Miracle-dz/UniFAR-FTUs huggingface dataset:
Convalescent serum therapy for COVID-19: A 19th century remedy for a 21st century disease

Coronavirus disease 2019 (COVID-19) is a viral respiratory disease that mysteriously emerged in late December 2019 in Wuhan City, China [1, 2]. The virus quickly spread worldwide and was announced a global pandemic by the World Health Organization (WHO) in March 2020. Shortly after, a novel coronavirus was identified as the etiologic agent and named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the seventh coronavirus to infect humans and the third to cause an outbreak [2–4]. SARS-CoV-2 continues to spread around the world, as of late July, 2020, over 17 million people have been infected, causing over 665,000 deaths (https://coronavirus.jhu.edu/) and these numbers continue to trend upwards. Despite concerted global efforts, only a few targeted therapeutics, such as remdesivir, are available to help prevent or treat this disease [5], therefore, convalescent plasma therapy, a century-old medical remedy is being revisited as a viable and immediate option for mitigating the impact of this disease [6]. Convalescent plasma therapy is a type of passive antibody therapy whereby blood plasma with neutralizing antibodies against a specific virus is recovered from people who have recuperated from an infection, and administered to patients with the infection in order to improve clinical outcome [6]. Although the potential clinical benefit of convalescent plasma therapy in COVID-19 is still uncertain, administering antibody-containing plasma from recovered patients is a near-term option that can be implemented relatively quickly. In fact, because of the high number of patients with severe COVID-19 and the mainstay of current clinical treatment consisting of symptomatic management and mechanical ventilation, administering convalescent plasma for treatment purposes is currently being deployed [7–12]. Although it is still early to tell whether this therapeutic approach is effective against this disease, evidence so far has shown promise in critically ill patients [7–10]. As new targeted therapies against COVID-19 take considerable time to develop, test and deploy, convalescent plasma therapy could buy time needed to develop more sophisticated targeted treatments.
Cigarette smoking and cognitive function among older adults living in the community

ABSTRACT Background. The present study aimed to examine the long-term impact of CS on Executive Function (EF) and memory among older adults living in the community. Methods. Clock Drawing Test (CDT) and Delayed Word Recall Test (DWRT) were used to examine EF and memory, respectively, using four waves of National Health and Aging Trend Study. The respondents were asked whether they have ever smoked, length of smoking, and age of start and quit smoking. Results. CS can have a long-term impact on both EF and memory. However, current smoking can increase the risk of EF impairment compared to former smokers. Lung disease and current smoking can have a synergic effect of impairment in EF. Conclusion. In the long-term, smoking can negatively affect cognitive. Lung diseases and smoking can synergize their impacts on EF. The impact of smoking on cognition varies across ethnic groups; hence, educational programs targeting minorities can reduce discrepancies.
DNA and protein based vaccines against Salmonella enterica Serovar Typhimurium

Salmonella enterica is a Gram negative, facultative, intracellular pathogen of clinical importance to both humans and animals. Current attenuated vaccines have shown great value. However, they provide only partial protection of the population and can have adverse effects. Also, use of antibiotics has lead to the widespread emergence of antibiotic-resistance and so, there is a need for development of alternative vaccines. To date, little research on typhoid vaccine development has focussed on the merits of subunit or DNA immunisation strategies. In the present study, immune responses to four candidate antigens were investigated. GroEL is a heat shock protein, involved in the folding of denatured proteins under stressed conditions. Flagellin is a structural protein of flagella, and can undergo phase variation so that at any one time, synthesis of flagellin occurs from either of two genes, fliC orfljB. Porins, of which OmpC is an example, allow passage of nutrients and small molecules through the bacterial cell outer membrane. All of these proteins have previously been described as being immunogenic. In the work described here, antibodies specific to each of these antigens were detected in both innately susceptible and resistant mice after infection with an attenuated strain of S. typhimurium, and after subsequent challenge with the virulent organism, suggesting that they may each be involved in protective immunity. The ability to stimulate both cell-mediated and humoral responses against protein antigens is thought to correlate with immunity to virulent Salmonella. Following cloning of the genes into suitable expression vectors, the immunogenicity of a vaccine consisting of these four recombinant Salmonella antigens was assessed in the mouse model. GroELand flagellin-specific antibodies were detected in innately susceptible mice after immunisation together with the adjuvant DDA. Moreover, analysis of IgG isotypes showed increased litres of both IgGl and lgG2a, the latter indicating that cellmediated immunity had been generated. However, challenge of immunised mice with virulent S. typhimurium demonstrated that the protective efficacy of the vaccine was of only low-level.
Olfactory markers for depression: Differences between bipolar and unipolar patients

Objectives The aim of the study was to compare olfactory functions between unipolar and bipolar patients according to the thymic states (depressed, euthymic) and determine specific olfactory variations between these different states. Methods We recruited 176 participants in 5 groups: depressed bipolar (DB), euthymic bipolar (EB), depressed unipolar (DU), euthymic unipolar (EU), and controls (HC). They were assessed using the Sniffin’ sticks threshold and identification tests. Odors’ pleasantness, intensity, familiarity and emotion were assessed. Clinical evaluation explored dimensions of depression, mania, anxiety, and anhedonia. Results Smell identification was lower in DU compared to EU patients and controls. Pleasant odors received lower hedonic rating in DU and DB patients compared to EU and EB patients respectively. Negative correlation was found in EB patients between hedonic rating and social anhedonia. In EU patients hedonic rating was negatively correlated with anxiety-state, and anhedonia. Conclusions Odor identification of pleasant odors is altered in both depressive states. Only unipolar patients would recover a regular identification level in symptomatic remission, while bipolar subjects would keep their deficits. Hedonic rating is lower in bipolar depressed patients compared to unipolar ones, and these deficits improve after remission. Hedonic rating of pleasant odors may distinguish bipolar depression from unipolar depression during periods of decompensation and phases of remission. Olfactory assessment may be useful to screen unipolar and bipolar depression, leading to possible future sensory markers in mood disorders.
The role of the corpus callosum in language network connectivity in children

Abstract The specific role of the corpus callosum (CC) in language network organization remains unclear, two contrasting models have been proposed: inhibition of homotopic areas allowing for independent functioning of the hemispheres versus integration of information from both hemispheres. This study aimed to add to this discussion with the first investigation of language network connectivity in combination with CC volume measures. In 38 healthy children aged 6–12, we performed task‐based functional magnetic resonance imaging to measure language network connectivity, used structural magnetic resonance imaging to quantify CC subsection volumes, and administered various language tests to examine language abilities. We found an increase in left intrahemispheric and bilateral language network connectivity and a decrease in right intrahemispheric connectivity associated with larger volumes of the posterior, mid‐posterior, and central subsections of the CC. Consistent with that, larger volumes of the posterior parts of the CC were significantly associated with better verbal fluency and vocabulary, the anterior CC volume was positively correlated with verbal span. Thus, children with larger volumes of CC subsections showed increased interhemispheric language network connectivity and were better in different language domains. This study presents the first evidence that the CC is directly linked to language network connectivity and underlines the excitatory role of the CC in the integration of information from both hemispheres.
Effects of larval swimming behavior on the dispersal and settlement of the eastern oyster Crassostrea virginica

: Large-scale efforts to restore oyster (Crassostrea virginica) habitat rely on the cre-ation of high-relief hard substrate to improve the natural recruitment of larvae originating from existing oyster populations. Delivery of competent larvae to reefs is influenced by larval behavior, which respond to elevated levels of turbulence by a downward swimming behavior. To determine the geographic dispersal of populations of oyster larvae and how swimming behavior of larvae alters settlement patterns within Virginia (USA) coastal bays, this study utilized a depth-averaged Delft3D © hydrodynamic model coupled to a larval behavior model which incorporates an increased downward swimming speed in response to elevated turbulence. Turbulence and flow measurements over oyster reefs, oyster restoration sites, and bare seafloor were quantified using velocimeters. Hydrodynamic cues were input into the larval behavior model to determine how changes in swimming behavior due to turbulence influence settlement patterns. Results indicate that alterations in settlement velocity, specifically maintaining approximate neutral buoyancy until larvae are both mature and over an existing reef, substantially increased the probability of settling on suitable substrate. We also found that oyster reefs in low velocity regions have a higher probability of self-colonization, while reefs found in less sheltered higher velocity environments receive comparatively little of their own larvae and depend upon connectivity with other areas. Data from in situ larval settlement plates agree with model results and indicate that rates of settlement are ~1.5 to 3× greater over existing reefs composed of primarily vertically oriented oysters than over restoration reefs that are less topographically complex.
Use of a Supportive Kidney Care Video Decision Aid in Older Patients: A Randomized Controlled Trial

Background: There are few studies of patient-facing decision aids that include supportive kidney care as an option. We tested the efficacy of a video decision aid on knowledge of supportive kidney care among older patients with advanced CKD. Methods: Participants (age ≥ 65 years with advanced CKD) were randomized to receive verbal or video education. Primary outcome was knowledge of supportive kidney care (score range 0–3). Secondary outcomes included preference for supportive kidney care, and satisfaction and acceptability of the video. Results: Among all participants (n = 100), knowledge of supportive kidney care increased significantly after receiving education (p < 0.01); however, there was no difference between study arms (p = 0.68). There was no difference in preference for supportive kidney care between study arms (p = 0.49). In adjusted analyses, total health literacy score (aOR 1.08 [95% CI: 1.003–1.165]) and nephrologists’ answer of “No” to the Surprise Question (aOR 4.87 [95% CI: 1.22–19.43]) were associated with preference for supportive kidney care. Most felt comfortable watching the video (96%), felt the content was helpful (96%), and would recommend the video to others (96%). Conclusions: Among older patients with advanced CKD, we did not detect a significant difference between an educational verbal script and a video decision aid in improving knowledge of supportive kidney care or preferences. However, patients who received video education reported high satisfaction and acceptability ratings. Future research will determine the effectiveness of a supportive kidney care video decision aid on real-world patient outcomes. Trial Registration: NCT02698722 (ClinicalTrials.gov).
Changes in biochemical parameters by gender and time: Effect of short-term vegan diet adherence

Background Vegetarian diets adapted for various reasons that may include religious, ethical, and health considerations have reasonable health benefits including weight loss, and favorable metabolic changes. However, studies that assessed health benefits associated with vegan diet practices during the Ethiopian Orthodox Christian (EOC) Lenten fasting remains limited. This study has, therefore, assessed how short-term vegan diet associated with metabolic traits, including weight, body mass index (BMI), circumference, blood pressure, total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C), through longitudinal cross-sectional study design. Methods Seventy-five subjects (34 females and 41 males) with a mean age of [+SD] 27.3 + 5.8 years (range, 18 and 35) took part in the study. The study followed three assessment sessions: at baseline, during the Lenten (week 7), and 7 weeks after the end of the Lenten (week 14). An automatic chemistry analyzer (Mindray, BE-2000, China) used for lipid profile analysis. We used paired sample t-test in pre and post-performance and repeated measures ANOVA with Bonferroni post hoc adjustment between time points. The statistical significance was set at p < 0.05. Results The EOC fasting with vegan diet induced significantly lower blood pressure, weight, BMI, TC, HDL-C, LDL-C, and TC: HDL-C ratios, during Lenten (that is vegan diet consumption), but a regain noted in these parameters 7-weeks after Lenten (that is omnivore diet). On gender differences, vegan diet associated with significantly lower blood pressure, TC, and LDL-C in females compared with age-matched male counterparts. Some methodological limitations of this study are discussed with particular reference to lack of a randomized control group and self-reported data that limit this study in establishing a causal relationship through observed associations. Conclusions Vegan diet consumption even for short period corroborate ideal metabolic traits, with more favorable changes noted in women than age-matched men counterparts. These findings might help to define vegetarian diets as part of religious fasting (beyond its spiritual goals) as a non-pharmacological prescription in different populations, and our findings add to growing evidence in these subjects.
Human FBXL8 Is a Novel E3 Ligase Which Promotes BRCA Metastasis by Stimulating Pro-Tumorigenic Cytokines and Inhibiting Tumor Suppressors

The initiation and progression of breast cancer (BRCA) is associated with inflammation and immune-overactivation, which is critically modulated by the E3 ubiquitin ligase. However, the underlying mechanisms and key factors involved in BRCA formation and disease advancement remains under-explored. By retrospective studies of BRCA patient tissues; and gene knockdown and gain/loss-of-function studies, we uncovered a novel E3 ligase, FBXL8, in BRCA. A signature expression profile of F-box factors that specifically target and degrade proteins involved in cell death/survival, was identified. FBXL8 emerged as a prominent member of the F-box factors. Ex vivo analysis of 1349 matched BRCA tissues indicated that FBXL8 promotes cell survival and tumorigenesis, and its level escalates with BRCA progression. Knockdown of FBXL8 caused: (i) intrinsic apoptosis, (ii) inhibition of cell migration and invasion, (iii) accumulation of two tumor-suppressors, CCND2 and IRF5, and (iv) downregulation of cancer-promoting cytokines/chemokines; all of which curtailed the tumor microenvironment and displayed potential to suppress cancer progression. Co-IP study suggests that two tumor-suppressors, CCND2 and IRF5 are part of the immune-complex of FBXL8. The protein levels of CCND2 and IRF5 inversely correlated with FBXL8 expression, implying that FBXL8 E3 ligase was associated with the degradation of CCND2 and IRF5. Altogether, we propose the exploitation of the ubiquitin signaling axis of FBXL8-CCND2-IRF5 for anti-cancer strategies and potential therapeutics.
Intensive care unit patients’ opinion on enrollment in clinical research: A multicenter survey

Background In most emergency situations or severe illness, patients are unable to consent for clinical trial enrollment. In such circumstances, the decision about whether to participate in a scientific study or not is made by a legally designated representative. Objective To address the willingness of patients admitted to the intensive care unit (ICU) to be enrolled in a scientific study as volunteers, and to assess the agreement between patients’ and their legal representatives’ opinion concerning enrollment in a scientific study. Methods This survey was conducted in two hospitals in São Paulo, Brazil. Patients (≥18 years) with preserved cognitive functions accompanied by a surrogate admitted to the ICU were eligible for this study. A survey containing 28 questions for patients and 8 questions for surrogates was applied within the first 48h from ICU admission. The survey for patients comprised three sections: demographic characteristics, opinion about participation in clinical research and knowledge about the importance of research. The survey for legal representatives contained two sections: demographic characteristics and assessment of legal representatives’ opinion in authorizing patients to be enrolled in research. Results Between January 2017 and May 2018, 208 pairs of ICU patients and their respective legal representatives answered the survey. Out of 208 ICU patients answering the survey, 73.6% (153/208) were willing to be enrolled in the study as volunteers. Of those patients, 65.1% (97/149) would continue participating in a research even if their legal representative did not support their enrollment. Agreement between patients’ and surrogates’ opinion concerning participation was poor [Kappa = 0.11 (IC95% -0.02 to 0.25)]. If a consent for study participation had been obtained, 69.1% (103/149) of patients would continue participating in the study until its conclusion, and 23.5% (35/149) would allow researchers to use data collected to date, but would withdraw from the study on that occasion. Conclusion The majority of patients admitted to the ICU were willing to be enrolled in a scientific study as volunteers, also after a deferred informed consent procedure has been used. Nevertheless, contradictory opinions between patients and their and their legal representatives’ concerning enrollment in a scientific study were often observed.
The Selection of Gamma-Ray Irradiated Higher Yield Rice Mutants by Directed Evolution Method

We have succeeded in selecting four higher yield mutants from five gamma-ray irradiated high-yielding Japanese rice varieties using a novel approach. A total of 464 M2 plants which had heavier total panicle weights per plant were first selected from 9801 irradiated M2 plants. Their higher yields were confirmed by yield trials conducted for three years with a six to ten-pairwise replicated plot design. FukuhibikiH6 and FukuhibikiH8 were selected from an irradiated high-yielding variety Fukuhibiki and showed 1.2% to 22.5% higher yield than their original significantly. YamadawaraH3 was selected from an irradiated high-yielding variety Yamadawara and its yield advantages were 2.7% to 3.9%. However, there was no difference in the genotypes of the 96 SNP (single nucleotide polymorphism) markers between the higher yield mutants and their respective original varieties. The differences in the measured phenotypical traits between each mutant and its original variety were not constant and the actual differences were marginal. Therefore, the higher yields of the selected mutants were likely to have been caused by physiological traits rather than phenotypical traits. The selection method used in this study is an application of the directed evolution method which has long been commonly used in the substantial improvements of microorganisms and their proteins.
Characterization of a New Intracellular Alginate Lyase with Metal Ions-Tolerant and pH-Stable Properties

Alginate lyases play an important role in alginate oligosaccharides (AOS) preparation and brown seaweed processing. Many extracellular alginate lyases have been characterized to develop efficient degradation tools needed for industrial applications. However, few studies focusing on intracellular alginate lyases have been conducted. In this work, a novel intracellular alkaline alginate lyase Alyw202 from Vibrio sp. W2 was cloned, expressed and characterized. Secretory expression was performed in a food-grade host, Yarrowia lipolytica. Recombinant Alyw202 with a molecular weight of approximately 38.3 kDa exhibited the highest activity at 45 °C and more than 60% of the activity in a broad pH range of 3.0 to 10.0. Furthermore, Alyw202 showed remarkable metal ion-tolerance, NaCl independence and the capacity of degrading alginate into oligosaccharides of DP2-DP4. Due to the unique pH-stable and high salt-tolerant properties, Alyw202 has potential applications in the food and pharmaceutical industries.
Body weight and high‐fat diet are associated with epigenetic aging in female members of the BXD murine family

DNA methylation (DNAm) is shaped by genetic and environmental factors and modulated by aging. Here, we examine interrelations between epigenetic aging, body weight (BW), and life span in 12 isogenic strains from the BXD family of mice that exhibit over twofold variation in longevity. Genome‐wide DNAm was assayed in 70 liver specimens from predominantly female cases, 6–25 months old, that were maintained on normal chow or high‐fat diet (HFD). We defined subsets of CpG regions associated with age, BW at young adulthood, and strain‐by‐diet‐dependent life span. These age‐associated differentially methylated CpG regions (age‐DMRs) featured distinct genomic characteristics, with DNAm gains over time occurring in sites such as promoters and exons that have high CpG density and low average methylation. CpG regions associated with BW were enriched in introns, tended to have lower methylation in mice with higher BW, and were inversely correlated with gene expression (i.e., higher mRNA levels in mice with higher BW). CpG regions associated with life span were linked to genes involved in life span modulation, including the telomerase reverse transcriptase gene, Tert, which had both lower methylation and higher expression in long‐lived strains. An epigenetic clock defined from age‐DMRs revealed accelerated aging in mice belonging to strains with shorter life spans. Both higher BW and the HFD were associated with accelerated epigenetic aging. Our results highlight the age‐accelerating effect of heavier BW. Furthermore, we demonstrate that the measure of epigenetic aging derived from age‐DMRs can predict genotype and diet‐induced differences in life span among female BXD members.