Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualization of Synchronous or Asynchronous Release of Single Synaptic Vesicle in Active-Zone-Like Membrane Formed on Neuroligin-Coated Glass Surface

Fast repetitive synaptic transmission depends on efficient exocytosis and retrieval of synaptic vesicles around a presynaptic active zone. However, the functional organization of an active zone and regulatory mechanisms of exocytosis, endocytosis and reconstruction of release-competent synaptic vesicles have not been fully elucidated. By developing a novel visualization method, we attempted to identify the location of exocytosis of a single synaptic vesicle within an active zone and examined movement of synaptic vesicle protein synaptophysin (Syp) after exocytosis. Using cultured hippocampal neurons, we induced formation of active-zone-like membranes (AZLMs) directly adjacent and parallel to a glass surface coated with neuroligin, and imaged Syp fused to super-ecliptic pHluorin (Syp-SEP) after its translocation to the plasma membrane from a synaptic vesicle using total internal reflection fluorescence microscopy (TIRFM). An AZLM showed characteristic molecular and functional properties of a presynaptic active zone. It contained active zone proteins, cytomatrix at the active zone-associated structural protein (CAST), Bassoon, Piccolo, Munc13 and RIM, and showed an increase in intracellular Ca2+ concentration upon electrical stimulation. In addition, single-pulse stimulation sometimes induced a transient increase of Syp-SEP signal followed by lateral spread in an AZLM, which was considered to reflect an exocytosis event of a single synaptic vesicle. The diffusion coefficient of Syp-SEP on the presynaptic plasma membrane after the membrane fusion was estimated to be 0.17–0.19 μm2/s, suggesting that Syp-SEP diffused without significant obstruction. Synchronous exocytosis just after the electrical stimulation tended to occur at multiple restricted sites within an AZLM, whereas locations of asynchronous release occurring later after the stimulation tended to be more scattered.
Diversity of Bacteria and the Characteristics of Actinobacteria Community Structure in Badain Jaran Desert and Tengger Desert of China

To assess the diversity of actinobacterial taxa in desert sands and obtain the novel microbial resources, 79 and 50 samples were collected from the Badain Jaran (BJD) and Tengger Deserts (TGD) of China, respectively. High-throughput sequencing (HTS) of environmental 16S rRNA genes within these samples was conducted on an Illumina Miseq platform, using universal bacterial primers targeting the V3–V4 hypervariable region. Based on the HTS analyses, cultivation-dependent (CULD) techniques were optimized to identify the cultivable Actinobacteria members. A total of 346,766 16S rRNA gene reads comprising 3,365 operational taxonomic units (OTUs) were obtained from the BJD sands using HTS, while 170,583 reads comprising 1,250 OTUs were detected in the TGD sands. Taxonomic classification indicated that Actinobacteria was the predominant phylum, comprising 35.0 and 29.4% of the communities in BJD and TGD sands, respectively. Among the Actinobacteria, members of the Geodermatophilaceae were considerably abundant in both deserts, indicating that they represent ubiquitous populations within the deserts. At the genus level, Arthrobacter spp. and Kocuria spp. were dominant, and corresponded to 21.2 and 5.3% of the actinobacterial communities in BJD and TGD deserts, respectively. A total of 786 and 376 actinobacterial strains were isolated and identified from BJD and TGD samples, respectively. The isolates comprised 73 genera of 30 families within the phylum Actinobacteria. In addition to the Geodermatophilaceae, Streptomyces spp. were a prominent component of the isolates, comprising 25% of the isolates from BJD and 17.5% of those from TGD. Comparison of the actinobacterial community structure in other ecosystems indicated that Geodermatophilaceae was the main actinobacterial group in desert sands, which is consistent with our results. Additionally, in these desert habits, Geodermatophilaceae and some other core groups may promote or inhabit the subsequent members' occurrence or prosper to shape the bacteria community structure. However, it should be noted that a number of other low-abundance bacteria appear to be specific to desert sands, which are worth further investigation. In antimicrobial activity assays, 10.36 % of the tested isolates showed antimicrobial activities in one or more screens. Importantly, 37 of the newly isolated strains reported here represent novel taxa that could be valuable resources for further research of novel secondary metabolites and their ecological significance in deserts.
Trustworthy multi-modal framework for life-critical systems security

With the advent of network connectivity and complex software applications, life-critical systems like medical devices are subject to a plethora of security risks and vulnerabilities. Security threats and attacks exploiting these vulnerabilities have been shown to compromise patient safety by hampering essential functionality. This necessitates incorporating security from the very design of software. Isolation of software functionality into different modes and switching between them based on risk assessment, while maintaining a fail-safe mode ensuring device's essential functionality is a compelling design. Formal modeling is an essential ingredient for verification of such a design. Hence, in this paper, we formally model a trustworthy multi-modal framework for life-critical systems security and in turn safety. We formalize a multiple mode based software design approach of operation with a fail-safe mode that maintains critical functionality. We ensure trustworthyness by formalizing a composite risk model incorporated into the design for run-time risk assessment and management.
Do nano-particles cause recalcitrant vulnerability curves in Robinia? Testing with a four-cuvette Cochard rotor and with water extraction curves

Cavitation resistance is a key trait for characterizing the drought adaption in plants and is usually presented in terms of vulnerability curves. Three principal techniques have been developed to produce vulnerability curves, but curves generated with centrifugation are reported to suffer from artifacts when applied to long-vesseled species. The main cause of this artifact is the issue of open vessels, resulting in a nano-particle effect that may seed premature embolism. We used two methods to test the potential mechanism behind the nano-particle effect in centrifuge-based vulnerability curves. A four-cuvette rotor system based on a traditional Cochard rotor was designed to inhibit effervescence while injecting water, but the recalcitrant vulnerability curves in Robinia could not be eliminated. There may be multiple sources, besides effervescence, of hypothetical nano-particles: they may arise from cut surfaces or they may be always present in the injected water, leading to the premature embolisms. To prevent the entry of the hypothetical nano-particles, water extraction curves in terms of PLV (percentage loss volume of extracted water from stems) vs tensions were constructed. The PLV curves of Robinia showed s-shaped characteristics after subtracting the first Weibull components from water extraction curves, which were not related to the water loss from vessels according to dye staining experiments. The differences between T50 (xylem tension at which 50% of hydraulic conductivity is lost) in mean PLV curve and T50 in percentage loss of conductivity curves determined by the four-cuvette rotor system and by the bench dehydration method were 3.9 MPa and 0.7 MPa, respectively. Hence, PLV curves may be a valid way to measure the cavitation resistance in long-vesseled species with centrifugation. Keeping bark intact in the process of measurement is recommended, otherwise it would increase evaporation from the entire system.
Skeleton-based region competition for automated gray matter and white matter segmentation of human brain MR images

Image segmentation is an essential process for quantitative analysis. Segmentation of brain tissues in magnetic resonance (MR) images is very important for understanding the structural-functional relationship for various pathological conditions, such as dementia vs. normal brain aging. Different brain regions are responsible for certain functions and may have specific implication for diagnosis. Segmentation may facilitate the analysis of different brain regions to aid in early diagnosis. Region competition has been recently proposed as an effective method for image segmentation by minimizing a generalized Bayes/MDL criterion. However, it is sensitive to initial conditions -- the "seeds", therefore an optimal choice of “seeds” is necessary for accurate segmentation. In this paper, we present a new skeleton-based region competition algorithm for automated gray and white matter segmentation. Skeletons can be considered as good "seed regions" since they provide the morphological a priori information, thus guarantee a correct initial condition. Intensity gradient information is also added to the global energy function to achieve a precise boundary localization. This algorithm was applied to perform gray and white matter segmentation using simulated MRI images from a realistic digital brain phantom. Nine different brain regions were manually outlined for evaluation of the performance in these separate regions. The results were compared to the gold-standard measure to calculate the true positive and true negative percentages. In general, this method worked well with a 96% accuracy, although the performance varied in different regions. We conclude that the skeleton-based region competition is an effective method for gray and white matter segmentation.
Alterations in Cellular Iron Metabolism Provide More Therapeutic Opportunities for Cancer

Iron is an essential element for the growth and proliferation of cells. Cellular iron uptake, storage, utilization and export are tightly regulated to maintain iron homeostasis. However, cellular iron metabolism pathways are disturbed in most cancer cells. To maintain rapid growth and proliferation, cancer cells acquire large amounts of iron by altering expression of iron metabolism- related proteins. In this paper, normal cellular iron metabolism and the alterations of iron metabolic pathways in cancer cells were summarized. Therapeutic strategies based on targeting the altered iron metabolism were also discussed and disrupting redox homeostasis by intracellular high levels of iron provides new insight for cancer therapy. Altered iron metabolism constitutes a promising therapeutic target for cancer therapy.
The Evolution of Genetics Alzheimer and Parkinson diseases

Genetic discoveries underlie the majority of the current research and thinking in neurodegenerative disease. This influence stretches from our basic notions of the etiologic architecture of these diseases through to the identification of both viable therapeutic targets and the populations in whom these therapies should be applied. In large part this work has been driven by the significant gains made in identifying causal mutations, even when these have been rare causes of disease; however, the translation of genetic causes of disease into pathobiological understanding remains a considerable challenge. While there have been some successes in this regard, providing therapeutic targets in prominent diseases such as Parkinson’s disease and Alzheimer’s disease, the absence of an effective treatment shows that more needs to be done. Geneticists continue to make progress in monogenic forms of disease, and this is increasingly facilitated by the application of a second generation of genetics methods. These methods also allow the dissection of moderate and mild genetic risk factors for disease, an area that had previously resisted systematic investigation. This raises several challenges and requires new thinking in two key areas: what constitutes proof of pathogenicity, and how do we translate these findings to biological understanding. Here we describe the progress that has been made thus far in genetics, and the ongoing evolution of this field; for illustration we use examples of progress in Parkinson’s disease and Alzheimer’s disease. We describe a changing view that rejects the tradition that genetic proof has to be absolute before functional characterization, and centers on a multi dimensional approach that integrates genetics, reference data, and functional work. This effort aims to simultaneously prove pathogenicity and understand the disease process. We also argue that in large part, the initial functional challenges cannot be efficiently met by traditional mechanistic hypothesis driven methods, but that high content system wide efforts are required.
MicroRNA-133a impairs perfusion recovery after hindlimb ischemia in diabetic mice

Objective: Peripheral arterial disease (PAD) patients with diabetes mellitus suffer from impaired neovascularization after ischemia which results in poorer outcomes. MicroRNA (miR)-133a is excessively expressed in endothelial cells under diabetic conditions. Here, we test whether diabetes-induced miR-133a up-regulation is involved in the impaired capability of neovascularization in experimental PAD models. Methods and results: MiR-133a level was measured by quantitative RT-PCR and showed a higher expression level in the ischemic muscle from diabetic mice when compared with nondiabetic mice. Knockdown of miR-133a using antagomir improved perfusion recovery and angiogenesis in experimental PAD model with diabetes day 21 after HLI. On the other hand, overexpression of miR-133a impaired perfusion recovery. Ischemic muscle was harvested day 7 after experimental PAD for biochemical test, miR-133a antagonism resulted in reduced malondialdehyde, and it increased GTP cyclohydrolase 1 (GCH1), and cyclic guanine monophosphate (cGMP) levels. In cultured endothelial cells, miR-133a antagonism resulted in reduced reactive oxygen species level, and it increased tube formation, nitric oxide (NO), and cGMP level. Moreover, miR-133a antagonism-induced angiogenesis was abolished by GCH1 inhibitor. In contrary, miR-133a overexpression impairs angiogenesis and it reduces GCH1, NO, and cGMP levels in nondiabetic models. Conclusion: Diabetes mellitus-induced miR-133a up-regulation impairs angiogenesis in PAD by reducing NO synthesis in endothelial cells. MiR-133a antagonism improves postischemic angiogenesis.
Testing a longitudinal compensation model in premanifest Huntington’s disease

Owing to compensatory processes, the initial stages of neurodegeneration are marked by normal performance despite the presence of pathology. Using their explicit mathematical model, Gregory et al. report the first empirical examination of compensation over time in neurodegeneration, showing evidence of motor and cognitive compensation in a Huntington’s disease cohort.
Sleep duration and mortality – Does weekend sleep matter?

Previous studies have found a U‐shaped relationship between mortality and (weekday) sleep duration. We here address the association of both weekday and weekend sleep duration with overall mortality. A cohort of 43,880 subjects was followed for 13 years through record‐linkages. Cox proportional hazards regression models with attained age as time‐scale were fitted to estimate multivariable‐adjusted hazard ratios and 95% confidence intervals for mortality; stratified analyses on age (<65 years, ≥65 years) were conducted. Among individuals <65 years old, short sleep (≤5 hr) during weekends at baseline was associated with a 52% higher mortality rate (hazard ratios 1.52; 95% confidence intervals 1.15–2.02) compared with the reference group (7 hr), while no association was observed for long (≥9 hr) weekend sleep. When, instead, different combinations of weekday and weekend sleep durations were analysed, we observed a detrimental association with consistently sleeping ≤5 hr (hazard ratios 1.65; 95% confidence intervals 1.22–2.23) or ≥8 hr (hazard ratios 1.25; 95% confidence intervals 1.05–1.50), compared with consistently sleeping 6–7 hr per day (reference). The mortality rate among participants with short sleep during weekdays, but long sleep during weekends, did not differ from the rate of the reference group. Among individuals ≥65 years old, no association between weekend sleep or weekday/weekend sleep durations and mortality was observed. In conclusion, short, but not long, weekend sleep was associated with an increased mortality in subjects <65 years. In the same age group, short sleep (or long sleep) on both weekdays and weekend showed increased mortality. Possibly, long weekend sleep may compensate for short weekday sleep.
Tumor-Infiltrating Lymphocytes in Patients Receiving Trastuzumab/Pertuzumab-Based Chemotherapy: A TRYPHAENA Substudy

Background There is an urgent requirement to identify biomarkers to tailor treatment in human epidermal growth factor receptor 2 (HER2)-amplified early breast cancer treated with trastuzumab/pertuzumab-based chemotherapy. Methods Among the 225 patients randomly assigned to trastuzumab/pertuzumab concurrently or sequentially with an anthracycline-containing regimen or concurrently with an anthracycline-free regimen in the Tryphaena trial, we determined the percentage of tumor-infiltrating lymphocytes (TILs) at baseline in 213 patients, of which 126 demonstrated a pathological complete response (pCR; ypT0/is ypN0), with 28 demonstrating event-free survival (EFS) events. We investigated associations between baseline TIL percentage and either pCR or EFS after adjusting for clinicopathological characteristics using logistic and Cox regression models, respectively. To understand TIL biology, we evaluated associations between baseline TILs and baseline tumor gene expression data (800 gene set by NanoString) in a subset of 173 patients. All statistical tests were two-sided. Results Among the patients with measurable TILs at baseline, the median level was 14.1% (interquartile range = 7.1%-32.4%). After adjusting for clinicopathological characteristics, baseline percentage TIL was not associated with pCR (adjusted odds ratio [aOR] for every 10-percentage unit increase in TILs = 1.12, 95% confidence interval [CI] = 0.95 to 1.31, P = .17). At a median follow-up of 4.7 years, for every increase in baseline TILs of 10%, there was a 25% reduction in the hazard for an EFS event (aOR = 0.75, 95% CI = 0.56 to 1.00, P = .05) after adjusting for baseline clinicopathological characteristics and pCR. Additionally, genes associated with epithelial-mesenchymal transition, angiogenesis, and T-cell inhibition such as SNAIL1, ZEB1, NOTCH3, and B7-H3 were statistically significantly inversely correlated with percentage TIL. Conclusions Baseline TIL percentage provides independent prognostic information in patients treated with trastuzumab/pertuzumab-based neoadjuvant chemotherapy. However, further validation is required.
Load-pull measurement of transistor negative input impedance

This paper presents a measurement-based way of forecasting some transistor's nonlinear effects. For some particular output impedances of the passive load-pull setup, a strange behavior of the Pout/Pin slopes can be obtained. Thanks to the LSNA, the non linear input impedance can be measured, it is useful to explain this phenomenon. The time domain slopes of a GaN HEMT up to 3.5 W/mm are proposed at these particular loci.
Multiple Causal Inference with Latent Confounding

Causal inference from observational data requires assumptions. These assumptions range from measuring confounders to identifying instruments. Traditionally, causal inference assumptions have focused on estimation of effects for a single treatment. In this work, we construct techniques for estimation with multiple treatments in the presence of unobserved confounding. We develop two assumptions based on shared confounding between treatments and independence of treatments given the confounder. Together, these assumptions lead to a confounder estimator regularized by mutual information. For this estimator, we develop a tractable lower bound. To recover treatment effects, we use the residual information in the treatments independent of the confounder. We validate on simulations and an example from clinical medicine.
Sequence Domain SISO Equivalent Models of a Grid-Tied Voltage Source Converter System for Small-Signal Stability Analysis

This paper presents a generalized method for converting multi-input and multi-output (MIMO) <inline-formula> <tex-math notation="LaTeX">$dq$</tex-math></inline-formula> impedance model of a grid-tied voltage source converter system into its sequence domain single-input and single-output (SISO) equivalents. As a result, two types of SISO impedance models were derived, one of which was derived from relatively strong and <inline-formula> <tex-math notation="LaTeX">$dq$</tex-math></inline-formula> symmetric grid assumption (reduced SISO model) and the other was based on closed-loop equivalent (accurate SISO model). It was proven that the accurate SISO model has the same marginal stability condition as the MIMO model. Accuracy of these models is assessed with respect to the measured impedances in PSCAD/EMTDC simulations, their effects on stability are analyzed as well. Findings show that the accurate SISO model presents identical stability conclusions as the MIMO model. However, the reduced SISO model may lead to inaccurate results if the system is highly <italic><inline-formula><tex-math notation="LaTeX">${\rm{dq}}$ </tex-math></inline-formula></italic> asymmetric, e.g., VSC with fast phase-locked loop or an actively controlled grid.
The Mauthner cell in a fish with top-performance and yet flexibly tuned C-starts. II. Physiology

ABSTRACT The parallel occurrence in archerfish of fine-tuned and yet powerful predictive C-starts as well as of kinematically identical escape C-starts makes archerfish an interesting system to test hypotheses on the roles played by the Mauthner cells, a pair of giant reticulospinal neurons. In this study, we show that the archerfish Mauthner cell shares all hallmark physiological properties with that of goldfish. Visual and acoustic inputs are received by the ventral and lateral dendrite, respectively, and cause complex postsynaptic potentials (PSPs) even in surgically anaesthetised fish. PSP shape did not indicate major differences between the species, but simple light flashes caused larger PSPs in archerfish, often driving the cell to fire an action potential. Probing archerfish in the classical tests for feedback inhibition, established in the Mauthner-associated networks in goldfish, revealed no differences between the two species, including the indications for electrical and chemical synaptic components. Also, the established hallmark experiments on feed-forward inhibition showed no differences between the goldfish and archerfish Mauthner system. Extending these experiments to visual stimuli also failed to detect any differences between the two species and suggested that acoustical and visual input cause feed-forward inhibition, the magnitude, time course and duration of which match that of the respective PSPs in both archerfish and goldfish. Our findings question simple views on the role of the Mauthner cell and suggest that the archerfish Mauthner cell should be a good system to explore the function of these giant neurons in more sophisticated C-start behaviours. Summary: The archerfish Mauthner neuron does not differ from that of goldfish in any hallmark physiological properties, a finding that questions current views on the role of these giant reticulospinal cells.