Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of MCNP4C, 4B and 4A Monte Carlo codes when calculating electron therapy depth doses

Background: Monte Carlo simulation of radiation transport is considered to be one of the most accurate methods of radiation therapy dose calculation. There are different Monte Carlo codes for simulation of photons, electrons and the coupled transport of electrons and photons. MCNP is a general purpose Monte Carlo code that can be used for electron, photon and coupled photon-electron transport. Materials and Methods: In this study the MCNP4A, 4B and 4C have been compared when calculating electron beam doses in water. For simulating, the geometry and other parameters were the same for three codes. By choosing two energy indexing algorithm (ITS & MCNP), absorbed doses were scored in water. 10 6 Particles were followed in these three cases. Results: MCNP4C and 4B gave different results compared to 4A when the ITS algorithm was used in 4B and 4C versions. There was a good agreement between versions 4B and 4C. For the energy spectrum, there were significant differences between these three versions in two planes. Conclusion: Because of new improvements in electron transport in 4C, this version is reliable for electron transport and also requires a shorter time than the two previous versions. These results, in addition to the practical measurements acquired with MCNP4B by other investigators, suggest that in electron transport the user should use the ITS indexing energy algorithm. Iran. J. Radiat. Res., 2005; 2 (4): 191-195
Telomeres and genomic evolution

The terminal regions of eukaryotic chromosomes, composed of telomere repeat sequences and sub-telomeric sequences, represent some of the most variable and rapidly evolving regions of the genome. The sub-telomeric regions are characterized by segmentally duplicated repetitive DNA elements, interstitial telomere repeat sequences and families of variable genes. Sub-telomeric repeat sequence families are shared among multiple chromosome ends, often rendering detailed sequence characterization difficult. These regions are composed of constitutive heterochromatin and are subjected to high levels of meiotic recombination. Dysfunction within telomere repeat arrays, either due to disruption in the chromatin structure or because of telomere shortening, can lead to chromosomal fusion and the generation of large-scale genomic rearrangements across the genome. The dynamic nature of telomeric regions, therefore, provides functionally useful variation to create genetic diversity, but also provides a mechanism for rapid genomic evolution that can lead to reproductive isolation and speciation. This article is part of the theme issue ‘Understanding diversity in telomere dynamics'. This article is part of the theme issue ‘Understanding diversity in telomere dynamics’.
HUMAN MUTATION Supplement 1 : SllO-Slll ( 1998 ) MUTATION IN BFUEF ~ ~ I M u t a t i o n i n the Y Gene Results in 46 , XY Gonadal Dysgenesis

The SRY gene was first cloned in 1990 and has subsequently been shown to be testis-determining factor on the Y chromosome (Sinclair et al., 1990; Koopman et al., 1991). Mutations inSRY have been found to account for 10-15% of cases of 46,XY gonadal dysgenesis (GD) (Hunter, 1995). To date, 26 mutations inSRY have been described (Cameron and Sinclair, in press). All but one of these have occurred within the HMG box region of the gene (Tajima et al., 1994). We describe a new mutation in the SRY HMG box region in a patient with 46,XY GD.
Major clades in Solanum based on ndhF sequence data

Analysis of sequence data from the chloroplast gene ndhF identifies at least 12 major well-supported clades within the genus Solanum. These are briefly described, given informal clade names, and compared with the groups recognized by previous Solanum workers. Non-molecular synapomorphies are proposed for many of the clades. Continued use of informal taxonomic designations is advocated for new infrageneric groups within Solanum.
Improvement in spread spectrum watermarking through convolutional codes

We present a watermarking approach using a directional multiresolution transform named contourlet. Contourlet transform offers a flexible image decomposition at various directions in multiple scales with flexible ratios, then it is easier to determine image areas which are less sensitive to human eye. We combine an spread spectrum scheme with a convolutional coding scheme to improve the capacity of watermark embedded through the host signal. We present some experimental results of our algorithm tested to common signal processing operation, which could be intentional or unintentional.
Segmentation- and Annotation-Free License Plate Recognition With Deep Localization and Failure Identification

Automated license plate recognition (ALPR) is essential in several roadway imaging applications. For ALPR systems deployed in the United States, variation between jurisdictions on character width, spacing, and the existence of noise sources (e.g., heavy shadows, non-uniform illumination, various optical geometries, poor contrast, and so on) present in LP images makes it challenging for the recognition accuracy and scalability of ALPR systems. Font and plate-layout variation across jurisdictions further adds to the difficulty of proper character segmentation and increases the level of manual annotation required for training classifiers for each state, which can result in excessive operational overhead and cost. In this paper, we propose a new ALPR workflow that includes novel methods for segmentation- and annotation-free ALPR, as well as improved plate localization and automation for failure identification. Our proposed workflow begins with localizing the LP region in the captured image using a two-stage approach that first extracts a set of candidate regions using a weak sparse network of winnows classifier and then filters them using a strong convolutional neural network (CNN) classifier in the second stage. Images that fail a primary confidence test for plate localization are further classified to identify localization failures, such as LP not present, LP too bright, LP too dark, or no vehicle found. In the localized plate region, we perform segmentation and optical character recognition (OCR) jointly by using a probabilistic inference method based on hidden Markov models (HMMs) where the most likely code sequence is determined by applying the Viterbi algorithm. In order to reduce manual annotation required for training classifiers for OCR, we propose the use of either artificially generated synthetic LP images or character samples acquired by trained ALPR systems already operating in other sites. The performance gap due to differences between training and target domain distributions is minimized using an unsupervised domain adaptation. We evaluated the performance of our proposed methods on LP images captured in several US jurisdictions under realistic conditions.
New Vector for Efficient Allelic Replacement in Naturally Nontransformable, Low-GC-Content, Gram-Positive Bacteria

ABSTRACT A shuttle vector designated pMAD was constructed for quickly generating gene inactivation mutants in naturally nontransformable gram-positive bacteria. This vector allows, on X-Gal (5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside) plates, a quick colorimetric blue-white discrimination of bacteria which have lost the plasmid, greatly facilitating clone identification during mutagenesis. The plasmid was used in Staphylococcus aureus, Listeria monocytogenes, and Bacillus cereus to efficiently construct mutants with or without an associated antibiotic resistance gene.
People and computers XI : proceedings of HCI '96

Fundamental Design Issues. - Towards the Total Quality Interface - Applying Taguchi TQM Techniques within the LUCID Method. - Games as a Metaphor for Interactive Systems. - Cultural Bases of Interface Acceptance: Foundations. - A Unified Concept of Style and its Place in User Interface Design. - Developing University Courses to Enable Students to Specify and Solve Human-Computer Interaction Design Problems. - 3D or not 3D: Is it Nobler in the Mind? - Specific Design Issues. - Can Design Choices for Language-Based Editors be Analysed with Keystroke-Level Models? - Deriving Information Requirement in the Design of a Mathematics Workstation or Visually Impaired Students. - Second-Language Help for Windows Applications. - Extending GUIs. - Eye-based Control of Standard GUI Software. - Non-visual Interaction with GUI Objects. - Earcons as a Method of Providing Navigational Cues in a Menu Hierarchy. - User Involvement. - Problems for User Involvement: A Human and Organizational Perspective. - Multidisciplinary Modelling for User-Centred System Design: An Air-traffic Control Case Study. - Costs and Benefits of User Involvement in Design: Practitioners' Views. - What You Don't Know Can Hurt You: Privacy in Collaborative Computing. - Computer-Supported Cooperative Work. - Behavioural Patterns of Collaborative Writing with Hypertext- A State Transition Approach. - Workspace Awareness in Real-Time Distributed Groupware: Framework, Widgets, and Evaluation. - Using Distortion-Oriented Displays to Support Workspace Awareness. - Working by Walking Around - Requirements of Flexible Interaction Management in Video-supported Collaborative Work. - Multimedia. - Matching Media to Goals: An Approach Based on Expressiveness. - DAVID: A Multimedia Tool for Accident Investigation. - A Web StoryBase. - Session Length and Subjective Satisfaction in Information Kiosk Research. - Author Index. - Keyword Index.
Autonomous underwater vehicles as a platform for underwater hyperspectral imaging

During an expedition to the Atlantic Mid-Ocean ridge in August 2016, an underwater hyperspectral imager (UHI) was utilized. The target was to investigate its applicability to exploration for marine minerals. The imager was deployed on both an autonomous underwater vehicle (AUV) and a remotely operated vehicle (ROV). To the authors knowledge, this is the first time a full scale hyperspectral imager has been mounted on an AUV. This new platform comes with many advantages and drawbacks which will be discussed, both in terms of future potential and observed data quality.
Influence of endotoxin‐induced acute lung injury on pulmonary innate and adaptive immunity

Objective. The aim of our study was to analyze pulmonary innate and adaptive immune responses during endotoxemia‐induced acute lung injury (ALI). Experimental design. Female BALB/c mice were challenged by endotoxin given intraperitoneally and followed for 24 h by unrestrained plethysmographic analysis. After this period, the mice were sacrificed by CO2 anesthesia and lung histopathology, pulmonary and serum levels of pro‐inflammatory cytokines, numbers of lymphocyte subsets in blood and lung, and lung‐derived macrophages (Mφ) were analyzed. Main results. Animals with endotoxemia demonstrated significant depression of tidal volumes indicating respiratory failure compared to control mice. Lung histopathology of endotoxin‐exposed animals revealed alveolar leakage characterizing ALI. Pulmonary levels of interleukin (IL)‐1β, IL‐6 and interferon (IFN)‐γ in animals with endotoxemia were significantly elevated, whereas serum levels of IL‐6 only were increased. IFN‐γ was strongly expressed by lung‐derived Mφ with high CD11b expression, and this subset significantly increased in the lungs after endotoxin challenge. Additionally, the numbers of lung‐resident CD4+ and total T‐lymphocytes were significantly reduced after challenge. Conclusion. These data suggest that endotoxemia‐induced ALI is associated with exaggerated and sustained pulmonary innate immune responses partly mediated by activated Mφ, whereas adaptive immunity in the lungs is compromised.
Identification and Validation of Targets for Cancer Immunotherapy: From the Bench-to-Bedside

The link between immune responses and cancer is evident from findings such as, a com‐ promised immune system resulting in an increased tumour incidence [1] and cancer pa‐ tient sera evidencing recognition of autologous cancer antigens [2]. The identification of tumour associated antigens (TAAs) plays a central role in our understanding of how can‐ cer cells can inhibit the immune system and how we can overcome this tumour immune suppression to break tolerance and achieve cancer destruction [3]. Antibodies reacting with TAAs on the surface of cancer cells provoke an extremely effective immune re‐ sponse [4] which can be exquisitely specific to the tumour cells present in the body. However not many surface proteins are present on tumour cells and limited otherwise in expression to healthy non-essential tissues.
Sphingomyelin trafficking in Chlamydia pneumoniae‐infected cells

Chlamydia pneumoniae is a bacterial obligate intracellular parasite with a developmental cycle common to all members of the genus Chlamydia. Like other chlamydiae, the developmental cycle of C. pneumoniae occurs entirely within a membrane‐bound intracellular vacuole, termed an inclusion, that is non‐fusogenic with endosomal or lysosomal compartments. To characterize the vesicular interactions of the C. pneumoniae inclusion, we used a fluorescent analogue of ceramide, {N‐[7‐(4‐nitrobenzo‐2‐oxa‐1,3‐diazole)]‐6‐aminocaproyl‐derythro‐sphingosine (C6‐NBD‐Cer), that has previously been used to characterize the endogenous synthesis and transport of sphingolipids from the Golgi apparatus to Chlamydia trachomatis and Chlamydia psittaci inclusions. Sphingolipids are trafficked to C. pneumoniae inclusions in a time‐, temperature‐ and energy‐dependent manner with properties very similar to the delivery of sphingomyelin to C. trachomatis inclusions. These results indicate that interactions of the inclusion with a subset of sphingomyelin‐containing exocytic vesicles is a property common to all species of chlamydiae.
Features of CRISPR-Cas Regulation Key to Highly Efficient and Temporally-Specific crRNA Production

Bacterial immune systems, such as CRISPR-Cas or restriction-modification (R-M) systems, affect bacterial pathogenicity and antibiotic resistance by modulating horizontal gene flow. A model system for CRISPR-Cas regulation, the Type I-E system from Escherichia coli, is silent under standard laboratory conditions and experimentally observing the dynamics of CRISPR-Cas activation is challenging. Two characteristic features of CRISPR-Cas regulation in E. coli are cooperative transcription repression of cas gene and CRISPR array promoters, and fast non-specific degradation of full length CRISPR transcripts (pre-crRNA). In this work, we use computational modeling to understand how these features affect the system expression dynamics. Signaling which leads to CRISPR-Cas activation is currently unknown, so to bypass this step, we here propose a conceptual setup for cas expression activation, where cas genes are put under transcription control typical for a restriction-modification (R-M) system and then introduced into a cell. Known transcription regulation of an R-M system is used as a proxy for currently unknown CRISPR-Cas transcription control, as both systems are characterized by high cooperativity, which is likely related to similar dynamical constraints of their function. We find that the two characteristic CRISPR-Cas control features are responsible for its temporally-specific dynamical response, so that the system makes a steep (switch-like) transition from OFF to ON state with a time-delay controlled by pre-crRNA degradation rate. We furthermore find that cooperative transcription regulation qualitatively leads to a cross-over to a regime where, at higher pre-crRNA processing rates, crRNA generation approaches the limit of an infinitely abrupt system induction. We propose that these dynamical properties are associated with rapid expression of CRISPR-Cas components and efficient protection of bacterial cells against foreign DNA. In terms of synthetic applications, the setup proposed here should allow highly efficient expression of small RNAs in a narrow time interval, with a specified time-delay with respect to the signal onset.
Hexpo: A vanishing-proof activation function

This article proposes “Hexpo”, an activation function that has ability to scale the gradient and hence overcome the vanishing gradient problem. Unlike rectified linear units family which produces identity mapping on positive inputs, Hexpo has scalable limits on both positive and negative values. With parametrization, the active domain of Hexpo and the output it maps to is flexible. Thus it can alleviate the vanishing gradient problem from both gradient flow and local gradient aspect, while preserving the upper and lower bound of output. Parametrization also offers Hexpo the ability to produce the output that is close to zero. On experiments involving MNIST hand digit recognition dataset, Hexpo outperforms rectified linear units family(rectified linear unit and exponential linear unit) by the accuracy and speed of learning. On the experiments involving CIFAR-10 tiny image recognition dataset and convolutional layers, Hexpo outperforms rectified linear unit and performs similar in comparison with exponential linear unit.
Reconfigurable lowpass filter based on signal interference techniques

This paper presents a novel reconfigurable filtering block based on signal interference techniques. The topology consists of the connection in parallel of three transmission lines of different electrical lengths. The lines can be switched on/off through the use of p-i-n diodes. In this way, the signal paths and their interferences are controlled providing different states (different cutoff frequencies). The proposed filter is easy to design and fabricate. As demonstration, a reconfigurable microstrip lowpass filter with three states (2.0, 3.0 and 4.0 GHz) is designed and implemented. The three states present selective responses with good rejection levels.
Electrical Characteristics of GaAs Nanowire-Based MESFETs on Flexible Plastics

GaAs nanowire (NW)-based metal-semiconductor field-effect transistors (MESFETs) were constructed on flexible plastic substrates by a conventional top-down approach. The top-down approach utilized in this paper combines photolithography of high-quality GaAs bulk wafers with anisotropic chemical etching processes for preparation of GaAs NWs and photolithographic processes for formation of metal electrodes. For a representative GaAs NW-based MESFET, peak transconductance, the Ion/Ioff ratio, and the subthreshold slope are estimated to be approximately 19.7 S, ~107, and ~100 mV/dec, respectively. The electrical characteristics of the GaAs NW-based MESFETs were maintained during 3000 times of bending cycles under maximal tensile strains of 0.77% and 1.02%. These results demonstrate the possibility of using these devices in high-speed and high-performance flexible electronics.
Once-weekly stereotactic radiotherapy for patients with oligometastases: compliance and preliminary efficacy.

AIMS AND BACKGROUND This retrospective analysis reports the outcomes obtained with an original once-weekly stereotactic radiotherapy fractionation given to patients affected by evolving oligometastases from different solid malignancies. METHODS From 2009 to 2011, patients with symptomatic and/or evolving oligometastases were submitted to a median 5-fraction cycle of stereotactic radiotherapy of one fraction per week in order to exploit a radiobiological rationale designed to increase the therapeutic index. Individual fractionation was mainly planned according to patient performance status, oligometastasis size and site, and record of previous irradiation in the same site. RESULTS Thirty-six patients in stage IV UICC-TNM affected by oligometastases were treated with image-guided intensity-modulated stereotactic tomotherapy with a single weekly radiation. Median age was 70 years (range, 34-89). The median weekly single dose, number of fractions and overall total radiation dose were 7 Gy, 5 fractions and 35 Gy, respectively. Thirty-five (97%) patients completed the treatment schedule. No patient suffered mild or severe radiation-related side effects. Twenty-one (87%) of 24 patients with local pain had complete symptomatic response within 30 days following the end of radiotherapy. Local control assessed at imaging after stereotactic radiotherapy was evidenced in 30 (83%) patients. Median time to response after the end of radiotherapy was 40 days. CONCLUSIONS The original radiotherapy regimen delivering only a single stereotactic dose per week seems to be highly feasible with an interesting high efficacy rate in patients with oligometastases from different solid tumors. Overall, the once-weekly treatment was very compliant in an advanced cancer stage especially for elderly and frail patients.
AMERICAN ASSOCIATION OF WINE ECONOMISTS AAWE WORKING PAPER No . 152 Economics Wine and Climate Change

In this article we provide an overview of the extensive literature on the impact of weather and climate on grapes and wine with the goal of describing how climate change is likely to affect their production. We start by discussing the physical impact of weather on vine phenology, berry composition and yields, and then survey the economic literature measuring the effects of temperature on wine quality, prices, costs and profits and how climate change will affect these. We also describe what has been learned so far about possible adaptation strategies for grape growers that would allow them to mitigate the economic effects of climate change. We conclude that climate change is likely to produce winners and losers, with the winners being those closer to the North and South Poles. There are also likely to be some substantial short run costs as growers adapt to climate change. Nevertheless, wine making has survived through thousands of years of recorded history, a history that includes large climate changes. I. Introduction Fine wine is an agricultural product that has characteristics that make it an especially interesting topic for economic analyses against the background of a changing climate. First, the quality and quantity of wine, and thus prices and revenues, are extraordinarily sensitive to the weather where the grapes were grown. Price differences for wines made a Department of Economics, Princeton University. Email: c6789@princeton.edu b Department of Economics, New York University. Email: karl.storchmann@nyu.edu 1 The close relation between weather and wine has also been exploited for reverse inferences. Historical climatologists use data on harvest dates and the phenological stages of ripeness to generate medieval weather data (see, e.g., Garcia de Cortázar-Atauri et al., 2010; Brázdil et al., 2005).
Hamiltonian boundary term and quasilocal energy flux

The Hamiltonian for a gravitating region includes a boundary term which determines not only the quasilocal values but also, via the boundary variation principle, the boundary conditions. Using our covariant Hamiltonian formalism, we found four particular quasilocal energy-momentum boundary term expressions; each corresponds to a physically distinct and geometrically clear boundary condition. Here, from a consideration of the asymptotics, we show how a fundamental Hamiltonian identity naturally leads to the associated quasilocal energy flux expressions. For electromagnetism one of the four is distinguished: the only one which is gauge invariant; it gives the familiar energy density and Poynting flux. For Einstein's general relativity two different boundary condition choices correspond to quasilocal expressions which asymptotically give the ADM energy, the Trautman-Bondi energy and, moreover, an associated energy flux (both outgoing and incoming). Again there is a distinguished expression: the one which is covariant.