nils-herrmann/clean_scirepeval huggingface dataset:
Cryopreservation and Banking of Dental Stem Cells.
Venue: Advances in experimental medicine and biology

Over the past decade, dental tissues have become an attractive source of mesenchymal stem cells (MSCs) Dental stem cells (DSCs) are not only able to differentiate into adipogenic, chondrogenic and osteogenic lineanges, but an increasing amount of research also pointed out their potential applicability in numerous clinical disorders, such as myocardial infarction, neurodegenerative diseases and diabetes. Together with their multilineage differentiation capacity, their easy availability from extracted third molars makes these stem cells a suitable alternative for bone marrow derived MSCs. More importantly, DSCs appear to retain their stem cell properties following cryopreservation, a key aspect in their long term preservation and upscale production. However, the vast number of different cryopreservation protocols makes it difficult to draw definite conclusions regarding the behavior of these stem cells. The routine application and banking of DSCs is also associated with some other pitfalls, such as interdonor variability, cell culture induced changes and the use of animal derived culture medium additives. Only thorough assessment of these challenges and the implementation of standardized, GMP procedures will successfully lead to better treatment options for patients who no longer benefit from current stem cell therapies.
Estimating 3D L5/S1 moments and ground reaction forces during trunk bending using a full body ambulatory inertial motion capture system.
Venue: Journal of biomechanics

Inertial motion capture (IMC) systems have become increasingly popular for ambulatory movement analysis. However, few studies have attempted to use these measurement techniques to estimate kinetic variables, such as joint moments and ground reaction forces (GRFs) Therefore, we investigated the performance of a full body ambulatory IMC system in estimating 3D L5/S1 moments and GRFs during symmetric, asymmetric and fast trunk bending, performed by nine male participants. Using an ambulatory IMC system (Xsens/MVN) L5/S1 moments were estimated based on the upper body segment kinematics using a top down inverse dynamics analysis, and GRFs were estimated based on full body segment accelerations. As a reference, a laboratory measurement system was utilized: GRFs were measured with Kistler force plates (FPs) and L5/S1 moments were calculated using a bottom up inverse dynamics model based on FP data and lower body kinematics measured with an optical motion capture system (OMC) Correspondence between the OMC+FP and IMC systems was quantified by calculating root mean square errors (RMSerrors) of moment/force time series and the interclass correlation (ICC) of the absolute peak moments/forces. Averaged over subjects, L5/S1 moment RMSerrors remained below 10Nm (about 5% of the peak extension moment) and 3D GRF RMSerrors remained below 20N (about 2% of the peak vertical force) ICCs were high for the peak L5/S1 extension moment (0.971) and vertical GRF (0.998) Due to lower amplitudes, smaller ICCs were found for the peak asymmetric L5/S1 moments (0.690 0.781) and horizontal GRFs (0.559 0.948) In conclusion, close correspondence was found between the ambulatory IMC based and laboratory based estimates of back load.
Percutaneous Endoscopic Lumbar Discectomy for L5 S1 Disc Herniation Via an Interlaminar Approach Versus a Transforaminal Approach: A Prospective Randomized Controlled Study With 2 Year Follow Up
Venue: Spine

A prospective, randomized controlled study of patients with L5 S1 lumbar disc herniations, operated with endoscopic discectomy through an interlaminar or transforaminal approach.  To compare the results of percutaneous endoscopic lumbar discectomy in L5 S1 disc herniation through an interlaminar or transforaminal approach.  The transforaminal and interlaminar techniques are both acceptable approaches for L5 S1 disc herniation. This is the first study to compare these two approaches in terms of their surgical effects and advantages.  From January 2010 to June 2010, 60 patients with L5 S1 disc herniation were randomly recruited into two groups; one group underwent percutaneous endoscopic interlaminar discectomy (PEID) and the other group underwent percutaneous endoscopic transforaminal discectomy (PETD) There were 30 patients in each group. The operation time, intraoperative radiation time, postoperative bed rest time, hospitalization time, and complications were compared between the groups. The surgical effectiveness was assessed according to the Oswestry Disability Index (ODI) Visual Analog Scale (VAS) and modified MacNab criteria.  All the patients completed follow up with a mean of 27.6 months (range, 24 37 months) In the PEID group, the mean operation time was 65.0 14.9 minutes, and the intraoperative radiation time was 0.60 0.24 seconds. For the PETD group, the mean operation time was 86.0 15.4 minutes, and the intraoperative radiation time was 6.50 1.52 seconds. There were significant differences in operation time and radiation time between the two groups (P 0.01) but not in the postoperative bed rest time, hospitalization time, or complication rate (P 0.05) The postoperative ODI and VAS were obviously improved in both groups when compared with preoperation (P 0.01) According to the MacNab criteria, the satisfactory rates were 93.3% and 90.0% in the two groups, without a significant difference (P 0.05)  PEID can escape the blockade of crista iliaca, and advantages include a faster puncture orientation, a shorter operation time, and less intraoperative radiation exposure. PETD requires higher punctuation skill and more intraoperative radiation exposure.
Clinical spectrum, diagnostic criteria, and polymerase chain reaction of aqueous humor in viral and toxoplasma detection in Fuchs' uveitis syndrome
Venue: Indian journal of ophthalmology

The aim of this study is to describe the clinical features and diagnostic criteria of Fuchs' uveitis (FU) and to determine whether it has an association with virus and toxoplasma in the aqueous humor during cataract surgery.  This is a prospective, case control study.  Patients with FU (n 25) anterior uveitis (n 15) and no uveitis (normal) (n 50) were included based on predefined inclusion and exclusion criteria for all three groups. Polymerase chain reaction (PCR) of aqueous humor and serum for rubella, herpes simplex virus (HSV) cytomegalovirus (CMV) varicella zoster virus (VZV) and toxoplasma was done using conventional uniplex PCR. Statistical Analysis It was done using SPSS software using Chi square test for categorical variables, and P 0.05 was considered statistically significant.  Ninety patients were enrolled in the study in three groups, comparable for age, gender, and laterality of ocular involvement. All patients had diffuse keratic precipitates in FU group (P 0001) with none having posterior synechiae (P 0.046) which was statistically significant when compared to anterior uveitis patients. Iris nodules were noted in one case in both groups. Serum and aqueous PCR was negative for detection of VZV, CMV, toxoplasma, and rubella in all groups. PCR for HSV was positive in one patient in "normal" group but was not statistically significant.  Our study shows that diagnosis of FU is mainly clinical. There appears to be no role of aqueous humor testing for viruses by PCR to aid in etiological diagnosis.
Assembly mechanisms determining high species turnover in aquatic communities over regional and continental scales

Niche and neutral processes drive community assembly and metacommunity dynamics, but their relative importance might vary with the spatial scale. The contribution of niche processes is generally expected to increase with increasing spatial extent at a higher rate than that of neutral processes. However, the extent to what community composition is limited by dispersal (usually considered a neutral process) over increasing spatial scales might depend on the dispersal capacity of composing species. To investigate the mechanisms underlying the distribution and diversity of species known to have great powers of dispersal (hundreds of kilometres) we analysed the relative importance of niche processes and dispersal limitation in determining beta diversity patterns of aquatic plants and cladocerans over regional (up to 300 km) and continental (up to 3300 km) scales. Both taxonomic groups were surveyed in five different European regions and presented extremely high levels of beta diversity, both within and among regions. High beta diversity was primarily explained by species replacement (turnover) rather than differences in species richness (i.e. nestedness) Abiotic and biotic variables were the main drivers of community composition. Within some regions, small scale connectivity and the spatial configuration of sampled communities explained a significant, though smaller, fraction of compositional variation, particularly for aquatic plants. At continental scale (among regions) a significant fraction of compositional variation was explained by a combination of spatial effects (exclusive contribution of regions) and regionally structured environmental variables. Our results suggest that, although dispersal limitation might affect species composition in some regions, aquatic plant and cladoceran communities are not generally limited by dispersal at the regional scale (up to 300 km) Species sorting mediated by environmental variation might explain the high species turnover of aquatic plants and cladocerans at regional scale, while biogeographic processes enhanced by dispersal limitation among regions might determine the composition of regional biotas
Effects of Roundup formulations, nutrient addition, and Western mosquitofish (Gambusia affinis) on aquatic communities
Venue: Environmental Science and Pollution Research

Aquatic communities can be affected by herbicides, nutrient addition, and non native fish species. We conducted a mesocosm experiment to examine the direct and interactive effects of three stressors: (1) Roundup formulations (Roundup Weed and Grass Killer(r) and Roundup Poison Ivy and Tough Brush Killer Plus(r) (2) nutrient addition, and (3) the presence of the non native Western mosquitofish (Gambusia affinis) on experimental pond communities. Roundup formulations had the most widespread effects on the zooplankton community, but effects varied between formulations and among taxa. The only significant effect of nutrient addition was a lowering of Daphnia abundance in the nutrient addition treatments. The abundances of Daphnia, mid sized cladocerans, and total zooplankton were lowered by mosquitofish, but no other taxa showed significant mosquitofish effects. We found several two way and three way interactions among the stressors, but these varied among zooplankton taxa. Chlorophyll a levels were higher with nutrient addition but were not significantly affected by Roundup formulation or mosquitofish. Our results suggest toxicity of Roundup formulations varies among taxa, and Roundup formulations differ in their toxicity to zooplankton, but with no cascading effects on primary producers. In addition, interactions among stressors affected the zooplankton community.
Wetland defense: naturally occurring pesticide resistance in zooplankton populations protects the stability of aquatic communities
Venue: Oecologia

Anthropogenic stressors are ubiquitous and have been implicated in worldwide declines of terrestrial and aquatic species. Pesticides are one such stressor that can have profound effects on aquatic communities by directly affecting sensitive species and indirectly affecting other species via trophic cascades, which can alter ecosystem function. However, there is growing evidence that non target species can evolve increased resistance. When such species are important drivers of the food web, then evolved resistance should help buffer communities from the effects of pesticides. To examine this possibility, we cultured four populations of the common zooplankton Daphnia pulex that we previously demonstrated were either sensitive or resistant to a common insecticide (i.e. chlorpyrifos) due to their proximity to agriculture. Using outdoor mesocosms that contained identical aquatic communities of phytoplankton, periphyton, and leopard frog tadpoles (Lithobates pipiens) we manipulated four D. pulex populations and four insecticide concentrations. As we monitored the communities for nearly 3 months, we found that the insecticide caused direct mortality of D. pulex in communities containing sensitive populations, and this led to a bloom of phytoplankton. In contrast, the insecticide caused much less direct mortality in communities containing resistant D. pulex populations, and the trophic cascade was prevented under low to moderate insecticide concentrations. Across all insecticide treatments, survivorship of leopard frogs was approximately 72 in communities with resistant D. pulex but only 35 in communities with sensitive D. pulex. To our knowledge, this is one of the first studies to use naturally occurring population variation in insecticide resistance to show that the evolution of pesticide resistance in zooplankton can mitigate the effects of insecticide induced trophic cascades, and that this outcome can have far reaching community effects.
Unravelling the drivers of aquatic communities using disparate organismal groups and different taxonomic levels

Bioassessment and monitoring methods should be as cost efficient as possible. Limiting the number of sites is not a practical solution to face the financial challenges related to bioassessment. Hence, it is highly important to find inexpensive ways to assess and monitor human impacted environments. Suggestions have been made to use coarser taxonomic levels because they require less expertise and time, or to use single surrogate taxonomic groups that indicate the overall state of ecosystems. In this study, we examined the level of within taxon and cross taxon congruence of aquatic bacterial, diatom and macroinvertebrate communities, while simultaneously assessing the chemical, physical and spatial drivers of community structure in these organismal groups. Our study area was an extensively sampled large lake system with high connectivity between sites. Thus, we ensured that spatial processes, if they existed, were well portrayed in our data. Our aim was to find out the taxonomic levels sufficient for the purposes of bioassessment and to detect possible surrogate taxonomic groups. We found that bacterial communities were best associated with pure effects of water chemistry, whereas diatom and macroinvertebrate communities were varyingly related to chemical, physical and spatial variables. Macroinvertebrates were the only group related to small scale spatial variables, while bacteria and diatoms were associated with variables illustrating spatial relations among sites at large and intermediate scales. Overall, the three organismal groups were mainly related to different chemical parameters. Also, the three organismal groups showed only weak, if any, congruent patterns in their community structure. Thus, we do not recommend the use of only one biological group as a surrogate in bioassessment. However, we found that higher taxonomic levels of all three studied organismal groups could be used as surrogates for finer level taxonomic assignments. Our findings are promising for the possible use of bacteria in future bioassessment and monitoring. Owing to the characteristics of very large lake systems, our findings may be applied to similarly highly connected ecosystems, such as marine coastal systems.
Carrier frequency offset estimation scheme for quasi constant envelope OFDM satellite system under AWGN channel
Venue: 2016 8th International Conference on Wireless Communications Signal Processing (WCSP)

Quasi Constant Envelope OFDM transmits dual stream simultaneously to improve the spectral efficiency of Constant Envelope OFDM. It can provide high data rate links and maintain a low PAPR to reduce the distortion caused by the nonlinear power amplifier. Thus, the quasi constant envelope OFDM is suitable for satellite communication system. However, the carrier frequency offset (CFO) in satellite communication must be estimated and compensated before the demodulation. In this paper a CFO estimation scheme is proposed for quasi constant envelope OFDM satellite system under additive white Gaussian noise (AWGN) channel. Since the null subcarrier at the transmitter can be considered as the prior information at the receiver, this null subcarrier can be used to estimate the CFO through phase demodulator and inverse discrete Fourier transform (IDFT) module at the receiver. Mathematical analysis reveals that the ideal estimation range of normalized CFO is nearly half of the size of IDFT under AWGN channel. Simulation results show that the proposed scheme performs well at moderate and high signal to noise ratio (SNR) conditions.
Hydrodynamic Characterization of USV Vessels with Innovative SWATH Configuration for Coastal Monitoring and Low Environmental Impact

The high costs associated with the use of research oceanographic vessels and the maturity of the unmanned surface vehicles (USV) makes now possible to develop systems for monitoring coastal areas based on networks of independent USVs. This type of vessels is a valid alternative to conventional vessels, which have a limited mission profile due to their high environmental impact (conventional propulsion systems based on polluting fossil fuels) inhibiting their access to protected coastal regions. Moreover, conventional vessels have high hydrodynamic resistance (limiting the autonomy) producing high levels of noise that can dramatically influence the monitoring equipment shipped: beside the environmental impact reduction, there is also the necessity of low resistance/low noise hydrodynamic specification. Consequently, the coastal monitoring (of also protected regions) needs unconventional vessels able to address both the issues related to the environmental impact and the hydrodynamic performance. In this framework, this work aims to characterize the hydrodynamic performance of a system based on USV units able to launch and recover autonomous vehicles of different nature (gliders, autonomous underwater vehicle (AUVs) motor gliders, wire guided Underwater Exploration Robots (ROVs) and able to acquire environmental data (in the column water from free surface to the sea floor) in order to meet the requirements of civil and military applications. The cutting edge aspects that characterize the USV studied are the hull SWATH type (Small Waterplane Area Twin Hulls) non conventional, optimized so as to ensure a unique seakeeping and a reduced resistance, along with the propulsion system with propellers in mantle, developed to combine propulsive efficiency and low noise. In the present paper, a SWATH shaped USV designed for monitoring of protected coastal regions is numerically studied solving the Navier Stokes equations on the fully appended vessels with several environmental conditions. An accurate hydrodynamic characterization will presented in order to investigate its performances and eventual maneuverability issues.
Primate TRIM5 proteins form hexagonal nets on HIV 1 capsids
Venue: eLife

TRIM5 proteins are restriction factors that block retroviral infections by binding viral capsids and preventing reverse transcription. Capsid recognition is mediated by C terminal domains on TRIM5a (SPRY) or TRIMCyp (cyclophilin A) which interact weakly with capsids. Efficient capsid recognition also requires the conserved N terminal tripartite motifs (TRIM) which mediate oligomerization and create avidity effects. To characterize how TRIM5 proteins recognize viral capsids, we developed methods for isolating native recombinant TRIM5 proteins and purifying stable HIV 1 capsids. Biochemical and EM analyses revealed that TRIM5 proteins assembled into hexagonal nets, both alone and on capsid surfaces. These nets comprised open hexameric rings, with the SPRY domains centered on the edges and the B box and RING domains at the vertices. Thus, the principles of hexagonal TRIM5 assembly and capsid pattern recognition are conserved across primates, allowing TRIM5 assemblies to maintain the conformational plasticity necessary to recognize divergent and pleomorphic retroviral capsids.
Expected number of real roots of random trigonometric polynomials

We investigate the asymptotics of the expected number of real roots of random trigonometric polynomials X_n(t)=u+\frac{1}\sqrt{n}\sum_{k=1}^n (A_k\cos(kt)+B_k\sin(kt) \quad t\in [0,2\pi]\quad u\in\mathbb{R} whose coefficients $A_k, B_k$ $k\in\mathbb{N} are independent identically distributed random variables with zero mean and unit variance. If $N_n[a, b] denotes the number of real roots of $X_n$ in an interval [a,b]\subseteq [0,2\pi] we prove that \lim_{n\rightarrow\infty} \frac{\mathbb{E} N_n[a,b]{n}\frac{b } e^ \frac{u^2}{2}
Denmark and UN peacekeeping: glorious past, dim future

Denmark became a staunch supporter of UN peacekeeping during the cold war because it simultaneously served its interests and values and this winning combination meant that it relatively quickly became internalized as part of Denmark's foreign policy identity. Denmark turned its back on UN peacekeeping when NATO took over from the UN in Bosnia in 1995. Since then Denmark has prioritized NATO and US led operations. The Danish shift was driven by the interest in supporting the Western great powers as well as an altruistic desire to improve United Nations Protection Force's (UNPROFOR) dismal humanitarian record in Bosnia. This belief was also generated by the positive lessons learned from Denmark's pioneering use of tanks in UNPROFOR. This tank deployment and subsequent participation in NATO and US led missions created a new warrior identity. This identity and the Danish interest in maintaining a close relationship to NATO's great powers make a major Danish return to UN peacekeeping unlikely.
How Accurate is the SMD Model for Predicting Free Energy Barriers for Nucleophilic Substitution Reactions in Polar Protic and Dipolar Aprotic Solvents

In the past seven years, the SMD (Solvent Model Density) method has been widely used by computational chemists. Thus, assessment on the reliability of this model for modeling chemical process in solution is worthwhile. In this report, it was investigated six anion molecule nucleophilic substitution reactions in methanol and dipolar aprotic solvents. Geometry optimizations have been done at SMD/X3LYP level and single point energy calculations at CCSD(T)/TZVPP diff level. Our results have indicated that the SMD model is not adequate for dipolar aprotic solvents, with a root of mean squared (RMS) error of 5.6 kcal mol 1, while the Polarizable Continuum Model (PCM) method with the Pliego and Riveros atomic cavities has led to RMS error of only 3.2 kcal mol 1. For methanol solvent, the SMD method has a RMS error of 3.0 kcal mol 1. The classical protic to dipolar aprotic solvent rate acceleration effect was not predicted by the SMD model for the tested systems.
Investigation on thermal characterization of low power SMD LED mounted on different substrate packages

Low power surface mounted device light emitting diode (SMD LED) is of high interest in research and development due to its portability and miniature size. However, high thermal resistance of low power SMD LED is a major concern due to lack of metal heat spreader. The evaluation of junction temperature and thermal resistance is important in understanding the thermal management and thermal reliability of low power SMD LEDs. In this paper, thermal parameters of low power SMD LED are determined. LED is mounted on different substrate packages which are FR4, 2W and 5W aluminum packages. Thermal parameters of LED are measured using Thermal Transient Tester (T3ster) at 50 and 100 mA. It is found that 5W aluminum package shows lower thermal resistance and junction temperature compared to the other two substrate packages. To validate the experiment, modeling and simulation using FloEFD is developed by considering geometrical model of the substrate packages.