Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Bottlenecks Driven by Population Disconnection

Abstract: Connectivity among populations plays a crucial role in maintaining genetic variation at a local scale, especially in small populations affected strongly by genetic drift. The negative consequences of population disconnection on allelic richness and gene diversity (heterozygosity) are well recognized and empirically established. It is not well recognized, however, that a sudden drop in local effective population size induced by such disconnection produces a temporary disequilibrium in allelic frequency distributions that is akin to the genetic signature of a demographic bottleneck. To document this effect, we used individual‐based simulations and empirical data on allelic richness and gene diversity in six pairs of isolated versus well‐connected (core) populations of European tree frogs. In our simulations, population disconnection depressed allelic richness more than heterozygosity and thus resulted in a temporary excess in gene diversity relative to mutation drift equilibrium (i.e., signature of a genetic bottleneck). We observed a similar excess in gene diversity in isolated populations of tree frogs. Our results show that population disconnection can create a genetic bottleneck in the absence of demographic collapse.
Complete Genome Sequence of Bacillus velezensis CBMB205, a Phosphate-Solubilizing Bacterium Isolated from the Rhizoplane of Rice in the Republic of Korea

ABSTRACT Bacillus velezensis CBMB205 (= KACC 13105T = NCCB 100236T) was isolated from the rhizoplane of rice (Oryza sativa L. cv. O-dae). According to previous studies, this bacterium has several genes that can promote plant growth, such as the phosphorus-solubilizing protein-coding gene. Here, we present the first complete genome of B. velezensis CBMB205.
On the branching of motoneurons

Innervation ratios were estimated for motor units supplying superficial lumbrical muscles of the cat after assigning units to one of three types, FF/FI, FR, and S, and estimating their axonal conduction velocity, based on published data. Similarly, unit tensions were converted to muscle fiber number using published values for specific tension and fiber cross‐sectional area. A relation was established between axonal area of cross‐section and number of fibers innervated which was matched reasonably well by a model of a branching motoneuron with preterminal diameter of 4.28 μm and a daughter‐to‐parent ratio of 1.48 at each level of branching. It is proposed that the main features of the model are likely to apply to all motoneurons. © 2001 John Wiley & Sons, Inc. Muscle Nerve 24: 372–379, 2001
Frequency-selective fading channel estimation with a polynomial time-varying channel model

A rectangular-windowed least-squares estimator using a polynomial model of the time-varying channel taps is proposed for estimating the impulse response of a frequency-selective fading channel. This method provides a significant improvement in mean square identification error (MSIE) over the conventional least mean squares (LMS) and the exponentially weighted recursive least squares (EW-RLS) algorithms without a polynomial model. A detailed study of the effects of channel parameters, such as the fading rate and the signal-to-noise ratio, on the proposed method is carried out. The performance of the method depends on the window size of the least squares estimator and the polynomial order being used. Algorithms to obtain the approximately optimal window size and polynomial order are proposed and are shown to perform well.
Adaptation and Combination of NMT Systems: The KIT Translation Systems for IWSLT 2016

In this paper, we present the KIT systems of the IWSLT 2016 machine translation evaluation. We participated in the machine translation (MT) task as well as the spoken language language translation (SLT) track for English→German and German→English translation. We use attentional neural machine translation (NMT) for all our submissions. We investigated different methods to adapt the system using small in-domain data as well as methods to train the system on these small corpora. In addition, we investigated methods to combine NMT systems that encode the input as well as the output differently. We combine systems using different vocabularies, reverse translation systems, multi-source translation system. In addition, we used pre-translation systems that facilitate phrase-based machine translation systems. Results show that applying domain adaptation and ensemble technique brings a crucial improvement of 3-4 BLEU points over the baseline system. In addition, system combination using n-best lists yields further 1-2 BLEU points.
Several Grassland Soil Nematode Species Are Insensitive to RNA-Mediated Interference.

Phenotypic analysis of defects caused by RNA mediated interference (RNAi) in Caenorhabditis elegans has proven to be a powerful tool for determining gene function. In this study we investigated the effectiveness of RNAi in four non-model grassland soil nematodes, Oscheius sp FVV-2. , Rhabditis sp, Mesorhabditis sp. , and Acrobeloides sp. In contrast to reference experiments performed using C. elegans and Caenorhabditis briggsae, feeding bacteria expressing dsRNA and injecting dsRNA into the gonad did not produce the expected RNAi knockdown phenotypes in any of the grassland nematodes. Quantitative reverse-transcribed PCR (qRT-PCR) assays did not detect a statistically significant reduction in the mRNA levels of endogenous genes targeted by RNAi in Oscheius sp. , and Mesorhabditis sp. From these studies we conclude that due to low effectiveness and inconsistent reproducibility, RNAi knockdown phenotypes in non-Caenorhabditis nematodes should be interpreted cautiously.
Pregnancy-associated Plasma Protein-A2 (PAPP-A2), a Novel Insulin-like Growth Factor-binding Protein-5 Proteinase*

A novel metalloproteinase with similarity to pregnancy-associated plasma protein-A (PAPP-A), which we denoted PAPP-A2, has been identified. Through expression in mammalian cells we showed that recombinant PAPP-A2 polypeptide of 1558 residues resulted from processing of a 1791-residue prepro-protein. Unlike PAPP-A, PAPP-A2 migrated as a monomer (of 220 kDa) in non-reducing SDS-polyacrylamide gel electrophoresis. The prepro-parts of PAPP-A2 and PAPP-A are not homologous, but mature PAPP-A2 shares 45% of its residues with PAPP-A. Because PAPP-A specifically cleaves insulin-like growth factor-binding protein (IGFBP)-4, one of six known modulators of IGF-I and -II, we looked for a possible PAPP-A2 substrate among the members of this family. We showed that PAPP-A2 specifically cleaved IGFBP-5 at one site, between Ser-143 and Lys-144. In contrast to the cleavage of IGFBP-4 by PAPP-A that strictly requires the presence of IGF, the cleavage of IGFBP-5 by PAPP-A2 was IGF-independent. Recent data firmly establish PAPP-A and IGFBP-4 as an important functional pair in several systems. Because of its close relationship with PAPP-A, both structurally and functionally, PAPP-A2 is a likely candidate IGFBP-5 proteinase in many tissues and conditioned media where IGFBP-5 proteolysis has been reported.
Percutaneous Endoscopic Placement of the “Button” Gastrostomy Tube as the Initial Procedure in Infants and Children

Summary Percutaneous endoscopic gastrostomy (PEG) tube placement is routinely performed in children with special nutritional needs. For convenience and cosmetic reasons, many parents prefer a skin-level, nonrefluxing, (“button”) gastrostomy tube. After healing of the track, a button gastrostomy tube can replace a PEG but this requires a second procedure. This study assessed the technique and complication rate of placement of a button gastrostomy tube mounted for endoscopic placement as the initial procedure. Seventeen patients (10 males), ages 4 months to 12 years were studied. All patients underwent successful placement of the button under conscious sedation using a standard endoscopic push technique. In the first 10 patients, an 18 French device was used. Four patients developed migration of the device into the track between 9 and 55 days after placement and the button was removed. Migration was preceded or accompanied by a wound infection in 3 of the 4 patients. In the next 7 patients, a larger, 24 French button was used without any wound infections or migration of the device. In thirteen patients with successful placement, a follow-up period of 110–450 days has revealed no further complications. Placement of the button gastrostomy tube in infants and children can be accomplished using standard endoscopic techniques. However, further study of the optimal size of the device and optimal placement procedure to prevent wound infection and migration should be undertaken.
The Use of DNA Microsatellite Loci for “Caretta Caretta” Identification

Caretta carettas, one of the members of Chelonidae family, live primarily in water, except the periods of their ovulation where they come out to the shores to lay their eggs. Following an incubation period of 50–60 days, the newborns return to sea water to continue their 10–12-year life. Studies using marking methodology of the animals have shown that females return to the same place for ovulation every 2–3 years. The development of molecular genetic studies gives us now opportunity to trace all these routes that Caretta carettas follow during their life cycle. One of the basic techniques that is used for identification in general is the polymorphic DNA microsatellite loci. These 2–4 base pair DNA segments are considered to be ideal for Caretta caretta identification also. In this study we tried to establish a protocol in order to identify both male and female carettas in tissue samples collected from animals in the Mediterranean shoreline in the southern Turkey once this shoreline is one of the main spots of them for ovulation. The sampling has been done from 89 locations (Dalyan, Dalaman, Fethiye, Patara, Kale, Kumluca, Belek, Kızılot, Demirtaş, Gazipaşa and Anamur) from 246 dead baby Caretta carettas. DNA was extracted using silica-based extraction technology from the tissue homogenates. Cc7 locus was selected for identification to be tested for its degree of polymorphic content and therefore power of discrimination in general. The methodology used is PCR, followed by polyacrilamide gel electrophoresis and silver staining.
Self-similarity Research on Scale-free Networks

Self-similarity of scale-free networks and volume-dimension are given based on the concept of fractal. The reason and the course of self-similarity networks formed and these three statistics characters of complex networks are discussed and analyzed in detail in this paper; besides, the concept of self-similarity groups is defined firstly. We propose that different local networks can be covered with different edges of box to reveal the self-similarity of special scale-free networks. Both theoretical analyses and simulation results are the evolution and characters more exactly for many scale-free networks of the real world.
A review of the development of a bloat-reduced alfalfa cultivar

The studies that led to the development of a bloat-reduced alfalfa began in 1970. Initial work focused on the causes of bloat, the characteristics of bloat-safe and bloat-causing legumes and the development of screening methodologies. The characteristics that were examined as causal factors of bloat in legume species included soluble proteins, saponins, absence of condensed tannins, and rapid breakdown of cells in the rumen. The factor or combination of factors responsible for causing bloat in animals grazing legumes have not been clearly identified; however, of the above, rapid cell breakdown was considered to be the most promising line of research to pursue in selecting a bloat-safe legume. A 4-h nylon-bag rumen digestion technique was developed, which was used to assess the initial rate of digestion (IRD) of fresh leaf material in large numbers of alfalfa genotypes. Using this technique on a population of four alfalfa cultivars, four cycles of recurrent selection for low initial rate of digestion (LIRD.
ormation of crystalline complexes between amylomaize dextrin and

Complexes between amylomaize dextrin (average DP 311) and ceramide were prepared by using two different blending systems: an aqueous batch system containing ethanol and a two-phase system of isopropyl ether and water. The organic solvents and complex formation temperature (50–90 ◦C) were important in determining the level of complex formation and its crystalline structure. Under X-ray diffraction analysis, the solvents as well as ceramide could form complexes with dextrin as weak V6I type crystals. However, the crystallinity of complexes was much higher in the presence of ceramide, which would enhance complex formation by forming ternary co-inclusion complexes of dextrin–solvent–ceramide.
Model-driven Engineering for the Configuration and Deployment of Data Processing Applications

This position paper reports our current endeavour towards a model-driven engineering framework to support the dynamic configuration and deployment of complex data processing applications. In particular, our approach includes a domain-specific modelling language that abstracts the data processing tasks and at the same time exposes the control of how these tasks are deployed on specific platforms and resources. A modelling framework of model transformation and models@runtime engines realises the semi-automatic configuration and deployment of the applications based on the abstract models.
Automated TES modeling of compressed video

TES (transform-expand-sample) is a versatile class of stationary stochastic processes which can model arbitrary marginals, a wide variety of autocorrelation functions, and a broad range of sample path behaviors. TES models include one set of parameters for exact fitting of the empirical distribution (histogram), and another for approximating the empirical autocorrelation function. The former is easy to determine algorithmically, but the latter involves a hard heuristic search on a large parametric function space. This paper describes an algorithmic procedure which largely automates TES modeling. The algorithm is cast in a nonlinear programming setting with the objective of minimizing a weighted square distance between the empirical autocorrelation function and its candidate TES-model counterpart. It combines a brute-force search with a steepest-descent nonlinear programming technique, and it performs well owing to the simplicity of the constraints and the nice local behavior of the objective function. Finally, we illustrate the efficacy of our approach via two examples from the domain of VBR (variable bit rate) compressed video.
A low-power 5 GHz CMOS LC-VCO optimized for high-resistivity SOI substrates

This paper discusses the power saving of an LC-VCO designed on high-resistivity SOI substrates (/spl rho/ > 1000/spl Omega//spl middot/cm). It demonstrates the drastic improvement in the varactors and inductors quality factor on these substrates. It stresses on the importance of optimizing the tank inductor and the VCO for high-resistivity substrates. A 5GHz VCO designed in a 0.13/spl mu/m partially depleted SOI CMOS confirms the low-power performance with a figure-of-merit greater than 190, placing this design at the top of the state-of-the-art.
EFFECT OF HYDROGEN PEROXIDE ON BACILLUS SUBTILIS SPORE REMOVAL IN AN ELECTROPHOTOCATALYTIC SYSTEM

Bacillus subtilis spores have been widely used in UV reactor validation as a possible surrogate for protozoa studies. UV light has become one of the most important methods of water disinfection. Hydrogen peroxide has been used as a strong oxidizing agent. The rate of disinfection of hydrogen peroxide is enhanced by UV and ozone. Bacillus subtilis spores are not sensitive to H2O2; thus, they have been the most important targets of peroxide sterilization. The goal of this study was to evaluate the potential of an electrophotocatalytic/hydrogen peroxide reactor for spore inactivation by studying this method with Bacillus subtilis spores. Contaminated water in an electrophotocatalytic reactor was prepared by adding 10 2 -10 3 spores of B. subtilis to the water. The batch electrophotocatalytic reactor was a 360-ml glass vessel. The characteristics of the electrodes were as follows: An electrode of ZnO nanoparticles immobilized on zinc and a copper electrode. The studied variables were pH (6-8), the number of spore suspensions (10 2 -10 3 spores / ml), the light emitting diodes (LED) UV-A lamps (2-4 W), time (5-40 min), layers of zinc oxide nanoparticles (1-3), the concentration of hydrogen peroxide (0.1-1000 mM), and voltage (10-20 V). The findings show that using H2O2 in the presence of UV-A irradiation (UV/H2O2) leads to an increase in spore removal efficiency. Optimal removal was obtained at pH 7, with a time of electrolysis of 5 minutes, 2 layers of nano ZnO, and a voltage of 10 V. This result suggests that this method is efficient for the enhanced disinfection of water.
Identifying the biomarker potential of telomerase activity and shelterin complex molecule, telomeric repeat binding factor 2 (TERF2), in multiple myeloma

Abstract Telomere length (TL) is maintained by telomere capping protein complex called shelterin complex. We studied the possible involvement and biomarker potential of shelterin complex molecules in naive multiple myeloma (MM) patients and controls. TL, relative telomerase activity (RTA), real-time PCR and Western blotting were performed in bonemarrow sample of 70 study subjects (patients = 50; controls = 20). Significantly lowered mean TL, increased RTA and higher mRNA expression of shelterin molecules were observed in patients, while PIN2/TERF1 interacting telomerase inhibitor 1 (PINX1) showed lower mRNA expression. Significantly increased protein expression of telomeric repeat binding factor 2 (TERF2), protection of telomeres 1, adrenocortical dysplasia homolog, Tankyrase 1 and telomere reverse transcriptase were observed in MM patients. Significant correlation was observed among genes and of genes with clinical parameters. In conclusion, our findings showed alteration of these molecules at mRNA and protein levels suggested their involvement in disease progression. Optimal sensitivity and specificity of TERF2 and RTA on receiver operating characteristics curve analysis and univariate analysis demonstrated their biomarkers potential in better prediction of disease course.
Bronchoscopic Lung Volume Reduction in Patients with Severe Emphysema: Anesthetic Management

Bronchoscopic lung volume reduction is a novel approach to the treatment of severe emphysema. Its objective is to achieve the same improvements in lung function and exercise tolerance as lung volume reduction surgery while avoiding the surgical morbidity and mortality. We describe the anesthetic experience in a series of seven patients who underwent a total of eight procedures (one patient underwent a second procedure on the contralateral side). The technique used was one of total IV anesthesia using remifentanil and propofol, with a ventilatory strategy aimed at avoiding gas trapping and dynamic hyperinflation. To achieve this pressure, limited ventilation with a prolonged expiratory phase was provided by a Draeger Evita 2 ventilator. This technique resulted in intraoperative hypercapnia (Paco2 6.75 kPa) compared with baseline values (median Paco2 5.1 kPa; P < 0.05), but 2 h postoperatively the arterial partial pressure of CO2 was returning to baseline (median Paco2 5.6 kPa; P < 0.01 compared with intraoperative data). There were no deaths or admissions to the intensive care unit after the procedure. One patient developed a pneumothorax that required drainage, three patients had acute exacerbations of chronic obstructive pulmonary disease, and one patient developed a cough that resolved spontaneously. Total hospital stay did not exceed 5 days for any of these patients.
Penile sparing surgical approaches for primary penile tumors: preserving function and appearance

Penile cancer is a rare and potentially disfiguring disease. There are multiple treatment options for primary penile lesions. Penile sparing approaches offer an attractive option as they can provide several quality of life benefits without detrimental oncologic outcomes. With appropriate diagnostic evaluation and staging, penile sparing techniques provide proper cancer control with improved cosmetic and functional results. Regardless of the chosen treatment modality, a commitment to close follow-up remains a critical component of all treatment considerations. The goal of this review is to provide an overview of the multiple treatment strategies for primary penile tumors with a focus on penile sparing surgical approaches.
Heterogeneous networks with LTE-Advanced technologies

Heterogeneous networks (HetNets) are a powerful solution to handle the rapidly increasing demand for mobile broadband bandwidth and are a key concept of Alcatel-Lucent's lightRadioTM strategy. HetNets consist of small cells embedded in a macrocellular network and enable flexible and scalable capacity enhancements. The first part of this paper discusses basic HetNet-specific aspects, e.g., small cell placement and fairness with respect to service quality. We present solutions for cell range expansion of small cells, which enables more user equipment (UEs) to profit from the additional capacity. The second part discusses advanced approaches for interference management optimized for HetNets. We present advanced solutions which exploit the possibilities offered by new Long Term Evolution (LTE)-Advanced features like enhanced inter-cell interference coordination (eICIC) and carrier aggregation (CA). We evaluate the performance of these advanced solutions based on standards compliant downlink (DL) system simulations in different application scenarios and provide recommendations on advanced scheduling strategies.
εPKC Is Required for the Induction of Tolerance by Ischemic and NMDA-Mediated Preconditioning in the Organotypic Hippocampal Slice

Glutamate receptors and calcium have been implicated as triggering factors in the induction of tolerance by ischemic preconditioning (IPC) in the brain. However, little is known about the signal transduction pathway that ensues after the IPC induction pathway. The main goals of the present study were to determine whether NMDA induces preconditioning via a calcium pathway and promotes translocation of the protein kinase C ε (εPKC) isozyme and whether this PKC isozyme is key in the IPC signal transduction pathway. We corroborate here that IPC and a sublethal dose of NMDA were neuroprotective, whereas blockade of NMDA receptors during IPC diminished IPC-induced neuroprotection. Calcium chelation blocked the protection afforded by both NMDA and ischemic preconditioning significantly, suggesting a significant role of calcium. Pharmacological preconditioning with the nonselective PKC isozyme activator phorbol myristate acetate could not emulate IPC, but blockade of PKC activation with chelerythrine during IPC blocked its neuroprotection. These results suggested that there might be a dual involvement of PKC isozymes during IPC. This was corroborated when neuroprotection was blocked when we inhibited εPKC during IPC and NMDA preconditioning, and IPC neuroprotection was emulated with the activator of εPKC. The possible correlation between NMDA, Ca2+, and εPKC was found when we emulated IPC with the diacylglycerol analog oleoylacetyl glycerol, suggesting an indirect pathway by which Ca2+ could activate the calcium-insensitive εPKC isozyme. These results demonstrated that the εPKC isozyme played a key role in both IPC- and NMDA-induced tolerance.