Miracle-dz/UniFAR-FTUs huggingface dataset:
SymPortal: A novel analytical framework and platform for coral algal symbiont next‐generation sequencing ITS2 profiling

We present SymPortal (SymPortal.org), a novel analytical framework and platform for genetically resolving the algal symbionts of reef corals using next‐generation sequencing (NGS) data of the ITS2 rDNA. Although the ITS2 marker is widely used to genetically characterize taxa within the family Symbiodiniaceae (formerly the genus Symbiodinium), the multicopy nature of the marker complicates its use. Commonly, the intragenomic diversity resultant from this multicopy nature is collapsed by analytical approaches, thereby focusing on only the most abundant sequences. In contrast, SymPortal employs logic to identify within‐sample informative intragenomic sequences, which we have termed ‘defining intragenomic variants' (DIVs), to identify ITS2‐type profiles representative of putative Symbiodiniaceae taxa. By making use of this intragenomic ITS2 diversity, SymPortal is able to resolve genetic delineations using the ITS2 marker at a level that was previously only possible by using additional genetic markers. We demonstrate this by comparing this novel approach to the most commonly used alternative approach for NGS ITS2 data, the 97% similarity clustering to operational taxonomic units (OTUs). The SymPortal platform accepts NGS raw sequencing data as input to provide an easy‐to‐use, standardization‐enforced, and community‐driven framework that integrates with a database to gain resolving power with increased use. We consider that SymPortal, in conjunction with ongoing large‐scale sampling and sequencing efforts, should play an instrumental role in making future sampling efforts more comparable and in maximizing their efficacy in working towards the classification of the global Symbiodiniaceae diversity.
Executive summary: heart disease and stroke statistics--2014 update: a report from the American Heart Association.

Author(s): Go, Alan S; Mozaffarian, Dariush; Roger, Veronique L; Benjamin, Emelia J; Berry, Jarett D; Blaha, Michael J; Dai, Shifan; Ford, Earl S; Fox, Caroline S; Franco, Sheila; Fullerton, Heather J; Gillespie, Cathleen; Hailpern, Susan M; Heit, John A; Howard, Virginia J; Huffman, Mark D; Judd, Suzanne E; Kissela, Brett M; Kittner, Steven J; Lackland, Daniel T; Lichtman, Judith H; Lisabeth, Lynda D; Mackey, Rachel H; Magid, David J; Marcus, Gregory M; Marelli, Ariane; Matchar, David B; McGuire, Darren K; Mohler, Emile R; Moy, Claudia S; Mussolino, Michael E; Neumar, Robert W; Nichol, Graham; Pandey, Dilip K; Paynter, Nina P; Reeves, Matthew J; Sorlie, Paul D; Stein, Joel; Towfighi, Amytis; Turan, Tanya N; Virani, Salim S; Wong, Nathan D; Woo, Daniel; Turner, Melanie B; American Heart Association Statistics Committee and Stroke Statistics Subcommittee
Edinburgh Research Explorer Association of apolipoprotein E with intracerebral hemorrhage risk by race/ethnicity

IMPORTANCE Genetic studies of intracerebral hemorrhage (ICH) have focused mainly on white participants, but genetic risk may vary or could be concealed by differing nongenetic coexposures in nonwhite populations. Transethnic analysis of risk may clarify the role of genetics in ICH risk across populations.
Self-prioritization of fully unfamiliar stimuli

Recently, Sui and colleagues introduced an experimental task to investigate prioritization of arbitrary stimuli associated with the self. They demonstrated that after being told to associate three identities (self, friend, stranger) with three arbitrary stimuli (geometrical shapes), participants were faster in a perceptual matching task to recognise matching pairs of self-associated shape with self-label, than respective friend or stranger-related pairings. They interpreted this as evidence that a brief self-association is sufficient to facilitate processing of previously neutral stimuli. However, in the matching trials of the self-prioritization task, participants are processing not only self-associated arbitrary stimuli but also familiar verbal labels with an established meaning. Therefore, the self-advantage may be caused by familiarity of the labels, rather than self-association of the shapes. To test whether self-prioritization can be elicited in a task employing exclusively neutral stimuli, we asked participants to associate avatar faces with three identities (self, name of best friend, and stranger) and replaced labels with unfamiliar abstract symbols that were associated to the words (you, friend, stranger) before the actual experiment started. The results presented the usual pattern of self-prioritization showing that this effect does not critically depend on the presence of familiar labels and that it can be elicited in the absence of any familiar stimuli.
Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis

Abstract Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf‐level water‐use efficiency (WUE). In Arabidopsis, little is known about the variation of whole‐plant water use (PWU) and whole‐plant WUE (transpiration efficiency). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large‐scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water use and drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water‐use strategies, namely, C24 (low PWU) and Col‐0 (high PWU). Subsequent quantitative trait loci mapping and validation through near‐isogenic lines identified two causal quantitative trait loci, which showed that a combination of weak and nonfunctional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water use due to their control of flowering time. Crucially, we observed that reducing flowering time and consequently water use did not penalize reproductive performance, as such water productivity (seed produced per unit of water transpired) improved. Natural polymorphisms of FRI and FLC have previously been elucidated as key determinants of natural variation in intrinsic WUE (δ13C). However, in the genetic backgrounds tested here, drought tolerance traits, stomatal conductance, δ13C. and rosette water use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining lifetime PWU but not always leaf‐level traits.
Evaluation of the impact of waterpipe tobacco smoke exposure on the activity and expression of rat hepatic CYP450: a pharmacokinetic study

Abstract Waterpipe smoke contains many toxic constituents that can alter drug pharmacokinetics. This study assessed the effect of waterpipe smoke exposure on the activity and expression of CYP450 enzymes in rats. Animals (n = 10/group) were exposed to either waterpipe smoke or side-stream cigarette smoke for 1 h/day (6 days/week) for 31 days, or fresh air (control). An intragastric cocktail solution containing three probe drugs, phenacetin, chlorzoxazone and testosterone was administered to assess the activity of CYP1A2, CYP2E1 and CYP3A, respectively. Serum concentrations were determined using LC-MS/MS and the pharmacokinetic parameters were calculated. The mRNA expression of hepatic enzymes was also quantified. Waterpipe and cigarette smoke exposure did not significantly alter the pharmacokinetics of phenacetin, chlorzoxazone and testosterone. For example, the clearance and drug exposure values were comparable among groups for all probe drugs. Additionally, there was no significant effect of waterpipe and cigarette smoke on mRNA expression of hepatic CYP1A2, CYP2E1 and CYP3A2. The results demonstrate that waterpipe smoke exposure had no effect on the functional expression of three key CYP450 isoforms in rats. Future research is required with longer exposure periods to waterpipe smoke. Such work serves to enhance current understanding of effect of waterpipe smoke exposure on pharmacokinetics.
Spinal Cord Regeneration in Amphibians: A Historical Perspective

In some vertebrates, a grave injury to the central nervous system (CNS) results in functional restoration, rather than in permanent incapacitation. Understanding how these animals mount a regenerative response by activating resident CNS stem cell populations is of critical importance in regenerative biology. Amphibians are of a particular interest in the field because the regenerative ability is present throughout life in urodele species, but in anuran species it is lost during development. Studying amphibians, who transition from a regenerative to a nonregenerative state, could give insight into the loss of ability to recover from CNS damage in mammals. Here, we highlight the current knowledge of spinal cord regeneration across vertebrates and identify commonalities and differences in spinal cord regeneration between amphibians.
Targeting biosynthetic networks of the proinflammatory and proresolving lipid metabolome

Nonsteroidal anti‐inflammatory drugs interfere with the metabolism of arachidonic acid to proinflammatory prostaglandins and leukotrienes by targeting cyclooxygenases (COXs), 5‐lipoxygenase (LOX), or the 5‐LOX–activating protein (FLAP). These and related enzymes act in conjunction with marked crosstalk within a complex lipid mediator (LM) network where also specialized proresolving LMs (SPMs) are formed. Here, we present how prominent LM pathways can be differentially modulated in human proinflammatory M1 and proresolving M2 macrophage phenotypes that, upon exposure to Escherichia coli, produce either abundant prostaglandins and leukotrienes (M1) or SPMs (M2). Targeted liquid chromatography–tandem mass spectrometry–based metabololipidomics was applied to analyze and quantify the specific LM profiles. Besides expected on‐target actions, we found that: 1) COX or 15‐LOX‐1 inhibitors elevate inflammatory leukotriene levels, 2) FLAP and 5‐LOX inhibitors reduce leukotrienes in M1 but less so in M2 macrophages, 3) zileuton blocks resolution‐initiating SPM biosynthesis, whereas FLAP inhibition increases SPM levels, and 4) that the 15‐LOX‐1 inhibitor 3887 suppresses SPM formation in M2 macrophages. Conclusively, interference with discrete LM biosynthetic enzymes in different macrophage phenotypes considerably affects the LM metabolomes with potential consequences for inflammation‐resolution pharmacotherapy. Our data may allow better appraisal of the therapeutic potential of these drugs to intervene with inflammatory disorders. —Werner, M. , Jordan, P. M. , Romp, E. , Czapka, A. , Rao, Z. , Kretzer, C. , Koeberle, A. , Garscha, U. , Pace, S. , Claesson, H. ‐E. , Serhan, C. N. , Werz, O. , Gerstmeier, J. Targeting biosynthetic networks of the proinflammatory and proresolving lipid metabolome. FASEB J. 33, 6140–6153 (2019). www.fasebj. org
Potential EEG biomarkers of sedation doses in intensive care patients unveiled by using a machine learning approach

Objective. Sedation of neurocritically ill patients is one of the most challenging situation in ICUs. Quantitative knowledge on the sedation effect on brain activity in that complex scenario could help to uncover new markers for sedation assessment. Hence, we aim to evaluate the existence of changes of diverse EEG-derived measures in deeply-sedated (RASS-Richmond agitation-sedation scale −4 and −5) neurocritically ill patients, and also whether sedation doses are related with those eventual changes. Approach. We performed an observational prospective cohort study in the intensive care unit of the Hospital de la Princesa. Twenty-six adult patients suffered from traumatic brain injury and subarachnoid hemorrhage were included in the present study. Long-term continuous electroencephalographic (EEG) recordings (2141 h) and hourly annotated information were used to determine the relationship between intravenous sedation infusion doses and network and spectral EEG measures. To do that, two different strategies were followed: assessment of the statistical dependence between both variables using the Spearman correlation rank and by performing an automatic classification method based on a machine learning algorithm. Main results. More than 60% of patients presented a correlation greater than 0.5 in at least one of the calculated EEG measures with the sedation dose. The automatic classification method presented an accuracy of 84.3% in discriminating between different sedation doses. In both cases the nodes’ degree was the most relevant measurement. Significance. The results presented here provide evidences of brain activity changes during deep sedation linked to sedation doses. Particularly, the capability of network EEG-derived measures in discriminating between different sedation doses could be the framework for the development of accurate methods for sedation levels assessment.
mTOR Signaling pathway as a master regulator of memory CD8+ T‐cells, Th17, and NK cells development and their functional properties

The mammalian target of rapamycin (mTOR) is a member of the evolutionary phosphatidylinositol kinase‐related kinases (PIKKs). mTOR plays a pivotal role in the regulation of diverse aspects of cellular physiology such as body metabolism, cell growth, protein synthesis, cell size, autophagy, and cell differentiation. Immunologically, mTOR has a fundamental part in controlling and shaping diverse functions of innate and adaptive immune cells, in particular, T‐cell subsets differentiation, survival, and metabolic reprogramming to ultimately regulate the fate of diverse immune cell types. Researchers report that rapamycin, a selective mTOR inhibitor, and immunosuppressive agent, has surprising immunostimulatory effects on inducing both quantitative and qualitative aspects of virus‐specific memory CD8+ T‐cells differentiation and homeostasis in a T‐cell‐intrinsic manner. The mTOR signaling pathway also plays a critical role in dictating the outcome of regulatory T cells (Treg), T helper 17 (Th17) cells, and natural killer (NK) cells proliferation and maturation, as well as the effector functions and cytotoxic properties of NK cells. Manipulation of mTOR activity is a critical therapeutic approach for pharmacological agents that seek to inhibit mTOR. This approach should enhance specific memory CD8 + T‐cells responses and induce fully functional effector properties of NK cells to provoke their antitumor and antiviral activities.
Contribution of Different Antiretroviral Regimens Containing Zidovudine, Lamivudine and Ritonavir-Boosted Lopinavir on HIV Viral Load Reduction during Pregnancy

Background Antiretroviral (ARV) regimens used for the prevention of mother-to-child transmission of HIV have evolved over time. We evaluated the contribution of different ARV regimens on the reduction of the plasma HIV RNA viral load (VL) during pregnancy. Methods A total of 1,833 VL measurements from ARV-naive pregnant women participating in perinatal prevention trials in Thailand were included. Women received either zidovudine (ZDV) monotherapy, ZDV plus lopinavir/ritonavir (LPV/r), or ZDV plus lamivudine (3TC) plus LPV/r. VL time-course during pregnancy was described as a function of pretreatment VL and treatment duration using an Emax non-linear mixed-effect model. VL reduction and median time to achieve a VL≤50 copies/ml were estimated for each regimen. Results Among 745 women, 279 (37%), 145 (20%) and 321 (43%) received ZDV monotherapy, ZDV+LPV/r and ZDV+3TC+LPV/r, respectively. The predicted VL reduction from baseline to delivery after a median of 10 weeks of treatment were 0.5, 2.7 and 2.9 log10 copies/ml with ZDV monotherapy, ZDV+LPV/r and ZDV+3TC+LPV/r, respectively. At delivery, 1%, 57% and 63% of women receiving ZDV monotherapy, ZDV+LPV/r or ZDV+3TC+LPV/r had a VL≤50 copies/ml. The addition of 3TC to ZDV+LPV/r reduced the time to achieve a VL≤50 copies/ml and the higher the pretreatment VL, the larger the effect 3TC had on reducing the time to VL≤50 copies/ml. Conclusions The addition of 3TC to ZDV+LPV/r was associated with a slight further VL reduction but the time to reach a VL≤50 copies/ml was shorter. This beneficial effect of 3TC is crucial for prevention of mother-to-child transmission in women who receive ARVs late and with high pretreatment VL.
Non- or Minimally Displaced Distal Radial Fractures in Adult Patients: Three Weeks versus Five Weeks of Cast Immobilization—A Randomized Controlled Trial

Abstract Background Patients with non- or minimally displaced distal radial fractures, that do not need repositioning, are mostly treated by a short-arm cast for a period of 4 to 6 weeks. A shorter period of immobilization may lead to a better functional outcome. Purpose We conducted a randomized controlled trial to evaluate whether the duration of cast immobilization for patients with non- or minimally displaced distal radial fractures can be safely shortened toward 3 weeks. Materials and Methods The primary outcomes were patient-reported outcomes measured by the Patient-Related Wrist Evaluation (PRWE) and Quick Disability of Arm, Shoulder and Hand (QuickDASH) score after 1-year follow-up. Secondary outcome measures were: PRWE and QuickDASH earlier in follow-up, pain (Visual Analog Scale), and complications like secondary displacement. Results Seventy-two patients (male/female, 23/49; median age, 55 years) were included and randomized. Sixty-five patients completed the 1-year follow-up. After 1-year follow up, patients in the 3 weeks immobilization group had significantly better PRWE (5.0 vs. 8.8 points, p = 0.045) and QuickDASH scores (0.0 vs. 12.5, p = 0.026). Secondary displacement occurred once in each group. Pain did not differ between groups (p = 0.46). Conclusion Shortening the period of immobilization in adult patients with a non- or minimally displaced distal radial fractures seems to lead to equal patient-reported outcomes for both the cast immobilization groups. Also, there are no negative side effects of a shorter period of cast immobilization. Therefore, we recommend a period of 3 weeks of immobilization in patients with distal radial fractures that do not need repositioning.
Hearing Conservation Surgery Using the Hybrid-L Electrode

Patients with high-frequency deafness and/or substantial residual hearing across frequencies might benefit from combined electro-acoustic stimulation. The Hybrid-L electrode was designed to address the issues of both hearing conservation and effective electrical stimulation in those recipients. The electrode with 22 contacts should be inserted through the round window membrane, and covers approximately 270° of the basal turn of the cochlear. This insertion length is equivalent to the one seen in many patients using the former Nucleus straight electrode. Twenty-four patients with low-frequency thresholds of 60 dB or better, up to 500 Hz, were implanted with a Hybrid-L device in a clinical trial at the Medical University of Hannover. Another group of 8 recipients with less residual hearing was included under extended inclusion criteria. Residual hearing was conserved in the majority of cases. One patient had a loss of more than 30 dB, but hearing partially recovered after 9 months. The median loss in all patients was 10 dB in both the Hybrid group and the extended group. Patients were able to use the residual hearing postoperatively to the same extent as preoperatively. In the Hybrid mode (cochlear implant + ipsilateral hearing aid), patients showed a significant improvement of 21% (p = 0.002) in speech understanding in quiet using the Freiburger Monosyllabic Word Test compared to the preoperative scores under aided conditions with their hearing aid. The Oldenburg Sentence Test in noise showed a remarkable average improvement of 10.2 dB (p < 0.001) compared to the preoperative hearing aid only mode. An additional improvement could be seen in the combined mode using an additional contralateral hearing aid. Recipients with a shorter duration of high-frequency hearing loss showed a larger benefit than those with a longer duration of hearing loss. Hearing conservation using the Hybrid-L electrode and a given surgical technique is possible with high probability in patients with high-frequency deafness or pantonal hearing loss. The use of the residual acoustic hearing offers specific advantages, especially for understanding speech in noise and for spatial hearing.
Encouraging the Use of eHealth Services: A Survey of Patients' Experiences

To promote eHealth services effectively, it is important to understand what motivates people to use these services and how they can be further supported. Our aim was to explore user experiences with eHealth services from the viewpoint of patients with chronic illnesses. The survey data included responses from 397 patients actively using eHealth services in Finland. Most of them had positive experiences using the services. We found that these positive experiences and the perceived benefits of eHealth services encouraged patients to continue using the services. In order to bolster the use of eHealth services, patients and other potential users must be informed about the new services and how to access them. Healthcare personnel play a key role in introducing eHealth services to patients and instructing them on their use.
Deep RNA Sequencing Reveals Dynamic Regulation of Myocardial Noncoding RNAs in Failing Human Heart and Remodeling With Mechanical Circulatory Support

Background— Microarrays have been used extensively to profile transcriptome remodeling in failing human heart, although the genomic coverage provided is limited and fails to provide a detailed picture of the myocardial transcriptome landscape. Here, we describe sequencing-based transcriptome profiling, providing comprehensive analysis of myocardial mRNA, microRNA (miRNA), and long noncoding RNA (lncRNA) expression in failing human heart before and after mechanical support with a left ventricular (LV) assist device (LVAD). Methods and Results— Deep sequencing of RNA isolated from paired nonischemic (NICM; n=8) and ischemic (ICM; n=8) human failing LV samples collected before and after LVAD and from nonfailing human LV (n=8) was conducted. These analyses revealed high abundance of mRNA (37%) and lncRNA (71%) of mitochondrial origin. miRNASeq revealed 160 and 147 differentially expressed miRNAs in ICM and NICM, respectively, compared with nonfailing LV. Among these, only 2 (ICM) and 5 (NICM) miRNAs are normalized with LVAD. RNASeq detected 18 480, including 113 novel, lncRNAs in human LV. Among the 679 (ICM) and 570 (NICM) lncRNAs differentially expressed with heart failure, ≈10% are improved or normalized with LVAD. In addition, the expression signature of lncRNAs, but not miRNAs or mRNAs, distinguishes ICM from NICM. Further analysis suggests that cis-gene regulation represents a major mechanism of action of human cardiac lncRNAs. Conclusions— The myocardial transcriptome is dynamically regulated in advanced heart failure and after LVAD support. The expression profiles of lncRNAs, but not mRNAs or miRNAs, can discriminate failing hearts of different pathologies and are markedly altered in response to LVAD support. These results suggest an important role for lncRNAs in the pathogenesis of heart failure and in reverse remodeling observed with mechanical support.