Miracle-dz/UniFAR-FTUs huggingface dataset:
Venous and Arterial Responses to Partial Gravity

Introduction: Chronic exposure to the weightlessness-induced cephalad fluid shift is hypothesized to be a primary contributor to the development of spaceflight-associated neuro-ocular syndrome (SANS) and may be associated with an increased risk of venous thrombosis in the jugular vein. This study characterized the relationship between gravitational level (Gz-level) and acute vascular changes. Methods: Internal jugular vein (IJV) cross-sectional area, inferior vena cava (IVC) diameter, and common carotid artery (CCA) flow were measured using ultrasound in nine subjects (5F, 4M) while seated when exposed to 1.00-Gz, 0.75-Gz, 0.50-Gz, and 0.25-Gz during parabolic flight and while supine before flight (0-G analog). Additionally, IJV flow patterns were characterized. Results: IJV cross-sectional area progressively increased from 12 (95% CI: 9–16) mm2 during 1.00-Gz seated to 24 (13–35), 34 (21–46), 68 (40–97), and 103 (75–131) mm2 during 0.75-Gz, 0.50-Gz, and 0.25-Gz seated and 1.00-Gz supine, respectively. Also, IJV flow pattern shifted from the continuous forward flow observed during 1.00-Gz and 0.75-Gz seated to pulsatile flow during 0.50-Gz seated, 0.25-Gz seated, and 1.00-Gz supine. In contrast, we were unable to detect differences in IVC diameter measured during 1.00-G seated and any level of partial gravity or during 1.00-Gz supine. CCA blood flow during 1.00-G seated was significantly less than 0.75-Gz and 1.00-Gz supine but differences were not detected at partial gravity levels 0.50-Gz and 0.25-Gz. Conclusions: Acute exposure to decreasing Gz-levels is associated with an expansion of the IJV and flow patterns that become similar to those observed in supine subjects and in astronauts during spaceflight. These data suggest that Gz-levels greater than 0.50-Gz may be required to reduce the weightlessness-induced headward fluid shift that may contribute to the risks of SANS and venous thrombosis during spaceflight.
Acquisition, Maintenance, and Ecological Roles of Kleptoplasts in Planoglabratella opercularis (Foraminifera, Rhizaria)

Kleptoplasty or acquisition of chloroplasts from ingested photosynthetic organisms, is thought to be a key factor in determining the trophic requirements and carbon mineralization of foraminifera, consequently influencing their ecology, evolution, and calcification. However, the acquisition, maintenance, and functions of “stolen” chloroplasts (kleptoplasts) in foraminiferal cells have not been well characterized. Using molecular phylogeny and experimental measurements of oxygen flux and intracellular (vacuole) pH, we characterized aspects of kleptoplast origin and function in Planoglabratella opercularis (d’Orbigny), a rocky-shore benthic foraminifera. We determined that the kleptoplasts in P. opercularis are derived from various species of epiphytic diatoms. The acquisition of epiphytic diatoms is congruent with the behavior of P. opercularis, which crawls on the thalli of coralline algae and grazes on the microalgae on the algal surface. Kleptoplasts were located near the host foraminiferal cell periphery, just under the pore plug, mainly along the dorsal side, which is important for oxygenic photosynthesis. The lifespan of kleptoplasts varied according to food availability and to the intensity and duration of light irradiation. Planoglabratella opercularis was able to capture not only diatom chloroplasts but also those from Chlorella. Kleptoplastids of diatom origin decreased in autofluorescence and were digested within 11 days under light in the absence of food. This suggests that host foraminifera frequently capture new diatoms to sustain kleptoplasts. Kleptoplastid autofluorescence was prolonged in the dark or 24:24-h light:dark cycle, and when food was available. Host foraminifera metabolized food to maintain the activity of kleptoplasts and effectively utilized photosynthetic products from both organic and inorganic materials in response to the ambient environment. This suggests that P. opercularis behaves as a mixotroph. Simultaneously, kleptoplasts maintain a high intracellular pH environment, indicating that foraminifera capture kleptoplasts not only to gain their photosynthates but also to control the intracellular pH levels to construct a high magnesian calcite test.
Dihydromyricetin Protects Against Gentamicin-Induced Ototoxicity via PGC-1α/SIRT3 Signaling in vitro

Aminoglycoside-induced ototoxicity can have a major impact on patients’ quality of life and social development problems. Oxidative stress affects normal physiologic functions and has been implicated in aminoglycoside-induced inner ear injury. Excessive accumulation of reactive oxygen species (ROS) damages DNA, lipids, and proteins in cells and induces their apoptosis. Dihydromyricetin (DHM) is a natural flavonol with a wide range of health benefits including anti-inflammatory, antitumor, and antioxidant effects; however, its effects and mechanism of action in auditory hair cells are not well understood. The present study investigated the antioxidant mechanism and anti-ototoxic potential of DHM using House Ear Institute-Organ of Corti (HEI-OC)1 auditory cells and cochlear explant cultures prepared from Kunming mice. We used gentamicin to establish aminoglycoside-induced ototoxicity models. Histological and physiological analyses were carried out to determine DHM’s pharmacological effects on gentamicin-induced ototoxicity. Results showed DHM contributes to protecting cells from apoptotic cell death by inhibiting ROS accumulation. Western blotting and quantitative RT-PCR analyses revealed that DHM exerted its otoprotective effects by up-regulating levels of peroxisome proliferator activated receptor γ-coactivator (PGC)-1α and Sirtuin (SIRT)3. And the role of PGC-1α and SIRT3 in the protective effects of DHM was evaluated by pharmacologic inhibition of these factors using SR-18292 and 3-(1H-1,2,3-triazol-4-yl) pyridine, respectively, which indicated DHM’s protective effect was dependent on activation of the PGC-1α/SIRT3 signaling. Our study is the first report to identify DHM as a potential otoprotective drug and provides a basis for the prevention and treatment of hearing loss caused by aminoglycoside antibiotic-induced oxidative damage to auditory hair cells.
Longitudinal Stroke Recovery Associated With Dysregulation of Complement System—A Proteomics Pathway Analysis

Currently the longitudinal proteomic profile of post-ischemic stroke recovery is relatively unknown with few well-accepted biomarkers or understanding of the biological systems that underpin recovery. We aimed to characterize plasma derived biological pathways associated with recovery during the first year post event using a discovery proteomics workflow coupled with a topological pathway systems biology approach. Blood samples (n = 180, ethylenediaminetetraacetic acid plasma) were collected from a subgroup of 60 first episode stroke survivors from the Australian START study at 3 timepoints: 3–7 days (T1), 3-months (T2) and 12-months (T3) post-stroke. Samples were analyzed by liquid chromatography mass spectrometry using label-free quantification (data available at ProteomeXchange with identifier PXD015006). Differential expression analysis revealed that 29 proteins between T1 and T2, and 33 proteins between T1 and T3 were significantly different, with 18 proteins commonly differentially expressed across the two time periods. Pathway analysis was conducted using Gene Graph Enrichment Analysis on both the Kyoto Encyclopedia of Genes and Genomes and Reactome databases. Pathway analysis revealed that the significantly differentiated proteins between T1 and T2 were consistently found to belong to the complement pathway. Further correlational analyses utilized to examine the changes in regulatory effects of proteins over time identified significant inhibitory regulation of clusterin on complement component 9. Longitudinal post-stroke blood proteomics profiles suggest that the alternative pathway of complement activation remains in a state of higher activation from 3-7 days to 3 months post-stroke, while simultaneously being regulated by clusterin and vitronectin. These findings also suggest that post-stroke induced sterile inflammation and immunosuppression could inhibit recovery within the 3-month window post-stroke.
The Importance of Cursive Handwriting Over Typewriting for Learning in the Classroom: A High-Density EEG Study of 12-Year-Old Children and Young Adults

To write by hand, to type, or to draw – which of these strategies is the most efficient for optimal learning in the classroom? As digital devices are increasingly replacing traditional writing by hand, it is crucial to examine the long-term implications of this practice. High-density electroencephalogram (HD EEG) was used in 12 young adults and 12, 12-year-old children to study brain electrical activity as they were writing in cursive by hand, typewriting, or drawing visually presented words that were varying in difficulty. Analyses of temporal spectral evolution (TSE, i.e., time-dependent amplitude changes) were performed on EEG data recorded with a 256-channel sensor array. For young adults, we found that when writing by hand using a digital pen on a touchscreen, brain areas in the parietal and central regions showed event-related synchronized activity in the theta range. Existing literature suggests that such oscillatory neuronal activity in these particular brain areas is important for memory and for the encoding of new information and, therefore, provides the brain with optimal conditions for learning. When drawing, we found similar activation patterns in the parietal areas, in addition to event-related desynchronization in the alpha/beta range, suggesting both similarities but also slight differences in activation patterns when drawing and writing by hand. When typewriting on a keyboard, we found event-related desynchronized activity in the theta range and, to a lesser extent, in the alpha range in parietal and central brain regions. However, as this activity was desynchronized and differed from when writing by hand and drawing, its relation to learning remains unclear. For 12-year-old children, the same activation patterns were found, but to a lesser extent. We suggest that children, from an early age, must be exposed to handwriting and drawing activities in school to establish the neuronal oscillation patterns that are beneficial for learning. We conclude that because of the benefits of sensory-motor integration due to the larger involvement of the senses as well as fine and precisely controlled hand movements when writing by hand and when drawing, it is vital to maintain both activities in a learning environment to facilitate and optimize learning.
Aberrant Correlation Between the Default Mode and Salience Networks in Mild Traumatic Brain Injury

Objectives: The specific intrinsic network coupling abnormalities in mild traumatic brain injury (mTBI) patients are poorly understood. Our objective is to compare the correlations among the default mode, salience, and central executive networks in patients with mTBI and healthy controls. Methods: This 2-year prospective study included 32 acute mTBI patients and 37 healthy comparisons. We calculated the functional connectivity scores among the default mode, salience, and central executive networks. Then we conducted multilevel correlation analysis to investigate component correlations, global graph, and local functional connectivity changes. Results: Patients with mTBI showed significant increased functional connectivity between the anterior part of the default mode network and the salience network compared with controls (p = 0.013, false discovery rate correction). Hyper-connectivity between the default mode and salience network was significantly positively correlated with the dimensional change card sort score in patients with mTBI (r = 0.40, p = 0.037). The average path length of mTBI patients was significantly higher than that of controls (p = 0.028). Conclusions: Aberrant functional coupling between the default mode and salience networks were identified in acute mTBI patients. Our finding has great potential to improve our understanding of the network architecture of mTBI.
Eimeria sciurorum (Apicomplexa, Coccidia) From the Calabrian Black Squirrel (Sciurus meridionalis): An Example of Lower Host Specificity of Eimerians

Host specificity plays one of the key roles in parasitism. It affects the evolution and diversification of both host and parasite, as well as it influences their geographical distribution, and epidemiological significance. For most of parasites, however, host specificity is unknown or misrepresented because it is difficult to be determined accurately. Here we provide the information about the lower host specificity of Eimeria sciurorum infecting squirrels, and its new host record for the Calabrian black squirrel Sciurus meridionalis, a southern Italian endemic species.
Planktonic Protists of the Eastern Nordic Seas and the Fram Strait: Spatial Changes Related to Hydrography During Early Summer

The European Arctic is rapidly changing where increasing water temperatures and rapid loss of sea ice will likely influence the structure and functioning of the entire ecosystem. This study aimed to describe the taxonomic composition and spatial distribution of early summer (2015–2016) nano- and microplanktonic protists in the Nordic (Norwegian, Greenland) Seas and the Fram Strait (70.99°N to 78.84°N; 1.52°E to 19.90°E) and to determine the distribution patterns of the communities from the aspect of hydrography, as deduced from in situ measurements. Here we identify some generalized regularity in the protistan distribution, indicating the two separated domains at the 6°C threshold. While Phaeocystis seemed to be a fairly conservative representative of the colder area (<6°C), the taxonomic structure of the warmer waters (>6°C) may vary significantly between successive summers: from mostly Bacillariophyceae-dominated communities in 2015 to flagellate-dominated in 2016. Based on our results, we hypothesized that the more intense phototroph development in the area, as deduced from higher remotely sensed chlorophyll a concentrations in 2016, i.e., record warm year in the observational period, could lead to faster depletion of nutrients and, thus, an earlier shift into the post-bloom community stage. Taking into account the possible phenological shift toward early summer domination of flagellates in a warmer year, as well as a higher number of heterotrophic protists associated with the warmer domain in two evaluated summers, it is highly likely that climatic warming of this region will have an impact on energy transfer to higher trophic levels. Although generalized patterns could be elucidated, more information is needed to predict and understand how the changing Arctic will alter protistan communities and, thus, higher-order consumers.
Microbiota in Dung and Milk Differ Between Organic and Conventional Dairy Farms

Organic farming is increasingly promoted as a means to reduce the environmental impact of artificial fertilizers, pesticides, herbicides, and antibiotics in conventional dairy systems. These factors potentially affect the microbial communities of the production stages (soil, silage, dung, and milk) of the entire farm cycle. However, understanding whether the microbiota representative of different production stages reflects different agricultural practices – such as conventional versus organic farming – is unknown. Furthermore, the translocation of the microbial community across production stages is scarcely studied. We sequenced the microbial communities of soil, silage, dung, and milk samples from organic and conventional dairy farms in the Netherlands. We found that community structure of soil fungi and bacteria significantly differed among soil types, but not between organic versus conventional farming systems. The microbial communities of silage also did not differ among conventional and organic systems. Nevertheless, the dung microbiota of cows and the fungal communities in the milk were significantly structured by agricultural practice. We conclude that, while the production stages of dairy farms seem to be disconnected in terms of microbial transfer, certain practices specific for each agricultural system, such as the content of diet and the use of antibiotics, are potential drivers of shifts in the cow’s microbiota, including the milk produced. This may reflect differences in farm animal health and quality of dairy products depending on farming practices.
Renal Precision Medicine in Neonates and Acute Kidney Injury: How to Convert a Cloud of Creatinine Observations to Support Clinical Decisions

Renal precision medicine in neonates is useful to support decision making on pharmacotherapy, signal detection of adverse (drug) events, and individual prediction of short- and long-term prognosis. To estimate kidney function or glomerular filtration rate (GFR), the most commonly measured and readily accessible biomarker is serum creatinine (Scr). However, there is extensive variability in Scr observations and GFR estimates within the neonatal population, because of developmental physiology and superimposed pathology. Furthermore, assay related differences still matter for Scr, but also exist for Cystatin C. Observations in extreme low birth weight (ELBW) and term asphyxiated neonates will illustrate how renal precision medicine contributes to neonatal precision medicine. When the Kidney Disease Improving Global Outcome (KDIGO) definition of acute kidney injury (AKI) is used, this results in an incidence up to 50% in ELBW neonates, associated with increased mortality and morbidity. However, urine output criteria needed adaptations to broader time intervals or weight trends, while Scr and its trends do not provide sufficient detail on kidney function between ELBW neonates. Instead, we suggest to use assay-specific centile Scr values to better describe postnatal trends and have illustrated its relevance by quantifying an adverse drug event (ibuprofen) and by explaining individual amikacin clearance. Term asphyxiated neonates also commonly display AKI. While oliguria is a specific AKI indicator, the majority of term asphyxiated cases are non-oliguric. Asphyxia results in a clinical significant—commonly transient—mean GFR decrease (−50%) with a lower renal drug elimination. But there is still major (unexplained) inter-individual variability in GFR and subsequent renal drug elimination between these asphyxiated neonates. Recently, the Baby-NINJA (nephrotoxic injury negated by just-in-time action) study provided evidence on the concept that a focus on nephrotoxic injury negation has a significant impact on AKI incidence and severity. It is hereby important to realize that follow-up should not be discontinued at discharge, as there are concerns about long-term renal outcome. These illustrations suggest that integration of renal (patho)physiology into neonatal precision medicine are an important tool to improve contemporary neonatal care, not only for the short-term but also with a positive health impact throughout life.
rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output

Searching for similar sequences in a database via BLAST or a similar tool is one of the most common bioinformatics tasks applied in general, and to non-coding RNAs in particular. However, the results of the search might be difficult to interpret due to the presence of partial matches to the database subject sequences. Here, we present rboAnalyzer – a tool that helps with interpreting sequence search result by (1) extending partial matches into plausible full-length subject sequences, (2) predicting homology of RNAs represented by full-length subject sequences to the query RNA, (3) pooling information across homologous RNAs found in the search results and public databases such as Rfam to predict more reliable secondary structures for all matches, and (4) contextualizing the matches by providing the prediction results and other relevant information in a rich graphical output. Using predicted full-length matches improves secondary structure prediction and makes rboAnalyzer robust with regards to identification of homology. The output of the tool should help the user to reliably characterize non-coding RNAs in BLAST output. The usefulness of the rboAnalyzer and its ability to correctly extend partial matches to full-length is demonstrated on known homologous RNAs. To allow the user to use custom databases and search options, rboAnalyzer accepts any search results as a text file in the BLAST format. The main output is an interactive HTML page displaying the computed characteristics and other context of the matches. The output can also be exported in an appropriate sequence and/or secondary structure formats.
Optimization of Viability Treatment Essential for Accurate Droplet Digital PCR Enumeration of Probiotics

Improvements offered by viability droplet digital PCR (v-ddPCR) include increased precision, specificity and decreased time to results making for an attractive alternative method to traditional plate count enumeration of probiotic products. A major hurdle faced in v-ddPCR, however, is distinguishing between live and dead cells. The objective of this study was to evaluate a combination of PMA and EMA (PE51) for viability treatment of freeze-dried probiotic powders. Lactobacillus acidophilus La-14 and Bifidobacterium animalis subsp. lactis Bi-07 were analyzed over a 2-log PE51 concentration gradient to investigate the efficiency across genus and assay targets. Results suggest a need to optimize viability dye concentration based on the genera of the organism, but also the assay target, even when analyzing the same organism. When optimized for PE51 concentration, strain specific v-ddPCR assays for both La-14 and Bi-07 were demonstrated to agree with plate count enumeration results. In conclusion, while these v-ddPCR assays require highly specific optimization, they are better suited for the future of the probiotic industry and are suggested to be implemented in probiotic product testing.
Abnormal Spontaneous Brain Activity in Left-Onset Parkinson Disease: A Resting-State Functional MRI Study

Objective: Motor asymmetry is characteristic in Parkinson disease (PD). This phenomenon is originated from uneven degeneration of bilateral substantia nigra. However, this asymmetry may not restrict to substantia nigra or striatum. We aimed to determine the effect of asymmetry on spontaneous brain activity across the whole brain. Methods: We consecutively recruited 71 patients with PD, as well as 35 healthy controls, and collected relevant demographic, clinical, and neuropsychological information. The PD patients were divided into two groups according to the side of motor symptom onset. All the participants underwent resting-state functional magnetic resonance imaging, and spontaneous brain activity was assessed using amplitude of low-frequency fluctuation (ALFF). The associations between areas showing significant group differences and various clinical and neuropsychological measures were analyzed. Results: Finally, the data of 30 PD patients with left-onset (LPD), 27 PD patients with right-onset (RPD), and 32 healthy controls were obtained. The three groups had similar age and gender ratios. Our results demonstrated that LPD patients had increased ALFF in the left inferior temporal gyrus and decreased ALFF in bilateral thalamus and cerebellum anterior lobes than the control group. The value of ALFF of the left inferior temporal gyrus was correlated with motor function, and ALFF value of the thalamus was associated with cognition. Comparisons between LPD and RPD patients and between RPD patients and the controls did not yield significant difference. Conclusions: The present study provides new insights into the distinct characteristics of spontaneous brain activity in LPD, which may be associated with motor and cognitive function.