Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxonium Ion-Guided Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro

Spatial separation of ions in the gas-phase, providing information about their size as collisional cross-sections, can readily be achieved through ion mobility. The timsTOF Pro series combines a trapped ion mobility device with a quadrupole, collision-cell and a time-of-flight analyser to enable the analysis of ions at great speed. Here, we show that the timsTOF Pro is capable of physically separating N-glycopeptides from non-modified peptides and producing high-quality fragmentation spectra, both beneficial for glycoproteomics analyses of complex samples. The glycan moieties enlarge the size of glycopeptides compared to non-modified peptides, yielding a clear cluster in the mobilogram that, next to increased dynamic range from the physical separation of glycopeptides and non-modified peptides, can be used to make an effective selection filter for directing the mass spectrometer to analytes of interest. This new approach was applied to selected glycoproteins, human plasma- and neutrophil-derived glycopeptides. We show that the achieved physical separation, combined with the focussing of the mass spectrometer, allows for improved extraction of information from the samples, even at shorter LC gradients of 15 min. We validated our approach on human neutrophil and plasma samples of known make-up, in which we captured the anticipated glycan heterogeneity (paucimannose, phosphomannose, high mannose, hybrid and complex glycans) from plasma and neutrophil samples at the expected abundances. As the method is compatible with off-the-shelve data acquisition routines and data analysis software, it can readily be applied by any laboratory with a timsTOF Pro and is reproducible as demonstrated by a comparison between two laboratories.
Dendrite architecture determines mitochondrial distribution patterns in vivo

Mitochondria are critical for neuronal function and must be reliably distributed through complex neuronal architectures. By quantifying in vivo mitochondrial transport and localization patterns in the dendrites of Drosophila visual system neurons, we show that mitochondria make up a dynamic system at steady-state, with significant transport of individual mitochondria within a stable global pattern. Mitochondrial motility patterns are unaffected by visual input, suggesting that neuronal activity does not directly regulate mitochondrial localization in vivo. Instead, we present a mathematical model in which four simple scaling rules enable the robust self-organization of the mitochondrial population. Experimental measurements of dendrite morphology validate key model predictions: to maintain equitable distribution of mitochondria across asymmetrically branched subtrees, dendritic branch points obey a parent-daughter power law that preserves cross-sectional area, and thicker trunks support proportionally bushier subtrees. Altogether, we propose that “housekeeping” requirements, including the need to maintain steady-state mitochondrial distributions, impose constraints on neuronal architecture.
Decoupling of interacting neuronal populations by time-shifted stimulation through spike-timing-dependent plasticity

The synaptic organization of the brain is constantly modified by activity-dependent synaptic plasticity. In several neurological disorders, abnormal neuronal activity and pathological synaptic connectivity may significantly impair normal brain function. Reorganization of neuronal circuits by therapeutic stimulation has the potential to restore normal brain dynamics. Increasing evidence suggests that the temporal stimulation pattern crucially determines the long-lasting therapeutic effects of stimulation. Here, we tested whether a specific pattern of brain stimulations can enable the suppression of pathologically strong inter-population synaptic connectivity through spike-timing-dependent plasticity (STDP). More specifically, we tested how introducing a time shift between stimuli delivered to two interacting populations of neurons can effectively decouple them. To that end, we first used a tractable model, i.e., two bidirectionally coupled leaky integrate-and-fire (LIF) neurons, to theoretically analyze the optimal range of stimulation frequency and time shift for decoupling. We then extended our results to two reciprocally connected neuronal populations (modules) where inter-population delayed connections were modified by STDP. As predicted by the theoretical results, appropriately time-shifted stimulation causes a decoupling of the two-module system through STDP, i.e., by unlearning pathologically strong synaptic interactions between the two populations. Based on the overall topology of the connections, the decoupling of the two modules, in turn, causes a desynchronization of the populations that outlasts the cessation of stimulation. Decoupling effects of the time-shifted stimulation can be realized by time-shifted burst stimulation as well as time-shifted continuous simulation. Our results provide insight into the further optimization of a variety of multichannel stimulation protocols aiming at a therapeutic reshaping of diseased brain networks.
Reciprocal recurrent selection based on genetic complementation: An efficient way to build heterosis in diploids due to directional dominance

Depending on the trait architecture and reproduction system, selection strategies in plant breeding focus on the accumulation of additive, dominance effects, or both. Innovation in the accumulation of dominance-effect-based heterosis has been limited since the proposal of GCA-based approaches and very few strategies to exploit it better have been proposed. We propose the use of a new surrogate of genetic complementation between genetic pools to increase accumulation of dominance effects and heterosis. We simulated breeding programs to show how reciprocal recurrent selection by genetic complementation would build the dominance-based heterosis but cheaper than GCA-based approaches and used real phenotypic data from hybrid maize to demonstrate the underlying concepts. We found reciprocal recurrent selection by genetic complementation to be an attractive and viable strategy to exploit dominance, build de novo heterotic pools and boost the current GCA-based approaches. If demonstrated in practice, we hypothesized that this approach would lower the cost of breeding drastically and contribute to food security. Key message Heterotic patterns can be developed quickly through genetic complementation surrogates to produce high-performance hybrids at a low cost in diploid species displaying dominance and boost GCA-based approaches in hybrid breeding.
StudentSADD

The growing prevalence of depression and suicidal ideation among college students further exacerbated by the Coronavirus pandemic is alarming, highlighting the need for universal mental illness screening technology. With traditional screening questionnaires too burdensome to achieve universal screening in this population, data collected through mobile applications has the potential to rapidly identify at-risk students. While prior research has mostly focused on collecting passive smartphone modalities from students, smartphone sensors are also capable of capturing active modalities. The general public has demonstrated more willingness to share active than passive modalities through an app, yet no such dataset of active mobile modalities for mental illness screening exists for students. Knowing which active modalities hold strong screening capabilities for student populations is critical for developing targeted mental illness screening technology. Thus, we deployed a mobile application to over 300 students during the COVID-19 pandemic to collect the Student Suicidal Ideation and Depression Detection (StudentSADD) dataset. We report on a rich variety of machine learning models including cutting-edge multimodal pretrained deep learning classifiers on active text and voice replies to screen for depression and suicidal ideation. This unique StudentSADD dataset is a valuable resource for the community for developing mobile mental illness screening tools.
The relationships between "augmented reality" and inclusive education in higher education

INTRODUCTION. Augmented reality is little by little becoming incorporated in the area of inclusive education as an emergent technology that fosters learning through discovery and experience by all in equal terms. METHOD. The study used a quasi-experimental design and a small sample of N=41 students enrolled in the Inclusive Education Master’s program, who were provided with an ad hoc-designed questionnaire —composed of 31 items and with a Likert-type response scale with 5 options—. The student’s opinions were used to answer if augmented reality could be used in the area of inclusive education. For this, an initial evaluation of their opinion on the subject matter was conducted —pre-test—, and afterwards an intervention was conducted in which they were exposed to the content and a variety of tasks linked to the subject matter. Once finished, they were provided with the questionnaire once again, for the post-test. RESULTS. The results achieved after the descriptive and inferential studies showed that augmented reality could be used to foster group and collaborative work in inclusive environments, and it can possibly be used with subjects who have diverse disabilities, as well as within inter and multicultural spheres. DISCUSSION. Augmented reality has possibilities for being used in inclusive education in general, and specifically for the development of the school curriculum. It might not be able to be used with subjects that have visual disabilities, and likewise it might not be able to be used to prevent cases of bullying at school, but it can emphasize the digital divide of the individuals.
Development of Window-Mounted Air Cap Roller Module

While previous research has shown the use of attachable air-caps on windows to efficiently reduce a building’s energy consumption, the air-caps considered had to be attached to the entire window’s surface, thus limiting the occupants’ view and creating the inconvenience of needing to detach and attach the air-caps. In this study, a window-mounted air-cap roller module using Velcro tape that may be easily attached, detached, and rolled up or down was developed and performance tested in a full-scale test bed. It was found that as the area of the air-caps attached on a window increased, the required indoor lighting energy increased. However, the window insulation improved, thus reducing the cooling and heating energy needed. Attaching the air-caps to the entire window surface effectively reduced the building’s energy consumption, but views through the window may be disturbed. Thus, the developed window-mounted air-caps enable an occupant to reduce the building energy consumption and maintain their view according to their need. The findings of this study may contribute to a reduction in building energy consumption without sacrificing a pleasant indoor environment. Further studies may be needed to verify their efficacy under varying indoor and outdoor conditions.
Real options models and analyses for energy transportation systems with jump and diffusion processes: Electric power transmission planning and fuel-carrying ship design

Investments in transportation sector have arisen as significant problems due to the substantial cost of maintaining required level of service. Energy transportation draws a particular attention. In this dissertation, we focus on two special forms of energy transportation problems. On the one hand, we study the quantification of value of expansion investments in high-voltage power lines. On the other hand, we quantify the value of expansion of capacities for U.S. Navy transportation ships. Problems are subject to severe uncertainties being in the form of smooth changes and discrete disruptions. We use geometric Brownian motion and Poisson arrival processes to model both types of evolutions, respectively. We utilize real options approach to quantify the values of expansion options and provide decision makers with managerial insights. My dissertation consists of three papers. In the first paper, we quantify the value of expansion options in transmission lines. Revenue of the investment is calculated based on differences between locational marginal prices. This research reveals that the proportion of susceptance of a power line to its power-carrying capacity is a significant factor to determine the value of an expansion investment. In the second paper, we quantify the value of option to expand the capacity of a U.S. Navy transportation ship. Decision maker can either choose flexible design (relatively more prepared for expansion) or fixed design at initial design phase. Our study indicates that flexible design should be preferred over fixed design if initial demand (for transported item) value is relatively lower. Third paper revisits transmission expansion problem and adopts installation of local generators as an uncertainty in the form of discrete disruption. It shows that the value of transmission network does not always reduce with the installation, instead location of the installation plays a key role.
Comparison of nondestructive testing techniques for the inspection of wind turbine blades' spar caps

Physics Department, University of Massachusetts Lowell, 1 University Avenue, Lowell 01854MA, USA Department of Mechanical Engineering, University of Massachusetts Lowell, 1 University Avenue, Lowell 01854MA, USA Composites Engineering Research Laboratory, TechPlace, 74 Orion Street, Brunswick 04011ME, USA Correspondence Robert W. Martin, Physics Department, University of Massachusetts Lowell, 1 University Avenue, Lowell, 01854 MA, USA. Email: robert_martin1@student.uml. edu Funding information National Science Foundation, Grant/Award Number: IIP‐1362022
Discrete Optimization in Architecture: Architectural & Urban Layout

This book presents three projects that demonstrate the fundamental problems of architectural design and urban composition the layout design, evaluation and optimization. Part I describes the functional layout design of a residential building, and an evaluation of the quality of a town square (plaza). The algorithm for the functional layout design is based on backtracking using a constraint satisfaction approach combined with coarse grid discretization. The algorithm for the town square evaluation is based on geometrical properties derived directly from its plan. Part II introduces a crowd-simulation application for the analysis of escape routes on floor plans, and optimization of a floor plan for smooth crowd flow. The algorithms presented employ agent-based modeling and cellular automata.
Impact of Surgery on Non-Functional Pancreatic Neuroendocrine Tumors ≤2 cm: Analyses With Propensity Score–Based Inverse Probability of Treatment Weighting

Purpose The impact of surgery on non-functional pancreatic neuroendocrine tumors (NF-PNETs) ≤2 cm is controversial. This study sought to demonstrate the impact of surgery on the prognosis of NF-PNETs ≤2 cm with different biological behaviors. Methods Patients with NF-PNETs ≤2 cm from 2004 to 2015 in the Surveillance, Epidemiology, and End Results database were included in this study. An inverse probability of treatment weighting (IPTW) method was used to reduce the selection bias. Kaplan–Meier survival analysis and Cox proportional hazards regression were used to evaluate the effect of surgery on the prognosis. Results In the IPTW-adjusted Cox proportional hazards regression analysis, surgery improved the cancer-specific survival (CSS) in the overall cohort (hazard ratio [HR], 0.187; 95% confidence interval [CI], 0.102–0.343; p < 0.001), patients with poorly differentiated or undifferentiated tumor grades (HR, 0.238; 95% CI, 0.105–0.64; p < 0.001), patients with distant metastasis (HR, 0.102; 95% CI, 0.021–0.496; p = 0.005), and patients with local invasion (HR, 0.059; 95% CI, 0.005–0.683; p = 0.002). Surgery did not improve the CSS in patients with lymph node metastasis only (HR, 0.26; 95% CI, 0.0462–1.461; p = 0.126) or patients with well or moderate differentiation while without distant and lymph node metastasis (HR, 0.387; 95% CI, 0.146–1.028; p = 0.057). Conclusions Among patients with NF-PNETs ≤2 cm, different biological behaviors correlate with different prognostic impacts of surgery. As long as distant metastasis does not occur and the grade is well–moderately differentiated, these patients will not benefit from surgery no matter whether lymph node metastasis occurs or not. However, when local invasion appears in this group of patients, surgery should be performed. Moreover, patients with a tumor grade of poorly differentiated or undifferentiated or those with distant metastases may benefit from surgery.
Equine Histoplasmosis in Ethiopia: Phylogenetic Analysis by Sequencing of the Internal Transcribed Spacer Region of rRNA Genes

Equine histoplasmosis commonly known as epizootic lymphangitis (EL) is a neglected granulomatous disease of equine that is endemic to Ethiopia. It is caused by Histoplasma capsulatum variety farciminosum, a dimorphic fungus that is closely related to H. capsulatum variety capsulatum. The objective of this study was to undertake a phylogenetic analysis of H. capsulatum isolated from EL cases of horses in central Ethiopia and evaluate their relationship with H. capsulatum isolates in other countries and/or clades using the internal transcribed spacer (ITS) region of rRNA genes. Clinical and mycological examinations, DNA extraction, polymerase chain reaction (PCR), Sanger sequencing, and phylogenetic analysis were used for undertaking this study. Additionally, sequence data of Histoplasma isolates were retrieved from GenBank and included for a comprehensive phylogenetic analysis. A total of 390 horses were screened for EL and 97 were positive clinically while H. capsulatum was isolated from 60 horses and further confirmed with PCR, of which 54 were sequenced. BLAST analysis of these 54 isolates identified 29 H. capsulatum isolates and 14 isolates from other fungal genera while the remaining 11 samples were deemed insufficient for further downstream analysis. The phylogenetic analysis identified five clades, namely, African, Eurasian, North American 1 and 2, and Latin African A and B. The Ethiopian isolates were closely aggregated with isolates of the Latin American A and Eurasian clades, whereas being distantly related to isolates from North American 1 and 2 clades as well as Latin American B clade. This study highlights the possible origins and transmission routes of Histoplasmosis in Ethiopia.
Human Diet Patterns During the Qijia Cultural Period: Integrated Evidence of Stable Isotopes and Plant Micro-remains From the Lajia Site, Northwest China

The diet of prehistoric humans in the Qijia period (4,400–3,500 BP) was significantly changed by the advent of dry agriculture and food globalization. However, it is yet to be proven whether wild plants were exploited despite the cultivation of millet, and whether wheat crops, cattle, and sheep originating from southwestern Asia were adopted into the regional human diet. This study presents stable isotope, starch grain, and phytolith analyses of 24 human teeth from the Lajia site in Qinghai, which is a representative Qijia culture settlement site. The carbon and nitrogen isotope results show that the subjects primarily ate C4 plants and had a high protein diet. Starch grain and phytolith results showed that the inhabitants consumed broomcorn millet (Panicum miliaceum), foxtail millet (Setaria italica), Triticeae, tubers and roots, along with other Pooideae and Poaceae plants. This data proves that although broomcorn and foxtail millet formed the mainstay of the Qijia diet, it also included a wide range of plants, such as the tribe Triticeae, tubers and roots, which would have been foraged rather than grown. Compared with the other three contemporaneous sites in Northern China, the proportion of millet starches was highest at the Lajia site, while the type and proportion of foraged plants were the lowest. This was probably because of the arid environment in the region, which could not have supported sufficient plant resources for foraging, which in turn might have led to enhanced millet cultivation and/or a greater reliance on hunting. No wheat or barley traces were found in human teeth in Lajia, and the high proportion of nitrogen was possibly related to the consumption of sheep because sheep bones were found in a zooarchaeological study. This study enhances our understanding of the subsistence strategies present in Qijia culture and of prehistoric food globalization, which is of pivotal significance for a deeper understanding of interactions between east and west Asia during the Neolithic and Bronze ages.
Hepatocellular Carcinoma Intrinsic Cell Death Regulates Immune Response and Prognosis

Ablative and locoregional treatment options, such as radiofrequency, ethanol injection, microwave, and cryoablation, as well as irreversible electroporation, are effective therapies for early-stage hepatocellular carcinoma (HCC). Hepatocyte death caused by ablative procedures is known to increase the release of tumor-associated antigen, thus enhancing tumor immunogenicity. In addition, the heat ablative resection induces pyroptotic cell death accompanied by the release of several inflammatory factors and immune-related proteins, including damage-associated molecular patterns (DAMPs), heat shock proteins (HSPs), ficolin 3, ATP, and DNA/RNA, which potentiate the antitumoral immune response. Surgical approaches that enhance tumor necrosis and reduce hypoxia in the residual liver parenchyma have been shown to increase the disease-free survival rate by reducing the host’s immunosuppressive response. Scalpel devices and targeted surgical approach combined with immune-modulating drugs are an interesting and promising area to maximize therapeutic outcomes after HCC ablation.
Immune Profiling in Gastric Cancer Reveals the Dynamic Landscape of Immune Signature Underlying Tumor Progression

The profiling of the tumor immune microenvironment (TIME) is critical for guiding immunotherapy strategies. However, how the composition of the immune landscape affects the tumor progression of gastric cancer (GC) is ill-defined. Here, we used mass cytometry to perform simultaneous in-depth immune profiling of the tumor, adjacent tissues, and blood cells from GC patients and revealed a unique GC tumor-immune signature, where CD8+ T cells were present at a lower frequency in tumor tissues compared to adjacent tissues, whereas regulatory T cells and tumor-associated macrophages (TAMs) were significantly increased, indicating strong suppressive TIME in GC. Incorporated with oncogenic genomic traits, we found that the unique immunophenotype was interactively shaped by a specific GC gene signature across tumor progression. Earlier-stage GC lesions with IFN signaling enrichment harbored significantly altered T-cell compartments while advanced GC featured by metabolism signaling activation was accumulated by TAMs. Interestingly, PD-1 expression on CD8+ T cells was relatively higher in earlier-stage GC patients, indicating that these patients may derive more benefits from PD-1 inhibitors. The dynamic properties of diverse immune cell types revealed by our study provide new dimensions to the immune landscape of GC and facilitate the development of novel immunotherapy strategies for GC patients.