Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid detection of novel coronavirus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by reverse transcription-loop-mediated isothermal amplification

Novel Corona virus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2 or 2019-nCoV), and the subsequent disease caused by the virus (coronavirus disease 2019 or COVID-19), is an emerging global health concern that requires a rapid diagnostic test. Quantitative reverse transcription PCR (qRT-PCR) is currently the standard for SARS-CoV-2 detection; however, Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) may allow for faster and cheaper field based testing at point-of-risk. The objective of this study was to develop a rapid screening diagnostic test that could be completed in 30–45 minutes. Simulated patient samples were generated by spiking serum, urine, saliva, oropharyngeal swabs, and nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. RNA isolated from nasopharyngeal swabs collected from actual COVID-19 patients was also tested. The samples were tested using RT-LAMP as well as by conventional qRT-PCR. Specificity of the RT-LAMP was evaluated by also testing against other related coronaviruses. RT-LAMP specifically detected SARS-CoV-2 in both simulated patient samples and clinical specimens. This test was performed in 30–45 minutes. This approach could be used for monitoring of exposed individuals or potentially aid with screening efforts in the field and potential ports of entry.
New cases of supernumerary chromosomes in characiform fishes

Supernumerary chromosomes were described for five species of Neotropical characiform fishes. These extra chromosomes were small, acrocentric and fully heterochromatic in Leporinus friderici from two different localities as well as in Leporinus sp. , but metacentric and fully heterochromatic in Cyphocharax modesta and Prochilodus nigricans. In Characidium cf. zebra, this element was small, acrocentric and euchromatic. GC-rich DNA blocks were observed in the supernumerary chromosome of Leporinus sp. using chromomycin A3. The widespread occurrence of these extra chromosomal elements suggests their independent origins.
Emerging atypical connectivity networks for processing angry and fearful faces in very preterm born children

Abstract Very preterm born (VPT) children are those born before 32/40 weeks' gestational age and comprise 10% of the 15 million babies born prematurely worldwide each year. Due to advancements in neonatal medicine, the survival rate of VPT birth has increased, but few studies have investigated the nonmedical, social‐cognitive morbidities that affect these children. In this study, we examined emotional face processing networks in VPT compared to age and sex matched full‐term born (FT) children. Magnetoencephalography (MEG) was used to test VPT and FT born children at 6 years (n = 78) and 8 years (n = 83). Children were assessed using an implicit emotion face‐processing task. Happy, fearful, and angry faces were presented for 150 ms, but children were asked to respond by button press to the location of a control pixelated image of the face displayed on the side of the screen opposite to the face. Children rated the valence of the images on a five‐point scale. Group differences showed that VPT children rated angry faces more positively than their FT peers. VPT children had reduced connectivity for angry and fearful faces at 8 years in networks including regions such as the bilateral amygdala, superior temporal sulci, and anterior cingulate gyrus. Interventions should target both emotion recognition, as well as higher cognitive processes related to emotional control and thinking about one's own emotions.
Dietary‐morphological relationships of fishes in Liangzi Lake, China

Species in Liangzi Lake were clustered into four trophic groups: Hemiramphus kurumeus and Hemiculter bleekeri bleekeri fed predominantly on terrestrial insects; Carassius auratus auratus and Abbottina rivularis on non-animal food; Hypseleotris swinhonis, Ctenogobius giurinus, Pseudorasbora parva and Toxabramis swinhonis on cladocerans or copepods; Culterichthys erythropterus on decapod shrimps. Gut length, mouth width, mouth height, gill raker length and gill raker spacing, varied widely among species. With the exception of three species pairs (H. swinhonis, C. glurinus; C. erythropterus, H. kurumeus; T. swinhonis, H. bleekeri bleekeri), principal components analysis of morphological variables revealed over-dispersion of species. Canonical correspondence analysis of dietary and morphological data revealed five significant dietary-morphological correlations. The first three roots explained > 85% of the total variance. The first root reflected mainly the relationship of gut length to non-animal feud, with an increase in gut length associated with an increase in non-animal food. The second root was influenced strongly by the relationship of the gill raker spacing to consumption of copepods, with an increase in gill raker spacing associated positively with copepods in the diet. The third root was influenced by the relationship of mouth gape to consumption of fish and decapod shrimps, with an increase in mouth gape associated with more fish and decapod shrimps in the diet. These significant dietary-morphological relationships supported the eco-morphological hypotheses that fish morphology influence food use, and morphological variation is important in determining ecological segregation of co-existing fish species. (C) 2001 The Fisheries Society of the British Isles.
Folate Receptor β (FRβ) Expression in Tissue-Resident and Tumor-Associated Macrophages Associates with and Depends on the Expression of PU.1

As macrophages exhibit a huge functional plasticity under homeostasis and pathological conditions, they have become a therapeutic target for chronic inflammatory diseases. Hence, the identification of macrophage subset-specific markers is a requisite for the development of macrophage-directed therapeutic interventions. In this regard, the macrophage-specific Folate Receptor β (FRβ, encoded by the FOLR2 gene) has been already validated as a target for molecular delivery in cancer as well as in macrophage-targeting therapeutic strategies for chronic inflammatory pathologies. We now show that the transcriptome of human macrophages from healthy and inflamed tissues (tumor; rheumatoid arthritis, RA) share a significant over-representation of the “anti-inflammatory gene set”, which defines the gene profile of M-CSF-dependent IL-10-producing human macrophages (M-MØ). More specifically, FOLR2 expression has been found to strongly correlate with the expression of M-MØ-specific genes in tissue-resident macrophages, tumor-associated macrophages (TAM) and macrophages from inflamed synovium, and also correlates with the presence of the PU.1 transcription factor. In fact, PU.1-binding elements are found upstream of the first exon of FOLR2 and most M-MØ-specific- and TAM-specific genes. The functional relevance of PU.1 binding was demonstrated through analysis of the proximal regulatory region of the FOLR2 gene, whose activity was dependent on a cluster of PU.1-binding sequences. Further, siRNA-mediated knockdown established the importance of PU.1 for FOLR2 gene expression in myeloid cells. Therefore, we provide evidence that FRβ marks tissue-resident macrophages as well as macrophages within inflamed tissues, and its expression is dependent on PU.1.
"Like Yin and Yang": Perceptions of Methamphetamine Benefits and Consequences Among People Who Use Opioids in Rural Communities.

OBJECTIVES The objective of this study was to investigate methamphetamine use among people who use opioids in rural Oregon communities to explore reasons for use and perceptions of methamphetamine consequences. METHODS We conducted interviews and surveys with participants who inject drugs or misuse prescription opioids in 2 rural Oregon counties with high opioid overdose rates. Survey participants were identified through participant-driven sampling initiated in syringe service programs and field outreach (n = 144). Semi-structured interviews with participants were recruited from the same locations (n = 52). RESULTS Of 144 surveys completed, 112 reported using opioids in the past 30 days; 96% of the 112 also report methamphetamine use. Among the 124 reporting injection drug use, 50% indicated they injected both methamphetamine and heroin in the past 30 days. Interview participants reported early exposure to methamphetamine and indicated that methamphetamine was more widely available, less expensive, and less stigmatized compared to heroin. Participants reported using methamphetamine to improve work-life functioning and because they enjoy the high produced from simultaneous use. Several participants reported a conscious effort to shift to methamphetamine from heroin as a harm reduction strategy.Some participants reported being involuntarily discharged from treatment for opioid use disorder due to methamphetamine use. Several participants perceived methamphetamine as conveying overdose prevention or reversal benefits, while fentanyl contamination in methamphetamine was reported or suspected. CONCLUSION As rural communities respond to evolving drug supply and demand, there is increasing need for public health efforts to address the emerging issue of concurrent methamphetamine and opioid use.
CRISPR/Cas9‐mediated knockout and overexpression studies reveal a role of maize phytochrome C in regulating flowering time and plant height

Summary Maize is a major staple crop widely used for food, feedstocks and industrial products. Shade‐avoidance syndrome (SAS), which is triggered when plants sense competition of light from neighbouring vegetation, is detrimental for maize yield production under high‐density planting conditions. Previous studies have shown that the red and far‐red photoreceptor phytochromes are responsible for perceiving the shading signals and triggering SAS in Arabidopsis; however, their roles in maize are less clear. In this study, we examined the expression patterns of ZmPHYC1 and ZmPHYC2 and found that ZmPHYC1, but not ZmPHYC2, is highly expressed in leaves and is regulated by the circadian clock. Both ZmPHYC1 and ZmPHYC2 proteins are localized to both the nucleus and cytoplasm under light conditions and both of them can interact with themselves or with ZmPHYBs. Heterologous expression of ZmPHYCs can complement the Arabidopsis phyC‐2 mutant under constant red light conditions and confer an attenuated SAS in Arabidopsis in response to shading. Double knockout mutants of ZmPHYC1 and ZmPHYC2 created using the CRISPR/Cas9 technology display a moderate early‐flowering phenotype under long‐day conditions, whereas ZmPHYC2 overexpression plants exhibit a moderately reduced plant height and ear height. Together, these results provided new insight into the function of ZmPHYCs and guidance for breeding high‐density tolerant maize cultivars.
Glomerulus-Selective Regulation of a Critical Period for Interneuron Plasticity in the Drosophila Antennal Lobe

Several features of the adult nervous systems develop in a “critical period” (CP), during which high levels of plasticity allow neural circuits to be tuned for optimal performance. Through an analysis of long-term olfactory habituation (LTH) in female Drosophila, we provide new insight into mechanisms by which CPs are regulated in vivo. LTH manifests as a persistently reduced behavioral response to an odorant encountered for 4 continuous days and occurs together with the growth of specific, odorant-responsive glomeruli in the antennal lobe. We show that the CP for behavioral and structural plasticity induced by ethyl butyrate (EB) or carbon dioxide (CO2) closes within 48 h after eclosion. The elaboration of excitatory projection neuron (PN) processes likely contribute to glomerular volume increases, as follows: both occur together and similarly require cAMP signaling in the antennal lobe inhibitory local interneurons. Further, the CP for structural plasticity could be extended beyond 48 h if EB- or CO2-responsive olfactory sensory neurons (OSNs) are silenced after eclosion; thus, OSN activity is required for closing the CP. Strikingly, silencing of glomerulus-selective OSNs extends the CP for structural plasticity only in respective target glomeruli. This indicates the existence of a local, short-range mechanism for regulating CP closure. Such a local mechanism for CP regulation can explain why plasticity induced by the odorant geranyl acetate (which is attractive) shows no CP although it involves the same core plasticity mechanisms as CO2 and EB. Local control of closure mechanisms during the critical period can potentially impart evolutionarily adaptive, odorant-specific features to behavioral plasticity. SIGNIFICANCE STATEMENT The critical period for plasticity represents a stage of life at which animals learn specific tasks or features with particular facility. This work provides fresh evidence that mechanisms for regulating critical periods are broadly conserved across evolution. Thus, a critical period for long-term olfactory habituation in Drosophila, which closes early in adulthood can, like the critical period for ocular dominance plasticity in mammals, be extended by blocking sensory neurons early in life. Further observations show that critical periods for plasticity can be regulated by spatially restricted mechanisms, potentially allowing varied critical periods for plasticity to stimuli of different ethological relevance.
COVID-19 and immunosuppression: a review of current clinical experiences and implications for ophthalmology patients taking immunosuppressive drugs

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in December 2019 in Wuhan city, Hubei province, China. This is the third and largest coronavirus outbreak since the new millennium after SARS in 2002 and Middle East respiratory syndrome (MERS) in 2012. Over 3 million people have been infected and the COVID-19 has caused more than 217 000 deaths. A concern exists regarding the vulnerability of patients who have been treated with immunosuppressive drugs prior or during this pandemic. Would they be more susceptible to infection by the SARS-CoV-2 and how would their clinical course be altered by their immunosuppressed state? This is a question the wider medical fraternity—including ophthalmologists, rheumatologists, gastroenterologist and transplant physicians among others—must answer. The evidence from the SARS and MERS outbreak offer some degree of confidence that immunosuppression is largely safe in the current COVID-19 pandemic. Preliminary clinical experiences based on case reports, small series and observational studies show the morbidity and mortality rates in immunosuppressed patients may not differ largely from the general population. Overwhelmingly, current best practice guidelines worldwide recommended the continuation of immunosuppression treatment in patients who require them except for perhaps high-dose corticosteroid therapy and in patients with associated risk factors for severe COVID-19 disease.
Clinical characteristics of COVID‐19 in patients with preexisting ILD: A retrospective study in a single center in Wuhan, China

Since the outbreak of 2019 novel coronavirus (SARS‐CoV‐2) pneumonia, many patients with underlying disease, such as interstitial lung disease (ILD), were admitted to Tongji hospital in Wuhan, China. To date, no data have ever been reported to reflect the clinical features of Corona Virus Disease 2019 (COVID‐19) among these patients with preexisting ILD. We analyzed the incidence and severity of COVID‐19 patients with ILD among 3201 COVID‐19 inpatients, and compared two independent cohorts of COVID‐19 patients with pre‐existing ILD (n = 28) and non‐ILD COVID‐19 patients (n = 130). Among those 3201 COVID‐19 inpatients, 28 of whom were COVID‐19 with ILD (0.88%). Fever was the predominant symptom both in COVID‐19 with ILD (81.54%) and non‐ILD COVID‐19 patients (72.22%). However, COVID‐19 patients with ILD were more likely to have cough, sputum, fatigue, dyspnea, and diarrhea. A very significantly higher number of neutrophils, monocytes, interleukin (IL)‐8, IL‐10, IL‐1β, and D‐Dimer was characterized in COVID‐19 with ILD as compared to those of non‐ILD COVID‐19 patients. Furthermore, logistic regression models showed neutrophils counts, proinflammatory cytokines (tumor necrosis factor‐alpha, IL6, IL1β, IL2R), and coagulation dysfunction biomarkers (D‐Dimer, PT, Fbg) were significantly associated with the poor clinical outcomes of COVID‐19. ILD patients could be less vulnerable to SARS‐CoV‐2. However, ILD patients tend to severity condition after being infected with SARS‐CoV‐2. The prognosis of COVID‐19 patients with per‐existing ILD is significantly worse than that of non‐ILD patients. And more, aggravated inflammatory responses and coagulation dysfunction appear to be the critical mechanisms in the COVID‐19 patients with ILD.
Post‐damage alkaloid concentration in sweet and bitter lupin varieties and its effect on subsequent herbivory

Abstract: While most lupin species possess quinolizidine alkaloids, sweet (low alkaloid) varieties are more palatable but at the same time more susceptible to herbivory. Nevertheless, as they are not totally devoid of alkaloids, it may be possible that their alkaloid levels increase after damage. The aim of this study was to compare inductive responses to herbivory in sweet and bitter varieties of Lupinus albus (L.) and Lupinus angustifolius (L.), and to assess if these responses were effective to stop subsequent herbivory. Two experiments were carried out; in the first, Anticarsia gemmatalis (Hübner; Lep., Noctuidae) caterpillars were introduced in field‐growing lupin plants and allowed to feed for 72 h, after which leaves were collected and analysed for alkaloid content and composition. The second experiment was a bioassay, in which leaves collected from experiment 1, from treated and control plants, were offered to another set of Anticarsia caterpillars, and consumption was recorded after 24 h. We found that both L. albus varieties (sweet and bitter) had an increase in their alkaloid concentration after damage, while none of the L. angustifolius varieties had. The sweet L. albus variety, Rumbo, had a greater inductive response than the bitter variety. When leaves were offered to caterpillars (bioassay), this variety showed the greatest difference between consumption of controls and previously eaten leaves, implying that alkaloid levels reached after damage were effective to deter subsequent herbivores as a result of plants probably overcoming a ‘palatability threshold’.
A quantitative serum biomarker of circulating collagen X effectively correlates with endochondral fracture healing

Currently, there are no standardized methods for quantitatively measuring fracture repair. Physicians rely on subjective physical examinations and qualitative evaluation of radiographs to detect mineralized tissue. Since most fractures heal indirectly through a cartilage intermediate, these tools are limited in their diagnostic utility of early repair. Prior to converting to the bone, cartilage undergoes hypertrophic maturation, characterized by the deposition of a provisional collagen X matrix. The objective of this study was to characterize the kinetics of a novel collagen X biomarker relative to other biological measurements of fracture healing using a murine model of endochondral fracture repair in which a closed, mid‐shaft tibia fracture was created using the classic drop‐weight technique. Serum was collected 5 to 42 days post‐fracture in male and female mice and compared to uninjured controls (n = 8‐12). Collagen X in the serum was quantified using a recently validated ELISA‐based bioassay (“Cxm”)1 and compared to genetic and histological markers of fracture healing and inflammation. We found the Cxm biomarker reliably increased from baseline to a statistically unique peak 14 days post‐fracture that then resolved to pre‐fracture levels by 3 weeks following injury. The shape and timing of the Cxm curve followed the genetic and histological expression of collagen X but did not show a strong correlation with local inflammatory states. Assessment of fracture healing progress is crucial to making correct and timely clinical decisions for patients. This Cxm bioassay represents a minimally invasive, inexpensive technique that could provide reliable information on the biology of the fracture to significantly improve clinical care.
Large-Scale Image Analysis for Investigating Spatio-Temporal Changes in Nuclear DNA Damage Caused by Nitrogen Atmospheric Pressure Plasma Jets

The effective clinical application of atmospheric pressure plasma jet (APPJ) treatments requires a well-founded methodology that can describe the interactions between the plasma jet and a treated sample and the temporal and spatial changes that result from the treatment. In this study, we developed a large-scale image analysis method to identify the cell-cycle stage and quantify damage to nuclear DNA in single cells. The method was then tested and used to examine spatio-temporal distributions of nuclear DNA damage in two cell lines from the same anatomic location, namely the oral cavity, after treatment with a nitrogen APPJ. One cell line was malignant, and the other, nonmalignant. The results showed that DNA damage in cancer cells was maximized at the plasma jet treatment region, where the APPJ directly contacted the sample, and declined radially outward. As incubation continued, DNA damage in cancer cells decreased slightly over the first 4 h before rapidly decreasing by approximately 60% at 8 h post-treatment. In nonmalignant cells, no damage was observed within 1 h after treatment, but damage was detected 2 h after treatment. Notably, the damage was 5-fold less than that detected in irradiated cancer cells. Moreover, examining damage with respect to the cell cycle showed that S phase cells were more susceptible to DNA damage than either G1 or G2 phase cells. The proposed methodology for large-scale image analysis is not limited to APPJ post-treatment applications and can be utilized to evaluate biological samples affected by any type of radiation, and, more so, the cell-cycle classification can be used on any cell type with any nuclear DNA staining.
Modulation of Tinospora rumphii and Zinc Salt on DNA Damage in Quinoline-Induced Genotoxicity and Hepatotoxicity in Male Albino Mice

Tinospora rumphii (T. rumphii) is a folkloric medicinal plant that is widely distributed in Asia and Africa. It has been widely used by locals to treat many diseases including jaundice, which is a manifestation of liver damage. We investigated the action of T. rumphii crude extract together with zinc sulphate, a known tumor modulator, on hepatic injuries induced by intraperitoneal (i.p) injections of quinoline on albino mice. The hepatotoxic effect was assessed by bilirubin concentration in the blood serum, while the genotoxic effect was determined by single-cell gel electrophoresis (SCGE). The mice orally fed with the crude extracts, following quinoline exposure, had reduced serum bilirubin concentration and DNA damage. Mice treated with Zinc sulphate, on the other hand, had remarkably reduced DNA damage on hepatocytes. Our findings showed that hepatoprotective potential of T. rumphii extract is dose-dependent and that utilization of the extract as medicinal remedy must be strictly monitored, while zinc was proven to reverse genotoxic effect of quinoline. This study unraveled the potential of T. rumphii extract and zinc as important hepatoprotective agents for future treatment of hepatic damage caused by chemotherapeutic agents used in cancer treatment.