Miracle-dz/UniFAR-FTUs huggingface dataset:
A Reconfigurable Platform for Magnetic Resonance Data Acquisition and Processing

Developments in magnetic resonance imaging (MRI) in the last decades show a trend towards a growing number of array coils and an increasing use of a wide variety of sensors. Associated cabling and safety issues have been addressed by moving data acquisition closer to the coil. However, with the increasing number of radio-frequency (RF) channels and trend towards higher acquisition duty-cycles, the data amount is growing, which poses challenges for throughput and data handling. As it is becoming a limitation, early compression and preprocessing is becoming ever more important. Additionally, sensors deliver diverse data, which require distinct and often low-latency processing for run-time updates of scanner operation. To address these challenges, we propose the transition to reconfigurable hardware with an application tailored assembly of interfaces and real-time processing resources. We present an integrated solution based on a system-on-chip (SoC), which offers sufficient throughput and hardware-based parallel processing power for very challenging applications. It is equipped with fiber-optical modules serving as versatile interfaces for modular systems with in-field operation. We demonstrate the utility of the platform on the example of concurrent imaging and field sensing with hardware-based coil compression and trajectory extraction. The preprocessed data are then used in expanded encoding model based image reconstruction of single-shot and segmented spirals as used in time-series and anatomical imaging respectively.
Genome-Wide CpG Island Methylation Profiles of Cutaneous Skin with and without HPV Infection

HPV infection is one of the most commonly transmitted diseases among the global population. While it can be asymptomatic, non-genital HPV infection often gives rise to cutaneous warts, which are benign growths arising from the epidermal layer of the skin. This study aimed to produce a global analysis of the ways in which cutaneous wart formation affected the CpG island methylome. The Infinium MethylationEPIC BeadChip microarray was utilized in order to quantitatively interrogate CpG island methylation in genomic DNA extracted from 24 paired wart and normal skin samples. Differential methylation analysis was carried out by means of assigning a combined rank score using RnBeads. The 1000 top-ranking CpG islands were then subject to Locus Overlap Analysis (LOLA) for enrichment of genomic ranges, while signaling pathway analysis was carried out on the top 100 differentially methylated CpG islands. Differential methylation analysis illustrated that the most differentially methylated CpG islands in warts lay within the ITGB5, DTNB, RBFOX3, SLC6A9, and C2orf27A genes. In addition, the most enriched genomic region sets in warts were Sheffield’s tissue-clustered DNase hypersensitive sites, ENCODE’s segmentation and transcription factor binding sites, codex sites, and the epigenome sites from cistrome. Lastly, signaling pathway analysis showed that the GRB2, GNB1, NTRK1, AXIN1, and SKI genes were the most common regulators of the genes associated with the top 100 most differentially methylated CpG islands in warts. Our study shows that HPV-induced cutaneous warts have a clear CpG island methylation profile that sets them apart from normal skin. Such a finding could account for the temporary nature of warts and the capacity for individuals to undergo clinical remission.
Lipidomic Analysis of Plastidial Octanoyltransferase Mutants of Arabidopsis thaliana

Plant de novo fatty acid synthesis takes place in the plastid using acetyl-coenzyme A (acetyl-CoA) as the main precursor. This first intermediate is produced from pyruvate through the action of the plastidial pyruvate dehydrogenase complex (PDH), which catalyses the oxidative decarboxylation of pyruvate to produce acetyl-CoA, CO2, and NADH. For the proper functioning of this complex, lipoic acid is required to be bound to the dihydrolipoamide S-acetyltransferase E2 subunit of PDH. Octanoyltransferase (LIP2; EC 2.3.1.181) and lipoyl synthase (LIP1; EC 2.8.1.8) are the enzymes involved in the biosynthesis of this essential cofactor. In Arabidopsis plastids, an essential lipoyl synthase (AtLIP1p) and two redundant octanoyltransferases (AtLIP2p1 and AtLIP2p2) have been described. In the present study, the lipidomic characterization of Arabidopsis octanoyltransferase mutants reveals new insight into the lipoylation functions within plastid metabolism. Lipids and fatty acids from mature seeds and seedlings from Atlip2p1 and Atlip2p2 mutants were analysed by gas chromatography (GC) and liquid chromatography–electrospray ionization high-resolution mass spectrometry (LC-ESI-HRMS2), the analysis revealed changes in fatty acid profiles that showed similar patterns in both mutant seeds and seedlings and in the lipid species containing those fatty acids. Although both mutants showed similar tendencies, the lack of the AtLIP2p2 isoform produced a more acute variation in its lipids profile. These changes in fatty acid composition and the increase in their content per seed point to the interference of octanoyltransferases in the fatty acid synthesis flux in Arabidopsis thaliana seeds.
Repurposing Salicylamide for Combating Multidrug-Resistant Neisseria gonorrhoeae

The U.S. Centers for Disease Control and Prevention (CDC) lists Neisseria gonorrhoeae as one of the most urgent antibiotic-resistant threats in the United States. This is due to the emergence of clinical isolates that have developed resistance to nearly every antibiotic used to treat gonorrhea and highlights the critical need to find new therapeutics. ABSTRACT The U.S. Centers for Disease Control and Prevention (CDC) lists Neisseria gonorrhoeae as one of the most urgent antibiotic-resistant threats in the United States. This is due to the emergence of clinical isolates that have developed resistance to nearly every antibiotic used to treat gonorrhea and highlights the critical need to find new therapeutics. The present study discovered salicylamide, an analgesic and antipyretic drug, has antibacterial activity against 40 different antibiotic-resistant strains of N. gonorrhoeae (MIC, 8 to 32 μg/ml) with low frequency of resistance <2.4 × 10−9. Interestingly, salicylamide did not inhibit growth of bacterial species in the vaginal microflora involved in defense against gonococcal infections, such as Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus johnsonii, and Lactobacillus crispatus. A time-kill assay revealed that salicylamide is a rapidly bactericidal drug, as it eradicated a high inoculum of N. gonorrhoeae within 10 h. Salicylamide was superior to the drug of choice, ceftriaxone, in reducing the burden of intracellular N. gonorrhoeae by 97% in infected endocervical cells. Furthermore, salicylamide outperformed ceftriaxone in reducing expression of the proinflammatory cytokine interleukin 8 (IL-8) from endocervical cells infected with N. gonorrhoeae. A checkerboard assay revealed that salicylamide exhibited a synergistic interaction with tetracycline and additive relationships with azithromycin, ciprofloxacin, and ceftriaxone. A more in-depth investigation of the structure-activity relationship of derivatives of salicylamide revealed the amide and hydroxyl groups are important for antigonorrheal activity. In conclusion, this study identified salicylamide as a promising candidate for further investigation as a novel treatment option for multidrug-resistant gonorrhea.
X chromosome and autosomal recombination are differentially sensitive to disruptions in SC maintenance

Significance This study investigates the function of a large protein complex, the synaptonemal complex (SC), that is necessary for the tightly controlled processes of DNA double-strand break (DSB) formation/repair and chromosome segregation during meiosis. The repair of programmed DSBs made during meiosis results in the exchange of genetic information between chromosomes and their subsequent segregation away from each other to produce haploid gametes. Failure to properly regulate these processes can lead to chromosomal abnormalities. Here we report that premature loss of full-length SC impairs proper maintenance of chromosome pairing throughout early meiosis and leads to improper crossover placement. This work will help further our understanding of the role of the SC in the regulation of homologous pairing and recombination. The synaptonemal complex (SC) is a conserved meiotic structure that regulates the repair of double-strand breaks (DSBs) into crossovers or gene conversions. The removal of any central-region SC component, such as the Drosophila melanogaster transverse filament protein C(3)G, causes a complete loss of SC structure and crossovers. To better understand the role of the SC in meiosis, we used CRISPR/Cas9 to construct 3 in-frame deletions within the predicted coiled-coil region of the C(3)G protein. Since these 3 deletion mutations disrupt SC maintenance at different times during pachytene and exhibit distinct defects in key meiotic processes, they allow us to define the stages of pachytene when the SC is necessary for homolog pairing and recombination during pachytene. Our studies demonstrate that the X chromosome and the autosomes display substantially different defects in pairing and recombination when SC structure is disrupted, suggesting that the X chromosome is potentially regulated differently from the autosomes.
Photobiomodulation Therapy Partially Restores Cartilage Integrity and Reduces Chronic Pain Behavior in a Rat Model of Osteoarthritis: Involvement of Spinal Glial Modulation

Objective Chronic pain associated with osteoarthritis (OA) often leads to reduced function and engagement in activities of daily living. Current pharmacological treatments remain relatively ineffective. This study investigated the efficacy of photobiomodulation therapy (PBMT) on cartilage integrity and central pain biomarkers in adult male Wistar rats. Design We evaluated the cartilage degradation and spinal cord sensitization using the monoiodoacetate (MIA) model of OA following 2 weeks of delayed PBMT treatment (i.e., 15 days post-MIA). Multiple behavioral tests and knee joint histology were used to assess deficits related to OA. Immunohistochemistry was performed to assess chronic pain sensitization in spinal cord dorsal horn regions. Furthermore, we analyzed the principal components related to pain-like behavior and cartilage integrity. Results MIA induced chronic pain-like behavior with respective cartilage degradation. PBMT had no effects on overall locomotor activity, but positive effects on weight support (P = 0.001; effect size [ES] = 1.01) and mechanical allodynia (P = 0.032; ES = 0.51). Greater optical densitometry of PBMT-treated cartilage was evident in superficial layers (P = 0.020; ES = 1.34), likely reflecting the increase of proteoglycan and chondrocyte contents. In addition, PBMT effects were associated to decreased contribution of spinal glial cells to pain-like behavior (P = 0.001; ES = 0.38). Conclusion PBMT during the chronic phase of MIA-induced OA promoted cartilage recovery and reduced the progression or maintenance of spinal cord sensitization. Our data suggest a potential role of PBMT in reducing cartilage degradation and long-term central sensitization associated with chronic OA.
Computational modelling predicts substantial carbon assimilation gains for C3 plants with a single-celled C4 biochemical pump

Achieving global food security for the estimated 9 billion people by 2050 is a major scientific challenge. Crop productivity is fundamentally restricted by the rate of fixation of atmospheric carbon. The dedicated enzyme, RubisCO, has a low turnover and poor specificity for CO2. This limitation of C3 photosynthesis (the basic carbon-assimilation pathway present in all plants) is alleviated in some lineages by use of carbon-concentrating-mechanisms, such as the C4 cycle—a biochemical pump that concentrates CO2 near RubisCO increasing assimilation efficacy. Most crops use only C3 photosynthesis, so one promising research strategy to boost their productivity focuses on introducing a C4 cycle. The simplest proposal is to use the cycle to concentrate CO2 inside individual chloroplasts. The photosynthetic efficiency would then depend on the leakage of CO2 out of a chloroplast. We examine this proposal with a 3D spatial model of carbon and oxygen diffusion and C4 photosynthetic biochemistry inside a typical C3-plant mesophyll cell geometry. We find that the cost-efficiency of C4 photosynthesis depends on the gas permeability of the chloroplast envelope, the C4 pathway having higher quantum efficiency than C3 for permeabilities below 300 μm/s. However, at higher permeabilities the C4 pathway still provides a substantial boost to carbon assimilation with only a moderate decrease in efficiency. The gains would be capped by the ability of chloroplasts to harvest light, but even under realistic light regimes a 100% boost to carbon assimilation is possible. This could be achieved in conjunction with lower investment in chloroplasts if their cell surface coverage is also reduced. Incorporation of this C4 cycle into C3 crops could thus promote higher growth rates and better drought resistance in dry, high-sunlight climates.
Patients with head and neck cancer: Are they frailer than patients with other solid malignancies?

Abstract Objective We aimed to compare frailty status between patients with head and neck cancer (HNC) and other solid malignancies. Methods Data collection was prospective, and the following were compared between cohorts at baseline: patient and tumour characteristics, Charlson Comorbidity Index (CCI), Groningen Frailty Indicator (GFI), Mini Mental State Examination (MMSE), Activities of Daily Living (ADLs), Instrumental ADLs (IADLs), Timed Up and Go (TUG) and Quality of Life (QoL). Univariate and multivariate logistic regression analyses were performed, and odds ratios (ORs) with their 95% confidence intervals (95% CIs) were estimated. Results In total, 242 patients with HNC and 180 with other oncology diagnoses were enrolled, of whom 32.6% and 21.8% were frail according to the GFI respectively. Comorbidity scores were not significantly different between the cohorts (7.4% vs. 13.1%; OR 0.54; 95% CI 0.28–1.02). In the univariate analysis, the GFI was significantly worse in the HNC cohort (OR 1.74; 95% CI 1.11–2.71). However, in the multivariate analysis, the MMSE, TUG and global QoL were significantly worse in the HNC cohort, with ORs of 20.03 (95% CI 2.44–164.31), 11.56 (95% CI 1.86–71.68) and 0.98 (95% CI 0.97–1.00) respectively. Conclusion Patients with HNC appear to be frailer than patients with other solid malignancies despite comparable levels of comorbidity.
Hybrid Nanocomposites of Cellulose/Carbon-Nanotubes/Polyurethane with Rapidly Water Sensitive Shape Memory Effect and Strain Sensing Performance

In this work, a fast water-responsive shape memory hybrid polymer based on thermoplastic polyurethane (TPU) was prepared by crosslinking with hydroxyethyl cotton cellulose nanofibers (CNF-C) and multi-walled carbon nanotubes (CNTs). The effect of CNTs content on the electrical conductivity of TPU/CNF-C/CNTs nanocomposite was investigated for the feasibility of being a strain sensor. In order to know its durability, the mechanical and water-responsive shape memory effects were studied comprehensively. The results indicated good mechanical properties and sensing performance for the TPU matrix fully crosslinked with CNF-C and CNTs. The water-induced shape fixity ratio (Rf) and shape recovery ratio (Rr) were 49.65% and 76.64%, respectively, indicating that the deformed composite was able to recover its original shape under a stimulus. The TPU/CNF-C/CNTs samples under their fixed and recovered shapes were tested to investigate their sensing properties, such as periodicity, frequency, and repeatability of the sensor spline under different loadings. Results indicated that the hybrid composite can sense large strains accurately for more than 103 times and water-induced shape recovery can to some extent maintain the sensing accuracy after material fatigue. With such good properties, we envisage that this kind of composite may play a significant role in developing new generations of water-responsive sensors or actuators.
δ-Oscillation Correlates of Anesthesia-induced Unconsciousness in Large-scale Brain Networks of Human Infants.

WHAT WE ALREADY KNOW ABOUT THIS TOPIC Electroencephalographic α-oscillations in the frontal cortex do not appear during general anesthesia in infants less than 3 to 4 months oldIn adults, functional connectivity and brain network integration appear to break down during anesthesia but whether this is true in infants is unknown WHAT THIS ARTICLE TELLS US THAT IS NEW: In infants younger than four months, slow-wave functional connectivity breaks down during general anesthesia and brain networks are less integratedFunctional disconnections in the cortex might be a common marker of anesthesia-induced unconsciousness in infants and adults BACKGROUND:: Functional brain connectivity studies can provide important information about changes in brain-state dynamics during general anesthesia. In adults, γ-aminobutyric acid-mediated agents disrupt integration of information from local to the whole-brain scale. Beginning around 3 to 4 months postnatal age, γ-aminobutyric acid-mediated anesthetics such as sevoflurane generate α-electroencephalography oscillations. In previous studies of sevoflurane-anesthetized infants 0 to 3.9 months of age, α-oscillations were absent, and power spectra did not distinguish between anesthetized and emergence from anesthesia conditions. Few studies detailing functional connectivity during general anesthesia in infants exist. This study's aim was to identify changes in functional connectivity of the infant brain during anesthesia. METHODS A retrospective cohort study was performed using multichannel electroencephalograph recordings of 20 infants aged 0 to 3.9 months old who underwent sevoflurane anesthesia for elective surgery. Whole-brain functional connectivity was evaluated during maintenance of a surgical state of anesthesia and during emergence from anesthesia. Functional connectivity was represented as networks, and network efficiency indices (including complexity and modularity) were computed at the sensor and source levels. RESULTS Sevoflurane decreased functional connectivity at the δ-frequency (1 to 4 Hz) in infants 0 to 3.9 months old when comparing anesthesia with emergence. At the sensor level, complexity decreased during anesthesia, showing less whole-brain integration with prominent alterations in the connectivity of frontal and parietal sensors (median difference, 0.0293; 95% CI, -0.0016 to 0.0397). At the source level, similar results were observed (median difference, 0.0201; 95% CI, -0.0025 to 0.0482) with prominent alterations in the connectivity between default-mode and frontoparietal regions. Anesthesia resulted in fragmented modules as modularity increased at the sensor (median difference, 0.0562; 95% CI, 0.0048 to0.1298) and source (median difference, 0.0548; 95% CI, -0.0040 to 0.1074) levels. CONCLUSIONS Sevoflurane is associated with decreased capacity for efficient information transfer in the infant brain. Such findings strengthen the hypothesis that conscious processing relies on an efficient system of integrated information transfer across the whole brain.
No overall change in the rate of weight gain after switching to an integrase-inhibitor in virologically suppressed adults with HIV.

OBJECTIVE Excessive weight gain has been reported with integrase strand transfer inhibitors (INSTIs). We evaluated weight changes in virologically-suppressed adults with HIV who switched from non-INSTI regimens to raltegravir- or dolutegravir-containing antiretroviral therapy. DESIGN Retrospective single-centre cohort. METHODS Adults who switched to raltegravir or dolutegravir before or between January-2015 and October-2017 were identified. Virologically-suppressed, treatment-experienced (≥2 years) individuals, ≥6 months on INSTI, with weight measurements ≤2years pre- and post-switch were included. Our analysis used a random effects model with linear slope pre- and post-INSTI with adjustment for age, gender, ethnicity, pre-switch-regimen (protease inhibitor vs. non-protease inhibitor), and raltegravir vs. dolutegravir use. RESULTS 378 individuals, 81.2% male, 70.1% white ethnicity, median age of 49 years, median of four weight measurements per participant, and median weight and body mass index (BMI) at switch, of 76.6 kg, and 25.3 kg/m respectively were included. Weight increased by an average of 0.63 kg/year (95% CI 0.17-1.09) pre-switch with no overall change in rate of weight gain post-switch [+0.05 kg/year (-0.61-0.71, p = 0.88)]. In our adjusted model, a transition from minimal weight change to weight gain post-switch was isolated to older individuals though this lacked statistical significance [e.g. +1.59 kg/year (-0.26-3.45) if aged 65 years]. Our findings did not differ by gender, ethnicity, pre-switch regimen, or raltegravir vs. dolutegravir. Similar results were seen for BMI and after adjusting for fixed nucleoside/nucleotide reverse transcriptase inhibitor backbone. CONCLUSION We found no clear evidence of an overall increase in rate of weight gain following switch to INSTI in virologically-suppressed individuals.
Altered Body Composition of Psoas and Thigh Muscles in Relation to Frailty and Severity of Parkinson’s Disease

Background: To investigate the relationship between fat content and the cross-sectional area of psoas and thigh muscles, and clinical severity in patients with Parkinson’s disease. Materials and Methods: Twenty-five patients and 20 age- and sex-matched normal controls were recruited. All subjects underwent MRI study to determine the fat content of the bilateral psoas and thigh muscles. Muscle quality was measured by grasp, walking speed, and cross-sectional area. All patients underwent clinical surveys to evaluate disease severity and frailty, and analyses of the correlations between muscle quality and disease severity were performed. Results: Compared with the controls, patients exhibited higher fatty content in the measured muscles. The higher fat infiltration of measured muscles was significantly correlated with increased disease severity and frailty in patients. The fat fraction of the bilateral medial compartment of the thigh was correlated with the Unified Parkinson Disease Rating Scale-I results and the fat fraction of the bilateral anterior compartment of the thigh was correlated with weakness and exhaustion in patients. Conclusions: Decreased quality in psoas and thigh muscles is prominent in Parkinson’s disease which is further associated with disease severity and frailty. Awareness of the risk of sarcopenia and associated sequelae might improve patient care and outcomes.