Miracle-dz/UniFAR-FTUs huggingface dataset:
Bilateral Ocular Necrotizing Fasciitis in an Immunosuppressed Patient on Prescription Eye Drops

Preseptal cellulitis is an infection of ocular tissue that is often unilateral and caused by extension of sinonasal disease. In rare instances it can lead to life-threatening necrotizing fasciitis. We present here a unique case of bilateral preseptal cellulitis incited by local conjunctivitis caused by prescription eye drops. The patient was immunosuppressed, which allowed her local inflammation to progress to severe infection and, ultimately, to necrotizing fasciitis. This necessitated serial debridement by ophthalmology and otolaryngology teams and a prolonged course of intravenous antibiotics monitored by an infectious disease team. Despite these interventions, the patient’s vision did not return to baseline and she had persistent cosmetic and functional deformity. This case is unique due to the inciting incident of new prescription eye drops, the patient’s immunosuppressed state leading to severity of infection, and the severe bilateral disease burden.
Climate and vegetation structure shape ant communities along elevational gradients on the Colorado Plateau

Abstract Terrestrial animal communities are largely shaped by vegetation and climate. With climate also shaping vegetation, can we attribute animal patterns solely to climate? Our study observes ant community changes along climatic gradients (i.e., elevational gradients) within different habitat types (i.e., open and forest) on the Colorado Plateau in the southwestern United States. We sampled ants and vegetation along two elevational gradients spanning 1,132 m with average annual temperature and precipitation differences of 5.7°C and 645mm, respectively. We used regression analyses and structural equation modeling to compare the explanatory powers and effect sizes of climate and vegetation variables on ants. Climate variables had the strongest correlations and the largest effect sizes on ant communities, while vegetation composition, richness, and primary productivity had relatively small effects. Precipitation was the strongest predictor for most ant community metrics. Ant richness and abundance had a negative relationship with precipitation in forested habitats, and positive in open habitats. Our results show strong direct climate effects on ants with little or no effects of vegetation composition or primary productivity, but contrasting patterns between vegetation type (i.e., forested vs. open) with precipitation. This indicates vegetation structure can modulate climate responses of ant communities. Our study demonstrates climate‐animal relationships may vary among vegetation types which can impact both findings from elevational studies and how communities will react to changes in climate.
Polymorphism Analysis of Genes Involved in Xenobiotic Metabolism and Circadian Rhythm in Human Breast Cancer

Individual response to xenobiotic exposures depends on the dynamics of xenobiotic metabolism and the circadian clock system, among other factors. Since these systems are closely related, polymorphisms in their key genes may have an impact on how carcinogenic compounds are metabolized, and therefore on the risk of tumor development. Whereas the mammary gland is exposed to agents that damage DNA, it was considered of high interest to study xenobiotic metabolizing genes (XMG) and clock genes in this tissue. Our aim was to analyze genotype and allele frequencies of polymorphisms in the XMG N-acetyl transferase 2 (NAT2) and glutathione S-transferase T1 (GSTT1), and in the clock genes period 3 (PER3) and CLOCK in human breast tumor samples. As well, it was if these polymorphisms were in linkage disequilibrium. 65 samples were genotyped for polymorphisms in GSTT1 (null), NAT2 (C481T, G590A and G857A), CLOCK (T3111C) and PER3 (length polymorphism), by PCR and PCR-RFLP. For GSTT1, 20% of the samples showed total absence of the gene. When NAT2 genotypes were grouped by their associated acetylator phenotype, 5% of rapid, 49% of intermediate and 46% of slow acetylator phenotypes were indicated. Allele frequencies for CLOCK were T=0.78 and C=0.22; for PER3, they were 0.66 for the 4repeats allele and 0.34 for the 5-repeats allele. Linkage disequilibrium test indicated evidence of strong linkage between NAT2 and CLOCK (χ 2 =13.076; p=0.005). With regard to allele and genotype frequencies, our results are in agreement with those reported for similar populations. The evidence of linkage disequilibrium in our breast cancer samples is interesting and requires further investigation. This work constitutes a first approximation to a combined study of polymorphisms in XMG and clock genes in breast cancer Argentinian patients. Future studies will attempt to address the role of these and other polymorphisms in cancer risk, prognosis and response to treatment.
Seed Composition and Amino Acid Profiles for Quinoa Grown in Washington State

Quinoa (Chenopodium quinoa Willd.) is a pseudocereal celebrated for its excellent nutritional quality and potential to improve global food security, especially in marginal environments. However, minimal information is available on how genotype influences seed composition, and thus, nutritional quality. This study aimed to provide a baseline for nutritional quality of Washington grown quinoa and test the hypothesis that these samples contain adequate amounts of essential amino acids to meet daily requirements set by the World Health Organization (WHO). One hundred samples, representing commercial varieties and advanced breeding lines adapted to Washington State, were analyzed for content of 23 amino acids, as well as crude protein, ash, moisture, and crude fat. Mean essential amino acid values for Washington grown quinoa met the daily requirements for all age groups for all essential amino acids, except for the amount of leucine required by infants. We found that only nine genotypes met the leucine requirements for all age groups. A total of 52 and 94 samples met the lysine and tryptophan requirements for all age groups, respectively. Mean values for isoleucine, leucine, lysine, tryptophan, valine, and the sulfur and aromatic amino acids are higher for Washington grown samples than those reported previously reported in the literature. Our results show that not all Washington grown quinoa samples meet daily requirements of essential amino acids, and we identify limiting amino acids for the germplasm and environments investigated. This study provides the first report of leucine as a limiting amino acid in quinoa. Additional research is needed to better understand variation in quinoa nutritional composition, identify varieties that meet daily requirements, and explore how genotype, environment, and management interactions influence nutritional quality.
Co-Overexpression of OsNAR2.1 and OsNRT2.3a Increased Agronomic Nitrogen Use Efficiency in Transgenic Rice Plants

The NO3 - transporter plays an important role in rice nitrogen acquisition and nitrogen-use efficiency. Our previous studies have shown that the high affinity systems for nitrate uptake in rice is mediated by a two-component NRT2/NAR2 transport system. In this study, transgenic plants were successful developed by overexpression of OsNAR2.1 alone, OsNRT2.3a alone and co-overexpression of OsNAR2.1 and OsNRT2.3a. Our field experiments indicated that transgenic lines expressing p35S:OsNAR2.1 or p35S:OsNAR2.1-p35S:OsNRT2.3a constructs exhibited increased grain yields of approximately 14.1% and 24.6% compared with wild-type (cv. Wuyunjing 7, WT) plants, and the agricultural nitrogen use efficiency increased by 15.8% and 28.6%, respectively. Compared with WT, the 15N influx in roots of p35S:OsNAR2.1 and p35S: OsNAR2.1-p35S:OsNRT2.3a lines increased 18.9%‑27.8% in response to 0.2 mM, 2.5 mM 15NO3 –, and 1.25 mM 15NH4 15NO3, while there was no significant difference between p35S:OsNAR2.1 and p35S:OsNAR2.1-p35S:OsNRT2.3a lines; only the 15N distribution ratio of shoot to root for p35S:OsNAR2.1-p35S:OsNRT2.3a lines increased significantly. However, there were no significant differences in nitrogen use efficiency, 15N influx in roots and the yield between the p35S:NRT2.3a transgenic lines and WT. This study indicated that co-overexpression of OsNAR2.1 and OsNRT2.3a could increase rice yield and nitrogen use efficiency.
DNA Encapsidation and Capsid Assembly Are Underexploited Antiviral Targets for the Treatment of Herpesviruses

Although there are effective nucleoside analogs to treat HSV, VZV, and HCMV disease, herpesvirus infections continue to contribute to significant morbidity and mortality. Acyclovir is the drug of choice for HSV encephalopathy, yet there is an estimated 6–19% mortality rate with half of the survivors experiencing moderate to severe chronic neurological deficits. For VZV, current treatments are inadequate to prevent acute and persistent pain due to zoster. Treatment of HCMV with GCV requires close monitoring particularly in patients with impaired renal function and there are no approved treatments for congenital HCMV infections. New therapeutic options to control cytomegalovirus reactivation in bone marrow and stem cell transplant patients are needed to improve patient outcome. No successful chemotherapeutic options are available for EBV, HHV-6, 7, and 8. Drug resistance is a concern for HCMV, HSV, and VZV since approved drugs share common mechanisms of action. Targeting DNA encapsidation or capsid assembly provide additional options for the development of non-nucleoside, small molecule anti-herpesviral drugs.
Pharmaco-fUS for Characterizing Drugs for Alzheimer’s Disease – The Case of THN201, a Drug Combination of Donepezil Plus Mefloquine

Donepezil is a potent acetylcholinesterase inhibitor, largely used worldwide to alleviate cognitive symptoms in Alzheimer’s disease (AD). Beyond the widely described neuronal impact of donepezil, it was recently shown that targeting connexins, the proteins involved in astrocyte network organization, potentiates donepezil efficacy profile using behavioral tests in AD rodent models. We herein present data demonstrating the potential of functional ultrasound imaging to monitor cerebral activity changes after pharmacological challenge in mice. As an example, we showed that although administration of donepezil or mefloquine alone at low dose had only very limited effects on the signal compared to the baseline, their combination produced marked hemodynamic effects in the hippocampus, in line with previously published behavioral data demonstrating a synergic interaction between both drugs. Thus, the present study provides new perspectives, (i) through the use of pharmaco-fUS, a new non-clinical imaging modality, to move forward drug discovery in AD and (ii) by the profiling of two drug treatments on brain dynamics, one used in AD: donepezil, and the other in development: donepezil combined with mefloquine (THN201) as a modulator of astrocyte network.
Reflections on Inner and Outer Silence and Consciousness Without Contents According to the Sphere Model of Consciousness

In the current hypothesis paper, we propose that focusing attention on silence can be used as a paradigm conceptually similar to sensory deprivation, to study consciousness without content. We briefly overview recent influential models of consciousness and consider how they assess the relationship between consciousness and contents. After discussing the strengths and weaknesses of current models, we suggest an extension based on the Sphere Model of Consciousness (SMC) and introduce new definitions for identification and self-awareness as states of consciousness. We further compare Paoletti’s theoretical model for the development of self with other influential models, highlighting similarities and differences. We conclude with a discussion of how attentional focus on silence can be empirically tested.
Molecular support of the classification of Greeniopsis Merr. in Aleisanthieae (Rubiaceae), with a revision of the genus

Greeniopsis Merr. is a small genus of Rubiaceae endemic to the Philippines. Previously, no molecular data have been available for Greeniopsis and its taxonomic position has remained controversial. Based on morphology, the genus was tentatively included in the tribe Aleisanthieae (Ixoroideae) along with the Southeast Asian genera Aleisanthia and Aleisanthiopsis. To determine the taxonomic position of Greeniopsis and evaluate the monophyly of the genus, sequences of the rps16 and trnT-F regions of cpDNA of all seven Greeniopsis species were generated. Parsimony and Bayesian analyses of the combined plastid dataset strongly support the inclusion of Greeniopsis in Aleisanthieae as well as its monophyly. Woolly hairs on the abaxial leaf surface occur in only one Greeniopsis species and can no longer be regarded a synapomorphy of the tribe. The generic status of Aleisanthia, Aleisanthiopsis, and Greeniopsis is maintained. A revision of Greeniopsis, including a key to species, descriptions, distribution maps, and illustrations, is provided.
Arousal and Executive Alterations in Attention Deficit Hyperactivity Disorder (ADHD)

Attention deficit hyperactivity disorder (ADHD) is the most common neurobehavioral disorder in childhood and can significantly affect a child’s personal and social development and academic achievement. Taking into account the model of attentional networks proposed by Posner et al., the aim of the present study was to review the literature regarding two main explicative models of ADHD, i.e., the inhibition model and the cognitive-energetic model, by discussing behavioral and neurological evidence of both models and the limitations of each model. The review highlights evidence that favors the energetic model and points to an unstable arousal as a potential pathogenetic factor in ADHD.
When the Damage Is Done: Injury and Repair in Thymus Function

Even though the thymus is exquisitely sensitive to acute insults like infection, shock, or common cancer therapies such as cytoreductive chemo- or radiation-therapy, it also has a remarkable capacity for repair. This phenomenon of endogenous thymic regeneration has been known for longer even than its primary function to generate T cells, however, the underlying mechanisms controlling the process have been largely unstudied. Although there is likely continual thymic involution and regeneration in response to stress and infection in otherwise healthy people, acute and profound thymic damage such as that caused by common cancer cytoreductive therapies or the conditioning regimes as part of hematopoietic cell transplantation (HCT), leads to prolonged T cell deficiency; precipitating high morbidity and mortality from opportunistic infections and may even facilitate cancer relapse. Furthermore, this capacity for regeneration declines with age as a function of thymic involution; which even at steady state leads to reduced capacity to respond to new pathogens, vaccines, and immunotherapy. Consequently, there is a real clinical need for strategies that can boost thymic function and enhance T cell immunity. One approach to the development of such therapies is to exploit the processes of endogenous thymic regeneration into novel pharmacologic strategies to boost T cell reconstitution in clinical settings of immune depletion such as HCT. In this review, we will highlight recent work that has revealed the mechanisms by which the thymus is capable of repairing itself and how this knowledge is being used to develop novel therapies to boost immune function.
Binding Ligands that Straddle an Important Contact Site on the RBD of the Covid-19 Spike Protein

The receptor binding domain (RBD) of the spike protein of the Covid-19 virus is responsible for attachment to human ACE2. A number of recent articles have studied monoclonal antibody blocking [8-11] and peptide inhibitors [12-16] of the Covid-19 virus. Here we report virtual ligand-based screening that targets pockets on each side of an important binding site with residues 502-504 on the RBD that contact residues 353-357 [15] of hACE2. These ligands are intended as pre-exposure therapy for Covid-19 infection.
Bacteria Remediate the Effects of Food Additives on Intestinal Function in an in vitro Model of the Gastrointestinal Tract

As the site of nutrient absorption, the small intestine is continuously exposed to preservatives and additives present in consumed food. While the effects of diet on the lower gastrointestinal tract are widely studied, the effects of food additives on the small intestinal epithelium and microbiota are less clearly understood. The goal of this work was to develop and establish a physiologically relevant model of the upper gastrointestinal tract to study the complex interactions between food additives, individual bacterial species, and intestinal function. To achieve this, an in vitro model incorporating simulated digestion, human intestinal epithelial cells, and the commensal, Gram-positive Lactobacillus rhamnosus, or the opportunistic, Gram-negative Escherichia coli was developed. This model was used to assess intestinal permeability and alkaline phosphatase activity following exposure to high glucose (HG), salt, emulsifier (TWEEN 20), food (milk chocolate candies) or chemical grade titanium dioxide nanoparticles (TiO2-NP), and food (whole wheat bread) or chemical grade gluten. It was found that HG increased intestinal permeability, the presence of bacteria remediated the negative effects of HG on intestinal permeability, and a decrease in permeability and IAP activity was observed with increasing concentration of TWEEN 20 both in the presence and absence of bacteria. While L. rhamnosus influenced the activity of intestinal alkaline phosphatase and tight junction protein distribution, E. coli produced indole to reinstate intestinal permeability. The source of TiO2 and gluten led to altered impacts on permeability and IAP activity. The growth of E. coli and L. rhamnosus was found to depend on the type of food additive used. Overall, the presence of bacteria in the in vitro model influenced the effects of food additives on intestinal function, suggesting a complex association between diet and upper GI microbiota. This model provides a method to study small intestinal function and host-microbe interactions in vitro in both healthy and diseased conditions.
Graphene-Assisted Narrow Bandwidth Dual-Band Tunable Terahertz Metamaterial Absorber

A tunable graphene terahertz metamaterial absorber is designed by treating a monolayer continuous dumbbell-shaped structure graphene layer, which can simultaneously realize the narrow bandwidth and dual-band absorption with transverse magnetic (TM) polarization and wide incident angle operation. Two pronounced absorption peaks are caused by the novel toroidal dipole phenomenon and magnetic plasmon polariton. By optimizing the geometry parameters, the relative narrow bandwidths of the two absorption peaks are 26.4 and 23.5 GHz at frequencies of 0.2242 THz and 0.5302 THz, respectively, with the absorption rate above 99.6%. Since the continuous dumbbell-shaped graphene structure is treated in the absorber, a more convenient way to realize the tuning ability by treating a bias voltage compared to the absorbers with discrete graphene structures. The designed device can work at a wide incident angles (up to 80°) under TM polarization with the absorption above 88% at low frequency. The simulation results are basically in good agreement with the results of the equivalent circuit model. This work offers huge potential applications in terahertz imaging, detecting and sensing, especially in the 6G communication systems.
COVID-19 in Guangdong: Immediate Perceptions and Psychological Impact on 304,167 College Students

The outbreak of COVID-19 has brought unprecedented psychological pressure to people across China and more widely across the entire globe. The aim of this study was to assess the immediate perceptions of COVID-19 among college students in Guangdong Province, China, and to assess the psychological impact of the outbreak. We conducted a cross-sectional survey of college students via online questionnaires between February 13th and February 22nd, 2020. A total of 304,167 students completed the Impact of Event Scale 6 (IES-6) and other items. The results showed that 155,077 (50.9%) of the students reported stress symptoms, 1,565 (0.5%) reported poor mental health, and 9,752 (3.2%) reported poor sleep quality. Analysis indicated that the students’ perceptions of COVID-19 were correlated with psychological stress, self-perceived mental health and sleep quality. Moreover, the analysis revealed that the relationship between types of perception and levels of stress symptoms varied according to the students’ demographic characteristics. These findings allow us to better understand psychological stress among students and the factors influencing stress during the COVID-19 outbreak. Understanding these factors will help us to design intervention programs with the aim of alleviating stress among students and reducing the potential for developing psychological disorders.
The CURE for the Typical Bioinformatics Classroom

Bioinformatics is a field that combines biology and computer science to investigate relevant current topics such as annotation of the Human Genome Project and other genomes, protein structure and function, examination of disease processes and personalized medicine, evolutionary relationships and conservation genetics (as reviewed in Luscombe et al., 2001; Can, 2014). Today it is difficult to find a published article in biochemistry and molecular biology/microbiology that does not have a bioinformatics component. Thus, it is important for majors in the life sciences to have exposure to bioinformatics in the curriculum. A blended course format (Garrison and Kanuka, 2004) allows for short lectures and hands-on learning in the classroom combined with computer-based learning outside of the classroom in the form of literature searches, computer tutorials, and independent research that use information from the course applied to specific projects. The topics and techniques that students learn will help them navigate the vast amounts of information that are freely available in databases and inform them about how to manage that data and derive new information. Bioinformatics is often a course taught in a workshop/computer lab format and in many instances a primarily lecture format. Adding a CURE, or Course-based Undergraduate Research Experience, has many advantages over traditional labs and lectures. CUREs have features of inquiry-based learning and also allow for participation in a larger project and community of researchers (Auchincloss et al., 2014). The Bioinformatics course described here incorporates many of the best teaching practices that have been called upon by numerous professional societies and are included in the 2011 Vision and Change Report (Brewer and Smith, 2011).