Prevalence and detection of low-allele-fraction variants in clinical cancer samples

Accurate detection of genomic alterations using high-throughput sequencing is an essential component of precision cancer medicine. We characterize the variant allele fractions (VAFs) of somatic single nucleotide variants and indels across 5095 clinical samples profiled using a custom panel, CancerSCAN. Our results demonstrate that a significant fraction of clinically actionable variants have low VAFs, often due to low tumor purity and treatment-induced mutations. The percentages of mutations under 5% VAF across hotspots in EGFR, KRAS, PIK3CA, and BRAF are 16%, 11%, 12%, and 10%, respectively, with 24% for EGFR T790M and 17% for PIK3CA E545. For clinical relevance, we describe two patients for whom targeted therapy achieved remission despite low VAF mutations. We also characterize the read depths necessary to achieve sensitivity and specificity comparable to current laboratory assays. These results show that capturing low VAF mutations at hotspots by sufficient sequencing coverage and carefully tuned algorithms is imperative for a clinical assay

25th annual computational neuroscience meeting: CNS-2016

The same neuron may play different functional roles in the neural circuits to which it belongs. For example, neurons in the Tritonia pedal ganglia may participate in variable phases of the swim motor rhythms [1]. While such neuronal functional variability is likely to play a major role the delivery of the functionality of neural systems, it is difficult to study it in most nervous systems. We work on the pyloric rhythm network of the crustacean stomatogastric ganglion (STG) [2]. Typically network models of the STG treat neurons of the same functional type as a single model neuron (e.g. PD neurons), assuming the same conductance parameters for these neurons and implying their synchronous firing [3, 4]. However, simultaneous recording of PD neurons shows differences between the timings of spikes of these neurons. This may indicate functional variability of these neurons. Here we modelled separately the two PD neurons of the STG in a multi-neuron model of the pyloric network. Our neuron models comply with known correlations between conductance parameters of ionic currents. Our results reproduce the experimental finding of increasing spike time distance between spikes originating from the two model PD neurons during their synchronised burst phase. The PD neuron with the larger calcium conductance generates its spikes before the other PD neuron. Larger potassium conductance values in the follower neuron imply longer delays between spikes, see Fig. 17.Neuromodulators change the conductance parameters of neurons and maintain the ratios of these parameters [5]. Our results show that such changes may shift the individual contribution of two PD neurons to the PD-phase of the pyloric rhythm altering their functionality within this rhythm. Our work paves the way towards an accessible experimental and computational framework for the analysis of the mechanisms and impact of functional variability of neurons within the neural circuits to which they belong

Cavity-dumped femtosecond optical parametric oscillator based on periodically poled stoichiometric lithium tantalate

A synchronously pumped cavity-dumped femtosecond optical parametric oscillator (OPO) based on a periodically poled stoichiometric lithium tantalate (PPSLT) crystal is reported. The OPO runs in positive group velocity dispersion (GVD) mode to deliver high pulse energy at high repetition rate. It delivers pulse energy over 130 nJ up to 500 kHz and 70 nJ at 1 MHz of repetition rate at 1100 nm. Pulse duration is as short as 42 fs, and the OPO is tunable in the near infrared region from 1050 to 1200 nm. Dispersion property of the OPO was also explored. The cavity-dumped output carries a positive GVD, which can be compensated easily by an external prism pair, and large negative third order dispersion (TOD), which results in a pedestal in the pulse shape. Approaches to obtain clean pulse shape by reducing the large TOD are proposed.111Nsciescopu

Vestibular syncope: clinical characteristics and mechanism

Background and Objectives: Vestibular syncope is a condition in which vertigo-induced hemodynamic changes cause syncope. This study investigated the clinical and laboratory findings of vestibular syncope and tried to refine our knowledge of the mechanism underlying this newly recognized entity. Methods: This study retrospectively analyzed 53 patients (33 women, median age = 63 years [interquartile range = 54-71 years]) with vestibular syncope from January 2017 to December 2021. To explain the mechanism of vestibular syncope, we incorporated a velocity-storage model into the dual reflex pathways comprising the vestibulo-sympathetic reflex and baroreflex and predicted the cardiovascular responses. Results: Twenty (37.7%) patients had multiple episodes of vestibular syncope, and seven (13.2%) had potentially life-threatening injuries. Meniere's disease (20.8%) and benign paroxysmal positional vertigo (9.4%) were the most common underlying vestibular disorders. Abnormal vestibular function tests included impaired cervical vestibular-evoked myogenic potentials (57.5%) and positive head impulse tests (31.0%). Orthostatic hypotension was found in 19.5% of patients. Dyslipidemia (30.2%) and hypertension (28.3%) were common medical comorbidities. The dual reflex pathways incorporating the function of the velocity-storage circuit in the brainstem and cerebellum suggest that vestibular syncope is a neurally mediated reflex syncope associated with a sudden hemodynamic change during vertigo. This change can be arterial hypertension triggered by a false downward inertial cue, as suggested previously, or hypotension driven by a false upward inertial cue. Conclusions: Vestibular syncope is associated with various vestibular disorders and requires careful evaluation and intervention to prevent recurrent falls and significant injuries.N

Retrieval of frequency spectrum from time-resolved spectroscopic data: comparison of Fourier transform and linear prediction methods

Femtosecond time-resolved signals often display oscillations arising from the nuclear and electronic wave packet motions. Fourier power spectrum is generally used to retrieve the frequency spectrum. We have shown by numerical simulations and coherent phonon spectrum of single walled carbon nanotubes (SWCNT) that the Fourier power spectrum may not be appropriate to obtain the spectrum, when the peaks overlap with varying phases. Linear prediction singular value decomposition (LPSVD) can be a good alternative for this case. We present a robust way to perform LPSVD analysis and demonstrate the method for the chirality assignment of SWCNT through the time-domain coherent phonon spectroscopy.X1133sciescopu

Cisplatin Induces Overactivation of the Dormant Primordial Follicle through PTEN/AKT/FOXO3a Pathway which Leads to Loss of Ovarian Reserve in Mice.

Cisplatin is a first-line chemotherapeutic agent for ovarian cancer that acts by promoting DNA cross links and adduct. However drug resistance and considerable side effects including reproductive toxicity remain a significant challenge. PTEN is well known as a tumor suppressor function which plays a fundamental role in the regulation of the cell cycle, apoptosis and development of cancer. At the same time PTEN has been revealed to be critically important for the maintenance of the primordial follicle pool. In this study, we investigated the role of PTEN/Akt/FOXO3 pathway in cisplatin-induced primordial follicle depletion. Cisplatin induced ovarian failure mouse model was used to evaluate how this pathway involves. In vitro maturation was used for oocyte rescue after cisplatin damage. We found that cisplatin treatment decreased PTEN levels, leading to a subsequent increase in the phosphorylation of key molecules in the pathway. The activation of the PTEN/Akt/FOXO3 pathway cascade increased cytoplasmic translocation of FOXO3a in cisplatin-treated follicles, which in turn increased the pool size of growing follicles, and rapidly depleted the number of dormant follicles. Once activated, the follicles were more prone to apoptosis, and their cumulus cells showed a loss of luteinizing hormone (LH) receptor expression, which leads to failure during final maturation and ovulation. In vitro maturation to rescue oocytes in a cisplatin-treated mouse model resulted in successful maturation and fertilization. This study is the first to show the involvement of the PTEN/Akt/FOXO3 pathway in premature ovarian failure after cisplatin treatment and the possibility of rescue through in vitro maturation

Bojungikgi-Tang, a Traditional Herbal Formula, Exerts Neuroprotective Effects and Ameliorates Memory Impairments in Alzheimer’s Disease-Like Experimental Models

Bojungikgi-tang (BJIGT; Bu Zhong Yi Qi Tang in China, Hochuekkito in Japan) is a traditional Oriental herbal formula comprised of eight medicinal herbs that has long been used for the treatment of digestive disorders. A recent clinical study from South Korea reported that BJIGT-gamibang administration may be effective in treating dementia. We aimed to establish scientific evidence for the anti-dementia effects of BJIGT using in vitro and in vivo experimental models. We measured amyloid- β (Aβ) aggregation, β-secretase (BACE), and antioxidant activity in a cell free system. Neuroprotective effects were assessed using CCK-8. Imprinting control region (ICR) mice were divided into the following six groups: Normal control, Aβ-injected, Aβ-injection + oral BJIGT gavage (200, 400, or 800 mg/kg/day), and Aβ-injection + oral morin administration (10 mg/kg/day). Subsequently, behavioral evaluations were conducted and brain samples were collected from all the animals and assessed. BJIGT enhanced inhibition of Aβ aggregation and BACE activity in vivo, as well as antioxidant activity in in vitro, cell-free systems. BJIGT also exerted neuroprotective effects in a hydroperoxide (H2O2)-induced damaged HT22 hippocampal cell line model. In addition, BJIGT administration significantly ameliorated cognitive impairments in Aβ-injected mice, as assessed by the passive avoidance and Y-maze tests. Furthermore, BJIGT treatment suppressed Aβ aggregation and expression, as well as expression of Aβ, NeuN, and brain-derived neurotrophic factor (BDNF) in the hippocampi of Aβ-injected mice. Overall, our results demonstrate that, with further testing in clinical populations, BJIGT may have great utility for the treatment of dementia and especially Alzheimer’s disease

Inferior divisional oculomotor nerve palsy due to orbital lymphoma

Y

High-Frequency Wave Generation in Magnetotail Reconnection : Nonlinear Harmonics of Upper Hybrid Waves

MMS3 spacecraft passed the vicinity of the electron diffusion region of magnetotail reconnection on 3 July 2017, observing discrepancies between perpendicular electron bulk velocities and (E) over right arrow x (B) over right arrow drift, and agyrotropic electron crescent distributions. Analyzing linear wave dispersions, Burch et al. (2019, https://doi.org/10.1029/2019GL082471) showed the electron crescent generates high-frequency waves. We investigate harmonics of upper-hybrid (UH) waves using both observation and particle-in-cell (PIC) simulation, and the generation of electromagnetic radiation from PIC simulation. Harmonics of UH are linearly polarized and propagate along the perpendicular direction to the ambient magnetic field. Compared with two-dimensional PIC simulation and nonlinear kinetic theory, we show that the nonlinear beam-plasma interaction between the agyrotropic electrons and the core electrons generates harmonics of UH. Moreover, PIC simulation shows that agyrotropic electron beam can lead to electromagnetic (EM) radiation at the plasma frequency and harmonics