Miracle-dz/UniFAR-FTUs huggingface dataset:
Site‐directed zebrafish transgenesis into single landing sites with the phiC31 integrase system

Background: Linear DNA‐based and Tol2‐mediated transgenesis are powerful tools for the generation of transgenic zebrafish. However, the integration of multiple copies or transgenes at random genomic locations complicates comparative transgene analysis and makes long‐term transgene stability unpredictable with variable expression. Targeted, site‐directed transgene integration into pre‐determined genomic loci can circumvent these issues. The phiC31 integrase catalyzes the unidirectional recombination reaction between heterotypic attP and attB sites and is an efficient platform for site‐directed transgenesis. Results: We report the implementation of the phiC31 integrase‐mediated attP/attB recombination for site‐directed zebrafish transgenics of attB‐containing transgene vectors into single genomic attP landing sites. We generated Tol2‐based single‐insertion attP transgenic lines and established their performance in phiC31 integrase‐catalyzed integration of an attB‐containing transgene vector. We found stable germline transmission into the next generation of an attB reporter transgene in 34% of all tested animals. We further characterized two functional attP landing site lines and determined their genomic location. Our experiments also demonstrate tissue‐specific transgene applications as well as long‐term stability of phiC31‐mediated transgenes. Conclusions: Our results establish phiC31 integrase‐controlled site‐directed transgenesis into single, genomic attP sites as space‐, time‐, and labor‐efficient zebrafish transgenesis technique. The described reagents are available for distribution to the zebrafish community. Developmental Dynamics 242:949–963, 2013. © 2013 Wiley Periodicals, Inc.
A Mutation in the Anticodon of a Single tRNAala Is Sufficient to Confer Auxin Resistance in Arabidopsis1

Auxin-resistant mutants have been useful for dissecting the mechanisms that underlie auxin-mediated biological processes. Here we report the isolation and molecular characterization of a novel auxin-resistant mutant in Arabidopsis (Arabidopsis thaliana). Like known mutated AUX/IAA transcription factors, the mutant described here displayed dominant resistance to exogenously supplied auxins (sirtinol, 2,4-dichlorophenoxyacetic acid, indole-3-acetic acid) and a host of pleiotropic phenotypes, including apical hook deformation, defects in lateral root development, reduced stature, and homozygous lethality. This mutant showed the same sensitivity to the ethylene precursor 1-aminocyclopropane carboxylic acid as wild-type plants, and retained the ability to induce IAA19 expression in response to exogenously supplied indole-3-acetic acid. To our surprise, these phenotypes were not caused by a mutation in an AUX/IAA gene, but rather a mutation in a tRNAala gene in which the anticodon was found changed from CGC to CAC. Such a change results in a tRNA that is charged with alanine but recognizes the second most highly used valine codon in Arabidopsis. Therefore, the observed phenotypes are likely the composite of stochastic mutations of many proteins, including downstream effectors.
Survival outcome of Borrmann type IV gastric cancer potentially improved by multimodality treatment.

BACKGROUND Type IV macroscopic gastric cancer has the poorest prognosis of all gastric cancer types. Although progress of multidisciplinary treatments is outstanding, the current survival outcome of such therapies is obscure. PATIENTS AND METHODS Among 5,172 patients with gastric cancer between 1971 and 2013, 287 cases of type IV were identified (5%). We divided time period into early (1971-2004) and late periods (2005-2013), and compared their prognosis. Multivariate Cox proportional hazards model was applied to the univariate prognostic factors, and identified independent prognostic factors and long-term survivors. RESULTS Five-year overall survival (OS) was 13% and 31% in the early and late periods, respectively (p=0.0010). Univariate prognostic factors were age, pathological tumor depth of invasion (pT), pathological lymph node metastasis (pN), peritoneal dissemination (P), intra-peritoneal cytology test (CY), and margin status. Multivariate analysis determined independent prognostic factors to be treatment period (p=0.0001), pT (p=0.0024) and P (p=0.035). Survival outcomes were stratified by combination of pT and P in both periods, where OS was improved in the late period. Long-term survivors often underwent long-term postoperative chemotherapy with S-1. CONCLUSION Long-term postoperative S-1 chemotherapy may improve survival outcome of patients with type IV gastric cancer, and their prognosis is predicted by pT and P status.
Enhancing single-trial mental workload estimation through xDAWN spatial filtering

Mental state monitoring is a topical issue in neuroengineering, more particularly for passive brain-computer interface (pBCI) applications. One of the mental states that are currently under focus is mental workload. The level of workload can be estimated from electroencephalographic activity (EEG) and markers derived from this signal. In active BCI applications, a well-known neurophysiological marker, the event-related potential (ERP), is commonly enhanced using a spatial filtering step. In this study, we evaluated how a spatial filtering method such as the xDAWN algorithm could improve mental workload classification performance. Twenty participants performed a Sternberg memory task for 18 minutes with pseudorandomized trials of low vs. high workload (2/6 digits to memorize). Three signal processing chains were compared on their performance to estimate mental workload from the single-trial ERPs of the test item (i.e. present/absent in the memorized list). All 3 included an FLDA classifier with a shrinkage covariance estimation and a 10-fold cross-validation. One chain used the ERPs of a relevant electrode for workload estimation (Cz) and the 2 others used the ERPs of the 32 electrodes and an xDAWN spatial filtering step with either 1 or 2 virtual electrodes kept for classification. Statistical analyses revealed that spatial filtering significantly improved mental workload estimation, with up to 98% of correct classification using the xDAWN algorithm and 2 virtual electrodes.
Evaluating youth development programs: Progress and promise

ABSTRACT Advances in theories of adolescent development and positive youth development have greatly increased our understanding of how programs and practices with adolescents can impede or enhance their development. In this article the authors reflect on the progress in research on youth development programs in the last two decades, since possibly the first review of empirical evaluations by Roth, Brooks-Gunn, Murray, and Foster (1998). The authors use the terms Version 1.0, 2.0, and 3.0 to refer to changes in youth development research and programs over time. They argue that advances in theory and descriptive accounts of youth development programs (Version 2.0) need to be coupled with progress in definitions of youth development programs, measurement of inputs and outputs that incorporate an understanding of programs as contexts for development, and stronger design and evaluation of programs (Version 3.0). The authors also advocate for an integration of prevention and promotion research, and for use of the term youth development rather than positive youth development.
Correction: When Less Is More: Non-monotonic Spike Sequence Processing in Neurons

Fundamental response properties of neurons centrally underly the computational capabilities of both individual nerve cells and neural networks. Most studies on neuronal input-output relations have focused on continuous-time inputs such as constant or noisy sinusoidal currents. Yet, most neurons communicate via exchanging action potentials (spikes) at discrete times. Here, we systematically analyze the stationary spiking response to regular spiking inputs and reveal that it is generically non-monotonic. Our theoretical analysis shows that the underlying mechanism relies solely on a combination of the discrete nature of the communication by spikes, the capability of locking output to input spikes and limited resources required for spike processing. Numerical simulations of mathematically idealized and biophysically detailed models, as well as neurophysiological experiments confirm and illustrate our theoretical predictions.
A microstrip filter with adjustable rejection band

This paper presents a novel microstrip filter design for tunable rejection band. The proposed was mainly with a defected ground structure. A ladder-shaped slot, which was located below the 50-Omega microstrip line, was embedded in the ground plane. For a fixed dimension, about 100% adjustment in rejection band was obtained by simply modifying the geometry parameters of the embedded slot. Experimental results indicate that the band control and design simplicity of the microstrip bandstop filter can be achieved simultaneously. In this article, the author discusses the design and experimental results for the adjustable bandstop filter
Modeling the sensitivity of outdoor recreation activities to climate change

This study develops a methodological framework to analyze the climate sensitivity as well as climate change impacts on outdoor recreation activities, applied to a case study of 2 lidos in the city of Zurich. A negative binomial regression is used to link daily data on lido entries with weather variables for the period 2003 to 2010, while controlling for non-climatic factors (such as weekends and school holidays). It shows that the number of lido visitors is significantly determined by weather conditions such as temperature and rainfall. Results from the regressions are combined with output of a stochastic weather generator to fully explore climate risks on a monthly and annual basis under current conditions. This setup is furthermore used to predict near future climate change impacts on lido entries using 3 emission scenarios. It shows that near future climate change characterized by temperature increases and reduced precipitation levels in late summer will have a positive effect on the number of lido visitors. While the expected increase of the annual number of visitors ranges from 9 to 19%, increases of >30% are expected for August and September
Is It the Cognitive or the Behavioral Component Which Makes Cognitive-Behavior Modification Effective in Test Anxiety?.

Components of Meichenbaum's cognitive-behavior modification treatment for test anxiety were varied in a 2 × 2 factorial design. Desensitization and cognitive treatments were either given or not given. The resultant conditions were (a) desensitization only, (b) cognitive only, (c) the combination cognitive plus desensitization,, and (d) neither cognitive nor desensitization (control). Each test-anxious subject was randomly assigned to one of the four groups. On a variety of test anxiety and self-rating measures the combined treatment and desensitization were less effective than the cognitive-only treatment. The results are discussed as consistent with traditional theories of test anxiety and antithetical to a recent behavioral reformulation of test anxiety theory.
On board measurements of the railway’s electromagnetic noise with moving train

The paper deals with the electromagnetic (EM) characterisation of the railway’s environment on a moving train, in the frequency band extended from 300 MHz to 1 GHz. A measurement method adapted to this context will be studied in order to characterise the interferences which can affect the on board telecommunication systems. Comparisons between measurements in time domain and frequency domain will be performed for different operating conditions.
Influence on Calculated Blood Pressure of Measurement Posture for the Development of Wearable Vital Sign Sensors

We studied a wearable blood pressure sensor using a fiber Bragg grating (FBG) sensor, which is a highly accurate strain sensor. This sensor is installed at the pulsation point of the human body to measure the pulse wave signal. A calibration curve is built that calculates the blood pressure by multivariate analysis using the pulse wave signal and a reference blood pressure measurement. However, if the measurement height of the FBG sensor is different from the reference measurement height, an error is included in the reference blood pressure. We verified the accuracy of the blood pressure calculation with respect to the measurement height difference and the posture of the subject. As the difference between the measurement height of the FBG sensor and the reference blood pressure measurement increased, the accuracy of the blood pressure calculation decreased. When the measurement height was identical and only posture was changed, good accuracy was achieved. In addition, when calibration curves were built using data measured in multiple postures, the blood pressure of each posture could be calculated from a single calibration curve. This will allow miniaturization of the necessary electronics of the sensor system, which is important for a wearable sensor.
The Need for Fourth Generation Static Analysis Tools for Security – From Bugs to Flaws

This paper discusses some of the limitations of the current (third) generation static code analyzers for security available on the market today and gives reasons for the plateau in their usefulness to a code reviewer. We further describe some of the characteristics of the next generation static analysis technology that will enable a new quantum leap in the space of static analysis with tools that are able to detect software security flaws, not merely implementation level bugs.
SPEECH PERCEPTION WITH PROMONTORY STIMULATION a

The present work of the EPI e group is characterized by a combination of four features. First, our patients are essentially all adults who have had largely normal speech communication ability prior to total bilateral loss of hearing. Second, the electrical stimulation that we use to give them a new sensation of hearing is always applied externally at the round window or on the cochlear promontory by means of a single active electrode. Third, the information that is transmitted along this single channel is designed to give maximum assistance to the deaf lipreader and is organized in terms of speech pattern components rather than the whole speech signal. These speech pattern components can be used separately or in combination, and are transformed to match the patient’s electrical hearing. Finally, our program of rehabilitation involves work with the patient’s speaking ability as well as the new sensation of hearing, and quantitative measures of both speech and hearing are made routinely.
Dynamic Information Acquisition and Strategic Trading

Consider a strategic trader who dynamically chooses when to acquire costly information about an asset’s payoff, instead of being endowed with this information. Whether the market maker observes acquisition is critical. Without observability, we show that an equilibrium with smooth trading and a pure acquisition strategy cannot exist. We also rule out the existence of a natural class of mixed-strategy equilibria. With observability, however, there exists an equilibrium in which optimal acquisition follows a pure strategy and generally exhibits delay. Our results suggest that many strategic trading equilibria considered in the literature are difficult to reconcile with dynamic information acquisition. JEL: D82, D84, G12, G14
An aperture-coupled linear microstrip leaky-wave antenna array with two-dimensional dual-beam scanning capability

This paper describes an X-band 4/spl times/1 aperture-coupled series-fed electronically steerable microstrip leaky-wave antenna (LWA) array design, which has dual-beam radiation pattern and two-dimensional (2-D) beam-scanning capability. The LWA array is operated in the first higher order mode and excited by center-fed aperture coupled for dual-beam operation. The varactor-tuned phase shifters are placed between the antenna elements. The measured half-power beamwidth of the H-plane and quasi-E-plane radiation patterns are less than 30/spl deg/. By tuning the reverse dc bias of the varactor diodes, the main beam can be scanned in azimuth plane from -13/spl deg/ to +13/spl deg/ off broadside. In the elevation plane, the beam-scanning angle is close to 20/spl deg/ as the operating frequency tuned from 11.58-12.5 GHz. Taking into account each phase-shifter insertion loss and phase progression, the measured results compared closely with the theoretical prediction. The proposed antenna array is suitable for wireless communication and collision warning radar systems.
NEMATODE INDUCED HYPERSENSITIVITY REACTIONS IN GUINEA PIGS: ONSET OF EOSINOPHILIA AND POSITIVE SCHULTZ‐DALE REACTIONS FOLLOWING GRADED INFECTIONS WITH TOXOCARA CANIS

In previous work, Sharp and Olson (1961, 1962) have demonstrated positive Schultz-Dale tests with gut segments from guinea pigs necropsied 25 to 32 days after oral infection with larvated Toxocara canis eggs. Sharp and Olson ( 1 9 6 2 ~ ) reported on the time of onset of positive Schultz-Dale reactions and eosinophilias in guinea pigs after a single infection with Toxocara. This report presents data on the dose response of guinea pigs to Toxocara in terms of the chronologic and quantitative aspects of eosinophilias and intestinal hypersensitiveness.
A School-Based Expressive Writing Intervention for At-Risk Urban Adolescents' Aggressive Behavior and Emotional Lability

This school-based randomized controlled trial tested the efficacy of 2 expressive writing interventions among youth living in high-violence urban neighborhoods. Seventeen classrooms (n = 258 seventh graders; 55% female; 91% African American/Black) from 3 public schools were randomized to 3 conditions in which they wrote 8 times about a nonemotional topic (control condition) or about experiencing and witnessing violence following either a standard or an enhanced expressive writing protocol. Outcomes were assessed 1 month prior and 2 and 6 months postintervention and included teacher-rated emotional lability and aggressive behavior and child-rated physical aggression. Intent-to-treat, mixed-model analyses controlled for preintervention measures of outcomes, sex, race, and family structure. At 2 months postintervention, relative to controls, students in the standard expressive writing condition had lower levels of teacher-rated aggression and lability (d = −.48). The beneficial effects of the writing interventions on aggression and lability were stronger at higher levels of community violence exposure.
Soluble Receptor for Advanced Glycation End-Products Predicts Impaired Alveolar Fluid Clearance in Acute Respiratory Distress Syndrome.

RATIONALE Levels of the soluble form of the receptor for advanced glycation end-products (sRAGE) are elevated during acute respiratory distress syndrome (ARDS) and correlate with severity and prognosis. Alveolar fluid clearance (AFC) is necessary for the resolution of lung edema but is impaired in most patients with ARDS. No reliable marker of this process has been investigated to date. OBJECTIVES To verify whether sRAGE could predict AFC during ARDS. METHODS Anesthetized CD-1 mice underwent orotracheal instillation of hydrochloric acid. At specified time points, lung injury was assessed by analysis of blood gases, alveolar permeability, lung histology, AFC, and plasma/bronchoalveolar fluid measurements of proinflammatory cytokines and sRAGE. Plasma sRAGE and AFC rates were also prospectively assessed in 30 patients with ARDS. MEASUREMENTS AND MAIN RESULTS The rate of AFC was inversely correlated with sRAGE levels in the plasma and the bronchoalveolar fluid of acid-injured mice (Spearman's ρ = -0.73 and -0.69, respectively; P < 10(-3)), and plasma sRAGE correlated with AFC in patients with ARDS (Spearman's ρ = -0.59; P < 10(-3)). Similarly, sRAGE levels were significantly associated with lung injury severity, and decreased over time in mice, whereas AFC was restored and lung injury resolved. CONCLUSIONS Our results indicate that sRAGE levels could be a reliable predictor of impaired AFC during ARDS, and should stimulate further studies on the pathophysiologic implications of RAGE axis in the mechanisms leading to edema resolution. Clinical trial registered with www.clinicaltrials. gov (NCT 00811629).
On Teaching Narrative Infographics in an Information Visualization Course

Although not currently a standard topic to teach in a technicallyfocused information visualization course, I have found assigning a Narrative Infographic an effective way to introduce narrative and story into the presentation of data visualization. By teaching the skills explicitly, I guide students towards using pictorial components responsibly for engagement, staying on the right side of chart junk. Although the assignment requires the creation of a stand-alone static design, I have observed positive transfer to web-based final projects. I also report on strategies I have developed to reduce problems of student anchoring on prior chart-based assignments. The most successful has been the instigation of a before-to-after practice assignment paired with a mid-project in-class progress review check.
Controlled Deposition of Size-Selected Silver Nanoclusters

Variable-temperature scanning tunneling microscopy was used to study the effect of kinetic cluster energy and rare-gas buffer layers on the deposition process of size-selected silver nanoclusters on a platinum(111) surface. Clusters with impact energies of ≤1 electron volt per atom could be landed nondestructively on the bare substrate, whereas at higher kinetic energies fragmentation and substrate damage were observed. Clusters with elevated impact energy could be soft-landed via an argon buffer layer on the platinum substrate, which efficiently dissipated the kinetic energy. Nondestructive cluster deposition represents a promising method to produce monodispersed nanostructures at surfaces.
Studies of Sick Building Syndrome. IV. Mycotoxicosis

There has been increasing public attention to the potential health risks of mold exposure, particularly in wet buildings. A variety of molds has been isolated from both damaged homes and businesses, including agents that secrete toxigenic materials. One area that is attracting particular notice is the relative toxigenic potential of mycotoxins. Although exposure to molds can produce significant mucosal irritation, there are very few data to suggest long-term ill effects. More importantly, there is no evidence in humans that mold exposure leads to nonmucosal pathology. In fact, many of the data on toxigenic molds are derived from animal toxicity studies, and these are based primarily on ingestion. Although every attempt should be made to improve the quality of indoor air, including avoidance of molds, the human illnesses attributed to fungal exposure are, with the exception of invasive infections and mold allergy, relatively rare. In this review we discuss selected aspects of the microbiology of mycotoxin-producing molds and their potential role in human immunopathology with respect to wet building environments.