Miracle-dz/UniFAR-FTUs huggingface dataset:
Species are hypotheses: avoid connectivity assessments based on pillars of sand

Connectivity among populations determines the dynamics and evolution of populations, and its assessment is essential in ecology in general and in conservation biology in particular. The robust basis of any ecological study is the accurate delimitation of evolutionary units, such as populations, metapopulations and species. Yet a disconnect still persists between the work of taxonomists describing species as working hypotheses and the use of species delimitation by molecular ecologists interested in describing patterns of gene flow. This problem is particularly acute in the marine environment where the inventory of biodiversity is relatively delayed, while for the past two decades, molecular studies have shown a high prevalence of cryptic species. In this study, we illustrate, based on marine case studies, how the failure to recognize boundaries of evolutionary‐relevant unit leads to heavily biased estimates of connectivity. We review the conceptual framework within which species delimitation can be formalized as falsifiable hypotheses and show how connectivity studies can feed integrative taxonomic work and vice versa. Finally, we suggest strategies for spatial, temporal and phylogenetic sampling to reduce the probability of inadequately delimiting evolutionary units when engaging in connectivity studies.
A neural circuit for gamma-band coherence across the retinotopic map in mouse visual cortex

Cortical gamma oscillations have been implicated in a variety of cognitive, behavioral, and circuit-level phenomena. However, the circuit mechanisms of gamma-band generation and synchronization across cortical space remain uncertain. Using optogenetic patterned illumination in acute brain slices of mouse visual cortex, we define a circuit composed of layer 2/3 (L2/3) pyramidal cells and somatostatin (SOM) interneurons that phase-locks ensembles across the retinotopic map. The network oscillations generated here emerge from non-periodic stimuli, and are stimulus size-dependent, coherent across cortical space, narrow band (30 Hz), and depend on SOM neuron but not parvalbumin (PV) neuron activity; similar to visually induced gamma oscillations observed in vivo. Gamma oscillations generated in separate cortical locations exhibited high coherence as far apart as 850 μm, and lateral gamma entrainment depended on SOM neuron activity. These data identify a circuit that is sufficient to mediate long-range gamma-band coherence in the primary visual cortex.
Capturing Chromosome Conformation

We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G1stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.
Invasive Management Strategies and Antithrombotic Treatments in Patients With Non–ST-Segment–Elevation Acute Coronary Syndrome in China: Findings From the Improving CCC Project (Care for Cardiovascular Disease in China)

Background— Early invasive strategies and antithrombotic treatments are key treatments of non–ST-segment–elevation acute coronary syndrome (NSTE-ACS). Few studies have examined the use of these strategies in patients with NSTE-ACS in China. This study aimed to assess the applications of invasive strategies and antithrombotic treatments in patients with NSTE-ACS and compare their outcomes. Methods and Results— A nationwide registry study, Improving CCC (Care for Cardiovascular Disease in China) ACS project, was launched in 2014 as a collaborative study of the American Heart Association and Chinese Society of Cardiology (CSC), with 142 participating hospitals reporting details of clinical management and outcomes of patients with NSTE-ACS. The use of invasive strategies and antithrombotic treatments was examined based on updated guidelines. Major adverse cardiovascular events were analyzed. A total of 9953 patients with NSTE-ACS were enrolled. Angiography was performed in 63.1% of these patients, and 58.2% underwent percutaneous coronary intervention (PCI). However, 40.6% of patients did not undergo early risk assessment, and very-high-risk patients had the lowest proportion of PCI (41.7%). PCI was performed within recommended times in 11.1% of very-high-risk patients and 26.3% of high risk patients. Those who underwent PCI within 2 hours had higher mortality in high-risk and very-high-risk patients who received PCI. Early dual antiplatelet treatment was given in 88.3% of patients. Conclusions— There are notable differences between guideline recommendations and the clinical management of patients with NSTE-ACS in China. The reasons for very-high-risk NSTE-ACS patients not undergoing PCI, and the optimal timing of PCI, require further clarification. Clinical Trial Registration— URL: http://www.clinicaltrials. gov. Unique identifier: NCT02306616.
Neonatal and Obstetrical Outcomes of Pregnancies in Systemic Lupus Erythematosus.

Objectives Systemic lupus erythematous (SLE) is a chronic autoimmune disease that affects women primarily of childbearing age. The objective of this study was to determine the neonatal and maternal outcomes of pregnancies in SLE patients compared to pregnancies in healthy controls. Methods We conducted a retrospective cohort study in a tertiary care hospital in Oman between January 2007 and December 2013. We analyzed 147 pregnancies and compared 56 (38.0%) pregnancies in women with SLE with 91 (61.9%) pregnancies in healthy control women. Disease activity was determined using the Systemic Lupus Erythematosus Disease Activity Index (SLEDAI). Results The mean age of the cohort was 30.0±5.0 years ranging from 19 to 44 years old. Patients with SLE were treated with hydroxychloroquine (n = 41; 73.2%), prednisolone (n = 38; 67.8%), and azathioprine (n = 17; 30.3%). There was no disease activity in 39.2% (n = 22) of patients while 41.0% (n = 23), 12.5% (n = 7), and 7.1% (n = 4) had mild (SLEDAI 1-5), moderate (SLEDAI 6-10), and severe (SLEDAI 3 11) disease activity, respectively, at onset of pregnancy. Pregnancies in patients with SLE were associated with higher abortions (42.8% vs. 15.3%; p < 0.001), gestational diabetes (28.3% vs. 10.2%; p = 0.004), polyhydramnios (7.1% vs. 0.0%; p = 0.020), previous preterm pregnancies (8.9% vs. 1.0%; p = 0.030), and intrauterine growth retardation (21.4% vs. 0.0%; p < 0.001) when compared to pregnancies in healthy control women. Furthermore, the neonates born to mothers with SLE were more likely to be preterm (28.5% vs. 1.0%; p < 0.001), have a low birth weight (< 2 500 g) (32.1% vs. 1.0%; p < 0.001), and were associated with stillbirth (7.1% vs. 0.0%; p = 0.010) when compared to neonates born to healthy control mothers. Conclusions Pregnancies in women with SLE were associated with higher neonatal and maternal complications. Therefore, pregnant women with SLE should have their pregnancy accurately planned, monitored, and managed according to a multidisciplinary treatment schedule.
Phase transition studies of Na3Bi system under uniaxial strain

We investigated the electronic properties and phase transitions of Na3Bi in four structural phases (space groups P63/mmc, P3¯c1, Fm3¯m and Cmcm) under constant-volume uniaxial strain using the first-principles method. For P63/mmc and P3¯c1-Na3Bi, an important phase transition from a topological Dirac semimetal (TDS) to a topological insulator appears under compression strain around 4.5%. The insulating gap increases with the increasing compressive strain and up to around 0.1 eV at a strain of 10%. However, both P63/mmc and P3¯c1-Na3Bi still keep the properties of a TDS within a tensile strain of 0–10%, although the Dirac points move away from the Γ point along Γ–A in reciprocal space as the tensile strain increases. The Na3Bi with space group Fm3¯m is identified as a topological semimetal with the inverted bands between Na-3s and Bi-6p and a parabolic dispersion in the vicinity of Γ point. Interestingly, for Fm3¯m-Na3Bi, both compression and tensile strain lead to a TDS which is identified by calculating surface Fermi arcs and topological invariants at time-reversal planes (kz = 0 and kz = π/c) in reciprocal space. Additionally, we confirmed the high pressure phase Cmcm-Na3Bi is an ordinary insulator with a gap of about 0.62 eV. It is noteworthy that its gap almost keeps constant around 0.60 eV within a compression strain of 0–10%. In contrast, a remarkable phase transition from an insulator to a metal phase appears under tensile strain. Moreover, this phase transition is highly sensitive to tensile strain and takes place only at a strain 1.0%. These strain-induced electronic structures and phase transitions of the Na3Bi system in various phases are important due to their possible applications under high pressure in future electronic devices.
Angiotensin 1–7 ameliorates caerulein-induced inflammation in pancreatic acinar cells by downregulating Toll-like receptor 4/nuclear factor-κB expression

The present study aimed to investigate the effects of angiotensin (Ang) 1–7 on caerulein (CAE)-stimulated nuclear factor (NF)-κB, Toll-like receptor (TLR4) and cytokine expression using pancreatic acinar AR42J cells. AR42J cells were treated with 10 nmol/l CAE for various durations. In addition, cells were pretreated with various concentrations of Ang 1–7 or A779, a specific antagonist of Ang 1–7, and were stimulated with CAE for 12 h. Control cells were treated with vehicle (F-12K complete medium with 2% fetal bovine serum, 10 U/ml penicillin and 100 mg/ml streptomycin) alone. The mRNA and protein expression levels of TLR4, NF-κB, interleukin (IL)-6, IL-8, IL-10 and tumor necrosis factor-α (TNF-α) were determined by western blotting, immunofluorescence and reverse transcription-quantitative polymerase chain reaction. CAE treatment stimulated TLR4 and NF-κB expression within AR42J cells. Immunofluorescence indicated that TLR4 was expressed on the membranes and in the cytoplasm of AR42J cells, whereas NF-κB expression accumulated in the cytoplasm and nuclei. CAE-induced expression of TLR4 and NF-κB within AR42J cells was abrogated by 10−5 mmol/l Ang 1–7; however, TLR4 and NF-κB expression was enhanced with the addition of A779, particularly 10−5 mmol/l. In addition, treatment with 10−6 and 10−5 mmol/l Ang 1–7 significantly mitigated CAE-induced expression of IL-6, IL-8 and TNF-α, whereas it enhanced IL-10 expression. Conversely, A779 treatment enhanced the CAE-induced expression of IL-6, IL-8 and TNF-α, and reduced IL-10 expression in AR42J cells. In conclusion, these results suggested that Ang 1–7 may attenuate CAE-induced inflammation by downregulating TLR4, NF-κB and proinflammatory cytokine expression within AR42J cells. Therefore, Ang 1–7 may exert protective effects against the pathological progression of AP in a cell model of AP induced by CAE and may be considered in the development of treatments for this disease.
Electrical tree growth retardation and acceleration model

In predicting electrical tree growth behaviour of practical insulation materials under operating alternating voltages, one must consider the effects of compressive and tensile residual stresses to retard and accelerate electrical tree growth. In this study a general model of electrical tree growth retardation and acceleration is firstly proposed. The present model combines both macroscopic and submicroscopic approaches to describe the local damage features around the tree tip and enables the effect of compressive and/or tensile residual stresses on electrical tree growth dynamics to be determined quantitatively. Electrical tree propagation rate equation and a lifetime formula that take into account the effect of the residual stresses have been derived. Taking the example of mechanically pre-stressed fibre-reinforced epoxy resins the application of the proposed model has been addressed.
The ancestral retinoic acid receptor was a low-affinity sensor triggering neuronal differentiation

Vitamin A–dependent intercellular signaling was originally regulated by a low-affinity sensor and acted in neural development. Retinoic acid (RA) is an important intercellular signaling molecule in vertebrate development, with a well-established role in the regulation of hox genes during hindbrain patterning and in neurogenesis. However, the evolutionary origin of the RA signaling pathway remains elusive. To elucidate the evolution of the RA signaling system, we characterized RA metabolism and signaling in the marine annelid Platynereis dumerilii, a powerful model for evolution, development, and neurobiology. Binding assays and crystal structure analyses show that the annelid retinoic acid receptor (RAR) binds RA and activates transcription just as vertebrate RARs, yet with a different ligand-binding pocket and lower binding affinity, suggesting a permissive rather than instructive role of RA signaling. RAR knockdown and RA treatment of swimming annelid larvae further reveal that the RA signal is locally received in the medial neuroectoderm, where it controls neurogenesis and axon outgrowth, whereas the spatial colinear hox gene expression in the neuroectoderm remains unaffected. These findings suggest that one early role of the new RAR in bilaterian evolution was to control the spatially restricted onset of motor and interneuron differentiation in the developing ventral nerve cord and to indicate that the regulation of hox-controlled anterior-posterior patterning arose only at the base of the chordates, concomitant with a high-affinity RAR needed for the interpretation of a complex RA gradient.
Detection of Vaccinia Virus in Urban Domestic Cats, Brazil

We investigated possible vaccinia virus (VACV) in urban house cats in Brazil. Serum samples from 6 cats were positive for VACV by PCR, indicating likely VACV circulation among house cats in urban areas of Brazil. This finding highlights the importance of epidemiologic surveillance to avoid outbreaks among urban human populations.
Efficacy of proprioceptive neuromuscular facilitation compared to other stretching modalities in range of motion gain in young healthy adults: A systematic review

ABSTRACT The objective of this study was to evaluate the efficacy of proprioceptive neuromuscular facilitation (PNF) on range of motion (ROM) gain in young healthy adults. We performed a systematic review of randomized controlled trials and quasi-randomized trials, including young healthy adults. The interventions were: PNF compared with different PNF techniques, control, other muscle stretching exercises and musculoskeletal manipulations. The outcome measures were: articular ROM and adverse effects. The final number of included studies was 46, involving 1,864 adults. There was difference on ROM comparing assisted hold-relax (HR) on diagonal plane to control, based on very low-quality evidence. There was also difference on ROM comparing assisted HR to self-HR; self-contract-relax (CR) to control; assisted CR contract to control; and assisted HR contract to control, based on low-quality evidence. Moderate-quality evidence shows that results differ between self HR and control (SMD: 0.95; 95%CI 0.03, 1.86; I249%; P = 0.16) in terms of ROM gain. When performing the other comparisons, the results were based on low or very low-quality evidence and do not allow to state if PNF is more or less effective than other stretches for improving ROM in healthy young adults. No adverse effects were mentioned.
Combined inhibition of CDK and HDAC as a promising therapeutic strategy for both cutaneous and uveal metastatic melanoma

Very little to no improvement in overall survival has been seen in patients with advanced non-resectable cutaneous melanoma or metastatic uveal melanoma in decades, highlighting the need for novel therapeutic options. In this study we investigated as a potential novel therapeutic intervention for both cutaneous and uveal melanoma patients a combination of the broad spectrum HDAC inhibitor quisinostat and pan-CDK inhibitor flavopiridol. Both drugs are currently in clinical trials reducing time from bench to bedside. Combining quisinostat and flavopiridol shows a synergistic reduction in cell viability of all melanoma cell lines tested, irrespective of their driver mutations. This synergism was also observed in BRAFV600E mutant melanoma that had acquired resistance to BRAF inhibition. Mechanistically, loss of cell viability was, at least partly, due to induction of apoptotic cell death. The combination was also effectively inducing tumor regression in a preclinical setting, namely a patient-derived tumor xenograft (PDX) model of cutaneous melanoma, without increasing adverse effects. We propose that the quisinostat/flavopiridol combination is a promising therapeutic option for both cutaneous and uveal metastatic melanoma patients, independent of their mutational status or (acquired) resistance to BRAF inhibition.
Impact of Fluoropolymer-Based Paclitaxel Delivery on Neointimal Proliferation and Vascular Healing: A Comparative Peripheral Drug-Eluting Stent Study in the Familial Hypercholesterolemic Swine Model of Femoral Restenosis

Background— A polymer-free peripheral paclitaxel-eluting stent (PES, Zilver PTX, Cook, IN) has shown to improve vessel patency after superficial femoral angioplasty. A new-generation fluoropolymer-based PES (FP-PES; Eluvia, Boston Scientific, MA) displaying more controlled and sustained paclitaxel delivery promise to improve the clinical outcomes of first-generation PES. We sought to compare the biological effect of paclitaxel delivered by 2 different stent-coating technologies (fluoropolymer-based versus polymer-free) on neointimal proliferation and healing response in the familial hypercholesterolemic swine model of femoral restenosis. Methods and Results— The biological efficacy of clinically available FP-PES (n=12) and PES (n=12) was compared against a bare metal stent control (n=12; Innova, Boston Scientific, MA) after implantation in the femoral arteries of 18 familial hypercholesterolemic swine. Longitudinal quantitative vascular angiography and optical coherence tomography were performed at baseline and at 30 and 90 days. Histological evaluation was performed at 90 days. Ninety-day quantitative vascular angiography results showed a lower percent diameter stenosis for FP-PES (38.78% [31.27–47.66]) compared with PES (54.16% [42.60–61.97]) and bare metal stent (74.52% [47.23–100.00]; P<0.001). Ninety-day optical coherence tomography results demonstrated significantly lower neointimal area in FP-PES (8.01 mm2 [7.65–9.21]) compared with PES (10.95 mm2 [9.64–12.46]) and bare metal stent (13.83 mm2 [11.53–17.03]; P<0.001). Histological evaluation showed larger lumen areas and evidence of higher biological activity (smooth muscle cell loss and fibrin deposition) in the FP-PES compared with PES and bare metal stent. Conclusions— In the familial hypercholesterolemic swine model of femoral restenosis, the implantation of an FP-PES resulted in lower levels of neointimal proliferation and sustained biological effect ⩽90 days compared with a polymer-free stent-based approach.
ABCG2 regulatory single-nucleotide polymorphisms alter in vivo enhancer activity and expression

Objectives The expression and activity of the breast cancer resistance protein (ABCG2) contributes toward the pharmacokinetics of endogenous and xenobiotic substrates. The effect of genetic variation on the activity of cis-regulatory elements and nuclear response elements in the ABCG2 locus and their contribution toward ABCG2 expression have not been investigated systematically. In this study, the effect of genetic variation on the in vitro and in vivo enhancer activity of six previously identified liver enhancers in the ABCG2 locus was examined. Methods Reference and variant liver enhancers were tested for their ability to alter luciferase activity in vitro in HepG2 and HEK293T cell lines and in vivo using a hydrodynamic tail vein assay. Positive in vivo single-nucleotide polymorphisms (SNPs) were tested for association with gene expression and for altered protein binding in electrophoretic mobility shift assays. Results Multiple SNPs were found to alter enhancer activity in vitro. Four of these variants (rs9999111, rs12508471, ABCG2RE1*2, and rs149713212) decreased and one (rs2725263) increased enhancer activity in vivo. In addition, rs9999111 and rs12508471 were associated with ABCG2 expression in lymphoblastoid cell lines, lymphocytes, and T cells, and showed increased HepG2 nuclear protein binding. Conclusion This study identifies SNPs within regulatory regions of the ABCG2 locus that alter enhancer activity in vitro and in vivo. Several of these SNPs correlate with tissue-specific ABCG2 expression and alter DNA/protein binding. These SNPs could contribute toward reported tissue-specific variability in ABCG2 expression and may influence the correlation between ABCG2 expression and disease risk or the pharmacokinetics and pharmacodynamics of breast cancer resistance protein substrates.
Characteristics of Initial Prescription Episodes and Likelihood of Long-Term Opioid Use — United States, 2006–2015

Because long-term opioid use often begins with treatment of acute pain (1), in March 2016, the CDC Guideline for Prescribing Opioids for Chronic Pain included recommendations for the duration of opioid therapy for acute pain and the type of opioid to select when therapy is initiated (2). However, data quantifying the transition from acute to chronic opioid use are lacking. Patient records from the IMS Lifelink+ database were analyzed to characterize the first episode of opioid use among commercially insured, opioid-naïve, cancer-free adults and quantify the increase in probability of long-term use of opioids with each additional day supplied, day of therapy, or incremental increase in cumulative dose. The largest increments in probability of continued use were observed after the fifth and thirty-first days on therapy; the second prescription; 700 morphine milligram equivalents cumulative dose; and first prescriptions with 10- and 30-day supplies. By providing quantitative evidence on risk for long-term use based on initial prescribing characteristics, these findings might inform opioid prescribing practices.
Object Onset and Parvocellular Guidance of Attentional Allocation

The parvocellular visual pathway in the primate brain is known to be involved with the processing of color. However, a subject of debate is whether an abrupt change in color, conveyed via this pathway, is capable of automatically attracting attention. It has been shown that the appearance of new objects defined solely by color is indeed capable of modulating attention. However, given evidence suggesting that the visual system is particularly sensitive to new onsets, it is unclear to what extent such results reflect effects of color change per se, rather than effects of object onset. We assessed attentional capture by color change that occurred as a result of either new objects appearing or already-present “old” objects changing color. Results showed that although new object onsets accrued attention, changing the color of old objects did not. We conclude that abrupt color change per se is not sufficient to capture attention.