Miracle-dz/UniFAR-FTUs huggingface dataset:
Levitated optomechanics in a hybrid electro-optical trap

This thesis describes the progress made in trapping and cooling silica nanoscale particles, levitating in a hybrid electro-optical trap. The light field of a high finesse Fabry-Perot cavity and the quadrupole field generated by an rf Paul trap are used for the first time to both trap and cool naturally charged 209 nm dielectric nanospheres in high vacuum. Particles are first loaded into the Paul trap at pressures of ∼ 10−1 mbar, after which their centre-of-mass motion is damped via optomechanical cooling, as the pressure is lowered to ∼ 10−6 mbar. The combined ion trap-optical cavity set-up exposes an interesting interplay between the ion trap dynamics and the cavity mode which lead to a novel optomechanical cooling mechanism of a cyclic nature. This eliminates the need for a second, dedicated cooling mode from the cavity, or feedback cooling in order to cool the levitated particles to the ground state. At the same time, we identify a previously unobserved shift of the Paul trap secular frequencies due to the optical cavity, which enables readout of key parameters, such as the nanoparticles charge and the mean number of photons in the cavity. The dynamical features of the levitated particle, driven by linear and nonlinear optomechanical coupling, are observed through the cavity output, as well as the light scattered by the particle. As the background pressure is lowered, we observe greater than 1000 fold reduction in the centre-of-mass temperature of particles, before temperatures fall below the read-out sensitivity of the set-up.
Transcriptomic responses to multigenerational environmental warming in a cold-adapted salmonid

Cold-adapted species are particularly threatened by climate change as rates of environmental warming outpace the ability of many populations adapt. Recent evidence suggest that transgenerational thermal plasticity may play a role in the response of cold-adapted organisms to long-term changes in temperature. Using RNA sequencing, we explored differential gene expression of lake trout (Salvelinus namaycush), a cold-adapted species, to examine the molecular processes that respond to elevated temperatures under conditions of within-generation (offspring) and transgenerational (parental) warm-acclimation. We hypothesized that genes associated with metabolism, growth and thermal stress/tolerance would be differentially expressed in juvenile lake trout offspring depending on their own acclimation temperature and that of their parents. We found enriched pathways for thermal stress, signaling processes, immune function, and transcription regulation, although the specific genes and direction of differential expression (up-or downregulation) depended on the combination of offspring and parental thermal rearing conditions. While parental warm-acclimation did have a transgenerational effect on gene expression in their offspring, within-generation warm-acclimation had a larger effect on differential expression, enriching more pathways. We provide evidence of the transgenerational response to warming at the transcriptional level in lake trout, which should be useful for future studies of transcriptomics and plasticity in these and other cold-adapted species.
Approximate Computing on Programmable SoCs via Neural Acceleration

Processor designs for portable, ubiquitous computing devices such as cell phones have widely incorporated hardware accelerators to support energy-efficient execution of common tasks. Porting applications to take advantage of these resources is often a difficult task due to the restricted programming model of the accelerator: FPGA-based acceleration, for instance, often requires the expertise of a hardware designer. Fortunately, many applications that can take advantage of accelerators are amenable to approximate execution, which prior work has shown can be exploited with a simple programming model. This paper presents a comprehensive and mostly automatic framework that allows general-purpose approximate code to use programmable logic without directly involving hardware design. We propose SNNAP, a flexible FPGA-based neural accelerator for approximate programs. We identify the challenges associated with this approach and design a hardware framework that offers this capability. We measure a real FPGA implementation on a state-of-the-art programmable systemon-a-chip (PSoC) and show an average 1.77× speedup and 1.71× energy savings.
Xylem sap residue in cut-open conduits can affect gas discharge in pneumatic experiments

Considerable progress has been made in understanding the mechanisms of embolism formation based on the pneumatic method, which relies on gas discharge measurements. Here, we test the assumption that cut-open conduits are gas-filled when samples are cut at high water potentials. We performed vulnerability curves (VC) with the Pneumatron and analysed sap extraction from cut-open vessels in Citrus branches, while the optical method was applied as a reference method. VCs of 11 additional angiosperms were analysed to generalise our findings. We found an increase in gas discharge during early stages of dehydration, which affected the VC of Citrus. Xylem sap was not absorbed immediately by surrounding tissue in cut Citrus branches. The gas amount discharged increased until all sap residue was absorbed, which was near the turgor loss point. By analysing the slope of VCs, we could correct pneumatic VC, as evidenced by the strong agreement in embolism resistance between the pneumatic and the optical method. Since residual sap in cut-open conduits of some species could slightly reduce embolism resistance in some species, we propose to apply an easy correction for this novel artefact. Automated measurements with a Pneumatron are also required because of its high time resolution.
5-HT 2A and 5-HT 2C receptor antagonism differentially modulates reinforcement learning and cognitive flexibility: behavioral and computational evidence

Cognitive flexibility, the ability to adapt behavior in response to a changing environment, is disrupted in several neuropsychiatric disorders, including obsessive–compulsive disorder (OCD) and major depressive disorder (MDD). Evidence suggests that flexibility, which can be operationalized using reversal learning tasks, is modulated by serotonergic transmission. However, how exactly flexible behavior and associated reinforcement learning (RL) processes are modulated by 5-HT action on specific receptors is unknown. We investigated the effects of 5-HT2A receptor (5-HT2AR) and 5-HT2C receptor (5-HT2CR) antagonism on cognitive flexibility and underlying RL mechanisms. Thirty-six male Lister hooded rats were trained on a touchscreen visual discrimination and reversal task. We evaluated the effects of systemic treatments with the 5-HT2AR and 5-HT2CR antagonists M100907 and SB-242084, respectively, on reversal learning performance and performance on probe trials where correct and incorrect stimuli were presented with a third, probabilistically rewarded, stimulus. Computational models were fitted to task choice data to extract RL parameters, including a novel model designed specifically for this task. 5-HT2AR antagonism impaired reversal learning during certain phases. 5-HT2CR antagonism, on the other hand, impaired learning from positive feedback. RL models further differentiated these effects. 5-HT2AR antagonism decreased punishment learning rate at high and low doses. The low dose also increased exploration (beta) and increased stimulus and side stickiness (kappa). 5-HT2CR antagonism also increased beta, but reduced side stickiness. These data indicate that 5-HT2A and 5-HT2CRs both modulate different aspects of flexibility, with 5-HT2ARs modulating learning from negative feedback and 5-HT2cRs for learning from positive feedback.
Phenotypic variation in maize can be largely explained by genetic variation at transcription factor binding sites

Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped nearly two-hundred thousand genetic variants (termed binding-QTLs) linked to cis-element occupancy. The functional significance of binding-QTLs is supported by three lines of evidence: i) they coincide with known causative loci that regulate traits, including novel alleles of Upright Plant Architecture2, Trehalase1, and the MITE transposon near ZmNAC111 under drought; ii) their footprint bias is mirrored between inbred parents and by ChIP-seq; iii) partitioning genetic variation across genomic regions demonstrates that binding-QTLs capture the majority of heritable trait variation across ∼70% of 143 phenotypes. Our study provides a promising approach to make previously hidden cis-variation more accessible for genetic studies and multi-target engineering of complex traits.
SwiSh: Distributed Shared State Abstractions for Programmable Switches

We design and evaluate SwiSh , a distributed shared state management layer for data-plane P4 programs. SwiSh enables running scalable stateful distributed network functions on programmable switches entirely in the data-plane. We explore several schemes to build a shared variable abstraction, which differ in consistency, performance, and in-switch implementation complexity. We introduce the novel Strong Delayed-Writes (SDW) protocol which offers consistent snapshots of shared data-plane objects with semantics known as 𝑟 -relaxed strong linearizability, enabling implementation of distributed concurrent sketches with precise error bounds. We implement strong, eventual, and SDW consistency protocols in Toﬁno switches, and compare their performance in microbenchmarks and three realistic network functions, NAT, DDoS detector, and rate limiter. Our results show that the distributed state management in the data plane is practical, and outperforms centralized solutions by up to four orders of magnitude in update throughput and replication latency.
Unravelling the complex biogeographic and anthropogenic history of Alaska’s mountain goats

Aim We used genetic tools to examine the population structure of mountain goats in Alaska, USA and assessed the demographic history of this species in relation to the natural and anthropogenic forces. Location Alaska, USA Taxon North American mountain goat (Oreamnos americanus) Methods Samples were collected between 2006 - 2020 from harvested animals and live captures. We genotyped 816 mountain goats at 18 microsatellite loci and identified the number of genetically distinct subpopulations across the state and assessed their genetic diversity. We used Bayesian computation software to investigate the demographic history relative to the known biogeographic history of the state. We also simulated island translocation events and compared simulations to empirical data to address the hypothesis that Baranof Island was a cryptic refugia. Results We showed that Alaska has four genetically distinct subpopulations of mountain goats with some additional genetic structure within those subpopulations. The main split of mountain goats between Southcentral and Southeast Alaska occurred ∼14,000 years ago. Simulations of translocation events largely aligned with the current populations observed today except for Baranof Island which showed greater diversity than the translocation simulation. Main Conclusions The distribution and genetic structure of mountain goats in Alaska reflects a combination of natural and anthropogenic forces. A rapid northerly expansion through an ice-free corridor in combination with the isolated nature of the landscape led to low diversity and isolation 14,000 years ago in Southcentral Alaska and higher diversity in Southeast Alaska. Two of the three islands where mountain goat translocations have occurred match genetically with their source population, while Baranof Island appears to have a divergent population, consistent with the hypothesis of an endemic or cryptic population prior to the translocation event. This study highlights the value of considering both the natural and anthropogenic forces when assessing the biogeographic history of a species.
Novel roles for the LRRC56 protein, an IFT cargo protein, in docking of dynein arms in Trypanosoma brucei

Outer dynein arms (ODAs) are responsible for ciliary beating in eukaryotes. They are assembled in the cytoplasm and shipped by intraflagellar transport (IFT) before attachment to microtubule doublets via the docking complex. The LRRC56 protein has been proposed to contribute to ODAs maturation. Mutations or deletion of the LRRC56 gene lead to reduced ciliary motility in all species investigated so far, but with variable impact on dynein arm presence. Here, we investigated the role of LRRC56 in the protist Trypanosoma brucei, where its absence results in distal loss of ODAs, mostly in growing flagella. We show that LRRC56 is a transient cargo of IFT trains during flagellum construction and surprisingly, is required for efficient attachment of a subset of docking complex proteins present in the distal portion of the organelle. This relation is interdependent since the knockdown of the distal docking complex prevents LRRC56’s association with the flagellum. Intriguingly, lrrc56-/- cells display shorter flagella whose maturation is delayed. Inhibition of cell division compensates for the distal ODAs absence thanks to the redistribution of the proximal docking complex, restoring ODAs attachment but not the flagellum length phenotype. This work reveals an unexpected connection between LRRC56 and the docking complex.
Novel Biomarkers and Distinct Transcriptomic Profile of Barrett’s Esophagus Epithelial Stem Cells

Barrett’s esophagus, a metaplastic condition that originates in the distal esophagus, is the only known precursor lesion for the development of esophageal adenocarcinoma, which has a devasting 5-year survival rate of <20%. The large number of subjects diagnosed with Barrett’s esophagus, and therefore at higher risk for esophageal adenocarcinoma, underscores the necessity for biomarkers that would benefit surveillance and potentially early treatment. To address this, we generated epithelial stem cell organoids from normal gastric cardia, non-dysplastic and dysplastic Barrett’s esophagus, and esophageal and gastric adenocarcinoma. Interestingly, non-dysplastic and dysplastic Barrett’s esophagus displayed higher expression of multiple archetypical cancer-associated genes compared with both esophageal and gastric adenocarcinoma in addition to expression of the novel biomarker CT83. ST6GAL1, a Golgi sialyltransferase upregulated in multiple epithelioid cancers, was strongly upregulated in dysplastic Barrett’s esophagus at both mRNA and protein levels. ST6GAL1 protein also was highly expressed in esophageal adenocarcinoma, suggesting that regulation of ST6GAL1 may play a role in Barrett’s esophagus progression to esophageal adenocarcinoma and serve as a potential biomarker of the development of esophageal cancer.
Non-homogenous axonal bouton distribution in whole-brain single cell neuronal networks

We examined the distribution of pre-synaptic contacts in axons of mouse neurons and constructed whole-brain single-cell neuronal networks using an extensive dataset of 1891 fully reconstructed neurons. We found that bouton locations were not homogeneous throughout the axon and also among brain regions. As our algorithm was able to generate whole-brain single-cell connectivity matrices from full morphology reconstruction datasets, we further found that non-homogeneous bouton locations have a significant impact on network wiring, including degree distribution, triad census and community structure. By perturbing neuronal morphology, we further explored the link between anatomical details and network topology. In our in silico exploration, we found that dendritic and axonal tree span would have the greatest impact on network wiring, followed by synaptic contact deletion. Our results suggest that neuroanatomical details must be carefully addressed in studies of whole brain networks at the single cell level.
Rechargeable Biomineral Induced by Sulfate Reducing Bacterium Cupidesulfovibrio sp. HK-II

A black precipitate produced by a sulfate reducing bacterium Cupidesulfovibrio sp. strain HK was investigated with multidisciplinary methods. X-ray diffraction (XRD) analysis revealed that the black precipitate was mackinawite. Cyclic voltammetry analysis showed the obvious redox peaks, and the biogenic mackinawite exhibited rechargeable properties. XRD analyses showed that the form of the rechargeable biogenic mackinawite (RBM-II) was changed by discharge and recharge treatments: Field-emission transmission electron microscope analyses revealed that lepidocrocite and amorphous iron oxide were appeared from mackinawite on discharged condition, and the three kinds of minerals were intermingled via the rechargeable treatments. Physicochemical parameters were changed regularly under the treatments, suggesting that discharge would be occurred by iron oxidation and sulfur reduction, and vice versa. These results indicated that dynamics of sulfur is important key process in rechargeable mechanism, supporting that a part of mackinawite was transformed to lepidocrocite and iron oxides, and vice versa. Microbial fuel cells (MFCs) equipped with lactate, strain HK-II and anode including RBM-II consumed lactate even under opened circuit conditions, after which MFCs generated higher current density at re-closed circuit conditions. These results demonstrated that the biogenic mackinawite is one of rechargeable materials and would play important roles in geomicrobiological reactions and biotechnology.
Efficient predictive vibration control of a building‐like structure

This paper presents the design of a model predictive controller (MPC) based on Laguerre functions for vibration control. The controller is tested in a building‐like structure consisting on a three‐story building with a passive vibration absorber. The structure is connected to an electromagnetic shaker, which excites the support of the superstructure, providing forces with a wide range of excitation frequencies, including some resonance frequencies of the structure. The overall controller is a hybrid vibration absorber conformed of (i) an active absorber, that is a predictive vibration control scheme, synthesised to actively attenuate the vibratory system response via (ii) a passive absorber, known as a tuned mass damper (TMD), located over the third story building to reduce the vibrations caused by harmonic forces acting on the base of the structure. The proposed predictive control strategy proves to be effective and efficient, improving system's performance with guaranteed stability and feasibility. Experimental and numerical results are included to illustrate the overall system performance.
Reverse Logistics: an approach to raising awareness of the risks caused by the incorrect disposal of expired drugs

The growth in the manufacture of medicines and their consumption has potentiated an exponential growth in the improper disposal of medicines. This improper disposal comes from the population's lack of information or choice to do it the right way, increasing the risks of contamination of the environment and of the human being. This research seeks to contribute to the awareness of the risks that the incorrect disposal of expired drugs produces in the environment. This study was applied to Brazil, specifically to the state of Ceará. A quantitative methodology by questionnaire was developed with the population (N=71) and pharmacies in Ceará (N=7). The main results of this investigation indicate that there is misinformation among most of the population regarding the correct disposal practices and the impact of doing it incorrectly on the environment and the population. As for the establishments that sell medicines, there is a lack of interest in creating policies for the awareness of correct disposal. This study is intended to be of added value to government organizations, the academic community, and all those interested in reverse logistics in health and sustainability.
A Cost-Effective and Smart Sensing Tissue-like Testbed for Surgical Training

A low-cost tissue-like testbed with six nodes of varying stiffness was developed for surgical training to provide pressure and force feedback data through image reception to human operators. Using SolidWorks, a 3D model of the box trainer housing was created. A pad for the distribution of smartsensing nodes and microcontroller connections was designed with open spaces for the respective components. The pad was 3D-printed with PLA filament. Flat piezoelectric pressure sensors were fabricated with conductive materials and velostat sensor material. Using static and dynamic analyses, three top sensors were chosen to be used in three pressure sensing nodes. A calibration process was performed on the pressure sensors to find the linear relationship between voltage and pressure, which was then used to create a conversion equation for each sensor. These equations were used to collect data at the three pressure sensing nodes on the silicone testbed pad. Conductive TPU filament was used to 3D-print vertical force sensors, which were designed using SolidWorks. The force sensors were calibrated with a squeezing mechanism to find a relationship between voltage and force and to subsequently develop a conversion equation for each sensor. We used these equations to collect force data from the three force sensing nodes on the testbed pad. Through static and dynamic analyses, the force sensors were found to be functional, but to need improvements in accuracy. The mechatronic system was designed and developed to integrate all six sensors and to collect data from the testbed pad using an Arduino microcontroller. The flat pressure and vertical force sensors were embedded in each node to measure the pressure and force that occurs during the deformation of the six nodes. Data was collected and imported into MATLAB. This data was used in displaying pressure and force mapping of the nodes over a live video of the silicone pad. Pressure and force mapping was realized by drawing color-coded circles on each of the six nodes that correspond to a range of force or pressure values. From this development, the surgical testbed provides multi-stiffness tissue training with live pressure and force mapping overlaid on a live video of the emulated surgical field.
Skynet: a Cyber-Aware Intrusion Tolerant Overseer

The increasing level of sophistication of cyber attacks which are employing cross-cutting strategies that leverage multi-domain attack surfaces, including but not limited to, software defined networking poisoning, biasing of machine learning models to suppress detection, exploiting software (development), and leveraging system design deficiencies.While current defensive solutions exist, they only partially address multi-domain and multi-stage attacks, thus rendering them ineffective to counter the upcoming generation of attacks. More specifically, we argue that a disruption is needed to approach separated knowledge domains, namely Intrusion Tolerant systems, cybersecurity, and machine learning.We argue that current solutions tend to address different concerns/facets of overlapping issues and they tend to make strong assumptions of supporting infrastructure, e.g., assuming that event probes/metrics are not compromised.To address these issues, we present Skynet, a platform that acts as a secure overseer that merges traditional roles of SIEMs with conventional orchestrators while being rooted on the fundamentals introduced by previous generations of intrusion tolerant systems. Our goal is to provide an open-source intrusion tolerant platform that can dynamically adapt to known and unknown security threats in order to reduce potential vulnerability windows.