nils-herrmann/clean_scirepeval huggingface dataset:
Intracellular localization and induction of a dynamic RNA-editing event of macro-algal V-ATPase subunit A (VHA-A) in response to copper.

A V-ATPase subunit A protein (VHA-A) transcript together with a variant (C793 to U), which introduces a stop codon truncating the subunit immediately downstream of its ATP binding site, was identified within a Fucus vesiculosus cDNA from a heavy metal contaminated site. This is intriguing because the VHA-A subunit is the crucial catalytic subunit responsible for the hydrolysis of ATP that drives ion transport underlying heavy metal detoxification pathways. We employed a chemiluminescent hybridization protection assay to quantify the proportion of both variants directly from mRNA while performing quantification of total transcript using Q-PCR. Polyclonal antisera raised against recombinant VHA-A facilitated simultaneous detection of parent and truncated VHA-A and revealed its cellular and subcellular localization. By exploiting laboratory exposures and samples from an environmental copper gradient, we showed that total VHA-A transcript and protein, together with levels of the truncated variant, were induced by copper. The absence of a genomic sequence representing the truncated variant suggests a RNA editing event causing the production of the truncated VHA-A. Based on these observations, we propose RNA editing as a novel molecular process underpinning VHA trafficking and intracellular sequestration of heavy metals under stress.

Field of study: Environmental science
The effects of reactants ratios, reaction temperatures and times on Maillard reaction products of the L-ascorbic acid/L-glutamic acid system

The transformation law of the Maillard reaction products with three different reactants ratios - equimolar reactants, excess L-glutamic acid and excess L-ascorbic acid reaction respectively, five different temperatures, and different time conditions for the L-ascorbic acid / L-glutamic acid system were investigated. Results showed that, the increase of the reaction time and temperature led to the increase of the browning products, uncoloured intermediate products, as well as aroma compounds. Compared with the equimolar reaction system, the excess L-ascorbic acid reaction system produced more browning products and uncoloured intermediate products, while the aroma compounds production remained the same. In the excess L-glutamic acid system, the uncoloured intermediate products increased slightly, the browning products remained the same, while the aroma compounds increased.

Field of study: Agricultural and Food sciences
Simulation of a solar driven aqua-ammonia absorption refrigeration system Part 1: mathematical description and system optimization

A theoretical thermodynamic analysis was performed on an aqua-ammonia refrigeration (AAR) cycle coupled to a solar water heating system using CPC-collectors and augmented with auxialiary energy. Thirteen AAR cycles were considered in the search for the maximum coefficient of performance. Also investigated was the exergetic performance of the AAR cycle. The adopted temperature and mass flow rate control strategy on the storage tank-auxiliary heater-AAR generator loop ensured operation of the refrigeration systems at design conditions. Consequently, the ratio between the pumps' electrical power and the designed evaporator heat transfer rate was kept to a minimum.

Field of study: Engineering
Thermal expansion in nanoresonators

Inspired by some recent experiments and numerical works related to nanoresonators, we perform classical molecular dynamics simulations to investigate the thermal expansion and the ability of the device to act as a strain sensor assisted by thermally-induced vibrations. The proposed model consists in a chain of atoms interacting anharmonically with both ends clamped to thermal reservoirs. We analyze the thermal expansion and resonant frequency shifts as a function of temperature and the applied strain. For the transversal modes the shift is approximately linear with strain. We also present analytical results from canonical calculations in the harmonic approximation showing that thermal expansion is uniform along the device. This prediction also works when the system operates in a nonlinear oscillation regime at moderate and high temperatures.

Field of study: Physics
Nubrigyn algal reefs (Devonian), eastern Australia: Allochthonous blocks and megabreccias

The widely known Lower Devonian “algal reef ” limestones of the Nubrigyn Formation, New South Wales, are enormous allochthonous blocks contained within a 400-m interval of interbedded mudstones, allodapic carbonates, and megabreccias that form part of a 5,000-m succession of Lower Devonian volcanics and flysch. Previous workers have interpreted these massive limestone bodies to be algal bioherms that developed in sublittoral to littoral environments around volcanic pedestals on a “Nubrigyn shelf.” The allochthonous nature of the limestone bodies is clearly indicated by (1) occurrence of a wide range of clast sizes, as much as 1 km across; (2) presence of a wide range of clast types and sizes in close juxtaposition; (3) discordance between stratigraphic facing of the large limestone bodies and stratification in surrounding beds; (4) lack of distinctive and regular facies changes within the limestone bodies, particularly near their margins; (5) abrupt and random truncation of internal fabrics at block margins; (6) lack of an autochthonous volcanic foundation for the “reefs”; and (7) anomalous lithofacies association of the massive bodies of shoal-water limestone with enclosing flysch. The limestones initially formed in a shoal-water carbonate complex to the west upon a geologically persistent volcanic archipelago, the Molong Arch, where source rocks for the Nubrigyn megaclasts and megabreccias crop out in the Lower Devonian Garra Formation and Cuga Burga Volcanics. The Nubrigyn megaclasts were transported eastward as debris flows into the adjacent and relatively deep water Hill End Trough after dislodgement from the eastern margin of the Garra shelf. Megaclasts isolated within hemipelagic mudstones and flysch were presumably transported by sliding or rolling. The loci of accumulation of the debris flows and exotic blocks occupy a meridional basin-margin position between the Molong Arch to the west and the predominantly turbidite-filled Hill End Trough to the east. Other debris-flow megabreccias, many previously unrecognized as having been transported and deposited in this manner, occur in the Paleozoic rocks of the Tasman mobile belt of eastern Australia.

Field of study: Geology
Front end electronics and trigger system for the KARMEN neutrino experiment

KARMEN is a 56-t liquid scintillation calorimeter for neutrino experiments using beam-dump neutrinos from the spallation neutron source ISIS of the Rutherford Appleton Laboratory. The central detector is surrounded by two layers of antidetectors to define the fiducial volume for v reactions. The architecture of the electronics system of the KARMEN detector is described. The readout of the position-sensitive calorimeter is controlled by a trigger processor that analyzes the sum energy and multiplicity of the 512 central detector modules. Zero suppression during the ADC (analog/digital converter) scan facilitates a fast readout. A sophisticated, high degree of multiplexing leads to an economical system.

Field of study: Physics
Impacts of HBsAg P24 conjugating extent on the antigenicity of the recombinant yeast expressed HBsAg

To identify the impact of the HBsAg P24 unit conjugating extent on the antigeni- city of the recombinant yeast expressed HBsAg.  Three lots of purified HBsAg derived from recombinant yeast were treated with or without thiocyanate to prepare non-transformed, semi-transformed and transformed HBsAg, the P24 unit is theoretically loose-conjugated, semi-tight-conjugated and tight-conjugated. The tight-conjugation of polypeptide P24 unit for HBsAg was detected by HPLC. The BALB/c mice NK activities and HBsAg specific spleen lymphocytes proliferation immunized with the loose-conjugated and tight-conjugated HBsAg were tested.  The average tight-conjugated P24 percentages of the three lots loose-conjugated, semi-tight-conjugated and tight-conjugated HBsAg are 23.00%-32.00%, 38.43%-50.98% and 39.65%-52.76%, respectively. The extent of tight-conjugated P24 semi-transformed HBsAg is similar to transformed ones. The NK activities induced by tight-conjugated HBsAg were higher than that induced by loose-conjugated antigen, the HBsAg specific spleen lymphocytes proliferation induced by loose-conjugated antigen was higher than that of tight-conjugated antigen in 4 weeks. All loose-conjugated, semi-tight-conjugated and tight-conjugated HBsAg effectively induced humoral immunoresponse. Although all vaccines showed effective immunogenicity, the semi-tight-conjugate vaccines are significantly more effective than that of loose-conjugated (P0.05). Both the median effective dose (ED_ 50 ) and in vitro relative potencies (RP) of the loose-conjugated and the semi-tight-conjugated trial hepatitis B vaccines meet the requirement of the recombinant yeast derived hepatitis B vaccine.  Various P24 unit conjugated degree HBsAg maintains antigenicity. The tight-conjugated HBsAg could induce stronger NK activities than loosed HBsAg. The semi-transform treatment may improve the immunogenicity of HBsAg.

Field of study: Biology
Die vele kante van suiwel : op die winkelrak

Van botter tot kaas - die veelsydigheid van suiwel bied aan verbruikers 'n wye verskeidenheid produkte om van te kies en te keur. Kaasmakers en verwerkers kan gereeld na die tekenbord terugkeer om aan hul kreatiewe kant uiting te gee. Verwerkers het egter nie net 'n verantwoordelikheid teenoor die verbruiker om aan die voorpunt van suiwelprodukontwikkeling te bly nie, maar word deur die vraag na produkte gedryf om innoverend te wees. So kan verbruikers deesdae tamatie-gegeurde jogurt, warm roomys en selfs gegeurde botter koop.

Field of study: Agricultural and Food sciences
Application of an O-ring pinch device as a constant-pressure inlet (CPI) for airborne sampling

We present a novel and compact design of a constant-pressure inlet (CPI) developed for use in airborne aerosol mass spectrometry. In particular, the inlet system is optimized for aerodynamic lenses commonly used in aerosol mass spectrometers, in which efficient focusing of aerosol particles into a vacuum chamber requires a precisely controlled lens pressure, typically of a few hectopascals. The CPI device can also be used in condensation particle counters (CPCs), cloud condensation nucleus counters (CCNCs), and gas-phase sampling instruments across a wide range of altitudes and inlet pressures. The constant pressure is achieved by changing the inner diameter of a properly scaled O-ring that acts as a critical orifice. The CPI control keeps air pressure and thereby mass flow rate ( ≈0.1  L min −1 ) upstream of an aerodynamic lens constant, deviating at most by only ±2  % from a preset value. In our setup, a pressure sensor downstream of the O-ring maintains control of the pinch mechanism via a feedback loop and setpoint conditions are reached within seconds. The device was implemented in a few instruments, which were successfully operated on different research aircraft covering a wide range of ambient pressures, from sea level up to about 55 hPa. Details of operation and the quality of aerosol particle transmission were evaluated by laboratory experiments and in-flight data with a single-particle mass spectrometer.

Field of study: Environmental science
Effects of stimulus and cell type on the expression of the -308 tumour necrosis factor promoter polymorphism.

The authors have previously demonstrated that the tumour necrosis factor (TNF) -308 G/A polymorphism affects the binding of transcription factors. In transient transfection assays in PMA stimulated U937 monocytes and Jurkat T cells, the A-containing TNF2 promoter has a 2-3-fold greater transcriptional activity than the TNF1 promoter in the presence of the TNF 3'UTR. In this study it was found that a difference in TNF1 and TNF2 promoter activities was only observed in U937 and Jurkat cells, and not in Raji (B cell line), HeLa (epithelial carcinoma cell line), HepG2 (hepatoma cell line) or THP-1 (monocyte), suggesting cell-type specific transcription factors or modifications may be involved in the formation of the -308 protein/DNA complex. Physiological stimulators, TNF and interferon gamma (IFN-gamma) did not cause differential promoter activity between TNF1 and TNF2, but LPS did with only the TNF2 promoter/3'UTR construct being significantly responsive to lipopolysaccharide (LPS) in U937 cells. In U937 cells, the -308 polymorphism affected transcription following differentiation by phorbol myristate acetate (PMA), retinoic acid, PMA plus LPS and PMA plus retinoic acid with an increase in nuclear factor binding to both TNF1 and TNF2 in the -323 to -285 region being observed. The greatest difference between TNF2 and TNF1 promoter activities (5-fold) was observed following PMA plus retinoic acid treatment of transfected U937 cells for 48h. During this time, U937 differentiated into cells with a macrophage-like morphology. An understanding of the cell type and stimuli specific requirements for differential expression of the -308 polymorphism may help elucidate the role the TNF -308 polymorphism plays in diseases where elevated TNF levels are thought to be important.

Field of study: Medicine
DNA transfer: informed judgment or mere guesswork?

With the advances of analytical sensitivity, it is now possible to detect a DNA profile from minute quantity of DNA. It opens new investigative avenues (in cold cases for example), but also new interpretative challenges. Here, forensic scientists deal with items bearing DNA cellular material from areas showing no visible stain and have limited means to identify the nature of the body fluid involved. Such DNA cells can be considered as trace evidence that can be exchanged for reasons connected to the alleged facts under investigation (generally a direct transfer) but also following alternative and versatile ways (through secondary or tertiary transfer) that have no connection to the facts under investigation. The trace becomes an ubiquitous material that can be found for unconnected reasons. In addition, and especially with trace quantities of DNA, the debate in court is less focused on the issue of the source of the DNA (often the parties will not dispute it), but on the mechanisms whereby the biological material has been transferred (Taroni et al., 2013). In other words, the well-known territory of source level DNA statistics (see Buckleton et al., 2005 for example) does not help with the interpretation process, but the forensic scientist is invited to assess how likely it would be to observe this amount of DNA given various transfer mechanisms. The review by Meakin and Jamieson (2013) led them to conclude that the quantity of DNA or the quality of the profile cannot be used “to reliably infer the mode of transfer by which the DNA came to be on the surface of interest.”

Field of study: Biology
Development of crumb rubber reinforced elastomeric/semielastomeric thermally conductive composite materials to be used as permanent ball grid array stencils in printed circuit board rework

Thiswork relates to the development of a newfamily ofmaterials to be used for the rework (removal, repair, and replacement) of BGA(BallGridArray) components that can be found on a PCB (Printed Circuit Board). The rework involves the use of stencils to solder an array of micro-balls arranged in a grid manner belowthe BGA.Astencil is a membrane consisting of arrays of perforations (micro-holes or apertures) arranged in a grid manner. The new stencils, with the balls fitted into the apertures, are initially attached below the BGA, and finally are fixed between the soldered balls, the BGA, and the PCB. Similarmethods employ polymer stencils that are initially fixed between the soldered balls and the PCB, and finally are fixed between the resoldered balls, the BGA, and the PCB. The development of the new stencils may uniquely provide a new, easier, repeatable, predictable, low cost, rework method eliminating resoldering of the balls that also gives the benefit of one fewer thermal cycle for the BGA component. Other benefits include reinforcementwith crumb rubber, increase in thermal conductivity, inhibition of whisker formation/growth, no need to use adhesives, and recycling of discarded stencils.

Field of study: Materials science
On linear combinations of independent exponential variables

The exact distribution of a linear combination of n indepedent negative exponential random variables , when the coefficients cf the linear combination are distinct and positive , is well-known. Recently Ali and Obaidullah (1982) extended this result by taking the coeff icients to be arbitrary real numbers. They used a lengthy geometric. al approach to arrive at the result . This article gives a simple derivation of the result with the help of a generalized partial fraction technique. This technique also works when the variables involved are gamma variables with certain types of parameters. Results are presented in a form which can easily be programmed for computational purposes. Connection of this problem t o various problems in different fields is also pointed out.

Field of study: Mathematics
A novel direct screening method for alkyl glucoside production by glucosidases expressed in E. coli in 96-well plates.

The present work describes the development of a novel direct screening method, assayed in 96-well format, for evaluation of enzymatic alkyl glycoside production in a hexanol-water two-phase system. Alkyl glycosides are surfactants with a range of applications and with good biodegradability and low toxicity. Enzymatic synthesis makes it possible to prepare beta-d-glucopyranosides with high purity. In the developed screening assay, hexyl-beta-d-glucopyranoside was chosen as a model product to be synthesised by reversed hydrolysis in a water-hexanol two-phase system. In a first step the model product is produced by glucosidases expressed in E. coli cells in 96-deep-well plates. After phase separation, the hexyl-beta-d-glucopyranoside in the organic phase is degraded enzymatically and the released glucose detected spectrophotometrically at 405nm utilizing peroxidase/glucose oxidase, and the reagent 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS). The aqueous phase is used to monitor hydrolysis of p-NPG at 405nm, allowing use of a ratio of the two assays to compensate for expression differences. The complete method was used for comparison of two different beta-glucosidases, classified under glycoside hydrolase family 1 and 3, respectively, showing a significant difference in their ability to synthesise hexyl-beta-d-glucopyranoside by reversed hydrolysis.

Field of study: Biology, Engineering
Bioactive cubitane diterpenoids from a Colombian gorgonian species of the genus Eunicea

Two new diterpenes having the rare cubitane skeleton were isolated from a southwestern Caribbean gorgonian coral of the genus Eunicea. The structures of the new metabolites, as well as those of three known cubitanes were elucidated by extensive spectroscopic analysis. One compound showed significant in vitro cytotoxic activity against a National Cancer Institute (NCI) panel of cancer cell lines, whereas the remaining metabolites were shown to exert mild antitubercular and antimalarial activities against the pathogenic microbes Mycobacterium tuberculosis and Plasmodium falciparum.

Field of study: Chemistry
Assessing the Influence of Social Networking Material on Adolescents' Sexual Behavior in Kampala.

Social media has been used to promote risky sexual behavior in form of unsolicited photos, videos and text from peers and strangers that is not regulated by parents or guardians. Therefore, it’s important to investigate the influence of social networking material on adolescents‘ sexual behavior in Ugandan in order to close the knowledge gap. Adolescents in Uganda may be at risk of indulging in risky sexual behavior if usage of social networking sites remains unrestricted.  A cross sectional study was conducted among 280 randomly selected adolescents in Kampala between August and October 2016.  Majority (68.9%) of the respondents thought that messages, photos, videos with sexual content shared/posted on social networking sites, changed their sexual behavior. Variables that were found to significantly explain the effect of exposure of social network  content on adolescent sexual behavior, among adolescents included: Gender (male) (OR 2.646, 95% CI 1.088-6.434, use of social networking sites during holidays (OR 2.581, 95% CI .836-7.965) and social sites being used for leisure activities (OR 4.516, 95% CI 1.232-16.548).  Parents may need to restrict access and use sexual content especially pictures and videos available on social networking site among the adolescents.  Adolescent, social networking sites, change, sexual behavior

Field of study: Education
Persistent escalation of alcohol drinking in C57BL/6J mice with intermittent access to 20% ethanol.

Intermittent access (IA) to drugs of abuse, as opposed to continuous access, is hypothesized to induce a kindling-type transition from moderate to escalated use, leading to dependence. Intermittent 24-hour cycles of ethanol access and deprivation can generate high levels of voluntary ethanol drinking in rats.



The current study uses C57BL/6J mice (B6) in an IA to 20% ethanol protocol to escalate ethanol drinking levels. Adult male and female B6 mice were given IA to 20% ethanol on alternating days of the week with water available ad libitum. Ethanol consumption during the initial 2 hours of access was compared with a short-term, limited access "binge" drinking procedure, similar to drinking-in-the-dark (DID). B6 mice were also assessed for ethanol dependence with handling-induced convulsion, a reliable measure of withdrawal severity.



After 3 weeks, male mice given IA to ethanol achieved high stable levels of ethanol drinking in excess of 20 g/kg/24 h, reaching above 100 mg/dl blood ethanol concentrations, and showed a significantly higher ethanol preference than mice given continuous access to ethanol. Also, mice given IA drank about twice as much as DID mice in the initial 2-hour access period. B6 mice that underwent the IA protocol for longer periods of time displayed more severe signs of alcohol withdrawal. Additionally, female B6 mice were given IA to ethanol and drank significantly more than males (ca. 30 g/kg/24 h).



The IA method in B6 mice is advantageous because it induces escalated, voluntary, and preferential per os ethanol intake, behavior that may mimic a cardinal feature of human alcohol dependence, though the exact nature and site of ethanol acting in the brain and blood as a result of IA has yet to be determined.

Field of study: Medicine
Multiscale analysis and computation for coupled conduction, convection and radiation heat transfer problem in porous materials

This paper discusses the multiscale analysis and numerical algorithms for coupled conduction, convection and radiation heat transfer problem in periodic porous materials. First, the multiscale asymptotic expansion of the solution for the coupled problem is presented, and high-order correctors are constructed. Then, error estimates and their proofs will be given on some regularity hypothesis. Finally, the corresponding finite element algorithms based on multiscale method are introduced and some numerical results are given in detail. The numerical tests demonstrate that the developed method is feasible and valid for predicting the heat transfer performance of periodic porous materials, and support the approximate convergence results proposed in this paper.

Field of study: Mathematics