nils-herrmann/clean_scirepeval huggingface dataset:
Enhanced Osteogenic Differentiation of Human Primary Mesenchymal Stem and Progenitor Cultures on Graphene Oxide/Poly(methyl methacrylate) Composite Scaffolds

Due to its versatility, small size, large surface area, and ability to interact with biological cells and tissues, graphene oxide (GO) is an excellent filler for various polymeric composites and is frequently used to expand their functionality. Even though the major advantage of the incorporation of GO is the enhancement of mechanical properties of the composite material, GO is also known to improve bioactivity during biomineralization and promote osteoblast adhesion. In this study, we described the fabrication of a composite bone cement made of GO and poly(methyl methacrylate) (PMMA), and we investigated its potential to enhance osteogenic differentiation of human primary mesenchymal stem and progenitor cells. Through the analysis of three differentiation markers, namely alkaline phosphatase, secreted protein acidic and rich in cysteine, and bone morphogenetic protein-2 in the presence and in the absence of an osteogenic differentiation medium, we were able to indicate a composite produced manually with a thick GO paper as the most effective among all investigated samples. This effect was related to its developed surface, possessing a significant number of voids and pores. In this way, GO/PMMA composites were shown as promising materials for the applications in bone tissue engineering.

Field of study: Materials science
Monte Carlo calculations and experimental measurements of dosimetry parameters of a new 103Pd source.

Permanent prostate implantation using 125I (iodine) or 103Pd (palladium) sources is a popular treatment option in the management of early prostate cancer. As sources of new designs are developed and marketed for application in permanent prostate implantations, their dosimetric characteristics must be carefully determined in order to maintain the accuracy of patient treatment. This report presents the results of experimental measurements and Monte Carlo calculations of the dosimetric parameters performed for a newly available 103Pd seed source. The measurements were performed in a large scanning water phantom using a diode detector. The positioning of the source and detector was achieved by a computer-controlled positioning mechanism in the scanning water phantom. The dose rate constant in water for the new 103Pd source was determined from measurements with the diode detector calibrated with 125I sources of known air-kerma strength. The radial dose function values for the source were measured using the diode detector. Monte Carlo photon transport calculations were then used to calculate the dosimetric parameters of dose rate constant, radial dose function, and anisotropy function using an accurate geometric model of the source. The measured dose rate constant of 0.693 cGy/U-hr compares well with the Monte Carlo calculated value of 0.677 cGy/U-hr. These results are further compared with data on existing 103Pd sources.

Field of study: Medicine, Physics
Parallel three-dimensional sensing by color-coded triangulation.

We discuss a three-dimensional sensor that combines coded illumination and triangulation. The sensor supplies the distance of ~ 250,000 object pixels (TV format) in 40 ms (one single TV frame period). Themethod is based on the following principle: a color spectrum of a white-light source is imaged onto the object by illumination from one certain direction. The object is observed by a color TV camera from a direction of observation, which is different from the direction of illumination. The color (hue) of each pixel is a measure of its distance from a reference plane. It can be evaluated by the three (red-green-blue) output channels of the CCD camera. This evaluation can be implemented within TV real time. Even colored objects can be measured. The resolution achieved is 50-150 depth steps.

Field of study: Physics
226: The transcription factor IRF8 is required for the development of basophils

Basophils are the rarest granulocytes circulating in the peripheral blood. Although their non-redundant roles in Th2-type immunity and allergic disorders have been clarified, little is known about the pathways and regulators of their development. Interferon Regulatory Factor-8 (IRF8) is a transcription factor known to promote the development of monocytes/macrophages and dendritic cells while inhibiting that of neutrophils. In this report, we show that this transcription factor is required for the development of the basophil lineage. Irf8 −/− mice display a severe reduction of basophil counts in the bone marrow, peripheral blood and spleen. Bone marrow transfer experiments showed that IRF8 functions in a bone marrow cell-intrinsic manner. Analysis of bone marrow progenitors revealed that the number of granulocyte-committed progenitors (GPs) in Irf8 −/− mice is comparable to that of wild-type mice, while that of basophil-committed progenitors (BaPs) is diminished. Using IRF8-GFP knock-in mice, we found that GPs but not BaPs and mature basophils express IRF8, suggesting that IRF8 may act in the stage of GPs. Indeed, GPs purified from Irf8 −/− mice failed to efficiently give rise to basophils in vitro in the presence of IL-3. Taken together, these results uncover a previously unrecognized role of IRF8 in granulocyte development.

Field of study: Medicine
High Rayleigh Number Turbulent Convection in a Gas near the Gas-Liquid Critical Point

$SF_6$ in the vicinity of its critical point was used to study turbulent convection up to exceptionally high Rayleigh numbers, $Ra$, (up to $5\cdot 10^{14}$) and to verify for the first time the generalized scaling laws for the heat transport and the large scale circulation velocity as a function of $Ra$ and the Prandtl number, $Pr$, in very wide range of these parameters. The both scaling laws obtained are consistent with theoretical predictions by B.Shraiman and E.Siggia, , 3650 (1990).

Field of study: Physics
Influence of superfluorescence on the operation of lasers with dye amplifiers

An investigation was made of a longitudinally pumped laser-single-pass dye amplifier system with a view to optimizing the total conversion efficiency. It was shown that competition between two processes–amplification of the external signal and of the spontaneous noise–determines the total efficiency of conversion of the pump into useful signal. The superfluorescence restricts the maximum gain and conversion efficiency of small external signals, as does the saturation by the signal being amplified in the case of large external signals. A quantitative analysis was made of the choice of optimal optical density of the amplifier and of the competition between two coupled waves in a nonlinearly amplifying medium.

Field of study: Engineering, Physics
K-nn active learning under local smoothness condition

There is a large body of work on convergence rates either in passive or active learning. Here we outline some of the results that have been obtained, more specifically in a nonparametric setting under assumptions about the smoothness and the margin noise. We also discuss the relative merits of these underlying assumptions by putting active learning in perspective with recent work on passive learning. We provide a novel active learning algorithm with a rate of convergence better than in passive learning, using a particular smoothness assumption customized for $k$-nearest neighbors. This smoothness assumption provides a dependence on the marginal distribution of the instance space unlike other recent algorithms. 
Our algorithm thus avoids the strong density assumption that supposes the existence of the density function of the marginal distribution of the instance space and is therefore more generally applicable.

Field of study: Computer science
Megatectonics of the Coast Ranges, California

The Coast Ranges are considered in the light of the “new global tectonics.” It is proposed that at the end of the Nevadan orogeny, a large prism of sediments, ranging in age from Late Jurassic to Late Cretaceous, was deposited across the boundary of the oceanic and the steep-sided sialic crusts. Westward movement of North America, away from the mid-Atlantic rise, caused the oceanic block to underthrust the continental block, in the Coast Range orogeny. The thrust fault, here named the Coast Ranges thrust, passed through the post-Nevadan sediment prism at a gentle angle and separated it into two blocks. The hanging-wall block is relatively undisturbed, and its sediments are identified as the Great Valley sequence. The footwall block is greatly disturbed into a tectonic jumble of sediment and ocean crustal igneous rocks, collectively identified as the Franciscan. Rocks in the footwall block are subjected to various facies of high-pressure and low-temperature metamorphism. On approaching the steep-sided sialic crust, the footwall block folded the crust downward and backward and continued under it at a steepened angle. Peridotite from the oceanic crust or from the mantle, mobilized by serpentinization, worked up the thrust plane and was dispersed in the footwall melange. No batholithic instrusions and no mountain making accompanied the Coast Range orogeny. The tectonic event of the Coast Range orogeny terminated with the propagation of the right-lateral transcurrent San Andreas fault. This change is estimated to have taken place in Eocene time. The San Andreas fault has offset the Coast Ranges thrust fault approximately 310 mi since its inception. The relative pressure of the ocean basin toward the continent was partly alleviated by strike-slip of the ocean basin, relatively northwesterly with respect to the continent. The orientation of the San Andreas is not ideal for the relief of this strain and compressional folding has also occurred. No evidence of the formation of deep-ocean trenches or island arcs has been found.

Field of study: Geology
Redefining community: towards an ecological republicanism

This paper makes some suggestions for a concept of community which arguably satisfies the most important criteria for both human communities, as defined in the social sciences and humanities, and natural communities, as defined in ecology and biology. Beginning with the former, I arrive at two such criteria: (1) a material and social connection among members, and (2) some kind and degree of awareness of other members. These are then supplemented with a third drawn from civic republicanism, with its focus on citizenship and the common good: communities (3) enable and require certain practices for their maintainence. Turning to ecological definitions of community, I find the dominant (reductionist) one seriously deficient as compared with a more holist and ecosystemic approach. However, I invoke a nonreductive holism to defend the idea of community, and go on to argue that each of the three above-mentioned criteria can be fruitfully extended to include both social and ecological communities in a nonreductionist way – that is, in a way that neither reduces ecosystemic properties to individual organisms nor the reverse. This culminates in a discussion of what I call ‘ecological republicanism’, which I suggest could have powerfully positive effects on the contemporary crisis of undue human impact on the natural world.

Field of study: Environmental science
A testable theoretical model for magnetotherapy potentially applicative to such diverse concerns as oncogenic, CNS trophic factor and viral disorders.

: Physiologic magnetic fields of the order 10(-8) gauss have been unified with their propitiators: quantum genetic particles, the gravitational potential of which is about an erg. As these fields are applied to the equation for solenoidal models, B = micro NI/L, currents of about a microampere are derived; in perfect accord with recent clinical data indicating the therapeutic efficacy of weak currents in repair and growth of soft tissue, bone and nerve. The mechanism of reorientation of spin angular momentum of leptons and baryons influencing molecular magnetic domains to bring about 'particle jumps' is presented so that a clinical picture results. The clinical picture is that of an organism placed at right angles to flux lines in the midst of a solenoid immersed in water exposed then to exogenously applied resonant physiologic magnetic fields which convert malalligned atomic lattices of oncogenes and associated particles to homologous normal structures.

Field of study: Biology, Chemistry, Physics
SoftAir: A software defined networking architecture for 5G wireless systems

One of the main building blocks and major challenges for 5G cellular systems is the design of flexible network architectures which can be realized by the software defined networking paradigm. Existing commercial cellular systems rely on closed and inflexible hardware-based architectures both at the radio frontend and in the core network. These problems significantly delay the adoption and deployment of new standards, impose significant challenges in implementing and innovation of new techniques to maximize the network capacity and accordingly the coverage, and prevent provisioning of truly- differentiated services which are able to adapt to growing and uneven and highly variable traffic patterns. In this paper, a new software-defined architecture, called SoftAir, for next generation (5G) wireless systems, is introduced. Specifically, the novel ideas of network function cloudification and network virtualization are exploited to provide a scalable, flexible and resilient network architecture. Moreover, the essential enabling technologies to support and manage the proposed architecture are discussed in details, including fine-grained base station decomposition, seamless incorporation of Openflow, mobility- aware control traffic balancing, resource-efficient network virtualization, and distributed and collaborative traffic classification. Furthermore, the major benefits of SoftAir architecture with its enabling technologies are showcased by introducing software- defined traffic engineering solutions. The challenging issues for realizing SoftAir are also discussed in details.

Field of study: Computer science
Pharmacy Students' Perceptions and Emotional Responses to Aggressive Incidents in Pharmacy Practice

To explore pharmacy students' experiences with and perceptions of aggressive incidents in pharmacy practice.  Data were taken from a survey completed by second-year pharmacy (P2) students and analyzed using a retrospective, cross-sectional design. Survey items were adapted using the following scales: Perception of Aggression Survey (POAS), List of Aggressive Incidents experienced by mental health staff, and List of Emotions experienced by nurses.  The majority of respondents did not identify aggression as normal, instead perceiving it as a violent reaction and functional. The 3 most frequent aggressive incidents experienced were: verbal abuse to face (40%); verbal abuse on the phone (39%); and refusal to cooperate with instructions (34%). The 3 most frequent emotions reported were: frustration (70%), empathy (65%), and no pride in their profession (70% rarely-never).  Pharmacy students reported experiencing aggressive incidents with patients in person and on the phone, and with patients not following instructions. Preparing future pharmacists in techniques to address and resolve patients' aggression must become a priority for pharmacy academia and further research in this area is needed.

Field of study: Education, Medicine
Biological-based optimization and volumetric modulated arc therapy delivery for stereotactic body radiation therapy.

To describe biological-based optimization and Monte Carlo (MC) dose calculation-based treatment planning for volumetric modulated arc therapy (VMAT) delivery of stereotactic body radiation therapy (SBRT) in lung, liver, and prostate patients.



Optimization strategies and VMAT planning parameters using a biological-based optimization MC planning system were analyzed for 24 SBRT patients. Patients received a median dose of 45 Gy [range, 34-54 Gy] for lung tumors in 1-5 fxs and a median dose of 52 Gy [range, 48-60 Gy] for liver tumors in 3-6 fxs. Prostate patients received a fractional dose of 10 Gy in 5 fxs. Biological-cost functions were used for plan optimization, and its dosimetric quality was evaluated using the conformity index (CI), the conformation number (CN), the ratio of the volume receiving 50% of the prescription dose over the planning target volume (Rx/PTV50). The quality and efficiency of the delivery were assessed according to measured quality assurance (QA) passing rates and delivery times. For each disease site, one patient was replanned using physical cost function and compared to the corresponding biological plan.



Median CI, CN, and Rx/PTV50 for all 24 patients were 1.13 (1.02-1.28), 0.79 (0.70-0.88), and 5.3 (3.1-10.8), respectively. The median delivery rate for all patients was 410 MU/min with a maximum possible rate of 480 MU/min (85%). Median QA passing rate was 96.7%, and it did not significantly vary with the tumor site.



VMAT delivery of SBRT plans optimized using biological-motivated cost-functions result in highly conformal dose distributions. Plans offer shorter treatment-time benefits and provide efficient dose delivery without compromising the plan conformity for tumors in the prostate, lung, and liver, thereby improving patient comfort and clinical throughput. The short delivery times minimize the risk of patient setup and intrafraction motion errors often associated with long SBRT treatment delivery times.

Field of study: Medicine, Physics
Social and olfactory experiences modify neuronal morphology of orbital frontal cortex.

Structural modifications in the dendritic morphology of neurons occur following many forms of experience, including exposure to drugs, complex housing, and training in specific behavioral tasks. The present study examined morphological changes in orbitofrontal (OFC) and medial prefrontal cortex (mPFC) neurons of female rats following experience with a variety of social partners or nonsocial olfactory stimuli. We reasoned that experience with various social partners or olfactory stimuli, and the associated behavioral adaptations, would drive structural modifications in prefrontal cortex neurons engaged by these stimuli. Social experience was manipulated by providing rats with a novel cage-mate or housing the animal with the same cage-mate throughout the study. Similarly, olfactory experience was manipulated by introducing novel, nonsocial odors in the home cage or exposing the animals to the same home-cage odor throughout the study. Both forms of experience resulted in altered dendritic morphology in OFC neurons, whereas morphological changes in mPFC were comparatively small and limited to changes in spine density. These observations indicate that OFC and mPFC neurons respond differently to social and nonsocial olfactory stimulation in adulthood and join the growing body of data illustrating differential effects of experience on structural plasticity in OFC and mPFC.

Field of study: Biology, Psychology
Toxicity of twenty-two plant essential oils against pathogenic bacteria of vegetables and mushrooms

ASBTRACT Toxicity of twenty-two essential oils to three bacterial pathogens in different horticultural systems: Xanthomonas campestris pv. phaseoli (causing blight of bean), Clavibacter michiganensis subsp. michiganensis (bacterial wilt and canker of tomato), and Pseudomonas tolaasii (causal agent of bacterial brown blotch on cultivated mushrooms) was tested. Control of bacterial diseases is very difficult due to antibiotic resistance and ineffectiveness of chemical products, to that essential oils offer a promising alternative. Minimal inhibitory and bactericidal concentrations are determined by applying a single drop of oil onto the inner side of each plate cover in macrodilution assays. Among all tested substances, the strongest and broadest activity was shown by the oils of wintergreen (Gaultheria procumbens), oregano (Origanum vulgare), and lemongrass (Cymbopogon flexuosus. Carvacrol (64.0–75.8%) was the dominant component of oregano oils, while geranial (40.7%) and neral (26.7%) were the major constituents of lemongrass oil. Xanthomonas campestris pv. phaseoli was the most sensitive to plant essential oils, being susceptible to 19 oils, while 11 oils were bactericidal to the pathogen. Sixteen oils inhibited the growth of Clavibacter michiganensis subsp. michiganensis and seven oils showed bactericidal effects to the pathogen. The least sensitive species was Pseudomonas tolaasii as five oils inhibited bacterial growth and two oils were bactericidal. Wintergreen, oregano, and lemongrass oils should be formulated as potential biochemical bactericides against different horticultural pathogens.

Field of study: Agricultural and Food sciences
Laparoscopic nephrectomy for Wilms' tumor: Can we expand on the current SIOP criteria?

Wilms' tumor now has a good overall prognosis with open radical nephrectomy having been the mainstay of surgical treatment. Recently laparoscopic nephrectomy (LN) has been growing in popularity. The aim of our study was to review our indications and outcomes for laparoscopic resections for Wilms' tumor and compare indications with International Society of Paediatric Oncology (SIOP) criteria for LN.



Patient demographics, preoperative management, surgical data, respect of SIOP criteria, complications, disease outcome, and follow-up were recorded on consecutive children who underwent nephrectomy for Wilms' tumor.



Fifty-four consecutive children with Wilms' tumor underwent a nephrectomy; 20 had a LN (Table). Nine of 20 (45%) patients who had LN did not meet SIOP criteria for LN. No patients had an intraoperative tumor rupture and one patient had positive margins because of preoperative rupture. There were two conversions: one caused by difficulty accessing the renal hilum and the other caused by difficulty maintaining oxygen saturations. There was one local recurrence.



SIOP criteria are conservative and safe. Indications can be extended for teams experienced in surgical oncology and laparoscopy after agreement at a multidisciplinary meeting (MDM).

Field of study: Medicine