Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vitro Mutational Analysis of the β2 Adrenergic Receptor, an In Vivo Surrogate Odorant Receptor

Many G-protein coupled receptors (GPCRs), such as odorant receptors (ORs), cannot be characterized in heterologous cells because of their difficulty in trafficking to the plasma membrane. In contrast, a surrogate OR, the GPCR mouse β2-adrenergic-receptor (mβ2AR), robustly traffics to the plasma membrane. We set out to characterize mβ2AR mutants in vitro for their eventual use in olfactory axon guidance studies. We performed an extensive mutational analysis of mβ2AR using a Green Fluorescent Protein-tagged mβ2AR (mβ2AR::GFP) to easily assess the extent of its plasma membrane localization. In order to characterize mutants for their ability to successfully transduce ligand-initiated signal cascades, we determined the half maximal effective concentrations (EC50) and maximal response to isoprenaline, a known mβ2AR agonist. Our analysis reveals that removal of amino terminal (Nt) N-glycosylation sites and the carboxy terminal (Ct) palmitoylation site of mβ2AR do not affect its plasma membrane localization. By contrast, when both the Nt and Ct of mβ2AR are replaced with those of M71 OR, plasma membrane trafficking is impaired. We further analyze three mβ2AR mutants (RDY, E268A, and C327R) used in olfactory axon guidance studies and are able to decorrelate their plasma membrane trafficking with their capacity to respond to isoprenaline. A deletion of the Ct prevents proper trafficking and abolishes activity, but plasma membrane trafficking can be selectively rescued by a Tyrosine to Alanine mutation in the highly conserved GPCR motif NPxxY. This new loss-of-function mutant argues for a model in which residues located at the end of transmembrane domain 7 can act as a retention signal when unmasked. Additionally, to our surprise, amongst our set of mutations only Ct mutations appear to lower mβ2AR EC50s revealing their critical role in G-protein coupling. We propose that an interaction between the Nt and Ct is necessary for proper folding and/or transport of GPCRs.
A Review of Evidence for a Therapeutic Application of Traditional Japanese Kampo Medicine for Oral Diseases/Disorders

Kampo medicines prescribed by specialized medical practitioners and Japanese physicians have gradually reemerged in Japan as alternatives to Western medications. Kampo formulations are composed of several plant extracts and, as such, the broad variety of phytochemicals they contain likely act synergistically to provide their beneficial effects. Kampo medicines have traditionally been prescribed for a number of health conditions, including chronic hepatitis, bronchial asthma, anemia, etc. The aim of this article is to review the beneficial effects of Kampos with respect to oral health. Pertinent papers published between 1970 and 2017 were retrieved by searching in PubMed, ScienceDirect, Web of Science, and Scopus using key words followed by evaluation of the relevant articles. In vitro studies have identified a number of properties that give credence to the potential of Kampos for treating or preventing oral diseases/disorders. Given their anti-microbial and anti-inflammatory properties, they may be promising agents for controlling periodontal diseases, oral mucositis, xerostomia, and drug-induced gingival overgrowth. Since some oral diseases have a complex etiology that involves microbial pathogens and the host immune response, agents with dual functionality such as Kampo phytochemicals may offer a therapeutic advantage.
A simulation study of outcome adaptive randomization in multi-arm clinical trials

Randomizing patients among treatments with equal probabilities in clinical trials is the established method to obtain unbiased comparisons. In recent years, motivated by ethical considerations, many authors have proposed outcome adaptive randomization, wherein the randomization probabilities are unbalanced, based on interim data, to favor treatment arms having more favorable outcomes. While there has been substantial controversy regarding the merits and flaws of adaptive versus equal randomization, there has not yet been a systematic simulation study in the multi-arm setting. A simulation study was conducted to evaluate four different Bayesian adaptive randomization methods and compare them to equal randomization in five-arm clinical trials. All adaptive randomization methods included an initial burn-in with equal randomization and some combination of other modifications to avoid extreme randomization probabilities. Trials either with or without a control arm were evaluated, using designs that may terminate arms early for futility and select one or more experimental treatments at the end. The designs were evaluated under a range of scenarios and sample sizes. For trials with a control arm and maximum same size 250 or 500, several commonly used adaptive randomization methods have very low probabilities of correctly selecting a truly superior treatment. Of those studied, the only adaptive randomization method with desirable properties has a burn-in with equal randomization and thereafter randomization probabilities restricted to the interval 0.10–0.90. Compared to equal randomization, this method has a favorable sample size imbalance but lower probability of correctly selecting a superior treatment. In multi-arm trials, compared to equal randomization, several commonly used adaptive randomization methods give much lower probabilities of selecting superior treatments. Aside from randomization method, conducting a multi-arm trial without a control arm may lead to very low probabilities of selecting any superior treatments if differences between the treatment success probabilities are small.
Reverse and forward engineering of protein pattern formation

Living systems employ protein pattern formation to regulate important life processes in space and time. Although pattern-forming protein networks have been identified in various prokaryotes and eukaryotes, their systematic experimental characterization is challenging owing to the complex environment of living cells. In turn, cell-free systems are ideally suited for this goal, as they offer defined molecular environments that can be precisely controlled and manipulated. Towards revealing the molecular basis of protein pattern formation, we outline two complementary approaches: the biochemical reverse engineering of reconstituted networks and the de novo design, or forward engineering, of artificial self-organizing systems. We first illustrate the reverse engineering approach by the example of the Escherichia coli Min system, a model system for protein self-organization based on the reversible and energy-dependent interaction of the ATPase MinD and its activating protein MinE with a lipid membrane. By reconstituting MinE mutants impaired in ATPase stimulation, we demonstrate how large-scale Min protein patterns are modulated by MinE activity and concentration. We then provide a perspective on the de novo design of self-organizing protein networks. Tightly integrated reverse and forward engineering approaches will be key to understanding and engineering the intriguing phenomenon of protein pattern formation. This article is part of the theme issue ‘Self-organization in cell biology’.
Identification of damage in composite structures based on feature guided ultrasonic waves

Complex-shaped composite laminates are increasingly utilized as Principal Structural Elements (PSE) such as spars, ribs, and the skin-stiffener combination in the aerospace industry. However, due to the stress concentration and out-of-plane impacts during the service life, various types of defects can be initiated in these structures, which have to be identified timely in case they propagate at subsurface laminae and ultimately lead to catastrophic failure. Therefore, this thesis explores the potential of exploiting a special type of ultrasonic guided wave, i.e. feature guided wave (FGW), for rapid screening of long-range composite structures. Such FGWs are capable of focusing their wave energy along the structural feature, with limited leakage into the adjacent plate. Two typical composite features are investigated in the thesis, which are laminated bends and adhesive composite joints, and the results are encouraging. Modal analysis of the laminated bend is carried out by using the Semi-Analytical Finite Element (SAFE) approach, in which the spatially-varying anisotropy is implemented to reveal the existing FGW modes. A shear horizontal type bend-guided (SHB) mode has been identified. The mode is almost non-dispersive and non-leaky, with strong energy confinement in the bend region, which is attractive to be applied as a screening tool for composite bends. Both 3D Finite Element (FE) simulations and experiments are performed to cross-validate the propagation characteristics of the SHB mode and to study its interaction with different defects occurred in the bend region, such as the interlaminar delamination and cracks, showing good agreement. The wave-defect resonance phenomenon and the reflection behaviour are investigated for localizing these two types of defects, and the capabilities of the SHB mode for efficient damage detection in long-range composite bends have been well demonstrated. Also, adhesive bonding is widely used in aerospace composites, and its integrity is crucial to the performance of the entire structure. This motivates the investigation of FGWs in another typical composite assembly, namely the stiffener-adhesive bond-
Computer‐assisted Orthopaedic Surgery

Nowadays, operating rooms can be inefficient and overcrowded. Patient data and images are at times not well integrated and displayed in a timely fashion. This lack of coordination may cause further reductions in efficiency, jeopardize patient safety, and increase costs. Fortunately, technology has much to offer the surgical disciplines and the ongoing and recent operating room innovations have advanced preoperative planning and surgical procedures by providing visual, navigational, and mechanical computerized assistance. The field of computer‐assisted surgery (CAS) broadly refers to surgical interface between surgeons and machines. It is also part of the ongoing initiatives to move away from invasive to less invasive or even noninvasive procedures. CAS can be applied preoperatively, intraoperatively, and/or postoperatively to improve the outcome of orthopaedic surgical procedures as it has the potential for greater precision, control, and flexibility in carrying out surgical tasks, and enables much better visualization of the operating field than conventional methods have afforded. CAS is an active research discipline, which brings together orthopaedic practitioners with traditional technical disciplines such as engineering, computer science, and robotics. However, to achieve the best outcomes, teamwork, open communication, and willingness to adapt and adopt new skills and processes are critical. Because of the relatively short time period over which CAS has developed, long‐term follow‐up studies have not yet been possible. Consequently, this review aims to outline current CAS applications, limitations, and promising future developments that will continue to impact the operating room (OR) environment and the OR in the future, particularly within orthopedic and spine surgery.
When to operate: online patient-reported outcome measures (PROMs) can help decide

We present a report on use of a web-based electronic patient-reported outcome measures (ePROMs) system to support decision-making for a patient with an osteoarthritic knee. After being placed on a waiting list for knee arthroplasty, the use of preoperative PROMs allowed the patient and surgical team to review ongoing disability, and, as a result, alter the management plan by deferring surgery. Ongoing clinical review and symptom management has been centred on ePROMs and has been tailored to the specific needs of the individual. PROMs data are increasingly becoming a necessary component of outcome measurement in many surgical areas. Often, these data are available to neither patient nor clinician in a way that prospectively allows meaningful management. This case highlights how ePROMs can directly influence patient care in real time.
Gene Therapy in Lipoprotein Lipase Deficiency: Case Report on the First Patient Treated with Alipogene Tiparvovec Under Daily Practice Conditions.

One-year results are reported of the first lipoprotein lipase deficiency (LPLD) patient treated with alipogene tiparvovec, which is indicated for the treatment of patients with genetically confirmed LPLD suffering from acute and recurrent pancreatitis attacks (PAs) despite dietary restrictions and expressing >5% of lipoprotein lipase (LPL) mass compared to a healthy control. During clinical development, alipogene tiparvovec has shown improvement of chylomicron metabolism and reduction of pancreatitis incidence up to 5.8 years post treatment. A 43-year-old female presented with severe hypertriglyceridemia (median triglyceride [TG] value of 3,465 mg/dL) and a history of 37 PAs within the last 25 years, despite treatment with fibrates, omega 3 fatty acids, and-since 2012-twice-weekly lipid apheresis. LPLD was confirmed by identification of two different pathogenic variants in the LPL gene located on separate alleles and therefore constituting a compound heterozygous state. With a detectable LPL mass level of 55.1 ng/mL, the patient was eligible for alipogene tiparvovec treatment, and in September 2015, she receved 40 injections (1 × 1012 genome copies/kg) in the muscles of her upper legs under epidural anesthesia and immunosuppressive therapy. Alipogene tiparvovec was well tolerated: no injection site or systemic reactions were observed. Median TG values decreased by 52%, dropping to 997 mg/dL at month 3 and increasing thereafter. Within the first 18 months post treatment, the patient discontinued plasmapheresis and had no abdominal pain or PAs. In March 2017, the patient suffered from a PA due to diet violation. Within the first 12 months post treatment, overall quality of life improved, and no change in humoral or cellular immune response against LPL or AAV-1 was observed. In conclusion, alipogene tiparvovec was well tolerated, with a satisfactory response to treatment. Long-term effects on the recurrence of pancreatitis continue to be monitored.
The CAN‐In network: A biologically inspired model for self‐sustained theta oscillations and memory maintenance in the hippocampus

During working memory tasks, the hippocampus exhibits synchronous theta‐band activity, which is thought to be correlated with the short‐term memory maintenance of salient stimuli. Recent studies indicate that the hippocampus contains the necessary circuitry allowing it to generate and sustain theta oscillations without the need of extrinsic drive. However, the cellular and network mechanisms supporting synchronous rhythmic activity are far from being fully understood. Based on electrophysiological recordings from hippocampal pyramidal CA1 cells, we present a possible mechanism for the maintenance of such rhythmic theta‐band activity in the isolated hippocampus. Our model network, based on the Hodgkin‐Huxley formalism, comprising pyramidal neurons equipped with calcium‐activated nonspecific cationic (CAN) ion channels, is able to generate and sustain synchronized theta oscillations (4–12 Hz), following a transient stimulation. The synchronous network activity is maintained by an intrinsic CAN current (ICAN), in the absence of constant external input. When connecting the pyramidal‐CAN network to fast‐spiking inhibitory interneurons, the dynamics of the model reveal that feedback inhibition improves the robustness of fast theta oscillations, by tightening the synchronization of the pyramidal CAN neurons. The frequency and power of the theta oscillations are both modulated by the intensity of the ICAN, which allows for a wide range of oscillation rates within the theta band. This biologically plausible mechanism for the maintenance of synchronous theta oscillations in the hippocampus aims at extending the traditional models of septum‐driven hippocampal rhythmic activity. © 2017 Wiley Periodicals, Inc.
Up in Vapor: Exploring the Health Messages of E-Cigarette Advertisements

ABSTRACT Electronic cigarettes (e-cigarettes) have gained popularity in the United States, and marketers are using advertising to recruit new users to their products. Despite outright bans on traditional cigarette advertisements, e-cigarettes have no specific regulations. This study uses framing theory to explore the themes in e-cigarette advertisements. Also, practical implications are discussed.
The Neuroprotection of Low-Dose Morphine in Cellular and Animal Models of Parkinson’s Disease Through Ameliorating Endoplasmic Reticulum (ER) Stress and Activating Autophagy

Parkinson’s disease (PD) is a common neurodegenerative disease characterized the progressive loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNc). Brain endogenous morphine biosynthesis was reported to be impaired in PD patients and exogenous morphine attenuated 6-hydroxydopamine (6-OHDA)-induced cell death in vitro. However, the mechanisms underlying neuroprotection of morphine in PD are still unclear. In the present study, we investigated the neuroprotective effects of low-dose morphine in cellular and animal models of PD and the possible underlying mechanisms. Herein, we found 6-OHDA and rotenone decreased the mRNA expression of key enzymes involved in endogenous morphine biosynthesis in SH-SY5Y cells. Incubation of morphine prevented 6-OHDA-induced apoptosis, restored mitochondrial membrane potential, and inhibited the accumulation of intracellular reactive oxygen species (ROS) in SH-SY5Y cells. Furthermore, morphine attenuated the 6-OHDA-induced endoplasmic reticulum (ER) stress possible by activating autophagy in SH-SY5Y cells. Finally, oral application of low-dose morphine significantly improved midbrain tyrosine hydroxylase (TH) expression, decreased apomorphine-evoked rotation and attenuated pain hypersensitivity in a 6-OHDA-induced PD rat model, without the risks associated with morphine addiction. Feeding of low-dose morphine prolonged the lifespan and improved the motor function in several transgenic Drosophila PD models in gender, genotype, and dose-dependent manners. Overall, our results suggest that neuroprotection of low-dose morphine may be mediated by attenuating ER stress and oxidative stress, activating autophagy, and ameliorating mitochondrial function.
Efficient in planta gene targeting in Arabidopsis using egg cell‐specific expression of the Cas9 nuclease of Staphylococcus aureus

Gene targeting (GT), the programmed change of genomic sequences by homologous recombination (HR), is still a major challenge in plants. We previously developed an in planta GT strategy by simultaneously releasing from the genome a dsDNA donor molecule and creating a double-stranded break (DSB) at a specific site within the targeted gene. Using Cas9 form Streptococcus pyogenes (SpCas9) under the control of a ubiquitin gene promoter, we obtained seeds harbouring GT events, although at a low frequency. In the present research we tested different developmentally controlled promotors and different kinds of DNA lesions for their ability to enhance GT of the acetolactate synthase (ALS) gene of Arabidopsis. For this purpose, we used Staphylococcus aureus Cas9 (SaCas9) nuclease and the SpCas9 nickase in various combinations. Thus, we analysed the effect of single-stranded break (SSB) activation of a targeted gene and/or the HR donor region. Moreover, we tested whether DSBs with 5' or 3' overhangs can improve in planta GT. Interestingly, the use of the SaCas9 nuclease controlled by an egg cell-specific promoter was the most efficient: depending on the line, in the very best case 6% of all seeds carried GT events. In a third of all lines, the targeting occurred around the 1% range of the tested seeds. Molecular analysis revealed that in about half of the cases perfect HR of both DSB ends occurred. Thus, using the improved technology, it should now be feasible to introduce any directed change into the Arabidopsis genome at will.
Intravenous Thrombolysis for Stroke and Presumed Stroke in Human Immunodeficiency Virus–Infected Adults: A Retrospective, Multicenter US Study

Background and Purpose— Human immunodeficiency virus (HIV) infection has been shown to increase both ischemic and hemorrhagic stroke risks, but there are limited data on the safety and outcomes of intravenous thrombolysis with tPA (tissue-type plasminogen activator) for acute ischemic stroke in HIV-infected patients. Methods— A retrospective chart review of intravenous tPA-treated HIV patients who presented with acute stroke symptoms was performed in 7 large inner-city US academic centers (various search years between 2000 and 2017). We collected data on HIV, National Institutes of Health Stroke Scale score, ischemic stroke risk factors, opportunistic infections, intravenous drug abuse, neuroimaging findings, and modified Rankin Scale score at last follow-up. Results— We identified 33 HIV-infected patients treated with intravenous tPA (mean age, 51 years; 24 men), 10 of whom were stroke mimics. Sixteen of 33 (48%) patients had an HIV viral load less than the limit of detection while 10 of 33 (30%) had a CD4 count <200/mm3. The median National Institutes of Health Stroke Scale score at presentation was 9, and mean time from symptom onset to tPA was 144 minutes (median, 159). The median modified Rankin Scale score for the 33-patient cohort was 1 and for the 23-patient actual stroke cohort was 2, measured at a median of 90 days poststroke symptom onset. Two patients had nonfatal hemorrhagic transformation (6%; 95% confidence interval, 1%–20%), both in the actual stroke group. Two patients had varicella zoster virus vasculitis of the central nervous system, 1 had meningovascular syphilis, and 7 other patients were actively using intravenous drugs (3 cocaine, 1 heroin, and 3 unspecified), none of whom had hemorrhagic transformation. Conclusions— Most HIV-infected patients treated with intravenous tPA for presumed and actual acute ischemic stroke had no complications, and we observed no fatalities. Stroke mimics were common, and thrombolysis seems safe in this group. We found no data to suggest an increased risk of intravenous tPA-related complications because of concomitant opportunistic infections or intravenous drug abuse.