Miracle-dz/UniFAR-FTUs huggingface dataset:
Dispersion, aberration and deconvolution in multi‐wavelength fluorescence images

The wavelength dependence of the incoherent point spread function in a wide‐field microscope was investigated experimentally. Dispersion in the sample and optics can lead to significant changes in the point spread function as wavelength is varied over the range commonly used in fluorescence microscopy. For a given sample, optical conditions can generally be optimized to produce a point spread function largely free of spherical aberration at a given wavelength. Unfortunately, deviations in wavelength from this value will result in spherically aberrated point spread functions. Therefore, when multiple fluorophores are used to localize different components in the same sample, the image of the distribution of at least one of the fluorophores will be spherically aberrated. This aberration causes a loss of intensity and resolution, thereby complicating the localization and analysis of multiple components in a multi‐wavelength image. We show that optimal resolution can be restored to a spherically aberrated image by constrained, iterative deconvolution, as long as the spherical aberration in the point spread function used for deconvolution matches the aberration in the image reasonably well. The success of this method is essentially independent of the initial degree of spherical aberration in the image. Deconvolution of many biological images can be achieved by collecting a small library of spherically aberrated and unaberrated point spread functions, and then choosing a point spread function appropriate for deconvolving each image. The co‐localization and relative intensities of multiple components can then be accurately studied in a multi‐wavelength image.
Improving DAC resolution in closed-loop control of precision mechatronic systems using dithering

The resolution of precision mechatronic systems is fundamentally limited by the the noise and distortion performance of digital-to-analog converters. The sources of noise and distortion include quantization error, non-linearity, thermal noise, and semiconductor noise. In precision control applications, the primary limitation is harmonic distortion due to quantization and element mismatch. In this article, quantization noise and harmonic distortion are reduced by combinations of small noise dithers and large high-frequency periodic dithers. Theoretical predictions are confirmed experimentally on a closed-loop nanopositioning system. The results show reasonable correspondence to simulation and a significant reduction in noise due to quantization and element mismatch.
Microarray meta‐analysis identifies candidate genes for human spermatogenic arrest

Male infertility affects approximately half of couples who have difficulty becoming pregnant, and its prevalence is continuously rising. Many studies have been performed using animal testes to reveal the mechanisms of male infertility, but few studies have investigated human testes due to various limitations. The aim of this study was to investigate the gene expression profile of impaired human testes through a meta‐analysis of microarray data sets, which was accomplished by using 178 human testis samples and 7 microarray data sets. Impaired testes were categorised into four pathological phenotypes or the normal phenotype based on their Johnsen score. Then, a meta‐analysis was performed to screen out the differentially expressed genes (DEGs) in each phenotype. The DEGs were used in a subsequent bioinformatics analysis. Our results identified several novel hub genes and pathways and suggested that G1 mitotic cell cycle arrest was a remarkable feature in pre‐meiotic arrest. Furthermore, fifteen p53‐interacting proteins, such as ABL1 and HDAC2, whose roles in spermatogenesis have not been well characterised, were selected from the DEGs through a strict screening procedure.
Description Logics-Based Modelling for Precise Information Retrieval

In professional environments, users have a good knowledge about their domain of interest as well as the documents they consult regularly. In order to carry out their professional tasks, they need an Information Retrieval System (IRS) that allows them to find a precise answer to their information needs. Generally speaking, they know about documents content that may satisfy their information needs. Thus, during the retrieval task, they try to complete the information that they have and that is insufficient. Their information needs are in this case formulated through precise queries. The qualifier ”precise” denotes a query that contains: i) a very specialised terminology and ii) a complex structure. Through a precise query, a user can describe his information need using explicit semantic relationships between the descriptors of his query. He also can use boolean operators or quantification (at least, all, etc.) in order to specify the number of elements that the desired document should contain. In order to illustrate some characteristics of precise queries, we present here some query examples.
Gaussian Modeling of Spatially Correlated LOS/NLOS Maps for Mobile Communications

The wireless channel behaves markedly different depending on whether a line-of-sight (LOS) between transmitter and receiver exists or not. State-of-the-art wireless channel models for mobile communications, such as, IST WINNER-II and the 3GPP 3D channel model specified in TR 36.873, define distinct macro- and microscopic fading parameters for LOS and non-LOS (NLOS) situations. Whether a user is in LOS/NLOS is randomly determined by a distance-dependent LOS probability; commonly, for each position in the network, the random realization of LOS/NLOS propagation is independently determined from this distance-dependent LOS probability. Since in this case random draws of neighboring positions are statistically independent, base station assignment regions in system-level simulations become highly irregular. To mitigate this problem, we propose an efficient method to generate spatially correlated LOS/NLOS channel maps that follow predefined distance-dependent LOS probability and additionally enable spatial clustering of LOS positions.
Common-Mode EMI Study and Reduction Technique for the Interleaved Multichannel PFC Converter

Interleaved multichannel power factor correction (PFC) converter is very popular today because of its ability to reduce input and output current ripples. In this paper, the common-mode (CM) electromagnetic interference noise emission model of the multichannel PFC converter is studied. A balance technique is introduced to reduce CM noise emission. To improve the high-frequency balance, a novel topology with coupled-inductor structure is proposed. Its CM noise model is derived and balance condition for minimizing CM noise is calculated. Effects of phase shift and channel shedding on this solution are also studied. The proposed topology has effectively reduced CM noise under any phase shift and channel shedding conditions. A two-channel PFC converter is built to verify the proposed balance technique. Experimental results show that CM noise can be reduced up to 20 dB between 150 kHz and 7 MHz.
The Mercury Resistance Operon: From an Origin in a Geothermal Environment to an Efficient Detoxification Machine

Mercuric mercury (Hg[II]) is a highly toxic and mobile element that is likely to have had a pronounced and adverse effect on biology since Earth’s oxygenation ∼2.4 billion years ago due to its high affinity for protein sulfhydryl groups, which upon binding destabilize protein structure and decrease enzyme activity, resulting in a decreased organismal fitness. The central enzyme in the microbial mercury detoxification system is the mercuric reductase (MerA) protein, which catalyzes the reduction of Hg(II) to volatile Hg(0). In addition to MerA, mer operons encode for proteins involved in regulation, Hg binding, and organomercury degradation. Mer-mediated approaches have had broad applications in the bioremediation of mercury-contaminated environments and industrial waste streams. Here, we examine the composition of 272 individual mer operons and quantitatively map the distribution of mer-encoded functions on both taxonomic SSU rRNA gene and MerA phylogenies. The results indicate an origin and early evolution of MerA among thermophilic bacteria and an overall increase in the complexity of mer operons through evolutionary time, suggesting continual gene recruitment and evolution leading to an improved efficiency and functional potential of the Mer detoxification system. Consistent with a positive relationship between the evolutionary history and topology of MerA and SSU rRNA gene phylogenies (Mantel R = 0.81, p < 0.01), the distribution of the majority of mer functions, when mapped on these phylograms, indicates an overall tendency to inherit mer-encoded functions through vertical descent. However, individual mer functions display evidence of a variable degree of vertical inheritance, with several genes exhibiting strong evidence for acquisition via lateral gene transfer and/or gene loss. Collectively, these data suggest that (i) mer has evolved from a simple system in geothermal environments to a widely distributed and more complex and efficient detoxification system, and (ii) merA is a suitable biomarker for examining the functional diversity of Hg detoxification and for predicting the composition of mer operons in natural environments.
Acquiring fear and threat related attentional biases through informational learning

Research has found that threat related attentional biases towards novel animals can be induced in children by giving threat information about the animals. Naturally occurring (i.e. non-induced) threat related attentional biases have also been found in both children and adults in the past research. The naturally occurring threat stimuli mainly include phobia stimuli and the threat stimuli that are assumed to have evolutionary roots (e.g., threatening facial expressions, and poisonous animals). In the present research, induced and naturally occurring threat related attentional biases were investigated and contrasted in children and adults. The participants' manual RTs and eye movements were measured in five experiments using the visual search paradigm to examine the attentional biases. The participating children, regardless of their trait anxiety scores, showed attentional bias toward angry faces as indexed by RT and eye movement measures. In the second and third experiments, children acquired fear of novel animals by listening to threat information about them. They later showed attentional bias to the newly feared stimuli: the presence of the animal's images interfered with detecting an irrelevant target, and the animal's images were detected faster than the control stimuli when presented as hidden targets in naturalistic scenes. In the fourth and fifth experiments, no enhancement of attentional bias towards fear-relevant stimuli due to receiving threat information was evident, as no difference was found between the threat information and the no information snake stimuli in terms of attention deployment measures. Strong evidence of naturally occurring attentional bias toward snake stimuli, however, was found in both RTs and overt attention indices. Overall, the RT data provided more robust evidence than the eye movement data in support of the predicted threat related attentional biases. It was argued that attentional biases to fear stimuli might have different levels which develop over time, with fast threat processing (indexed by faster RTs) appearing soon after the fear is acquired
MicroRNA-34a regulates liver regeneration and the development of liver cancer in rats by targeting Notch signaling pathway

Objective This study aimed to investigate the role of microRNA-34a (miR-34a) in regulating liver regeneration (LR) and the development of liver cancer in rats by targeting Notch signaling pathway. Methods Thirty male Sprague-Dawley (SD) rats were randomly assigned into partial hepatectomy (PH) group and sham hepatectomy (SH) group. Hematoxylin and eosin (HE) staining was used to observe the histological change in liver tissues. Enzyme-linked immunosorbent assay (ELISA) was used to measure the serum tumor necrosis factor α (TNF-α) and interleukin-6 (IL-6) levels. Dual-luciferase reporter gene assay was performed to examine whether miR-34a targeted Notch1 gene. Human liver cancer Huh7 cells were transfected and divided into blank, negative control (NC), miR-34a mimics and miR-34a inhibitors groups. MTT and flow cytometry were used to detect cell growth, and cell cycle and apoptosis, respectively. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied detect to the expressions of miR-34a and Notch receptor mRNA. Western blotting was performed to detect the protein expressions of Notch receptors, P21, Bax, Bcl-2 and Bcl-xL. Tumor xenograft in nude mice was done to observe tumor formation in different groups. Results Compared to the SH group, miR-34a expression in liver tissues in the PH group decreased first and then increased to the normal level during LR. In early stage of LR, the expressions of Notch receptors and miR-34a were negatively correlated. Compared to the blank and NC groups, the cell growth was inhibited, cell cycle was mainly arrested in the G2/M phase and cell apoptosis rate increased in the miR-34a mimics group. Moreover, the expressions of miR-34a, P21 and Bax were up-regulated, while the expressions of Notch receptors, and Bcl-2 and Bcl-xL were down-regulated in this group. Additionally, the tumor growth in the miR-34a mimics group was reduced. The miR-34a inhibitors group showed contrary tendencies. Conclusion Our study demonstrates that miR-34a regulated LR and the development of liver cancer by inhibiting Notch signaling pathway.
Systems Analysis of Drug-Induced Receptor Tyrosine Kinase Reprogramming Following Targeted Mono- and Combination Anti-Cancer Therapy

The receptor tyrosine kinases (RTKs) are key drivers of cancer progression and targets for drug therapy. A major challenge in anti-RTK treatment is the dependence of drug effectiveness on co-expression of multiple RTKs which defines resistance to single drug therapy. Reprogramming of the RTK network leading to alteration in RTK co-expression in response to drug intervention is a dynamic mechanism of acquired resistance to single drug therapy in many cancers. One route to overcome this resistance is combination therapy. We describe the results of a joint in silico, in vitro, and in vivo investigations on the efficacy of trastuzumab, pertuzumab and their combination to target the HER2 receptors. Computational modelling revealed that these two drugs alone and in combination differentially suppressed RTK network activation depending on RTK co-expression. Analyses of mRNA expression in SKOV3 ovarian tumour xenograft showed up-regulation of HER3 following treatment. Considering this in a computational model revealed that HER3 up-regulation reprograms RTK kinetics from HER2 homodimerisation to HER3/HER2 heterodimerisation. The results showed synergy of the trastuzumab and pertuzumab combination treatment of the HER2 overexpressing tumour can be due to an independence of the combination effect on HER3/HER2 composition when it changes due to drug-induced RTK reprogramming.
The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example

What is the mechanism through which transcription factors (TFs) assemble specifically along the enhancer DNA? The IFN-β enhanceosome provides a good model system: it is small; its components' crystal structures are available; and there are biochemical and cellular data. In the IFN-β enhanceosome, there are few protein-protein interactions even though consecutive DNA response elements (REs) overlap. Our molecular dynamics (MD) simulations on different motif combinations from the enhanceosome illustrate that cooperativity is achieved via unique organization of the REs: specific binding of one TF can enhance the binding of another TF to a neighboring RE and restrict others, through overlap of REs; the order of the REs can determine which complexes will form; and the alternation of consensus and non-consensus REs can regulate binding specificity by optimizing the interactions among partners. Our observations offer an explanation of how specificity and cooperativity can be attained despite the limited interactions between neighboring TFs on the enhancer DNA. To date, when addressing selective TF binding, attention has largely focused on RE sequences. Yet, the order of the REs on the DNA and the length of the spacers between them can be a key factor in specific combinatorial assembly of the TFs on the enhancer and thus in function. Our results emphasize cooperativity via RE binding sites organization.
Working memory moderates the association between early institutional care and separation anxiety symptoms in late childhood and adolescence

Abstract Adverse caregiving, for example, previous institutionalization (PI), is often associated with emotion dysregulation that increases anxiety risk. However, the concept of developmental multifinality predicts heterogeneity in anxiety outcomes. Despite this well-known heterogeneity, more work is needed to identify sources of this heterogeneity and how these sources interact with environmental risk to influence mental health. Here, working memory (WM) was examined during late childhood/adolescence as an intra-individual factor to mitigate the risk for separation anxiety, which is particularly susceptible to caregiving adversities. A modified “object-in-place” task was administered to 110 youths (10–17 years old), with or without a history of PI. The PI youths had elevated separation anxiety scores, which were anticorrelated with morning cortisol levels, yet there were no group differences in WM. PI youths showed significant heterogeneity in separation anxiety symptoms and morning cortisol levels, and WM moderated the link between caregiving and separation anxiety and mediated the association between separation anxiety and morning cortisol in PI youth. Findings suggest that (a) institutional care exerts divergent developmental consequences on separation anxiety versus WM, (b) WM interacts with adversity-related emotion dysregulation, and (c) WM may be a therapeutic target for separation anxiety following early caregiving adversity.
Becoming a Nurse: Role Formation Among Accelerated Baccalaureate Students

To understand nursing role formation for students enrolled in an accelerated baccalaureate nursing program, end-of-term narrative reflections from 34 students were analyzed over the course of the 15-month program. Using thematic analysis, 4 major themes were identified: evolving role perception, extending nursing student-patient interaction, engaging with health care team and systems of care, and expanding clinical thinking.
Computer-assisted surgical trainer for minimally invasive surgery

The paper presents the current state of research on developing a computer-assisted surgical trainer to be used in a minimally-invasive surgery training program. Along with wide adoption of laparoscopic surgery a strong need for systematic training in the field of minimally-invasive surgery has developed. The goal of the described system is to provide surgeons specialising in minimally-invasive operating techniques an objective performance evaluation method and a safe setting for practicing elementary laparoscopic skills.
Dares to addiction: youth definitions and perspectives on gambling.

BACKGROUND Over the past decade, there has been a rapid growth of gambling in Canada and internationally. Although youth are a potentially vulnerable group, little is known about what they understand and if they are being affected by the recent increase in gambling. METHODS This study examined how youth view gambling using an inductive qualitative research design and analysis based on grounded theory principles. Twelve focus groups were conducted comprising 103 participants (median age = 15 years) with diverse representation of Ontario youth. Focus-group questions were designed to capture youth's experiences and opinions about gambling. RESULTS Youth participants defined a spectrum of gambling from a dare and friendly betting to legalized forms of gambling (lotteries, casinos) and addiction. Their opinions varied according to age and gambling type. For example, daring and friendly betting were identified as positive activities used by younger adolescents to relieve boredom and establish social relationships. Gambling was separate from daring because of its association with money. Many participants had minimal awareness of the potential negative impact of gambling. Information technology (Internet) was seen as an attractive medium for playing games and gambling where no money was involved. CONCLUSION Lack of awareness of gambling among youth and its consequences underscores the need for public education. The diverse range of gambling behaviour and age-dependent access to money need careful consideration in defining youth gambling "problems" and in designing public health interventions.
Calretinin: A Valuable Marker of Normal and Neoplastic Leydig Cells of the Testis

Sex cord–stromal tumors represent approximately 4% of all testicular neoplasms. Leydig cell tumor (LCT) is the most common entity, followed by Sertoli cell tumor (SCT). Leydig cell tumor histologic diagnosis is usually easy, but occasional forms of LCT could mimic others neoplasms, especially SCT or variants of yolk sac tumor. The aim of this study was to investigate calretinin expression in LCT and SCT of the testis. We evaluated calretinin reactivity in formalin-fixed, paraffin-embedded sections of 10 LCT, three SCT, five Leydig cell hyperplasia, two Sertoli cell adenomas, eight seminomatous tumors, five nonseminomatous germ cell tumors (mixed tumor), one adenomatoid tumor, and two normal testes using a standard immunohistochemical technique with a microwave-mediated epitope retrieval. All cases of LCT showed a positive staining that was diffuse and intense, constantly cytoplasmic, and sometimes nuclear. A positive strong and diffuse cytoplasmic and sometimes nuclear staining was also observed in Leydig cell hyperplasia and in normal Leydig cells. No staining was seen in two of three cases of SCT, and focal staining was observed in the third case. Only rare scattered cells were weakly immunostained in the Sertoli cell nodules. Seminomatous and nonseminomatous germ cell tumors were negative. Calretinin is an interesting marker of normal and neoplastic Leydig cells of the testis and may be of value in the diagnosis of atypical LCT.