturbed cholesterol homeostasis. Compared with flaxseed oil, fish oil was more effective in inhibiting TMAO-induced atherogenesis by lowering plasma cholesterol and inflammatory cytokines. Both oils could reverse TMAO-induced decrease in fecal acidic sterols. Fish oil promoted fecal output of neutral sterols and downregulated hepatic cholesterol biosynthesis. Fish oil was more effective than flaxseed oil in promoting the growth of short-chain fatty acid-producing bacteria and lowering microbial generation of lipopolysaccharide. In conclusion, fish oil is more potent than flaxseed oil to ameliorate TMAO-exacerbated atherogenesis.
Cross-Reactivity of Herpesvirus-Specific CD8 T Cell Lines Toward Allogeneic Class I MHC Molecules (2010)

Although association between persistent viral infection and allograft rejection is well characterized, few examples of T-cell cross-reactivity between self-MHC/viral and allogeneic HLA molecules have been documented so far. We appraised in this study the alloreactivity of CD8 T cell lines specific for immunodominant epitopes from human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV). CD8 T cell lines were generated after sorting with immunomagnetic beads coated with either pp65(495-503)/A*0201, BMLF1(259-267)/A*0201, or BZLF1(54-64)/B*3501 multimeric complexes. Alloreactivity of the CD8 T cell lines against allogeneic class I MHC alleles was assessed by screening of (i) TNF-alpha production against COS-7 cells transfected with as many as 39 individual HLA class I-encoding cDNA, and (ii) cytotoxicity activity toward a large panel of HLA-typed EBV-transformed B lymphoblastoid cell lines. We identified several cross-reactive pp65/A*0201-specific T cell lines toward allogeneic HLA-A*3001, A*3101, or A*3201. Moreover, we described here cross-recognition of HLA-Cw*0602 by BZLF1/B*3501-specific T cells. It is noteworthy that these alloreactive CD8 T cell lines showed efficient recognition of endothelial cells expressing the relevant HLA class I allele, with high level TNF-alpha production and cytotoxicity activity. Taken together, our data support the notion that herpes virus-specific T cells recognizing allo-HLA alleles may promote solid organ rejection.
System integration and fin trajectory design for a robotic sea-turtle (2013)

This paper presents a novel underwater robot based on biological locomotion principle.A robotic platform imitating sea-turtle fin propulsion is described and tested.As fin locomotion is a novel and complex research area, basic control concepts are analyzed and implemented.Based on a simulation, a fin-trajectory morphing control strategy is developed in order to control the robots roll, pitch and yaw rates, thus allowing the robot to follow a given vector.Absolute position control or depth control, however, is not yet implemented.The paper concludes with the presentation of a working system that demonstrated motion capabilities in air as well as the first dive test in a swimming pool.
Low-Temperature Modification of Mesoporous MCM-41 Material with Sublimated Aluminum Chloride in Vacuum (2002)

Treatment of siliceous MCM-41 with aluminum chloride was performed in a vacuum at a temperature of 403 K. The obtained AlCl3/MCM-41 material was characterized by multinuclear solid-state NMR spectroscopy and by application of probe molecules. The results of NMR spectroscopy indicate a reaction of aluminum chloride with vicinal silanol groups at the surface of conditioned MCM-41 and the formation of tetrahedrally coordinated aluminum species bound to chlorine and framework oxygen atoms. In the local structures of 3% of these aluminum atoms, strong Brønsted acid sites are formed causing a 1H MAS NMR signal at 6.0 ppm. According to 13C MAS NMR spectroscopy of acetone-2-13C adsorbed on AlCl3/MCM-41 (241 and 245 ppm), these Brønsted acid sites are characterized by an acid strength higher than that of bridging OH groups in H−ZSM-5 (223 ppm).
Targeted screening for third-generation cephalosporin-resistant Enterobacteriaceae carriage among patients admitted to intensive care units: a quasi-experimental study (2015)

Targeted screening of 3GC-RE carriers at ICU admission was not associated with an increase in 3GC-RE-related HAI incidence compared with universal screening. Total number of rectal swabs decreased significantly. These findings suggest that targeted screening may be worth assessing as an alternative to universal screening.
Predicting lncRNA-miRNA Interaction via Graph Convolution Auto-Encoder (2019)

The interaction of miRNA and lncRNA is known to be important for gene regulations. However, the number of known lncRNA-miRNA interactions is still very limited and there are limited computational tools available for predicting new ones. Considering that lncRNAs and miRNAs share internal patterns in the partnership between each other, the underlying lncRNA-miRNA interactions could be predicted by utilizing the known ones, which could be considered as a semi-supervised learning problem. It is shown that the attributes of lncRNA and miRNA have a close relationship with the interaction between each other. Effective use of side information could be helpful for improving the performance especially when the training samples are limited. In view of this, we proposed an end-to-end prediction model called GCLMI (Graph Convolution for novel lncRNA-miRNA Interactions) by combining the techniques of graph convolution and auto-encoder. Without any preprocessing process on the feature information, our method can incorporate raw data of node attributes with the topology of the interaction network. Based on a real dataset collected from a public database, the results of experiments conducted on k-fold cross validations illustrate the robustness and effectiveness of the prediction performance of the proposed prediction model. We prove the graph convolution layer as designed in the proposed model able to effectively integrate the input data by filtering the graph with node features. The proposed model is anticipated to yield highly potential lncRNA-miRNA interactions in the scenario that different types of numerical features describing lncRNA or miRNA are provided by users, serving as a useful computational tool.
Determination of baroreflex gain using auto‐regressive moving‐average analysis during spontaneous breathing (1999)

The heart rate component of the arterial baroreflex gain (BRG) was determined with auto-regressive moving-average (ARMA) analysis during each of spontaneous (SB) and random breathing (RB) protocols. Ten healthy subjects completed each breathing pattern on two different days in each of two different body positions, supine (SUP) and head-up tilt (HUT). The R-R interval, systolic arterial pressure (SAP) and instantaneous lung volume were recorded continuously. BRG was estimated from the ARMA impulse response relationship of R-R interval to SAP and from the spontaneous sequence method. The results indicated that both the ARMA and spontaneous sequence methods were reproducible (r = 0.76 and r = 0.85, respectively). As expected, BRG was significantly less in the HUT compared to SUP position for both ARMA (mean +/- SEM; 3.5 +/- 0.3 versus 11.2 +/- 1.4 ms mmHg-1; P < 0.01) and spontaneous sequence analysis (10.3 +/- 0.8 versus 31.5 +/- 2.3 ms mmHg-1; P < 0.001). However, no significant difference was found between BRG during RB and SB protocols for either ARMA (7.9 +/- 1.4 versus 6.7 +/- 0.8 ms mmHg-1; P = 0.27) or spontaneous sequence methods (21.8 +/- 2.7 versus 20.0 +/- 2.1 ms mmHg-1; P = 0.24). BRG was correlated during RB and SB protocols (r = 0.80; P < 0.0001). ARMA and spontaneous BRG estimates were correlated (r = 0.79; P < 0.0001), with spontaneous sequence values being consistently larger (P < 0.0001). In conclusion, we have shown that ARMA-derived BRG values are reproducible and that they can be determined during SB conditions, making the ARMA method appropriate for use in a wider range of patients.
Inter-Sample Avoidance in Trajectory Optimizers using Mixed-Integer Linear Programming (2013)

Summary
This paper proposes an extension to trajectory optimization using mixed-integer linear programming. The purpose of the extension is to ensure that avoidance constraints are respected at all times between discrete samples, not just at the sampling times themselves. The method is very simple and involves applying the same switched constraints at adjacent time steps. This requires fewer additional constraints than the existing approach and is shown to reduce computation time. A key benefit of efficient inter-sample avoidance is the facility to reduce the number of time steps without having to compensate by enlarging the obstacles. A further extension to the principle is presented to account for curved paths between samples, proving useful in cases where narrow passageways are traversed. Copyright © 2013 John Wiley & Sons, Ltd.
Sidewall gratings in ultra-low-loss Si_3N_4 planar waveguides (2013)

We demonstrate sidewall gratings in an ultra-low-loss Si3N4 planar waveguide platform. Through proper geometrical design we can achieve coupling constant values between 13 and 310 cm(-1). The TE waveguide propagation loss over the range of 1540 to 1570 nm is below 5.5 dB/m.
Electrodeposited semiconducting molybdenum selenide films. I. Preparatory technique and structural characterisation (1984)

Molybdenum selenide films have been electrodeposited cathodically on titanium substrates from an ammoniacal solution of H2MoO4 and SeO2 under galvanostatic conditions. The initial layers of the film were of Se followed by an increasing amount of Mo in the deposit. Some intermediate layer has a composition equivalent to molybdenum selenide (MoSe2). An 'induced codeposition' mechanism for the MoSe2 film deposition has been suggested. Structural characterisation of the electrodeposited films using EDAX, EM and SEM studies has been carried out.