nils-herrmann/clean_scirepeval huggingface dataset:
Folding of influenza virus hemagglutinin in insect cells is fast and efficient.

Folding of influenza virus hemagglutinin (HA) in the endoplasmic reticulum has been well defined in mammalian cells. In different mammalian cell lines the protein follows the same folding pathway with identical folding intermediates, but folds with very different kinetics. To examine the effect of cellular context on HA folding and to test to which extent insect cells would support the HA folding process, we expressed HA in Sf9 insect cells. Strikingly, in this invertebrate system HA folded faster and more efficiently, still via the same folding intermediates as in vertebrate cells. Our results suggest that insect cells provide a highly efficient and effective folding environment for influenza virus HA and the ideal production platform for HA (emergency) vaccines.

Field of study: Biology, Engineering
An incremental pressure correction finite element method for the time-dependent Oldroyd flows

In this paper, we present an incremental pressure correction finite element method for the time-dependent Oldroyd flows. This method is a fully discrete projection method. As we all know, most projection methods have been studied without space discretization. Then the ensuing analysis may not extend to this case. We also give the stability analysis and the optimal error analysis. The analysis is based on a time discrete error and a spatial discrete error. In order to show the effectiveness of the method, we also present some numerical results. The numerical results confirm our analysis and show clearly the stability and optimal convergence of the incremental pressure correction finite element method for the time-dependent Oldroyd flows.

Field of study: Mathematics
Deglacial CO2 buildup: Constraints on the coral-reef model

The coral-reef hypothesis of degalcial CO2 buildup in the atmosphere can account for about one-half of the signal seen in ice cores, assuming additional coral-reef growth releases 2 atmospheric carbon masses (ACM). The carbonate dissolution signal on the deep sea floor suggest titration of only 1 ACM. At least 4 ACM of CO2 must be made available to satisfy the requirements of pCO2-increases, growth of biosphere and of sedimentary carbon pool, carbonate dissolution on the sea floor, and saturation of newly introduced meltwater. A drop in ocean fertility is called for to provide the missing CO2. Such a drop is evident in deep-sea cores from the western equatorial Pacific. CO2 buildup appears to occur as a step, near 13,500 years B.P. Dissolution on the deep sea floor begins near 11,000 years B.P. The difference of 2500 years may describe a mixing lag due to meltwater input (the “Worthington Effect”).

Field of study: Environmental science, Geography
Synthesis of Zirconium Phosphonate Supported L‐Proline as an Effective Organocatalyst for Direct Asymmetric Aldol Addition

Stable L-proline-functionalized zirconium methyl- and/or phenylphosphonates have been prepared as amorphous solids by the precipitation of (4R)-4-[(4′-phosphonobenzyl)oxy]-L-proline and methyl- and/or phenylphosphonic acid with ZrOCl2. The supported L-proline catalysts were tested in the direct asymmetric aldol addition between several ketones and p-substituted benzaldehydes. High yields, diastereoselectivities (anti/syn up to 92:8) and enantiomeric excesses (up to 99 % ee) have been achieved. Moreover, an easy protocol for the efficient recovery of the catalytic system by simple centrifugation has been defined, and the effective reuse of the catalyst has been reported in the representative aldol addition of cyclohexanone with p-nitrobenzaldehyde. This study has shown that these L-proline immobilized catalytic systems can be used at least six times without loss of activity and with reproducible anti/syn and ee values.

Field of study: Chemistry
The New Method to Analysis the Influence of Trapped Pressure on Casing Stress in Multi-stage Fracturing of Shale Gas

Currently, most of the shale gas development in China's Sichuan region adopts the large-displacement staged fracturing technology. Some of the shale gas wells undergo casing deformation during stimulation of the reservoir, where the trapped pressure of cementing section has a non-negligible effect on the casing stress in the multi-stage fracturing process. To this end, this paper constructs a finite element model of casing-cement sheath-formation assemblage under shale anisotropy based on the step-by-step finite element method by taking into account the whole construction process of drilling, completion and fracturing, in order to analyze the effect of trapped pressure on the casing stress under varying missing degrees, temperature field variations and cement sheath-formation property variations of cementing section in the multi-stage fracturing process. The results show that: 1) the larger the temperature drop in the wellbore during fracturing, the greater the effect of trapped pressure on casing stress during instantaneous pumping termination. 2) The smaller the missing degree of cementing section, the greater the effect of trapped pressure on casing stress under variations of cement sheath and formation. Therefore, optimization of cementing quality and reasonable optimization of relevant fracturing operation parameters are necessary in the future shale gas fracturing stimulation, so as to ensure the normal proceeding of subsequent well completion works.

Field of study: Engineering
Ichnology of fair-weather and storm deposits in an Upper Cretaceous estuary (Eutaw Formation, western Georgia, USA)

Exposures of the Eutaw Formation in western Georgia, eastern Gulf coastal plain, USA, were examined to evaluate the ichnologic signature of fair-weather and storm-related strata deposited within the central bay of a Late Cretaceous estuary. Ichnofabrics of fair-weather sandy muds and muddy sands compare favorably with those of previously well-documented estuarine facies of the Cretaceous Western Interior foreland basin. Trace fossil assemblages vary with sediment texture, reflecting proximity to sources and frequency of deposition of sands, but they generally are dominated by simple structures attributed to activities of trophic generalists (Terebellina, Teichichnus, and Planolites). Although this likely reflects environmental stress associated with estuarine dynamics, the degree to which salinity fluctuations governed trace fossil assemblages cannot be confidently assessed. Trace fossil assemblages in estuarine storm sands also are variable. Distal central bay tempestites include fair-weather ichnofossil suites. However, commonly in proximal parts of the central bay, rapid event-related accumulation of suspended clays immediately followed sand emplacement and thereby precluded burrowing of sands by subsequently established fair-weather organisms. By virtue of proximity to fluvial point sources and/or salinity gradients, this phenomenon may be unique to and diagnostic of certain estuarine settings. Ophiomorpha is nearly ubiquitous in storm sands. Normally attributed to post-storm colonization by opportunistic organisms, these burrow systems instead may represent the work of storm-transported crustaceans.

Field of study: Environmental science, Geography
Serendipity in Physics Research

This paper relates several serendipitous discoveries in physics in the 19th and 20th centuries. They are all experimental in nature and the places range from reputable universities to modern research laboratories. The discoverers could be working in solo or in group. The subject discovered ranges from the finest nucleus to the limitless cosmos.  Bob Berman in his book Strange Universe related a classic case of serendipity in science which culminated in the award of Nobel Prize to the discoverers. Page 164 of the book says that in 1965 Robert Wilson and Arno Penzias while using a Bell Laboratories radio telescope to survey the sky's radio background in preparation for planned communications satellites, found omnipresent noise they could not explain. At first they assumed it was caused by heat from droppings left behind by the many pigeons roosting in the metallic horn-shaped antenna, but repeated cleanings didn't clear out the static. The noise was the signal of cosmic background radiation, residue of the birth of the universe through the Big Bang. The author opined that who would have imagined that the birth of the universe would have been discovered in New Jersey? Ivan Kaminow, a colleague of Wilson and Penzias later remarked to a reporter, "They looked for dung and found gold, which is just the opposite of the experience of most of us." Serendipity or fortuitous finds in research is rather common. Someone likened it to looking for the rake in a stack of hay and instead finding the farmer's daughter in there. Other Cases of Serendipity In 1927, Clinton Davisson and Lester Germer again from the Bell Telephone Laboratories, were studying the surface of a piece of nickel by directing a beam of electrons at it and observing how many electrons bounced off at various angles . During the experiment, an accident occurred that permitted air to enter the vacuum chamber resulting in the oxidation of the metal surface. In order to remove the oxidized film, Davisson and Germer heated up the specimen in a high-temperature oven, almost hot enough to melt it. They were oblivious of the fact that the heating had the effect of annealing the specimen making it a large piece of single crystal. The crystal planes thus formed make diffraction of electron beam possible. Thus by an accident in the laboratory, the duo had discovered electron diffraction and they were awarded the coveted Nobel later on. The discovery of X-rays or Rontgent rays in 1895 was also considered as serendipitous in nature. The discoverer Wilhelm Rontgent was awarded the first Nobel Prize in physics in 1901. He didn't know much of the nature of the rays, hence he conveniently dubbed it 'X-rays'. But in Germany it is still called Rontgent rays in honour of the discoverer. …

Field of study: Education
[A systematic review of using myorelaxants in treatment of low back pain].

A systematic review summarizes the results of studies on the efficacy of myorelaxants (tolperisone, tizanidine, thiocolchicoside or baclofen) in the treatment of acute nonspecific low back pain published up to Dec. 2017. The authors conclude that there are enough data to confirm the efficacy of myorelaxants in treatment of nonspecific low back pain, myorelaxants are recommended as monotherapy or in combination with analgesics or NSAID, the nonsedative drugs tolperisone or thiocolchicoside should be preferred.

Field of study: Medicine, Psychology
Method for State Recognition of Egg Embryo in Vaccines Production Based on Support Vector Machine

The method for state recognition of egg embryo in biological vaccines production based on computer image processing and support vector machine was researched. Firstly, the median filtering method was applied to eliminate noises in the images of egg embryo that were classified by the requirements of practical production, then the threshold segmentation method was used to segment the images, then the blood vessels and black blocks in the egg embryo images were selected as major characteristics to extract. The decision tree classification model with structure of binary tree was built on support vector machine, and the model was trained with the toolkit LIBSVM, the penalty factor C=2, RBF kernel parameter =3.0512e-05 and the precision of cross validation accuracy is 98.913%. Finally, 100 egg embryos were randomly selected as the test samples to do pattern recognition, and compared with manual test result.

Field of study: Engineering
Protocol Specification, Testing and Verification - Guest Editorial

Carl Sunshine is with the University of Southern California Information Sciences Institute where he is engaged in research on computer networks and their protocols. He is particularly interested in protocol design, modeling, and analysis, and network interconnection. Dr. Sunshine received a PhD in computer science in 1975 from Stanford University where he worked on the first major network interconnection projects within the ARPA and IFIP communities. From 1975 to 1979 he worked at the Rand Corporation on various protocol design and network planning projects. Dr. Sunshine is active in 1FIP, ISO, and ANSI network groups and is Vice Chairman of the AC M Special Interest Group on Data Communication. He serves on the editorial board of Computer Networks journal, and is Associate Editor for Protocols of the IEEE Transactions on Communications. He has lectured and published widely.

Field of study: Computer science
Exact expressions for the energy current and stress tensor operators in many-particle systems

For some purposes in statistical physics, such as, for example, the calculation of various transport coefficients, it is necessary to have expressions for the energy current operatorS and stress tensor operatorTlm. In this work it is shown that by using a simple identity, exact expressions forS andTlm which satisfy the conservation laws for the energy densityɛ and momentum densityP, respectively, exist.S andTlm can each be written as a sum of two parts,S=S(A)+S(B)Tlm=Tlm(A)+Tlm(B). The “A” part is the ordinary convective or kinetic part while the “B” part is shown to be expressible as a gradient and hence its homogeneous component vanishes identically. The expressions are compared with approximate forms found in the literature. The operators are Fourier analyzed and written in terms of the field operators in the second quantization formalism.

Field of study: Physics
Effects of CD134 monoclonal antibody on hemolysis activities and expression of perforin in peripheral blood mononuclear cells of systemic lupus erythematosus patients.

Perforin had been demonstrated to play important roles in the pathology of systemic lupus erythematosus (SLE), which was a potential target of clinical treatment of SLE. CD134 was a member of the tumor necrosis factor receptor family, which had been demonstrated to inhibit expression of perforin mRNA. The aim of the present study was to determine the effects of CD134 monoclonal antibody (MAb) on expression and hemolysis activities of perforin and its mechanisms. Effects of CD134 MAb on hemolysis activities of perforin were measured by rabbit red blood cells. Effects of CD134 MAb on expression of perforin in peripheral blood mononuclear cells (PBMCs) were determined by reverse transcription-polymerase chain reaction (RT-PCR) method and flow cytometry. Then, expression of NF-kappaB P65 was detected by Western blot. The results showed that CD134 MAb could inhibit hemolysis activities and expression of perforin through decreasing expression of NF-kappaB P65. The inhibition effects were positively correlated to the SLE disease activity index (SLEDAI) and 24-hour protein-uria of SLE patients in active state. CD134 MAb is suggested to be a potential treatment for SLE patients.

Field of study: Biology
Changes in growing season duration and productivity of northern vegetation inferred from long-term remote sensing data

Monitoring and understanding climate-induced changes in the boreal and arctic vegetation is critical to aid in prognosticating their future.We used a 33 year (1982–2014) long record of satellite observations to robustly assess changes inmetrics of growing season (onset: SOS, end: EOS and length: LOS) and seasonal total gross primary productivity. Particular attentionwas paid to evaluating the accuracy of thesemetrics by comparing them tomultiple independent direct and indirect growing season and productivitymeasures. These comparisons reveal that the derivedmetrics capture the spatio-temporal variations and trendswith acceptable significance level (generally p<0.05).We find that LOS has lengthened by 2.60 d dec (p<0.05) due to an earlier onset of SOS (−1.61 d dec, p<0.05) and a delayed EOS (0.67 d dec, p<0.1) at the circumpolar scale over the past three decades. Relatively greater rates of changes in growing seasonwere observed in Eurasia (EA) and in boreal regions than inNorthAmerica (NA) and the arctic regions. However, this tendency of earlier SOS and delayed EOSwas prominent only during the earlier part of the data record (1982–1999). During the later part (2000–2014), this tendencywas reversed, i.e. delayed SOS and earlier EOS. As for seasonal total productivity, wefind that 42.0%of northern vegetation shows a statistically significant (p<0.1) greening trend over the last three decades. This greening translates to a 20.9%gain in productivity since 1982. In contrast, only 2.5%of northern vegetation shows browning, or a 1.2% loss of productivity. These trends in productivity were continuous through the period of record, unlike changes in growing seasonmetrics. Similarly, wefind relatively greater increasing rates of productivity in EA and in arctic regions than inNA and the boreal regions. These results highlight spatially and temporally varying vegetation dynamics and are reflective of biome-specific responses of northern vegetation during last three decades.

Field of study: Environmental science
The Impact of Induced Affect on the Perception of Variability in Social Groups

Two studies examined the effects of mood on perceptions of intragroup variability. Following exposure to positive, neutral, or negative mood-inducing stimuli, subjects read information about behaviors performed by members of a group. The group was either high or low in intragroup behavioral variability. In contrast to those in a neutral mood, subjects in a positive or negative mood did not produce differential variability judgments for the two groups. Experiment 2 replicated this finding and indicated that happy, but not sad, subjects showed other indexes of reduced processing. Possible cognitive and motivational mechanisms underlying reduced perception of intragroup variability are discussed.

Field of study: Psychology
Patients with acute respiratory distress syndrome exhibit increased stromelysin1 activity in the blood samples.

Enzyme activity analyses in the blood are expected to be reliable, non-invasive diagnostic as well as prognostic markers to reflect disease progression in acute lung injury (ALI). The objective of the current study was to evaluate the enzymatic activity of stromelysin1 (matrix metalloprotease-3) in the plasma/serum samples collected from ALI patients compared to the samples collected from healthy controls. Gene expression omnibus (GEO) database analysis indicated a correlation between increased stromelysin1 gene expression and the incidence of ALI in various animal models. Our analysis of patient plasma/serum samples from healthy controls and ALI patients revealed a significant, 3-fold increase in stromelysin1 activity in ALI plasma/serum compared to healthy subjects with no difference in stromelysin1 activity between the serum and plasma samples. Interestingly, no significant difference in stromelysin1 activity between non-smoking and smoking subjects was observed. These findings provide fundamental information on the potential reliability of stromelysin1 activity analysis, combined with other biomarkers in development, in blood samples for the early detection of ALI.

Field of study: Medicine
Hunting for low-surface brightness features in nearby galaxy groups

On the scale of dwarf galaxies, several tensions between observations and the theory of structure formation have been identified in the Local Group of galaxies. One of them, the plane-of-satellite problem describes the distribution and motion of dwarf galaxies around their hosts being planar and co-moving. To extend these studies, we have surveyed the nearby Centaurus group and found again evidence for co-rotation within a planar structure of dwarf galaxies, posing a challenge to the current LambdaCDM paradigm. To further study the distribution of satellite systems around other galaxy groups, we have tested MTO - a program to detect astronomical sources - and found that it works well in combination with surface brightness fluctuation distance measurements to get a complete sample of dwarf galaxies. Such an approach will improve the census of dwarf galaxies in nearby galaxy groups, bringing the study of the small-scale problems to a solid statistical foundation.

Field of study: Physics
Linc00518 Contributes to Multidrug Resistance Through Regulating the MiR-199a/MRP1 Axis in Breast Cancer

Long non-coding RNAs (LncRNAs) have been validated to be pivotal mediators in multidrug resistance (MDR) of various cancers. This study aims to explore the roles and molecular mechanisms of linc00518 implicated in chemoresistance in breast cancer.  Expressions of linc00518, miR-199a and MRP1 were evaluated by RT-qPCR or western blot. IC50 values of adriamycin (ADR), vincristine (VCR) and paclitaxel (PTX) were determined by XTT assays and cell apoptosis was assessed by flow cytometry. Luciferase reporter and RIP assays were employed to detect the interaction of linc00518, miR-199a and MRP-1.  linc00518 expression increased nearly 2 fold and MRP1 level elevated about 2.5 fold in breast cancer tissues as compared to that in adjacent normal tissues. Also, almost 2 fold upregulation of linc00518 and MRP-1 expressions was observed in MCF-7 cells than in MCF-10A cells. Additionally, linc00518 level was almost 2.5 fold higher and MRP1 level was about 2 fold increased in ADR-resistant MCF-7 cells (MCF-7/ADR) than in parental cell line MCF-7. Linc00518 knockdown enhanced chemosensitivity to ADR, VCR and PTX, and boosted ADR-, VCR- and PTX-induced apoptosis in MCF-7/ADR cells. miR-199a inhibitor conferred chemoresistance to ADR, VCR and PTX in MCF-7/ADR cells, and suppressing miR-199a reversed multi-drug susceptibility induced by linc00518 knockdown. Furthermore, linc00518 could act as a molecular sponge of miR-199a to repress MRP1 expression. MRP1 depletion increased the sensitivity of MCF-7/ADR cells to ADR, VCR and PTX, and this effect was attenuated following miR-199a inhibition or linc00518 overexpression. Also, linc00518 silencing increased ADR-mediated anti-tumor effect in vivo.  linc00518 downregulation reduced MDR by regulating miR-199a/MRP1 axis in breast cancer.

Field of study: Biology, Chemistry
Abscisic acid activates ATPase in developing apple fruit especially in fruit phloem cells

Abscisic acid (ABA) improves the sink strength by promoting the phloem unloading and regulating the assimilate metabolism in the economic sink organs of crops, although its mechanism remains unknown. The present experiment, using the techniques of the in vivo injection of ABA into the intact apple fruit attached to a growing apple tree and the in vivo incubation of the fruit tissue in the ABA-contained medium, showed that ABA strongly activated the fruit ATPase especially P-ATPase, of which the activity was doubled by ABA treatment. This ATPase activation was shown to be in vivo tissue-dependent. The ABA-induced P-ATPase activation was fruit developmental stage-, ABA dose-, medium pH- and incubation time-dependent. Physiological active (+)ABA was shown more effective to stimulate P-ATPase activity than (+/–)ABA, and two ABA analogues (–)ABA and trans-ABA, had no effect on P-ATPase activation, indicating that only physiologically active cis(+)ABA can induce the enzyme activation, and so the ABA-induced effects are stereospecific. The protein synthesis inhibitor cycloheximide was shown to have no effect on P-ATPase activation by ABA, suggesting that synthesis of new proteins was not involved in the enzyme activation. The cytochemical assay revealed that P-ATPase was activated by ABA in both the phloem and its surrounding flesh parenchyma cells, and that the most strongly P-ATPase activation was observed in the plasma membrane of sieve element/companion cell complex. These data suggest that the improvement of phloem unloading by ABA previously reported in this fruit as in other crop sink organs may be attributed, at least partly, to the ABA-induced ATPase activation especially in phloem cells.

Field of study: Environmental science