Miracle-dz/UniFAR-FTUs huggingface dataset:
Endogenous 2μ Plasmid Editing for Pathway Engineering in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, conventional 2μ-plasmid based plasmid (pC2μ, such as pRS425) have been widely adopted in pathway engineering for multi-copy overexpression of key genes. However, the loss of partition and copy number control elements of yeast endogenous 2μ plasmid (pE2μ) brings the issues concerning plasmid stability and copy number of pC2μ, especially in long-term fermentation. In this study, we developed a method based on CRISPR/Cas9 to edit pE2μ and built the pE2μ multi-copy system by insertion of the target DNA element and elimination of the original pE2μ plasmid. The resulting plasmid pE2μRAF1 and pE2μREP2 demonstrated higher copy number and slower loss rate than a pC2μ control plasmid pRS425RK, when carrying the same target gene. Then, moving the essential gene TPI1 (encoding triose phosphate isomerase) from chromosome to pE2μRAF1 could increase the plasmid viability to nearly 100% and further increase the plasmid copy number by 73.95%. The expression using pE2μ multi-copy system demonstrated much smaller cell-to-cell variation comparing with pC2μ multi-copy system. With auxotrophic complementation of TPI1, the resulting plasmid pE2μRT could undergo cultivation of 90 generations under non-selective conditions without loss. Applying pE2μ multi-copy system for dihydroartemisinic acid (DHAA) biosynthesis, the production of DHAA was increased to 620.9 mg/L at shake-flask level in non-selective rich medium. This titer was 4.73-fold of the strain constructed based on pC2μ due to the more stable pE2μ plasmid system and with higher plasmid copy number. This study provides an improved expression system in yeast, and set a promising platform to construct biosynthesis pathway for valuable products.
Clinical Study of Correlation for the Intestinal and Pharyngeal Microbiota in the Premature Neonates

Objective: There are mutual influences between intestine and lung, that propose a concept of the gut-lung axis, but the mechanism is still unclear. Microbial colonization in early life plays an important role in regulating intestinal and lung function. In order to explore the characteristics of early microbiota on the gut-lung axis, we studied the correlation between intestinal and pharyngeal microbiota on day 1 and day 28 after birth in premature neonates. Methods: Thirteen neonates born at 26–32 weeks gestational age (GA) hospitalized at the neonatal intensive care unit (NICU) of the West China Second Hospital of Sichuan University were enrolled in this study. Stool samples and pharyngeal swabs samples were collected from each neonate on the first day (T1) and the 28th day (T28) after birth. Total bacterial DNA was extracted and sequenced using the Illumina MiSeq Sequencing System based on the V3–V4 hyper-variable regions of the 16S rRNA gene. Based on the sequencing results, the composition of the intestinal and pharyngeal microbiota was compared and analyzed. Results: At T1, the difference in microbial composition between intestine and pharynx was not statistically significant. The intestinal microbiota was mainly composed of Unidentified Enterobacteriaceae, Ralstonia, Streptococcus, Fusobacterium, Ureaplasma, etc. The pharyngeal microbiota was mainly composed of Ureaplasma, Bacteroides, Fusobacterium, etc. Ureaplasma and Fusobacterium were detected in both intestine and pharynx. At T28, there was a significant difference in microbial composition between intestine and pharynx (p < 0.001). The intestinal microbiota was mainly composed of Unidentified Clostridiales, Klebsiella, Unidentified Enterobacteriaceae, Enterobacter, Streptococcus, etc. Pharyngeal microbiota was mainly composed of Streptococcus, Rothia, etc. Streptococcus was detected in both intestine and pharynx. Conclusions: The intestine and pharynx of premature neonates have a unique microbial composition, and share some common microbiota. Whether these microbiotas play a role in the mechanism of gut-lung crosstalk needs further study.
Altered Frequency-Dependent Brain Activation and White Matter Integrity Associated With Cognition in Characterizing Preclinical Alzheimer’s Disease Stages

Background Subjective cognitive decline (SCD), non-amnestic mild cognitive impairment (naMCI), and amnestic mild cognitive impairment (aMCI) are regarded to be at high risk of converting to Alzheimer’s disease (AD). Amplitude of low-frequency fluctuations (ALFF) can reflect functional deterioration while diffusion tensor imaging (DTI) is capable of detecting white matter integrity. Our study aimed to investigate the structural and functional alterations to further reveal convergence and divergence among SCD, naMCI, and aMCI and how these contribute to cognitive deterioration. Methods We analyzed ALFF under slow-4 (0.027–0.073 Hz) and slow-5 (0.01–0.027 Hz) bands and white matter fiber integrity among normal controls (CN), SCD, naMCI, and aMCI groups. Correlation analyses were further utilized among paired DTI alteration, ALFF deterioration, and cognitive decline. Results For ALFF calculation, ascended ALFF values were detected in the lingual gyrus (LING) and superior frontal gyrus (SFG) within SCD and naMCI patients, respectively. Descended ALFF values were presented mainly in the LING, SFG, middle frontal gyrus, and precuneus in aMCI patients compared to CN, SCD, and naMCI groups. For DTI analyses, white matter alterations were detected within the uncinate fasciculus (UF) in aMCI patients and within the superior longitudinal fasciculus (SLF) in naMCI patients. SCD patients presented alterations in both fasciculi. Correlation analyses revealed that the majority of these structural and functional alterations were associated with complicated cognitive decline. Besides, UF alterations were correlated with ALFF deterioration in the SFG within aMCI patients. Conclusions SCD shares structurally and functionally deteriorative characteristics with aMCI and naMCI, and tends to convert to either of them. Furthermore, abnormalities in white matter fibers may be the structural basis of abnormal brain activation in preclinical AD stages. Combined together, it suggests that structural and functional integration may characterize the preclinical AD progression.
Correlation and Reliability of Behavioral and Otoacoustic-Emission Estimates of Contralateral Medial Olivocochlear Reflex Strength in Humans

The roles of the medial olivocochlear reflex (MOCR) in human hearing have been widely investigated but remain controversial. We reason that this may be because the effects of MOCR activation on cochlear mechanical responses can be assessed only indirectly in healthy humans, and the different methods used to assess those effects possibly yield different and/or unreliable estimates. One aim of this study was to investigate the correlation between three methods often employed to assess the strength of MOCR activation by contralateral acoustic stimulation (CAS). We measured tone detection thresholds (N = 28), click-evoked otoacoustic emission (CEOAE) input/output (I/O) curves (N = 18), and distortion-product otoacoustic emission (DPOAE) I/O curves (N = 18) for various test frequencies in the presence and the absence of CAS (broadband noise of 60 dB SPL). As expected, CAS worsened tone detection thresholds, suppressed CEOAEs and DPOAEs, and horizontally shifted CEOAE and DPOAE I/O curves to higher levels. However, the CAS effect on tone detection thresholds was not correlated with the horizontal shift of CEOAE or DPOAE I/O curves, and the CAS-induced CEOAE suppression was not correlated with DPOAE suppression. Only the horizontal shifts of CEOAE and DPOAE I/O functions were correlated with each other at 1.5, 2, and 3 kHz. A second aim was to investigate which of the methods is more reliable. The test–retest variability of the CAS effect was high overall but smallest for tone detection thresholds and CEOAEs, suggesting that their use should be prioritized over the use of DPOAEs. Many factors not related with the MOCR, including the limited parametric space studied, the low resolution of the I/O curves, and the reduced numbers of observations due to data exclusion likely contributed to the weak correlations and the large test–retest variability noted. These findings can help us understand the inconsistencies among past studies and improve our understanding of the functional significance of the MOCR.
Disrupted Regional Homogeneity in Melancholic and Non-melancholic Major Depressive Disorder at Rest

Background: Melancholic depression has been viewed as one severe subtype of major depressive disorder (MDD). However, it is unclear whether melancholic depression has distinct changes in brain imaging. We aimed to explore specific or distinctive alterations in melancholic MDD and whether the alterations could be used to separate melancholic MDD from non-melancholic MDD or healthy controls. Materials and Methods: Thirty-one outpatients with melancholic MDD and thirty-three outpatients with non-melancholic MDD and thirty-two age- and gender-matched healthy controls were recruited. All participants were scanned by resting-state functional magnetic resonance imaging (fMRI). Imaging data were analyzed with the regional homogeneity (ReHo) and support vector machine (SVM) methods. Results: Melancholic MDD patients exhibited lower ReHo in the right superior occipital gyrus/middle occipital gyrus than non-melancholic MDD patients and healthy controls. Merely for non-melancholic MDD patients, decreased ReHo in the right middle frontal gyrus was negatively correlated with the total HRSD-17 scores. SVM analysis results showed that a combination of abnormal ReHo in the right fusiform gyrus/cerebellum Crus I and the right superior occipital gyrus/middle occipital gyrus exhibited the highest accuracy of 83.05% (49/59), with a sensitivity of 90.32% (28/31), and a specificity of 75.00% (21/28) for discriminating patients with melancholic MDD from patients with non-melancholic MDD. And a combination of abnormal ReHo in the right fusiform gyrus/cerebellum VI and left postcentral gyrus/precentral gyrus exhibited the highest accuracy of 98.41% (62/63), with a sensitivity of 96.77% (30/31), and a specificity of 100.00%(32/32) for separating patients with melancholic MDD from healthy controls. Conclusion: Our findings showed the distinctive ReHo pattern in patients with melancholic MDD and found brain area that may be associated with the pathophysiology of non-melancholic MDD. Potential imaging markers for discriminating melancholic MDD from non-melancholic MDD or healthy controls were reported.
Relationships Between Aerobic Performance, Hemoglobin Levels, and Training Load During Small-Sided Games: A Study in Professional Soccer Players

The purposes of this study were (1) to analyze between-session variations of external and internal load measures during small-sided games (SSGs) and (2) to test the relationships between the maximum speed reached (VIFT) during the last stage of the 30-15 Intermittent Fitness Test, hemoglobin levels, and training load measures during SSG intervals among professional soccer players. Sixteen professional soccer players (mean ± SD; age 27.2 ± 3.4 years, height 174.2 ± 3.6 cm, body mass 69.1 ± 6.4 kg, and body fat 10.4 ± 4.1%) participated in this study. Hemoglobin and aerobic performance were first tested, and then a 3-week SSG program was applied using a 3 vs. 3 format. During those 3 weeks, internal and external load of entire sessions were also monitored for all training sessions. Trivial-to-small, standardized differences were observed between sessions for external and internal measures during SSGs. Total distance (TD) and mechanical work (MW) were the only variables that indicated small changes. Large-to-very-large relationships were found between VIFT and external loads: TD (r range: 0.69; 0.87), high-intensity running (HIR; r range: 0.66; 0.75), and MW (r range: 0.56; 0.68). Moderate-to-large negative relationships were found between hemoglobin levels and internal loads: Edwards’ TRIMP (r range: −0.36; −0.63), %HRmax (r range: −0.50; −0.61), and red zone (r range: −0.50; −0.61). VIFT had unclear relationships with overall internal loads, while hemoglobin levels presented unclear relationships with overall external loads. In conclusion, no meaningful changes were found between sessions considering the format of play used. Additionally, the detected relationships indicate that VIFT and hemoglobin levels are good indicators of the performance capacity and physiological profile of players during SSGs. Also, the use of SSGs protocols as a monitoring complement of the 30-15IFT is suggested.
Anxiety Behavior in Pigs (Sus scrofa) Decreases Through Affiliation and May Anticipate Threat

Anxiety is a physio-psychological state anticipating an imminent threat. In social mammals it is behaviorally expressed via displacement activities and buffered via affiliation. Anxiety research on domestic pigs (Sus scrofa) has mostly focused on abnormal/stereotypic behavior associated with intensive farming. We investigated how anxiety is expressed and modulated in semi-free ranging pigs, in natural habitats. Owing to pigs' socio-cognitive complexity, we posited that displacement activities, if such, would increase after a (stressful) intra-group aggression (Prediction 1), be reduced by affiliation (Prediction 2) and influenced by individual/contextual factors (Prediction 3). From 224 videos recorded on adult individuals (Mean ± SD/subject: 4.84 ± 1.85 h) at the “Ethical Farm Parva Domus” (Turin, Italy), we extracted possible displacement activities (vacuum-chewing, scratching/body-rubbing, head/body-shaking, and yawning) in four 3-min conditions: before (BA) and after aggression events, in the absence (AA) or presence (AP) of post-aggression affiliation, and a matched-control (no event; MC). We conducted a minute-by-minute analysis in AE/AA and assessed the effect of subjects' involvement in a conflict (aggressor, aggression's recipient, bystander). All activities were higher in AA than in BA condition—thus being anxiety markers—and all of them decreased to baseline levels in AP, faster compared to AE. Hence, anxiety behavior in pigs was socially buffered. Intriguingly, anxiety behavior was expressed significantly more by bystanders than opponents, which suggests that pigs may be able to anticipate imminent threats. By highlighting how anxiety is managed under extensive farming, this study contributes to the understanding of pig welfare and biology.
Genes Regulating Spermatogenesis and Sperm Function Associated With Rare Disorders

Spermatogenesis is a cell differentiation process that ensures the production of fertilizing sperm, which ultimately fuse with an egg to form a zygote. Normal spermatogenesis relies on Sertoli cells, which preserve cell junctions while providing nutrients for mitosis and meiosis of male germ cells. Several genes regulate normal spermatogenesis, some of which are not exclusively expressed in the testis and control multiple physiological processes in an organism. Loss-of-function mutations in some of these genes result in spermatogenesis and sperm functionality defects, potentially leading to the insurgence of rare genetic disorders. To identify genetic intersections between spermatogenesis and rare diseases, we screened public archives of human genetic conditions available on the Genetic and Rare Diseases Information Center (GARD), the Online Mendelian Inheritance in Man (OMIM), and the Clinical Variant (ClinVar), and after an extensive literature search, we identified 22 distinct genes associated with 21 rare genetic conditions and defective spermatogenesis or sperm function. These protein-coding genes regulate Sertoli cell development and function during spermatogenesis, checkpoint signaling pathways at meiosis, cellular organization and shape definition during spermiogenesis, sperm motility, and capacitation at fertilization. A number of these genes regulate folliculogenesis and oogenesis as well. For each gene, we review the genotype–phenotype association together with associative or causative polymorphisms in humans, and provide a description of the shared molecular mechanisms that regulate gametogenesis and fertilization obtained in transgenic animal models.
Cooling Between Exercise Bouts and Post-exercise With the Fan Cooling Jacket on Thermal Strain in Hot-Humid Environments

This study investigated the effects of cooling between exercise bouts and post-exercise with a commercially available fan cooling jacket on thermal and perceptual responses during and following exercise in hot-humid environments. Ten male athletes completed two 30 min cycling bouts at a constant workload (1.4 watts⋅kg–1 of body mass) with a 5 min recovery period in between. Exercise was followed by a 10 min recovery period. In an environmental chamber (33°C, 65% relative humidity), participants performed two trials with (FCJ) or without (CON) the fan cooling jacket on a T-shirt during the 5 min inter-exercise and 10 min post-exercise recovery periods. Mean, chest and upper arm skin temperatures, and thermal sensation and comfort were lower in FCJ than CON trial during and following exercise (P < 0.05). Thigh and calf skin temperatures, infrared tympanic temperature and heart rate were lower in FCJ than CON trial during the experimental trials (P < 0.05). The rates of fall in mean, chest and upper arm skin temperatures, infrared tympanic temperature and thermal sensation and comfort were faster in FCJ than CON trial during both recovery periods (P < 0.05). There were faster rates of fall in thigh and calf skin temperatures and heart rate in FCJ than CON trial during the post-exercise recovery period (P < 0.05). No difference was observed between trials in the rating of perceived exertion (P > 0.05). This study indicates that cooling between exercise bouts and post-exercise with the fan cooling jacket would effectively mitigate thermal strain and perception/discomfort during and following exercise in hot-humid environments. This garment would reduce whole-body skin temperature quickly while promoting falls in lower-body as well as upper-body skin temperatures.
Virtual Reality as a Technological-Aided Solution to Support Communication in Persons With Neurodegenerative Diseases and Acquired Brain Injury During COVID-19 Pandemic

The COVID-19 poses an ongoing threat to lives around the world and challenges the existing public health and medical service delivery. The lockdown or quarantine measures adopted to prevent the spread of COVID-19 has caused the interruption in ongoing care and access to medical care including to patients with existing neurological conditions. Besides the passivity, isolation, and withdrawal, patients with neurodegenerative diseases experience difficulties in communication due to a limited access to leisure opportunities and interaction with friends and relatives. The communication difficulties may exacerbate the burden on the caregivers. Therefore, assistive-technologies may be a useful strategy in mitigating challenges associated with remote communication. The current paper presents an overview of the use of assistive technologies using virtual reality and virtual body ownership in providing communication opportunities to isolated patients, during COVID-19, with neurological diseases and moderate-to-severe communication difficulties. We postulate that the assistive technologies-based intervention may improve social interactions in patients with neurodegenerative diseases and acquired brain injury-thereby reducing isolation and improving their quality of life and mental well-being.
Co-Reactivation of Cytomegalovirus and Epstein-Barr Virus Was Associated With Poor Prognosis After Allogeneic Stem Cell Transplantation

Reactivation of cytomegalovirus (CMV) or Epstein-Barr virus (EBV) is common after hematopoietic stem cell transplantation (HSCT). Previous researches have demonstrated that either CMV or EBV reactivation is associated with poor outcomes of HSCT. However, few studies investigate the impact of CMV and EBV co-reactivation after HSCT. In this study, we described the clinical characteristics of HSCT recipients with CMV and EBV co-reactivation (defined as CMV and EBV viremia occur at the same period of time). We conducted a longitudinal study of 247 patients who underwent HSCT in our center. A total of 24 (9.7%) patients had CMV and EBV co-reactivation. These patients showed higher incidence of viral pneumonitis (P=0.005). Patients with CMV and EBV co-reactivation had significant lower 1-year overall survival (OS) (P=0.004) and lower 1-year leukemia free survival (LFS) (P=0.016). Our further analysis suggested that duration of CMV (P=0.014), EBV (P<0.001), and CD4+CD25+ T cell counts at day 30 post-transplantation (P=0.05) are independent risk factors of virus co-reactivation. In conclusion, patients who developed co-reactivation of CMV and EBV had poor prognosis in terms of lower 1-year OS and LFS, and the CMV and EBV co-reactivation was associated with prolonged CMV or EBV duration and poor CD4+CD25+ T cell reconstitution at day 30 post-transplantation.
Therapeutic Use of Mesenchymal Stromal Cells: The Need for Inclusive Characterization Guidelines to Accommodate All Tissue Sources and Species

Following their discovery over 50 years ago, mesenchymal stromal cells (MSCs) have become one of the most studied cellular therapeutic products by both academia and industry due to their regenerative potential and immunomodulatory properties. The promise of MSCs as a therapeutic modality has been demonstrated by preclinical data yet has not translated to consistent, successful clinical trial results in humans. Despite the disparities across the field, MSC shareholders are unified under one common goal—to use MSCs as a therapeutic modality to improve the quality of life for those suffering from a malady in which the standard of care is suboptimal or no longer effective. Currently, there is no Food and Drug Administration (FDA)-approved MSC therapy on the market in the United States although several MSC products have been granted regulatory approval in other countries. In this review, we intend to identify hurdles that are impeding therapeutic progress and discuss strategies that may aid in accomplishing this universal goal of widespread therapeutic use.