Miracle-dz/UniFAR-FTUs huggingface dataset:
Microstructure Informed Tractography: Pitfalls and Open Challenges

One of the major limitations of diffusion MRI tractography is that the fiber tracts recovered by existing algorithms are not truly quantitative. Local techniques for estimating more quantitative features of the tissue microstructure exist, but their combination with tractography has always been considered intractable. Recent advances in local and global modeling made it possible to fill this gap and a number of promising techniques for microstructure informed tractography have been suggested, opening new and exciting perspectives for the quantification of brain connectivity. The ease-of-use of the proposed solutions made it very attractive for researchers to include such advanced methods in their analyses; however, this apparent simplicity should not hide some critical open questions raised by the complexity of these very high-dimensional problems, otherwise some fundamental issues may be pushed into the background. The aim of this article is to raise awareness in the diffusion MRI community, notably researchers working on brain connectivity, about some potential pitfalls and modeling choices that make the interpretation of the outcomes from these novel techniques rather cumbersome. Through a series of experiments on synthetic and real data, we illustrate practical situations where erroneous and severely biased conclusions may be drawn about the connectivity if these pitfalls are overlooked, like the presence of partial/missing/duplicate fibers or the critical importance of the diffusion model adopted. Microstructure informed tractography is a young but very promising technology, and by acknowledging its current limitations as done in this paper, we hope our observations will trigger further research in this direction and new ideas for truly quantitative and biologically meaningful analyses of the connectivity.
Smart Home System Design based on Artificial Neural Networks

Management and security of electric power plays a key role in economy and sustainable development. The major concerns in optimal usage of Power are reduction in wastage and creating intelligent switching systems to make optimal use of the power available. This paper proposes an adaptive smart home system for optimal utilization of power, through Artificial Neural Network (ANN). The system proposed comprises of a Recurrent Neural Network to capture Human behavior patterns and a Feed Forward Architecture in ANN for security applications in the smart homes. The technique is used to minimize the power wastage by studying and adapting to the consumption behavior patterns of the consumers. Index Terms — Temporal response, Human behavior mapping, Recurrent Neural Network, single layer perceptron model.
A Mouse Model of Latent Tuberculosis Infection to Study Intervention Strategies to Prevent Reactivation

Infection with Mycobacterium tuberculosis (Mtb) is the leading cause of death in human immunodeficiency virus (HIV)+ individuals, particularly in Sub-Saharan Africa. Management of this deadly co-infection is a significant global health challenge that is exacerbated by the lack of efficient vaccines against both Mtb and HIV, as well as the lack of reliable and robust animal models for Mtb/HIV co-infection. Here we describe a tractable and reproducible mouse model to study the reactivation dynamics of latent Mtb infection following the loss of CD4+ T cells as it occurs in HIV-co-infected individuals. Whereas intradermally (i.d.) infected C57BL/6 mice contained Mtb within the local draining lymph nodes, depletion of CD4+ cells led to progressive systemic spread of the bacteria and induction of lung pathology. To interrogate whether reactivation of Mtb after CD4+ T cell depletion can be reversed, we employed interleukin (IL)-2/anti-IL-2 complex-mediated cell boost approaches. Although populations of non-CD4 lymphocytes, such as CD8+ memory T cells, natural killer (NK) cells and double-negative (DN) T cells significantly expanded after IL-2/anti-IL-2 complex treatment, progressive development of bacteremia and pathologic lung alterations could not be prevented. These data suggest that the failure to reverse Mtb reactivation is likely not due to anergy of the expanded cell subsets and rather indicates a limited potential for IL-2-complex-based therapies in the management of Mtb/HIV co-infection.
FGFR1-Frs2/3 Signalling Maintains Sensory Progenitors during Inner Ear Hair Cell Formation

Inner ear mechanosensory hair cells transduce sound and balance information. Auditory hair cells emerge from a Sox2-positive sensory patch in the inner ear epithelium, which is progressively restricted during development. This restriction depends on the action of signaling molecules. Fibroblast growth factor (FGF) signalling is important during sensory specification: attenuation of Fgfr1 disrupts cochlear hair cell formation; however, the underlying mechanisms remain unknown. Here we report that in the absence of FGFR1 signaling, the expression of Sox2 within the sensory patch is not maintained. Despite the down-regulation of the prosensory domain markers, p27Kip1, Hey2, and Hes5, progenitors can still exit the cell cycle to form the zone of non-proliferating cells (ZNPC), however the number of cells that form sensory cells is reduced. Analysis of a mutant Fgfr1 allele, unable to bind to the adaptor protein, Frs2/3, indicates that Sox2 maintenance can be regulated by MAP kinase. We suggest that FGF signaling, through the activation of MAP kinase, is necessary for the maintenance of sensory progenitors and commits precursors to sensory cell differentiation in the mammalian cochlea.
Nitric oxide regulation of myocardial O2 consumption and HEP metabolism.

NO and O(2) compete at cytochrome-c oxidase, thus potentially allowing NO to modulate mitochondrial respiration. We previously observed a decrease of myocardial phosphocreatine (PCr)/ATP during very high cardiac work states, corresponding to an increase in cytosolic free ADP. This study tested the hypothesis that NO inhibition of respiration contributes to this increase of ADP. Infusion of dobutamine + dopamine (DbDp, each 20 microg.kg(-1). min(-1) iv) to more than double myocardial oxygen consumption (MVo(2)) in open-chest dogs caused a decrease of myocardial PCr/ATP measured with (31)P NMR from 2.04 +/- 0.09 to 1.85 +/- 0.08 (P < 0.05). Inhibition of NO synthesis with N(omega)-nitro-L-arginine (L-NNA), while catecholamine infusion continued, caused PCr/ATP to increase to the control value. In a second group of animals, L-NNA administered before catecholamine stimulation (reverse intervention of the first group) increased PCr/ATP during basal conditions. In these animals L-NNA did not prevent a decrease of PCr/ATP at the high cardiac work state but, relative to MVo(2), PCr/ATP was significantly higher after L-NNA. In a third group of animals, pharmacological coronary vasodilation with carbochromen was used to prevent changes in coronary flow that might alter endothelial NO production. In these animals L-NNA again restored depressed myocardial PCr/ATP during catecholamine infusion. The finding that inhibition of NO production increased PCr/ATP suggests that during very high work states NO inhibition of mitochondrial respiration requires ADP to increase to drive oxidative phosphorylation.
A Systematic Comparison of Smoothing Techniques for Sentence-Level BLEU

BLEU is the de facto standard machine translation (MT) evaluation metric. How- ever, because BLEU computes a geo- metric mean of n-gram precisions, it of- ten correlates poorly with human judg- ment on the sentence-level. There- fore, several smoothing techniques have been proposed. This paper systemati- cally compares 7 smoothing techniques for sentence-level BLEU. Three of them are first proposed in this paper, and they correlate better with human judgments on the sentence-level than other smoothing techniques. Moreover, we also compare the performance of using the 7 smoothing techniques in statistical machine transla- tion tuning.
Splash seed dispersal by raindrops

Splash seed dispersal by raindrops was investigated for plants in southern Japan. Nine families, 10 genera and 19 species were confirmed as raindrop-dispersed plants. The 10 genera were Gentiana, Gratiola, Chrysosplenium, Mazus, Mitella, Ophiorrhiza, Sagina, Sedum, Trigonotis and Veronica. The method of splash rain dispersal in these species was clarified. Raindrop-dispersed species were all small herbaceous plants with a vertical pedicel and an apically opening fresh capsule when the seeds mature. Open capsules were cup-shaped or boat-shaped and can accommodate raindrops easily. The raindrops splashed the seeds from the capsule. In general, the seeds weighed very little, but they were heavier than powder or dust seeds dispersed by wind. A strong negative correlation was found between seed weight and the number of seeds per capsule. In the case of Trigonotis brevipes (Maxim.) Maxim. , raindrops were received into the cup-shaped calyx-tube and dispersed the fruitlets. Some species, such as Gentiana thunbergii (G. Don) Griseb. , Gentiana zollingeri Fawcett and Ophiorrhiza japonica Blume, had hydroscopic movement capsules that opened widely only when wet. Raindrop-dispersed plants were found in various habitats. For example, some plants grew together on rocks along the mountain torrents where splash water could easily be caught. The results of the laboratory and field experiments indicated that the dispersal distance of seeds by raindrops was 1 m or less. For small herbaceous plants, splash dispersal by rain might be an effective and advantageous method of seed dispersal because dispersal is not affected by plant height.
Sex differences in human performance

The book brings together for the first time research on sex differences that affect human performance. The first section of the book reviews basic research in the areas of sensation, learning, response to stress, and social factors, as they provide a basic for observed sex differences. The next section contains more specific information about response differences and anthropometric factors. The contributors, many of whom are international authorities in their field, offer a wide but selective review across psychology and fields related to human performance, such as ergonomics, education and personnel work with objective and information based chapters, supported by extensive and valuable bibliographies.
Electronic medical record systems are associated with appropriate placement of HIV patients on antiretroviral therapy in rural health facilities in Kenya: a retrospective pre-post study

Background and objective There is little evidence that electronic medical record (EMR) use is associated with better compliance with clinical guidelines on initiation of antiretroviral therapy (ART) among ART-eligible HIV patients. We assessed the effect of transitioning from paper-based to an EMR-based system on appropriate placement on ART among eligible patients. Methods We conducted a retrospective, pre-post EMR study among patients enrolled in HIV care and eligible for ART at 17 rural Kenyan clinics and compared the: (1) proportion of patients eligible for ART based on CD4 count or WHO staging who initiate therapy; (2) time from eligibility for ART to ART initiation; (3) time from ART initiation to first CD4 test. Results 7298 patients were eligible for ART; 54.8% (n=3998) were enrolled in HIV care using a paper-based system while 45.2% (n=3300) were enrolled after the implementation of the EMR. EMR was independently associated with a 22% increase in the odds of initiating ART among eligible patients (adjusted OR (aOR) 1.22, 95% CI 1.12 to 1.33). The proportion of ART-eligible patients not receiving ART was 20.3% and 15.1% for paper and EMR, respectively (χ2=33.5, p<0.01). Median time from ART eligibility to ART initiation was 29.1 days (IQR: 14.1–62.1) for paper compared to 27 days (IQR: 12.9–50.1) for EMR. Conclusions EMRs can improve quality of HIV care through appropriate placement of ART-eligible patients on treatment in resource limited settings. However, other non-EMR factors influence timely initiation of ART.
Robustness and generalization of model-free learning for robot kinematic control using a nested-hierarchical multi-agent topology

This paper focuses on evaluating the robustness and knowledge generalization properties of a model-free learning mechanism, applied for the kinematic control of robot manipulation chains based on a nested-hierarchical multi-agent architecture. In the proposed topology, the agents correspond to independent degrees-of-freedom (DOF) of the system, managing to gain experience over the task that they collaboratively perform by continuously exploring and exploiting their state-to-action mapping space. Each agent forms a local (partial) view of the global system state and task progress, through a recursive learning process. By organizing the agents in a nested topology, the goal is to facilitate modular scaling to more complex kinematic topologies, with loose control coupling among the agents. Reinforcement learning is applied within each agent, to evolve a local state-to-action mapping in a continuous domain, thus leading to a system that exhibits developmental properties. This work addresses problem settings in the domain of kinematic control of dexterous-redundant robot manipulation systems. The numerical experiments performed consider the case of a single-linkage open kinematic chain, presenting kinematic redundancies given the desired task-goal. The focal issue in these experiments is to assess the capacity of the proposed multi-agent system to progressively and autonomously acquire cooperative sensorimotor skills through a self-learning process, that is, without the use of any explicit model-based planning strategy. In this paper, generalization and robustness properties of the overall multi-agent system are explored. Furthermore, the proposed framework is evaluated in constrained motion tasks, both in static and non-static environments. The computational cost of the proposed multi-agent architecture is also assessed.
Learning the Similarity of Audio Music in Bag-of-frames Representation from Tagged Music Data

Due to the cold-start problem, measuring the similarity between two pieces of audio music based on their low-level acoustic features is critical to many Music Information Retrieval (MIR) systems. In this paper, we apply the bag-offrames (BOF) approach to represent low-level acoustic features of a song and exploit music tags to help improve the performance of the audio-based music similarity computation. We first introduce a Gaussian mixture model (GMM) as the encoding reference for BOF modeling, then we propose a novel learning algorithm to minimize the similarity gap between low-level acoustic features and music tags with respect to the prior weights of the pre-trained GMM. The results of audio-based query-by-example MIR experiments on the MajorMiner and Magnatagatune datasets demonstrate the effectiveness of the proposed method, which gives a potential to guide MIR systems that employ BOF modeling.
Collective Decision with 100 Kilobots Speed vs Accuracy in Binary Discrimination Problems

Achieving fast and accurate collective decisions with a large number of simple agents without relying on a central planning unit or on global communication is essential for developing complex collective behaviors. In this paper, we investigate the speed versus accuracy trade-oﬀ in collective decision-making in the context of a binary discrimination problem—i.e., how a swarm can collectively determine the best of two options. We describe a novel, fully distributed collective decision-making strategy that only requires agents with minimal capabilities and is faster than previous approaches. We evaluate our strategy experimentally, using a swarm of 100 Kilobots, and we study it theoretically, using both continuum and ﬁnite-size models. We ﬁnd that the main factor aﬀecting the speed versus accuracy trade-oﬀ of our strategy is the agents neighborhood size—i.e., the number of agents with whom the current opinion of each agent is shared. The proposed strategy and the associated theoretical framework can be used to design swarms that take collective decisions at a given level of speed and/or accuracy.
A novel design method for highly selective and tunable microwave bandpass filter

A cascaded filter design method is proposed and realized by combline topology for the flexible bandpass filters with tunable centre frequency and tunable bandwidth without the need for adjusting the inter-resonator couplings. This is achieved by cascading a quasi low-pass filter and a quasi high-pass filter, while minimizing interaction between the filters without the need for an isolator between the filters. Simulated results are presented.
Intracellular routing of GLcNAc-bearing molecules in thyrocytes: selective recycling through the Golgi apparatus

Previous experiments led us to speculate that thyrocytes contain a recycling system for GlcNAc-bearing immature thyroglobulin molecules which prevents these molecules from lysosomal degradation (Miquelis, R., C. Alquier, and M. Monsigny. 1987. J. Biol. Chem. 262:15291-15298). To confirm this hypothesis, the fate of GlcNAc-bearing proteins after internalization by thyrocytes was monitored and compared to that of fluid phase markers. Kinetic internalization studies were performed using 125I-GlcNAc-BSA and 131I-Man-BSA. We observed that the apparent intake rate as well as the amount of hydrolyzed GlcNAc-BSA are smaller than the corresponding values for Man-BSA. These differences were reduced by GlcNAc competitors (thyroglobulin and ovomucoid) or a weak base (chloroquine). Part of the internalized GlcNAc-BSA was released into the extracellular milieu at a higher rate and shorter half life (t1/2 = approximately 30 min) than the Man-BSA (t1/2 = approximately 8 h). Subcellular homing was first studied by cell fractionation after internalization using 125I-ovomucoid and 131I-BSA. During Percoll density gradient fractionation, endogenous thyroperoxidase was used to separate subsets of organelles involved in the biosynthetic exocytotic pathway. Incubation of the cell homogenate in the presence of DAB and H2O2 before cell fractionation give rise to a shift in the density of organelles containing 3.5 times more ovomucoid than BSA. Discontinuous sucrose gradient showed that: (a) thyroperoxidase was colocalized with galactosyltransferase-contraining organelles in Golgi-rich subfractions; and (b) that at every time studied from 10 to 100 min, the ovomucoid/BSA ratio was higher in these organelles than in other subfractions. Finally we also observed that: (a) ovomucoid sequestered in the Golgi-rich subfraction incorporated [3H]galactose; and (b) that part of internalized ovomucoid was localized on the Golgi stacks as well as elements of the trans-Golgi, as revealed by immunogold labeling on ultrathin cryosections. These data prove that in thyrocytes GlcNAc accessible sugar moieties on soluble internalized molecules are sufficient to trigger their recycling via the Golgi apparatus.
Deep Sea Image Mosaic Based on SIFT Algorithm

This paper presents a new technique of deep sea image mosaic based on SIFT(Scale-invariant feature transform) algorithm. The SIFT algorithm by means of the median filter to the noise processing and itself has a good ability to resist scale changes, It can effectively match the characteristics of the two deep-sea biological images in the case of parallax. In the same coordinate system, the corresponding coordinate transformation is made according to the matching characteristic points. And the neighborhood average algorithm is used to optimize the processing. The whole process of using MATLAB to achieve, The program interface is simplified to enter two images.
Whole Brain Resting-State Analysis Reveals Decreased Functional Connectivity in Major Depression

Recently, both increases and decreases in resting-state functional connectivity have been found in major depression. However, these studies only assessed functional connectivity within a specific network or between a few regions of interest, while comorbidity and use of medication was not always controlled for. Therefore, the aim of the current study was to investigate whole-brain functional connectivity, unbiased by a priori definition of regions or networks of interest, in medication-free depressive patients without comorbidity. We analyzed resting-state fMRI data of 19 medication-free patients with a recent diagnosis of major depression (within 6 months before inclusion) and no comorbidity, and 19 age- and gender-matched controls. Independent component analysis was employed on the concatenated data sets of all participants. Thirteen functionally relevant networks were identified, describing the entire study sample. Next, individual representations of the networks were created using a dual regression method. Statistical inference was subsequently done on these spatial maps using voxel-wise permutation tests. Abnormal functional connectivity was found within three resting-state networks in depression: (1) decreased bilateral amygdala and left anterior insula connectivity in an affective network, (2) reduced connectivity of the left frontal pole in a network associated with attention and working memory, and (3) decreased bilateral lingual gyrus connectivity within ventromedial visual regions. None of these effects were associated with symptom severity or gray matter density. We found abnormal resting-state functional connectivity not previously associated with major depression, which might relate to abnormal affect regulation and mild cognitive deficits, both associated with the symptomatology of the disorder.
Spider hosts (Arachnida, Araneae) and wasp parasitoids (Insecta, Hymenoptera, Ichneumonidae, Ephialtini) matched using DNA barcodes

Abstract The study of parasitoids and their hosts suffers from a lack of reliable taxonomic data. We use a combination of morphological characters and DNA sequences to produce taxonomic determinations that can be verified with reference to specimens in an accessible collection and DNA barcode sequences posted to the Barcode of Life database (BOLD). We demonstrate that DNA can be successfully extracted from consumed host spiders and the shed pupal case of a wasp using non-destructive methods. We found Acrodactyla quadrisculpta to be a parasitoid of Tetragnatha montana; Zatypota percontatoria and Zatypota bohemani both are parasitoids of Neottiura bimaculata. Zatypota anomala is a parasitoid of an as yet unidentified host in the family Dictynidae, but the host species may be possible to identify in the future as the library of reference sequences on BOLD continues to grow. The study of parasitoids and their hosts traditionally requires specialized knowledge and techniques, and accumulating data is a slow process. DNA barcoding could allow more professional and amateur naturalists to contribute data to this field of study. A publication venue dedicated to aggregating datasets of all sizes online is well suited to this model of distributed science.