Miracle-dz/UniFAR-FTUs huggingface dataset:
Highly Stereoselective Synthesis of the Anti-Platelet Activating Factor, 4-Thiazolidinones, Using Silyl Derivatives of 2-Mercaptoalkanoic Acids

The cyclo-condensation of silyl 2-mercaptoalkanoates and arylmethyleneamines proceeded with high stereoselectivity to give alternatively both the cis- and trans-2,5-disubstituted 4-thiazolidinones, some of which are known as anti-platelet activating factor-active drugs. The use of the piperidine catalyst and no catalyst showed very high cis-stereoselectivity (cis/trans = 10/1—50/1) during the reaction. On the other hand, the trans-selective reaction was promoted by Ti(O-i-Bu)4 and Al(O-s-Bu)3 catalysts (cis/trans = 1/8—1/25). Both reactions were conducted with higher cis- and trans-selectivities as compared with those of the alkyl 2-mercaptoalkanoates under mild conditions. The cyclo-condensation using trimethylsilyl 2-(trimethylsilylthio)propionate and methyl 2-(trialkylsilylthio)propionates proceeded by the action of a catalytic amount (0.02 molar amount) of tetrabutylammonium fluoride with moderate cis-selectivity.
Boron-doped polycrystalline SixGe1-x films : Dopant activation and solid solubility

The solid solubility of B in is determined over the entire composition range from x = 1 (Si) to x = 0 (Ge). Polycrystalline films deposited using and were employed for the solubility study. Boron was introduced into the films either ex situ by ion‐implantation of or in situ by addition of to the gas mixture. The solubility results were obtained in the ion‐implanted films, and confirmed with the in situ doped ones. The solubility of B in Si is 8.1 × 1019 and at 800 and 900°C, respectively, in accordance with the results obtained in single crystal Si. The solubility of B in Ge is approximately at 800 or 900°C, in agreement with the reported value in the limited literature. The solubility of B in decreases with increasing Ge content, but does not follow a single exponential function that would link the solubility in Si and that in Ge. Furthermore, in situ doping is found superior to ion‐implantation because already at 500°C, low resistivity films are deposited with uniformly distributed high concentrations of electrically active B atoms exceeding the respective solubility limits.
Simulation of forces on entangled polymers due to slippage

We consider the force on the end of a polymer chain being pulled through a network at velocity v, using computer simulations. We develop algorithms for measuring the force on the end of the chain using lattice models of polymers. Our algorithm attaches a spring to the end being pulled and uses its average extension to calculate the force. General problems associated with the use of lattice models in obtaining forces are discussed. Variants of this method are used to obtain upper and lower bounds to the force. The results obtained are in agreement with recent analytical predictions and experiments.
V–Ti and V–Al silicate molecular sieves of MFI topology: synthesis and characteristics

Doubly substituted V–Ti and V–Al derivatives of silicalite-1 have been synthesized hydrothermally with full yield and crystallinity. The materials have been examined using XRD, SEM, EPM, ICP, SIMS, XRF, DTG/DTA, TPD of ammonia, EPR, static and MAS NMR, UV–VIS, FTIR and Raman spectroscopy. The investigation indicate incorporation of the heteroelements into the framework, give further support for the framework siting of V ions in MFI-type materials and reveal the good thermal and chemical stabilities of the substituted materials. The vanadium ions occur in several different coordinations and can be reversibly oxidized and reduced between V4+ and V5+. Introduction of Al or Ti together with V does not influence the state and/or coordination of the V ions.
Medical application-oriented nanostructure design: physical basics and limitations

We present a theoretical overview of key physical limitations for application-oriented nanostructure design. We focus on such promising applications as: nanodot-assisted optical imaging, and photo-thermal therapy with the help of nanostructures. For these applications we consider the following nanostructures: metal-coated nanoshells and metal nanoparticles. The actual design of relevant nanoobjects for particular applications must include consideration of such phenomena as: plasmon resonance, light scattering, light absorption. These phenomena are considered for model systems of various designs for different parameters of radiation. Our model estimations are compared with experimental results when such results are available. The conclusions are formulated as a paradigm "desired vs. feasible".
Molekulardynamik-Simulationen von amyloidogenen Proteinen in Lösung: Stabilitätsuntersuchungen und Weiterentwicklung einer Kontinuumsmethode

Viele neurodegenerative Erkrankungen, wie die transmissiblen spongiformen Enzephalopathien (TSE), die Alzheimer- und die Huntington-Krankheit, sind durch charakteristische Ablagerungen im Gehirn, sogenannte Amyloide, gekennzeichnet. Amyloide sind oftmals fibrillare Aggregate von normalerweise loslichen Proteinen, deren dreidimensionale Strukturen sich bei der Aggregation verandern. Bedauerlicherweise waren hochauflosende Methoden biophysikalischer Strukturaufklarung bislang auf Amyloide nicht anwendbar. Dagegen konnen Molekulardynamik (MD)-Simulationen amyloidogener Proteine und Peptide in ihrer Losungsmittelumgebung dazu beitragen, die Mechanismen der auftretenden Konformationsanderungen zu verstehen und die Strukturen amyloider Fasern aufzuklaren. Die korrekte und effiziente Beschreibung der Losungsmittelumgebung spielt dabei eine entscheidende Rolle. Im ersten Teil dieser Arbeit wird die Konformationsdynamik Amyloid bildender Peptide und Proteine in expliziter wassriger Umgebung untersucht. In MD-Simulationen des zellularen Prion Proteins (PrPC) werden durch Einfuhrung der Punktmutationen M205S und M205R entscheidende Faktoren fur die korrekte Faltung und strukturelle Stabilitat des Proteins identifiziert. Ferner wird fur die Grundstruktur der bei TSE auftretenden pathogenen Isoform PrPSc ein Modell basierend auf dem Strukturmotiv einer parallelen beta-Helix entwickelt. Analog dazu werden Peptide aus poly-Glutamin, die den mutmaslichen Aggregationskeim bei der Huntington-Krankheit darstellen, als parallele beta-Helizes unterschiedlicher Formen und Grosen modelliert. In MD-Simulationen ermitteln wir aus diesen Strukturen thermodynamisch stabile monomere und dimere Aggregationskeime. Da die erreichbaren Simulationszeiten in expliziten Losungsmitteln verglichen mit den Zeitskalen der Proteindynamik zu kurz sind, wird im zweiten Teil dieser Arbeit eine effiziente Kontinuumsmethode fur Proteine in polaren Losungsmitteln weiterentwickelt. In dieser Methode wird das durch die Polarisation des Losungsmittels hervorgerufene Reaktionsfeld (RF) durch normalverteilte RF-Dipoldichten an den Orten der Proteinatome beschrieben. Die sich daraus ergebenden RF-Krafte auf die Proteinatome berucksichtigen aber nicht den Druck an den dielektrischen Grenzflachen, der vom Kontinuum auf das Protein ausgeubt wird, und verletzen damit das 3. Newtonsche Gesetz. Dies fuhrt in MD-Simulationen zu erheblichen Artefakten. In dieser Arbeit wird diese Kontinuumsmethode so umformuliert und erweitert, dass die resultierenden RF-Krafte dem Prinzip Actio=Reactio gehorchen. Die modifizierte Kontinuumsmethode wird in ein MD-Programm implementiert und an Hand geeigneter Systeme parametrisiert. In ausgedehnten MD-Simulationen des Alanin-Dipeptids wird die Korrektheit und Effizienz der Methode demonstriert.
Adsorption of Phenolic Compounds onto the Activated Carbon Synthesized from Pulp and Paper Mill Sludge: Equilibrium Isotherm, Kinetics, Thermodynamics and Mechanism Studies

Adsorption Precursor ABSTRACT New activated carbon was produced from pulp and paper mill sludge as a low cost precursor via chemical activation by zinc chloride. The activated carbon was successfully used for the adsorption of phenol and two of its derivatives, i.e. 2-chlorophenol and 4-nitrophenol from aqueous solutions. The characterization of the prepared activated carbon demonstrated high textural properties for the synthesized activated carbon. The results revealed superior adsorption performance of the prepared activated carbon in this study compared to the commercial one. The effect of main affecting parameters such as pH, contact time, concentration and temperature on adsorption of phenolic compounds was experimentally investigated in discontinuous system. The adsorption capacities followed the order of 4-nitrophenol > 2-chlorophenol >phenol which was attributed to the property of substituent groups in their chemical structure. Amongst the isotherm models used to describe experimental equilibrium data, the best match was obtained by Sips isotherm which revealed the heterogeneous behavior of the adsorption sites on the adsorbent surface. Kinetic study demonstrated that the adsorption kinetics followed pseudo-second-order kinetic model. Based on thermodynamical analysis, the negative values obtained for Gibbs free energy, enthalpy and entropy indicated spontaneous, exothermic and random behavior of the adsorption process.
Electronic structure of the substitutional vacancy in graphene: density-functional and Green's function studies

We study the electronic structure of graphene with a single substitutional vacancy using a combination of the density-functional, tight-binding and impurity Green's function approaches. Density-functional studies are performed with the all-electron spin-polarized linear augmented plane wave (LAPW) method. The three sp2σ dangling bonds adjacent to the vacancy introduce localized states (Vσ) in the mid-gap region, which split due to the crystal field and a Jahn–Teller distortion, while the pzπ states introduce a sharp resonance state (Vπ) in the band structure. For a planar structure, symmetry strictly forbids hybridization between the σ and the π states, so that these bands are clearly identifiable in the calculated band structure. As to the magnetic moment of the vacancy, the Hund's rule coupling aligns the spins of the four localized Vσ1↑↓, Vσ2↑ and Vπ↑ electrons, resulting in an S = 1 state, with a magnetic moment of 2μB, which is reduced by about 0. 3μB due to the anti-ferromagnetic spin polarization of the π band itinerant states in the vicinity of the vacancy. This results in the net magnetic moment of 1. 7μB. Using the Lippmann–Schwinger equation, we reproduce the well-known ∼1/r decay of the localized Vπ wave function with distance, and in addition, find an interference term coming from the two Dirac points, previously unnoticed in the literature. The long-range nature of the Vπ wave function is a unique feature of the graphene vacancy and we suggest that this may be one of the reasons for the widely varying relaxed structures and magnetic moments reported from the supercell band calculations in the literature.
On the complex conductivity signatures of calcite precipitation

On the complex conductivity signatures of calcite precipitation Yuxin Wu 1 , Susan Hubbard 1 , Kenneth Hurst Williams 1 , Jonathan Ajo-Franklin 1 1. Earth Sciences Division, Lawrence Berkeley National Laboratory, MS 90-1116, 1 Cyclotron Road, Berkeley, CA 94720 Abstract Calcite is a mineral phase that frequently precipitates during subsurface remediation or geotechnical engineering processes. This precipitation can lead to changes in the overall behavior of the system, such as flow alternation and soil strengthening. Because induced calcite precipitation is typically quite variable in space and time, monitoring its distribution in the subsurface is a challenge. In this research, we conducted a laboratory column experiment to investigate the potential of complex conductivity as a mean to remotely monitor calcite precipitation. Calcite precipitation was induced in a glass bead (3 mm)-packed column through abiotic mixing of CaCl 2 and Na 2 CO 3 solutions. The experiment continued for 12 days with a constant precipitation rate of ~0.6 milimole/day. Visual observations and Scanning Electron Microscope (SEM) imaging revealed two distinct phases of precipitation: an earlier phase dominated by well distributed, discrete precipitates and a later phase characterized by localized precipitate aggregation and associated pore clogging. Complex conductivity measurements exhibited polarization signals that were characteristic of both phases of calcite precipitation, with the precipitation volume and crystal size controlling the overall polarization magnitude and relaxation time constant. We attribute the observed responses to polarization at the electrical double layer (EDL) surrounding calcite crystals. Our experiment illustrates the potential of electrical methods for characterizing the distribution and aggregation state of nonconductive minerals like calcite. Advancing our ability to quantify geochemical transformations using such non-invasive methods is expected to facilitate our understanding of complex processes associated with natural subsurface systems as well as processes induced through engineered treatments (such as environmental remediation and carbon sequestration).
Effect of moisture regime on recovery and utilization of fertilizer n applied to corn

Abstract Environmental and economic concerns have resulted in renewed interest in the potential for N loss under various climatic conditions. Experiments were conducted over a three‐year period at three locations in Illinois to evaluate the effects of soil type and soil moisture conditions on the fate of fertilizer N during the growing season. At each location, a factorial arrangement of four N rates (0, 100, 150, and 200 lb N/acre) and three soil moisture levels (ambient, ambient + 4 in. over a 3‐d period, and ambient + 6 in. over an 8‐d period) was established with com (Zea mays L.). Isotopic 15N was used for the 150 lb N/acre plots. After the moisture treatments had been imposed, moisture levels were allowed to return to conditions drier than 0.33 bar and plots were split with one half receiving a supplemental application of 50 lb N/acre. Regression equations relating total recovered N and plant N uptake to soil moisture condition and N application were developed for each site. Fertilizer N recovery on.
Mobilité des métaux dans les systèmes sol-plante-biochar

Les biochars sont au cœur de la lutte contre les changements globaux. Ils constituent aussi un enjeu pour la gestion durable des sols contamines. Ces travaux ont ete conduits afin de mieux comprendre les effets du biochar sur la mobilite des metaux dans les sols et leur transfert vers les plantes. Une serie d’experiences de complexite croissante ont ete conduites, impliquant un biochar obtenu par pyrolyse de bois a 450 °C, et deux sols, l’un acide et l’autre alcalin, contamines par Cd, Pb et Zn suite a l'activite d'une fonderie. Une gamme d’especes vegetales aux reponses contrastees vis-a-vis des metaux a ete testee. Des essais de sorption en batch et de lixiviation en colonnes couples a une caracterisation microscopique et spectroscopique du biochar ont ete realises, ainsi que des experiences de croissance vegetale en vases de vegetation, en rhizotrons et en lysimetres. Les resultats demontrent que les phases minerales carbonatees du biochar jouent un role preponderant dans l'immobilisation des metaux. Elles interviennent dans la sorption directe des metaux a la surface du biochar par co-precipitation. Leur dissolution contribue egalement a l'augmentation du pH du sol, conduisant a une retention accrue des metaux a la surface des particules du sol. Le biochar modifie le transfert des metaux vers la plante en diminuant la disponibilite des metaux, mais egalement en diminuant la mobilite de cations majeurs et en modifiant la surface racinaire developpee par la plante. Une diminution du transfert du metal vers les parties aeriennes de la plante a generalement ete observee avec Lolium perenne ou Zea mays, alors qu'une augmentation du prelevement de Cd et Zn par l'hyperaccumulateur Noccaea caerulescens a ete mise en evidence. En conclusion, le biochar controle la mobilite des metaux dans les systemes sol-plante grâce a une serie de mecanismes differents. Au plan pratique, le biochar favorise les strategies de phytostabilisation et de phytoextraction des metaux dans les sols contamines
Automated force field optimisation of small molecules using a gradient-based workflow package

In this study, the recently developed gradient-based optimisation workflow for the automated development of molecular models is for the first time applied to the parameterisation of force fields for molecular dynamics simulations. As a proof-of-concept, two small molecules (benzene and phosgene) are considered. In order to optimise the underlying intermolecular force field (described by the (12,6)-Lennard-Jones and the Coulomb potential), the energetic and diameter parameters ε and σ are fitted to experimental physical properties by gradient-based numerical optimisation techniques. Thereby, a quadratic loss function between experimental and simulated target properties is minimised with respect to the force field parameters. In this proof-of-concept, the considered physical target properties are chosen to be diverse: density, enthalpy of vapourisation and self-diffusion coefficient are optimised simultaneously at different temperatures. We found that in both cases, the optimisation could be successfully concluded by fulfillment of a pre-defined stopping criterion. Since a fairly small number of iterations were needed to do so, this study will serve as a good starting point for more complex systems and further improvements of the parametrisation task.
The structure of a model ionic melt in a planar slit

The structure of the primitive model fused salt in planar slit is studied by Monte Carlo simulation. The density profile of the ionic melt in the slit with respect to the walls displays oscillations similar to those observed with simple liquids. At the pore width of about seven ionic diameters, the pressure exerted on the walls is comparable to the virial pressure of the bulk melt. The calculated surface energy of 210+20 mN m−1 is close to the experimental value for molten potassium chloride at similar conditions.
Ochratoxin A in liquorice and liquorice root products.

The analysis of 83 food and drug samples containing liquorice root shows partially important contamination rates and singulary high contents, as they are observed within crude products but not in consumer products. There exists a big difference between peeled and unpeeled root. Drugs with special indication show depending on the percentage of liquorice in the product, extrem levels. Results of some samples had been confirmed by LC-tandem-MS, as this combination of chromatographic separation and spectroscopy allows the selective detection of analytes in a complex matrix like food.
Multi Agent Team Learning in Disaggregated Virtualized Open Radio Access Networks (O-RAN)

As we are moving towards the new era of 5G supported verticals and their services, there is a surge in the mobile network investments and equipment deployments. The traditional monolithic mobile network radio access equipment, generally called as the base station (BS), houses radio units (RU), processors and accelerators along with proprietary software. With the advances in cloud technologies, disaggregated Radio Access Network (RAN) architectures emerged in the past decade, where Network Functions (NFs) are ripped away from specialized hardware and placed on bare metal servers. Although the concept of RAN evolution has been around for some time starting from Cloud Radio Access Networks (C-RANs), continuing with Virtual Radio Access Networks (vRANs) and most recently Open Radio Access Networks (ORANs), we are seeing commercial implementations and tests of disaggregated, virtualized and open RANs only since the beginning of 2020. One unique aspect that motivates this paper is the availability of new opportunities that arise from applying machine learning to optimize the RAN in closed-loop, i.e. without human intervention, where the complexity of disaggregation and virtualization makes well-known Self-Organized Networking (SON) solutions inadequate. In particular, Multi-agent systems (MASs) is expected to play an essential role in the control and coordination of near-real-time and nonreal-time RAN Intelligent Controller (RIC). In this visionary article, we first present the state-of-the-art research in multiagent systems and team learning, then we provide an overview of the landscape in RAN disaggregation, virtualization, as well as ORAN which emphasizes the open interfaces introduced by the O-RAN Alliance. We present a case study for ML-based disaggregation, and finally, we identify challenges and open issues to provide a roadmap for researchers.
AIDE: Annotation-efficient deep learning for automatic medical image segmentation

Accurate image segmentation is crucial for medical imaging applications. The prevailing deep learning approaches typically rely on very large training datasets with high-quality manual annotations, which are often not available in medical imaging. We introduce Annotation-effIcient Deep lEarning (AIDE) to handle imperfect datasets with an elaborately designed cross-model self-correcting mechanism. AIDE improves the segmentation Dice scores of conventional deep learning models on open datasets possessing scarce or noisy annotations by up to 30%. For three clinical datasets containing 11,852 breast images of 872 patients from three medical centers, AIDE consistently produces segmentation maps comparable to those generated by the fully supervised counterparts as well as the manual annotations of independent radiologists by utilizing only 10% training annotations. Such a 10-fold improvement of efficiency in utilizing experts' labels has the potential to promote a wide range of biomedical applications.
Spatiotemporal Variations of Bioaerosols in the Vicinity of an Animal Feeding Operation Facility in the US

Bioaerosol emissions from animal feeding operation (AFO) facilities are of increasing interest due to the magnitude of the emissions and their potential health effect on local communities. There is limited information about fate and transport of AFO bioaerosol emissions. In this study, concentrations of airborne bacteria and fungi were measured at four ambient stations in four wind directions surrounding an egg production farm through winter, spring and summer using Andersen six-stage samplers. Mean concentrations of ambient bacteria and fungi ranged from 8.7 × 102 CFU m-3 to 1.3 × 103 CFU m-3 and from 2.8 × 102 CFU m-3 to 1.4 × 103 CFU m-3, respectively. Ambient bacterial concentrations were not significantly different over the seasons, while ambient fungal concentrations were the highest in summer and the lowest in winter. There were significant differences between downwind and upwind bacterial concentrations (p < 0.0001). Downwind bacterial and fungal concentrations responded differently to the influencing factors. Bacterial concentrations were quadratically correlated with wind vector (combined effects of wind speed and direction) and emission rate, were positively correlated with temperature, and were negatively correlated with solar radiation. Fungal concentrations were positively correlated with temperature, RH, and emission rate, and were negatively correlated with wind vector.
Two-loop scalar kinks

At one loop, quantum kinks are described by a sum of quantum harmonic oscillator Hamiltonians, and the ground state is just the product of the oscillator ground states. Two-loop kink masses are only known in integrable and supersymmetric cases and two-loop states have never been found. We find the two-loop kink mass and explicitly construct the two-loop kink ground state in a scalar field theory with an arbitrary nonderivative potential. We use a coherent state operator which maps the vacuum sector to the kink sector, allowing all states to be treated with a single Hamiltonian which needs to be renormalized only once, eliminating the need for regulator matching conditions. Our calculation is greatly simplified by a recently introduced alternative to collective coordinates, in which the kink momentum is fixed perturbatively.