Miracle-dz/UniFAR-FTUs huggingface dataset:
Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as “photosynthesis” and “starch and sucrose metabolism,” were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.
Splitting Matching Pursuit Method for Reconstructing Sparse Signal in Compressed Sensing

In this paper, a novel method named as splitting matching pursuit (SMP) is proposed to reconstructK-sparse signal in compressed sensing.The proposedmethod selectsFl (Fl > 2K) largest components of the correlation vector c, which are divided intoF split sets with equal length l.The searching area is thus expanded to incorporatemore candidate components, which increases the probability of finding the true components at one iteration. The proposed method does not require the sparsity level K to be known in prior. The Merging, Estimation and Pruning steps are carried out for each split set independently, which makes it especially suitable for parallel computation. The proposed SMP method is then extended to more practical condition, e.g. the direction of arrival (DOA) estimation problem in phased array radar systemusing compressed sensing. Numerical simulations show that the proposedmethod succeeds in identifying multiple targets in a sparse radar scene, outperforming other OMP-type methods. The proposed method also obtains more precise estimation of DOA angle using one snapshot compared with the traditional estimation methods such as Capon, APES (amplitude and phase estimation) and GLRT (generalized likelihood ratio test) based on hundreds of snapshots.
Some thoughts on bibliometrics, usage metrics and altmetrics concerning the International Journal of Rehabilitation Research.

Department of Physical and Rehabilitation Medicine, Faculty of Medicine, Ljubljana, Slovenia and ICS Maugeri, IRCCS, Department of Physical and Rehabilitation Medicine of Lissone Institute, Lissone (MB), Italy Correspondence to Franchignoni Franco, MD, ICS Maugeri, IRCCS, Department of Physical and Rehabilitation Medicine, Via Bernasconi 16, 20851 Lissone (MB), Italy Tel: +39 039 46571; fax: +39 039 4657254; e-mail: franco.franchignoni@icsmaugeri.it
Differential effects of aging and physical activity on corticospinal excitability of upper and lower limb muscles.

Corticospinal tract excitability can be altered by age, physical activity (PA) and possibly sex, but whether these effects differ between upper and lower limb muscles is unknown. We determined the influence of age, PA and sex on corticospinal excitability of an upper and lower limb muscle during submaximal contractions by comparing stimulus-response curves of motor evoked potentials (MEPs). Transcranial magnetic stimulation was used to evoke stimulus-response curves in active muscles by incrementally increasing the stimulator intensity from below the active motor threshold (AMT) until a plateau in MEP amplitudes was achieved. Stimulus-response curves were analyzed from the first dorsal interosseous (FDI) of 30 young (23.9±3.8 years) and 33 older men and women (72.6±5.6 years) and the vastus lateralis (VL) of 13 young (23.2±2.2 years) and 25 older men and women (72.7±5.5 years). Corticospinal excitability was determined by fitting the curves with a 4-parameter sigmoidal curve and calculating the maximal slope (slopemax). PA was assessed with tri-axial accelerometry and participants were dichotomized into high- (>10,000 steps∙day-1, n=15) or low-PA (<10,000 steps∙day-1, n=43). Young adults had larger FDI MEP amplitudes (%Mmax) at higher TMS intensities (120-150%AMT) and greater slopemax than older adults (P<0.05), with no differences between high- and low-PA groups (P>0.05). VL MEP amplitudes and slopemax, however, were lower in the high-PA than low-PA participants, with no age or sex differences. These data suggest that aging and physical activity, but not sex, differentially influence the excitability of the corticospinal tracts projecting to muscles of the upper compared with the lower limb.
The impact of mycophenolate mofetil dosing patterns on clinical outcome after renal transplantation

Abstract: Background: Mycophenolate mofetil (MMF) has proven to be a very effective drug for the prevention of acute rejection following renal transplantation when dosed as prescribed at 2 or 3 g/d. However, circumstances arise in clinical transplantation where the dose must be lowered, either to avoid drug toxicity or because of concurrent infection. The impact on the incidence of acute rejection and graft survival when the MMF dose must be lowered has not previously been investigated.
Antibiotic resistomes of healthy pig faecal metagenomes

Antibiotic resistance reservoirs within food-producing animals are thought to be a risk to animal and human health. This study describes the minimum natural resistome of pig faeces as the bacteria are under no direct antibiotic selective pressure. The faecal resistome of 257 different genes comprised 56 core and 201 accessory resistance genes. The genes present at the highest relative abundances across all samples were tetW, tetQ, tet44, tet37, tet40, mefA, aadE, ant(9)-1, ermB and cfxA2. This study characterized the baseline resistome, the microbiome composition and the metabolic components described by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in healthy pig faeces, without antibiotic selective pressures. The microbiome hierarchical analysis resulted in a cluster tree with a highly similar pattern to that of the accessory resistome cluster tree. Functional capacity profiling identified genes associated with horizontal gene transfer. We identified a statistically significant positive correlation between the total antibiotic resistome and suggested indicator genes, which agree with using these genes as indicators of the total resistomes. The correlation between total resistome and total microbiome in this study was positive and statistically significant. Therefore, the microbiome composition influenced the resistome composition. This study identified a core and accessory resistome present in a cohort of healthy pigs, in the same conditions without antibiotics. It highlights the presence of antibiotic resistance in the absence of antibiotic selective pressure and the variability between animals even under the same housing, food and living conditions. Antibiotic resistance will remain in the healthy pig gut even when antibiotics are not used. Therefore, the risk of antibiotic resistance transfer from animal faeces to human pathogens or the environment will remain in the absence of antibiotics.
TIM1 (HAVCR1): an Essential “Receptor” or an “Accessory Attachment Factor” for Hepatitis A Virus?

aLineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA bDepartment of Microbiology, University of Iowa, Iowa City, Iowa, USA cDepartment of Microbiology & Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA dDepartment of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
Implementing a self-management mobile app for spinal cord injury during inpatient rehabilitation and following community discharge: A feasibility study

Objective: To determine the feasibility of implementing and evaluating a self-management mobile app for spinal cord injury (SCI) during inpatient rehabilitation and following community discharge. Design: Pilot feasibility study. Setting: Rehabilitation hospital and community. Participants: Inpatients from rehabilitation hospital following admission for their first SCI. Intervention: A mobile app was developed to facilitate self-management following SCI. The app consisted of 18 tools focusing on goal setting, tracking various health aspects, and identifying confidence regarding components of self-management. In-person training and follow-up sessions were conducted during inpatient rehabilitation and follow-up calls were provided after participants were discharged into the community. Main outcome measures: Participants completed outcome measures at baseline, community discharge, and 3-months post discharge. This study focused on feasibility indicators including recruitment, retention, respondent characteristics, adherence, and app usage. Additionally, participants’ self-management confidence relating to SCI (e.g. medication, skin, bladder, pain) was evaluated over time. Results: Twenty participants (median age 39, IQR: 31 years, 85% male) enrolled in the study. Participants’ Spinal Cord Injury Independence Measure (SCIM-III) median score was 23 and IQR was 33 (range: 7–84), which did not correlate with app usage. Retention from admission to discharge was 85% and 70% from discharge to 3-months post discharge. Individuals in the study who used the app entered data an average of 1.7x/day in rehabilitation (n = 17), and 0.5x/day in the community (n = 7). Participants’ bowel self-management confidence improved between admission and discharge (P < 0.01). Conclusions: Feasibility indicators support a larger clinical trial during inpatient rehabilitation; however, there were challenges with retention and adherence following community discharge.
The Effect of Vitamin D Supplementation on Insulin Resistance among Women with Polycystic Ovary Syndrome

Objective: To explore the effect of vitamin D supplementation on insulin resistance in a group of Iranian patients with polycystic ovary syndrome and vitamin D deficiency. Methods: This was a clinical trial conducted in a tertiary medical center in Tehran, the capital city of Iran, from May 2015 to September 2015. The participants included 41 women between 20 and 40 years of age with polycystic ovary syndrome based on the Rotterdam criteria and vitamin D deficiency. The fasting blood glucose and insulin levels, as well as serum 25-hydroxyvitamin D and homeostasis model assessment of insulin resistance (HOMA-IR) levels were measured at baseline and two months post treatment with a single dose of 300,000IU intramuscular vitamin D₃. The main outcome measures were plasma levels of vitamin D, fasting blood sugar and insulin levels, as well as insulin resistance. Results: The mean age of participants was 26.6±4.1. The serum level of 25-hydroxyvitamin D increased (5.7±1.77 to 16.34±8.99 ng/mL, p<0.001). The mean fasting blood glucose reading significantly decreased from 109.56±14.59mg/dL in pre-treatment to 103.71±13.72mg/dL post treatment (p=0.003). There was a significant decrease in the mean fasting serum insulin level from 8.52±5.48 mcU/mL before treatment with vitamin D to 7.07±5.03 (p=0.019) µU/mL after the treatment. The mean HOMA-IR, as a sign of insulin resistance, significantly decreased from 2.37±1.76 to 1.87±1.49, indicating less insulin resistance. Conclusions: A single injection of vitamin D significantly decreased serum insulin levels and insulin resistance among patients with polycystic ovary syndrome.
Neutrophil kinetics shortly after initial administration of recombinant human granulocyte colony‐stimulating factor: Neutrophil alkaline phosphatase activitv as an endorrenous marker

Abstract: Recombinant human granulocyte colony‐stimulating factor (rhG‐CSF) was administered (1.5 pg/kg body weight) subcutaneously once daily for 5 to 9 days to 5 patients with malignant lymphoma. In all patients, initial administration of rhG‐CSF induced a rapid fall in the neutrophil count within 30 minutes, followed by a recovery and an increase in the neutrophil count within 150 min. A rapid fall in the neutrophil count was accompanied by increased expression of neutrophil C3bi‐receptors, and neutrophils left in the circulation had lower activity of neutrophil alkaline phosphatase (NAP) and phagocytosis. A decrease in the NAP scores observed at 30 min reflected a preferential decrease of neutrophils with high NAP activity. A recovery and an increase in the neutrophil count were accompanied by a further decrease of NAP scores, which was caused by a preferential increase of neutrophils with lower NAP activity. The NAP scores of mature neutrophils from peripheral blood were not affected by in vitro treatment of cells with rhG‐CSF for up to 150 min at 37 °C. These findings and the previous observations that neutrophils in the circulating and marginal pools have high NAP activity and neutrophils in the bone marrow pool have low NAP activity taken together suggest that, following initial administration of rhG‐CSF, functionally active neutrophils leave the bloodstream preferentially, which is primarily followed by an influx of neutrophils from the bone marrow, but not by demargination of sequestered neutrophils.
A transgenic zebrafish model of hepatocyte function in human Z α1-antitrypsin deficiency

Abstract In human α1-antitrypsin deficiency, homozygous carriers of the Z (E324K) mutation in the gene SERPINA1 have insufficient circulating α1-antitrypsin and are predisposed to emphysema. Misfolding and accumulation of the mutant protein in hepatocytes also causes endoplasmic reticulum stress and underpins long-term liver damage. Here, we describe transgenic zebrafish (Danio rerio) expressing the wildtype or the Z mutant form of human α1-antitrypsin in hepatocytes. As observed in afflicted humans, and in rodent models, about 80% less α1-antitrypsin is evident in the circulation of zebrafish expressing the Z mutant. Although these zebrafish also show signs of liver stress, they do not accumulate α1-antitrypsin in hepatocytes. This new zebrafish model will provide useful insights into understanding and treatment of α1-antitrypsin deficiency.
Cascaded Tuning to Amplitude Modulation for Natural Sound Recognition

The auditory system converts the physical properties of a sound waveform to neural activities and processes them for recognition. During the process, the tuning to amplitude modulation (AM) is successively transformed by a cascade of brain regions. To test the functional significance of the AM tuning, we conducted single-unit recording in a deep neural network (DNN) trained for natural sound recognition. We calculated the AM representation in the DNN and quantitatively compared it with those reported in previous neurophysiological studies. We found that an auditory-system-like AM tuning emerges in the optimized DNN. Better-recognizing models showed greater similarity to the auditory system. We isolated the factors forming the AM representation in the different brain regions. Because the model was not designed to reproduce any anatomical or physiological properties of the auditory system other than the cascading architecture, the observed similarity suggests that the AM tuning in the auditory system might also be an emergent property for natural sound recognition during evolution and development. SIGNIFICANCE STATEMENT This study suggests that neural tuning to amplitude modulation may be a consequence of the auditory system evolving for natural sound recognition. We modeled the function of the entire auditory system; that is, recognizing sounds from raw waveforms with as few anatomical or physiological assumptions as possible. We analyzed the model using single-unit recording, which enabled a fair comparison with neurophysiological data with as few methodological biases as possible. Interestingly, our results imply that frequency decomposition in the inner ear might not be necessary for processing amplitude modulation. This implication could not have been obtained if we had used a model that assumes frequency decomposition.
Optimized training for jumping performance using the force-velocity imbalance: Individual adaptation kinetics

Aims We analysed the changes in force-velocity-power variables and jump performance in response to an individualized training program based on the force-velocity imbalance (FVimb). In particular, we investigated (i) the individual adaptation kinetics to reach the optimal profile and (ii) de-training kinetics over the three weeks following the end of the training program. Methods Sixty subjects were assigned to four sub-groups according to their initial FVimb: high or low force-deficit (FD) and high or low velocity-deficit (VD). The duration of training intervention was set so that each individual reached their “Optimal force-velocity (F-v) profile”. Mechanical and performance variables were measured every 3 weeks during the program, and every week after the end of the individualized program. Results All subjects in the FD sub-groups showed extremely large increases in maximal theoretical force output (+30±16.6% Mean±SD; ES = 2.23±0.28), FVimb reduction (-74.3±54.7%; ES = 2.17±0.27) and large increases in jump height (+12.4±7.6%; ES = 1.45±0.23). For the VD sub-groups, we observed moderate to extremely large increases in maximal theoretical velocity (+15.8±5.1%; ES = 2.72±0.29), FVimb reduction (-19.2±6.9%; ES = 2.36±0.35) and increases in jump height (+10.1±2.7%; ES = 0.93±0.09). The number of weeks needed to reach the optimal F-v profile (12.6 ± 4.6) was correlated to the magnitude of initial FVimb (r = 0.82, p<0.01) for all participants regardless of their initial subgroup. No significant change in mechanical variables or jump performance was observed over the 3-week de-training period. Conclusions Collectively, these results provide useful insights into a more specific, individualized (i.e. based on the type and magnitude of FVimb) and accurate training prescription for jumping performance. Considering both training content and training duration together with FVimb may enable more individualized, specific and effective training monitoring and periodization.
N-acetyltransferase: the practical consequences of polymorphic activity in man

Abstract Over the years, numerous studies have supported the premise that individuals possessing the “slow acetylator” phenotype are more at risk from developing drug side-effects. Most prominent amongst these reports are those concerned with hepatotoxicity and peripheral neuropathy following treatment with isoniazid, lupus-like symptoms during procainamide therapy and experiencing hypersensitivity reactions to the various sulphonamide derivatives. Similarly, “slow acetylators” undergoing heavy exposure to arylamines and related carcinogens are more likely to develop bladder cancer. Contrariwise, there appears a slight risk of “rapid acetylators” developing pancreatic tumours. Other therapeutic agents for which polymorphic N-acetylation plays a minor role in their metabolism have been investigated but any impact of this metabolic difference on clinical efficacy or associated toxicity is still under question. In the search for clues as to the underlying aetiology, patient groups with many disease states have been examined for association with differences in N-acetylation and the majority have provided data that could be interpreted as equivocal. Studies have given contradictory, often opposing, results, calculated risk factors that are (perhaps) just significant but certainly not high, and patients within the cohorts who are always exceptions. Undoubtedly, other as yet unappreciated factors are at play.
Placental aromatase expression decreased in severe neonatal opioid withdrawal syndrome

Abstract Background: Severe neonatal opioid withdrawal syndrome (NOWS) cannot be predicted. Placental aromatase metabolizes both methadone and buprenorphine and may contribute to the severity of NOWS. Objectives: To determine whether placental aromatase mRNA expression differs in methadone- or buprenorphine-exposed placentas and is associated with NOWS severity. Study design: Prospective multicenter observational cohort study from July 2016 to December 2017. Inclusion: pregnant, ≥18 years old, singleton fetus, nonanomalous, ≥34 weeks at delivery, documented methadone or buprenorphine use. Exclusion: declined sample collection. Severe NOWS is defined as three consecutive Finnegan scores ≥8 or sum of three consecutive scores ≥24 within 72 hours of birth. Finnegan scoring was correlated with placental mRNA expression and compared to umbilical cord drug and metabolite levels. Data were analyzed using descriptive, parametric, and nonparametric statistics and regression analysis. p-Value <. 05 was considered significant. Results: Thirty-eight out of 45 (84%) patients were included. Methadone and buprenorphine were used by 29/38 (76%) and 9/38 (24%) of patients, respectively. 19/38 (50%) infants had severe NOWS. Placental aromatase/actin mRNA expression was significantly lower in the placentas of infants with severe NOWS (p = .04). Mean umbilical cord 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP)/methadone ratios were significantly higher in infants with severe NOWS (p = .03). Placental aromatase mRNA expression was weakly to moderately correlated with umbilical cord methadone, buprenorphine, and their metabolite concentrations (r = 0.4–0.8). Conclusion: Placental aromatase mRNA expression was lower and umbilical cord EDDP/methadone ratios were higher in infants with severe NOWS. Additional investigation of placental aromatase in methadone- and buprenorphine-exposed pregnancies is needed.
Zebrafish Carrying pycr1 Gene Deficiency Display Aging and Multiple Behavioral Abnormalities

Aging is a natural process that internal gene control and external stimuli mediate. Clinical data pointed out that homozygotic or heterozygotic mutation in the pyrroline-5-carboxylate reductase 1 (PYCR1) gene in humans caused cutis laxa (ARCL) disease, with progeroid appearance, lax and wrinkled skin, joint laxity, osteopenia, and mental retardation phenotypes. In this study, we aimed to generate pycr1 knockout (KO) zebrafish and carried out biochemical characterizations and behavior analyses. Marked apoptosis and senescence were detected in pycr1 KO zebrafish, which started from embryos/larvae stage. Biochemical assays showed that adult pycr1 KO fish have significantly reduced proline and extracellular matrix contents, lowered energy, and diminished superoxide dismutase (SOD) and telomerase activity when compared to the wild type fish, which suggested the pycr1 KO fish may have dysfunction in mitochondria. The pycr1 KO fish were viable; however, displayed progeria-like phenotype from the 4 months old and reach 50% mortality around six months old. In adult stage, we found that pycr1 KO fish showed reduced locomotion activity, aggression, predator avoidance, social interaction interest, as well as dysregulated color preference and circadian rhythm. In summary, we have identified multiple behavioral alterations in a novel fish model for aging with pycr1 gene loss-of-function by behavioral tests. This animal model may not only provide a unique vertebrate model to screen potential anti-aging drugs in the future, but also be an excellent in vivo model towards a better understanding of the corresponding behavioral alterations that accompany aging.