Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence of a Reduced and Modified Mitochondrial Protein Import Apparatus in Microsporidian Mitosomes

ABSTRACT Microsporidia are a group of highly adapted obligate intracellular parasites that are now recognized as close relatives of fungi. Their adaptation to parasitism has resulted in broad and severe reduction at (i) a genomic level by extensive gene loss, gene compaction, and gene shortening; (ii) a biochemical level with the loss of much basic metabolism; and (iii) a cellular level, resulting in lost or cryptic organelles. Consistent with this trend, the mitochondrion is severely reduced, lacking ATP synthesis and other typical functions and apparently containing only a fraction of the proteins of canonical mitochondria. We have investigated the mitochondrial protein import apparatus of this reduced organelle in the microsporidian Encephalitozoon cuniculi and find evidence of reduced and modified machinery. Notably, a putative outer membrane receptor, Tom70, is reduced in length but maintains a conserved structure chiefly consisting of tetratricopeptide repeats. When expressed in Saccharomyces cerevisiae, EcTom70 inserts with the correct topology into the outer membrane of mitochondria but is unable to complement the growth defects of Tom70-deficient yeast. We have scanned genomic data using hidden Markov models for other homologues of import machinery proteins and find evidence of severe reduction of this system.
Cognitive Interventions Targeting Subjective Cognitive Complaints

Subjective cognitive complaints (SCCs) are being increasingly recognized as a preclinical phase of dementia. Thus, SCCs may represent a “promising” stage for planning and implementing preventive interventions aimed at reducing the incidence of cognitive disorders. The aim of the present study is to present and discuss the available evidence coming from clinical trials adopting cognitive interventions in individuals with SCCs. A systematic review of literature was conducted to evaluate the available trials testing nonpharmacological cognitive interventions for the prevention of dementia in subjects with SCCs. Six studies were included in the present study. Overall, most interventions showed to objectively improve cognitive performance in subjects with SCCs. A relevant heterogeneity was found concerning their characteristics and feasibility. Conversely, there is a current lack of evidence in the literature about the efficacy of nonpharmacological cognitive interventions for preventing dementia or cognitive impairment.
Suicidal Behavior in Dementia

Background: Some studies report a low suicide risk in general dementia and in Alzheimer’s disease (AD). Objective: To evaluate suicidal behavior among patients with semantic dementia (SD), a disorder that impairs semantic knowledge. Methods: We reviewed the presence of active suicidal behavior and related factors among 25 patients with SD compared to 111 age-matched patients with early-onset AD. Results: In all, 5 (20%) patients with SD had suicidal behavior (2 successfully killed themselves) compared to 1 (0.9%) with AD (P < .001). There was significantly more depression and greater premorbid history of suicidal behavior among the patients with SD compared to those with AD. Among the patients with SD, those with suicidal behavior, compared to those without, had more depression and greater insight into their deficits. Conclusions: Patients with SD are at special risk of committing suicide, particularly if they have depression and preserved insight. Possible mechanisms include an impaired sense of semantic competence with increased impulsivity.
Farnesol Induces Hydrogen Peroxide Resistance in Candida albicans Yeast by Inhibiting the Ras-Cyclic AMP Signaling Pathway

ABSTRACT Farnesol, a Candida albicans cell-cell signaling molecule that participates in the control of morphology, has an additional role in protection of the fungus against oxidative stress. In this report, we show that although farnesol induces the accumulation of intracellular reactive oxygen species (ROS), ROS generation is not necessary for the induction of catalase (Cat1)-mediated oxidative-stress resistance. Two antioxidants, α-tocopherol and, to a lesser extent, ascorbic acid effectively reduced intracellular ROS generation by farnesol but did not alter farnesol-induced oxidative-stress resistance. Farnesol inhibits the Ras1-adenylate cyclase (Cyr1) signaling pathway to achieve its effects on morphology under hypha-inducing conditions, and we demonstrate that farnesol induces oxidative-stress resistance by a similar mechanism. Strains lacking either Ras1 or Cyr1 no longer exhibited increased protection against hydrogen peroxide upon preincubation with farnesol. While we also observed the previously reported increase in the phosphorylation level of Hog1, a known regulator of oxidative-stress resistance, in the presence of farnesol, the hog1/hog1 mutant did not differ from wild-type strains in terms of farnesol-induced oxidative-stress resistance. Analysis of Hog1 levels and its phosphorylation states in different mutant backgrounds indicated that mutation of the components of the Ras1-adenylate cyclase pathway was sufficient to cause an increase of Hog1 phosphorylation even in the absence of farnesol or other exogenous sources of oxidative stress. This finding indicates the presence of unknown links between these signaling pathways. Our results suggest that farnesol effects on the Ras-adenylate cyclase cascade are responsible for many of the observed activities of this fungal signaling molecule.
Tagging of Endogenous Genes in a Toxoplasma gondii Strain Lacking Ku80

ABSTRACT As with other organisms with a completed genome sequence, opportunities for performing large-scale studies, such as expression and localization, on Toxoplasma gondii are now much more feasible. We present a system for tagging genes endogenously with yellow fluorescent protein (YFP) in a Δku80 strain. Ku80 is involved in DNA strand repair and nonhomologous DNA end joining; previous studies in other organisms have shown that in its absence, random integration is eliminated, allowing the insertion of constructs with homologous sequences into the proper loci. We generated a vector consisting of YFP and a dihydrofolate reductase-thymidylate synthase selectable marker. The YFP is preceded by a ligation-independent cloning (LIC) cassette, which allows the insertion of PCR products containing complementary LIC sequences. We demonstrated that the Δku80 strain is more effective and efficient in integrating the YFP-tagged constructs into the correct locus than wild-type strain RH. We then selected several hypothetical proteins that were identified by a proteomic screen of excreted-secreted antigens and that displayed microarray expression profiles similar to known micronemal proteins, with the thought that these could potentially be new proteins with roles in cell invasion. We localized these hypothetical proteins by YFP fluorescence and showed expression by immunoblotting. Our findings demonstrate that the combination of the Δku80 strain and the pYFP.LIC constructs reduces both the time and cost required to determine localization of a new gene of interest. This should allow the opportunity for performing larger-scale studies of novel T. gondii genes.
DYF-1 Is Required for Assembly of the Axoneme in Tetrahymena thermophila

ABSTRACT In most cilia, the axoneme can be subdivided into three segments: proximal (the transition zone), middle (with outer doublet microtubules), and distal (with singlet extensions of outer doublet microtubules). How the functionally distinct segments of the axoneme are assembled and maintained is not well understood. DYF-1 is a highly conserved ciliary protein containing tetratricopeptide repeats. In Caenorhabditis elegans, DYF-1 is specifically needed for assembly of the distal segment (G. Ou, O. E. Blacque, J. J. Snow, M. R. Leroux, and J. M. Scholey. Nature. 436:583-587, 2005). We show that Tetrahymena cells lacking an ortholog of DYF-1, Dyf1p, can assemble only extremely short axoneme remnants that have structural defects of diverse natures, including the absence of central pair and outer doublet microtubules and incomplete or absent B tubules on the outer microtubules. Thus, in Tetrahymena, DYF-1 is needed for either assembly or stability of the entire axoneme. Our observations support the conserved function for DYF-1 in axoneme assembly or stability but also show that the consequences of loss of DYF-1 for axoneme segments are organism specific.
Lung motion correction on respiratory gated 3-D PET/CT images

Motion is a source of degradation in positron emission tomography (PET)/computed tomography (CT) images. As the PET images represent the sum of information over the whole respiratory cycle, attenuation correction with the help of CT images may lead to false staging or quantification of the radioactive uptake especially in the case of small tumors. We present an approach avoiding these difficulties by respiratory-gating the PET data and correcting it for motion with optical flow algorithms. The resulting dataset contains all the PET information and minimal motion and, thus, allows more accurate attenuation correction and quantification.
Wavelet Based Noise Reduction in CT-Images Using Correlation Analysis

The projection data measured in computed tomography (CT) and, consequently, the slices reconstructed from these data are noisy. We present a new wavelet based structure-preserving method for noise reduction in CT-images that can be used in combination with different reconstruction methods. The approach is based on the assumption that data can be decomposed into information and temporally uncorrelated noise. In CT two spatially identical images can be generated by reconstructions from disjoint subsets of projections: using the latest generation dual source CT-scanners one image can be reconstructed from the projections acquired at the first, the other image from the projections acquired at the second detector. For standard CT-scanners the two images can be generated by splitting up the set of projections into even and odd numbered projections. The resulting images show the same information but differ with respect to image noise. The analysis of correlations between the wavelet representations of the input images allows separating information from noise down to a certain signal-to-noise level. Wavelet coefficients with small correlation are suppressed, while those with high correlations are assumed to represent structures and are preserved. The final noise-suppressed image is reconstructed from the averaged and weighted wavelet coefficients of the input images. The proposed method is robust, of low complexity and adapts itself to the noise in the images. The quantitative and qualitative evaluation based on phantom as well as real clinical data showed, that high noise reduction rates of around 40% can be achieved without noticeable loss of image resolution.
International Ballroom Dancing Against Neurodegeneration: A Randomized Controlled Trial in Greek Community-Dwelling Elders With Mild Cognitive impairment

Background: Many studies have highlighted the positive effects of dance in people with neurodegenerative diseases. Objectives: To explore the effects of International Ballroom Dancing on cognitive function in elders with amnestic mild cognitive impairment (aMCI). Methods: One-hundred twenty-nine elderly patients with aMCI diagnosis (mean age 66.8 ± 10.1 years) were randomly assigned into 2 groups: intervention group (IG, n = 66) and control group (CG, n = 63). The IG exercised systematically for 10 months, and both groups were submitted to extensive neuropsychological assessment prior and after the 10-month period. Results: According to the independent sample t test at the follow-up, significant differences between groups were found in benefit of the IG while the CG showed worse performance in the majority of neuropsychological tests. According to the Student t test, better performance is detected in IG in contrast with CG, which had worse performance almost in all scales. Conclusion: Dance may be an important nonpharmacological approach that can benefit cognitive functions.
Leg Wound Infections Following Greater Saphenous Vein Harvesting: Minimally Invasive Vein Harvesting Versus Conventional Vein Harvesting

Wound complications associated with long incisions used to harvest the greater saphenous vein are common and well documented. We compared leg wound infection rates, wound healing disturbances (WHDs), length of vein harvested, vein harvest time, and total surgical time between minimally invasive saphenous vein harvesting (MIVH) and conventional vein harvesting (CVH) techniques. This meta-analysis showed a significant reduction in wound infections in favor of the MIVH group (odds ratio = 0.19; 95% confidence interval = 0.14-0.25) and a significant reduction in WHDs in favor of the MIVH group (odds ratio = 0.26; 95% confidence interval = 0.20-0.34). The MIVH and CVH techniques are equivalent with respect to saphenous vein harvest time, saphenous vein harvest length, and total surgical time. A visual inspection of “funnel” plots suggests a mild to moderate publication bias. This meta-analysis suggests that leg wound infections and wound healing disturbances are reduced using MIVH techniques.
Ultrafast Doppler Imaging of Blood Flow Dynamics in the Myocardium

Imaging intramyocardial vascular flows in real-time could strongly help to achieve better diagnostic of cardiovascular diseases. To date, no standard imaging modality allows describing accurately myocardial blood flow dynamics with good spatial and temporal resolution. We recently introduced a novel ultrasonic Doppler imaging technique based on compounded plane waves transmissions at ultrafast frame rate. The high sensitivity of this ultrafast Doppler technique permits to image the intramyocardial blood flow and its dynamics. A dedicated demodulation-filtering process is implemented to compensate for the large tissue velocity of the myocardium during the cardiac cycle. A signed power Doppler processing provides the discrimination between arterial and venous flows. Experiments were performed in vivo in a large animal open chest model (N = 5 sheep) using a conventional ultrasonic probe placed at the surface of the heart. Results show the capability of the technique to image intramyocardial vascular flows in normal physiological conditions with good spatial and temporal resolution (10 ms). Flow dynamics over the cardiac cycle were investigated and the imaging method demonstrated a phase opposition of flow waveforms between arterial and venous flows. Finally, ultrafast Doppler combined with tissue motion compensation was found able to reveal vascular flow disruption in ischemic regions during occlusion of the main diagonal coronary artery.
List-Mode PET Motion Correction Using Markerless Head Tracking: Proof-of-Concept With Scans of Human Subject

A custom designed markerless tracking system was demonstrated to be applicable for positron emission tomography (PET) brain imaging. Precise head motion registration is crucial for accurate motion correction (MC) in PET imaging. State-of-the-art tracking systems applied with PET brain imaging rely on markers attached to the patient's head. The marker attachment is the main weakness of these systems. A healthy volunteer participating in a cigarette smoking study to image dopamine release was scanned twice for 2 h with 11C-racolopride on the high resolution research tomograph (HRRT) PET scanner. Head motion was independently measured, with a commercial marker-based device and the proposed vision-based system. A list-mode event-by-event reconstruction algorithm using the detected motion was applied. A phantom study with hand-controlled continuous random motion was obtained. Motion was time-varying with long drift motions of up to 18 mm and regular step-wise motion of 1-6 mm. The evaluated measures were significantly better for motion-corrected images compared to no MC. The demonstrated system agreed with a commercial integrated system. Motion-corrected images were improved in contrast recovery of small structures.
Investigation of the Role of Feature Selection and Weighted Voting in Random Forests for 3-D Volumetric Segmentation

This paper describes a novel 3-D segmentation technique posed within the Random Forests (RF) classification framework. Two improvements over the traditional RF framework are considered. Motivated by the high redundancy of feature selection in the traditional RF framework, the first contribution develops methods to improve voxel classification by selecting relatively “strong” features and neglecting “weak” ones. The second contribution involves weighting each tree in the forest during the testing stage, to provide an unbiased and more accurate decision than provided by the traditional RF. To demonstrate the improvement achieved by these enhancements, experimental validation is performed on adult brain MRI and 3-D fetal femoral ultrasound datasets. In a comparison of the new method with a traditional Random Forest, the new method showed a notable improvement in segmentation accuracy. We also compared the new method with other state-of-the-art techniques to place it in context of the current 3-D medical image segmentation literature.
FMT-PCCT: Hybrid Fluorescence Molecular Tomography—X-Ray Phase-Contrast CT Imaging of Mouse Models

The implementation of hybrid fluorescence molecular tomography (FMT) and X-ray computed tomography (CT) has been shown to be a necessary development, not only for combining anatomical with functional and molecular contrast, but also for generating optical images of high accuracy. FMT affords highly sensitive 3-D imaging of fluorescence bio-distribution, but in stand-alone form it offers images of low resolution. It was shown that FMT accuracy significantly improves by considering anatomical priors from CT. Conversely, CT generally suffers from low soft tissue contrast. Therefore utilization of CT data as prior information in FMT inversion is challenging when different internal organs are not clearly differentiated. Instead, we combined herein FMT with emerging X-ray phase-contrast CT (PCCT). PCCT relies on phase shift differences in tissue to achieve soft tissue contrast superior to conventional CT. We demonstrate for the first time FMT-PCCT imaging of different animal models, where FMT and PCCT scans were performed in vivo and ex vivo, respectively. The results show that FMT-PCCT expands the potential of FMT in imaging lesions with otherwise low or no CT contrast, while retaining the cost benefits of CT and simplicity of hybrid device realizations. The results point to the most accurate FMT performance to date.
Promising Role of ANGPTL4 Gene in Diabetic Wound Healing

Diabetes mellitus (DM) is one of the severe metabolic disorders of carbohydrate metabolism worldwide. Developing countries are at higher risk of DM, and there is significant evidence that it is epidemic in many economically developing and newly industrialized countries. Among all other complications associated with DM, delayed wound healing is a major concern in diabetic patients. Wound healing is a natural healing process that starts immediately after injury. This involves interaction of a complex cascade of cellular events that generates resurfacing, reconstitution, and restoration of the tensile strength of injured skin. There are multiple factors responsible for delayed wound healing among which the contribution of DM has been well documented. The wound healing process is also delayed by the metabolic, vascular, neurological, and inflammatory alterations, which are well known in both type 1 and type 2 diabetes. Keratinocytes are crucial for wound re-epithelialization, and defects in directed migration of keratinocytes due to DM are associated with the delayed wound healing process. Many factors responsible for re-epithelialization have been identified, characterized, and well described; however, the genes responsible for the healing process have only partially been illustrated. This article will therefore focus on the efficacy of ANGPTL4 (angiopoietin-like 4) gene, which plays a novel role in keratinocyte migration during wound healing.
The Use of Negative Pressure in Critical Necrotizing Fasciitis Treatment

Surgery complemented by antibiotics forms the backbone of the successful management of necrotizing fasciitis. But it will be very difficult to clear away extensive necrotizing tissue thoroughly in critically ill patients when their vital signs are unstable. The authors report the case of a 33-year-old woman who had extensive necrotizing fasciitis of the right lower limb with septic shock. The patient was severely anemic and malnutrition and had been given conservative debridement at bedside, that is, only detached necrotizing tissues was taken away while some other necrotizing tissue still remained, so that the skin tissue within the same area could be saved as much as possible. After debridement, negative pressure was applied at 125 mm Hg. Broad-spectrum antibiotics and effective supplementation were also complemented, thus controlling the septic shock. All necrotizing tissues were detached, and the sparing vital skin on necrotizing fascia was preserved successfully after negative pressure treatment. The patient was finally saved. In conclusion, negative pressure treatment may help diminish toxin absorbance, detach gangrene tissue, and preserve sparing vital tissue. This case suggests the value of combined use of negative pressure therapy and conservative debridement in critically ill patients with extensive necrotizing fasciitis.
Draft Genome Sequence of Frankia sp. Strain BMG5.23, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina glauca Grown in Tunisia

ABSTRACT Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.27-Mbp draft genome sequence for Frankia sp. strain BMG5.23, a salt-tolerant nitrogen-fixing actinobacterium isolated from root nodules of Casuarina glauca collected in Tunisia.
An Introduction to the Visual System: References

In recent years there has been a host of new advances in our understanding of how we see. From molecular genetics come details of the photopigments and the molecular causes of disorders like colour blindness. In-depth analysis has shown how a cell converts light into a neural signal using the photopigments. Traditional techniques of microelectrode recording along with new techniques of functional imaging - such as PET scans - have made it possible to understand how visual information is processed in the brain. This processing results in the single coherent perception of the world we see in our 'mind's eye'. An Introduction to the Visual System provides a concise, but detailed, overview of this field. It is clearly written, and each chapter ends with a helpful 'key points' section. It is ideal for anyone studying visual perception, from the second year of an undergraduate course onwards.
Draft Genome Sequences of Three European Laboratory Derivatives from Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933, Including Two Plasmids

ABSTRACT Escherichia coli O157:H7 EDL933, isolated in 1982 in the United States, was the first enterohemorrhagic E. coli (EHEC) strain sequenced. Unfortunately, European labs can no longer receive the original strain. We checked three European EDL933 derivatives and found major genetic deviations (deletions, inversions) in two strains. All EDL933 strains contain the cryptic EHEC-plasmid, not reported before.
Complete Genome Sequence of Bovine Polyomavirus Type 1 from Aborted Cattle, Isolated in Belgium in 2014

ABSTRACT The complete and fully annotated genome sequence of a bovine polyomavirus type 1 (BPyV/BEL/1/2014) from aborted cattle was assembled from a metagenomics data set. The 4,697-bp circular dsDNA genome contains 6 protein-coding genes. Bovine polyomavirus is unlikely to be causally related to the abortion cases.