Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome analysis of bread wheat leaves in response to salt stress

Salinity is one of the main abiotic stresses limiting crop productivity. In the current study, the transcriptome of wheat leaves in an Iranian salt-tolerant cultivar (Arg) was investigated in response to salinity stress to identify salinity stress-responsive genes and mechanisms. More than 114 million reads were generated from leaf tissues by the Illumina HiSeq 2500 platform. An amount of 81.9% to 85.7% of reads could be mapped to the wheat reference genome for different samples. The data analysis led to the identification of 98819 genes, including 26700 novel transcripts. A total of 4290 differentially expressed genes (DEGs) were recognized, comprising 2346 up-regulated genes and 1944 down-regulated genes. Clustering of the DEGs utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that transcripts associated with phenylpropanoid biosynthesis, transporters, transcription factors, hormone signal transduction, glycosyltransferases, exosome, and MAPK signaling might be involved in salt tolerance. The expression patterns of nine DEGs were investigated by quantitative real-time PCR in Arg and Moghan3 as the salt-tolerant and susceptible cultivars, respectively. The obtained results were consistent with changes in transcript abundance found by RNA-sequencing in the tolerant cultivar. The results presented here could be utilized for salt tolerance enhancement in wheat through genetic engineering or molecular breeding.
The demand for a COVID-19 vaccine in Kenya

ABSTRACT The goal of achieving herd immunity to the coronavirus requires high vaccination acceptance levels on the part of the population. The objectives of this study were to: 1) Measure individuals’ willingness to pay (WTP) for a COVID-19 vaccine in Kenya; 2) evaluate the effect of vaccine characteristics (duration of protection and efficacy) and individuals’ socioeconomic variables on WTP, and 3) estimate the aggregate demand and economic value of a COVID-19 vaccine. The contingent valuation (CV) method was used as the basis for the analyses. Data for this study were obtained from a survey of 1,050 individuals in Kenya conducted from April 7 to April 15, 2020. The survey included CV questions using a double-bounded dichotomous choice format. Results reveal that most of the individuals in Kenya (at least 96%) were willing to accept a COVID-19 vaccine. Approximately 80% of individuals were willing to pay a positive amount. Conservative estimates of individuals’ mean WTP for the vaccine range from USD 49.81 to USD 68.25 (depending on vaccine characteristics). Both vaccine duration of protection and efficacy were found to influence WTP (p < .10). The perceived probability of being hospitalized, age, gender, education, location and region of residence, and household income were also found to be associated with WTP for the vaccine (p < .10). In conclusion, the COVID-19 vaccine is highly valued and accepted by the Kenyan population; however, a high percent of the population is unwilling to pay for it or is only willing to pay a low price.
The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large‐scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here, we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post‐glacial expansion northwards along two colonization routes. Based on our analyses of a large SNP data set, we find evidence that both climate and demographic history have shaped the genetic structure of populations. Pronounced genetic differentiation was evident between populations occupying cold versus hot deserts, and we detected numerous loci with significant associations with climate. The genetic signal of founder effects, however, is still present in the genomes of the recently expanded populations, which comprise subsets of genetic variation found in the southern populations.
Assessment of the effect of vacuum-formed retainers and Hawley retainers on periodontal health: A systematic review and meta-analysis

Background Recently, increasing attention has been paid to the periodontal health of orthodontic patients in the maintenance stage in clinical practice. The focus of this meta-analysis was to compare the effects of vacuum-formed retainers (VFR) and Hawley retainers (HR) on periodontal health, in order to provide a reference for clinical selection. Methods From the establishment of the database until November 2020, a large number of databases were searched to find relevant randomized control trials, including the Cochrane Library databases, Embase, PubMed, Medline via Ovi, Web of Science, Scopus, Grey Literature in Europe, Google Scholar and CNKI. Related literature was manually searched and included in the analysis. Two researchers screened the literature according to relevant criteria. The size of the effect was determined using RevMan5.3 software, and the mean difference and 95% confidence intervals (CI) were used to estimate the results using a random effects model. Results This meta-analysis included six randomized controlled trials involving 304 patients. The results of the meta-analysis showed that there was no statistical difference in sulcus probing depth status between the VFR group and the HR group, including at 1, 3, and 6 months. Compared with the VFR group, the HR group showed a lower gingival index at 1 month (mean difference = 0.12, 95%CI: 0.06 to 0.19) and 3 months (mean difference = 0.11, 95%CI: 0.06 to 0.17), while there was no statistically significant difference at 6 months (mean difference = 0.10, 95%CI: -0.07 to 0.27). The plaque index of the HR group also showed a good state at 1 month (mean difference = 0.06, 95%CI: 0.01 to 0.12), 3 months (mean difference = 0.12, 95%CI: 0.08 to 0.16), and 6 months (mean difference = 0.19, 95%CI: 0.09 to 0.29). Subgroup analysis of PLI showed that when all teeth were measured, PLI status was lower in the HR group at 6 months (mean difference = 0.32, 95%CI: 0.18 to 0.46). PLI status was also low for the other teeth group (mean difference = 0.15, 95%CI: 0.08 to 0.22). Conclusion Our meta-analysis showed that patients using the Hawley retainer had better periodontal health compared with those using vacuum-formed retainers. However, more research is needed to look at the periodontal health of patients using these two retainers.
A multi-centre, post-marketing surveillance study of Vi polysaccharide–tetanus toxoid conjugate vaccine (Typbar TCV®) in India

ABSTRACT A typhoid Vi capsular-polysaccharide tetanus toxoid conjugate vaccine (Typbar-TCV®) was recommended by the World Health Organization for use in children >6 months of age. The present post-marketing surveillance study was intended to assess the clinical safety of approximately 11 million doses of TCV sold till 2019 in a diverse age range Indian population. Both active and passive post-marketing surveillance studies were conducted at multiple centers. Active surveillance was performed in two periods, Period-I: February to October 2016, Period-II: April 2017 to October 2018. In Period-II, the Brighton Collaboration Criteria adverse event case definitions were used. Passive surveillance was performed from February 2016 to December 2019 through voluntary reporting by pediatricians across India. During the active surveillance, 1147 adverse events were reported among 4,991 (23.0%) subjects in Period-I, and 596 adverse events among 3898 (21.3%) subjects in Period-II. The most frequent adverse events were fever (9.2% and 12.02%in Periods I and II, respectively), pain at the injection site (8.3% and 7.33%), and swelling (4.0% and 1.93%). No serious adverse events (SAEs) were reported during either Period. Passive surveillance revealed 235 adverse events, including 25 SAEs requiring hospitalization, of which two were due to typhoid fever. All the events mentioned above occurred within one week of vaccination, and all the subjects have recovered from AEs with medications. All reported adverse events resolved with no clinical sequelae. Observations in this study are consistent with the pre-licensure studies with no additional safety signals detected, confirming that Typbar-TCV® is safe. Abbreviations: AE: Adverse event; LMIC: low- and middle-income countries; PMS: Post-marketing surveillance; SAE: Serious adverse event; TCV: Vi-polysaccharide tetanus –toxoid conjugate vaccine (Typbar-TCV®)
Phenotyping long COVID

The public health consequences of the epidemic of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections may well go beyond the current burden on hospital services and the indirect effects of social distancing and lockdowns. Patients, particularly older ones with comorbidities, experience persistent dyspnoea, fatigue, body aches and brain fog for months after the acute phase of coronavirus disease 2019 (COVID-19) [1]. Post-acute sequelae of SARS-CoV-2 infection, more commonly called “long COVID”, attract considerable media attention, patient advocacy group-initiated research and, recently, USD 1.15 billion of funding by the US National Institutes of Health (NIH) [1]. Cellular damage, inflammatory cytokine production and pro-coagulant state induced by SARS-CoV-2 infection provide a pathophysiological rationale for long-lasting symptomatology [2]. Given the magnitude of the COVID-19 pandemic, with currently over 150 million reported cases, long COVID may emerge as a huge worldwide medical problem [1, 2]. Patients who recover from an acute SARS-CoV-2 infection often present with persistent symptoms lasting for months. The cardiopulmonary exercise test profile of those with “long COVID” is suggestive of deconditioning with a tendency to hyperventilation. https://bit.ly/3y8n0Bt
Do technically efficient surgeons continue to provide active clinical services in a university hospital?

It is difficult for university hospitals to recruit and retain technically efficient surgeons because their missions include teaching and research as well as clinical services. The authors hypothesized that technically efficient surgeons do not continue to provide active clinical services in a university hospital. The authors collected data from all the surgical procedures performed at Teikyo University Hospital from April 1 through September 30 in 2013–2018. The dependent variable was defined as a length of each surgeon’s active clinical services measured by month. Data envelopment analysis was employed to calculate each surgeon’s technical efficiency score. Five control variables were selected; experience, medical school, surgical volume, gender, and academic ranks. Multiple regression analysis was performed. Efficiency scores had significantly negative association with length of active clinical services. Experience and surgical volume had significantly positive association with length of active clinical services. The other coefficients of control variables were insignificant. Technically efficient surgeons provide shorter active clinical services in a university hospital.
Autoimmunity to annexin A2 predicts mortality among hospitalised COVID-19 patients

The pathophysiology of severe coronavirus disease 2019 (COVID-19) has largely been attributed to a hyper-inflammatory response without a clear indication of the underlying mechanism [1]. There is a characteristic delay in the onset of respiratory distress, approximately 6 to 12 days after the start of symptoms, which is somewhat atypical for other severe viral respiratory infections [2]. Several theories have been proposed for this delay, such as an indolent infection or viral persistence. However, data from viral cultures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (not PCR) demonstrate a lack of positive cultures beyond day 9 of illness [3]. Levels of anti-annexin A2 antibodies at admission strongly predicted mortality among hospitalised COVID-19 patients. Given its critical protective function in the lung, annexin A2 antagonism may play an important role in the pathophysiology of COVID-19. https://bit.ly/2UMPr9w
Coronary microcirculation assessment using functional angiography: Development of a wire‐free method applicable to conventional coronary angiograms

We aimed to develop a novel wire‐ and adenosine‐free microcirculatory resistive index from functional angiography (angio‐IMR) to estimate coronary microcirculatory resistance, and to investigate how this method can improve clinical interpretation of physiological stenosis assessment with quantitative flow ratio (QFR).
Common Analgesic Use for Menstrual Pain and Ovarian Cancer Risk

This study investigates whether analgesic use specifically for menstrual pain during the premenopausal period influences ovarian cancer risk. Our results suggest use of aspirin or acetaminophen for severe menstrual pain may be associated with lower risk of ovarian cancer among women with severe menstrual pain. Menstrual pain has been associated with increased ovarian cancer risk, presumably through increased inflammation, which is known to play a critical role in ovarian carcinogenesis. Analgesic medications are frequently used to treat menstrual pain, some of which lower ovarian cancer risk. In this study, we examined the association between analgesic use for menstrual pain during the premenopausal period and ovarian cancer risk among women with history of menstrual pain. We used data from the New England Case-Control Study, including 1,187 epithelial ovarian cancer cases and 1,225 population-based controls enrolled between 1998 and 2008 with detailed information on analgesic use for their menstrual pain. We used unconditional logistic regression to calculate the odds ratios (ORs) and 95% confidence intervals (CIs) for the association between analgesic use (i.e., aspirin, ibuprofen, acetaminophen) for menstrual pain and ovarian cancer risk. We further conducted a stratified analysis by intensity of menstrual pain (mild/moderate, severe). Among women with menstrual pain during their 20s and 30s, ever use of analgesics for menstrual pain was not significantly associated with ovarian cancer risk. However, among women with severe menstrual pain, ever use of aspirin or acetaminophen for menstrual pain was inversely associated with risk (OR, 0.41; 95% CI, 0.18–0.94 and OR, 0.43; 95% CI, 0.21–0.88 compared with never users, respectively). No significant association was observed between analgesic use and ovarian cancer risk among women with mild/moderate menstrual pain (Pinteraction ≤ 0.03). Our results suggest that use of aspirin or acetaminophen for severe menstrual pain may be associated with lower risk of ovarian cancer. Prevention Relevance: This study investigates whether analgesic use specifically for menstrual pain during the premenopausal period influences ovarian cancer risk. Our results suggest use of aspirin or acetaminophen for severe menstrual pain may be associated with lower risk of ovarian cancer among women with severe menstrual pain.
Dynamic Change of Endocannabinoid Signaling in the Medial Prefrontal Cortex Controls the Development of Depression After Neuropathic Pain

Many patients with chronic pain conditions suffer from depression. The mechanisms underlying pain-induced depression are still unclear. There are critical links of medial prefrontal cortex (mPFC) synaptic function to depression, with signaling through the endocannabinoid (eCB) system as an important contributor. We hypothesized that afferent noxious inputs after injury compromise activity-dependent eCB signaling in the mPFC, resulting in depression. Depression-like behaviors were tested in male and female rats with traumatic neuropathy [spared nerve injury (SNI)], and neuronal activity in the mPFC was monitored using the immediate early gene c-fos and in vivo electrophysiological recordings. mPFC eCB Concentrations were determined using mass spectrometry, and behavioral and electrophysiological experiments were used to evaluate the role of alterations in eCB signaling in depression after pain. SNI-induced pain induced the development of depression phenotypes in both male and female rats. Pyramidal neurons in mPFC showed increased excitability followed by reduced excitability in the onset and prolonged phases of pain, respectively. Concentrations of the eCBs, 2-arachidonoylglycerol (2-AG) in the mPFC, were elevated initially after SNI, and our results indicate that this resulted in a loss of CB1R function on GABAergic interneurons in the mPFC. These data suggest that excessive release of 2-AG as a result of noxious stimuli triggers use-dependent loss of function of eCB signaling leading to excessive GABA release in the mPFC, with the final result being behavioral depression. SIGNIFICANCE STATEMENT Pain has both somatosensory and affective components, so the complexity of mechanisms underlying chronic pain is best represented by a biopsychosocial model that includes widespread CNS dysfunction. Many patients with chronic pain conditions develop depression. The mechanism by which pain causes depression is unclear. Although manipulation of the eCB signaling system as an avenue for providing analgesia per se has not shown much promise in previous studies. An important limitation of past research has been inadequate consideration of the dynamic nature of the connection between pain and depression as they develop. Here, we show that activity-dependent synthesis of eCBs during the initial onset of persistent pain is the critical link leading to depression when pain is persistent.
The spatial distribution of the photosynthetic picoeukaryotes community structure in Lake Hongze.

The spatial dynamics of picophytoplankton were investigated by flow cytometry and high-throughput sequencing in Lake Hongze, a large river-connecting lake. Picophytoplankton were mainly composed of phycocyanin-rich picocyanobacteria (PCY) and photosynthetic picoeukaryotes (PPEs). PCY was the dominant picophytoplankton group since the contribution of PPEs to total picophytoplankton was only 11.78%. However, PPEs were highly diverse and were composed of Chlorophyta, Bacillariophyta and Chrysophyceae. Environmental factors showed spatial differences, particularly in total phosphorus (TP), suspended solids (SS) and chemical oxygen demand (CODMn), which showed relatively high concentrations around the river channel. The abundances of PPEs and PCY showed similar spatial patterns, which were relatively low in the river course since they were negatively related to SS and CODMn. The top 10 OTUs contributed 79.18% of the total PPEs reads and affiliated with main species in PPEs. CCA results showed that, PPEs community composition was significantly impacted by temperature and DO at sites away from river channel, while was only influenced by nitrite at sites around the river channel.
Clinical utility of the BioFire FilmArray Blood Culture Identification panel in the adjustment of empiric antimicrobial therapy in the critically ill septic patient

Sepsis and septic shock are key contributors to mortality in critically ill patients and thus prompt recognition and management thereof is central to achieving improved patient outcomes. Early initiation of appropriate antimicrobial therapy constitutes a crucial component of the management strategy and thus early identification of the causative pathogen is essential in informing antimicrobial therapeutic choices. The BioFire FilmArray blood culture identification (BCID) panel is a US Food and Drug Administration (FDA) approved rapid, multiplex polymerase chain reaction assay for use on positive blood cultures. This study evaluated its clinical utility in the intensive care unit (ICU) setting, in terms of amendment of empiric antimicrobial therapy in critically ill patients with sepsis. The assay proved useful in this setting as final results were made available to clinicians significantly earlier than with conventional culture methods. This, in turn, allowed for modification of empirical antimicrobial therapy to more appropriate agents in 32% of patients. Additionally, the use of the BioFire FilmArray BCID panel permitted the prompt implementation of additional infection prevention and control practices in a sizeable proportion (14%) of patients in the study who were harbouring multidrug resistant pathogens. These findings support the use of the BioFire FilmArray BCID panel as a valuable adjunct to conventional culture methods for the diagnosis and subsequent management of critically ill patients with sepsis.
Development and analytical validation of a novel bioavailable 25-hydroxyvitamin D assay

Background Bioavailable 25-hydroxyvitamin D (25OHD) may be a better indicator of vitamin D sufficiency than total 25OHD. This report describes a novel assay for measuring serum bioavailable 25OHD. Methods We developed an assay for 25OHD % bioavailability based on competitive binding of 25OHD tracer between vitamin D-binding protein (DBP)-coated affinity chromatography beads and serum DBP. Bioavailable 25OHD, total 25OHD, albumin, and DBP protein concentrations were measured in 89 samples from hospitalized patients and 42 healthy controls to determine how the DBP binding assay responds to differences in concentrations of DBP and compares to calculated bioavailable 25OHD values. Results DBP binding assay showed a linear relationship between DBP-bound 25OHD tracer recovered from bead supernatant and DBP calibrator concentrations (y = 0.0017x +0.731, R2 = 0.9961, p<0.001). Inversion of this relationship allowed interpolation of DBP binding equivalents based upon 25OHD tracer recovered. The relationship between DBP binding equivalents and % bioavailability fits a non-linear curve, allowing calculation of % bioavailable 25OHD from DBP binding equivalents (y = 10.625x-0.817, R2 = 0.9961, p<0.001). In hospitalized patient samples, there were linear relationships between DBP protein concentrations and DBP binding equivalents (y = 0.7905x + 59.82, R2 = 0.8597, p<0.001), between measured vs. calculated % bioavailability (y = 0.9528 + 0.0357, R2 = 0.7200, p<0.001), and between absolute concentrations of measured vs. calculated bioavailable 25OHD (y = 1.2403 + 0.1221, R2 = 0.8913, p<0.001). Conclusions The DBP-binding assay for bioavailable 25OHD shows expected changes in 25OHD % bioavailability in response to changes in DBP concentrations and concordance with calculated bioavailable 25OHD concentrations.