Miracle-dz/UniFAR-FTUs huggingface dataset:
The resting release of acetylcholine by a retinal neuron

The cholinergic amacrine cells of the rabbit retina secrete acetylcholine by two mechanisms. One is activated by stimulation of the retina by light or depolarization of the amacrine cells by K+ ions. It requires the presence of extracellular Ca2+. The second is independent of extracellular Ca2+ and is unaffected by large depolarizations of the cells. It bears some similarity to the acetylcholine ‘leakage’ described at the neuromuscular junction. Although the Ca2+-independent mechanism accounts for about two thirds of the total acetylcholine release in the dark, the amount of acetylcholine released in this way is small compared with the release of acetylcholine triggered by stimulation of the retina with light. Its biological significance is unclear.
An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells

The ability to adapt to diverse micro-environmental challenges encountered within a host is of pivotal importance to the opportunistic fungal pathogen Candida albicans. We have quantified C. albicans and M. musculus gene expression dynamics during phagocytosis by dendritic cells in a genome-wide, time-resolved analysis using simultaneous RNA-seq. A robust network inference map was generated from this dataset using NetGenerator, predicting novel interactions between the host and the pathogen. We experimentally verified predicted interdependent sub-networks comprising Hap3 in C. albicans, and Ptx3 and Mta2 in M. musculus. Remarkably, binding of recombinant Ptx3 to the C. albicans cell wall was found to regulate the expression of fungal Hap3 target genes as predicted by the network inference model. Pre-incubation of C. albicans with recombinant Ptx3 significantly altered the expression of Mta2 target cytokines such as IL-2 and IL-4 in a Hap3-dependent manner, further suggesting a role for Mta2 in host–pathogen interplay as predicted in the network inference model. We propose an integrated model for the functionality of these sub-networks during fungal invasion of immune cells, according to which binding of Ptx3 to the C. albicans cell wall induces remodeling via fungal Hap3 target genes, thereby altering the immune response to the pathogen. We show the applicability of network inference to predict interactions between host–pathogen pairs, demonstrating the usefulness of this systems biology approach to decipher mechanisms of microbial pathogenesis.
Community Detection Based on Variable Vertex Influence

In recent years community detection has been a hot research topic in network science, which helps to explain the characteristics of the network structure. This paper analyzed the effect of vertices with high influence in community detection, and found that such vertices have different roles in different networks. A variable influence community detection algorithm based on PageRank is proposed in this paper, which can resize the community involving vertices with high influence. A variable influence local community detection algorithm based on a single initial vertex is also proposed, which introduces the mechanism of influence decay and is able to find communities with different sizes according to users' requirements.
X‐linked recessive chondrodysplasia punctata: Spectrum of arylsulfatase E gene mutations and expanded clinical variability

X‐linked chondrodysplasia punctata (CDPX1), due to mutations of the arylsulfatase E (ARSE) gene, is a congenital disorder characterized by abnormalities in cartilage and bone development. We performed mutational analysis of the ARSE gene in a series of 16 male patients, and we found mutations in 12 subjects. Clinical variability was observed among the patients, including severe presentations with early lethality in one of them, and symptoms such as cataract and respiratory distress. This indicates that the clinical spectrum of CDPX1, commonly considered a relatively mild form of chondrodysplasia punctata, is wider than previously reported. Different types of mutations were found among the patients examined. Three missense mutations (I80N, T481M, P578S) were expressed in Cos7 cells to study the effects on arylsulfatase E catalytic activity. These mutations caused impaired enzymatic activity suggesting that they are responsible for the disease. Two nonsense mutations, W581X in four patients and R540X in one, were found. One patient showed an insertion (T616ins). In three patients we found deletions of the ARSE gene: in one the deletion involved only the 3′ end of the gene, while in two the ARSE gene was completely deleted. © 2002 Wiley‐Liss, Inc.
Gross Anatomy of the Brachial Plexus in the Giant Anteater (Myrmecophaga tridactyla)

Ten forelimbs of five Myrmecophaga tridactyla were examined to study the anatomy of the brachial plexus. The brachial plexuses of the M. tridactyla observed in the present study were formed by the ventral rami of the last four cervical spinal nerves, C5 through C8, and the first thoracic spinal nerve, T1. These primary roots joined to form two trunks: a cranial trunk comprising ventral rami from C5‐C7 and a caudal trunk receiving ventral rami from C8‐T1. The nerves originated from these trunks and their most constant arrangement were as follows: suprascapular (C5‐C7), subscapular (C5‐C7), cranial pectoral (C5‐C8), caudal pectoral (C8‐T1), axillary (C5‐C7), musculocutaneous (C5‐C7), radial (C5‐T1), median (C5‐T1), ulnar (C5‐T1), thoracodorsal (C5‐C8), lateral thoracic (C7‐T1) and long thoracic (C6‐C7). In general, the brachial plexus in the M. tridactyla is similar to the plexuses in mammals, but the number of rami contributing to the formation of each nerve in the M. tridactyla was found to be larger than those of most mammals. This feature may be related to the very distinctive anatomical specializations of the forelimb of the anteaters.
Reduction in resting metabolic rate and ratio of plasma leptin to urinary nitric oxide: influence on obesity-related hypertension.

BACKGROUND Multiple factors are involved in the pathogenesis of hypertension in the obese individual OBJECTIVE To evaluate the role of a decrease in sympathetically mediated thermogenesis and the effect of the correlation between the plasma leptin and daily urinary nitric oxide levels on obesity-related hypertension. METHODS We evaluated three groups: 25 obese hypertensive patients (age 45.7 +/- 1.37 years, body mass index 34.2 +/- 1.35 kg/m2, systolic/diastolic blood pressure 155 +/- 2.9/105 +/- 1.3, mean arterial pressure 122 +/- 1.50 mmHg); 21 obese normotensive patients (age 39.6 +/- 1.72, BMI 31.3 +/- 0.76, SBP/DBP 124 +/- 2.1/85.4 +/- 1.8, MAP 98.2 +/- 1.80); and 17 lean normotensive subjects (age 38.1 +/- 2.16, BMI 22.1 +/- 0.28, SBP/DBP 117 +/- 1.7/76.8 +/- 1.5, MAP 90.1 +/- 1.50). We determined basal resting metabolic rates, plasma insulin (radio-immunoassay), norepinephrine (high performance liquid chromatography) in all subjects. Thereafter, 14 obese hypertensives underwent a weight reduction diet. At weeks 6 (n = 14) and 14 (n = 10) of the diet the above determinations were repeated. Plasma leptin (enzyme-linked immunosorbent assay) and UNOx (spectrophotometry) were assayed in 17 obese hypertensives and 17 obese normotensives, and in 19 obese hypertensives versus 11 obese normotensives, respectively. RESULTS Obese hypertensive patients had significantly higher basal RMR and plasma NE levels insulin levels were lower in the lean group, with no difference between the hypertensive and normotensive obese groups. At weeks 6 and 14, BMI was significantly lower, as were insulin and NE levels. RMR decreased to values of normotensive subjects. MAP normalized but remained significantly higher than in obese normotensives. Leptin blood levels and the leptin/UNOx ratio were significantly higher in the obese hypertensive compared to the obese normotensive patients. Both these parameters were strongly correlated to BMI, MAP, RMR, and plasma NE and insulin. Obese hypertensive patients excreted less urinary NO metabolites. A strong correlation was found between MAP and the leptin/UNOx ratio. CONCLUSIONS A reduction in sympathetically mediated thermogenesis, as reflected by RMR, results in normalization of obesity-related hypertension. In contrast, insulin does not seem to play a major role in the pathogenesis of hypertension associated with obesity. Increased leptin levels in conjunction with decreased NO production in the presence of enhanced sympathetic activity may contribute to blood pressure elevation in the obese.
Diverse rupture processes in the 2015 Peru deep earthquake doublet

The nearby Mw 7.5 and Mw 7.6 events in a deep earthquake doublet under Peru have diverse stress drops and radiation efficiency. Earthquakes in deeply subducted oceanic lithosphere can involve either brittle or dissipative ruptures. On 24 November 2015, two deep (606 and 622 km) magnitude 7.5 and 7.6 earthquakes occurred 316 s and 55 km apart. The first event (E1) was a brittle rupture with a sequence of comparable-size subevents extending unilaterally ~50 km southward with a rupture speed of ~4.5 km/s. This earthquake triggered several aftershocks to the north along with the other major event (E2), which had 40% larger seismic moment and the same duration (~20 s), but much smaller rupture area and lower rupture speed than E1, indicating a more dissipative rupture. A minor energy release ~12 s after E1 near the E2 hypocenter, possibly initiated by the S wave from E1, and a clear aftershock ~165 s after E1 also near the E2 hypocenter, suggest that E2 was likely dynamically triggered. Differences in deep earthquake rupture behavior are commonly attributed to variations in thermal state between subduction zones. However, the marked difference in rupture behavior of the nearby Peru doublet events suggests that local variations of stress state and material properties significantly contribute to diverse behavior of deep earthquakes.
New Diagnosis of Acquired Immunodeficiency Syndrome in a Patient With Crohn's Disease

ABSTRACT There are limited data on the natural history of Crohn's disease (CD) in the presence of human immunodeficiency virus infection and the safety of available treatments. We report a patient with CD who presented with pneumocystis pneumonia secondary to newly diagnosed acquired immunodeficiency syndrome. One month before his admission, his gastrointestinal symptoms were well controlled without treatment but gradually reappeared after antiretroviral therapy was initiated. Clinical remission was achieved with vedolizumab treatment. We review the management challenges of CD in a patient with human immunodeficiency virus and describe the unique mechanism of anti-α4β7 integrin therapy in this setting.
Serum PTH reference values established by an automated third-generation assay in vitamin D-replete subjects with normal renal function: consequences of diagnosing primary hyperparathyroidism and the classification of dialysis patients.

OBJECTIVE To determine parathyroid hormone (PTH) reference values in French healthy adults, taking into account serum 25-hydroxyvitamin D (25OHD), renal function, age, gender, and BMI. PARTICIPANTS AND MAIN BIOLOGICAL MEASUREMENTS We studied 898 healthy subjects (432 women) aged 18-89 years with a normal BMI and estimated glomerular filtration rate (eGFR), 81 patients with surgically proven primary hyperparathyroidism (PHPT), and 264 dialysis patients. 25OHD and third-generation PTH assays were implemented on the LIAISON XL platform. RESULTS Median PTH and 25OHD values in the 898 healthy subjects were 18.8 ng/l and 23.6 ng/ml respectively. PTH was lower in subjects with 25OHD ≥30 ng/ml than in those with lower values. Among the 183 subjects with 25OHD ≥30 ng/ml, those aged ≥60 years (n=31) had higher PTH values than younger subjects, independent of 25OHD, BMI, and eGFR (P<0.001). Given the small number of subjects aged ≥60 years, we adopted the 95% CI of PTH values for the entire group of 183 vitamin D-replete subjects (9.4-28.9 ng/l) as our reference values. With 28.9 ng/l as the upper limit of normal (ULN) rather than the manufacturer's ULN of 38.4 ng/l, the percentage of PHPT patients with 'high' PTH values rose to 90.1% from 66.6% (P<0.001), and 18.6% of the dialysis patients were classified differently in view of the KDIGO target range (two to nine times the ULN). CONCLUSION When only subjects with 25OHD ≥30 ng/ml were included in the reference population, the PTH ULN fell by 22.4%, diagnostic sensitivity for PHPT improved, and the classification of dialysis patients was modified.
EARE-1, a Transcriptionally Active Ty1/Copia-Like Retrotransposon Has Colonized the Genome of Excoecaria agallocha through Horizontal Transfer

Long terminal repeat (LTR) retrotransposons constitute the majority of the content of angiosperm genomes, but their evolutionary dynamics remain poorly understood. Here, we report the isolation and characterization of a putative full-length (~9550 bp) Ty1/copia-like retrotransposon in Excoecaria agallocha and its evolution in Euphorbiaceae. The so-called EARE-1 is phylogenetically closely related to RIRE-1 from Oryza australiensis, and has proliferated recently (~7.19 Mya) in the E. agallocha genome. An RT-PCR analysis revealed substantial transcription of EARE-1 in all examined organs (leaves, staminate flowers, pistillate flowers, seeds, and roots) in unstressed E. agallocha plants and indications of elevated expression under stress. We conducted sequence analyses of 256 RT-RH fragments (~860 bp) of EARE-1 from 34 species representing four subfamilies of Euphorbiaceae that exist in China. EARE-1 copies from two Excoecaria species and Phyllanthus urinaria showed incongruent phylogeny with the host species and exhibited high sequence similarity to the host genes, suggesting a horizontal transfer from P. urinaria to the common ancestor of Excoecaria. However, SSAP analysis detected no new insertions of EARE-1 among full-sibling progeny plants of E. agallocha, despite considerable SSAP polymorphisms among half-siblings. EARE-1 is the first transcriptionally active Ty1/copia-like retrotransposon isolated from E. agallocha. Our results provide empirical evidence of the horizontal transfer of LTR retrotransposons in plants, and may suggest a significant role of post-transcriptional host control in the life cycles of transposable elements.
Expected Conditional Characteristic Function-based Measures for Testing Independence

Abstract We propose a novel class of independence measures for testing independence between two random vectors based on the discrepancy between the conditional and the marginal characteristic functions. The relation between our index and other similar measures is studied, which indicates that they all belong to a large framework of reproducing kernel Hilbert space. If one of the variables is categorical, our asymmetric index extends the typical ANOVA to a kernel ANOVA that can test a more general hypothesis of equal distributions among groups. In addition, our index is also applicable when both variables are continuous. We develop two empirical estimates and obtain their respective asymptotic distributions. We illustrate the advantages of our approach by numerical studies across a variety of settings including a real data example. Supplementary materials for this article are available online.
Robust Linear MIMO in the Downlink: A Worst-Case Optimization with Ellipsoidal Uncertainty Regions

This paper addresses the joint robust power control and beamforming design of a linear multiuser multiple-input multiple-output (MIMO) antenna system in the downlink where users are subjected to individual signal-to-interference-plus-noise ratio (SINR) requirements, and the channel state information at the transmitter (CSIT) with its uncertainty characterized by an ellipsoidal region. The objective is to minimize the overall transmit power while guaranteeing the users' SINR constraints for every channel instantiation by designing the joint transmitreceive beamforming vectors robust to the channel uncertainty. This paper first investigates a multiuser MISO system (i.e., MIMO with single-antenna receivers) and by imposing the constraints on an SINR lower bound, a robust solution is obtained in a way similar to that with perfect CSI. We then present a reformulation of the robust optimization problem using S-Procedure which enables us to obtain the globally optimal robust power control with fixed transmit beamforming. Further, we propose to find the optimal robust MISO beamforming via convex optimization and rank relaxation. A convergent iterative algorithm is presented to extend the robust solution for multiuser MIMO systems with both perfect and imperfect channel state information at the receiver (CSIR) to guarantee the worst-case SINR. Simulation results illustrate that the proposed joint robust power and beamforming optimization significantly outperforms the optimal robust power allocation with zeroforcing (ZF) beamformers, and more importantly enlarges the feasibility regions of a multiuser MIMO system.
Sleep Apnea Phenotyping: Implications for Dental Sleep Medicine

New knowledge of obstructive sleep apnea (OSA) pathophysiology has highlighted the heterogeneity of this common chronic health condition. Recent advances in OSA ‘phenotyping’ concepts have provided a novel framework in which to understand OSA pathophysiology on an individual patient basis. This has also provided new potential precision medicine strategies to optimize efficacy and success rates with current OSA treatments including mandibular advancement therapy.
Ontology-based skill matching algorithms

Automatic recommendations based on skill matching techniques can prove to be an important component of an online recruitment platform, being able to lower the costs for employers, ease the process for candidates and increase the hiring quality overall. This is important nowadays, when online recruitment plays a major role in the hiring process. The main challenges in this area consist in providing relevant and computationally inexpensive results. In this paper we propose a semantic approach to the skill matching problem in the context of online recruitment. We present a metric of similarity based on a skills ontology and three algorithms on top of this metric, with the intent of obtaining a ranked skill-based matching between candidates and job offers. We also provide an analysis of those algorithms in terms of advantages, disadvantages and complexity.
AND BACTERIAL EXPRESSION OF THE β-AMYRIN SYNTHASE GENE FROM PANAX JAPONICUS C . A . MEY

Panax japonicus C. A. Mey. is one of the rare traditional Chinese herbal medicines; its main active ingredient is ginsenosides. β-amyrin synthase (βAS) is the rate-limiting enzyme in the biosynthesis pathway of oleanane-type ginsenosides. We cloned for the first time the full-length cDNA of βAS from P. japonicus (GenBank: KP658156) using reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE), and we named it PjβAS, which contained an open reading frame (ORF) of 2,286 bp in length and encoded a protein of 761-amino acids in length and about 87.8 kDa in molecular weight. Bioinformatics analysis showed that PjβAS had more than 80% homology with βAS from P. ginseng, Aralia elata, Betula platyphylla, and Malusx domestica, etc. PjβAS consists of six functional domains of the terpene synthase family and the functional domain of the prenyltransferase/squalene oxidase family. The coding sequence of PjβAS was cloned into a prokaryotic expression vector pET-41a(+); and the recombinant vector pET-AS was transformed into the Escherichia coli BL21(DE3) strain. Real-time fluorescence quantitative PCR (qRT-PCR) and sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis showed that PjβAS could be over-expressed by IPTG-induction in BL21(DE3). High performance liquid chromatography (HPLC) analysis showed that pET-AS could synthesize β-amyrin in BL21 (DE3) cells. These results indicated that PjβAS functions as a βAS gene. Introduction Panax japonicus C.A. Mey. , belonging to Araliaceae Panax, is one of the rare traditional Chinese herbal medicines. All plants of the Panax genus have high medicinal value and their main active ingredient is ginseng saponins (Yun 2001). The total saponin content of the roots of P. ginseng is 2 7%, whereas the total saponin content in the roots of P. japonicus can be as high as 15%, which is 2 to seven-fold higher than that observed in P. ginseng and three-fold higher than reported in P. quinquefolius. Ginsenosides are further classified into the oleanane type and the dammarane type; and the oleanane-type saponins are the main saponins in P. japonicus (Haralampidis et al. 2002, Lichtenthaler et al. 1997). Ginsenosides are triterpenoid saponins of plant secondary metabolites, i.e. the product of the triterpenoid saponin biosynthesis branch in the isoprenoid pathway (Fig. 1). Triterpenoid saponins are formed by different cyclizations of squalene (Haralampidis et al. 2002; Lichtenthaler et al. 1997). There are two pathways for the synthesis of isopentenyl pyrophosphate (IPP) in the isoprenoid pathway, one is mevalonate (MVA) pathway (Chappell 1995, Goldstein and Brown 1990), and the other is the 1-deoxy-D-xylulose-5-phosphate (DOXP) pathway, also known as the non-mevalonate pathway (Lichtenthaler 1999, Wanke et al. 2001). IPP in the triterpenoid biosynthesis pathway comes from the MVA pathway, and IPP can further synthesize squalene. *Author for correspondence: <zjg231@126.com>. College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Performance Analysis of Layered ACO-OFDM

Layered asymmetrically clipped optical orthogonal frequency division multiplexing (LACO-OFDM) has been proposed for improving the spectral efficiency of conventional asymmetrically clipped optical OFDM. Multiple base layers that are orthogonal in the frequency domain are sequentially superimposed to form LACO-OFDM, where each superimposed layer fills the empty subcarriers left by the previous layer. As our contribution, the bit error ratio (BER) considering the effect of thermal noise, clipping distortion, inter-layer interference, and the bit rate difference between layers is analysed in this paper. Since the BER performance of LACO-OFDM is closely related to its peak-to-average power ratio (PAPR) distribution, we also provide the analytical expression of the PAPR distribution in this paper, which quantifies how the number of layers in LACO-OFDM reduces the PAPR. As a further advance, we propose a tone-injection aided PAPR reduction design for LACO-OFDM, which in turn improves the BER performance. Simulations are provided for verifying both the analytical BER performance and the PAPR distribution of LACO-OFDM. The results show that the expressions derived match well with the simulations. Furthermore, the PAPR reduction method proposed attains a 5 dB PAPR reduction at the $10^{-3}$ probability-point of the complementary cumulative distribution function, as well as a better BER performance than the original LACO-OFDM scheme.