nils-herrmann/clean_scirepeval huggingface dataset:
Oocyte Cytoplasmic Gas6 and Heparan Sulfate (HS) are Required to Establish the Open Chromatin State in Nuclei During Remodeling and Reprogramming

Previously, we found that silencing of growth arrest-specific gene 6 (Gas6) in oocytes impaired cytoplasmic maturation, resulting in failure of sperm chromatin decondensation (SCD) and pronuclear (PN) formation after fertilization. Thus, we conducted this study to determine the effect of Gas6 RNAi on downstream genes and to elucidate the working mechanism of Gas6 on oocyte cytoplasmic maturation and SCD.  Using RT-PCR, Western blot and immunofluorescence, the expression levels of various target genes and the localization of heparan sulfate (HS) were analyzed after Gas6 RNAi. The roles of Gas6 in HS biosynthesis, production of ATP and GSH, ROS generation and ΔΨm were also investigated. SCD and micrococcal nuclease (MNase) analyses were used to examine the effects of HS on the open chromatin state in sperm and somatic cell nuclei, respectively.  Disruption of Gas6 expression led to the inhibition of HS biosynthesis through the reduction of several HS biosynthetic enzymes. The rescue experiment, HS treatment in vitro, significantly recovered SCD and PN formation, confirming that HS had the ability to induce sperm head remodeling during fertilization. Interestingly, excessive mitochondrial activation in Gas6-depleted MII oocytes caused ROS generation and glutathione (GSH) degradation via mitochondrial activation, such as elevated ΔΨm and ATP production. Indeed, HS-treated NIH3T3 cell nuclei showed an open chromatin state, as determined by diffuse DAPI staining and increased sensitivity to MNase.  We propose that the addition of HS to sperm and/or oocyte maturation would improve the efficiency of in vitro fertilization and somatic cell nuclear transfer (SCNT) reprogramming.

Field of study: Biology, Chemistry
M-ideals of homogeneous polynomials

We study the problem of whether $\mathcal{P}_w(^nE)$, the space of $n$-homogeneous polynomials which are weakly continuous on bounded sets, is an $M$-ideal in the space of continuous $n$-homogeneous polynomials $\mathcal{P}(^nE)$. We obtain conditions that assure this fact and present some examples. We prove that if $\mathcal{P}_w(^nE)$ is an $M$-ideal in $\mathcal{P}(^nE)$, then $\mathcal{P}_w(^nE)$ coincides with $\mathcal{P}_{w0}(^nE)$ ($n$-homogeneous polynomials that are weakly continuous on bounded sets at 0). We introduce a polynomial version of property $(M)$ and derive that if $\mathcal{P}_w(^nE)=\mathcal{P}_{w0}(^nE)$ and $\mathcal{K}(E)$ is an $M$-ideal in $\mathcal{L}(E)$, then $\mathcal{P}_w(^nE)$ is an $M$-ideal in $\mathcal{P}(^nE)$. We also show that if $\mathcal{P}_w(^nE)$ is an $M$-ideal in $\mathcal{P}(^nE)$, then the set of $n$-homogeneous polynomials whose Aron-Berner extension do not attain the norm is nowhere dense in $\mathcal{P}(^nE)$. Finally, we face an analogous $M$-ideal problem for block diagonal polynomials.

Field of study: Mathematics
A theory of sticky rents: Search and bargaining with incomplete information

The housing rental market offers a unique laboratory for studying price stickiness. This paper is motivated by two facts: 1. Tenants’ rents are remarkably sticky even though regular and expected recontracting would, by itself, suggest substantial rent flexibility. 2. Rent stickiness varies significantly across structure type; for example, detached unit rents are far stickier than large apartment unit rents. We offer the first theoretical explanation of rent stickiness that is consistent with these facts. In this theory, search and bargaining with incomplete information generates stickiness in the absence of menu costs or other commonly used modeling assumptions. Tenants’ valuations of their units, and whether they are considering other units, are both private information. At lease end, the behavior of risk-averse landlords differs according to the number of units managed. Multi-unit landlords, aided by the law of large numbers, exploit tenant moving costs. When renegotiating rent contracts, they set rent increases that exceed the inflation rate; while the majority of tenants stay, those who place low value on the unit search elsewhere and leave. Landlords with one unit loathe vacancy and offer tenants the identical contract to pre-empt search; only those who really hate the unit leave.

Field of study: Economics
Diketone cleaving enzyme Dke1 production by Acinetobacter johnsonii--optimization of fermentation conditions.

The main objective of this work was the optimization of the production of the novel dioxygenase diketone cleaving enzyme (Dke1) from Acinetobacter johnsonii. Acetylacetone was used as an inducer for enzyme production. In the first step, the growth medium was optimized by using screening designs for finding the optimal carbon and nitrogen source. In the second step, a genetic algorithm was used to optimize the concentrations of all medium components. After six generations the stopping criterion was reached and a growth medium was obtained which produced sixteen times more enzyme than the starting medium. In the next step, an addition profile for the inducer acetylacetone was developed to further increase enzyme production by using a genetic algorithm. In this case, after four generations the stopping criterion was fulfilled. By using the obtained optimal addition profile Dke1 activity was enhanced from 826 to 2584Ul(-1). In comparison to the starting conditions activity could even be increased by a factor of 50.

Field of study: Biology, Engineering
Comments on "Timing Estimation and Resynchronization for Amplify-and-Forward Communication Systems"

This comment first shows that the Cramer-Rao lower bound (CRLB) derivations in the above paper are not exact. In addition, contrary to the claims in the above paper, the assumptions of perfect timing offset estimation and matched-filtering at the relays affect the generality of the analytical results and cannot be justified.

Field of study: Engineering
Seamless post-operative removal of JJ stents in the paediatric population: Securing the JJ stent to the tip of the urethral balloon catheter avoids a further operation.

In children, removal of a post-procedural JJ stent requires a further cystoscopy under general anaesthetic. We describe securing the distal end of the ureteric stent to the tip of a balloon catheter at the end of the primary procedure. Once post-operative oedema has subsided, the stent is removed seamlessly in tandem with the balloon catheter. This can be done on the ward by nursing staff without the need for general anaesthesia or sedation. Our experience in the first 10 successive patients (aged 1.6-16.3 years) demonstrates this technique to be safe, easy to learn and well tolerated.

Field of study: Medicine
Expansion of C4 grasses in the Late Miocene of Northern Pakistan: evidence from stable isotopes in paleosols

Stable-isotopic, clay-mineralogic, and bulk-chemical analyses were conducted on paleosols of the Neogene Siwalik sections in northern Pakistan in order to reconstruct floodplain environments over the past ∼ 17 Ma. The stable carbon isotopic composition of soil carbonate (mean δ13C (PDB) = -10.2%) and associated organic matter (mean δ13C (PDB) = −24.1%) in paleosols representing 17− ∼ 7.3 Ma reveal that floodplain vegetation was dominated by C3 plants. At 7.3 Ma, a shift toward more positive carbon isotopic values began, signaling the gradual expansion of C4 grasses onto the floodplain. From 6 Ma to present, carbon isotopic values for paleosol carbonate (mean δ13C (PDB) = +0.6%) and organic matter (mean δ13C (PDB) = −14.4%) are uniformly enriched in 13C, indicating the presence of nearly pure C4 grassland. 
 
The scarcity of kaolinite and abundance of smectite and pedogenic carbonate in most paleosols suggest that rainfall in the region remained 1.0–1.25 m/yr or less for the entire 17 Ma of record. Paleosols in the lower portion of the section lack organic A horizons but have reddish B horizons often containing secondary iron-oxide nodules. Leaching depths of soil carbonate in these older paleosols are typically greater than those in the Plio-Pleistocene part of the section, where organic A horizons are common, and B horizons are markedly more yellow. The combined evidence suggests that the mature paleosols in the pre-7.3 Ma part of the record are dominantly calcareous Alfisols or Mollisols that once underlay nearly pure C3 vegetation, perhaps trees and shrubs, while calcareous Mollisols underlying C4 grassland dominate the upper part of the record. 
 
The carbon- and oxygen-isotopic trends in the paleosol record in Pakistan are also evident in the diet of fossil mammals, and in paleosols from Nepal, thus demonstrating that these paleoenvironmental changes in floodplain vegetation may be continent-wide. Local effects, such as the development or intensification of the Asian Monsoon driven by uplift of the Tibetan Plateau, may have led to the expansion of C4 grasses. If, however, the expansion of C4 grasses proves globally synchronous, then a larger scale cause, such as a marked decrease in ϱCO2, may be the driving mechanism.

Field of study: Environmental science, Geography
Sialyltransferase activity as a marker for the differentiation of lymphocytes. Increase in sialyltransferase activity of blasts from acute lymphoblastic leukaemia cases by 12-o-tetradecanoylphorbol-13-acetate (TPA).

The level of sialyltransferase activity in leukaemic blasts from acute lymphoblastic leukaemia (ALL) cases was significantly lower (3.29 +/- 2.09 pmoles/5 X 10(7) cells or 1.77 +/- 1.16 pmoles/mg protein) than those (18.80 +/- 4.91 pmoles/5 X 10(7) cells or 7.72 +/- 1.75 pmoles/mg protein) of mature lymphocytes from normal volunteers (T less than 0.001). An inverse relationship between the level of sialyltransferase activity and the level of terminal transferase (TdT)activity was seen in blasts from eight TdT-positive ALL cases. No significant difference was observed in the level of sialyltransferase activity between ALL and cells of chronic myelogenous leukemia (CML) in blast crisis. Short Term culture of ALL blast cells with 12-0-tetradecanoylphorbol-13-acetate (TPA) at the concentration of 10-(6)M to 10-(9)M caused a marked increase in sialyltransferase activity. In one of these three ALL cases the population of TdT-positive cells and the TdT activity of the blasts decreased significantly after culture with TPA. These results suggest that biochemical differentiation of leukaemic lymphoblasts has been induced by the addition of TPA, although morphological changes were not observed. Sialyltransferase activity may be a useful indicator for the analysis of differentiation of lymphocytes.

Field of study: Biology, Medicine
A plant proton-pumping inorganic pyrophosphatase functionally complements the vacuolar ATPase transport activity and confers bafilomycin resistance in yeast.

V-ATPases (vacuolar H+-ATPases) are a specific class of multi-subunit pumps that play an essential role in the generation of proton gradients across eukaryotic endomembranes. Another simpler proton pump that co-localizes with the V-ATPase occurs in plants and many protists: the single-subunit H+-PPase [H+-translocating PPase (inorganic pyrophosphatase)]. Little is known about the relative contribution of these two proteins to the acidification of intracellular compartments. In the present study, we show that the expression of a chimaeric derivative of the Arabidopsis thaliana H+-PPase AVP1, which is preferentially targeted to internal membranes of yeast, alleviates the phenotypes associated with V-ATPase deficiency. Phenotypic complementation was achieved both with a yeast strain with its V-ATPase specifically inhibited by bafilomycin A1 and with a vma1-null mutant lacking a catalytic V-ATPase subunit. Cell staining with vital fluorescent dyes showed that AVP1 recovered vacuole acidification and normalized the endocytic pathway of the vma mutant. Biochemical and immunochemical studies further demonstrated that a significant fraction of heterologous H+-PPase is located at the vacuolar membrane. These results raise the question of the occurrence of distinct proton pumps in certain single-membrane organelles, such as plant vacuoles, by proving yeast V-ATPase activity dispensability and the capability of H+-PPase to generate, by itself, physiologically suitable internal pH gradients. Also, they suggest new ways of engineering macrolide drug tolerance and outline an experimental system for testing alternative roles for fungal and animal V-ATPases, other than the mere acidification of subcellular organelles.

Field of study: Biology, Computer science
β+ ratio andβ-delayedγ-decay of146Eu

The positron decay of146Eu was investigated, firstly to derive for the allowed transition to the 2046 keV state in146Sm the electron capture to positron decay ratio. The experimental valueEC/β+=43.7(42) is found to be in agreement within the respective error intervals with the ones calculated from the formalism of allowed decay using the recentQ-values of146Eu. Further on, theγ-decay properties of146Eu have been reinvestigated with emphasis on implied modifications of the hitherto accepted decay scheme: 42 new levels and 33 newγ-transitions were placed in the revised level scheme, 12 of the previously reported levels were deleted. The level distribution of146Sm is discussed within a statistical model. The indication for a non-statisticalβ-strength function is observed.

Field of study: Physics
Segregation as a Factor in the Racial Identification of Negro Pre-School Children

In conjunction with an investigation (1,2) of racial identification of Negro pre-school children as indicative of a phase in the de velopment of consciousness of self, some Negro children from mixed New York nurs ery schools were compared with the main group of Negro children from segregated Washington, D. C. nursery schools. It was believed that such a comparison would give an indication of the possible effects of segre gation as a factor affecting the problem investigated.

Field of study: Education
Women Graduate Students

When I started teaching solid‐state‐physics courses at MIT, nearly 20 years ago, there were very few women at MIT and very few women students in my classes. It was unusual for women students to ask questions in class or to participate in class discussions. As the number of women students increased, they participated more and more, and in very recent years their class participation has become essentially indistinguishable from that of the men. A turning point appeared to occur when the number of women reached a “critical mass” of about 10–15% of the students in a class. But in some other physics courses at MIT the critical mass hasn't been reached.

Field of study: Physics
Rheology of Highly Filled Polypropylenes Prepared with Surface Treated Fillers

Highly filled polypropylene (PP) composites have been produced by extrusion of polypropylenes with surface treated fillers. The aim is to include the highest proportion of filler that can provide hardness and high density, without undue brittleness. Modification of the filler surface provided significant enhancement of the processing properties that have been studied with parallel plate rheometry. The experimental results indicated that the viscoelastic behavior of melt flow of highly filled polypropylene composites significantly depended on the following properties of the fillers: aspect ratio, specific surface area and particle size in talc, calcium carbonate and barium sulfate filled polypropylene composites. Traditional surface modifiers such as stearic acid are useful, but titanates and in particular small amounts of silicones have provided the greatest rheological modification.

Field of study: Materials science
An extension of the Piatetski-Shapiro prime number theorem

Balog and Harman proved that for any λ in the interval 1/2 ≤ λ < 1 and any real θ there are infinitely many primes p satisfying (with an asymptotic result). In the present paper we prove that for 59/85 = 0-694... < λ < 1 the above exponent -(1-λ)/2+ε may be replaced by - min{max{(35-22λ)/129, 1/7}, 5/18-λ/6}+ε. This result in particular contains the Piatetski-Shapiro prime number theorem in the version given by Liu and Rivat: We have |{n ≤ N : [nc] prime}) ~ N/(c log N) as N → 8734 if 1 < c < 15/13. For the proof of our result we use exponential sum techniques.

Field of study: Philosophy
Tracking of group-housed pigs using multi-ellipsoid expectation maximisation

Maintaining the health and well-being of animals is critical to the efficiency and profitability of livestock operations. However, it can be difficult to monitor the health of animals in large group-housed settings without the assistance of technology. This study presents a system that uses depth images to continuously track individual pigs in a group-housed environment. It is an alternative to traditional manual observation used by both researchers and producers for the analysis of animal activities and behaviours. The tracking method used by the system exploits the consistent shape and fixed number of the targets in the environment by applying expectation maximisation as a policy for fitting an ellipsoid to each target. Results demonstrate that the system can maintain the correct positions and orientations of 15 group-housed pigs for an average of 19.7 min between failure events.

Field of study: Computer science
Changes in primary care provision in Turkey: A comparison of 1993 and 2012.

Since the early 1990s, the primary care system in Turkey has undergone fundamental changes. In the first decade of the millennium family doctor scheme was introduced to the Turkish primary care sector and the name of the primary care doctors (PCDs) changed from "general practitioner" (GP) to "family doctor" (FD). This study aims to give an insight into those changes and to compare the service profiles of PCDs in 1993 and 2012. Data, based on cross sectional surveys among Turkish doctors working in primary care are derived from the 1993 European GP Task Profile study (n=199) and the 2012 Quality and Costs of Primary Care in Europe (QUALICOPC) study (n=299). The study focuses on the changes in the primary care service provision based on selected aspects such as the first contact of care, preventive care, and the knowledge exchange and collaboration with other health professionals. Compared to GPs in 1993, FDs in 2012 reported that their involvement in treatment of chronic diseases, first contact care, antenatal and child health care have increased. FDs have more contact with other primary healthcare workers but their contact with hospital consultants have decreased. Overall, the services provided by PCDs seem to be expanded. However, the quality of care given by FDs and its effects on health indicators are needed to be explored by further studies.

Field of study: Medicine, Political science
Analysis of Minimum Quantity Lubrication (MQL) for Different Coating Tools during Turning of TC11 Titanium Alloy

The tool coating and cooling strategy are two key factors when machining difficult-to-cut materials such as titanium alloy. In this paper, diamond coating was deposited on a commercial carbide insert as an attempt to increase the machinability of TC11 alloy during the turning process. An uncoated carbide insert and a commercial Al2O3/TiAlN-coated tool were also tested as a comparison. Furthermore, MQL was applied to improve the cutting condition. Cutting performances were analyzed by cutting force, cutting temperate and surface roughness measurements. Tool wears and tool lives were evaluated to find a good matchup between the tool coating and cooling strategy. According to the results, using MQL can slightly reduce the cutting force. By applying MQL, cutting temperatures and tool wears were reduced by a great amount. Besides, MQL can affect the tool wear mechanism and tool failure modes. The tool life of an Al2O3/TiAlN-coated tool can be prolonged by 88.4% under the MQL condition. Diamond-coated tools can obtain a good surface finish when cutting parameters and lubrication strategies are properly chosen.

Field of study: Materials science
Minimum Variance Estimation Without Regularity Assumptions

Following the essential steps of the proof of the Cramer-Rao inequality [1,2] but avoiding the need to transform coordinates or to differentiate under integral signs, a lower bound for the variance of estimators is obtained which is (a) free from regularity assumptions and (b) at least equal to and in some cases greater than that given by the Cramer-Rao inequality. The inequality of this paper might also be obtained from Barankin’s general result . Only the simplest case—that of unbiased estimation of a single real parameter—is considered here but the same idea can be applied to more general problems of estimation.

Field of study: Mathematics
Iprrdiation Damage of MOS-FETS Operating in the Common Source Mode

Thirty-three MOS-FETS were operated at various bias points under 60Co gamma irradiation up to a total dose of approximately 107 R. The n-channel depletion, n-channel enhancement, and p-channel enhancement devices were operated at constant drain voltage in the common source mode. The results demonstrate effects of lateral oxide charge distributions along the channel between source and drain terminals. A tendency for the n-channel devices to gradually turn off is observed in addition to the threshold voltage shifts previously reported. A factor of ten improvement in radiation resistance can be obtained by using optimum device types (n-channel) at gate voltages which minimize threshold voltage shift (approximately zero volts).

Field of study: Physics
Size-frequency and population structure of brachiopods

The living terebratulids, Terabratulina unguicula, Terebratalia transversa, Laqueus vancouverensis, and the rhynchonelid Hemithiris psittacea were studied in the San Juan Islands, Washington, U.S.A. Those results and a review of a the literature lead to the conclusion that most brachiopod populations experience episodic recruitment at intervals which may be irregular. The occurrence of juveniles attached to adults, brooding, and bi- or multimodal size-frequency distributions demonstrate that, contrary to a previously suggested hypothesis, adult brachiopods do not generally exclude juveniles from the same area. The commony observed rarity of small individuals is regarded as a product of local recruitment failure due to patchy distribution of larvae; it does not justify the assumption that brachiopods are unaffected by high post-larval juvenile mortality. However, the frequent rarity of small individuals confirms that this cannot be used as a criterion of transport in assemblages of fossil brachiopods.

Field of study: Environmental science, Geography
Solvent-free enzymatic transesterification of ethyl ferulate and monostearin: optimized by response surface methodology.

In this study, enzymatic transesterification of ethyl ferulate (EF) and monostearin for feruloylated lipids production was investigated. Enzyme screening and the effect of feruloyl acceptors on the transesterification were also studied. Effects of reaction variables (reaction temperatures, enzyme load, and reaction time) on the transesterification were optimized using response surface methodology (RSM). The optimum conditions were as follows: reaction temperature 74°C, reaction time 23h, and enzyme load 20% (w/w, relative to the weight of substrates). Under these conditions, EF conversion was 98.3±1.1%, and the transesterification product was consisted of 19.2±2.1% glyceryl ferulate (FG), 32.9±1.9% diferuloylated glycerols (DFG), 36.6±2.2% feruloylated monoacylglycerols (FMAG), 9.1±2.0% feruloylated diacylglycerols (FDAG), and 0.5% ferulic acid (FA). Analysis of variance (ANOVA) showed that the regression equation was adequate for predicting EF conversion. The activation energies for hydrolysis to form FG+DFG and transesterification to form FMAG+FDAG were calculated as 22.45 and 51.05kJ/mol, respectively, based on Arrhenius law.

Field of study: Biology, Engineering