Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarray analysis of developing flax hypocotyls identifies novel transcripts correlated with specific stages of phloem fibre differentiation.

BACKGROUND AND AIMS Hypocotyls are a commonly used model to study primary growth in plants, since post-germinative hypocotyls increase in size by cell elongation rather than cell division. Flax hypocotyls produce phloem fibres in bundles one to two cell layers thick, parallel to the protoxylem poles of the stele. Cell wall deposition within these cells occurs rapidly at a well-defined stage of development. The aim was to identify transcripts associated with distinct stages of hypocotyl and phloem fibre development. METHODS Stages of flax hypocotyl development were defined by analysing hypocotyl length in relation to fibre secondary wall deposition. Selected stages of development were used in microarray analyses to identify transcripts involved in the transition from elongation to secondary cell wall deposition in fibres. Expression of specific genes was confirmed by qRT-PCR and by enzymatic assays. KEY RESULTS Genes enriched in the elongation phase included transcripts related to cell-wall modification or primary-wall deposition. Transcripts specifically enriched at the transition between elongation and secondary wall deposition included beta-galactosidase and arabinogalactan proteins. Later stages of wall development showed an increase in secondary metabolism-related transcripts, chitinases and glycosyl hydrolases including KORRIGAN. Microarray analysis also identified groups of transcription factors enriched at one or more stages of fibre development. Subsequent analysis of a differentially expressed beta-galactosidase confirmed that the post-elongation increase in beta-galactosidase enzyme activity was localized to phloem fibres. CONCLUSIONS Transcripts were identified associated with specific stages of hypocotyl development, in which phloem fibre cells were undergoing thickening of secondary walls. Temporal and spatial regulation of beta-galactosidase activity suggests a role for this enzyme in remodelling of flax bast fibre cell walls during secondary cell wall deposition.
USER CONTROLLABILITY IN A HYBRID RECOMMENDER SYSTEM

Since the introduction of Tapestry in 1990, research on recommender systems has traditionally focused on the development of algorithms whose goal is to increase the accuracy of predicting users’ taste based on historical data. In the last decade, this research has diversified, with human factors being one area that has received increased attention. Users’ characteristics, such as trusting propensity and interest in a domain, or systems’ characteristics, such as explainability and transparency, have been shown to have an effect on improving the user experience with a recommender. This dissertation investigates on the role of controllability and user characteristics upon the engagement and experience of users of a hybrid recommender system. A hybrid recommender is a system that integrates the results of different algorithms to produce a single set of recommendations. This research examines whether allowing the user to control the process of fusing or integrating different algorithms (i.e., different sources of relevance) results in increased engagement and a better user experience. The essential contribution of this dissertation is an extensive study of controllability in a hybrid fusion scenario. In particular, the introduction of an interactive Venn diagram visualization, combined with sliders explored in a previous work, can provide an efficient visual paradigm for information filtering with a hybrid recommender that fuses different prospects of relevance with overlapping recommended items. This dissertation also provides a three-fold evaluation of the user experience: objective metrics, subjective user perception, and behavioral measures.
Effects of Pulse Width, Pulse Rate and Paired Electrode Stimulation on Psychophysical Measures of Dynamic Range and Speech Recognition in Cochlear Implants

Objectives: In this article results are described of a study on the effects of stimulation rate (PR), pulse duration (PW), and paired pulsatile stimulation (PPS) versus continuous interleaved sampling (CIS) on speech perception and psychophysical loudness measures. Methods: During 3 nonconsecutive days, 27 postlingually deafened patients, implanted with either a CII or a HiRes90K with a HiFocus electrode array, were fitted with nine 12-channel strategies after a Latin-square design, systematically investigating the effect of stimulation rate (774–3868 pps/channel), PW (11–43 µsec/phase), and PPS versus CIS. Speech perception was measured in phonemes using open-set monosyllabic words. Minimum (T level) and maximum stimulation (M level) levels were measured. Results: In general, performance was better with CIS strategies than with PPS strategies. There was little variation in speech perception performance between the different CIS strategies. As expected, PW and rate influenced the T and M levels in a systematic way for all electrode array positions. The T levels decreased by 2.11 dB per doubling of the pulse rate, whereas the M levels were considerably less influenced (slope −0.81 dB per doubling of the rate). T levels decreased 6.46 dB per doubling of pulse width, with an associated decrease in M levels of 5.58 dB, which is expressed in a closed-set formula. Changing from CIS to PPS led to a reduction of T levels by 1.34 dB and of M levels by 1.91 dB. This reduction was superimposed on the changes caused by doubling the rate, inherent to the PPS paradigm. Conclusions: CIS strategies tend to perform better than PPS strategies. PW, rate and paired stimulation have little effect on speech perception scores. However, they do have predictable and independent effects on both T and M levels for all strategies tested. The relationships found allow the improvement of the versatility of current fitting software and provide a basis to let the fitting software automatically adjust T and M levels if the PW or rate are adjusted in an existing program.
Identification of transcription factors perturbed by the synthesis of high levels of a foreign protein in yeast saccharomyces cerevisiae

For years, micro‐organisms have been used for the industrial production of heterologous proteins. However, the production of foreign proteins causes undesirable problems for the host organism. The analysis of this phenomenon is desirable to improve the production of relevant proteins and so far no analysis of the effects of recombinant protein production on genetic regulation has been reported. In this work, network component analysis (NCA) was used to deduce transcription factor activities (TFAs) in a recombinant strain of Saccharomyces cerevisiae that produces a foreign protein, human superoxide dismutase (SOD) and compared the behavior of this yeast strain to the wild‐type host to see the effect of the expression of the protein at the regulatory level. NCA identified a network of 817 genes regulated by 87 transcription factors (TFs). From the identified TFs, 45 show significant change in their activities at least in one of the three phases of diauxic growth (glucose, ethanol, and early stationary phase). The major effect of the expression of SOD on the activity of the TFs was observed in the early stationary phase with 34 of them perturbed in comparison with 12 on glucose and 20 on ethanol. These TFs cover the main functions of the cell, such as developmental processes, cell cycle, metabolism, and environmental response. Five of them are present in all growth phases: Hal9, Mac1, Oaf3, Stp1, and Urc2. In addition, TFA analysis corroborates the hypothesis that copper plays a key role as a stress factor and suggests that YJL206C, a TF with unknown function, could be related to Ace2, a cell cycle regulator. © 2011 American Institute of Chemical Engineers Biotechnol. Prog. , 2011
Post-Conflict Aid, Real Exchange Rate Adjustment, and Catch-Up Growth

Post-conflict countries receive substantial aid flows after the start of peace. While post-conflict countries' capacity to absorb aid (that is, the quality of their policies and institutions) is built up only gradually after the onset of peace, the evidence suggests that aid tends to peak immediately after peace is attained and decline thereafter. Aid composition broadly reflects post-conflict priorities, with large parts of aid financing social expenditure and infrastructure investment. Aid has significant short-term effects on the real exchange rate (RER), as inferred from the behavior of RER in the world. While moderate RER overvaluation is observed in post-conflicts, it cannot be traced down to the aid flows. The empirical evidence on world growth reveals new findings about the pattern of catch-up growth during post-conflicts and the role of key growth determinants on post-conflict growth. Aid is an important determinant of growth, both generally and more strongly during post-conflict periods. Because RER misalignment reduces growth, RER overvaluation during post-conflicts reduces catch-up growth. Aid and RER overvaluation combined also lower growth. But the negative growth effect of RER overvaluation declines with financial development.
Finding Relevant Sources in Twitter Based on Content and Social Structure

As an increasingly large amount of knowledge is shared between users in Twitter, it is becoming a popular source of relevant information to many people. In Twitter, information is transferred primarily via a social relationship called following. Identifying users to follow who are highly relevant to a particular topic of interest can be a difficult task. To address this problem, we introduce a novel method of automatically identifying and ranking Twitter users according to their relevancy to a given topic. The algorithm combines the standard Twitter text search mechanism with information about the social relationships in the network, effectively leveraging the opinions of the crowd. We performed a study comparing the ranked lists generated by the algorithm with lists provided by a commercial website specifically designed for the same purpose. Our initial findings show a good potential for automatically identifying interesting and relevant users.
Development and psychometric testing of the attitude toward potential pregnancy scale.

OBJECTIVE To develop and test a comprehensive tool for measuring women's attitudes toward the possibility of becoming pregnant. DESIGN Cross-sectional mixed methods study. SETTING Two obstetric/gynecologic (OB/GYN) clinics and one family planning clinic in Baltimore, Maryland. PARTICIPANTS One-hundred thirty (130) nonpregnant, primarily African American women (84%) age 18 to 29. METHODS Participants completed a computer-based survey as part of a larger retrospective mixed-methods study. The Attitude Toward Potential Pregnancy Scale (APPS) was assessed using exploratory factor analysis and hypothesis testing. RESULTS Cronbach's alpha for internal consistency for the APPS was 0.86. Item-total correlations ranged from 0.56 to 0.75. All items loaded on one factor. Support for construct validity was demonstrated using logistic regression, where the odds of being a highly effective contraceptive user decreased by 8% with each one-point increase in score on the APPS (odds ratio = 0.92; confidence interval [0.87, 0.98]). CONCLUSIONS This study provides support for reliability and validity of the APPS. The APPS may be a useful tool for understanding pregnancy attitude in future studies and in clinical practice. Further research is needed to assess the usefulness of the scale with other groups of women, its utility in the clinical practice setting, and its potential predictive validity for unintended pregnancy.
The Temporal Muscle of the Head Can Cause Artifacts in Optical Imaging Studies with Functional Near-Infrared Spectroscopy

Background: Extracranial signals are the main source of noise in functional near-infrared spectroscopy (fNIRS) as light is penetrating the cortex but also skin and muscles of the head. Aim: Here we performed three experiments to investigate the contamination of fNIRS measurements by temporal muscle activity. Material and methods: For experiment 1, we provoked temporal muscle activity by instructing 31 healthy subjects to clench their teeth three times. We measured fNIRS signals over left temporal and frontal channels with an interoptode distance of 3 cm, in one short optode distance (SOD) channel (1 cm) and electromyography (EMG) over the edge of the temporal muscle. In experiment 2, we screened resting state fNIRS-fMRI (functional magnetic resonance imaging) data of one healthy subject for temporal muscle artifacts. In experiment 3, we screened a dataset of sound-evoked activity (n = 33) using bi-temporal probe-sets and systematically contrasted subjects presenting vs. not presenting artifacts and blocks/events contaminated or not contaminated with artifacts. Results: In experiment 1, we could demonstrate a hemodynamic-response-like increase in oxygenated (O2Hb) and decrease in deoxygenated (HHb) hemoglobin with a large amplitude and large spatial extent highly exceeding normal cortical activity. Correlations between EMG, SOD, and fNIRS artifact activity showed only limited evidence for associations on a group level with rather clear associations in a sub-group of subjects. The fNIRS-fMRI experiment showed that during the temporal muscle artifact, fNIRS is completely saturated by muscle oxygenation. Experiment 3 showed hints for contamination of sound-evoked oxygenation by the temporal muscle artifact. This was of low relevance in analyzing the whole sample. Discussion: Temporal muscle activity e.g., by clenching the teeth induces a large hemodynamic-like artifact in fNIRS measurements which should be avoided by specific subject instructions. Data should be screened for this artifact might be corrected by exclusion of contaminated blocks/events. The usefulness of established artifact correction methods should be evaluated in future studies. Conclusion: Temporal muscle activity, e.g., by clenching the teeth is one major source of noise in fNIRS measurements.
PBG-Net: Object detection with a multi-feature and iterative CNN model

We introduce PBG-Net, an object detection system based on an elaborately designed multi-feature deep CNN which works without proposal algorithms. Firstly, PBG-Net aggregates hierarchical features into multi-feature maps and discretizes the output of Conv5 feature map into a set of predicting boxes, namely Predicting Boxes Generation (PBG). Then, PBG-Net crops multi-feature maps via mapping the predicting boxes and handles the outcome into multi-feature concatenation. Finally, we exploit an iterative regression localization model based on a novel overlap loss function and online hard boxes selection. PBG-Net with around 100 boxes and an end-to-end joint training can achieve 74.2% and 71.1% mAP on the detection of PASCAL VOC 2007 and PASCAL VOC 2012 correspondingly at 12 fps on a NVIDIA GTX 1070p GPU, better than the Faster R-CNN counterparts.
Rotational control of an omnidirectional mobile robot using a fuzzy servo controller

It is known that the equation of motions for an omnidirectional mobile robot is nonlinear with respect to the rotational angle between the moving and absolute coordinate systems. In this paper, a fuzzy model approach is applied to the control of a time-varying rotational angle, in which multiple linear models are obtained by utilizing the original nonlinear model in some representative angles and they are used to derive the optimal type 2 servo gain matrices. The effectiveness of the proposed method is illustrated by giving some simulations for the trajectory tracking control problem.
Spiking Chemical Sensor (SCS): A new platform for neuro-chemical sensing

A spiking chemical sensor (SCS) is presented for detection of neurogenic ion concentration associated with active nerve fibres in nerve bundles. Based on the "integrate-and-fire" circuit, the SCS uses a chemically-modified ISFET front end encoding the sense data in the spike domain. Used in an array, it provides a spatio-temporal map of chemical activity around the nerve bundle which may be relayed off chip using low power asynchronous communication hardware. The circuit is shown to be tunable to yield a linear relation with either pH or actual hydrogen ion concentration. Furthermore, its compact pixel footprint in addition to efficient use of the sensing surface, makes it ideal for use in neuro-chemical imaging.
Association of glucose transporter 1 polymorphisms with type 2 diabetes in the Tunisian population

T2DM is a complex metabolic disease. Genetic studies on T2DM have been of little help so far because several genetic association studies have shown conflicting results. In this study, we report the findings of a case‐control study on three SNPs in the GLUT1 gene. For this, we investigated the association of GLUT1 genotypes and haplotypes with T2DM.
Use of heme and hemoglobin by Escherichia coli O157 and other Shiga-like-toxin-producing E. coli serogroups

The virulence properties of Escherichia coli O157 isolates were compared with those of Shiga-like-toxin-producing E. coli of non-O157 serogroups. The growth of all E. coli O157 isolates was stimulated by both heme and hemoglobin, and all produced enterohemolysin. The incidence of these properties was significantly lower in the non-O157 isolates. This may contribute to the greater virulence and higher incidence of human infection caused by E. coli O157.
A Modified Bow-Tie Antenna for Improved Pulse Radiation

The analysis, design, and realization of a modified bow-tie antenna optimized for impulse ground penetrating radar (GPR) applications is described. The proposed antenna shows improved properties important for GPR, which include its compact size (in comparison with a conventional bow-tie antenna) and ability to radiate UWB pulses with increased amplitude and very small late-time ringing. A substantial increase in the amplitude of the transmitted pulse is achieved by utilizing radiation from discontinuities introduced by the resistive loading employed in the antenna to suppress late-time ringing. By choosing an optimal distance between the antenna's feed point and the location of the resistive loading, radiations that occur from the antenna's feed point and the mentioned discontinuities at the resistive loading will combine constructively in the boreside direction of the antenna. As a result, one will observe a substantial increase of the amplitude of the transmitted pulse in the boreside direction. Furthermore, an analytical expression describing approximate time-harmonic current distribution is derived to indicate an optimal resistive loading profile for the proposed antenna. Additionally, the traveling-wave current distribution of the antenna is theoretically analyzed to examine the applicability of the obtained time-harmonic expression for pulse excitation. It has been found that when the antenna is resistively loaded both the time-harmonic and traveling-wave currents decay to approach nearly the same value at the end section of the antenna. As the amount of current at the antenna ends corresponds to the level of reflection which occurs there, the derived expression is found to be useful to indicate an optimal loading profile for the proposed antenna. A theoretical model of the proposed antenna has been developed to perform numerical analysis using a modified NEC-2 code. In addition, an experimental verification has been carried out and both the simulation and experiment confirmed the improved properties of the proposed antenna.
Net forces during tethered simulation of underwater streamlined gliding and kicking techniques of the freestyle turn

Weassessed the net forces created when towing swimmers while gliding and kicking underwater to establish an appropriate speed for initiating underwater kicking, and the most effective gliding position and kicking technique to be applied after a turn. Sixteen experienced male swimmers of similar body shape were towed by a motorized winch and pulley system. A load cell measured net force (propulsive force - drag force) at speeds of 1.6, 1.9, 2.2, 2.5 and 3.1 m· s-1 . At each speed, the swimmers performed a prone streamline glide, a lateral streamline glide, a prone freestyle kick, a prone dolphin kick and a lateral dolphin kick. A two-way repeated-measures analysis of variance revealed significant differences between the gliding and kicking conditions at different speeds. The results demonstrated an optimal range of speeds (1.9 to 2.2 m· s-1 ) at which to begin underwater kicking to prevent energy loss from excessive active drag. No significant differences were found between the prone and lateral streamline glide positions or between the three underwater kicking techniques. Therefore, there appears to be no significant advantage in using one streamlining technique over another or in using one kicking style over another.
A preliminary study of active compared with passive imputation of missing body mass index values among non-Hispanic white youths.

BACKGROUND Addressing missing data on body weight, height, or both is a challenge many researchers face. In calculating the body mass index (BMI) of study participants, researchers need to impute the missing data. OBJECTIVE A multiple imputation through a chained equations approach was used to determine whether one should first impute the missing anthropometric data and then calculate BMI or use an imputation model to obtain BMI. DESIGN The present study used computer simulation to address the question of how to calculate BMI when there is missing data on weight and height. The simulated data reflected data gathered on non-Hispanic white youths (n = 905) aged 2-18 y, who participated in the 1999-2000 National Health and Nutrition Examination Survey (NHANES). RESULTS The simulation indicated that it made little difference in the accuracy with which the youths' mean BMIs were estimated when the data were missing completely at random. However, the use of a model to impute BMI was favored slightly when the data were missing at random and the imputation model included the variable used to determine missingness. CONCLUSION The present findings extend the use of passive imputation and the use of multiple imputation through a chained equations approach to an area of critical public health importance.