Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiphoton microscopy in defining liver function

Abstract. Multiphoton microscopy is the preferred method when in vivo deep-tissue imaging is required. This review presents the application of multiphoton microscopy in defining liver function. In particular, multiphoton microscopy is useful in imaging intracellular events, such as mitochondrial depolarization and cellular metabolism in terms of NAD(P)H changes with fluorescence lifetime imaging microscopy. The morphology of hepatocytes can be visualized without exogenously administered fluorescent dyes by utilizing their autofluorescence and second harmonic generation signal of collagen, which is useful in diagnosing liver disease. More specific imaging, such as studying drug transport in normal and diseased livers are achievable, but require exogenously administered fluorescent dyes. If these techniques can be translated into clinical use to assess liver function, it would greatly improve early diagnosis of organ viability, fibrosis, and cancer.
Partial band noise jamming rejection with S-CFFH/16-QAM optimum and suboptimum maximum-likelihood receivers over rayleigh fading channels with imperfect CSI

The recently proposed subset-based coherent fast frequency hopping (S-CFFH) scheme enables reliable channel estimation for FFH over fading channel. With S-CFFH/16-QAM, we propose the optimum and suboptimum maximum-likelihood (ML) receivers in the presence of partial band noise jamming (PBNJ), frequency-selective Rayleigh fading, and Gaussian channel estimation errors. We analyze the bit error ratio (BER) of the suboptimum ML receiver, whose BER performance is nearly the same as the optimum ML receiver. The analyses are verified by simulations. It is shown that, the proposed ML receivers significantly outperform the maximum ratio combining (MRC) and the equal gain combining (EGC). Furthermore, as compared with the conventional non-coherent FFH/BFSK, the S-CFFH/16- QAM shows better BER performance and a much higher spectral efficiency.
Atypical Features in Regenerating Tubules Point to a Risk for Implantation of Renal Stem/Progenitor Cells

Stem/progenitor cells are seen as a therapeutic option for repair of diseased renal parenchyma. However, actual data show that survival of implanted stem/progenitor cells is impeded by harmful interstitial environment. To learn about parameters for cell adaptation, renal stem/progenitor cells were mounted in a polyester (POSI-4) interstitium during perfusion culture. Controlled fluid environment was maintained by chemically defined CO 2 - independent culture media for 13 days. Cell biological features were then analyzed by immunohistochemistry, while structural details were investigated by advanced fixation of specimens for microscopy. When stem/progenitor cells are kept in Leibovitz's L-15 Medium or CO 2 Independent Medium, spatial development of numerous tubules is observed. Immunolabel for TROMA- III, cingulin and laminin ɣ1 depicts that a homogenous cell population is contained. Semithin sections of specimens fixed in traditional glutaraldehyde (GA) solution reflect an unobtrusive morphology. In contrast, fixation by GA solution including ruthenium red unveils in tubules a thickened basal lamina. Fixation by GA solution including tannic acid illustrates atypical development of a heterogeneous epithelium consisting of bright and dark cells. Thus, advanced fixation of specimens makes pathological features visible, when regeneration is investigated by renal stem/ progenitor cells. To what extent a comparable risk lurks behind an implantation, has to be elaborated.
Adipose differentiation-related protein knockdown inhibits vascular smooth muscle cell proliferation and migration and attenuates neointima formation

Vascular smooth muscle cells (VSMCs) have an important role in atherosclerosis development. Evidence has demonstrated that adipose differentiation-related protein (ADRP) is associated with foam cell formation and atherosclerosis progression. However, to the best of our knowledge, no previous studies have investigated the role of ADRP knockdown in platelet-derived growth factor (PDGF)-stimulated proliferation and migration of VSMCs in vitro. Furthermore, the effect of ADRP knockdown on neointima formation in vivo remains unclear. In the present study, primary human aortic VSMCs were incubated with PDGF following ADRP small interfering (si)RNA transfection. Cell viability, migration and cell cycle distribution were analyzed by MTT, wound healing and Transwell assays and flow cytometry, respectively. Extracellular signal-regulated kinase (ERK), phosphorylated (p)-ERK, Akt, p-Akt, proliferating cell nuclear antigen (PCNA), matrix metalloproteinase (MMP)-2 and MMP-9 protein levels were determined by western blotting. Apolipoprotein E−/− mice fed an atherogenic diet were injected with siADRP or control siRNA twice a week. After 3 weeks of therapy, aortas were excised and ADRP mRNA and protein expression was determined. Neointima formation was assessed by hematoxylin and eosin staining. The results of the current study demonstrated that ADRP knockdown significantly inhibited PDGF-induced increases in VSMC viability, caused G1 phase cell cycle arrest and decreased PCNA expression. Knockdown of ADRP inhibited PDGF-induced migration of VSMCs by reducing MMP protein expression and activity. In addition, the present study also demonstrated that ADRP knockdown inhibited ERK and Akt signaling pathways in response to PDGF. Furthermore, siADRP administration suppressed neointima formation in the mouse model. The results of the present study indicate that ADRP may be a potential target for the treatment of atherosclerosis.
Congestion Control across a Video-Dominated Internet Tight Link

Existing congestion controllers have been desig ned with TCP traffic in mind. Changing traffic patterns on the Internet imply that on some tight links all UDP video stre ams will occur. Three different congestion controllers (RAP, TFRC, and fuzzy-logic based), already su ccessful in avoiding instability in current TCPdominated internets, were tested across a tight link in whic h v deo traffic dominated. Congestion control is either achieved by modulating the sending rate in response t o feedback of packet loss rates and/or round-trip delays (RAP/TFRC) or a congestion level based on packet disp ersion across a network path (fuzzy controller). The controllers were found to differ in the smoothness of res ulting video clip streams, with the fuzzy and TFRC controllers, in that order, producing the smoothest re ceiv d video. Tests also demonstrated that, when controlled flows of different types compete across a tight li nk, t is possible for the sending rate of TFRC to exceed the available bandwidth, resulting in excess packet loss and implying quite poor video quality at the receiver. The results show that fuzzy-logic control is more flexible when video streams dominate.
ICA for Surface Electromyogram

Surface electromyogram (SEMG) is an indicator of the underlying muscle activity and can be useful for human control interface. One difficulty in the use of SEMG for identifying complex movements is the mixing of muscle activity from other muscles, referred to cross-talk. Similarity in frequency and time domain makes the separation of muscle activity from different muscles extremely difficult. Independent Component Analysis (ICA) is a useful technique for blind source separation. This paper reports investigations to test the effectiveness of using ICA for such applications. It determines the impact of different conditions on the reliability of the separation. The paper reports the evaluation of issues related to the properties of the signals and number of sources. The paper also tests Zibulevsky’s method of temporal plotting to identify number of independent sources in SEMG recordings. The results demonstrate that ICA is suitable for SEMG signals when the numbers of sources are not greater than the number of recordings. The inability of the system to identify the correct order and magnitude of the signals is also discussed. It is observed that even when muscle contraction is minimal, and signal is filtered using wavelets and band pass filters, Zibulevsky’s sparse decomposition technique does not identify number of independent sources.
Interrogating the Escherichia coli cell cycle by cell dimension perturbations

Significance How bacteria regulate cell division to achieve cell size homeostasis, with concomitant coordination of DNA replication, is a fundamental question. Currently, there exist several competing models for cell cycle regulation in Escherichia coli. We performed experiments where we systematically perturbed cell dimensions and found that average cell volume scales exponentially with the product of the growth rate and the time from initiation of DNA replication to the corresponding cell division. Our data support a model in which cells initiate replication on average at a constant volume per origin and divide a constant time thereafter. Bacteria tightly regulate and coordinate the various events in their cell cycles to duplicate themselves accurately and to control their cell sizes. Growth of Escherichia coli, in particular, follows a relation known as Schaechter’s growth law. This law says that the average cell volume scales exponentially with growth rate, with a scaling exponent equal to the time from initiation of a round of DNA replication to the cell division at which the corresponding sister chromosomes segregate. Here, we sought to test the robustness of the growth law to systematic perturbations in cell dimensions achieved by varying the expression levels of mreB and ftsZ. We found that decreasing the mreB level resulted in increased cell width, with little change in cell length, whereas decreasing the ftsZ level resulted in increased cell length. Furthermore, the time from replication termination to cell division increased with the perturbed dimension in both cases. Moreover, the growth law remained valid over a range of growth conditions and dimension perturbations. The growth law can be quantitatively interpreted as a consequence of a tight coupling of cell division to replication initiation. Thus, its robustness to perturbations in cell dimensions strongly supports models in which the timing of replication initiation governs that of cell division, and cell volume is the key phenomenological variable governing the timing of replication initiation. These conclusions are discussed in the context of our recently proposed “adder-per-origin” model, in which cells add a constant volume per origin between initiations and divide a constant time after initiation.
Riemannian Classification for SSVEP-Based BCI : Offline versus Online Implementations

This chapter focus on the different implementations of brain-computer interface (BCI) based on Steady-State Visually Evoked Potentials (SSVEPs). In offline BCI, feature extraction and the classification are performed at the end of the session, when all trials are available. Whereas, in on-line settings, they are performed several times during each trial, usually for each available epoch recorded by the electroencephalogram (EEG) device, enabling real-time and asynchronous BCI. A recent successful approach in feature extraction and signal processing for BCI is Riemannian geometry , which deals with covariance matrices. They capture the degree of correlation between several random variables, that is how the brain signals change relatively to each other. These techniques have demonstrated their benefit on several occasions, leading to winning algorithms in international competitions and to state-of-the-art results on renowned BCI benchmarks. After reviewing some of the most robust approaches in feature extraction for SSVEP, this chapter will introduce newer tools based on Riemannian geometry. With an application to SSVEP, this article shows through a comparison how Riemannian geometry allows one to easily define offline and online implementations that have better accuracies than state of the art.
Exploiting Strategy-Space Diversity for Batch Bayesian Optimization

This paper proposes a novel approach to batch Bayesian optimisation using a multiobjective optimisation framework with exploitation and exploration forming two objectives. The key advantage of this approach is that it uses a suite of strategies to balance exploration and exploitation and thus can efficiently handle the optimisation of a variety of functions with small to large number of local extrema. Another advantage is that it automatically determines the batch size within a specified budget avoiding unnecessary function evaluations. Theoretical analysis shows that the regret not only reduces sub-linearly but also by an additional reduction factor determined by the batch size. We demonstrate the efficiency of our algorithm by optimising a variety of benchmark functions, performing hyperparameter tuning of support vector regression and classification, and finally heat treatment process of an Al-Sc alloy. Comparisons with recent baseline algorithms confirm the usefulness of our algorithm.
Identifying the target genes of SUPPRESSOR OF GAMMA RESPONSE 1, a master transcription factor controlling DNA damage response in Arabidopsis

In mammalian cells, the transcription factor p53 plays a crucial role in transmitting DNA damage signals to maintain genome integrity. However, in plants, orthologous genes for p53 and checkpoint proteins are absent. Instead, the plant-specific transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) controls most of the genes induced by gamma irradiation and promotes DNA repair, cell cycle arrest, and stem cell death. To date, the genes directly controlled by SOG1 remain largely unknown, limiting the understanding of DNA damage signaling in plants. Here, we conducted a microarray analysis and chromatin immunoprecipitation (ChIP)-sequencing, and identified 146 Arabidopsis genes as direct targets of SOG1. By using ChIP-sequencing data, we extracted the palindromic motif [CTT(N)7 AAG] as a consensus SOG1-binding sequence, which mediates target gene induction in response to DNA damage. Furthermore, DNA damage-triggered phosphorylation of SOG1 is required for efficient binding to the SOG1-binding sequence. Comparison between SOG1 and p53 target genes showed that both transcription factors control genes responsible for cell cycle regulation, such as CDK inhibitors, and DNA repair, whereas SOG1 preferentially targets genes involved in homologous recombination. We also found that defense-related genes were enriched in the SOG1 target genes. Consistent with this finding, SOG1 is required for resistance against the hemi-biotrophic fungus Colletotrichum higginsianum, suggesting that SOG1 has a unique function in controlling the immune response.
Membrane fluidification by ethanol stress activates unfolded protein response in yeasts

The toxic effect of ethanol is one of the most important handicaps for many biotechnological applications of yeasts, such as bioethanol production. Elucidation of ethanol stress response will help to improve yeast performance in biotechnological processes. In the yeast Saccharomyces cerevisiae, ethanol stress has been recently described as an activator of the unfolded protein response (UPR), a conserved intracellular signalling pathway that regulates the transcription of ER homoeostasis‐related genes. However, the signal and activation mechanism has not yet been unravelled. Here, we studied UPR's activation after ethanol stress and observed the upregulation of the key target genes, like INO1, involved in lipid metabolism. We found that inositol content influenced UPR activation after ethanol stress and we observed significant changes in lipid composition, which correlate with a major membrane fluidity alteration by this amphipathic molecule. Then, we explored the hypothesis that membrane fluidity changes cause UPR activation upon ethanol stress by studying UPR response against fluidification or rigidification agents and by studying a mutant, erg2, with altered membrane fluidity. The results suggest that the membrane fluidification effects of ethanol and other agents are the signal for UPR activation, a mechanism that has been proposed in higher eukaryotes.
The Power of the Web: A Systematic Review of Studies of the Influence of the Internet on Self-Harm and Suicide in Young People

Background There is concern that the internet is playing an increasing role in self-harm and suicide. In this study we systematically review and analyse research literature to determine whether there is evidence that the internet influences the risk of self-harm or suicide in young people. Methods An electronic literature search was conducted using the PsycINFO, MEDLINE, EMBASE, Scopus, and CINAHL databases. Articles of interest were those that included empirical data on the internet, self-harm or suicide, and young people. The articles were initially screened based on titles and abstracts, then by review of the full publications, after which those included in the review were subjected to data extraction, thematic analysis and quality rating. Results Youth who self-harm or are suicidal often make use of the internet. It is most commonly used for constructive reasons such as seeking support and coping strategies, but may exert a negative influence, normalising self-harm and potentially discouraging disclosure or professional help-seeking. The internet has created channels of communication that can be misused to ‘cyber-bully’ peers; both cyber-bullying and general internet use have been found to correlate with increased risk of self-harm, suicidal ideation, and depression. Correlations have also been found between internet exposure and violent methods of self-harm. Conclusions Internet use may exert both positive and negative effects on young people at risk of self-harm or suicide. Careful high quality research is needed to better understand how internet media may exert negative influences and should also focus on how the internet might be utilised to intervene with vulnerable young people.
Safety of Checkpointing and Rollback-Recovery Protocol for Mobile Systems with RYW Session Guarantee

This paper presents rVsRYW checkpointing and rollback-recovery protocol, which preserves Read Your Writes session guarantee and includes the proof of safety property of the proposed protocol. In order to provide RYW guarantee required by mobile clients, despite failures of servers, in rVsRYW protocol semantics of consistency protocol operations is exploited and build in recovery mechanisms.
Telocytes and Their Extracellular Vesicles—Evidence and Hypotheses

Entering the new millennium, nobody believed that there was the possibility of discovering a new cellular type. Nevertheless, telocytes (TCs) were described as a novel kind of interstitial cell. Ubiquitously distributed in the extracellular matrix of any tissue, TCs are regarded as cells with telopodes involved in intercellular communication by direct homo- and heterocellular junctions or by extracellular vesicle (EVs) release. Their discovery has aroused the interest of many research groups worldwide, and many researchers regard them as potentially regenerative cells. Given the experience of our laboratory, where these cells were first described, we review the evidence supporting the fact that TCs release EVs, and discuss alternative hypotheses about their future implications.
Development of a luminous textile for reflective pulse oximetry measurements

In this paper, a textile-based sensing principle for long term photopletysmography (PPG) monitoring is presented. Optical fibers were embroidered into textiles such that out-coupling and in-coupling of light was possible. The “light-in light-out” properties of the textile enabled the spectroscopic characterization of human tissue. For the optimization of the textile sensor, three different carrier fabrics and different fiber modifications were compared. The sample with best light coupling efficiency was successfully used to measure heart rate and SpO2 values of a subject. The latter was determined by using a modified Beer-Lambert law and measuring the light attenuation at two different wavelengths (632 nm and 894 nm). Moreover, the system was adapted to work in reflection mode which makes the sensor more versatile. The measurements were additionally compared with commercially available system and showed good correlation.
Theoretical Elucidation of the Unusually High [HNC]/[HCN] Abundance Ratio in Interstellar Space: Two-dimensional and Two-State Quantum Wave Packet Dynamics Study on the Branching Ratio of the Dissociative Recombination Reaction HCNH+ + e– → HNC/HCN + H

In order to elucidate the unusually high [HNC]/[HCN] abundance ratio observed in interstellar space, we have carried out wave packet simulations for the dissociative recombination reaction HCNH+ + e- → HNC/HCN + H on the two-dimensional potential energy surfaces (PESs) of two dissociative electronic states of HCNH, 1 2Σ+ and 2 2Σ+. Two adiabatic PESs of 1 2Σ+ and 2 2Σ+ have been determined as functions of NH and CH bond lengths for a linear geometry of HCNH with a fixed CN bond length, by the multireference single and double configuration interaction plus Davidson's quadruple excitation correction [MR-SDCI(+Q)] method. The wave packets, generated from the low-lying vibrational eigenstates of HCNH+, have been put initially on the 2 2Σ+ adiabatic PES. The resulting branching ratios of [HNC]/[HCN] vary from 0.77 to 1.32, depending on the initial vibrational quantum numbers, which support that HCNH+ is the precursor of both HNC and HCN in interstellar space.
The role of neutrophil to lymphocyte ratio for the assessment of liver fibrosis and cirrhosis: a systematic review

ABSTRACT Introduction: Neutrophil to lymphocyte ratio (NLR) is widely used to assess inflammatory diseases. We performed a systematic review to explore the prognostic role of NLR for the assessment of liver fibrosis and cirrhosis. Areas covered: We searched the PubMed and EMBASE databases for the eligible papers which explored the association between NLR and liver fibrosis/cirrhosis or investigated the prognostic value of NLR in cirrhotic patients. Expert commentary: In accordance with assessment of liver fibrosis stage, we classified papers into four subgroups by etiology. For the patients with nonalcoholic fatty liver disease (NAFLD) there was a significant association between NLR and fibrosis stage and nonalcoholic fatty liver disease activity score (NAS), while NLR had a negative correlation with fibrosis stage for the patients with chronic hepatitis B (CHB). As for the patients with and chronic hepatitis C (CHC), NLR might not be significantly associated with fibrosis stage. Moreover, NLR seemed to be significantly useful for predicting outcomes in cirrhotic patients. Hence, NLR might be associated with liver fibrosis stage, especially in patients with NAFLD. Furthermore, NLR might be a useful biomarker for evaluating the prognosis in cirrhotic patients.
Spontaneous dormancy protects Trypanosoma cruzi during extended drug exposure

The ability of the Chagas disease agent Trypanosoma cruzi to resist extended in vivo exposure to highly effective trypanocidal compounds prompted us to explore the potential for dormancy and its contribution to failed drug treatments in this infection. We document the development of non-proliferating intracellular amastigotes in vivo and in vitro in the absence of drug treatment. Non-proliferative amastigotes ultimately converted to trypomastigotes and established infections in new host cells. Most significantly, dormant amastigotes were uniquely resistant to extended drug treatment in vivo and in vitro and could re-establish a flourishing infection after as many as 30 days of drug exposure. These results demonstrate a dormancy pathway in T. cruzi that accounts for the failure of highly cytotoxic compounds to completely resolve the infection. The ability of T. cruzi to establish dormancy throws into question current methods for identifying curative drugs but also suggests alternative therapeutic approaches.