Miracle-dz/UniFAR-FTUs huggingface dataset:
Swing phase estimation in paralyzed persons walking

In the paper we present the sensory system aimed for FES gait reeducation of incomplete spinal cord injured persons. The proposed system consists of four accelerometers, gyro and two goniometers placed along the shank of the paralyzed leg. The data assessed are input into mathematical algorithms estimating the swing phase quality. The estimation is based on swing phase detection and signal correlation and is used to determine the cognitive feedback signal. The feedback signal is delivered to the patient as an auditory signal. The preliminary measurements were performed in three healthy and two incomplete spinal cord injured persons with C6 and C6-7 lesion during treadmill walking. FES was manually triggered by a physiotherapist. The results have shown that the proposed multisensory system was successful in gait quality estimation. Therefore, the use of FES multisensory system and cognitive feedback could be an efficient rehabilitative approach in gait reeduction.
Sphyrapicus varius (Yellow-Bellied Sapsucker) Use of Cotinus obovatus (American Smoketree) in the Ozark Mountains

Abstract Sphyrapicus varius (Yellow-bellied Sapsucker) has been reported drilling sap wells in more than 250 species of trees and woody vines in eastern North America. Criteria for species selection and use of geographically restricted endemics are poorly understood. Here I report drilling frequencies in Cotinus obovatus (American Smoketree), a rare endemic whose center of abundance occurs in the wintering range of Yellow-bellied Sapsuckers in the Ozark Mountains. Horizontal bands of sap wells were present on 4.5% of specimens (DBH ≥ 7 cm; n = 402) and 12.1% of larger-diameter classes (DBH ≥ 20 cm; n = 149). Sapsuckers preferred larger trees exhibiting little cambial dieback. Latticed arrays of sap wells similar to those observed on breeding territories were present on several large specimens. This survey indicates that the Yellow-bellied Sapsucker exploits rare species that may only be encountered on their winter territories. Documentation of a yearling inspecting a preexisting array of sap wells suggests that yearlings may obtain cues for appropriate tree species selection by examining sapsucker drillings encountered on wintering grounds. Because sap wells persist for years, cultural transmission of sapping information is likely transgenerational.
An integrated Asian human SNV and indel benchmark combining multiple sequencing methods

Precision medicine of human requires an accurate and complete reference variant benchmark for different populations. A human standard cell line of NA12878 provides a good reference for part of the human populations, but it is still lack of a fine reference standard sample and variant benchmark for the Asians. Here, we constructed a stabilized cell line of a Chinese Han volunteer. We received about 4.16T clean data of the sample using eight sequencing strategies in different laboratories, including two BGI regular NGS platforms, three Illumina regular NGS platforms, two linked-read libraries, and PacBio CCS model. The sequencing depth and reference coverage of eight sequencing strategies have reached the saturation. We detected small variants of SNPs and Indels using the eight data sets and obtained eight variant sets by performing a series of strictly quality control. Finally, we got 3.35M SNPs and 349K indels supported by all of sequencing data, which could be considered as a high confidence standard small variant sets for the studies. Besides, we also detected 5,913 high quality SNPs located in the high homologous regions supported by both linked-reads and CCS data benefited by their long-range information, while these regions are recalcitrant to regular NGS data due to the limited mappability and read length. We compared the later SNPs against the public databases and 969 sites of them were novel SNPs, indicating these SNPs provide a vital complement for the variant database. Moreover, we also phased more than 99% heterozygous SNPs also supported by linked-reads and CCS data. This work provided an integrated Asians SNV and indel benchmark for the further basic studies and precision medicine.
A field panel/finite difference method for potential unsteady transonic flow

A hybrid method for calculating time-linearized transonic potential flows is described. The method combines the advantages of finite difference and integral methods such that computation times are reduced to a level acceptable for routine flutter applications. The corresponding computer code FTRAN3 has been applied to several wing planforms. The results correlate satisfactorily with experimental data and results of other calculation methods.
CTA Quantification and Multi-modal Visualization for Assessing Coronary Artery Disease

textabstractIn cardiovascular disease, relating a coronary stenosis to a cardiac perfusion defect is of importance for selecting and planning the proper treatment. However, this is challenging owing to the high anatomical variability of the coronary arteries between patients. Anatomical and functional imaging is routinely obtained from multiple imaging modalities. The goal of the work described in this thesis is to develop and evaluate techniques to quantify cardiac and coronary geometry from computed tomography angiography (CTA), and to combine this anatomical information with functional information extracted from either perfusion magnetic resonance imaging (MRI) or single-photon emission computed tomography myocardial perfusion imaging (SPECT-MPI) to support diagnosis and therapy planning in coronary artery disease (CAD). In the remainder of this chapter, the cardiac anatomy and pathologies will be introduced (Section 1.1 and 1.2), and the imaging techniques currently used to assess coronary artery disease will be presented in Section 1.3, with a highlight on hybrid imaging. Following the introduction, an outline of this thesis is proposed in Section 1.4
Visual working memory representations in visual and parietal cortex do not remap after eye movements

Previous studies have suggested that stimulus representations in the visual system are remapped across eye movements during perception. Interestingly, our visual system does not only process stimuli that are directly available to our eyes, but may also have a role in maintaining information in VWM over a period of seconds. It remains unclear if saccadic remapping also occurs for stimuli that are held in working memory and whether eye movements degrade VWM representations in visual cortex. Here, we directly compared the content of VWM in early visual areas for saccade and no-saccade conditions using MVPA of delay-related activity measured with fMRI. Specifically, we probed item-related VWM representations of the remembered grating orientation from contralateral and ipsilateral early visual areas (V1 – V3) and the intraparietal sulcus (IPS). When participants did not make a saccade, VWM representations were robustly present in contralateral early visual cortex. Surprisingly, VWM representations disappeared from contralateral V1-V3 after the saccade shifted the location of the remembered grating to the opposite visual field. In contrast to our saccadic remapping hypothesis, we found no evidence for the representations of the remembered grating at the saccadic target location in the opposite visual field, suggesting that there is no evidence for remapping of VWM in early visual cortex. Interestingly, IPS showed persistent VWM representations in both the saccade and no-saccade condition. Together, our results indicate that VWM representations in early visual cortex are not remapped across eye movements, potentially limiting the role of early visual cortex in VWM storage. Significance Statement It has been well documented that our visual system does not only process stimuli that are directly available to our eyes, but may also have a role in maintaining information in visual working memory over a few seconds. Previous research has indicated that stimulus features are remapped across eye movement to aid visual stability. In the current study, we show that visual working memory information does not remap after eye movements. In addition, visual working memory representations are degraded after eye movements in early visual cortex, but not in parietal cortex, potentially limiting the role of early visual cortex in VWM storage.
Quantitative Trait Loci Mapping for Lameness Associated Phenotypes in Holstein–Friesian Dairy Cattle

Lameness represents a significant challenge for the dairy cattle industry, resulting in economic losses and reduced animal health and welfare. The existence of underlying genomic variation for lameness associated traits has the potential to improve selection strategies by using genomic markers. Therefore, the aim of this study was to identify genomic regions and potential candidate genes associated with lameness traits. Lameness related lesions and digital cushion thickness were studied using records collected by our research team, farm records, and a combination of both. Genome-wide analyses were performed to identify significant genomic effects, and a combination of single SNP association analysis and regional heritability mapping was used to identify associated genomic regions. Significant genomic effects were identified for several lameness related traits: Two genomic regions were identified on chromosome 3 associated with digital dermatitis and interdigital hyperplasia, one genomic region on chromosome 23 associated with interdigital hyperplasia, and one genomic region on chromosome 2 associated with sole haemorrhage. Candidate genes in those regions are mainly related to immune response and fibroblast proliferation. Quantitative trait loci (QTL) identified in this study could enlighten the understanding of lameness pathogenesis, providing an opportunity to improve health and welfare in dairy cattle with the addition of these regions into selection programs.
Fitness functions, genetic and non-genetic inheritance, and why ecological dynamics and evolution are inevitably linked

Fitness functions are at the heart of ecology and evolution as they simultaneously determine both population dynamics and the strength of selection. We link the Breeders and Price equations with structured population models constructed from fitness functions to show how ecological and evolutionary dynamics are intimately linked. Analyses of our models reveal i) how multi-generational predictions of evolution are sensitive to assumptions about phenotypic plasticity and non-genetic inheritance, ii) that factors that reduce the per time-step population growth rate such as negative density-dependence and antagonistic species interactions are generally expected to accelerate rates of evolution compared to cases when they are absent, iii) that evolution is expected to occur fastest when it is cryptic (all other things being equal) and iv) that eco-evolutionary dynamics are likely widespread and can be studied using evolutionarily explicit structured population models.
Strong population structure and limited gene flow between Yellow-billed Ducks and Mallards in southern Africa

ABSTRACT Secondary contact and hybridization between recently diverged taxa have been increasing due to anthropogenic changes to the environment. Determining whether secondary contact leads to gene flow between species is important for understanding both the evolutionary consequences of such events (i.e. genetic swamping, speciation reversal, hybrid speciation) and for establishing proper conservation measures. Mallards (Anas platyrhynchos), which natively have a Holarctic distribution, have been introduced nearly worldwide due to game-farm and domestic pet releases. Their expanding range has resulted in secondary contact and increased incidences of hybridization with many closely related Mallard-like ducks that comprise the Mallard complex. Here, we assay molecular diversity for 19 nuclear introns and the mitochondrial DNA for wild Mallards (n = 50) across their Holarctic range and Yellow-billed Ducks (n = 30–75; Anas undulata) from southern Africa to determine population genetic structure and test for evidence of Mallard introgression into Yellow-billed Ducks. While we found limited support for contemporary gene flow across nuclear markers, we provide evidence from mitochondrial DNA that best supports ancient gene flow between Yellow-billed Ducks and Mallards. Yellow-billed Ducks best fit a single population at nuclear markers but show some location-specific mtDNA structure that suggests recent founder or bottleneck events. Although we find that introgression from Mallards into Yellow-billed Duck is limited, Yellow-billed Duck populations should be monitored to determine if expanding feral Mallard populations in southern Africa are increasing introgression.
Occupancy patterns and upper range limits of lowland Bornean birds along an elevational gradient

The traditional view of species’ distributions is that they are less abundant near the edges of their ranges and more abundant towards the centre. Testing this pattern is difficult because of the complexity of distributions across wide geographical areas. An alternative strategy, however, is to measure species’ distributional patterns along elevational gradients. We applied this strategy to examine whether lowland forest birds are indeed less common near their upper range limits on a Bornean mountain, and tested co‐occurrence patterns among species for potential causes of attenuation, including signatures of habitat selection and competition at the periphery of their ranges.
THE DIVERSITY OF UNDERSTOREY BIRDS IN FOREST FRAGMENTS AND OIL PALM PLANTATION, SARAWAK, BORNEO

Much of the Bornean rainforest has been converted to oil palm plantation. This has resulted in forest fragmentation, which in turn has led to changes in avian assemblages in these fragments. This study: (1) examines the diversity of understorey birds at the edge, in forest fragments, and in neighbouring oil palm plantation; (2) compares the bird assemblages along distance gradients from the forest edge; 3) identifies the species common to both forest and oil palm plantation; and 4) examines seasonal variation (dry and wet season) in bird diversity. Understorey birds were mist-netted from November 2013 to April 2015 (22 680 net-hours). A total of 342 individuals comprising 58 species from 25 families were captured. Sampling effort did not yield an asymptotic species accumulation curve and an estimated 77% of all species were captured. Species diversity was greatest at the edge compared to the forest interior and oil palm interior. Species composition differed along the forest-oil palm gradient, with some species confined to the edge, oil palm and forest habitat. Those edge species that also occurred in the oil palm plantation were relatively abundant. Regular surveys of avian assemblage will aid monitoring of habitat quality and change, as well as ecosystem functionality and the maintenance of vital ecosystem services that benefit both native vegetation and oil palm.
Prognostic value of Red Blood Cell Distribution Width in Acute Kidney Injury Patients: A Systematic Review and Meta-analysis

Background The conflicting result with regard to Red Cell Distribution Width (RDW) with Acute Kidney Injury (AKI) has been reported. This systematic review and meta-analysis were aimed to investigate RDW and prognostic value in AKI patients. Methods/Main Results This meta-analysis included 1251 cases and 1663 controls with a total of 7 enrolled published papers. The results of RDW levels were significantly associated with patients of AKI (WMD=1.127, 95% CI=0.426-1.827; P=0.002), with statistically significant heterogeneity (I2 =95.80%, Pheterogeneity =0.000, random-effects model). Conclusions In conclusion, the results of this present meta-analysis suggest that the RDW value is a positive prognostic indicator in patients with AKI. However, these results were obtained on the basis of RCS or small sample sizes studies. Further functional studies with additional data would be needed to validate our findings.
Southern Flying Squirrels (Glaucomys volans) as Major Predators of Avian Nest Boxes in Conecuh National Forest, Alabama

Abstract Bird population dynamics are strongly affected by the ability to successfully reproduce, and nest predation is the primary cause of reproductive failure for most birds. Efforts to understand nest predation and manage its effects on species of conservation concern require knowledge of the ecology of associated predator assemblages. Recently, studies using cameras to record events at nests have illuminated this previously under-studied avian life stage, but such studies have been largely limited to open-cup nests. Cavity nests may be depredated by a different suite of predators, and incubating or brooding females occupying such nests may be more vulnerable to predation relative to open-cup nests. Here, we used motion-activated, infrared trail cameras to record predators of artificial nest boxes in a Pinus palustris Mill. (Longleaf Pine) forest in southern Alabama. Although Glaucomys volans L. (Southern Flying Squirrel) have only rarely been captured on film preying on nests, we found them to be responsible for the vast majority (84%) of bird-nest depredations at nest boxes, and these depredations contributed to a surprisingly low overall rate of nest success (∼20%). These results may have implications for the conservation of birds that nest in artificial cavities in Longleaf Pine forests and highlight the importance of further studies on predator assemblages and their effects on nesting birds.
Caracterização molecular da população viral associada ao mosaico comum em trigo no Brasil.

O mosaico comum e uma importante doenca viral da cultura do trigo, sendo atribuido ao Soil-borne wheat mosaic virus (SBWMV - Furovirus) e Wheat spindle streak mosaic virus (WSSMV - Bymovirus), ambos transmitidos por Polymyxa graminis. A doenca ocasiona reducoes significativas de produtividade se cultivares suscetiveis forem semeadas em areas com a presenca do vetor e em condicoes favoraveis como inverno frio e umido (Lau, 2014).
Novel nanomaterial-based antibacterial photodynamic therapies to combat oral bacterial biofilms and infectious diseases

Abstract Oral diseases such as tooth caries, periodontal diseases, endodontic infections, etc., are prevalent worldwide. The heavy burden of oral infectious diseases and their consequences on the patients’ quality of life indicates a strong need for developing effective therapies. Advanced understandings of such oral diseases, e.g., inflammatory periodontal lesions, have raised the demand for antibacterial therapeutic strategies, because these diseases are caused by viruses and bacteria. The application of antimicrobial photodynamic therapy (aPDT) on oral infectious diseases has attracted tremendous interest in the past decade. However, aPDT had a minimal effect on the viability of organized biofilms due to the hydrophobic nature of the majority of the photosensitizers (PSs). Therefore, novel nanotechnologies were rapidly developed to target the delivery of hydrophobic PSs into microorganisms for the antimicrobial performance improvement of aPDT. This review focuses on the state-of-the-art of nanomaterials applications in aPDT against oral infectious diseases. The first part of this article focuses on the cutting-edge research on the synthesis, toxicity, and therapeutic effects of various forms of nanomaterials serving as PS carriers for aPDT applications. The second part discusses nanomaterials applications for aPDT in treatments of oral diseases. These novel bioactive nanomaterials have demonstrated great potential to serve as carriers for PSs to substantially enhance the PDT therapeutic effects. Furthermore, the novel aPDT applications not only have exciting therapeutic potential to inhibit bacterial plaque-initiated oral diseases, but also have a wide applicability to other biomedical and tissue engineering applications.
Antidepressants act by binding to the cholesterol-interaction site at TRKB neurotrophin receptor

It is unclear how binding of antidepressant drugs to their targets gives rise to the clinical antidepressant effect. We found that both typical and fast-acting antidepressants bind to a cholesterol interaction motif in the BDNF receptor TRKB, a known mediator of neuronal plasticity and antidepressant responses. Cholesterol stabilized a cross-shaped configuration of TRKB transmembrane domain dimers and prolonged TRKB cell surface expression and activation by BDNF. Mutation of the TRKB cholesterol interaction site or cholesterol depletion by pravastatin impaired BDNF-mediated plasticity and cellular and behavioral responses to antidepressants in vitro and in vivo. We suggest that binding to and facilitation of TRKB activity is the common mechanism for antidepressant action, and propose a framework for how molecular effects of antidepressants are translated into clinical mood recovery.
Cell motion as a stochastic process controlled by focal contacts dynamics

Directed cell motion is essential in physiological and pathological processes such as morphogenesis, wound healing and cancer spreading. Chemotaxis has often been proposed as the driving mechanism, even though evidence of long-range gradients is often lacking in vivo. By patterning adhesive regions in space, we control cell shape and the associated potential to move along one direction in another mode of migration coined ratchetaxis. We report that focal contacts distributions collectively dictate cell directionality, and bias is non-linearly increased by gap distance between adhesive regions. Focal contact dynamics on micro-patterns allow to integrate these phenomena in a consistent model where each focal contact can be translated into a force with known amplitude and direction, leading to quantitative predictions for cell motion in every condition. Altogether, our study shows how local and minutes timescale dynamics of focal adhesions and their distribution lead to long term cellular motion with simple geometric rules.
Perirectal injection of imaging materials for computed tomographic lymphography and near infrared fluorescent thoracoscopy in cats

For the treatment of chylothorax, the most common procedure is a thoracic duct ligation; however, recurrence of the issue is often common, generally due to the incomplete ligation of all thoracic duct tributaries. Therefore, accurate localisation of the thoracic duct tributaries is required to determine the ligation sites in each patient. The concept of the perirectal injection of the imaging materials, which provides a simple and minimally invasive approach, is investigated for computed tomographic (CT) lymphography and near infrared fluorescent thoracoscopy in cats. Three clinically healthy cats were used for the CT lymphography, and two clinically healthy cats were used for the near infrared fluorescent thoracoscopy. Iodine contrast agent for the CT or indocyanine green for the thoracoscopy was injected subcutaneously into the peri-anal tissue. The injection site was massaged for 5 min post-injection. However, in the indirect injection of the imaging materials, in three iohexol-administered cats, the abdominal lymphatics, cisterna chyle, and thoracic duct could be depicted by the CT lymphography; and in both indocyanine green-administered cats, the thoracic duct was depicted running alongside the aorta by the near infrared fluorescent thoracoscopy. The ideal imaging procedure for the thoracic duct ligation involves the pre-operative CT lymphography of the entire pathway of the lymphatic vessels in advance, followed by the direct visualisation using a thoracoscopy. A combined CT lymphography and thoracoscopy could be a reliable method for successful surgeries. Crucially, the subcutaneous peri-anal injection of a contrast/dye provides a simple and minimally invasive method for the pre-operative and intra-operative depiction of the lymphatic pathways.