gebhart/patrepeval huggingface dataset:
The lectin complement pathway and Ficolin-2 in patients with necrotizing soft tissue infection (2016)

Abstract Background Mannose-binding lectin (MBL) and ficolins are pattern recognition molecules (PRMs) that play an important role during infection through activation of the lectin complement pathway. We assessed whether blood concentrations of the PRMs were associated with mortality in patients with necrotizing soft tissue infection (NSTI). Methods We conducted a prospective, observational study over 25 months involving 135 NSTI patients with a maximum follow-up time of 2.7 years. Plasma PRM level were measured upon admission. Non-infected surgical patients served as controls. Results PRMs levels of the lectin complement pathway were significantly lower compared to non-infected patients. Ficolin-2 level below median was associated with mortality at the end of follow-up (p = 0.007, log-rank), whereas no significant association was found for MBL, Ficolin-1 and Ficolin-3. Ficolin-2 level below median had a positive predictive value of 0.27 and a negative predictive value of 0.94 for 28-day mortality. When optimal cut-off was used, the multivariate cox-regression analysis revealed that low Ficolin-2 level was independently associated with 28-day mortality when adjusted for age, gender and chronicity (HR 6.27 [95% CI, 2.28–17.21], p &amp;lt; 0.0001) and also when SAPS II was included (HR 3.16 [95% CI, 1.03–9.73], p = 0.045). Conclusions All PRMs of the lectin complement pathway were significantly lower in patients with NSTI than in non-infected controls upon admission. Only plasma Ficolin-2 was significantly associated with both short-term and long-term mortality. Additionally, a high Ficolin-2 level above the median indicated a 94% chance of surviving the first 28 days after admission. ClinicalTrials.gov Identifier: NCT2180906.
Correction: Heterologous Reconstitution of the Intact Geodin Gene Cluster in Aspergillus nidulans through a Simple and Versatile PCR Based Approach (2013)

Fungal natural products are a rich resource for bioactive molecules. To fully exploit this potential it is necessary to link genes to metabolites. Genetic information for numerous putative biosynthetic pathways has become available in recent years through genome sequencing. However, the lack of solid methodology for genetic manipulation of most species severely hampers pathway characterization. Here we present a simple PCR based approach for heterologous reconstitution of intact gene clusters. Specifically, the putative gene cluster responsible for geodin production from Aspergillus terreus was transferred in a two step procedure to an expression platform in A. nidulans. The individual cluster fragments were generated by PCR and assembled via efficient USER fusion prior to transformation and integration via re-iterative gene targeting. A total of 13 open reading frames contained in 25 kb of DNA were successfully transferred between the two species enabling geodin synthesis in A. nidulans. Subsequently, functions of three genes in the cluster were validated by genetic and chemical analyses. Specifically, ATEG_08451 (gedC) encodes a polyketide synthase, ATEG_08453 (gedR) encodes a transcription factor responsible for activation of the geodin gene cluster and ATEG_08460 (gedL) encodes a halogenase that catalyzes conversion of sulochrin to dihydrogeodin. We expect that our approach for transferring intact biosynthetic pathways to a fungus with a well developed genetic toolbox will be instrumental in characterizing the many exciting pathways for secondary metabolite production that are currently being uncovered by the fungal genome sequencing projects.
Proteomic and Genomic Studies on Lizard Venoms in the Last Decade (2010)

Traditionally man has looked to nature to provide cures for diseases. This approach still exists today in the form of ‘bio-prospecting’ for therapeutically-active compounds in venoms. For example, the venoms of many reptiles offer a spectacular laboratory of bioactive molecules, including peptides and proteins. In the last 10–15 years, there have been a number of major proteomic and genomic research breakthroughs on lizard venoms. In this current review, the key findings from these proteomic and genomic studies will be critically discussed and suggestions will be offered for future focused investigations. It is our intention that this article will not only provide a comprehensive picture of the state of current knowledge of the components of lizard venoms, but also engender awareness in readers of the need to protect and conserve such uniquely precious natural resources for several reasons, including the potential benefit of humankind.
Enzymatic Esterification by Surfactant‐Coated Lipase in Organic Media (1994)

Abstract Surfactant‐coated lipases have been prepared with a synthesized surfactant. Preparation conditions to obtain a suitable surfactant‐coated lipase were investigated. The enzymatic activity of the lipase in an organic solvent significantly increased with the coating of the surfactant. The esterification rate from the surfactant‐coated lipase was much higher than that from the powder lipase. An aliphatic solvent showed higher activity than did alcohol, aromatic, and chloric solvents. Among them, isooctane gave the highest activity. The reactivity of the surfactant‐coated lipase depends on the pH of the aqueous solution in the preparation and on the buffer solution. Surfactant‐coated lipase prepared in the middle pH range using phosphate buffer showed high enzymatic activity. The surfactant‐coated lipase was thermostable at high temperature compared to the native lipase. A kinetic study enabled a ping‐pong bi‐bi reaction mechanism with alcohol inhibition to be suggested. From the kinetic analysis, it was found that an alcohol substrate inhibits enzymatic esterification by lipase. The reaction rate of the coated lipase was about 100 times that of the powder lipase.
Model-based compensation of pixel crosstalk in liquid crystal spatial light modulators (2019)

Spatial light modulators (SLMs) based on liquid crystals are widely used for wavefront shaping. Their large number of pixels allows one to create complex wavefronts. The crosstalk between neighboring pixels, also known as fringing field effect, however, can lead to strong deviations. The realized wavefront may deviate significantly from the prediction based on the idealized assumption that the response across a pixel is uniform and independent of its neighbors. Detailed numerical simulations of the SLM response based on a full 3D physical model accurately match the measured response and properly model the pixel crosstalk. The full model is then used to validate a simplified model that enables much faster crosstalk evaluation and pattern optimization beyond standard performance. General conclusions on how to minimize crosstalk in liquid crystal on silicon (LCoS) SLM systems are derived, as well as a readily accessible estimation of the amount of fringing in a given SLM.
An opening in mortal produced from gas evolution of aluminum (1999)

アルミニウムを僅かでも含む固体状廃棄物をモルタルにて固型化する場合，アルミニウムから発生するガスが充填固化体の性能に与える影響を調べ，評価しておくことは重要である. 本研究では種々のモルタルを用いて模擬充填固化体を試作し，固化体中の空隙率を測定した. その結果，アルミニウムと炭素鋼の接触によって固化体中でのガス発生を起因とする空隙率は減少することが認められた. また，鉄とアルミニウム接触条件下において，両金属の表面積比とガス発生による固化体の空隙率との関係はモルタル平衡水中での両金属の表面積比とガス発生量との関係と良く一致した. さらに，モルタルの物性値，アルミニウムからのガス発生量の定量結果等から固化体の空隙率を推定する手法を提案した. その手法によって，数種類のモルタル中でのアルミニウムからのガス発生を起因とする空隙率を推定した. その結果，現在想定されている充填固化体の最も保守的な条件で，しかもアルミニウムが炭素鋼と接触していない条件においても空隙率は1%以下と推定された.
Did Lorenzo Lotto use optical projections while painting “Husband and Wife”? (2004)

We apply optical and perspective tests to the carpet in Lorenzo Lotto’s “Husband and Wife” (c. 1543) to test the claim that this painting was executed by tracing an optically projected image. While the perspective exhibits many inaccuracies consistent with this claim, such inaccuracies are equally consistent with non-optical explanations, such as artistic freehand for features that are peripheral to the theme of the painting. Further, a number of properties–specifically the perspective inconsistencies within some putative projection regions–are incompatible with the use of projections. We explore perspective in carpets in other Lotto paintings and find perspective incoherence that is unlikely due to refocusing or depth of field problems in a projection, the putative source in “Husband and wife.” Our analyses and the lack of supporting historical evidence lead us to reject claims for “proofs” that projections were used in the creation of this painting.
Protein Classification with Improved Topological Data Analysis (2018)

Automated annotation and analysis of protein molecules have long been a topic of interest due to immediate applications in medicine and drug design. In this work, we propose a topology based, fast, scalable, and parameter-free technique to generate protein signatures. We build an initial simplicial complex using information about the protein's constituent atoms, including its radius and existing chemical bonds, to model the hierarchical structure of the molecule. Simplicial collapse is used to construct a filtration which we use to compute persistent homology. This information constitutes our signature for the protein. In addition, we demonstrate that this technique scales well to large proteins. Our method shows sizable time and memory improvements compared to other topology based approaches. We use the signature to train a protein domain classifier. Finally, we compare this classifier against models built from state-of-the-art structure-based protein signatures on standard datasets to achieve a substantial improvement in accuracy.
Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis (2000)

We have analyzed the cyclic nucleotide (cNMP)-binding protein and nucleotide cyclase superfamilies using Bayesian computational methods of protein family identification and classification. In addition to the known cNMP-binding proteins (cNMP-dependent kinases, cNMP-gated channels, cAMP-guanine nucleotide exchange factors, and bacterial cAMP-dependent transcription factors), new functional groups of cNMP-binding proteins were identified, including putative ABC-transporter subunits, translocases, and esterases. Classification of the nucleotide cyclases revealed subtle differences in sequence conservation of the active site that distinguish the five classes of cyclases: the multicellular eukaryotic adenylyl cyclases, the eukaryotic receptor-type guanylyl cyclases, the eukaryotic soluble guanylyl cyclases, the unicellular eukaryotic and prokaryotic adenylyl cyclases, and the putative prokaryotic guanylyl cyclases. Phylogenetic distribution of the cNMP-binding proteins and cyclases was analyzed, with particular attention to the 22 complete archaeal and eubacterial genome sequences. Mycobacterium tuberculosis H37Rv and Synechocystis PCC6803 were each found to encode several more putative cNMP-binding proteins than other prokaryotes; many of these proteins are of unknown function. M. tuberculosis also encodes several more putative nucleotide cyclases than other prokaryotic species.
An Experimental Evaluation of the Oil Fouling Effects of Two-Stroke Oxidation Catalysts (1998)

&lt;div class="htmlview paragraph"&gt;Washcoat sintering and substrate meltdown have traditionally been the principle deactivating mechanisms of catalysts fitted to two-stroke engines. The reduction of the excessively high HC and CO levels responsible for these effects has therefore been the focus of considerable research which has led to the introduction of direct in-cylinder fuel injection to some larger versions of this engine. However, much less attention has been paid to the effects of oil and its additives on the performance and durability of the two-stroke catalyst. The quantity of oil emitted to the exhaust system of the majority of two-stroke engines is much greater than in four-stroke engines of comparable output due to the total loss lubrication system employed. The fundamental design of the two-stroke also permits some of this oil to ‘short-circuit’ to the exhaust in a neat or unburned form. The effect of this oil on the catalyst and the subsequent effect of the catalyst on the oil is the subject of this paper.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Two separate experimental test facilities were used during this investigation. The first was a computer-controlled catalyst test rig which uses a synthetic exhaust gas to examine the light-off characteristics of the catalyst in an accurate and repeatable manner. The second was based on a propane gas burner and was used to subject the catalyst to oil under conditions representative of those experienced on an operating engine.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Two oil types were formulated specifically for this study, one containing a minimal sulphur concentration and one containing 1.02% sulphur. It was found that oil with a low sulphur content caused only temporary deactivation which could be removed by simply heating the catalyst while oil which contained a high level of sulphur caused immediate and permanent deactivation. It was also found that the temperature at which the oil was layered onto the catalyst had a significant effect on the post-oiling light-off performance with CO conversion being inhibited to a greater degree than HC conversion. BET surface area measurements revealed a significant reduction in the number of micropores in the 5-10Å region while surface reaction rate considerations suggested a loss in metal surface area of over 50%.&lt;/div&gt;
Attacking and Defending Masked Polynomial Comparison for Lattice-Based Cryptography (2021)

In this work, we are concerned with the hardening of post-quantum key encapsulation mechanisms (KEM) against side-channel attacks, with a focus on the comparison operation required for the Fujisaki-Okamoto (FO) transform. We identify critical vulnerabilities in two proposals for masked comparison and successfully attack the masked comparison algorithms from TCHES 2018 and TCHES 2020. To do so, we use first-order side-channel attacks and show that the advertised security properties do not hold. Additionally, we break the higher-order secured masked comparison from TCHES 2020 using a collision attack, which does not require side-channel information. To enable implementers to spot such flaws in the implementation or underlying algorithms, we propose a framework that is designed to test the re-encryption step of the FO transform for information leakage. Our framework relies on a specifically parametrized t-test and would have identified the previously mentioned flaws in the masked comparison. Our framework can be used to test both the comparison itself and the full decapsulation implementation.
On Consumption-Indexed Public Pension Plans (1982)

Using the known result that life-cycle investors will optimally hold portfolios whose returns are perfectly correlated with aggregate consumption, this paper uses a simple intertemporal general equilibrium model to explore the merits and feasibility of pension plans where both accumulations and benefits are linked to aggregate per capita consumption.Although the analysis is made within the framework of a public pension plan, it applies equally well to organized private pension plans where participation is virtually mandatory and where individually designed programs are not practical.An additional feature of the plans examined is that they provide for life annuities during both the accumulation and retirement phases of the life cycle.
Systemic neuropeptide levels as predictive indicators for lethal outcome in patients with postoperative sepsis (2002)

High systemic CGRP levels were associated with lethal outcome already at the onset of sepsis, whereas high substance P levels were identified as late predictive indicators of lethal outcome. These results are consistent with the view that the neuropeptides, CGRP and substance P, may be involved in the pathogenesis of sepsis.
Synthesis of novel aminoquinolines with potential leishmanicidal and antimalarial biological activity / Síntese de novas aminoquinolinas com potencial actividade biológica leishmanicida e antimalárica (2021)

Leishmaniasis is a disease transmitted by different parasite species of the genus Leishmania, while malaria, by protozoa of the genus Plasmodium sp. These diseases affect tropical and subtropical regions, where about half of the world's population live. However, leishmaniasis and malaria are considered neglected diseases because these regions are poor, and consequently have precarious essential sanitation networks. In response to the lack of vaccines and effective medical measures, some natural and synthetic medicines are used as forms of treatment, such as quinoline derivatives necessary to treat malaria. Even so, the parasites have shown resistance to forms of treatment, which makes needed the constant development of new drugs with potential against them. Quinoline derivatives, chloroquine analogues, have potential activity for the diseases of interest, while anilines are molecules used in nucleophilic reactions on different substrates. Therefore, the work consisted of exploring the synthesis between these two compounds through subsequent reactions involving the formation of intermediates that resulted in the products of interest. Twelve novel derivatives with potential leishmanicidal and antimalarial biological activity were synthesized. The molecules produced were purified and rightly characterized by several methods, such as mass spectrometry, infrared spectroscopy, and Nuclear Magnetic Resonance of Carbon (13C) and Hydrogen (1H). Also, were obtained the melting points of the synthesized molecules. Finally, all products were sent for biological tests against the parasites, getting highly effective results for the protozoa responsible for leishmaniasis.
Field Determination of Saturated and Unsaturated Hydraulic Conductivities Using the IP Method (2006)

An instantaneous profile (IP) test was conducted at Sandia National Laboratories, Albuquerque, New Mexico. The IP method was used to determine the field-saturated and unsaturated hydraulic conductivities of a natural soil profile. The soil profile was instrumented with two neutron probe access tubes and three clusters of paired tensiometers and time domain reflectometry (TDR) probes. The soil profile was flooded for a period of 48 hours. Flooding was discontinued when the soil was field-saturated. Neutron probe and tensiometer data were acquired on a continual basis for 890 days and 200 days, respectively. As the soil profile was allowed to drain, soil moisture and suction data were recorded throughout the soil profile. These data from the IP test were used to calculate the unsaturated hydraulic conductivity as a function of the volumetric moisture content of the soil profile. The curves representing hydraulic head, H, change with depth, z, exhibit a clear change in slope between 90 cm and 120 cm due to a caliche layer. Values of hydraulic conductivity were calculated from the slope of the ∂H/∂z curves corresponding to a given depth and time. The hydraulic conductivity of the soil profile is represented by a family of curves that represent the variations in soil characteristics within this soil profile.
Redundant PLC control ensures flexible storage (1992)

This paper reports on new compressor control system at a fast storage field operated by Illinois Power that enables the utility to provide customers with gas on even the coldest days. High peak-demand for natural gas on even the coldest winter days is no problem for Illinois Power Co., thanks to a new control system at its gas storage facility at Central, Ill. The system consists of two programmable logic controllers running identical software in a hot backup configuration, with distributed I/O, sophisticated monitoring and control software, and software-based flow computers. Illinois Power's Central compressor station, activated in 1964, is located above an old sandstone gas field that was converted to gas storage once it stopped producing. The facility is of the dry-gas type with an average depth of 836 ft and reservoir pressure of 320 psig. It has a daily sendout capacity of f14 MMcf and a total working gas inventory of 143 MMcf. Illinois Power uses the stored gas for meeting peak winter demand as well as annual economic dispatch. The utility's winter peak daily load is about five times greater than its normal summer load. The Central storage compressor station is powered by an electric motor-driven, 800-hp,more » Cooper-Bessemer double-acting, three-cylinder compressor. The unit stands idle most of the year, but must respond flawlessly on demand during the coldest days of the winter heating season.season.« less
Probucol decreases total body fat loss in VX2-carcinoma-induced cachectic rabbits (2001)

We previously reported the continuous decrease of total body fat in VX2-carcinoma-bearing rabbits after tumor implantation, as well as changes in the serum lipid profile. Probucol, an antioxidant drug, has a cholesterol lowering effect against hyperlipidemic subjects. VX2-carcinoma-bearing rabbits fed with a diet containing 1% probucol did not show any difference in serum lipid compositions as compared with rabbits fed with a control diet. Similarly serum lipolytic activity showed no differences, whether probucol was administered or not, while the decrease in total body fat was significantly less when probucol was administered.
Polarization-Based Reconfigurable Tags for Robust Ambient Backscatter Communications (2020)

Ambient backscatter communication is an emerging and promising low-energy technology for the Internet of Things. In such a system, a tag sends a binary message to a reader by backscattering a radio frequency signal generated by an ambient source. The tag can operate without battery and without generating additional radio waves. However, the tag-to-reader link suffers from the source-to-reader interference. In this paper, we propose a polarization-based reconfigurable antenna in order to improve the robustness of the tag-to-reader link against the source-to-reader direct interference. More precisely, we compare different types of tags' antennas, different tags' encoding schemes, and different detectors at the reader. By using analysis, numerical simulations, and experiments, we show that a polarization-based reconfigurable tag with four polarization directions significantly outperforms a non-reconfigurable tag, and provides almost the same performance as an ideal reconfigurable tag with a large number of reconfigurable polarization patterns.