nils-herrmann/clean_scirepeval huggingface dataset:
HOX Antisense lincRNA HOXA-AS2 Promotes Tumorigenesis of Hepatocellular Carcinoma

Recent studies reveal that long non-coding RNAs (LncRNAs) play critical roles in the proliferation and migration of human cancer. Previous report has shown that LncRNA HOXA-AS2 was involved in carcinoma processes. However, the expression and biological function of HOXA-AS2 in hepatocellular carcinoma (HCC) are poorly understood.  Quantitative real-time PCR (qRT-PCR) was performed to detect the expression of HOXA-AS2 in HCC tissues and cell lines. The relation between lncRNA HOXA-AS2 expression and clinicopathological characteristics was assessed by chi-square test. The prognosis was analyzed using Kaplan-Meier method, and compared differences between the two groups by log-rank test. The biological function of HOXA-AS2 on HCC cells were determined both in vitro and in vivo.  In the present study, we found that HOXA-AS2 expression was increased in HCC tissues and adjacent normal tissues and high HOXA-AS2 expression was associated with bigger tumor size, advanced tumor stage, and shorter survival time. Knockdown of HOXA-AS2 significantly inhibited HCC cell proliferation and invasion and resulted in an increase of apoptosis. Furthermore, inhibition of HOXA-AS2 in HCC cells significantly repressed tumorigenicity in nude mice.  Our results indicated that the inhibition of HOXA-AS2 in HCC cells significantly inhibited cell proliferation in vitro and in vivo, which might provide a potential possibility for targeted therapy of HCC.

Field of study: Biology, Chemistry
Efficient modeling and optimizing of checkpointing in concurrent component-based software systems

A common mechanism to improve availability and performance is checkpointing and rollback. When it is time to checkpoint, a system stores a job’s state to nonvolatile memory, and, when a failure occurs, it rolls back to the latest stored state instead of restarting the job from the beginning, thus improving performance in the presence of failures. Too frequent checkpointing reduces the amount of work to be redone in case of failures but generates excessive overhead, degrading performance. This paper presents a novel and very efficient queuing network model that addresses software component contention for hardware resources and shows how it can be used to model checkpointing in heterogeneous component-based software systems. We validated this model against a previous model, developed by the authors, that used Markov Chains. Our new model is orders of magnitude faster than the previous one and can be used to plan for checkpointing at run-time. As an additional contribution of this paper, we present an optimizer to find, for each software component, the optimal checkpointing interval that minimizes execution time, maximizes availability, or minimizes checkpointing overhead.

Field of study: Computer science, Engineering
Complement activation in postpartum thyroiditis.

Postpartum thyroid dysfunction (PPTD) develops in 50% of pregnant women who have raised levels of circulating thyroid peroxidase autoantibodies (TPOAb) at booking. Although these antibodies are able to activate the complement cascade in vitro, it is not known whether complement activation plays any role in the pathogenesis of this disease.



To investigate potential and actual activation of the complement system in women with postpartum thyroiditis.



Complement activation was monitored on a weekly basis in 24 postpartum women who had raised TPOAb at 16 weeks gestation, attending an antenatal clinic in Mid-Glamorgan, Wales.



ELISA procedures were used to measure both in-vitro complement C3 activation by TPOAb and circulating terminal complement complexes (TCC) in serum.



Higher levels of bioactive TPOAb activity were seen in women who developed PPTD when compared to those who did not. However, TCC remained undetectable in serum throughout the period of study.



In PPTD, despite the presence of circulating bioactive TPOAbs, the extent of complement activation is inadequate to cause detectable increases in peripheral blood TCC, suggesting that the complement system may not play a major role in PPTD pathogenesis.

Field of study: Medicine
Precipitable water characteristics during the 2013 Colorado flood using ground-based GPS measurements

During 9 th –16 th September 2013, the Front Range region of Colorado experienced heavy rainfall that resulted in severe flooding. Precipitation totals for the event exceeded 450 mm, damages to public and private properties were estimated to be over $ 2 billion, and nine lives were lost. This study analyzes the characteristics of precipitable water (PW) surrounding the event using 10 years of high-resolution GPS PW data in Boulder, Colorado, which was located within the region of maximum rainfall. PW in Boulder is dominated by seasonal variability with an average summertime maximum of 36 mm. In 2013, the seasonal PW maximum extended into early September and the September monthly mean PW exceeded the 99 th percentile of climatology with a value 25 % higher than the 40 year climatology. Prior to the flood, around 18 UTC on 8 September, PW rapidly increased from 22 mm to 32 mm and remained around 30 mm for the entire event as a result of the nearly saturated atmosphere. The frequency distribution of September PW for Boulder is typically normal, but in 2013 the distribution was bimodal due to a combination of above average PW values from September 1 st –15 th and much drier conditions from 16 th –30 th September. The above normal, near saturation PW values during the flood were the result of large-scale moisture transport into Colorado from the eastern tropical Pacific and the Gulf of Mexico. This moisture transport was the product of a stagnating, cutoff low over the southwestern United States working in conjunction with an anticyclone located over the southeastern United States. A blocking ridge located over the Canadian Rocky Mountains kept both of the synoptic features in place over the course of several days, which helped to provide continuous moisture to the storm, thus enhancing the accumulated precipitation totals.

Field of study: Environmental science
Acoustic Tracking of Supersonic Objects

Nonequilibrium, multicomponent air calculations for electron-density distributions in the stagnation point, merged viscous shock layer have been presented using a shock-slip analysis in conjunction with a coupled, iterative finitedifference numerical solution. The present study yielded four main conclusions summarized as follows: 1) Including of shock-slip effects are necessary for analysis of merged viscous-layer electron density using a thin viscous shock-layer model. Such a shock-slip approach appears to be valid based on comparison with solutions which include details of the shock structure. 2) Predicted electron-density distributions are relatively insensitive to choice of diffusion model (constant Lewis-Semenov number for all species vs full multicomponent diffusion). 3) For an equilibrium catalytic-wall condition, a factor of four maximum difference in peak electron density resulted from the four different sets of reaction rates used in the present study. The catalytic condition of the wall influences the entire shock layer with the principal effect concentrated in the near-wall region. 4) Decoupled calculations in which the species concentrations are solved for using frozen-flow fluid-dynamic solutions appear to overpredict the electron density as compared to coupled calculations such as that of Dellinger3 and the present work.

Field of study: Physics
Multicast/broadcast network convergence in next generation mobile networks

The 3GPP Multimedia Broadcast Multicast Service (MBMS) aims to introduce group communications into the 3G networks. One of the current key challenges is how to evolve these incipient features towards the ''beyond 3G vision'' of a converged global network where multimedia content can be delivered over one or more selected broadcast transport bearers. This paper presents potential multicast/broadcast technologies convergence and discusses the issues and challenges in moving towards this next generation network vision from the viewpoint of evolving MBMS.

Field of study: Computer science
Two-dimensional multiple non-homogeneous harmonic equation and its boundary integral equations

The paper discusses 2-dimensional multiple non-homogeneous harmonic equation and its boundary integral equation, and gives recurrence formulae of fundamental solution. Under the assumption that non-homogeneous term is m-degree harmonic, the integral term in domain is shifted into boundary integral. Therefore the boundary integral equations are obtained that the integral in domain is not included, and the special solution can be expressed by boundary integrals. Furthermore, the error and convergence analysis are given by Taylor's polynomial approximating non-homogeneous term f(x), and analytic expressions of boundary integral for 2-dimensional harmonic equation are given in local right-angle coordinate system.

Field of study: Mathematics
Molecular analysis of the diversity of genus Psychrobacter present within a temperate estuary.

Many members of the genus Psychrobacter are endemic in extremely cold and saline environments and the genus has been described as only marginally successful in warmer habitats. In a previous study the Psychrobacter genus was, unexpectedly, the most frequently isolated bacterial genus from the sea-surface microlayer (SML) and the underlying water (UW) of a temperate estuary (Ria de Aveiro, Portugal). Here we analysed the diversity in Psychrobacter populations inhabiting this estuary. Samples were collected at three dates and three locations from sea-SML and UW. Isolated Psychrobacter strains were well-adapted to temperatures and salt concentrations above the ones described as optimal for most members of this genus. Hydrocarbon-degrading potential was not confirmed for these strains. We developed and optimized a reliable and specific denaturing gradient gel electrophoresis (DGGE)-based method for the analysis of Psychrobacter populations in aquatic systems. DGGE profiles inferred that Psychrobacter populations were very stable in the estuary, a strong indication for the presence of well-adapted phylotypes. The analysis of genus-specific clone libraries revealed a surprisingly high diversity among Psychrobacter in Ria de Aveiro. Results indicated that novel species were probably cultivated. Significant differences between sea-SML and UW Psychrobacter communities were revealed. Observed diversity trends may be related to environmental factors such as salinity and/or anthropogenic pressures such as contamination with hydrocarbons.

Field of study: Biology, Environmental science
Response and time allocation in concurrent second-order schedules.

Six pigeons were trained on two-key concurrent variable-interval schedules in which the required response was the completion of a fixed number of key pecks. When the required number of pecks was equal on the two keys, response- and time-allocation ratios under-matched obtained reinforcement rate ratios. A similar result was found when the required number of pecks was unequal, except that performance, measured in response terms, was biased to the shorter required number of pecks and was less sensitive to reinforcement-rate changes. No such differences were found in the data on time spent responding. When the variable-interval schedules were kept constant and the required numbers of pecks were systematically varied, response ratios changed inversely with the ratio of the required number of pecks, but time-allocation ratios varied directly with the same independent variable. Thus, on response measures, pigeons "prefer" the schedule with the smaller peck requirement, but on time measures they "prefer" the schedule with the larger peck requirement. This finding is inconsistent with a commonsense notion of choice, which sees response and time-allocation measures as equivalent.

Field of study: Biology, Psychology
Two model-independent results for the momentum dependence of ϱ-ω mixing

Two model-independent results on the momentum-dependence of ϱ-ω mixing are described. First, an explicit choice of interpolating fields for the vector mesons is displayed for which both the mixing in the propagator and the isospin-breaking at the nucleon-vector meson vertices (and hence also the one-vector-meson-exchange contribution to NN charge symmetry breaking) vanish identically at q 2 = 0. Second, it is shown, using the constraints of unitarity and analyticity on the spectral function of the vector meson propagator, that there is no possible choice of interpolating fields for the ϱ 0 , ω 0 mesons such that, with the ϱω element of the propagator defined by Δ μν ϱω (q 2 ) = (g μν − q μ q ν q 2 )θ(q 2 ) (q 2 − m ϱ 2 )(q 2 − m ω 2 ) , θ(q 2 ) is independent of momentum. It follows that the standard treatment of charge symmetry breaking in few-body systems cannot be interpreted as arising from any realizable effective meson-baryon Lagrangian and must, therefore, be considered purely phenomenological in content.

Field of study: Physics
Sensitization of Gastric Cancer Cells to 5-FU by MicroRNA-204 Through Targeting the TGFBR2-Mediated Epithelial to Mesenchymal Transition

Gastric cancer (GC) is the most common gastrointestinal malignancy, causing cancer-related deaths in East Asia. MicroRNAs (miRNAs) are small non-coding RNAs aberrantly expressed in human tumors. In this study, we aim to investigate the roles of miR-204 in the epithelial to mesenchymal transition (EMT)-associated chemosensitivity.  The expression of miR-204 was detected in clinical tumor samples and GC cell lines by real time PCR. Tumor cell’s growth, invasion, and migration were measured by MTT assay, wound healing assay, and transwell invasion assay, respectively. Western blot method was used to detect the protein levels of indicated genes. Luciferase reporter assay was performed to validate the target gene of miR-204. The in vivo role of miR-204 was measured using a xenograft mouse model of GC.  By comparing the expressions of miR-204 in human gastric tumors and their adjacent normal tissues, it was disclosed that miR-204 was significantly downregulated in gastric tumors. Moreover, miR-204 was downregulated in multiple GC cell lines compared with normal gastric epithelial cells. Overexpression of miR-204 suppressed GC cells’ proliferation, invasion, and migration. It is noteworthy that 5-FU treatments induced miR-204 expression and suppressed TGF-β pathway. By establishment of 5-FU resistant GC cell line, it was revealed that miR-204 was significantly downregulated in 5-FU resistant GC cells, representing mesenchymal features with downregulation of epithelial marker, while mesenchymal markers were upregulated. We identified TGFBR2 as a direct target of miR-204 by Western blot method and luciferase assay in GC cells and tumor samples as well. In addition, overexpression of miR-204 sensitized GC cells to 5-FU in vitro. Xenograft experiments demonstrated that the combination of miR-204 and 5-FU efficiently inhibited tumor growth and improved survival rate of mice as well. Eventually, we illustrated the restoration of TGFBR2 in miR-204 overexpression GC cells, which recovered resistance to 5-FU treatments compared with miR-204 overexpression GC cells.  This study describes a miRNA-based therapeutic strategy against 5-FU resistance in GC, contributing to the development of anti-chemoresistance therapeutic agents.

Field of study: Biology, Chemistry
RISK BEHAVIORS IN THE MULTIVARIATE CONCENTRIC SQUARE FIELD ASSOCIATED WITH ALCOHOL PREFERENCE IN CHROMOSOME 4 RECIPROCAL CONGENIC (P. NP, NP. P) RATS

RISK BEHAVIORS IN THE MULTIVARIATE CONCENTRIC SQUARE FIELD ASSOCIATED WITH ALCOHOL PREFERENCE IN CHROMOSOME 4 RECIPROCAL CONGENIC (P. NP, NP. P) RATS

Field of study: Medicine
Using vanishing points to estimate parameters of fisheye camera

This study presents an approach for estimating the fisheye camera parameters using three vanishing points corresponding to three sets of mutually orthogonal parallel lines in one single image. The authors first derive three constraint equations on the elements of the rotation matrix in proportion to the coordinates of the vanishing points. From these constraints, the rotation matrix is calculated under the assumption of the image centre known. The experimental results with synthetic images and real fisheye images validate this method. In contrast to the existing methods, the authors method needs less image information and does not know the three-dimensional reference point coordinates.

Field of study: Computer science
Weak localization in monolayer and bilayer graphene

We describe the weak localization correction to
conductivity in ultra-thin graphene films, taking into account
disorder scattering and the influence of trigonal warping of the
Fermi surface. A possible manifestation of the chiral nature of
electrons in the localization properties is hampered by trigonal
warping, resulting in a suppression of the weak anti-localization
effect in monolayer graphene and of weak localization in bilayer
graphene. Intervalley scattering due to atomically sharp
scatterers in a realistic graphene sheet or by edges in a narrow
wire tends to restore weak localization resulting in negative
magnetoresistance in both materials.

Field of study: Physics
Bayesian estimation and prediction based on generalized Type-I hybrid censored sample

In this paper, we consider an exponential form for the underlying distributionand a conjugate prior, and develop a procedure for deriving the maximum likelihood and Bayesian estimators based on an observed generalized Type-I hybrid censored sample. The problems of predicting the future order statistics from the same sample and that from a future sample are also discussed from a Bayesian viewpoint. For the illustration of the developed results, the exponential and Pareto distributions are used as examples. Finally, two numerical examples are presented for illustrating all the inferential procedures developed here.

Field of study: Mathematics
The Effect of Self-Evaluation on Teaching Behavior in Classrooms for Students with Emotional and Behavioral Disorders

This study examined the effect of a self-evaluation intervention using audiotaped samples of teachers' instructional behavior on the rates of praise in classrooms for students with emotional and behavioral disorders (EBD). It also examined the effect of the intervention on other teaching behaviors and determined whether implementation of the intervention is feasible for teachers of students with EBD. Results suggested that the intervention had positive short-term effects on teacher praise and correct academic responses by students. Post hoc analyses suggested that the mean ratio of praise to reprimands changed across phases for teachers in both the self-evaluation and no treatment groups. Implications for future research and study limitations are discussed.

Field of study: Education
Freezing time of a slab using the method of lines

A one-dimensional mathematical model has been developed to solve the heat conduction equation and simulate the freezing process for a slab. The mathematical model was solved using finite differences and the method of lines (MOL). 
 
In MOL, spatial derivatives are discretized by finite differences, and the resulting system in time is integrated using an appropriate solver. Several sets of thermal properties were selected to simulate the process. Predicted freezing time values were compared to 142 published experimental data sets. Predictions obtained by published numerical methods were compared to the experimental data. The freezing time predictions of the proposed model give a percentage error in the range of −4.55 < E(%) < 4.09, which includes the 142 data sets using the best calculation results. In summary, the MOL is a good numerical prediction method since an adequate set of thermophysical properties is especially tested and selected for each data set.

Field of study: Engineering
Ecological and socioeconomic impacts of marine protected areas in the South Pacific: assessing the evidence base

Marine protected areas (MPAs) in the South Pacific have a unique history that calls for a regional-scale synthesis of MPA impacts and the factors related to positive ecological and socioeconomic change. However, recommendations of best approaches to MPA implementation can be made only when evaluation techniques are sound. Impact evaluation involves quantifying the effects of an intervention over and above the counterfactual of no intervention or a different intervention. Determining the true impact of an MPA can be challenging because additional factors beyond the presence of an MPA can confound the observed results (e.g. differences in ecological or socioeconomic conditions between MPA and control sites). While impact evaluation techniques employing counterfactual thinking have been well developed in other fields, they have been embraced only slowly in the MPA evaluation literature. We conducted a structured literature search and synthesis of MPA evaluation studies from the South Pacific to determine: (i) the overall ecological and socioeconomic impacts of MPAs in the region, (ii) what factors were associated with positive, neutral, or negative impacts, and (iii) to what extent the MPA evaluation literature from the region has incorporated counterfactual thinking and robust impact evaluation techniques. Based on 52 identified studies, 42% of measured ecological impacts were positive. While 72% of socioeconomic impacts were positive, these were from only eight studies. The proportion of positive impacts was comparable between community-based and centrally governed MPAs, suggesting that both governance approaches are viable options in the region. No-take MPAs had a greater number of positive ecological impacts than periodic closures and there was little evidence of any long-term ecological recovery within periodic closures following harvesting. Importantly, more than half of the studies examined (59%) did not provide any clear consideration of factors beyond the presence of the MPA that might have confounded their results. We conclude that counterfactual thinking has yet to be fully embraced in impact evaluation studies in the region and recommend pathways by which progress can be made.

Field of study: Environmental science