Miracle-dz/UniFAR-FTUs huggingface dataset:
COLD-REGULATED GENE27 Integrates Signals from Light and the Circadian Clock to Promote Hypocotyl Growth in Arabidopsis

COR27 inhibits the biochemical activity of HY5, and up-regulates PIF4 expression especially in the afternoon to promote hypocotyl elongation. Light and the circadian clock are two essential external and internal cues affecting seedling development. COLD-REGULATED GENE27 (COR27), which is regulated by cold temperatures and light signals, functions as a key regulator of the circadian clock. Here, we report that COR27 acts as a negative regulator of light signaling. COR27 physically interacts with the CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)–SUPPRESSOR OF PHYTOCHROME A1 (SPA1) E3 ubiquitin ligase complex and undergoes COP1-mediated degradation via the 26S proteasome system in the dark. cor27 mutant seedlings exhibit shorter hypocotyls, while transgenic lines overexpressing COR27 show elongated hypocotyls in the light. In addition, light induces the accumulation of COR27. On one hand, accumulated COR27 interacts with ELONGATED HYPOCOTYL5 (HY5) to repress HY5 DNA binding activity. On the other hand, COR27 associates with the chromatin at the PHYTOCHROME INTERACTING FACTOR4 (PIF4) promoter region and upregulates PIF4 expression in a circadian clock–dependent manner. Together, our findings reveal a mechanistic framework whereby COR27 represses photomorphogenesis in the light and provide insights toward how light and the circadian clock synergistically control hypocotyl growth.
Spring phytoplankton phenology: are patterns and drivers of change consistent among lakes in the same climatological region?

1. Advancement of phytoplankton peaks has been reported from a large variety of aquatic systems, attributed mostly to climate warming. Most studies have used chlorophyll a as a proxy for phytoplankton biomass. Here, we investigated phenology of three phytoplankton taxa (Asterionella formosa, Aulacoseira spp. and Cryptomonas spp.) in four lakes of the English Lake District situated within the same catchment over a 58-year period (1945–2003). 2. We used two methods (the centre of gravity method and a fitted Weibull-type function) to quantify the timing of the spring bloom. Both methods gave similar results for the diatoms, but not for Cryptomonas spp. 3. The timing of the spring bloom advanced over the study period for A. formosa but was delayed for Aulacoseira spp. and Cryptomonas spp. These changes were consistent in all four lakes. 4. We tested whether surface water temperatures prior to the time of phytoplankton peak abundance, winter soluble reactive phosphorus (SRP) and silicate concentrations, winter taxon inoculum, Schmidt stability or a combination of these affected phytoplankton phenology in the four lakes. Results were remarkably consistent: each driver either advanced or delayed the peak of each taxon in all four lakes. However, the different drivers affected the taxa differently. 5. Contrary to our expectations, the regional driver, temperature, did not have a consis-tent effect on the three phytoplankton taxa, significantly advancing A. formosa and Aulacoseira spp. in the North Basin of Windermere but significantly delaying Cryptomonas spp. peaks in three lakes. Overall, the locally variable driver, SRP concentration, had a more consistent effect upon phenology, affecting all taxa in nearly all lakes.
The species composition—ecosystem function relationship: A global meta-analysis using data from intact and recovering ecosystems

The idea that biodiversity is necessary in order for ecosystems to function properly has long been used as a basic argument for the conservation of species, and has led to an abundance of research exploring the relationships between species richness and ecosystem function. Here we present a meta-analysis of global ecosystems using the Bray-Curtis index to explore more complex changes in the species composition of natural ecosystems, and their relationship with ecosystem functions. By using data recorded, firstly in reference sites and secondly in recovering sites, captured in restoration ecology studies, we pose the following questions: Firstly, how much variation is there in species composition and in ecosystem function in an intact ecosystem? Secondly, once an ecosystem has become degraded, is there a general relationship between its recovery in species composition and its recovery in ecosystem function? Thirdly, is this relationship the same for all types of ecosystem functions? Data from 21 studies yielded 478 comparisons of mean values for ecosystems. On Average, sites within the same intact natural ecosystems shared only a 48% similarity in species composition but were 69% similar in ecosystem functioning. In recovering ecosystems the relationship between species composition and ecosystem function was weak and saturating (directly accounting for only 2% of the variation). Only two of the six types of ecosystem function examined, biomass and biotic structure, showed a significant relationship with species composition, and the three types that measured soil functions showed no significant relationship. To date, most biodiversity—ecosystem function (BEF) research has been conducted in simplified ecosystems using the simple species richness metric. This study encourages a broader examination of the drivers of ecosystem functions under realistic scenarios of biodiversity change, and highlights the need to properly account for the extensive natural variation.
Clonal Hematopoiesis and Mutations of Myeloproliferative Neoplasms

Myeloproliferative neoplasms (MPNs) are associated with the fewest number of mutations among known cancers. The mutations propelling these malignancies are phenotypic drivers providing an important implement for diagnosis, treatment response monitoring, and gaining insight into the disease biology. The phenotypic drivers of Philadelphia chromosome negative MPN include mutations in JAK2, CALR, and MPL. The most prevalent driver mutation JAK2V617F can cause disease entities such as essential thrombocythemia (ET) and polycythemia vera (PV). The divergent development is considered to be influenced by the acquisition order of the phenotypic driver mutation relative to other MPN-related mutations such as TET2 and DNMT3A. Advances in molecular biology revealed emergence of clonal hematopoiesis (CH) to be inevitable with aging and associated with risk factors beyond the development of blood cancers. In addition to its well-established role in thrombosis, the JAK2V617F mutation is particularly connected to the risk of developing cardiovascular disease (CVD), a pertinent issue, as deep molecular screening has revealed the prevalence of the mutation to be much higher in the background population than previously anticipated. Recent findings suggest a profound under-diagnosis of MPNs, and considering the impact of CVD on society, this calls for early detection of phenotypic driver mutations and clinical intervention.
Growth and Major Inorganic Cation Budgets of Atlantic Salmon Alevins at Three Ambient Acidities

Abstract Budgets of Ca++, Mg++, Na+, and K+ were determined for alevins of Atlantic salmon Salmo salar incubated at pH 6.8, 5.1, or 4.5. Accumulation of Ca++, K +, and Na + by larvae was reduced at pH 4.5 whereas Mg++ accumulation was unaffected. The extrapolated dry weight of larvae at terminal yolk resorption was reduced from 27 mg at pH 6.8 and 5.1 to 20 mg at pH 4.5. The findings support the hypothesis that high acidity affects ion uptake from the ambient water more than yolk-to-larva transfer of cations.
Vaccine Design from the Ensemble of Surface Glycoprotein Epitopes of SARS-CoV-2: An Immunoinformatics Approach

The present study aimed to work out a peptide-based multi-epitope vaccine against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We predicted different B-cell and T-cell epitopes by using the Immune Epitopes Database (IEDB). Homology modeling of the construct was done using SWISS-MODEL and then docked with different toll-like-receptors (TLR4, TLR7, and TLR8) using PatchDock, HADDOCK, and FireDock, respectively. From the overlapped epitopes, we designed five vaccine constructs C1–C5. Based on antigenicity, allergenicity, solubility, different physiochemical properties, and molecular docking scores, we selected the vaccine construct 1 (C1) for further processing. Docking of C1 with TLR4, TLR7, and TLR8 showed striking interactions with global binding energy of −43.48, −65.88, and −60.24 Kcal/mol, respectively. The docked complex was further simulated, which revealed that both molecules remain stable with minimum RMSF. Activation of TLRs induces downstream pathways to produce pro-inflammatory cytokines against viruses and immune system simulation shows enhanced antibody production after the booster dose. In conclusion, C1 was the best vaccine candidate among all designed constructs to elicit an immune response SARS-CoV-2 and combat the coronavirus disease (COVID-19).
Stem Cell Transplantation and Vinblastine Monotherapy for Relapsed Pediatric Anaplastic Large Cell Lymphoma: Results of the International, Prospective ALCL-Relapse Trial.

PURPOSE To analyze the efficacy of a risk-stratified treatment of children with relapsed anaplastic large cell lymphoma (ALCL). The ALCL-Relapse trial (ClinicalTrials.gov identifier: NCT00317408) stratified patients according to the time of relapse and CD3 expression to prospectively test reinduction approaches combined with consolidation by allogeneic or autologous hematopoietic stem cell transplantation (SCT) and vinblastine monotherapy. PATIENTS AND METHODS Patients with progression during frontline therapy (very high risk) or a CD3-positive relapse (high risk) were scheduled for allogeneic SCT after reinduction chemotherapy. Patients with a CD3-negative relapse within 1 year after initial diagnosis or prior exposure to vinblastine (intermediate risk) received autologous SCT after carmustine-etoposide-cytarabine-melphalan. This arm was terminated prematurely, and subsequent patients received vinblastine monotherapy instead. Patients with a CD3-negative relapse > 1 year after initial diagnosis (low risk) received vinblastine monotherapy. RESULTS One hundred sixteen patients met the inclusion criteria; 105 evaluable patients with CNS-negative disease had a 5-year event-free survival (EFS) of 53% ± 5% and a 5-year overall survival (OS) of 78% ± 4%. Before termination of autologous SCT, EFS rates of patients in the very-high- (n = 17), high- (n = 26), intermediate- (n = 32), and low- (n = 21) risk groups were 41% ± 12%, 62% ± 10%, 44% ± 9%, and 81% ± 9%; the respective OS rates were 59% ± 12%, 73% ± 9%, 78% ± 7%, and 90% ± 6%. Analyzing only the patients in the intermediate-risk group consolidated per protocol by autologous SCT, EFS and OS of 23 patients were 30% ± 10% and 78% ± 9%, respectively. All 5 patients with intermediate risk receiving vinblastine monotherapy after the amendment experienced relapse again. CONCLUSION Shorter time to relapse was the strongest predictor of subsequent relapse. Allogeneic SCT offers a chance for cure in patients with high-risk ALCL relapse. For early relapsed ALCL autologous SCT was not effective. Vinblastine monotherapy achieved cure in patients with late relapse; however, it was not effective for early relapses.
Telomere Length Increase in HIV/HCV-Coinfected Patients with Cirrhosis after HCV Eradication with Direct-Acting Antivirals †

Introduction: Human immunodeficiency virus (HIV) infection and cirrhosis are associated with a senescent phenotype that decreases telomere length. We evaluated the impact of hepatitis C virus (HCV) elimination on telomere length in patients with advanced HCV-related cirrhosis after sustained virological response (SVR), with all-oral direct-acting antiviral agents (DAAs). Methods: Prospective study of 60 HIV/HCV-coinfected and 30 HCV-monoinfected patients with advanced HCV cirrhosis (liver decompensation or liver stiffness measurement (LSM) ≥ 25 kPa, hepatic liver pressure gradient (HVPG) ≥ 10 mmHg, or Child–Pugh–Turcotte (CPT) ≥ 7). The relative telomere length (RTL) was quantified by real-time multiplex PCR (MMqPCR) on peripheral blood mononuclear cells at baseline and 48 weeks after HCV treatment. Generalized linear models (GLMs) adjusted for the most relevant clinical and epidemiological variables and mixed GLMs were used. Results: In comparison with HCV-monoinfected patients, HIV/HCV-coinfected patients were younger (p < 0.001), had lower body mass index (BMI) (p = 0.002), and had been exposed less frequently to interferons (p = 0.011). In addition, they were more frequently men (p = 0.011), smokers (p = 0.005), prior intravenous drug users (IVDUs) (p < 0.001), and alcohol abusers (p = 0.005). RTL was significantly lower in HIV/HCV-coinfected patients than in HCV-monoinfected patients, both at baseline (p < 0.001), and at the end of follow-up (p = 0.032). A significant RTL increase over time was found only for HIV/HCV-coinfected patients (p < 0.001), especially in those patients with compensated cirrhosis (p < 0.001). Conclusion: HCV eradication with all-oral DAAs was associated with an increase in telomere length in HIV/HCV-coinfected patients with advanced cirrhosis, particularly in compensated patients. This finding suggests that HCV clearance may have implications in age-related conditions in this population group.
Stromal CCL2 Signaling Promotes Mammary Tumor Fibrosis through Recruitment of Myeloid-Lineage Cells

Obesity is correlated with breast tumor desmoplasia, leading to diminished chemotherapy response and disease-free survival. Obesity causes chronic, macrophage-driven inflammation within breast tissue, initiated by chemokine ligand 2 (CCL2) signaling from adipose stromal cells. To understand how CCL2-induced inflammation alters breast tumor pathology, we transplanted oncogenically transformed human breast epithelial cells with breast stromal cells expressing CCL2 or empty vector into murine mammary glands and examined tumor formation and progression with time. As tumors developed, macrophages were rapidly recruited, followed by the emergence of cancer-associated fibroblasts (CAFs) and collagen deposition. Depletion of CD11b + myeloid lineage cells early in tumor formation reduced tumor growth, CAF numbers, and collagen deposition. CCL2 expression within developing tumors also enhanced recruitment of myeloid progenitor cells from the bone marrow into the tumor site. The myeloid progenitor cell population contained elevated numbers of fibrocytes, which exhibited platelet-derived growth factor receptor-alpha (PDGFRα)-dependent colony formation and growth in vitro. Together, these results suggest that chronic inflammation induced by CCL2 significantly enhances tumor growth and promotes the formation of a desmoplastic stroma through early recruitment of macrophages and fibrocytes into the tumor microenvironment. Fibrocytes may be a novel target in the tumor microenvironment to reduce tumor fibrosis and enhance treatment responses for obese breast cancer patients.
The impact of COVID-19 on Bangladeshi readymade garment (RMG) workers

Abstract This paper describes the potential impact of the coronavirus disease 2019 (COVID-19) pandemic on the readymade garment (RMG) workers of Bangladesh. It articulates the RMG workers’ existing vulnerability during the COVID-19 pandemic based on currently available evidence and personal conversations/communications with RMG workers. COVID-19 has already impacted RMG workers’ health (both physical and mental health status) and wellbeing, and resulted in loss of employment. We argue that the COVID-19 pandemic will have long-lasting effects on the garment workers, especially related to their health issues, financial hardship and inability to pay for essentials such as food, and future employment opportunities. The stakeholders (such as the international retailers/brands, Bangladesh Garment Manufacturers and Exporters Association, Government of Bangladesh) responsible for the global supply chain RMG factories should reconsider the health and overall wellbeing needs of the RMG workers during the ongoing COVID-19 pandemic.
Effectiveness of Resistance Training with the Use of a Suspension System in Patients after Myocardial Infarction

The aim of the study was to assess the effects of resistance training with the use of a suspension system on exercise tolerance, evaluated through an exercise test, and the changes in selected echocardiographic parameters of patients after myocardial infarction. The study involved 44 males. The subjects were divided into two groups: Standard (20) and Suspension system (24). All the subjects had undergone an angioplasty with stent implantation. The standard and suspension system groups carried out a 24-day improvement program comprising 22 training units. Each session consisted of endurance, general stamina and resistance training. Instead of resistance training, the experimental group made multijoint exercises with a suspension system. Statistically significant changes in both groups were observed in the parameters of the echocardiographic exercise test, such as test duration (p = 0.000), distance covered (p = 0.000), MET (p = 0.000), VO2max (p = 0.000) and SBPrest (p = 0.013). Additionally, SBPmax in the suspension system group improved (p = 0.035). The echocardiographic test revealed significant improvement of Left Ventricular Ejection Fraction in both groups (SP group p = 0.001, standard group p = 0.005). The lipid profile test in the SP group revealed statistically significant improvement of TC (p = 0.003), HDL (p = 0.000) and LDL (p = 0.005). Training with the suspension system had a positive effect on the change of exercise tolerance level, left ventricular function and blood lipid profile.
Undetectable equals untransmittable (U = U): awareness and associations with health outcomes among people living with HIV in 25 countries

Objectives ‘Undetectable equals Untransmittable’ (U=U) is an empowering message that may enable people living with HIV (PLHIV) to reach and maintain undetectability. We estimated the percentage of PLHIV who ever discussed U=U with their main HIV care provider, and measured associations with health-related outcomes. Secondarily, we evaluated whether the impact of the U=U message varied between those who heard it from their healthcare provider (HCP) vs from elsewhere. Methods Data were from the 25-country 2019 Positive Perspectives Survey of PLHIV on treatment (n=2389). PLHIV were classified as having discussed U=U with their HCP if they indicated that their HCP had ever told them about U=U. Those who had not discussed U=U with their HCP but were nonetheless aware that ‘My HIV medication prevents me from passing on HIV to others’ were classified as being made aware of U=U from non-HCP sources. Multivariable logistic regression was used to measure associations between exposure to U=U messages and health outcomes. Results Overall, 66.5% reported ever discussing U=U with their HCP, from 38.0% (South Korea) to 87.3% (Switzerland). Prevalence was lowest among heterosexual men (57.6%) and PLHIV in Asia (51.3%). Compared with those unaware of U=U, those reporting U=U discussions with their HCP had lower odds of suboptimal adherence (AOR=0.59, 95% CI 0.44 to 0.78) and higher odds of self-reported viral suppression (AOR=2.34, 95% CI 1.72 to 3.20), optimal sexual health (AOR=1.48, 95% CI 1.14 to 1.92) and reporting they ‘always shared’ their HIV status (AOR=2.99, 95% CI 1.42 to 6.28). While exposure to U=U information from non-HCP sources was beneficial too, the observed associations were attenuated relative to those seen with reported discussions with HCPs. Conclusion HCP discussion of U=U with PLHIV was associated with favourable health outcomes. However, missed opportunities exist since a third of PLHIV reported not having any U=U discussion with their HCP. U=U discussions with PLHIV should be considered as a standard of care in clinical guidelines.
Sex differences in the human reward system: convergent behavioral, autonomic and neural evidence

Abstract Several studies have suggested that females and males differ in reward behaviors and their underlying neural circuitry. Whether human sex differences extend across neural and behavioral levels for both rewards and punishments remains unclear. We studied a community sample of 221 young women and men who performed a monetary incentive task known to engage the mesoaccumbal pathway and salience network. Both stimulus salience (behavioral relevance) and valence (win vs loss) varied during the task. In response to high- vs low-salience stimuli presented during the monetary incentive task, men showed greater subjective arousal ratings, behavioral accuracy and skin conductance responses (P < 0.006, Hedges’ effect size g = 0.38 to 0.46). In a subsample studied with functional magnetic resonance imaging (n = 44), men exhibited greater responsiveness to stimulus salience in the nucleus accumbens, midbrain, anterior insula and dorsal anterior cingulate cortex (P < 0.02, g = 0.86 to 1.7). Behavioral, autonomic and neural sensitivity to the valence of stimuli did not differ by sex, indicating that responses to rewards vs punishments were similar in women and men. These results reveal novel and robust sex differences in reward- and punishment-related traits, behavior, autonomic activity and neural responses. These convergent results suggest a neurobehavioral basis for sexual dimorphism observed in the reward system, including reward-related disorders.
Molecular Identification and Prevalence of Entamoeba histolytica, Entamoeba dispar and Entamoeba moshkovskii in Erbil City, Northern Iraq

Abstract The present study was conducted to evaluate the infection rates of Entamoeba histolytica, Entamoeba dispar, and Entamoeba moshkovskii among asymptomatic individuals in Erbil City, northern Iraq. The research intent was to discover whether pathogenic or nonpathogenic species cause a high rate of symptomless Entamoeba infections. Stool samples were microscopically examined, and the 18S-rRNA gene was targeted utilizing the nested PCR technique in the positive specimens. Initial results based on morphological features showed that the Entamoeba prevalence rate was 7.4%. Significantly higher rates of infections were seen in females than in males and in low-income people than in moderate-income people. The incidence rates among the asymptomatic individuals, as determined by molecular analysis, were as follows: E. histolytica – 6%, E. dispar – 4.3%, and E. moshkovskii – 0.3%. Of all the Entamoeba positive samples, a single infection with E. histolytica was identified in 41.4% samples; the single infection with E. dispar in 18.6% samples, 35.7% samples had mixed infections with two Entamoeba species, and 4.3% had mixed infections with three species. The current study concluded that 7.4% of healthy people, who live in the endemic area under investigation, carry Entamoeba species asymptomatically. Additionally, the majority of asymptomatic Entamoeba infections were caused by the pathogenic E. histolytica (81.4%) compared to E. dispar (58.6%), and E. moshkovskii with the lowest rate of infection. Single and co-infections with E. histolytica and E. dispar were noted. E. moshkovskii, which was identified for the first time in the region, was only seen in mixed infections.