Miracle-dz/UniFAR-FTUs huggingface dataset:
Discordant population structure inferred from male- and female-type mtDNAs from Macoma balthica, a bivalve species characterized by doubly uniparental inheritance of mitochondria

Doubly Uniparental Inheritance (DUI) of mitochondria is a remarkable exception to the Strictly Maternal Inheritance (SMI) in metazoans. In species characterized by DUI --almost exclusively gonochoric bivalve mollusks--, females (F) transmit mitochondria to offspring of both sexes, while males (M) pass on their mitochondria exclusively to their sons. Under DUI, males are heteroplasmic, somatic tissues containing F-transmitted mtDNA and gametic cells containing M-transmitted mtDNAs. The aforementioned transmission routes make M- and F- transmitted mtDNA interesting as sex-specific markers which can differ in their effective population sizes, mutation rates, and selective constraints. For these reasons, looking at both markers can provide significant insights into the genetic structure of populations and investigate its determinants. In this study, we document differences in genetic diversity, divergence, inter-populational genetic differentiation and biogeographic structure between M- and F-type cox1 mt genes in the Baltic tellin (Macoma balthica) to test whether cox1m and cox1f genes bear the marks of similar phylogeographic histories. Both markers were sequenced for 302 male individuals sampled from the North Sea to the Gironde Estuary (Southern France). Nucleotide diversity and net divergence were over twice higher in cox1m compared to cox1f. A strong southward decrease in nucleotide diversity was observed only at cox1m. Genetic differentiation between northern and southern populations was nearly 3 times higher at cox1m compared to cox1f (global ΦST = 0.345 and 0.126 respectively) and the geographic localization of the strongest genetic break significantly differed between the markers (Finistère Peninsula at cox1f; Cotentin Peninsula at cox1m). A higher mutation rate, relaxed negative selection and differences in effective population sizes (depending on locations) at cox1m could explain differences in population genetic structure. As both F- and M-type mtDNAs interact with nuclear genes for oxidative phosphorylation and ATP production, geographical discordances in genetic clines could be linked to mito-nuclear genetic incompatibilities in this system.
Modeling of individual neurophysiological brain connectivity

Introduction Computational models are often used to assess how functional connectivity (FC) patterns emerge from neuronal population dynamics and anatomical connections in the brain. However, group averaged data is often used in this context and it remains unclear whether individual predictions of FC patterns using this approach can be made. Here, we assess the value of using individualized structural data for simulation of individual whole-brain FC. Methods The Jansen and Rit neural mass model was employed, where masses were coupled using individual structural connectivity (SC) obtained from diffusion weighted imaging. Simulated FC was correlated to individual magnetoencephalography-derived empirical FC. FC was estimated using both phase-based (phase lag index (PLI), phase locking value (PLV)) and amplitude-based (amplitude envelope correlation (AEC)) metrics to analyze the goodness-of-fit of different metrics for individual predictions. Prediction of individual FC was compared against the prediction of group averaged FC. We further tested whether SC of a different participant could equally well predict a participants FC pattern. Results The AEC provided a significantly better match between individually simulated and empirical FC than phase-based metrics. Simulations with individual SC provided higher correlations between simulated and empirical FC compared to using the group-averaged SC. However, using SC from other participants resulted in similar correlations between simulated and empirical FC compared to using participants own SC. Discussion This work underlines the added value of FC simulations based on individual instead of group-averaged SC, and could aid in a better understanding of mechanisms underlying individual functional network trajectories in neurological disease. Impact statement In this work, we investigated how well individual empirical functional connectivity can be simulated using the individual’s structural connectivity matrix combined with neural mass modeling. Our research highlights the potential added value of using individual simulations of functional connectivity, and could aid in a better understanding of mechanisms underlying individual functional network trajectories in neurological disease. Moreover, individualized prediction of disease trajectories could enhance patient care and may provide better treatment options.
Stable nebulization and muco‐trapping properties of regdanvimab/IN‐006 support its development as a potent, dose‐saving inhaled therapy for COVID‐19

The respiratory tract represents the key target for antiviral delivery in early interventions to prevent severe COVID-19. While neutralizing monoclonal antibodies (mAb) possess considerable efficacy, their current reliance on parenteral dosing necessitates very large doses and places a substantial burden on the healthcare system. In contrast, direct inhaled delivery of mAb therapeutics offers the convenience of self-dosing at home, as well as much more efficient mAb delivery to the respiratory tract. Here, building on our previous discovery of Fc-mucin interactions crosslinking viruses to mucins, we showed that regdanvimab, a potent neutralizing mAb already approved for COVID-19 in several countries around the world, can effectively trap SARS-CoV-2 virus-like-particles in fresh human airway mucus. IN-006, a reformulation of Regdanvimab, was stably nebulized across a wide range of concentrations, with no loss of activity and no formation of aggregates. Finally, nebulized delivery of IN-006 resulted in 100-fold greater mAb levels in the lungs of rats compared to serum, in marked contrast to intravenously dosed mAbs. These results not only support our current efforts to evaluate the safety and efficacy of IN-006 in clinical trials, but more broadly substantiate nebulized delivery of human antiviral mAbs as a new paradigm in treating SARS-CoV-2 and other respiratory pathologies.
Combining transgenesis with paratransgenesis to fight malaria

Malaria is among the deadliest infectious diseases and Plasmodium, the causative agent, needs to complete a complex development cycle in its vector mosquito for transmission to occur. Two promising strategies to curb transmission are transgenesis, consisting of genetically engineering mosquitoes to express anti-malarial effector molecules and paratransgenesis, consisting of introducing into the mosquito, commensal bacteria engineered to express anti-malarial effector molecules. Although both approaches restrict parasite development in the mosquito, it is not known how their effectiveness compares. Here we provide an in-depth assessment of transgenesis and paratransgenesis and evaluate the combination of the two approaches. Using the Q-system to drive gene expression, we engineered mosquitoes to produce and secrete two effectors – scorpine and the MP2 peptide – into the mosquito gut and salivary glands. We also engineered Serratia, a commensal bacterium capable to spread through mosquito populations, to secrete the same two effectors into the mosquito gut. Whereas both mosquito-based and bacteria-based approaches strongly reduced the oocyst and sporozoite intensity, a substantially stronger reduction of P. falciparum development was achieved when transgenesis and paratransgenesis were combined. Most importantly, transmission of P. berghei from infected to naïve mice was maximally inhibited by the combination of the two approaches. Combining these two strategies promise to become a powerful approach to combat malaria. Significance Malaria kills hundreds of thousand persons yearly. Clearly, new approaches are needed to fight this disease. Two promising approaches are based on the concept of genetically modifying the mosquito to make it a poor vector for the parasite: 1) transgenesis (engineering the mosquito to deliver anti-malarial compounds) and 2) paratransgenesis (engineering mosquito symbiotic bacteria to deliver anti-malarial compounds). The key questions addressed by this manuscript are: which of the two is the most promising approach? And because transgenesis and paratransgenesis are not mutually exclusive, would the combination of both be the most effective strategy? Our results argue for the combination of the two, showing the additive impact that these two strategies may have in controlling malaria transmission in the field.
Reconstruction and simulation of thalamoreticular microcircuitry

Thalamoreticular circuitry is central to sensory processing, attention, and sleep, and is implicated in numerous brain disorders, but the cellular and synaptic mechanisms remain intractable. Therefore, we developed the first detailed microcircuit model of mouse thalamus and thalamic reticular nucleus that captures morphological and biophysical properties of ~14,000 neurons connected via ~6M synapses, and recreates biological synaptic and gap junction connectivity. Realistic spontaneous and evoked activity during wakefulness and sleep emerge allowing dissection of cellular and synaptic contributions. Computer simulations suggest that reticular inhibition shapes thalamic responses and cortex can drive frequency-selective thalamic enhancement during wakefulness, whereas in sleep, reticular inhibition and cortical UP-states can trigger thalamic bursts and spindles. Gap junctions and short-term synaptic plasticity underlie spindle properties such as waxing and waning, and neuromodulation influences the occurrence of spindles. The model is openly available to support testing hypotheses of thalamoreticular circuitry in normal brain function and in disease.
Design and development of electric vehicle charging station equipped with RFID

This paper reports the development of electric charging station from distributed renewable for electric vehicle (EV). This designed refer to the input voltage standard of IEC 61851, plugs features of IEC 62196 and standard communication of ISO 15118. The developed electric charging station used microcontroller ATMEGA8535 and RFID as controller and identifier of the EV users, respectively. The charging station successfully developed as desired features for electric vehicle from renewable energy resources grid with solar panel, wind power and batteries storage.
Identifying Root Causes of Long Review Times for Engineering Shop Drawings

Every construction project requires approved shop drawings. Design drawings do not show details required for installation, so (sub)contractors cannot construct/install without approved shop drawings. Shop drawings are generally produced by subcontractors and should be reviewed and approved by appropriate parties promptly in order to avoid production delays. Observations on the shop drawing review process reveal that engineering review times of such major construction components as structural steels and reinforcing bars are unnecessarily long and often fail to meet the time frames within which contractors expect to receive responses from the design team. The primary goal of the study is to identify and speculate about possible measures for eliminating the root causes of long review times for engineering shop drawings. Since it is not a simple task to identify and eliminate root causes of any problem because problems are always coupled with their business and work processes, the study uses a systematic problem-solving technique: problem understanding, problemcause brainstorming, problem-cause data collection and analysis, and root-cause identification. The study reveals that the root cause of long engineering review time is insufficient and unclear information, rather than capability or availability of reviewers.
Design of a DPA based on the dual‐level supply voltage modulation for efficiency improvement

In this article, a Doherty power amplifier (DPA) based on the dual‐level supply voltage modulation is proposed. To improve efficiency, the drain of the carrier amplifier in the DPA is supplied with two different voltage levels based on the input RF power. The switching between these two different voltage levels is modulated by a voltage control circuit. The DPA is fabricated using two LDMOSFETs at the working frequency of 2.14 GHz. The measured results show that, compared with the conventional DPA, the power‐added efficiency (PAE) has been enhanced at low RF input power, and the feasibility of the proposed method has been verified. © 2016 Wiley Periodicals, Inc. Microwave Opt Technol Lett 58:759–762, 2016
Investigation on the Quality of 3D Sound Reproduction

Standard audio reproduction formats assume that the loudspeakers are positioned in the horizontal plane. The last missing dimension – height – offers many opportunities and challenges. In this paper we focus on one challenge, i.e., the evaluation of reproduction systems with additional height channels. First, the results of an expert survey regarding the importance of 3D sound for different applications are presented. Secondly, the overall quality of 3D sound reproduction is evaluated by listening tests. Because the selection of sound items is critical for the evaluation a broad selection of different sound items is used. To classify sound items, we extend an existing 2D sound categorisation concept to 3D. The test signals were derived from original 22-channel sound items. The 2-, 5-, and 9-channel sound items were generated by passive down-mixing algorithms and selective muting of reproduction channels. In addition, we investigate the influence of an external reference. Therefore, one listening test with a reference and a second one without a reference were conducted. A companion paper focuses on controlling physical relevant parameters of a 3D audio setup.
RFID and Wireless Sensing

The efforts in realizing ubiquitous integrated circuits for ambient intelligence networks increased over the past few years. In particular, the passive radio frequency identification (RFID) presents a key technology for unattended wireless networks. A typical state of the art passive RFID system consists of an interrogator/reader and several passive Transponders. The interrogator communicates with the transponders by a wireless peer-to-peer connection and is responsible for the power supply of the passive transponders. To achieve a higher reading range and to improve the operational reliability of passive RFID sensor tags, the design of integrated circuits with an ultra low-power consumption and novel concepts for high-efficiency energy scavenging are required.
Conceptual Framework For Visual Question And Answering System

: Visual question answering is a field of study in the Artificial Intelligence domain. Visual Question Answering (VQA) is a trained system which provides an answer to the questions asked in respect to the given image in English Natural Language. VQA is a general system and has a power that can VQA be used in any image based scenario with enough training on the relevant dataset. To achieve this, neural networks are used, particularly Convolutional Neural Networks and Recurrent Neural Networks. In this research work, we have compared different approaches of VQA, out of which we are exploring CNN based models. This paper proposes the conceptual framework to a VQA model by using the combination of CNNs and RNNs under the computer vision tasks and NLP tasks.
Task-based Evaluation of 3D Radial Layouts for Centrality Visualization

In this paper we propose improvements to the 3D radial layouts that make it possible to visualize centrality measures of nodes in a graph. Our improvements mainly relate edge drawing and the evaluation of the 3D radial layouts. First, we projected the edges onto the visualization surfaces in order to reduce the nodes overlap. Secondly, we proposed a human-centered evaluation in order to compare the efficiency score, the time to complete tasks and the number of clicks of the 3D radial layouts to those of the 2D radial layouts. The results showed that even if the overall improvements in terms of time or errors are not statistically significant between the various visualization surfaces, the participants have a better feeling on the 3D and therefore the user experience is able to be improved in data visualization.
Random-walk Segmentation of Nuclei in Fluorescence Microscopic Images with Automatic Seed Detection

: In personalized immunotherapy against cancer analysis of cell nuclei in tissue samples can provide helpful information to predict whether the beneﬁts of the therapy outweigh the usually severe side effects. Since segmentation of nuclei is the basis for all further analyses of cell images, research into suitable methods is of particular relevance. In this paper we present and evaluate two versions of a segmentation pipeline based on the established random-walk method. These versions contain automatic seed detection, using a distance transformation in one of them. In addition, we present a method to select the required hyper-parameter of the random-walk algorithm. The evaluation using a benchmark dataset shows that promising results can be achieved with respect to common evaluation metrics. Furthermore, the segmentation accuracy can compete with a reference CellProﬁler segmentation pipeline, based on the watershed transformation. Based on the presented pipeline, the random-walk method can also be integrated into more advanced pipelines to further improve segmentation results.
PENCARIAN JALUR TERBAIK MENGGUNAKAN PARTICLE SWARM OPTIMIZATION UNTUK MENGOPTIMASI LALU LINTAS KENDARAAN

Dalam berkendara, penting halnya untuk mencari jalur terbaik untuk menuju suatu tempat. Dengan semakin bertambahnya jumlah kendaraan dari tahun ke tahun, maka berkendara secara efektif menjadi sangatlah penting agar waktu pengendara tidak habis terpakai di jalan. Particle Swarm Optimization adalah salah satu metode untuk melakukan optimasi dalam pencarian jalan terbaik. Metode Particle Swarm Optimization ini menggunakan populasi acak dan mencari solusi optimal dengan memperbarui posisi tiap generasi. Solusi terbaik (fitness) yang telah dicapai akan disimpan dan diperbaharui di setiap generasi. Dalam Penelitian ini disimulasikan salah satu metode dalam Pencarian jalan terbaik dengan menggunakan Blender sebagai penyedia lingkungan virtual untuk simulasi jalur dan jalannya suatu obyek 3D sebagai pengganti obyek nyata. Dari hasil penelitian, didapatkan hasil bahwa Particle Swarm Optimization berhasil diterapkan pada obyek multi agent pada penyimulasian. Dari hasil percobaan, diketahui juga bahwa jumlah penggunaan partikel akan meningkat sebanding dengan kekompleksan yang dimiliki oleh jalan lalu lintas. Pada percobaan, untuk menyelesaikan permasalahan dengan besar jalan satu blok dibutuhkan partikel berjumlah 4. Setelah dilakukan penambahan blok menjadi 3 blok jalan dibutuhkan penambahan jumlah partikel sebanyak 21 agar pencarian jalan dapat dilakukan.
Cognitive and Physical Intervention in Metals’ Dysfunction and Neurodegeneration

Metals—especially iron, copper and manganese—are important elements of brain functions and development. Metal-dysregulation homeostasis is associated with brain-structure damage to the motor, cognitive and emotional systems, and leads to neurodegenerative processes. There is more and more evidence that specialized cognitive and motor exercises can enhance brain function and attenuate neurodegeneration in mechanisms, such as improving neuroplasticity by altering the synaptic structure and function in many brain regions. Psychological and physical methods of rehabilitation are now becoming increasingly important, as pharmacological treatments for movement, cognitive and emotional symptoms are limited. The present study describes physical and cognitive rehabilitation methods of patients associated with metal-induced neurotoxicity such as Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis, Huntington’s disease and Wilson’s disease. In our review, we describe physical (e.g., virtual-reality environments, robotic-assists training) and psychological (cognitive training, cognitive stimulation, neuropsychological rehabilitation and cognitive-behavioral and mindfulness-based therapies) methods, significantly improving the quality of life and independence of patients associated with storage diseases. Storage diseases are a diverse group of hereditary metabolic defects characterized by the abnormal cumulation of storage material in cells. This topic is being addressed due to the fact that rehabilitation plays a vital role in the treatment of neurodegenerative diseases. Unfortunately so far there are no specific guidelines concerning physiotherapy in neurodegenerative disorders, especially in regards to duration of exercise, type of exercise and intensity, as well as frequency of exercise. This is in part due to the variety of symptoms of these diseases and the various levels of disease progression. This further proves the need for more research to be carried out on the role of exercise in neurodegenerative disorder treatment.
Simulation Model of Thyristor Controlled Reactor

Controlled power is a fundamental pre-requisite of various sectors. This paper discuss one of the FACT device i.e. Thyristor Controlled Reactor which is used to compensate the reactive power and controls the voltage profile of the power transmission line. Firing control scheme for triggering Thyristor is performed in MATLAB SIMULINK software. This paper deals with the Simulink model of TCR and results ofThyristor controlledreactor (TCR) system. Generation of harmonics in TCRsystem, operation of TCR under different conditionsare also discussed. Keywords—Thyristor Controlled Reactor, SVC, Flexible AC Transmission System, Variable Shunt Compensation, Ferranti Effect.
Does Contact with the Justice System Influence Situational Action Theory's Causes of Crime? A Study of English and German Juveniles

To explore why system contact often has no crime-preventative effect, the current study examined the effects of juvenile justice contact on Situational Action Theory's (SAT) causes of crime, including personal morals, deviant peer associations, and detection risk perceptions. The analysis is based on a sample of English (Peterborough Adolescent and Young Adult Development Study) and German (Crime in the modern City study) juveniles. Propensity score matching was applied to estimate whether the lenient system contacts influenced the causes of crime in the year after the contact. The treatment effect estimates are mostly insignificant and relatively small. The few significant estimates in the English sample suggest that official contact slightly increased deviant peer associations and decreased feelings of moral guilt. Overall, the findings suggest that system contact may often have no crime-preventative effect as it does not (Germany), or only slightly (England) affect SAT's causes of crime. Previous studies, primarily based on the U.S. data, often reported more substantial effects that mostly operated in a crime-amplifying direction. It is speculated whether the less substantial impact in the current study can be attributed to the overall more lenient, diversion-oriented handling of the examined English and German offenders.