Miracle-dz/UniFAR-FTUs huggingface dataset:
Hill function‐based models of transcriptional switches: impact of specific, nonspecific, functional and nonfunctional binding

We explore minimalist models of transcription in which we take into account that a cis‐regulatory sequence is embedded in, and interacts with, a complex genome. The classical Hill equation is the simplest way to represent a transcriptional response. However, it may overlook the fact that a transcription factor (TF) establishes specific and nonspecific nonfunctional interactions with chromatin. Classical papers have shown that nonfunctional binding (not leading to transcription) may influence gene expression. We examine how the presence of additional binding sites for a TF, besides those on the gene(s) of interest, affect the shape and parameters of the transcriptional response. We consider two conditions: at equilibrium and at steady‐state. In many cases the TF level is determined by the position of the cell within a spatial or temporal gradient. We show that such gradients can be adjusted by evolutionary selection to compensate for the alteration of the gene transcription response by the presence of nonfunctional binding sites. Finally, we analyse how the transcriptional response is affected by a decrease in TF concentration, as in cases of haploinsufficiency. We show that the nonlinearity of the transcriptional response as a function of [TF] exacerbates the effect of a decrease in the latter, at least for weakly expressed TFs. Although decades of work on TFs have led to the impression that almost everything is known about the control of gene expression, we show that even the simplest models of transcription control have not delivered all their secrets yet.
Comprehensive analysis of clinical Burkholderia pseudomallei isolates demonstrates conservation of unique lipid A structure and TLR4-dependent innate immune activation

Burkholderia pseudomallei is an environmental bacterium that causes melioidosis, a major community-acquired infection in tropical regions. Melioidosis presents with a range of clinical symptoms, is often characterized by a robust inflammatory response, may relapse after treatment, and results in high mortality rates. Lipopolysaccharide (LPS) of B. pseudomallei is a potent immunostimulatory molecule comprised of lipid A, core, and O-polysaccharide (OPS) components. Four B. pseudomallei LPS types have been described based on SDS-PAGE patterns that represent the difference of OPS–type A, type B, type B2 and rough LPS. The majority of B. pseudomallei isolates are type A. We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) followed by electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-QqTOF MS) and gas chromatography to characterize the lipid A of B. pseudomallei within LPS type A isolates. We determined that B. pseudomallei lipid A is represented by penta- and tetra-acylated species modified with 4-amino-4-deoxy-arabinose (Ara4N). The MALDI-TOF profiles from 171 clinical B. pseudomallei isolates, including 68 paired primary and relapse isolates and 35 within-host isolates were similar. We did not observe lipid A structural changes when the bacteria were cultured in different growth conditions. Dose-dependent NF-κB activation in HEK cells expressing TLR4 was observed using multiple heat-killed B. pseudomallei isolates and corresponding purified LPS. We demonstrated that TLR4-dependent NF-κB activation induced by heat-killed bacteria or LPS prepared from OPS deficient mutant was significantly greater than those induced by wild type B. pseudomallei. These findings suggest that the structure of B. pseudomallei lipid A is highly conserved in a wide variety of clinical and environmental circumstances but that the presence of OPS may modulate LPS-driven innate immune responses in melioidosis.
Canoe: An Autonomous Infrastructure-Free Indoor Navigation System

The development of the Internet of Things (IoT) has accelerated research in indoor navigation systems, a majority of which rely on adequate wireless signals and sources. Nonetheless, deploying such a system requires periodic site-survey, which is time consuming and labor intensive. To address this issue, in this paper we present Canoe, an indoor navigation system that considers shopping mall scenarios. In our system, we do not assume any prior knowledge, such as floor-plan or the shop locations, access point placement or power settings, historical RSS measurements or fingerprints, etc. Instead, Canoe requires only that the shop owners collect and publish RSS values at the entrances of their shops and can direct a consumer to any of these shops by comparing the observed RSS values. The locations of the consumers and the shops are estimated using maximum likelihood estimation. In doing this, the direction of the target shop relative to the current orientation of the consumer can be precisely computed, such that the direction that a consumer should move can be determined. We have conducted extensive simulations using a real-world dataset. Our experiments in a real shopping mall demonstrate that if 50% of the shops publish their RSS values, Canoe can precisely navigate a consumer within 30 s, with an error rate below 9%.
Low-level laser therapy for treatment of neurosensory disorders after orthognathic surgery: A systematic review of randomized clinical trials

Background Low-level laser has been widely used in Dentistry and many studies have focused on its application in oral surgeries. This study was conducted with the aim of searching for scientific evidence concerning the effectiveness of laser to reduce pain or paresthesia related to orthognathic surgery. Material and Methods An electronic search was performed in PubMed, Scopus, Science Direct, LILACS, SciELO, CENTRAL, Google Scholar, OpenGrey, and ClinicalTrials.gov, up to November 2016, with no restrictions on language or year of publication. Additionally, a hand search of the reference list of the selected studies was carried out. The PICOS strategy was used to define the eligibility criteria and only randomized clinical trials were selected. Results Out of 1,257 identified citations, three papers fulfilled the criteria and were included in the systematic review. The risk of bias was assessed according to the Cochrane Guidelines for Clinical Trials and results were exposed based on a descriptive analysis. One study showed that laser therapy was effective to reduce postoperative pain 24 hours (P=0.007) and 72 hours (P=0.007) after surgery. Other study revealed the positive effect of laser to improve neurosensory recovery 60 days after surgery, evaluated also by the two-point discrimination (P=0.005) and sensory (P=0.008) tests. The third study reported an improvement for general sensibility of 68.75% for laser group, compared with 21.43% for placebo (P=0.0095), six months after surgery. Conclusions Individual studies suggested a positive effect of low-level laser therapy on reduction of postoperative pain and acceleration of improvement of paresthesia related to orthognathic surgery. However, due to the insufficient number and heterogeneity of studies, a meta-analysis evaluating the outcomes of interest was not performed, and a pragmatic recommendation about the use of laser therapy is not possible. This systematic review was conducted according to the statements of PRISMA and was registered at PROSPERO under the number CRD42016043258. Key words:Low-level laser therapy, orthognathic surgery, parestesia, postoperative pain.
The relationship between DNA single-stranded damage response and double-stranded damage response

ABSTRACT The damage response of DNA single-stranded breaks(SSBs) and double-stranded breaks(DSBs) are two relatively independent processes involving different signaling pathways and protein factors, but there are still many overlapping parts. All of them can activate p53 protein, then the activated p53 regulates the damage response of single-stranded breaks or double-stranded breaks in transcriptional regulation and non-transcriptional regulation. Especially, the two types of damage would compete for RPA and ATR resources in damage repair process. The research has been focused on damage response of DNA single-stranded breaks or DNA double-stranded breaks. However, when single-stranded breaks and double-stranded breaks exist simultaneously, the DNA damage response remains to be elucidated. Here, we present a hybrid numerical model of p53 response and a hybrid numerical model of DNA damage repair exploring DNA damage repair and apoptosis mechanisms when DNA single-stranded breaks and DNA double-stranded breaks exist simultaneously. Firstly, when two kinds of damage are present at the same time, the response of p53 is graded, it means that p53 responds to single-stranded breaks preferentially; Secondly, DNA single-stranded breaks are repaired preferentially, and single-stranded breaks and double-stranded breaks can be repaired simultaneously after most of single-stranded breaks having been repaired; Moreover, single-stranded breaks are more likely to cause apoptosis, because the accumulation of p53 in DNA single-stranded breaks is faster than it in DNA double-stranded breaks and single-stranded breaks has lower threshold of apoptosis.
The Impact of Caring for Grandchildren on Grandparents’ Physical Health Outcomes: The Role of Intergenerational Support

Little longitudinal data exist on grandparent caregivers and few studies have examined their physical health outcomes. This study examined the effect of caring for grandchildren on grandparents’ physical health and the role of intergenerational support from adult children. Longitudinal data derived from a survey on the well-being of older adults in China were used to conduct path analysis of previous grandparent caregivers (vs. noncaregivers) and repeated grandparent caregivers (vs. noncaregivers). The final sample was 799 grandparents aged 60 or older living in rural China. Three aspects of intergenerational support were measured: financial, emotional, and instrumental support. Repeated grandparent caregivers had better self-rated health (SRH) and fewer limitations than noncaregivers. Previous grandparent caregivers had better SRH compared to noncaregivers. Emotional support mediated the relationship between caregiving and SRH among repeated caregivers. Findings suggest that any caregiving experience (previous or repeated) provides health benefits to grandparents.
High Expression of Human Cathepsin S by Recombinant Pichia pastoris with Cod Skin as an Organic Co-Nitrogen Source

Human cathepsin S production by recombinant Pichia pastoris using cod skin as the co-nitrogen source was investigated in this study. The addition of carbon sources of glycerol in the fed-batch phase and of methanol in the induction stage was also investigated. A new approach to the highly expression of human cathepsin S was developed using 90 g/L of cod skin (wet weight). After 24 h of the initial fermentation, 4% glycerol (v/v, glycerol/culture) was added once to enhance the cell density (OD600) in the cultivation. Then, adding and maintaining methanol at 0.5% (v/v, methanol/cultivation) after about 48 h of fermentation achieved a high expression of human cathepsin S in a 5-L bioreactor. The results demonstrate that the maximum activity of human cathepsin S in the fermentation supernatant reached 7,152 U/L after 96 h of methanol induction. The methylotrophic yeast P. pastoris grown in the medium containing cod skin (90 g/L) as the co-nitrogen source provided a 21% higher cell density (OD600) and 18.3% higher human cathepsin S yield than P. pastoris grown in BMGY medium. For the first time, human cathepsin S was successfully expressed by P. pastoris with cod skin as the co-nitrogen source. The glycerol fed-batch controlling strategy and method of maintaining methanol at a constant concentration of 0.5% (v/v, methanol/cultivation) in the induction stage was efficient for P. pastoris growth and the expression of human cathepsin S.
Spatial risk factors of felonious battery to police officers

Purpose – The purpose of this paper is to examine the spatial influence of features of the physical environment on the risk of aggression toward law enforcement. Design/methodology/approach – The spatial analytic technique, risk terrain modeling was performed on felonious battery data provided by the Chicago Police Department. Findings – Out of the 991 batteries against law enforcement officers (LEOs) in Chicago, 11 features of the physical environment were identified as presenting a statistically significant spatial risk of battery to LEOs. Calls for service within three blocks of foreclosures and/or within a dense area of problem buildings pose as much as two times greater risk of battery to police officers than what is presented by other significant spatial factors in the model. Originality/value – An abundance of existing research on aggression toward law enforcement is situated from the perspective of characteristics of the suspect or officer. The research advances the field of violence studies by il.
Implementation of single precision conventional and fused floating point add-sub unit using Verilog

Floating-point arithmetic is enhancive for the realization of a vast application of Digital Signal Processing (DSP) such as Fast Fourier Transform, Discrete Cosine Transform. In this paper, architecture of floating point adder and floating point Subtractor were compared with their fused counterpart known as Fused Addition-Subtract Unit. Since, most of the DSP algorithms require FFT and DCT in their structures hence analysis and implementation were done specifically for complex addition and subtraction involved in FFT computation. Butterfly unit consisting of arithmetic operations like additions, subtractions and multiplications of complex valued data were first implemented using conventional single precision floating point adder and Subtractor. Thereafter, single compressed structure for floating point addition-subtraction was implemented using Verilog HDL. After simulation run on Xilinx ISE tool, it was observed that fused Add-Sub FPU provides better latency results compared to conventional FPU.
microRNA in Cardiovascular Aging and Age-Related Cardiovascular Diseases

Over the last decades, life expectancy has significantly increased although several chronic diseases persist in the population, with aging as the leading risk factor. Despite improvements in diagnosis and treatment, many elderlies suffer from cardiovascular problems that are much more frequent in an older, more fragile organism. In the long term, age-related cardiovascular diseases (CVDs) contribute to the decline of quality of life and ability to perform normal activities of daily living. microRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression at the posttranscriptional level in both physiological and pathological conditions. In this review, we will focus on the role of miRNAs in aging and age-related CVDs as heart failure, hypertension, atherosclerosis, atrial fibrillation, and diabetes mellitus. miRNAs are key regulators of complex biological mechanisms, representing an exciting potential therapeutic target in CVDs. Moreover, one major challenge in geriatric medicine is to find reliable biomarkers for diagnosis, prognosis, and prediction of the response to specific drugs. miRNAs represent a very promising tool due to their stability in the circulation and unique signature in CVDs. However, further studies are needed to investigate their translational potential in the real clinical practice.
Circuit Design of a Compact 5-kV W-Band Extended Interaction Klystron

A low voltage (5 kV) ladder-type circuit is designed for the compact W-band extended interaction Klystron (EIK). Characteristics of the low voltage circuit are studied, synchronism relationship and electric field distribution are analyzed and optimized, and discussions on the circuit stability are embedded in the circuit design. In this paper, efficiency decline of the low voltage circuit is studied; two competing modes (<inline-formula> <tex-math notation="LaTeX">$2\pi $ </tex-math></inline-formula> cavity mode and upper <inline-formula> <tex-math notation="LaTeX">$\pi /8$ </tex-math></inline-formula> mode) are observed, analyzed and suppressed. All of these efforts resulted in a low voltage W-band ladder-type EIK circuit with high stability and feasibility.
Efficient Sequential Compression of Multichannel Biomedical Signals

This paper proposes lossless and near-lossless compression algorithms for multichannel biomedical signals. The algorithms are sequential and efficient, which makes them suitable for low-latency and low-power signal transmission applications. We make use of information theory and signal processing tools (such as universal coding, universal prediction, and fast online implementations of multivariate recursive least squares), combined with simple methods to exploit spatial as well as temporal redundancies typically present in biomedical signals. The algorithms are tested with publicly available electroencephalogram and electrocardiogram databases, surpassing in all cases the current state of the art in near-lossless and lossless compression ratios.
Immigrant reproductive dysfunction facilitates ecological speciation

The distributions of species are not only determined by where they can survive – they must also be able to reproduce. Although immigrant inviability is a well‐established concept, the fact that immigrants also need to be able to effectively reproduce in foreign environments has not been fully appreciated in the study of adaptive divergence and speciation. Fertilization and reproduction are sensitive life‐history stages that could be detrimentally affected for immigrants in non‐native habitats. We propose that “immigrant reproductive dysfunction” is a hitherto overlooked aspect of reproductive isolation caused by natural selection on immigrants. This idea is supported by results from experiments on an externally fertilizing fish (sand goby, Pomatoschistus minutus). Growth and condition of adults were not affected by non‐native salinity whereas males spawning as immigrants had lower sperm motility and hatching success than residents. We interpret these results as evidence for local adaptation or acclimation of sperm, and possibly also components of paternal care. The resulting loss in fitness, which we call “immigrant reproductive dysfunction,” has the potential to reduce gene flow between populations with locally adapted reproduction, and it may play a role in species distributions and speciation.
CIP2A acts as a scaffold for CEP192-mediated microtubule organizing center assembly by recruiting Plk1 and aurora A during meiotic maturation

In somatic cells spindle microtubules are nucleated from centrosomes that act as major microtubule organizing centers (MTOCs), whereas oocytes form meiotic spindles by assembling multiple acentriolar MTOCs without canonical centrosomes. Aurora A and Plk1 are required for these events, but the underlying mechanisms remain largely unknown. Here we show that CIP2A regulates MTOC organization by recruiting aurora A and Plk1 at spindle poles during meiotic maturation. CIP2A colocalized with pericentrin at spindle poles with a few distinct cytoplasmic foci. Although CIP2A has been identified as an endogenous inhibitor of protein phosphatase 2A (PP2A), overexpression of CIP2A had no effect on meiotic maturation. Depletion of CIP2A perturbed normal spindle organization and chromosome alignment by impairing MTOC organization. Importantly, CIP2A was reciprocally associated with CEP192, promoting recruitment of aurora A and Plk1 at MTOCs. CIP2A was phosphorylated by Plk1 at S904, which targets CIP2A to MTOCs and facilitates MTOC organization with CEP192. Our results suggest that CIP2A acts as a scaffold for CEP192-mediated MTOC assembly by recruiting Plk1 and aurora A during meiotic maturation in mouse oocytes. Summary: Plk1-mediated phosphorylation at the coiled-coil domain targets CIP2A to the microtubule organizing center, where it acts independently of PP2A in spindle assembly during meiotic maturation of mouse oocytes.
Income Taxation in an Empirical Collective Household Labour Supply Model with Discrete Hours

Most empirical studies on the impact of labour income taxation on the labour supply behaviour of households use a unitary modelling approach. In this paper we empirically analyze income taxation and the choice of working hours by combining the collective approach for household behaviour and the discrete hours choice framework with fixed costs of work. We identify the sharing rule parameters with data on working hours of both the husband and the wife within a couple. Parameter estimates are used to evaluate various model outcomes, like the wage elasticities of labour supply and the impacts of wage changes on the income sharing between husband and wife. We also simulate the consequences of a policy change in the tax system. We find that the collective model has different empirical outcomes of income sharing than a restricted model that imposes pooling of men's earnings and the household's non-labour income in the female's budget constraint. These differences in outcomes have consequences for the evaluation of a policy change in the tax system.
Friction fluctuations of gold nanoparticles in the superlubric regime

Superlubricity, or alternatively termed structural (super)lubrictiy, is a concept where ultra-low friction is expected at the interface between sliding surfaces if these surfaces are incommensurate and thus unable to interlock. In this work, we now report on sudden, reversible, friction changes that have been observed during AFM-based nanomanipulation experiments of gold nanoparticles sliding on highly oriented pyrolythic graphite. These effects can be explained by rotations of the gold nanoparticles within the concept of structural superlubricity, where the occurrence of ultra-low friction can depend extremely sensitively on the relative orientation between the slider and the substrate. From our theoretical simulations it will become apparent how even miniscule magnitudes of rotation are compatible to the observed effects and how size and shape of the particles can influence the dependence between friction and relative orientation.
Structure, Magnetostriction and Magnetic Properties of the Mn100-xFex (x=50, 58) Alloys Prepared by SPS

Mn100-xFex (x=50, 58) alloys were prepared by spark plasma sintering (SPS), and the structure, magnetostriction and magnetic properties of the polycrystalline Mn100-xFex alloys were investigated. The results of XRD and SEM showed that the as-cast and annealed samples presented a single face center cubic γ-phase, which is austenite structure. The magnetic measurement showed that Mn100-xFex (x=50, 58) alloys annealed at 700oC were a typical ferromagnet at low temperature and there was a gradual transition from the ferromagnetic phase to the paramagnetic phase in a wide temperature region (about 150-250K). The magnetostriction for the annealed samples, measured by strain-gauge bridge up to 3T, was ~100 ppm at 300K, but the results was chaotic. The results are not in agreement with the results reported. The further research on the mechanism of the magnetostriction is needed.