Miracle-dz/UniFAR-FTUs huggingface dataset:
Lateral Gene Transfer from the Dead

In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer, however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modeling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared with the total number of existing species, the overwhelming majority of gene transfers involve speciation to and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum-likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near-universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events (28%) appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria. [Gene tree reconciliation; lateral gene transfer; macroevolution; phylogeny. ]
Relevance information: a loss of entropy but a gain for IDF?

When investigating alternative estimates for term discriminativeness, we discovered that relevance information and idf are much closer related than formulated in classical literature. Therefore, we revisited the justification of idf as it follows from the binary independent retrieval (BIR) model. The main result is a formal framework uncovering the close relationship of a generalised idf and the BIR model. The framework makes explicit how to incorporate relevance information into any retrieval function that involves an idf-component.In addition to the idf-based formulation of the BIR model, we propose Poisson-based estimates as an alternative to the classical estimates, this being motivated by the superiority of Poisson-based estimates for the within-document term frequencies. The main experimental finding is that a Poisson-based idf is superior to the classical idf, where the superiority is particularly evident for long queries.
NADPH-Diaphorase-Containing Neurons in Cortex, Subcortical White Matter and Neostriatum Are Selectively Spared in Alzheimer’s Disease

To investigate the involvement of NADPH-diaphorase (NADPH-d)-containing neurons in Alzheimer’s disease (AD), NADPH-d enzyme histochemistry in vibratome sections was applied to the superior frontal and superior temporal cortex and the neostriatum in 5 AD and 6 aged control brains. Overall there was a neuronal loss and atrophy in the cortex of AD. Despite slight morphological neuronal changes in the cortex of AD, we found no significant difference in the number of NADPH-d-positive neurons in both cortex and neostriatum between control and AD cases. These results provide further evidence for a selective preservation of NADPH-d neurons in AD. In order to check whether nNOS-immunoreactive neurons are identical to NADPH-d-positive neurons in the human brain, we examined the frontal and temporal cortex and neostriatum of normal human brains in serial cryostat sections. We found that nNOS-containing neurons paralleled NADPH-d-positive neurons in these brain regions.
Developing and Disseminating Effective Psychological Treatments: Science, Practice and Economics

In many countries there is growing interest in the identification, development, and dissemination of evidence based psychological therapies. The cognitive– behaviour therapy (CBT) movement has been particularly successful in developing effective new treatments. It has been suggested this is partly because of the close interplay between theory, experimental psychopathology, and treatment development that characterizes much of CBT research. This article provides an illustration of such an interplay before moving on to discuss one of the world’s largest attempts to disseminate evidence-based therapies to the general public. The English Improving Access to Psychological Therapies (IAPT) program aims to vastly increase the availability of evidence-based psychological treatments for anxiety disorders and depression by training an extra 6,000 psychological therapists and deploying them in new, stepped care therapy services. Outcomes are assessed with a session-by-session monitoring system that achieves unusually high levels of data completeness. Around 600,000 patients per year are currently being seen in IAPT services. The background to the initiative, the scientific and economic arguments on which it is based, the training and clinical service models, a summary of progress to date, and future developments are described.
A simulator of the manufacturing of induction motors

A simulator of the manufacturing process of induction motors is presented whose main purpose is to provide feedback in the form of motor cost and production scheduling during the design process. Emphasis is on modeling and simulating a factory, modeling production costs, and providing examples of how the design of electric motors can be improved by taking manufacturing information into account via software. The simulator uses principles of system dynamics and technical cost modeling to model the flows of materials and evolution of the product through manufacturing stages across the factory floor. The inputs to the simulator are blueprint data for motor design and the status of the factory. The output is cost and schedule information. The simulator also provides a mechanism whereby design variables can be tested for variations that produce cost improvements. <<ETX>>
Decontamination of Pesticide Residues for Sustainable Agriculture

Sustainable Agriculture satisfies human food and fiber needs, makes the most efficient use of on-farm resources and integrates natural biological cycles, enhances the quality of life for farmers and society as a whole, and sustains the economic viability of farm operations. A farm that is able to produce continuously, yet has negative effects on environmental quality elsewhere, does not support sustainable agriculture. Over-application of synthetic pesticides and fertilizers or animal manure, which can improve productivity of a farm but can pollute nearby rivers and coastal waters does not contribute to sustainable agriculture. The lack of pesticide field dissipation data and the increasing concern about agricultural chemicals and their impact on surface and ground water quality have made this an international issue. Pesticide adsorption to soil is related more to soil organic matter than to other soil chemical and physical properties, therefore, addition of recycled waste as soil amendments having high organic matter content is a management practice that should be exploited to trap pesticides in situ in agricultural fields that would have been transported into rivers and streams contaminating natural water resources. The use of recycled waste for land farming could decrease dependence on synthetic fertilizers and provide alternatives to farmers dealing with the escalating production costs associated with increasing costs of energy. Soil management practices that bind pesticides and excess nutrients to soil particles, reducing pesticides, nitrate, nitrate, and phosphate in runoff and seepage water are vital to sustainable crop production systems and environmental quality. Soil organic matter has an important effect on the bioavailability, persistence, biodegradability, leaching, and volatility of chemicals in soil that could intercept pesticide-contaminated runoff from agricultural fields and provide a potential solution to pesticide contamination of surface and seepage water from farmlands. Mitigation and removal of excess pesticide residues before they runoff and enter bodies of water is the main focus of the research plan at Kentucky State University (KSU)/Environmental Science at the College of Agriculture. Studies at KSU research farm indicated that bio filters installed down the field slope reduced runoff water volume by 44% and herbicides (trifluralin and clomazone) residues in runoff water by 55% and 38%, respectively. These findings revealed that bio filters offer a viable means of treating pesticides in runoff water arising from agricultural fields.
Push and spin: A complete multi-robot path planning algorithm

In multi-robot path planning problem domain, robots must move from their start locations to their goal locations avoiding collisions with each other. There are various cooperative algorithms in this domain with their specialized strengths. Notable amongst them are Push and Swap (PAS), Push and Rotate (PAR) which appear as most favorable for such problems. This can be attributed to the reason that they don't impose as many restrictions on the graph topology. Our analysis, however, shows that a wider class of solvable instances is excluded from PAS and PAR domain. In this paper, we have proposed Push and Spin (PASp) algorithm, as a new complete cooperative algorithm for Multi-robot Path Planning problem with rotation (MPPr) for any instance recognized by the solvability test as solvable without any assumption. The algorithm employed two operations i.e. a "push" operation where robots move towards their goals up to the point that no progress can be made, and "spin" operation that allows two robots to swap positions without altering the configuration of other robots. The experimental results show that the PASp performs competitively in terms of number of moves compared to PAS, PAR and tractable multi-robot path planning (MAPP) algorithms, on a set of benchmark problems from the video game industry, in reasonable execution time. In addition, results show the scalability and robustness of PASp in problems that can be solved only by PASp. Such problems require high levels of coordination with an efficient number of moves, in short execution time. In bi-connected graphs, with too many cycles, PASp produces a higher number of moves than PAS, PAR and Bibox algorithms in a higher time. However, PASp is the only one capable of solving such instances with only one empty vertex.
Modeling of Gas Production from Shale Reservoirs Considering Multiple Transport Mechanisms

Gas transport in unconventional shale strata is a multi-mechanism-coupling process that is different from the process observed in conventional reservoirs. In micro fractures which are inborn or induced by hydraulic stimulation, viscous flow dominates. And gas surface diffusion and gas desorption should be further considered in organic nano pores. Also, the Klinkenberg effect should be considered when dealing with the gas transport problem. In addition, following two factors can play significant roles under certain circumstances but have not received enough attention in previous models. During pressure depletion, gas viscosity will change with Knudsen number; and pore radius will increase when the adsorption gas desorbs from the pore wall. In this paper, a comprehensive mathematical model that incorporates all known mechanisms for simulating gas flow in shale strata is presented. The objective of this study was to provide a more accurate reservoir model for simulation based on the flow mechanisms in the pore scale and formation geometry. Complex mechanisms, including viscous flow, Knudsen diffusion, slip flow, and desorption, are optionally integrated into different continua in the model. Sensitivity analysis was conducted to evaluate the effect of different mechanisms on the gas production. The results showed that adsorption and gas viscosity change will have a great impact on gas production. Ignoring one of following scenarios, such as adsorption, gas permeability change, gas viscosity change, or pore radius change, will underestimate gas production.
Genomic Imprinting in Mammals: Emerging Themes and Established Theories

The epigenetic events that occur during the development of the mammalian embryo are essential for correct gene expression and cell-lineage determination. Imprinted genes are expressed from only one parental allele due to differential epigenetic marks that are established during gametogenesis. Several theories have been proposed to explain the role that genomic imprinting has played over the course of mammalian evolution, but at present it is not clear if a single hypothesis can fully account for the diversity of roles that imprinted genes play. In this review, we discuss efforts to define the extent of imprinting in the mouse genome, and suggest that different imprinted loci may have been wrought by distinct evolutionary forces. We focus on a group of small imprinted domains, which consist of paternally expressed genes embedded within introns of multiexonic transcripts, to discuss the evolution of imprinting at these loci.
Efficient Electrochemical Synthesis, Antimicrobial and Antiinflammatory Activity of 2–amino-5-substituted- 1,3,4-oxadiazole Derivatives

An efficient electrochemical method for the preparation of 2-amino-5-substituted-1,3,4-oxadiazoles (4a-k) at platinum anode through the electrooxidation of semicarbazone (3a-k) at controlled potential electrolysis has been reported in the present study. The electrolysis was carried out in the acetic acid solvent and lithium perchlorate was used as supporting electrolyte. The products were characterized by IR,1H-NMR,13C-NMR, mass spectra and elemental analysis. The synthesized compounds were screened for their in vitro growth inhibiting activity against different strains of bacteria viz., Klebsilla penumoniae, Escherichia coli, Bassilus subtilis and Streptococcus aureus and antifungal activity against Aspergillus niger and Crysosporium pannical and results have been compared with the standard antibacterial streptomycin and antifungal griseofulvin. Compounds exhibits significant antibacterial activity and antifungal activity. Compounds 4a and g exhibited equal while 4c, d, i and j slightly less antibacterial activity than standard streptomycin. Compounds 4a and g exhibited equal while 4b, c, d, f and i displayed slightly less antifungal activity than standard griseofulvins.
Difficult Management of a Rapidly Growing Benign Phyllodes Tumor in a 49‐Year‐Old Woman

hyllodes breast tumors are rare, representing 0.3% to 1.0% of all breast tumors.1,2 These tumors present a difficult management issue because of the chance of recurrence, which has been reported to occur in 15% of patients overall; therefore, careful clinical observation of these patients is recommended after surgical excision. Hajdu et al3 reported a high incidence of local relapse of phyllodes breast tumors, with an incidence of 18%. Phyllodes tumors are difficult to diagnose because these tumors can be extremely difficult to differentiate from fibroadenomas. These tumors may masquerade as fibroadenomas and may be difficult to assess, even at core biopsy. The patients affected by these tumors vary in age at presentation, most typically 30 to 70 years old.4,5 An article by Yohe and Yeh6 discussed features suggesting phyllodes tumors that the pathologist can look for when analyzing a specimen and stated that increased sampling of a large tumor will likely yield a more accurate diagnosis. We report a case of a rapidly growing phyllodes tumor in a 49-year-old patient. In this case, the tumor grew very quickly in a short time and initially required wide surgical excision; fast recurrence led to a mastectomy for complete removal and clear margins. Even in the spectrum of what may be considered benign disease, a phyllodes tumor can locally recur and can be troublesome to treat.2,3 This can lead to multiple diagnostic and invasive procedures and, as in this patient, mastectomy.
Dynamic range enhanced readout circuit for a capacitive touch screen panel with current subtraction technique

A dynamic range enhanced readout circuit using current subtraction technique is presented for a capacitive touch screen panels. A low-voltage, analog front-end circuit using a high-voltage input signal is implemented. A high voltage (> 10 V) parallel pulse signal is used as the transmitter signal. The receiver system was designed with low voltage (<; 5 V). A current-subtraction circuit (CSC) with a current mirror and switches is proposed to improve the signal-to-noise ratio (SNR). SNR is improved by removing excessive current from the touch screen panel. High-voltage parallel signaling method is used to further enhance the dynamic range. Dynamic range was increased by a factor of four and reduced the feedback capacitance from 20 to 5 pF. The proposed IC was implemented in a TSMC 0.18-μm high-voltage CMOS process. The power consumption of the chip is 11.2 mW and the chip size is 2.5 mm × 2.5 mm.
The role of joint stiffness enhancing collision reaction performance of collaborative robot manipulators

For robots working in human environment, human safety is one of the most serious and important aspects to be considered. Appropriate intrinsic and / or functional safety design must be employed for collaborative robots in order to reduce the human injury risks through physical human-robot interaction. Above all the situations that such interactions are possible to occur, it is reported that clamping humans with robot and its environment is of great danger in a sense of human injury risks. We have conducted experiments and simulations that mimic clamping-human accident in some different situations varying robot's inertia, velocity, thickness of robot's soft cover and joint stiffness. Furthermore, some collision detection and reaction measures are implemented on the experimental system and their contributions to human safety were evaluated. From the results of these experiments and simulations, the joint stiffness was found to play an important role on human safety considerably affecting the performance of collision reaction.
Molecular and Cellular Pathobiology KRas Induces a Src / PEAK 1 / ErbB 2 Kinase Ampli fi cation Loop That DrivesMetastatic Growth and Therapy Resistance in Pancreatic Cancer

Early biomarkers and effective therapeutic strategies are desperately needed to treat pancreatic ductal adenocarcinoma (PDAC), which has a dismal 5-year patient survival rate. Here, we report that the novel tyrosine kinase PEAK1 is upregulated in human malignancies, including human PDACs and pancreatic intraepithelial neoplasia (PanIN). Oncogenic KRas induced a PEAK1-dependent kinase amplification loop between Src, PEAK1, and ErbB2 to drive PDAC tumor growth and metastasis in vivo. Surprisingly, blockade of ErbB2 expression increased Src-dependent PEAK1 expression, PEAK1-dependent Src activation, and tumor growth in vivo, suggesting a mechanism for the observed resistance of patients with PDACs to therapeutic intervention. Importantly, PEAK1 inactivation sensitized PDAC cells to trastuzumab and gemcitabine therapy. Our findings, therefore, suggest that PEAK1 is a novel biomarker, critical signaling hub, and new therapeutic target in PDACs. Cancer Res; 72(10); 2554–64. 2012 AACR.
The problem of penicillin resistant staphylococcal infection.

AND CONCLUSIONS A case of cerebral thrombosis following the administration of a mercurial diuretic is reported. While this may have been coincidental, it is pertinent that recent studies indicate thrombotic phenomena are more prone to occur in congestive failure following initiation of diuresis. Hamoconcentration and prothrombin increase predispose to these complications. Where time permits a gradual rather than intensive plan of treatment, while less dramatic, may be a safer method of management. There is good evidence that anticoagulant therapy is effective in reducing thromboembolic complications with their attendant mortality during the early treatment of congestive heart failure. A brief summary is also given of other reported untoward effects of mercurials. In conclusion it is again emphasized that mercurials are valuable and often indispensable for our treatment of heart failure, but undesirable effects may occur and we should be alert to recognize their occurrence.
Electronic Colloquium on Computational Complexity a Note on Read-k times Branching Programs

A syntactic read-k times branching program has the restriction that no variable occurs more than k times on any path (whether or not consistent). We exhibit an explicit Boolean function f; which cannot be computed by nondeterministic syntactic read-k times branching programs of size less than exp p n k 2k ; although its complement :f has a nondeterministic syntactic read-once branching program of polynomial size. This, in particular, means that the nonuniform analogue of NLOGSPACE = co? NLOGSPACE fails for syntactic read-k times networks with k = o(log n): We also show that (even for k = 1) the syntactic model is exponentially weaker then more realistic "nonsyntactic" one. subject "MAIL ME CLEAR", body "pub/eccc/ftpmail.txt"
The Role of 3 Tesla MRA in the Detection of Intracranial Aneurysms

Intracranial aneurysms constitute a common pathological entity, affecting approximately 1–8% of the general population. Their early detection is essential for their prompt treatment. Digital subtraction angiography is considered the imaging method of choice. However, other noninvasive methodologies such as CTA and MRA have been employed in the investigation of patients with suspected aneurysms. MRA is a noninvasive angiographic modality requiring no radiation exposure. However, its sensitivity and diagnostic accuracy were initially inadequate. Several MRA techniques have been developed for overcoming all these drawbacks and for improving its sensitivity. 3D TOF MRA and contrast-enhanced MRA are the most commonly employed techniques. The introduction of 3 T magnetic field further increased MRA's sensitivity, allowing detection of aneurysms smaller than 3 mm. The development of newer MRA techniques may provide valuable information regarding the flow characteristics of an aneurysm. Meticulous knowledge of MRA's limitations and pitfalls is of paramount importance for avoiding any erroneous interpretation of its findings.
Effect of selected non-ionic surfactants on the flow behavior of aqueous veegum suspensions

The aim of this work was to investigate the influence of some non-ionic surfactants, Tween 80 and Brij 98, on the viscosity and flow behavior of a commercial montmorillonite clay, Veegum Granules. The effect of different concentrations of the surfactants on the shear stress-shear rate rheograms of hydrated concentrated clay suspensions was determined by shear viscometry. The addition of either surfactant increased the plastic viscosity and the yield stress of the suspensions. Furthermore both surfactants altered the thixotropy of the suspensions to an extent that depended on both the surfactant concentration and the time of equilibration of the surfactant and Veegum. Brij 98 had a greater and more rapid effect. It is proposed that the surfactant polar head-groups anchor at the tetrahedral sheet surface, leaving the alkyl chains extending away from the edges and faces. Consequently, the alkyl chains undergo hydrophobic interactions that facilitate the association between the platelets and increase the physical structure within the suspension. Stereochemical differences between the polar groups may lead to differences in the way the surfactants associate with the tetrahedral sheet and hence their ultimate effect on the rheological behavior. There is a significant interaction between these surfactants and montmorillonite clays, and the rheological changes that occur could have a major impact on any pharmaceutical formulation that uses these ingredients.