nils-herrmann/clean_scirepeval huggingface dataset:
Structure-based glycoengineering of interferon lambda 4 enhances its productivity and anti-viral potency

Abstract
 
 Interferon lambda 4 (IFNλ4) has been recently known and studied for its role in hepatitis C virus (HCV) infection, but its clinical potential is significantly hampered due to its poor expression in vitro. Our study reports the successful production of IFNλ4 from a mammalian cell line through a glycoengineering and structure-based approach. We introduced de novo N-glycosylation of IFNλ4, guided by structural analysis, and produced IFNλ4 variants in Expi293F that displayed improved expression and potency. To preserve the structure and functionality of IFNλ4, the model structure of the IFNλ4 signaling complex was analyzed and the N-glycosylation candidate sites were selected. The receptor binding activity of engineered IFNλ4 variants and their receptor-mediated signaling pathway were similar to the E. coli version of IFNλ4 (eIFNλ4), while the antiviral activity and induction levels of interferon-stimulated gene (ISG) were all more robust in our variants. Our engineered IFNλ4 variants may be further developed for clinical applications and utilized in basic research to decipher the immunological roles of IFNλ4.

Field of study: Medicine
Zur Theorie und Praxis der Phosphoroxidation

Based on the theoretically calculated; and on experimentally investigated thermodynamic data of the molecular phosphorus oxides °6 P407, P408, P09 and P010 which are metastable under normal conditions respectively their dissociation products P0, P02, P3, P2, P, .02 and 0, which probably exist under the conditions of hot phosphorus oxidation, thermodynamic calculations yield their equilibrium states in dependence on temperature, pressure and the P:0—ratio. Accordingly there . are characteristic ranges of temperature in which the respective molecular phosphorus oxides at constant total pressure exist only in depextdence..on the P:0—ratio. With increasing total pressure the existence ranges of the pure components extend towards higher temperatures. For instance at a total. pressure of I05 Pa the P406—molecule is stable at the P:02—ratio of 1:3 nearly 2000K. and the P4010—molecule is stable at the .P4 02—ratio of 1:5 up to 1900K. On introducting 00 as an additional component influencing the equilibrium,002 is formed and the equilibrium is changed in the direction of decreasing P:O—rati.o. Above 3500K. no more 002 is present in the equilibrium whereas the molecular phosphorus oxides cease to exist above 2500K. Since at temperatures above 1800K kinetic factors have practically .no effect on. the rate of the equilibrium, the rate of reaction depends only on factors which influence the rate of mixing of gases7 such as the viscosity of the gases. The quenching of the hot phosphorus flame was investigated basing on the theoretical understandings. Depending on the temperature gradient, on the P:O—ratio and on the mean temperature in the reaction zone by a suitable carrying of energy. practically pure normally metastable products may be obtained, if an ideal mixing regime can be approached. As a consequence an alteration of the total pressure effects as well the required temperature gradient of the

Field of study: Chemistry
Integration of Markov random field with Markov chain for efficient event detection using wireless sensor network

Event detection is an important task required in various applications of wireless sensor network (WSN). The existing approaches consider the spatial and temporal correlation of sensor data separately or not in a cohesive way. In this paper an event detection scheme with WSN is introduced, which adopts a hierarchical structure to efficiently integrate the spatial and temporal correlation of sensor data. Here a fusion algorithm considering both the weight of the sensors and spatial information is applied to Markov random field to properly fuse the decisions of the neighboring nodes. Markov chain is also adopted to effectively extract the temporal correlation after the spatial correlation is decided. The simulation results demonstrate that the proposed scheme can effectively increase the detection accuracy and reduce communication cost, in comparison with the existing schemes.

Field of study: Computer science
Evidence for semi-sessile early juvenile life history in Cretaceous ammonites

Here we present evidence for a semi-sessile early juvenile stage of ammonites. Our hypothesis is based on fossil evidence in early diagenetic limestone concretions discovered in platy limestone deposits of Cenomanian age in the northern state of Coahuila, Mexico. In these locations densely packed post-embryonic shell assemblages were attached to fossilized algal or bacterial mats and preserved in sediments deposited under permanently anoxic bottom conditions. Tiny ammonites, as well as gastropods and byssate pectinid bivalves are abundant and restricted to these mats. They do not occur elsewhere in the sediment. The ammonite hatchlings were apparently unable to escape from mats sinking to the hostile sea floor and must thus have been semi-sessile, similar to the associated gastropods and bivalves.

Field of study: Environmental science, Geography
“Preliminary Exploration of the Thought of Social Education”——From the Rural Construction Practice of Liang Shu-ming

Liang Shu-ming was a famous educator and organizer of rural movement in modern times. He connected the theory of social education with the practice of rural construction, which had great efforts on the rural reform and social development of modern times. This paper mainly talks about Liang Shu-ming's social educational concepts and its important enlightenment for current all-life education ideal and building learning society.

Field of study: Education
Transitional and Turbulent Heat-Transfer Measurements on a Yawed Blunt Conical Nosetip

Transitional and turbulent heat-transfer rates measured on a blunt (RN = 2.5 in.) nine degree half-angle cone in a Mx = 5 air flow at various angles of attack are presented. Measurements were made at nominal freestream Reynolds numbers of 48.5,19, and ll(10)6/ft and nominal angles of attack of a = 0°, 5°, 10°, 15°, 20 , and 27°. The wall to stagnation temperature ratio varied between 0.20 and 0.29. Detailed circumferential (A0 « 30°) and axial (S/RN ^ 5.25) distributions of both the heat-transfer rate and surface pressure were obtained over the entire model at each test condition and angle of attack. Natural transition occurred on the hemisphereical cap near the stagnation region at the Re^ = 48.5 and 19(10)6 test conditions. Heat-transfer rates computed along inviscid surface streamlines using various simplified heat-transfer formulations are compared to the data. The Vaglio-Laurin type turbulent heat-transfer formulations are shown to be in good agreement with the data at all test conditions, while those formulations which use reference rather than edge conditions to define the local rate, substantially overpredict the heattransfer rate over the entire surface. The applicability of the angle-of-attack turbulent heat-transfer correlation previously proposed by Widhopf is demonstrated for the present test results.

Field of study: Physics
Semantic false memories in the form of derived relational intrusions following training.

Contemporary behavior analytic research is making headway in characterizing memory phenomena that typically have been characterized by cognitive models, and the current study extends this development by producing "false memories" in the form of functional equivalence responding. A match-to-sample training procedure was administered in order to encourage participants to treat groups of unrelated English words as being interchangeable. Following training, participants were presented with a list of words from within one of the groups for a free recall test and a recognition test. Results showed that participants were more likely to falsely recall and recognize words that had been assigned to the same group as the list words during prior training, relative to words not assigned to the same group and relative to words that co-occurred with list words. These results indicate that semantic relatedness can be experimentally manipulated in order to produce specific false memories.

Field of study: Biology, Psychology
Spaceborne imaging radar-C (SIR-C) observations of groundwater discharge and wetlands associated with the Chicxulub impact crater, northwestern Yucatan Peninsula, Mexico

Analyses of spaceborne imaging radar-C (SIR-C) data and field data from the northwestern Yucatan Peninsula, Mexico, demonstrate that spaceborne multifrequency polarimetric radars are excellent tools for characterizing patterns of wetland flooding. Seasonal flooding can be detected in most types of forest and marsh in the radar backscatter magnitude and phase data of both L and C band. Field observations made in the wet and dry seasons concurrent with the space missions and chemical analyses of floodwaters confirm that flooding is the product of discharge from the Yucatan aquifer, which consists of a fresh-water lens floating on seawater. This discharge controls the distribution of wetlands. Therefore, vegetation and flooding patterns, mapped with SIR-C imagery, provide valuable information on the hydrogeology of the region. Radar-image maps of wetlands and flooding indicate that there are three major zones of groundwater discharge that correlate with structures of the buried Chicxulub crater—zone 1 with the peak ring, zone 2 with the crater rim, and zone 3 with the exterior ring. Zone 1 has sulfate-poor discharge, unlike the sulfate-rich discharge in zones 2 and 3. The highest discharge is in zone 3, where the buried crater is closest to the surface. This groundwater-discharge pattern can be explained by tidal pumping of fresh water to the surface through high permeability zones developed in the Tertiary carbonates overlying crater faults and escarpments.

Field of study: Geology
Inhibition Effect of Three-Dimensional (3D) Nanostructures on the Corrosion Resistance of 1-Dodecanethiol Self-Assembled Monolayer on Copper in NaCl Solution

A novel and simple method to improve the corrosion resistance of copper by constructing a three-dimensional (3D) 1-dodecanethiol self-assembled monolayer (SAM) in 3.5% NaCl solution is reported in this study. Several drops of 1% H3PO4 solution are thinly and uniformly distributed on copper surface to form a 3D nanostructure constituted by Cu3(PO4)2 nanoflowers. The anticorrosion properties of 1-dodecanethiol SAM on copper surface and on copper surface that is treated with H3PO4 solution were evaluated. Results demonstrated that 1-dodecanethiol SAM on bare copper surface exhibits good protection capacity, whereas a copper surface that is pretreated with H3PO4 solution can substantially enhance the corrosion resistance of 1-dodecanethiol SAM.

Field of study: Materials science
Deformable image registration based automatic CT-to-CT contour propagation for head and neck adaptive radiotherapy in the routine clinical setting.

To evaluate the clinical potential of deformable image registration (DIR)-based automatic propagation of physician-drawn contours from a planning CT to midtreatment CT images for head and neck (H&N) adaptive radiotherapy.



Ten H&N patients, each with a planning CT (CT1) and a subsequent CT (CT2) taken approximately 3-4 week into treatment, were considered retrospectively. Clinically relevant organs and targets were manually delineated by a radiation oncologist on both sets of images. Four commercial DIR algorithms, two B-spline-based and two Demons-based, were used to deform CT1 and the relevant contour sets onto corresponding CT2 images. Agreement of the propagated contours with manually drawn contours on CT2 was visually rated by four radiation oncologists in a scale from 1 to 5, the volume overlap was quantified using Dice coefficients, and a distance analysis was done using center of mass (CoM) displacements and Hausdorff distances (HDs). Performance of these four commercial algorithms was validated using a parameter-optimized Elastix DIR algorithm.



All algorithms attained Dice coefficients of >0.85 for organs with clear boundaries and those with volumes >9 cm(3). Organs with volumes <3 cm(3) and/or those with poorly defined boundaries showed Dice coefficients of ∼ 0.5-0.6. For the propagation of small organs (<3 cm(3)), the B-spline-based algorithms showed higher mean Dice values (Dice = 0.60) than the Demons-based algorithms (Dice = 0.54). For the gross and planning target volumes, the respective mean Dice coefficients were 0.8 and 0.9. There was no statistically significant difference in the Dice coefficients, CoM, or HD among investigated DIR algorithms. The mean radiation oncologist visual scores of the four algorithms ranged from 3.2 to 3.8, which indicated that the quality of transferred contours was "clinically acceptable with minor modification or major modification in a small number of contours."



Use of DIR-based contour propagation in the routine clinical setting is expected to increase the efficiency of H&N replanning, reducing the amount of time needed for manual target and organ delineations.

Field of study: Medicine, Physics
Towards polariton neuromorphic engineering

The ubiquity of nonlinear oscillatory motion is perhaps best demonstrated with a pendulum which is harmonic only at small angles. Just as the harmonic oscillator provides a natural description of bosons in a quantum field, the Stuart-Landau oscillator provides a universal description of nonlinear oscillators close to a Hopf bifurcation. In the case of coupled nonlinear oscillators, time-delayed interactions increase the complexity of many physical systems ranging from coupled lasers, epidemiology, predator-prey, and road traffic systems to neuronal networks. Here, we explore the phase-space of ballistically coupled polariton condensates and demonstrate that the dynamics of the system are driven by the Lang-Kobayashi equation, and in the limit of fast relaxation of the exciton-reservoir feeding the condensates they can be described by time-delayed coupled Stuart-Landau oscillators. The controllability, complexity and similarity of ballistically coupled polariton condensates to many physical interacting systems establishes a strong motivation to apply polaritonics towards continuous recurrent artificial neural networks and is the first step forward in realizing integrated time delayed polariton networks for high speed optical neuromorphic computation.

Field of study: Physics
Evidence for diversifying selection of genetic regions of encoding putative collagen-like host-adhesive fibers in Pasteuria penetrans

&NA; Pasteuria spp. belong to a group of genetically diverse endospore‐forming bacteria (phylum: Firmicutes) that are known to parasitize plant‐parasitic nematodes and water fleas (Daphnia spp.). Collagen‐like fibres form the nap on the surface of endospores and the genes encoding these sequences have been hypothesised to be involved in the adhesion of the endospores of Pasteuria spp. to their hosts. We report a group of 17 unique collagen‐like genes putatively encoded by Pasteuria penetrans (strain: Res148) that formed five different phylogenetic clusters and suggest that collagen‐like proteins are an important source of genetic diversity in animal pathogenic Firmicutes including Pasteuria. Additionally, and unexpectedly, we identified a putative collagen‐like sequence which had a very different sequence structure to the other collagen‐like proteins but was similar to the protein sequences in Megaviruses that are involved in host‐parasite interactions. We, therefore, suggest that these diverse endospore surface proteins in Pasteuria are involved in biological functions, such as cellular adhesion; however, they are not of monophyletic origin and were possibly obtained de novo by mutation or possibly through selection acting upon several historic horizontal gene transfer events. &NA;  Collagen‐like genes that are expressed on the surface of spores are hypothesised to have been obtained by horizontal gene transfer and are involved in the spores' adhesion to nematode cuticle.

Field of study: Biology, Environmental science
Blue-shift photoluminescence from porous InAlAs

A porous InAlAs structure was first obtained by electrochemical etching. Nano-pore arrays were formed when the In0.52Al0.48As membrane was anodized at constant voltages in an HF aqueous solution. These self-assembled structures showed evident blue-shift photoluminescence emissions. While a quantum size effect alone underestimates the blue-shift energy for a sample with a relatively large average pore wall thickness, a novel effect caused by the asymmetric etching is proposed to account for this phenomenon. The results inferred from the x-ray double crystal diffraction are in good agreement with the experimental data.

Field of study: Materials science
Dynamic Scheduling Algorithm of Real-time Tasks with End-to-end Time Constraints

Uniprocessor schedulability theory made great strides,in part,due to the simplicity of composing the delay of a task from the execution time of higher-priority tasks that preempt it. In this paper,a scheduling algorithm of real-time tasks with end-to-end time constraints is proposed. When a real-time task arrives at the system,the algorithm reserves computing time for each of its subtasks on the processor assigned,so that the multiprocessor schedulability has been transformed to uniprocessor schedulability. The wealth of schedulability analysis techniques derived for uniprocessors can then be applied to decide the schedulability of real-time task with end-to-end time constraints. The experimental results demonstrate that the CPU utilization ratio and tasks accept ratio increase greatly.

Field of study: Computer science
INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow‐leafed lupin (Lupinus angustifolius L.)

Narrow‐leafed lupin (Lupinus angustifolius L.) cultivation was transformed by 2 dominant vernalization‐insensitive, early flowering time loci known as Ku and Julius (Jul), which allowed expansion into shorter season environments. However, reliance on these loci has limited genetic and phenotypic diversity for environmental adaptation in cultivated lupin. We recently predicted that a 1,423‐bp deletion in the cis‐regulatory region of LanFTc1, a FLOWERING LOCUS T (FT) homologue, derepressed expression of LanFTc1 and was the underlying cause of the Ku phenotype. Here, we surveyed diverse germplasm for LanFTc1 cis‐regulatory variation and identified 2 further deletions of 1,208 and 5,162 bp in the 5' regulatory region, which overlap the 1,423‐bp deletion. Additionally, we confirmed that no other polymorphisms were perfectly associated with vernalization responsiveness. Phenotyping and gene expression analyses revealed that Jul accessions possessed the 5,162‐bp deletion and that the Jul and Ku deletions were equally capable of removing vernalization requirement and up‐regulating gene expression. The 1,208‐bp deletion was associated with intermediate phenology, vernalization responsiveness, and gene expression and therefore may be useful for expanding agronomic adaptation of lupin. This insertion/deletion series may also help resolve how the vernalization response is mediated at the molecular level in legumes.

Field of study: Environmental science
Thermal Decomposition of 3-Nitro-1-nitromethyl-1,2,4-1H-triazole in Solution

The thermal decomposition of 3-nitro-1-nitromethyl-1,2,4-1H-triazole in 1% solution in phenyl benzoate proceeds homolytically with initial rupture of the CH2-NO2 bond. Activation parameters of the process were Ea = 172.6 kJ/mol, log A = 14.25. The initial basic pathway of fragmentation of the molecule under electron impact coincides with the first step of thermal decomposition, which is in agreement with X-ray structural and calculated quantum chemical data on bond stability in the molecule.

Field of study: Chemistry
Simulations of the changes o f the heating energy demand and transmission losses of buildings in central European climate: Combination of experiments and simulations

Recently, it has become extremely important to reduce the heating energy demand and the CO2 emission of buildings. This reduction can easily be achieved by insulating the shell of buildings. By thermal insulation not only the heating energy demand can be reduced but also higher thermal efficiency can be reached. Therefore, measurements, calculations and simulations are carried out on the energy efficiency of buildings. Furthermore, the combination of methods is of great importance. Combination of experiments with building simulations solution can make design practices and sizing processes easier in the investigation of building performance. The purpose of this article is to demonstrate how the energy balance of a building can be changed in function of the wet building envelope in the Central European Region. A real and available building (old family house) was tested and it was placed (hypothetically) in three different countries (Austria, Hungary and Slovakia). In this study two types of load-bearing str...

Field of study: Engineering
The optimal duration of alarm therapy use in children with primary monosymptomatic nocturnal enuresis.

The prevalence of primary monosymptomatic nocturnal enuresis (PMNE) has a range of 1.6-5.3% in adolescents and 7.5-12.4% in children of 5-10 years. Alarm intervention has been well known for more than 30 years. This method is a reliable and safe means of treating primary monosymptomatic nocturnal enuresis, being effective in 60-80% of cases.



The objective of this study was to determine the efficacy of alarm intervention prolongation after the cure in order to reduce the risk of disease recurrence.



Two hundred ninety-four boys and 161 girls (455 persons in total) of age 9-14 years (average 11.4 years) took part in the prospective randomized study. After preselection and establishing diagnosis, all patients were randomly divided in three groups. In group А (n = 139) alarm system treatment was carried out within 12 weeks, in group В (n = 136) 16 weeks, and in group С (n = 139) 20 weeks.



The percentage of patients who no longer wet the bed (for 2 weeks or more) immediately after treatment in groups B (80.7%) and C (85.5%) was higher than in group A (67.4%) if the probability of error is pB/A < 0.05; pC/A < 0.05. There was no statistically significant difference in treatment success between groups B and C immediately after treatment. The percentage of patients who no longer wet the bed 3 months after the end of treatment in groups B (71.2%) and C (77.1%) was higher than in the group A (45.9%) if the probability of error is pB/A < 0.05; pC/A < 0.05. There was no statistically significant difference in treatment success between groups B and C 3 months after treatment. During the year this ratio did not change.



These data suggest that the effective duration of alarm intervention is found in the range 16-20 weeks and involves an uninterrupted course of treatment. Perhaps this range of time is optimal for the formation of a neuroreflexive mechanism that creates a habit for independent awakening in children with primary monosymptomatic nocturnal enuresis.



The effective duration of alarm intervention is likely to be 16-20 weeks of an uninterrupted course of treatment. This time interval ensures the maximum effectiveness of treatment and the stability of long-term results.

Field of study: Medicine