gebhart/patrepeval huggingface dataset:
Optimizing Xylindein from Chlorociboria spp. for (Opto)electronic Applications (2020)

Xylindein, a stable quinonic blue-green fungal pigment, has shown potential for use not only as a colorant but also as an (opto)electronic material. As no method presently exists to synthesize the pigment, organic production by slow-growing fungi from the genus Chlorociboria is the only method to obtain it. This has resulted in limited quantities of impure xylindein, hampering research. In order to improve quantity and quality of pigment for optoelectronic applications, speed of xylindein production by Chlorociboria aeruginosa and its relative purity were compared across liquid and solid-state fermentation conditions on selected nutrient sources. Liquid 2% malt shaking cultures produced the same amount of pigment in 5 weeks that previous testing produced in 2 months. Xylindein generation speed, purity, and conductive properties of produced pigment for (opto)electronics was then compared between two Chlorociboria species native to North America, Chlorociboria aeruginosa and Chlorociboria aeruginascens. Differences were seen in the conductivity of extracted pigment between species and strains, with xylindein from C. aeruginascens strain UAMH 7614 producing films with the highest effective electron mobility. The identification of the most effective growth conditions and the strain with highest purity xylindein production should support further development of sustainable organic (opto)electronics. Future work identifying new strains with reduced production of interfering metabolites and new extraction methodologies will help to produce very low cost xylindein, supporting sustainable technologies based on the pigment.
Gut Bacteria May Be Involved in Interactions between Plants, Herbivores and Their Predators: Microbial Biosynthesis of N-Acylglutamine Surfactants as Elicitors of Plant Volatiles (2000)

N-Acylamino acids are dominant and widespread constituents of insect oral secretions (regurgitants), serving the insect as biosurfactants in the digestive process. During feeding the conjugates may be introduced into damaged leaves and contribute there to the elicitation of plant defenses such as the induction of volatile biosynthesis. From gut segments of Spodoptera exigua, Mamestra brassicae and Agrotis segetum 23 bacterial strains were isolated, ten of which were able to synthesise typical lepidopteran N-acylamino acids from externally added precursors. Four strains, Providencia rettgeri, Ochrobactrum spec., Myroides odoratus and Acinetobacter sp. genospecies 11 were identified on the basis of their 16 S rDNA. The organisms displayed a very broad substrate tolerance, since fatty acids of different chain length and different degree of saturation were converted into N-acylamino acids. Moreover, most of the proteinogenic amino acids, but not glutamic and aspartic acid, were used as substrates. The dominant occurrence of fatty acids conjugated with glutamine may result from a preferred transport of glutamine from the hemolymph into the gut of the insects. The involvement of bacteria in the biosynthesis of compounds which play a pivotal role in the interaction of plants, herbivores and their predators adds a new trophic level to this complex network of interactions. Due to their short generation cycle and the ease of adaptation endosymbiontic bacteria may have an outstanding importance for the coevolution of plant-insect interactions.
Reinvestigation of the Catalytic Mechanism of Formyl-CoA Transferase, a Class III CoA-transferase (2007)

Formyl-coenzyme A transferase from Oxalobacter formigenes belongs to the Class III coenzyme A transferase family and catalyzes the reversible transfer of a CoA carrier between formyl-CoA and oxalate, forming oxalyl-CoA and formate. Formyl-CoA transferase has a unique three-dimensional fold composed of two interlaced subunits locked together like rings of a chain. We here present an intermediate in the reaction, formyl-CoA transferase containing the covalent beta-aspartyl-CoA thioester, adopting different conformations in the two active sites of the dimer, which was identified through crystallographic freeze-trapping experiments with formyl-CoA and oxalyl-CoA in the absence of acceptor carboxylic acid. The formation of the enzyme-CoA thioester was also confirmed by mass spectrometric data. Further structural data include a trapped aspartyl-formyl anhydride protected by a glycine loop closing down over the active site. In a crystal structure of the beta-aspartyl-CoA thioester of an inactive mutant variant, oxalate was found bound to the open conformation of the glycine loop. Together with hydroxylamine trapping experiments and kinetic as well as mutagenesis data, the structures of these formyl-CoA transferase complexes provide new information on the Class III CoA-transferase family and prompt redefinition of the catalytic steps and the modified reaction mechanism of formyl-CoA transferase proposed here.
Huntingtin expression influences spontaneous seizure disorder susceptibility in FVN/B mice (2022)

ABSTRACT Huntington disease (HD) is an adult-onset neurodegenerative disorder that is caused by a trinucleotide CAG repeat expansion in the HTT gene that codes for the protein huntingtin (HTT or Htt in mice). HTT is a multi-functional, ubiquitously expressed protein that is essential for embryonic survival, normal neurodevelopment, and adult brain function. The ability of wild-type HTT to protect neurons against various forms of death raises the possibility that loss of normal HTT function may worsen disease progression in HD. Huntingtin-lowering therapeutics are being evaluated in clinical trials for HD, but concerns have been raised that decreasing wild-type HTT levels may have adverse effects. Here we show that Htt levels modulate the occurrence of an idiopathic seizure disorder that spontaneously occurs in FVB/N mice. These abnormal FVB/N mice demonstrate various cardinal features of mouse models of epilepsy including spontaneous seizures, astrocytosis, neuronal hypertrophy, upregulation of brain-derived neurotrophic factor (BDNF), and sudden seizure-related death. Interestingly, decreasing wild-type Htt levels increased the frequency of this disorder, while over-expression of HTT completely prevented it. Examination of the mechanism underlying huntingtin’s ability to modulate the frequency of this seizure disorder indicated that over-expression of full length HTT can promote neuronal survival following seizures. Overall, our results demonstrate a protective role for huntingtin in this form of epilepsy and provide a plausible explanation for the observation of seizures in the juvenile form of HD, Lopes-Maciel-Rodan syndrome, and Wolf-Hirschhorn syndrome. Adverse effects caused by altering huntingtin levels has ramifications related to Huntingtin-lowering therapies in development to treat HD.
Textured conducting glass by nanosphere lithography for increased light absorption in thin-film solar cells (2014)

Nanoscale surface texturing in thin-film solar cells has been shown to enhance device efficiency by increasing light absorption through reduced reflectance and increased light scattering across a broad range of wavelengths and angles. However, light trapping in the industrial thin-film cells is still sub-optimal and creating optimized nanoscale texture over a large area remains challenging. In this article, we present a well-controlled low-cost process to fabricate a periodic nanocone texture optimized for maximum light absorption in thin-film microcrystalline silicon solar cells. The texture is fabricated using nanosphere lithography with the period controlled by the nanosphere diameter and the texture shape and aspect ratio controlled by the reactive ion etching conditions. Finite-difference time-domain optical simulations are used to optimize the texture in the state-of-the-art microcrystalline cells, and optical absorption measurements show that the same cells fabricated on the optimized nanocone-textured substrates exhibit a relative short-circuit current increase of close to 30% compared to a reference state-of-the-art cell with a randomly textured zinc oxide layer. This nanocone texturing technique is compatible with standard thin-film cell fabrication processes and can also be used for other thin-film cells (CIGS, CdTe, CZTS, etc) to maximize light absorption and minimize layer thickness enabling more efficient carrier collection and lower overall cost.
High coercive L10 FePt–C (001) nanocomopsite films with small grain size for perpendicular recording media (2008)

FePt–C films with various C concentrations were deposited on MgO∕CrRu/glass substrate by cosputtering FePt and C at 350°C. The evolution of magnetic properties and microstructure of FePt–C films with the C concentration were investigated. All FePt films showed (001) preferred orientation regardless of C concentrations. With C doping, a two-layer structure of FePt–C films was formed. The FePt–C underlying layer epitaxially grown on MgO intermediate layer were L10 FePt grains, while the FePt overlayer consisted of fcc FePt phase and L10 FePt phase. The out-of-plane coercivity measured at room temperature increased from 10.2to19kOe when C concentrations increased from 0% to 15%. Further increasing the C contents to 20% and 25% caused the decrease of coercivity to 17.2 and 14.8kOe, respectively.
Synthesis of nanoporous poly-melamine-formaldehyde (PMF) based on Schiff base chemistry as a highly efficient adsorbent (2018)

This study proposes the construction of nanoporous poly-melamine-formaldehyde (PMF) through the Schiff base condensation reaction of paraformaldehyde and melamine. The PMF nanoparticles showed a good adsorption capability to some benzene-ring-containing dyes including acid fuchsine, nigrosine, and methyl orange. Moreover, the as-prepared PMF nanoparticles were employed as the coating adsorbent for the solid-phase microextraction (SPME) of seven volatile fatty acids (VFAs) with high enrichment factors. A PMF-assisted SPME method was established for the enrichment of VFAs from environmental water samples with satisfactory recoveries (88.5%-102.0%) and acceptable precisions (relative standard deviations <10.9%). This contribution might furnish an advanced benchmark for the exploitation of new porous organic polymers as the effective adsorbents for SPME or other fields of utilization.
CORRECTION OF ANOMALOUS VENOUS RETURN FROM THE RIGHT LUNG TO THE INFERIOR VENA CAVA (SCIMITAR DEFORMITY). (1976)

Anomalous pulmonary venous drainage to the inferior vena cava is a rare congenital cardiac defect. Oxygenated blood from the right lung enters the right atrium resulting in a left-to-right shunt. Because the radiographic shadow of the anomalous vein resembles a curved saber, this defect has been called the "scimitar" deformity. From 1958 through June 30, 1975, 11 patients underwent surgical correction of this anomaly at our institution with 10 survivors. Diagnosis was made by routine roentgenography of the chest in all but one patient. Eight patients had total correction which consisted of implanting the anomalous vein into the right atrium, opening the interatrial septum and applying a patch graft as a baffle to direct pulmonary venous blood into the left atrium. Five patients had associated cardiac defects which were also repaired. Three patients underwent pneumonectomy and all survived. The only operative death occurred in a 5-year-old female with an atrial septal defect and endocardial cushion defect. We believe the existence of a large left-to-right shunt justifies surgical intervention. The prognosis appears to depend upon the presence of other cardiac or pulmonary anomalies.
Bridge architecture, performance, and management (1989)

A bridge allows the physical interconnection of local area networks (LANs) whilst retaining their logical independence. Such interconnection extends the physical limits of LAN technologies and provides the mechanism for filtering LAN traffic in a manner which is both independent of end-station involvement and operates at full LAN data rates. A bridge operates at the medium access control (MAC) sub-layer of the data link layer and as a result is independent of all high-level protocols. This paper identifies and discusses areas of crucial concern to the correct operation of bridges focusing particularly on the issues of functionality, architecture, performance, interworking and management.
Redundancy architectures for channel-based 3D DRAM yield improvement (2014)

The three-dimensional integrated circuit (3D IC) is considered a promising approach that can obtain high data band-width and low power consumption for future electronic systems that require high integration level. One of the popular drivers for 3D IC is the integration of a memory stack and a logic die. Because the yield of a 3D IC is the product of respective yields of the mounted dies, the yields of the memory dies and logic die must be high enough, or the 3D IC will be too expensive to be manufactured. To obtain a high yield of 3D ICs, efficient test and repair methodologies for memories are necessary. In this paper, we target the channel-based 3D dynamic random access memory (DRAM) and propose two 3D redundancy architectures, i.e., Cubical Redundancy Architectures 1 and 2 (CRA1 and CRA2). We use Wide-IO DRAM as an example for discussion. In CRA1, spares are associated with each DRAM die as in a conventional 2D architecture. In CRA2, we use a static random access memory (SRAM) on the logic die as spares. Experimental results show that the CRA1 can achieve up to 18% higher stack yield than traditional redundancy architecture with the same area overhead. On the other hand, the CRA2 can achieve the same yield as the CRA1 with 40% less spares, but 1.3% higher area overhead.
Using Local Dependencies within Batches to Improve Large Margin Classifiers (2009)

Most classification methods assume that the samples are drawn independently and identically from an unknown data generating distribution, yet this assumption is violated in several real life problems. In order to relax this assumption, we consider the case where batches or groups of samples may have internal correlations, whereas the samples from different batches may be considered to be uncorrelated. This paper introduces three algorithms for classifying all the samples in a batch jointly: one based on a probabilistic formulation, and two based on mathematical programming analysis. Experiments on three real-life computer aided diagnosis (CAD) problems demonstrate that the proposed algorithms are significantly more accurate than a naive support vector machine which ignores the correlations among the samples.
Stereoselection at the Steady State by Stereoconvergent Reaction Topography (1998)

A novel strategy for achieving stereoselection by engineering reactions to occur through a unique kinetic scheme is introduced. The strategy, named “complex stereoselection”, effects stereoselection as a result of intermediates at the steady state partitioning successively between competing chemical transformations. A mathematical description of the ratio of products produced in the kinetic strategy is derived, and computer simulation of that model demonstrates two principal advantages of this method: higher selectivity and more efficient conversion of substrates. These computer simulations were subsequently used to determine conditions for maximum stereoselection in these reactions via the framework of a series of hypothetical scenarios in six different incarnations of complex stereoselection. The resulting predictions present challenges to the field of experimental stereochemistry.
Hidden earthquakes unveil the dynamic evolution of a large-scale explosive eruption (2020)

&amp;lt;p&amp;gt;Volcanic eruptions progress by co-evolving the fluid and solid systems. The fluid mechanics can be observed through the evolution of plumes and ejecta. How does the solid evolve? When does the conduit open? When does it close? Seismology can potentially tell us about these processes by measuring the failure of the solid rock. However, such inferences require detection of earthquakes during an explosive eruption. Standard earthquake detection methods often fail during this time as the eruption itself produces seismic noise that obscures the earthquakes. In this work, we address this problem by applying both a supervised and unsupervised search techniques to the existing catalog of the 2008 Okmok Caldera eruption to find brittle failure signals during the continuous eruptive sequence. We were able to detect &amp;gt;4500 new earthquakes using the 419 events previously located by the Alaska Volcano Observatory (AVO). A spatiotemporal analysis of the occurrence of earthquakes during the eruption reveal interesting observations: Seismic bursts during the eruption are not synchronized with the exhalation of large ash and steam plumes, suggesting that the dynamics of the eruption are controlled by a clog-and-crack mechanism; most of the Caldera co-eruptive seismicity that is not located at the focus of the eruption occurs under the intra-Caldera cones, showing the activation of their hydrological system due to a system-wide pressurization; the end of the eruption is marked by a large burst of small, deep earthquakes trending SW-NE, possibly related to a propagating lateral dike similar to those observed in other basaltic calderas; the magnitude distribution of seismicity through time shows that the largest earthquakes in the bursts do not happen at the beginning of the sequence like in typical mainshock-aftershock sequences. Furthermore, high precision earthquake relocations highlight a ring-fault structure inside of Okmok Caldera which is thought to be acting as the pathway for fluids to the surface.&amp;lt;/p&amp;gt;
Nitrogen-dependent regulation of gluconic and/or citric acid production by Aspergillus niger (2000)

Surface culture fermentation using Aspergillus niger was studied for gluconic and citric acid production at different C/N ratios. A culture of A. niger was found to produce either gluconic acid alone, a mixture of gluconic and citric acid, or citric acid alone depending on the level of nitrogen in the medium (4 to 18 mM). Glucose oxidase from the mycelial mat was also analyzed at different levels of nitrogen in the media. By choosing the level of nitrogen in the medium at the start of fermentation, it is possible to produce either of the two acids as the dominant product or the two together as a mixture.
Dynamic Characterization of Rubber O-Rings: Squeeze and Size Effects (2017)

This paper concerns the dynamic characterization of rubber O-rings used to introduce damping in high speed gas bearing systems. O-shaped rubber rings composed of high temperature rubber compounds are characterized in terms of stiffness and damping coefficients in the frequency range 100–800 Hz. Simple formulas with frequency independent coefficients were identified to express the viscoelastic properties of the O-rings. The formulas proposed approximate the stiffness and damping coefficients of O-rings of general size.
On Threshold Selection for Principal Component Based Network Anomaly Detection (2011)

Principal component based anomaly detection has emerged as an important statistical tool for network anomaly detection. It works by projecting summary network information onto a signal and noise sub-spaces and detecting anomalies in the noise sub-space. Recently some major problems where detected with this network anomaly approach. The chief among the problems is the difficulty in selecting a threshold used to declare that the energy in the noise sub-space contains a network anomaly. We show that the reason for this problem is that some of the assumption previously used to select the threshold, namely that the traffic follows a Normal distribution, do not fit the reality of the available network traces. Then, we show that the energy in the noise sub-space can be modeled with the long-tailed Cauchy distribution and use this approximation to calculate reliable thresholds. Our analysis of network traces indicates that the Cauchy distribution approximation of the energy distribution should significantly lower the false alarm rate.
Crowding between first- and second-order letter stimuli in normal foveal and peripheral vision (2007)

Evidence that the detection of first- and second-order visual stimuli is processed by separate pathways abounds. This study asked whether first- and second-order stimuli remain independent at the stage of processing where crowding occurs. We measured thresholds for identifying a first-order (luminance defined) or second-order (contrast defined) target letter in the presence of two second- or first-order flanking letters. For comparison, we also measured thresholds when the target and flanking letters were all first or second order. Contrast of the flankers was 1.6 times their respective contrast thresholds. Measurements were obtained at the fovea and 10 degrees in the lower visual field of four normally sighted observers. Two observers were also tested at 10 degrees nasal visual field. As expected, in both the fovea and periphery, the magnitude of crowding (threshold elevation) was maximal at the closest letter separation and decreased as letter separation increased. The magnitude of crowding was greater for second- than for first-order target letters, independent of the order type of flankers; however, the critical distance for crowding was similar for first- and second-order letters. Substantial crossover crowding occurred when the target and flanking letters were of different order type. Our finding of substantial interaction between first- and second-order stimuli suggests that the processing of these stimuli is not independent at the stage of processing at which crowding occurs.
Synthesis and Thermolysis of 2H-1,2,3-Benzothiadiazine 1,1-Dioxide and 2,1-Benzoxathiin-3-one 1,1-Dioxide (1971)

2H-1,2,3-Benzothiadiazine 1,1-dioxide (6) and 2,l-benzoxathiin-3-one 1,1-dioxide (5), representatives of little-known heterocyclic systems, have been synthesized from sodium o-formylbenzenesulfonate (7). Thermolysis of 5 and 6 was investigated in the hope of finding evidence for the formation of a sulfene. No characterized product was obtained from 5, but 6 gave the sultine 3H-2,1-benzoxathiole 1-oxide (21), the compound expected from the sulfene 20.
Tribology Data Handbook (1997)

This handbook is a useful aid for anyone working to achieve more effective lubrication, better control of friction and wear, and a better understanding of the complex field of tribology. Developed in cooperation with the Society of Tribologists and Lubrication Engineers and containing contributions from 74 experts in the field, the Tribology Data Handbook covers properties of materials, lubricant viscosities, and design, friction and wear formulae.The broad scope of this handbook includes military, industrial and automotive lubricant specifications; evolving areas of friction and wear; performance and design considerations for machine elements, computer storage units, and metal working; and more. Important guidelines for the monitoring, maintenance, and failure assessment of lubrication in automotive, industrial, and aircraft equipment are also included. Current environmental and toxicological concerns complete this one-stop reference.With hundreds of figures, tables, and equations, as well as essential background information explaining the information presented, this is the only source you need to find virtually any tribology information.