nils-herrmann/clean_scirepeval huggingface dataset:
Deposition of silver nanoparticles in geochemically heterogeneous porous media: predicting affinity from surface composition analysis.

The transport of uncoated silver nanoparticles (AgNPs) in a porous medium composed of silica glass beads modified with a partial coverage of iron oxide (hematite) was studied and compared to that in a porous medium composed of unmodified glass beads (GB). At a pH lower than the point of zero charge (PZC) of hematite, the affinity of AgNPs for a hematite-coated glass bead (FeO-GB) surface was significantly higher than that for an uncoated surface. There was a linear correlation between the average nanoparticle affinity for media composed of mixtures of FeO-GB and GB collectors and the relative composition of those media as quantified by the attachment efficiency over a range of mixing mass ratios of the two types of collectors, so that the average AgNPs affinity for these media is readily predicted from the mass (or surface) weighted average of affinities for each of the surface types. X-ray photoelectron spectroscopy (XPS) was used to quantify the composition of the collector surface as a basis for predicting the affinity between the nanoparticles for a heterogeneous collector surface. A correlation was also observed between the local abundances of AgNPs and FeO on the collector surface.

Field of study: Environmental science
Straight multimode interference phased array structure using periodic segmented waveguide phase array.

A new design of a multimode interference (MMI) phased array structure is proposed. This design is based on replacing the arrayed delay arms between the first MMI power splitter and the second MMI combiner by periodic segmented waveguides. This allows a straight structure without curved waveguides and thus reduces greatly the size of the structure. A design example of an 8 channel multiplexer is presented showing a size reduction by a factor of 23 when compared with conventional design, while keeping nearly the same performance.

Field of study: Physics
Inhibition of histone binding by supramolecular hosts.

The tandem PHD (plant homeodomain) fingers of the CHD4 (chromodomain helicase DNA-binding protein 4) ATPase are epigenetic readers that bind either unmodified histone H3 tails or H3K9me3 (histone H3 trimethylated at Lys⁹). This dual function is necessary for the transcriptional and chromatin remodelling activities of the NuRD (nucleosome remodelling and deacetylase) complex. In the present paper, we show that calixarene-based supramolecular hosts disrupt binding of the CHD4 PHD2 finger to H3K9me3, but do not affect the interaction of this protein with the H3K9me0 (unmodified histone H3) tail. A similar inhibitory effect, observed for the association of chromodomain of HP1γ (heterochromatin protein 1γ) with H3K9me3, points to a general mechanism of methyl-lysine caging by calixarenes and suggests a high potential for these compounds in biochemical applications. Immunofluorescence analysis reveals that the supramolecular agents induce changes in chromatin organization that are consistent with their binding to and disruption of H3K9me3 sites in living cells. The results of the present study suggest that the aromatic macrocyclic hosts can be used as a powerful new tool for characterizing methylation-driven epigenetic mechanisms.

Field of study: Biology, Computer science
2-Carbethoxy-4H-3,1-benzoxazin-4-one. 1. Synthesis and reaction mechanism of formation

The possibility was examined of using various condensing agents in the intramolecular cyclization reaction of ethyl ester of 2-carbomalonanilic acid into 2-carboethoxymethyl-4H-3,1-benzoxazin-4-one. It was found that the optimal reagent is dicyclohexylcarbodiimide. By using NMR spectroscopy and deutero-exchange it was shown that the cyclization proceeds with the participation of the hydroxyl group of the carboxyl and a proton of the amide function.

Field of study: Chemistry
Microbial mats as bioreactors: populations, processes, and products

Microbial mats are dynamic and complex ecosystems exhibiting spatial and temporal heterogeneity. The physical/chemical environment is typified by steep gradients and distinct microenvironments. These microenvironments support a great diversity of species with a wide range of metabolic processes. These processes often result in coupled reactions and biogeochemical cycles, and produce important end products such as trace gases and mineral precipitates. The latter can impact the composition and character of the sediment, imparting a “biosignature.” These biosignatures can be preserved in the rock record and are useful in the interpretation of fossil record on Earth and possibly as an indication of life on other planetary bodies. The modern marine stromatolites of the Exuma Cays, Bahamas, provide an ideal system for studying the populations, processes, and products in a microbial ecosystem using a multidisciplinary approach. In order to acquire redox energy, microbial populations need to carry out metabolic reactions at rates faster than the equivalent chemical (abiotic) reactions. As such, microbes can be viewed as bioreactors that preferably oxidize carbon to CO2 to maximize the energy yield. The study of the microbial role in carbonate sedimentation and lithification in these stromatolites provides a picture of microbial mats as bioreactors producing a biosignature.

Field of study: Environmental science, Geography
Comment on "Spontaneous breaking of time-reversal symmetry in the pseudogap state of a high-T$_c$ superconductor"

We argue that that in their recent experiment in which they claim to have found evidence for a time-reversal symmetry broken state, Kaminski et al. overlooked small temperature dependent changes in the superstructure of Bi2212. These subtle changes may manifest themselves by changing the final state configurations of the photoemission process and thus invalidate their ultimate conclusions.

Field of study: Physics
Structural diversity and ligand specificity of lectins. The Bangalore effort

Structural studies in this laboratory encompass four of the five major classes of plant lectins, including the one discovered by us. In addition to addressing issues specific to individual lectins, the work provided insights into protein folding, quaternary association and generation of ligand specificity. Legume and β-prism fold lectins constitute families of proteins in which small alterations in essentially the same tertiary structure lead to large variations in quaternary structure, including that involving an open structure. Strategies for generating ligand specificity include water bridges, variation in loop length, post translational modification and oligomerization. Three of the structural classes investigated have subunits with three-fold symmetry. The symmetry in the structure is reflected in the sequence to different extents in different sub-classes. The evolutionary implications of this observation have been explored. The work on lectins has now been extended to those from mycobacteria.

Field of study: Chemistry
Analysis of an autonomous phase model for neuronal parabolic bursting

An understanding of the nonlinear dynamics of bursting is fundamental in unraveling structure-function relations in nerve and secretory tissue. Bursting is characterized by alternations between phases of rapid spiking and slowly varying potential. A simple phase model is developed to study endogenous parabolic bursting, a class of burst activity observed experimentally in excitable membrane. The phase model is motivated by Rinzel and Lee's dissection of a model for neuronal parabolic bursting ( (1987)). Rapid spiking is represented canonically by a one-variable phase equation that is coupled bi-directionally to a two-variable slow system. The model is analyzed in the slow-variable phase plane, using quasi steady-state assumptions and formal averaging. We derive a reduced system to explore where the full model exhibits bursting, steady-states, continuous and modulated spiking. The relative speed of activation and inactivation of the slow variables strongly influences the burst pattern as well as other dynamics. We find conditions of the bistability of solutions between continuous spiking and bursting. Although the phase model is simple, we demonstrate that it captures many dynamical features of more complex biophysical models.

Field of study: Biology, Mathematics
Holographic optical generation of prism anamorphs.

Analyses of prism anamorphic optical systems with single and multiple prisms in plane and spherical wave illumination geometries are presented. A theoretical evaluation and experimental demonstration of a new technique for recording holographic anamorphic elements by using prism anamorphic optical systems is discussed. It is seen that this technique offers the advantage of generating elements with low f/number. Another advantage of this recording is the easy generation of elements with different anamorphic factors by using a single configuration.

Field of study: Physics
Stimulation of thaumarchaeal ammonia oxidation by ammonia derived from organic nitrogen but not added inorganic nitrogen.

Ammonia oxidation, the first step in nitrification, is performed by autotrophic bacteria and thaumarchaea, whose relative contributions vary in different soils. Distinctive environmental niches for the two groups have not been identified, but evidence from previous studies suggests that activity of thaumarchaea, unlike that of bacterial ammonia oxidizers, is unaffected by addition of inorganic N fertilizer and that they preferentially utilize ammonia generated from the mineralization of organic N. This hypothesis was tested by determining the influence of both inorganic and organic N sources on nitrification rate and ammonia oxidizer growth and community structure in microcosms containing acidic, forest soil in which ammonia oxidation was dominated by thaumarchaea. Nitrification rate was unaffected by the incubation of soil with inorganic ammonium but was significantly stimulated by the addition of organic N. Oxidation of ammonia generated from native soil organic matter or added organic N, but not added inorganic N, was accompanied by increases in abundance of the thaumarchaeal amoA gene, a functional gene for ammonia oxidation, but changes in community structure were not observed. Bacterial amoA genes could not be detected. Ammonia oxidation was completely inhibited by 0.01% acetylene in all treatments, indicating ammonia monooxygenase-dependent activity. The findings have implications for current models of soil nitrification and for nitrification control strategies to minimize fertilizer loss and nitrous oxide production.

Field of study: Biology, Environmental science
Modeling and computing throughput capacity of wireless multihop networks

Capacity is an important property for QoS support in Mobile Ad Hoc Networks (MANETs) and has been extensively studied. However, most approaches rely on simplified models (e.g., protocol interference, unidirectional links, perfect scheduling or perfect routing) and either provide asymptotic bounds or are based on integer linear programming solvers. In this paper, we present a probabilistic approach to capacity calculation by linking the normalized throughput of a communicating pair in an ad hoc network to the connection probability of the two nodes in a so-called schedule graphG"T(N,E). The effective throughput of a random network is modeled as a random variable and its expected value is computed using Monte-Carlo methods. A schedule graph G"T(N,E) for a given network is directly derived from the physical properties of the network like node distribution, radio propagation and channel assignment. The modularity of the approach leads to a capacity analysis under more realistic network models. In the paper, throughput capacity is computed for various forms of network configurations and the results are compared to simulation results obtained with ns-2.

Field of study: Computer science
An ESPRIT-like method for quadratic phase coupling estimation

Two algorithms are proposed for estimating the quadratically coupled frequency pairs (QC pairs) in a signal consisting of complex sinusoids in white noise. Three matrices are constructed from the complex third-order cumulants of the noisy signal, the second and third being time shifted versions of the first. The list of coupled frequencies is obtained from the rank reducing numbers of the matrix pencil formed from the first matrix and either of the latter two. The first algorithm then pairs these components by relating quadratic coupling to the intersection of generalized eigenspaces corresponding to two of these frequencies. The coupling strengths are also obtained in terms of generalized eigenvectors in this intersection space. The second algorithm constructs a two-parameter matrix pencil using all the three matrices. The rank reducing pairs of this pencil on the unit circle yield the QC pairs and the associated generalized eigenvectors: the coupling strengths.

Field of study: Engineering
[Recommandations de Choisir avec soin Canada].

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N’utilisez pas d’antipsychotiques comme intervention de premiere intention pour traiter les symptomes comportementaux et psychologiques de la demence. 

Pour reduire le nombre de prescriptions d’antipsychotiques, mon equipe et moi avons concu un plan. D’abord, nous

Field of study: Medicine
Coulomb-coupled quantum-dot thermometers

A novel design concept that Coulomb-coupled quantum dots can be used as quantum probes to determine the temperature of a sample (i.e., an electronic reservoir) is proposed. Through the regulation of the positive or negative voltage bias in the thermometer, we are able to judge whether the temperature of the sample is higher or lower than that of the reference heat reservoir in the measure environment and to determine the precise temperature of the sample by using a particularly simple temperature-voltage bias relationship in the reversible condition. One outstanding characteristic of the thermometer is that when the sample is at low temperatures, a small temperature change will lead to a large voltage bias change. It means that the proposed thermometer has a high sensitivity when low-temperature samples are measured.

Field of study: Physics
The influence of brachiplex nerves patient-controlled analgesia to immune functions of amutated limb(finger) replantation patients

To study the influence of brachiplex nerves patient-controlled analgesia to immune functions of amutated limb(finger) replantation patients. Twenty amutated limb(finger) replantation patients were randomly divided into PCRA and PCIA group ,and measured circulating cytokines , C-reactive protein(CRP),cortisol ,and immune cells (neutrophilic leukocyte, histoleucocyte, lymphocytes) respectively.  PCRA, compared with PCIA , had no influence on altered levels of circulating cytokines (IL-6,IL-8,IL-10,TNF-α,CRP and cortisol )and histoleucocyte(P0.05). In contrast, the postoperative decrease in B lymphocytes and T-helper cells was significant in the PCRA group.Nature killer cells also decreased significantly in patients receiving PCRA compared with PCIA(P0.05).Conclusion:Postoperative epidural pain therapy had no influence on histoleucocyte function but reduced natural killer cells and preserved B-cell and T-helper cell populations .Epidural analgesia thus influenced the specific rather than the innate immune system and potentially blunts the post surgical lymphocyte depression, which was relevant to infectious resistance.

Field of study: Medicine
Simultaneous methanogenesis and oxygen reduction by Methanobrevibacter cuticularis at low oxygen fluxes.

Methanogenic Archaea are often encountered in habitats that are not entirely anoxic in space or time. Recent biochemical and genomic studies have revealed the capacity of methanogens to reduce molecular oxygen. O(2) reduction by Methanobrevibacter species was investigated. Cell suspensions incubated in agar tubes under a headspace of H(2)-CO(2) and increasing concentrations of O(2) formed a distinct growth band, which coincided with the oxic-anoxic interface and indicated that the influx of O(2) into the band was balanced by its consumption. However, in batch cultures methanogenesis ceased as soon as traces of O(2) were added. Focusing on Methanobrevibacter cuticularis, a species colonizing the microoxic gut epithelium of termites, a diffusion-limited setup was used that allowed the exposure of dense cell suspensions to controlled O(2) fluxes. Here, Methanobrevibacter cuticularis was capable of simultaneous CH(4) production and O(2) consumption. Low O(2) fluxes (10% of the CH(4) production rate) had virtually no influence on methanogenesis [4.5 micromol CH(4) (mg dry wt)(-1) h(-1)], whereas higher O(2) fluxes (up to 30% of the initial CH(4) production rate) caused a reversible decrease in methanogenesis, which was accompanied by a reversible, partial conversion of coenzyme F(420) to factor F(390). The maximum O(2) reduction rate [4.8 micromol O(2) (mg dry wt)(-1) h(-1)] that could be maintained over extended time periods (>30 min) was similar to the CH(4) production rate under anoxic conditions.

Field of study: Biology, Environmental science
7Li NMR relaxation by diffusion in hexagonal and cubic LixTiS2

The motion of Li ions in the quasi-two-dimensional (2D) hexagonal and the three-dimensional (3D) cubic structures of the two modifications of the intercalation compound Li x TiS 2 (0 x ⩽1) has been studied by means of nuclear magnetic relaxation spectroscopy. The 7 Li spin-lattice relaxation (SLR) times in the laboratory and the rotating frame were measured at various frequencies as a function of temperature. The results are discussed with regard to the influence of dimensionality and correlation effects.

Field of study: Materials science
Infant Cues and Stopping at the Crosswalk

An experiment was conducted in a field setting to study the effects of infant cues on inhibiting antisocial behavior-driving through a crosswalk while a pedestrian is waiting to cross the street. A female experimenter either stood alone, with a shopping cart, or with an infant stroller. As predicted, motorists stopped more frequently in the presence of the stroller than in the other two conditions.

Field of study: Psychology
Application of EGS-4 code for evaluating a Compton suppression system

The response evaluation of the Compton suppression system is usually conducted in controlled experiments with specific radiation sources. However, such sources alone cannot be used to evaluate the advanced system designs to be used in the high background radiation field of a nuclear power plant. A computational code is required to evaluate such a system. We experimentally determined the responses of a Ge detector, a scintillation detector, and a Compton suppression system; and we evaluated the validity of the results using the EGS-4 Monte Carlo Simulation code. Results showed that when the Compton suppression system is simulated, high accuracy cannot be achieved without spending at least 100 hours developing the model for the peripheral structures of the detector and for the /spl gamma/-ray scattering. However, the experimental results agreed closely with the simulation results, and the EGS-4 code was validated to be applicable to the advanced system design.

Field of study: Physics
Facilitation of ejaculation induced by 8-OH-DPAT does not produce conditioned place preference in male rats.

The serotonin 1A receptor agonist 8-hydroxy-2-(di-n-propylamino)tetralin (8-OH-DPAT) produces a drastic facilitation of ejaculation characterized by a significant reduction in the number of pre-ejaculatory intromissions and a shortening of ejaculation latency. In the present study, the authors evaluated whether this facilitation of ejaculation can induce a reward state assessed by conditioned place preference. Males treated with 0.1 or 1.0 mg/kg of 8-OH-DPAT showed a clear facilitation of ejaculation but did not develop conditioned place preference. These results clearly indicate that the pharmacological facilitation of ejaculation and the reduction of the number of intromissions does not necessarily make sex rewarding.

Field of study: Biology, Psychology
Simultaneous Optimization of SMES Coil Size and Control Parameters for Robust Power System Stabilization

As the coil size is the heart of superconducting magnetic energy storage (SMES), the simultaneous optimization of coil size and control parameters of SMES for robust power system stabilization is proposed. The structure of active and reactive power controllers of SMES is the practical first-order lead/lag compensator. To handle system uncertainties such as various generating and loading conditions, unpredictable network structures etc., the multiplicative uncertainty model is embedded in the system modeling. As a result, the optimization problem of SMES coil size and controller parameters based on the enhancement of system damping and robust stability margin against system uncertainties can be formulated. Solving the problem by a particle swarm optimization, both optimal coil size and controller parameters are obtained simultaneously and automatically. Simulation study in the West Japan six-area interconnected power system with two SMES units confirms the superior robustness and damping performance of the proposed SMES controller with an optimal coil size under various situations in comparison with the conventional SMES controller.

Field of study: Physics
Collaborating with our adult colleagues: A case series of robotic surgery for suspicious and cancerous lesions in children and young adults performed in a free-standing children's hospital.

In adult urologic oncology the use of robotics has become commonplace; in pediatric urology it is rare. Herein, we describe a collaboration between an adult and a pediatric urologist performing robotic surgery for children and young adults with suspicious or cancerous genitourinary (GU) lesions.



To evaluate clinical and oncologic outcomes in children and young adults undergoing robotic surgery for suspicious or cancerous lesions of the GU tract; to describe our collaborative model between an adult and pediatric surgeon at a free-standing children's hospital.



We retrospectively reviewed all robotic cases performed at our institution from 2014 to 2016 for patients with a GU malignancy or a suspicious mass. The surgeries were performed by a pediatric urologist with robotic experience and a fellowship-trained MIS adult urologist specializing in oncology. Perioperative and oncologic outcomes were recorded.



A total of eight robotic cases were performed: four partial nephrectomies (PN) with retroperitoneal lymph node dissection (LND) (OT 269-338 min, EBL 5-300 mL, LOS 3-6 days), one adrenalectomy with LND (6.4 cm mass; OT 172 min, EBL 5 mL, LOS 3 days), one nephrectomy with pericaval LND (9.8 cm mass; 234 min, EBL 25 mL, LOS 3 days), and two retroperitoneal LNDs (OT 572 and 508 min, EBL 250 and 100, LOS 3 and 4 days). Patient weights ranged from 14 to 79 kg (mean 53.4 kg). There were no major complications (Clavien 3-5). Pathology results for PN included papillary RCC (AJCC pT1aNx) and two cases of segmental cystic renal dysplasia with nephrogenic rests. Bilateral template RPLNDs yielded paratesticular rhabdomyosarcoma (43 nodes; COG low risk group II stage I) and mixed non-seminomatous germ cell tumor (74 nodes; COG stage III). The nephrectomy yielded an undifferentiated sarcoma, low grade; the adrenalectomy favorable-type ganglioneuroma.



In pediatrics, urologic oncology cases are often managed with open surgery. Our series demonstrates the feasibility of using the robotic approach in carefully selected cases. In doing so, the patient benefits from a minimally invasive surgery, while the surgeon benefits from robotic surgical dexterity. We seamlessly advanced these new techniques through a step-wise collaboration between an adult urologist who routinely performs robotic oncology procedures and a pediatric urologist experienced in robotics for benign conditions.



In this small series, we safely and effectively adapted adult robotic techniques for genitourinary oncology cases in children and young adults.

Field of study: Medicine