Miracle-dz/UniFAR-FTUs huggingface dataset:
Extended Molecular Evolutionary Biology: Artificial Life Bridging the Gap Between Chemistry and Biology

Molecular evolution provides an ample field for the extension of Nature's principles towards novel applications. Several examples are discussed here, among them are evolution in the test tube, nucleotide chemistry with new base pairs and new backbones, enzyme-free replication of polynucleotides and template chemistry aiming at replicating structures that have nothing in common with the molecules from nature. Molecular evolution in the test tube provides a uniquely simple system for the study of evolutionary phenomena: genotype and phenotype are two features of one and the same RNA molecule. Then fitness landscapes are nothing more than combined mappings from sequences to structures and from structures to functions, the latter being expressed in terms of rate constants. RNA landscapes are presented as examples for which an access to phenomena in reality by mathematical analysis and computer simulations is feasible. New questions concerning stability of structures in evolution can be raised and quantitative answers are given. Evolutionary biotechnology is a spin-off from molecular evolution. Darwin's principle of variation and selection is applied to design novel biopolymers with predetermined functions. Different approaches to achieve this goal are discussed and a survey of the current state of the art is given.
Facile Synthesis of CeO2-LaFeO3 Perovskite Composite and Its Application for 4-(Methylnitrosamino)-1-(3-Pyridyl)-1-Butanone (NNK) Degradation

A facile and environmentally friendly surface-ion adsorption method using CeCO3OH@C as template was demonstrated to synthesize CeO2-LaFeO3 perovskite composite material. The obtained composite was characterized by X-ray diffraction (XRD), fourier transform infrared spectra (FT-IR), field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), thermo-gravimetric analysis and differential scanning calorimetry (TG-DSC), N2 adsorption/desorption isotherms and X-ray photoelectron spectra (XPS) measurements. The catalytic degradation of nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) was tested to evaluate catalytic activity of the CeO2-LaFeO3 composite. Much better activity was observed for the CeO2-LaFeO3 composite comparing with CeO2 and LaFeO3. These results suggested that perovskite composite materials are a promising candidate for the degradation of tobacco-specific nitrosamines (TSNAs).
TARIFF OF TELECOMMUNICATIONS SERVICE

In this article, optimal two-part tariffs of a bi-directional telecommunications service are examined. Heterogeneous users are assumed to formulate social demand for the service. Two regimes of supplier are considered: monopoly and non-monopoly. In the latter, the supplier which enjoyed monopoly is faced with the entry of a competitive mpplier. Demand externalities which are conspicuous in telecommunications service are introduced into the model. The supplier is assumed to maximize the profit or to be forced to maximize the social benefit derived from the service. A nonlinear optimization method is applied to derive the optimal tariff. It is shown that the tariff diverges from conventional rules for public utility pricing.
Epidemiological aspects of venezuelan equine encephalitis virus infections.

INTRODUCTION. 65 ETIOLOGY. 65 DETECTION AND DIAGNoss. 66 Clinical Features. 66 Virus Isolation Procedures. 66 Serological Techniques. 67 EPIDEMIOLOGY. 68 Natural Distribution in Man. 68 Laboratory Infections. 70 Distribution in Domestic Animals. 70 Distribution in Wild Mammals. 70 Distribution in Birds. 71 Possible Arthropod Vectors. 72 CONTROL PROCEDURES. 74 SUMMARY AND OUTLOOK. 76 LITERATURE CITED. 77
Snail Shell Derived Natural Hydroxyapatite: Effects on NIH-3T3 Cells for Orthopedic Applications

Hydroxyapatite [HAP] and tricalcium phosphate [ß-TCP] are a class of calcium phosphate related ceramic materials that are widely used in tissue regeneration and biomedical applications owing to their excellent bioactivity and biocompatibility. In this investigation, nanocrystalline pure HAP was prepared via sol–gel method by incorporating snail shell as calcium precursor with different phosphorus sources such as triethyl phosphate/phosphite (without using any additives like pH maintaining solutions or gelling agents). Nanocrystalline HAP and biphasic calcium phosphate (HAP + ß TCP) were prepared from triethyl phosphate and triethyl phosphite precursors, respectively. The prepared material was further characterized by powder XRD, IR, Raman spectroscopy, and thermo-gravimetrical analysis to confirm the phase purity, functional groups, and thermal stability. SEM coupled with EDAX was also used to examine the size, shape of particles, and elemental composition of Ca to P ratio in the material. Different phosphorus based HAP has shown rod and spherical shaped surface morphology which was further confirmed by TEM analysis. MTT assay was performed using NIH-3T3 fibroblast cell lines which indicated that the viability was not affected in various concentrations of pure nanocrystalline HAP (12.5–100 µg/ml). This study confirms the improved biocompatibility of biowaste converted HAP which would have implications in biomedical applications.
Evaluating the Use of Snow-Covered Ranges to Estimate the Explosives Residues that Result From Detonation of Army Munitions

Abstract : Estimating the amounts of residues remaining after munitions detonate is complicated by the presence of residues from previous detonations and the difficulty in easily obtaining adequately sized samples to overcome spatial heterogeneity in residue deposition. This study was conducted to assess the use of snow-covered ranges to provide these types of estimates. Specifically, two snow-covered ranges were used to estimate the amount of explosives residues that result from detonation of individual mortar rounds. At Fort Drum, New York, 60-mm mortar rounds were fired, and at Camp Ethan Allen, Vermont, 81-mm mortar rounds were detonated by EOD personnel using C4 (RDX) and a blasting cap. The locations where residues were deposited were identified by the presence of soot from the detonation of TNT on the surface of the otherwise clean snow. Large surface snow samples were collected with a snow shovel and the melted snow was extracted and analyzed by gas chromatography with an electron capture detector ((GC-ECD) and reversed-phase high performance liquid chromatography (RP-HPLC). For both types of rounds, the main charge was Composition B (60% RDX and 39% TNT). The major residues produced were RDX and nitroglycerine (NG), with lesser amounts of HMX and TNT. Surface concentrations ranged from as high as 4430 micrograms/sq m for RDX to less than 0.05 microgram/sq m for TNT, both at Camp Ethan Allen.
Countering criticisms of single mitochondrial DNA gene barcoding in birds

General criticisms of a single mtDNA gene barcodes include failure to identify newly evolved species, use of species‐delimitation thresholds, effects of selective sweeps and chance occurrence of reciprocal monophyly within species, inability to deal with hybridization and incomplete lineage sorting, and superiority of multiple genes in species identification. We address these criticisms in birds because most species are known and thus provide an ideal test data set, and we argue with selected examples that with the exception of thresholds these criticisms are not problematic for avian taxonomy. Even closely related sister species of birds have distinctive COI barcodes, but it is not possible to universally apply distance thresholds based on ratios of within‐species and among‐species variation. Instead, more rigorous methods of species delimitation should be favoured using coalescent‐based techniques that include tests of chance reciprocal monophyly, and times of lineage separation and sequence divergence. Incomplete lineage sorting is also easily detected with DNA barcodes, and usually at a younger time frame than a more slowly evolving nuclear gene. Where DNA barcodes detect divergent reciprocally monophyletic lineages, the COI sequences can be combined with multiple nuclear genes to distinguish between speciation or population subdivision arising from high female philopatry or regional selective sweeps. Although selective sweeps are increasingly invoked to explain patterns of shallow within‐species coalescences in COI gene trees, caution is warranted in this conjecture because of limited sampling of individuals and the reduced power to detect additional mtDNA haplotypes with one gene.
DC biased input stage with differential photocurrent sensing for VLC front-ends

The reverse bias voltage across the PIN photodiode is essential for the photodiode to operate in the photoconductive mode. This paper presents an input bias stage with differential photocurrent sensing for VLC front-ends. The bias voltage is provided from within the transimpedance amplifier's (TIA) circuit eliminating the need of external bias voltage. The amount of bias voltage could be optimised according to the photodiode required sensitivity and capacitance. The differential configuration makes the TIA immune to any common mode noise. The proposed method is applied to a hypothetical TIA and results are compared with single ended structure. Simulation results showed that using this approach it is possible to achieve a transimpedance gain of 120 dBΩ over a maximum bandwidth of 14.5 MHz with a common mode rejection ratio of 61 dB while the circuit provides a controlled bias voltage of up to 6 V across the PIN photodiode eliminating the need for external bias voltage source.
Compressive Strain Behaviour under Different Strain Rates in Multi-Walled Carbon Nanotubes-Polycarbonate Composites

Polycarbonate (PC) based composites were fabricated with different concentrations of Multi Walled Carbon Nanotubes (MWCNTs) and were subjected to dynamic impact loading using Split Hopkinson Pressure Bar (SHPB). Impact tests using this instrument were performed under varying strain rates ranging from 1096 to 4017/s on pure PC samples and samples with 0.1, 0.5 and 1% by weight of MWCNT concentrations in PC. A comparison of maximum strains produced in these samples due to different strain rates was done. It was found that the maximum strain produced for every sample increases with increase in strain rate. Maximum strain is a measure of the toughness and deformation of the sample which increases as strain rate increases.
Irisin Is Elevated in Skeletal Muscle and Serum of Mice Immediately after Acute Exercise

Recent findings regarding the response of fibronectin type III domain-containing protein 5 (Fndc5) and irisin to exercise are partly controversial. While the 25 kDa form of Fndc5 can be observed in muscle and serum of different species, the ~12 kDa irisin band was not detectable up to now. The present study aimed to clarify whether irisin exists in its theoretical size of ~12 kDa in mice and if it is affected by exercise. Male mice were randomly assigned to a sedentary control group (CO), a group with free access to running wheels (RW), and a treadmill group (TM). Blood and leg muscles were collected to investigate the regulatory cascade including peroxisome proliferator-activated receptor gamma co-activator 1-alpha (Ppargc1a) and Fndc5. In western blot analysis, antibodies were used capable of differentiation between full-length Fndc5 and irisin. This enabled us to demonstrate that irisin exists in muscle and serum of mice independent of exercise and that it is increased immediately after acute exercise. Different transcripts of Ppargc1a mRNA, but not Fndc5 mRNA, were up-regulated in the TM group. Furthermore, neither Fndc5 (25 kDa) nor Ppargc1a protein was elevated in muscle tissue. The Ppargc1a-Fndc5/irisin pathway did not clearly respond to mild exercise in the RW group. Our results provide evidence for the existence of irisin and for its immediate response to acute exercise in mice.
Tuberculosis Toxin Blocking Phagosome Maturation Inhibits a Novel Ca2+/Calmodulin-PI3K hVPS34 Cascade

The capacity of Mycobacterium tuberculosis to infect latently over one billion people and cause two million fatalities annually rests with its ability to block phagosomal maturation into the phagolysosome in infected macrophages. Here we describe how M. tuberculosis toxin lipoarabinomannan (LAM) causes phagosome maturation arrest, interfering with a new pathway connecting intracellular signaling and membrane trafficking. LAM from virulent M. tuberculosis, but not from avirulent mycobacteria, blocked cytosolic Ca2+ increase. Ca2+ and calmodulin were required for a newly uncovered Ca2+/calmodulin phosphatidylinositol (PI)3 kinase hVPS34 cascade, essential for production of PI 3 phosphate (PI3P) on liposomes in vitro and on phagosomes in vivo. The interference of the trafficking toxin LAM with the calmodulin-dependent production of PI3P described here ensures long-term M. tuberculosis residence in vacuoles sequestered away from the bactericidal and antigen-processing organelles in infected macrophages.
A general strategy for the evolution of bond-forming enzymes using yeast display

The ability to routinely generate efficient protein catalysts of bond-forming reactions chosen by researchers, rather than nature, is a long-standing goal of the molecular life sciences. Here, we describe a directed evolution strategy for enzymes that catalyze, in principle, any bond-forming reaction. The system integrates yeast display, enzyme-mediated bioconjugation, and fluorescence-activated cell sorting to isolate cells expressing proteins that catalyze the coupling of two substrates chosen by the researcher. We validated the system using model screens for Staphylococcus aureus sortase A–catalyzed transpeptidation activity, resulting in enrichment factors of 6,000-fold after a single round of screening. We applied the system to evolve sortase A for improved catalytic activity. After eight rounds of screening, we isolated variants of sortase A with up to a 140-fold increase in LPETG-coupling activity compared with the starting wild-type enzyme. An evolved sortase variant enabled much more efficient labeling of LPETG-tagged human CD154 expressed on the surface of HeLa cells compared with wild-type sortase. Because the method developed here does not rely on any particular screenable or selectable property of the substrates or product, it represents a powerful alternative to existing enzyme evolution methods.
A New Insight into Hepatitis C Vaccine Development

Chronic hepatitis C virus (HCV) infection remains a serious burden to public health worldwide. Currently, HCV-infected patients could undergo antiviral therapy by giving pegylated IFN-α with ribavirin. However, this therapy is only effective in around 50% of patients with HCV genotype 1, which accounts for more than 70% of all HCV infection, and it is not well tolerated for most patients. Moreover, there is no vaccine available. The efforts on identifying protective immunity against HCV have progressed recently. Neutralizing antibodies and robust T cell responses including both CD4+ and CD8+ have been shown to be related to the clearance of HCV, which have shed lights on the potential success of HCV vaccines. There are many vaccines developed and tested before entering clinical trials. Here, we would first discuss strategies of viral immune evasion and correlates of protective host immunity and finally review some prospective vaccine approaches against chronic HCV infection.
Development of sol–gel processed semi-transparent and self-cleaning superhydrophobic coatings

Optically transparent, mechanically durable, and self-cleaning superhydrophobic coatings are greatly awaited for applications in daily life. An attempt has been made to develop sol–gel processed semi-transparent, durable and self-cleaning superhydrophobic coatings on glass using a silica–PMMA composite. A water drop acquires a near spherical shape on the coating exhibiting a water contact angle of ∼159° and immediately rolled off under small disturbance. A 10 μl water drop could individually collect around 10 mg of dirt particles along the way whilst rolling off the coating surface. The superhydrophobicity of the coatings remained intact under the impact of a water jet. A water jet hits the superhydrophobic coating and was repelled straightaway off the surface, without leaving any trace of water. These coatings showed both strong superhydrophobicity and superoleophilicity. We observed an improvement in mechanical stability, as well as optical transparency of the coatings in the visible range after low loadings of PMMA polymer (2 vol%) in silica. The prepared coatings maintained excellent superhydrophobicity even after 6 months storage under normal conditions in air.
Natural Direct and Indirect Effects on the Exposed: Effect Decomposition under Weaker Assumptions

Summary We define natural direct and indirect effects on the exposed. We show that these allow for effect decomposition under weaker identification conditions than population natural direct and indirect effects. When no confounders of the mediator‐outcome association are affected by the exposure, identification is possible under essentially the same conditions as for controlled direct effects. Otherwise, identification is still possible with additional knowledge on a nonidentifiable selection‐bias function which measures the dependence of the mediator effect on the observed exposure within confounder levels, and which evaluates to zero in a large class of realistic data‐generating mechanisms. We argue that natural direct and indirect effects on the exposed are of intrinsic interest in various applications. We moreover show that they coincide with the corresponding population natural direct and indirect effects when the exposure is randomly assigned. In such settings, our results are thus also of relevance for assessing population natural direct and indirect effects in the presence of exposure‐induced mediator‐outcome confounding, which existing methodology has not been able to address.
Cord-forming property, lethality and pathogenicity of Mycobacteria.

CONCLUSIONS The pathogenicity of 245 strains of Mycobacteria was tested by means of guinea pig inoculations; in another laboratory the same cultures were tested for their cord-forming ability in the liquid medium. Both methods, the guinea pig inoculation and the cord-forming ability, recognized 192 lethal and 40 saprophytic strains with equal efficiency. The two above mentioned groups of Mycobacteria represented 94.3 per cent of the strains tested. The remaining material consisted of eight N strains showing rudiment of cord formation. These strains were not lethal to guinea pigs but caused considerable morbid lesions in them. The origin of these strains from the lethal ones was presumed. Five isoniazid-resistant R strains formed true cords; they were classified as lethal. Two of these strains were lethal to guinea pigs; when injected intravenously, the other three were lethal to mice.
Optimal Scheduling of Information Extraction Algorithms

Most research on run-time efficiency in information extraction is of empirical nature. This paper analyzes the efficiency of information extraction pipelines from a theoretical point of view in order to explain empirical findings. We argue that information extraction can, at its heart, be viewed as a relevance filtering task whose efficiency traces back to the run-times and selectivities of the employed algorithms. To better understand the intricate behavior of information extraction pipelines, we develop a sequence model for scheduling a pipeline’s algorithms. In theory, the most efficient schedule corresponds to the Viterbi path through this model and can hence be found by dynamic programming. For real-time applications, it might be too expensive to compute all run-times and selectivities beforehand. However, our model implies the benchmarks of filtering tasks and illustrates that the optimal schedule depends on the distribution of relevant information in the input texts. We give formal and experimental evidence where necessary. TITLE AND ABSTRACT IN GERMAN Optimales Scheduling von Information-Extraction-Verfahren Nahezu alle Forschung zur Laufzeiteffizienz in der Information Extraction ist empirischer Natur. Die vorliegende Arbeit analysiert die Effizienz von Information-Extraction-Pipelines aus theoretischer Sicht, um empirische Erkenntnisse zu erklären. Wir sehen Information Extraction im Kern als Relevanz-Filteraufgabe an, deren Effizienz auf die Laufzeiten und Selektivitäten der eingesetzten Algorithmen zurückgeht. Zum besseren Verständnis des komplexen Verhaltens von Information-Extraction-Pipelines entwickeln wir ein Sequenzmodell für das Scheduling der Algorithmen einer Pipeline. Theoretisch entspricht der effizienteste Schedule dem Viterbi-Pfad durch dieses Modell und lässt sich daher mittels dynamischer Programmierung finden. Für Echtzeitanwendungen kann es zu teuer sein, alle Laufzeiten und Selektivitäten im Vorhinein zu berechnen. Unser Modell impliziert jedoch die Benchmarks von Filteraufgaben und zeigt, dass der optimale Schedule von der Verteilung relevanter Informationen in den Eingabetexten abhängt. Wo nötig, führen wir sowohl formale als auch experimentelle Belege an.
The Effect of Ball Milling on the Electrochemical Behavior of Silicon Composite Electrode

Silicon material possesses the highest theoretic capacity (4200mAh/g, ten times of the capacity of commercialized carbon anode materials) of all known anode materials for lithium ion batteries and thus receives lots of attention to date. Silicon-containing composite electrode for lithium ion batteries was prepared by high-energy ball milling process. The microstructure and morphology of silicon electrode was investigated in detail. The effect of the structure transformation of the electrode by ball milling on the electrochemical behavior was systematically analyzed. Electrode precursors after a mediate ball milling time of 45min is beneficial to get a better cycling performance, due to the well distributed and less destroy of Carboxyl Methyl Cellulose (CMC). Weak lithium insertion into CMC occurs unavoidably in the charging-discharging process of the composite electrodes, which should be the main reason for the sudden disability of electrode. The electrochemical properties can get a dramatic enhancement within voltage window of 0.02-1.5V. Excellent cyclability with high capacity retention above 1800mAh/g after 40 cycles could be gained by controlling the ball-milling time and the voltage windows. It might be a feasible way to obtain satisfactory cyclability for high capacity anode materials.
Fast construction of nets in low dimensional metrics, and their applications

We present a near linear time algorithm for constructing hierarchical nets in finite metric spaces with constant doubling dimension. This data-structure is then applied to obtain improved algorithms for the following problems: Approximate nearest neighbor search, well-separated pair decomposition, spanner construction, compact representation scheme, doubling measure, and computation of the (approximate) Lipschitz constant of a function. In all cases, the running (preprocessing) time is near-linear and the space being used is linear.