Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting 1‐year post‐COVID‐19 mortality based on chest computed tomography scan

To the Editor, Post‐discharge mortality in patients with coronavirus disease 2019 (COVID‐19) is an important yet unraveled aspect of this disease. In a study in UK, mortality was reported to occur in 13.4% of patients with COVID‐19 after discharge from hospital. In our study, we reviewed a total of 1078 patients with COVID‐ 19 pneumonia who underwent chest computed tomography (CT) at Baqiyatallah Hospital, Tehran, Iran, and were hospitalized from March to April 2020. Data were extracted from hospital registry records including age, sex, date of admission, date of discharge, history of readmission, mortality (in‐hospital or out‐of‐hospital), and chest CT scan information including lesion distribution, opacity score and underlying disease (according to chest CT). The mean age of study population was 53 ± 14.38 years, and 773 patients (68.4%) were men. The lesion type of 414 patients (38.4%) was only ground‐glass opacification/opacity (GGO), 133 (12.3%) was GGO plus crazy paving, 42 (3.9%) was consolidation only, and 489 (45.4%) was GGO plus consolidation. The mean opacity score was 6.13 ± 5.55. According to registry records, 29 patients (2.7%) had the history of readmission after discharge. The post‐discharge mortality was assessed by telephone interview during the next 365 days (up to March 2021). In‐hospital mortality was 25 of 1078 (1.9%) and post‐discharge mortality of patients was 97 of 1053 (9.2%) within 365 days of diagnosis. The most frequent causes of death were vascular and thromboembolic events. Age was a prognostic factor for long‐term mortality in COVID‐19 patients after discharge from hospital. Using a Cox regression model, the hazard of death in patients from 50 to 60 years was 2.03 more than patients under 50 years (95% CI, 1.15–3.58) and this hazard increased to 3.00 for patients over 60 years of age (95% CI, 1.75–5.16) (Graph 1). Moreover, a Cox regression model was used to predict the mortality and post‐discharge mortality, using chest CT, adjusted for age, sex, readmission, and diagnosed underlying disease (according to chest CT). According to the results, both opacity score and lesion type could predict the overall mortality and mortality after discharge
Stability of neocortical synapses across sleep and wake states during the critical period in rats

Sleep is important for brain plasticity, but its exact function remains mysterious. An influential but controversial idea is that a crucial function of sleep is to drive widespread downscaling of excitatory synaptic strengths. Here, we used real-time sleep classification, ex vivo measurements of postsynaptic strength, and in vivo optogenetic monitoring of thalamocortical synaptic efficacy to ask whether sleep and wake states can constitutively drive changes in synaptic strength within the neocortex of juvenile rats. We found that miniature excitatory postsynaptic current amplitudes onto L4 and L2/3 pyramidal neurons were stable across sleep- and wake-dense epochs in both primary visual (V1) and prefrontal cortex (PFC). Further, chronic monitoring of thalamocortical synaptic efficacy in V1 of freely behaving animals revealed stable responses across even prolonged periods of natural sleep and wake. Together, these data demonstrate that sleep does not drive widespread downscaling of synaptic strengths during the highly plastic critical period in juvenile animals. Whether this remarkable stability across sleep and wake generalizes to the fully mature nervous system remains to be seen.
Identification of Full-Length Wild-Type and Mutant Huntingtin Interacting Proteins by Crosslinking Immunoprecipitation in Mice Brain Cortex

Background: Huntington’s disease is a neurodegenerative disorder caused by a CAG expansion in the huntingtin gene, resulting in a polyglutamine expansion in the ubiquitously expressed mutant huntingtin protein. Objective: Here we set out to identify proteins interacting with the full-length wild-type and mutant huntingtin protein in the mice cortex brain region to understand affected biological processes in Huntington’s disease pathology. Methods: Full-length huntingtin with 20 and 140 polyQ repeats were formaldehyde-crosslinked and isolated via their N-terminal Flag-tag from 2-month-old mice brain cortex. Interacting proteins were identified and quantified by label-free liquid chromatography-mass spectrometry (LC-MS/MS). Results: We identified 30 interactors specific for wild-type huntingtin, 14 interactors specific for mutant huntingtin and 14 shared interactors that interacted with both wild-type and mutant huntingtin, including known interactors such as F8a1/Hap40. Syt1, Ykt6, and Snap47, involved in vesicle transport and exocytosis, were among the proteins that interacted specifically with wild-type huntingtin. Various other proteins involved in energy metabolism and mitochondria were also found to associate predominantly with wild-type huntingtin, whereas mutant huntingtin interacted with proteins involved in translation including Mapk3, Eif3h and Eef1a2. Conclusion: Here we identified both shared and specific interactors of wild-type and mutant huntingtin, which are involved in different biological processes including exocytosis, vesicle transport, translation and metabolism. These findings contribute to the understanding of the roles that wild-type and mutant huntingtin play in a variety of cellular processes both in healthy conditions and Huntington’s disease pathology.
Effects of evidence-based nursing on psychological well-being, postoperative complications and quality of life after breast cancer surgery.

OBJECTIVE To evaluate the influence of evidence-based nursing (EBN) on psychological well-being, postoperative complications and quality of life (QOL) after breast cancer (BC) surgery. METHODS A total of 263 patients with BC who were surgically treated in Zhejiang Provincial People's Hospital from May, 2018 to August, 2019 were as assigned to observation group (EBN, n=142) and control group (routine nursing care, n=121). Clinical indicators and any complications after intervention were recorded. And the exercise compliance in the affected limbs was evaluated. Barthel index (BI), self-rating anxiety scale (SAS) and self-rating depression scale (SDS), Pittsburgh Sleep Quality Index (PSQI) were employed for the assessment of self-care ability, psychological status, and sleep quality, respectively. In addition, we utilized the numerical rating scale (NRS) to evaluate postoperative pain, the functional assessment of cancer therapy-breast (FACT-B) scale to assesse the quality of life (QOL), and the self-made questionnaire to quantify patient satisfaction. RESULTS After intervention, the observation group presented greater improvement in symptoms, higher exercise compliance and BI scores, as well as lower SAS, SDS, and PSQI scores; the incidence of postoperative pain and complications decreased in observation group, and FACT-B scores and patient satisfaction increased. CONCLUSION EBN is effective in relieving symptoms, reducing negative emotions and postoperative complications, as well as enhancing the QOL of patients undergoing BC surgery.
Solution structure of the anticancer p28 peptide in biomimetic medium

The p28 peptide derived from Pseudomonas aeruginosa azurin shows an anticancer activity after binding to p53 protein and is currently in Phase I of clinical trials. We have studied its structure in water and in a biomimetic media and show that the peptide is unstructured in water but when studied in a biomimetic medium assumes a structure very similar to the one observed in azurin, suggesting a high propensity of this peptide to maintain this secondary structure. Analysis of p28 sequences from different bacterial species indicates conservation of the secondary structure despite amino acid replacement in different positions, suggesting that others, similar peptides could be tested for binding to p53.
Defining Clinical Public Health.

PURPOSE To solve complex health issues, an innovative and multidisciplinary framework is necessary. The Clinical Public Health (CPH) Division was established at the University of Toronto (UofT), Canada to foster inte-gration of primary care, preventive medicine and public health in education, practice and research. To better understand how the construct of CPH might be applied, we surveyed clinicians, researchers and public health professionals affiliated with the CPH Division to assess their understanding of the CPH concept and its utility in fostering broad collaboration. METHODS A two-wave anonymous survey of the active faculty of the CPH Division, UofT was conducted across Canada. Wave 1 participants (n = 187; 2016) were asked to define CPH, while Wave 2 participants (n = 192; 2017) were provided a synthesis of Wave 1 results and asked to rank each definition. Both waves were asked about the need for a common definition, and to comment on CPH. RESULTS Response rates for the first and second waves were 25% and 22%, respectively. Of the six definitions of CPH from Wave 1, "the intersection of clinical practice and public health," was most highly ranked by Wave 2 participants. Positive perceptions of CPH included multidisciplinary collaboration, new fields and insights, forward thinking and innovation. Negative perceptions included CPH being a confusing term, too narrow in scope or too clinical. CONCLUSION The concept of Clinical Public Health can foster multidisciplinary collaboration to address com-plex health issues because it provides a useful framework for bringing together key disciplines and diverse professional specialties.
Correction to “Development and Use of a Cyclic Voltammetry Simulator To Introduce Undergraduate Students to Electrochemical Simulations”

Cyclic voltammetry (CV) is a popular technique for the study of electrochemical mechanisms because the method can provide useful information on the redox couple. The technique involves the application of a potential ramp on an unstirred solution while the current is monitored, and then the ramp is reversed for a return sweep. CV is sometimes introduced in undergraduate chemistry laboratories. The CV waveform is dependent on several processes including charge transfer, diffusion, and coupled homogeneous reactions. Computer simulations are sometimes used to study these effects. An easy-to-use CV simulator was written in Microsoft Excel for the purpose of teaching undergraduate students and to serve as an entryway to more sophisticated electrochemical simulations.
The effect of docetaxel on survival, fertilization rate and apoptosis-related genes mRNA expression in mouse metaphase II oocytes following vitrification.

Background Docetaxel is beneficial in oocyte cryopreservation. Aims The effect of docetaxel, on the survival, fertilization rate and mRNA expression of apoptosis-related genes of vitrified mature oocytes was investigated. Methods Mature oocytes were divided into eight experimental groups, including I) control, II) docetaxel, III) docetaxel + cryoprotectant agent 1 (CPA1), IV) docetaxel + CPA2, V) docetaxel + vitrification 1 (Vit1), VI) docetaxel + Vit2, VII) Vit1, and VIII) Vit2. The survival and fertilization rates, and the mRNA expression level of Bcl-xl, Bax and caspase-3 as apoptosis-related genes were evaluated. Results The survival rates in Vit1, and Vit2 groups were significantly lower than in the control group (P<0.05). The fertilization rates in docetaxel + Vit1, docetaxel + Vit2, Vit1, and Vit2 were significantly lower than the control, docetaxel, and related groups using docetaxel and CPAs. Bax expression was significantly increased in groups which oocytes vitrified. Also, its expression in the Vit2 group increased significantly in comparison to the docetaxel + Vit2 group. The expression of the Bcl-xl gene was downregulated in docetaxel + CPA2, docetaxel + Vit2 and Vit2 compared to docetaxel group. The Bax/Bcl-xl ratio significantly increased in docetaxel + CPA2, docetaxel + Vit1, docetaxel + Vit2, Vit1 and Vit2 groups compared to control, docetaxel and the docetaxel + CPA1 group. Caspase-3 expression significantly increased in all six groups in comparison to the control, and docetaxel groups. Its expression significantly increased in the Vit1 and Vit2 groups in comparison with docetaxel + Vit1, and docetaxel + Vit2, respectively. Conclusion Docetaxel ameliorates the damages to oocytes during vitrification by altering the expression of apoptosis-related genes and its effects are dependent on the vitrification solution used in cryopreservation of oocytes.
Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains

Streptococcus agalactiae evasion from the human defense mechanisms has been linked to the production of DNases. These were proposed to contribute to the hypervirulence of S. agalactiae ST17/capsular-type III strains, mostly associated with neonatal meningitis. We performed a comparative genomic analysis between ST17 and ST19 human strains with different cell tropism and distinct DNase production phenotypes. All S. agalactiae ST17 strains, with the exception of 2211-04, were found to display DNase activity, while the opposite scenario was observed for ST19, where 1203-05 was the only DNase(+) strain. The analysis of the genetic variability of the seven genes putatively encoding secreted DNases in S. agalactiae revealed an exclusive amino acid change in the predicted signal peptide of GBS0661 (NucA) of the ST17 DNase(-), and an exclusive amino acid change alteration in GBS0609 of the ST19 DNase(+) strain. Further core-genome analysis identified some specificities (SNVs or indels) differentiating the DNase(-) ST17 2211-04 and the DNase(+) ST19 1203-05 from the remaining strains of each ST. The pan-genomic analysis evidenced an intact phage without homology in S. agalactiae and a transposon homologous to TnGBS2.3 in ST17 DNase(-) 2211-04; the transposon was also found in one ST17 DNase(+) strain, yet with a different site of insertion. A group of nine accessory genes were identified among all ST17 DNase(+) strains, including the Eco47II family restriction endonuclease and the C-5 cytosine-specific DNA methylase. None of these loci was found in any DNase(-) strain, which may suggest that these proteins might contribute to the lack of DNase activity. In summary, we provide novel insights on the genetic diversity between DNase(+) and DNase(-) strains, and identified genetic traits, namely specific mutations affecting predicted DNases (NucA and GBS0609) and differences in the accessory genome, that need further investigation as they may justify distinct DNase-related virulence phenotypes in S. agalactiae.
Understanding Civilian Mental Health Providers’ Knowledge in Providing Care for Active Duty Service Members: Opportunities for Improvement

INTRODUCTION: There are a growing number of civilian mental health providers who are treating active duty service members (ADSM) from referrals of local emergency rooms, directly from military installations, or when a military mental health program is unavailable. Civilian providers may be unprepared to address issues that are unique to this population. AIM: The purpose of this quality improvement project was to develop and implement a survey-based knowledge assessment, in order to assess civilian psychiatric advanced practice nurse’s (APN) perceptions, knowledge, and practice of treating ADSMs. METHOD: The investigator developed and validated a survey that was posted on the American Psychiatric Nurses Association All-Purpose Discussion Forum, and the snowball technique was utilized to enhance psychiatric APN colleague recruitment. RESULTS: Seventy-eight participants scored extremely low with average score of 40.4%; however, the psychiatric APNs who received formal training from the Department of Defense on unique mental health issues of ADSMs scored significantly higher (49.6%) than participants without the formal training (38.2%; p = .03). CONCLUSIONS: Understanding the knowledge gap of psychiatric APNs as it relates to the care of ADSMs will allow educators to recommend available trainings or develop trainings that are tailored to meet their needs.
Muscarinic regulation of the neuronal Na+/K+‐ATPase in rat hippocampus

Stimulation of postsynaptic muscarinic receptors was shown to excite principal hippocampal neurons by modulating several membrane ion conductances. We show here that activation of postsynaptic muscarinic receptors also causes neuronal excitation by inhibiting Na+/K+‐ATPase activity. Muscarinic Na+/K+‐ATPase inhibition is mediated by two separate signalling pathways that lead downstream to enhanced Na+/K+‐ATPase phosphorylation by activating protein kinase C and protein kinase G. Muscarinic excitation through Na+/K+‐ATPase inhibition is probably involved in cholinergic modulation of hippocampal activity and may turn out to be a widespread mechanism of neuronal excitation in the brain.
Characterizing Decisional Conflict in Patients Presenting to Sleep Surgery Clinic and an Exploration of Resource Limitations

Numerous therapies exist for adult obstructive sleep apnea (OSA), creating potential for patient decisional conflict (DC) that impacts treatment adherence and post‐treatment regret. We evaluated the prevalence of elevated DC in OSA patients presenting for positive airway pressure (PAP) alternative therapies and identified gaps in available resources about OSA therapies.
Structure-based pharmacophore modeling, virtual screening and simulation studies for the identification of potent anticancerous phytochemical lead targeting cyclin-dependent kinase 2

Abstract Cyclin-dependent kinases are of critical importance in directing various cell cycle phases making them as potential tumor targets. Cyclin-dependent kinase 2 (CDK2) in particular plays a significant part during cell cycle events and its imbalance roots out tumorogenic environment. Herein, we built a structure-based pharmacophore model complementing the ATP pocket site of CDK2 with four pharmacophoric features, using a series of structures obtained from cluster analysis during MD simulation assessment. This was followed by its validation and further database screening against Taiwan indigenous plants database (5284 compounds). The screened compounds were subjected toward Lipinski’s rule (RO5) and ADMET filter followed by docking analysis and simulation study. In filtering hits (10 compounds) via molecular docking against CDK2, Schinilenol with −8.1 kcal/mol fetched out as a best lead phytoinhibitor in the presence of standard drug (Dinaciclib). Additionally, pharmacophore mapping analysis also indicated relative fit values of dinaciclib and schinilenol as 2.37 and 2.31, respectively. Optimization, flexibility prediction and the stability of CDK2 in complex with the ligands were also ascertained by means of molecular dynamics for 50 ns, which further proposed schinilenol having better binding stability than dinaciclib with RMSD values ranging from 0.31 to 0.34 nm. Reactivity site, biological activity detection and cardiotoxicity assessment also proposed schinilenol as a better phytolead inhibitor than the existing dinaciclib. Abbreviations: CDK2: Cyclin dependent kinase2; ATP: Adenosine triphosphate; MD: Molecular dynamics, RO5: Rule of five; ADMET: Absorption, distribution, metabolism, and excretion; RMSD: Root mean square deviation; DS: Discovery Studio; SOM: Site of metabolism; RBPM: receptor based pharmacophore model; TIP: Schinilenol; hERG: human Ether-à-go-go - Related Gene Communicated by Ramaswamy H. Sarma
Alteration of the PKA-CREB cascade in the mPFC accompanying prepulse inhibition deficits: evidence from adolescent social isolation and chronic SKF38393 injection during early adolescence

Prepulse inhibition (PPI) refers to the inhibition of the startle reflex that occurs when the startling stimulus is preceded by a weak prestimulus. Altered adolescent mPFC circuitry induced by early-life adversity might be a key source of PPI deficits. The current study focused on variations in the cyclic AMP (cAMP)/protein kinase A (PKA)-cAMP-response element-binding protein (CREB) pathway in the medial prefrontal cortex (mPFC). We found a negative relationship between PPI and the PKA-CREB cascade during adolescence by employing both developmental and pharmacologic manipulations. Experiment 1, with the early adolescent social isolation model [postnatal days (PNDs), 21–34), displayed a disrupted PPI at PND 35 and significantly altered PKA, phosphorylated CREB (p-CREB) and the ratio of p-CREB to CREB. In particular, the level of p-CREB was negatively related to PPI performance. In Experiment 2, SKF38393, a well-characterized activator of adenylate cyclase and cAMP/PKA, was chronically injected during early adolescence (PNDs 28–34). We sought to mimic potential biochemical changes, particularly PKA activation, which is possibly altered by adolescent social isolation, and to determine if PPI was disrupted, similar to the disruption associated with adolescent social isolation. On PND 35, PPI deficits were detected, as well as increased PKA, marginally increased CREB and no change occurred in p-CREB or the ratio of p-CREB to CREB. In particular, PKA activity was negatively related to PPI performance. Although these results are limited in suggesting a causal link between PPI deficits and PKA-CREB signaling, they may help to elucidate the role played by PKA-CREB in the mPFC in regulating PPI.
Reciprocal allopolyploid grasses (Festuca × Lolium) display stable patterns of genome dominance

Summary Allopolyploidization entailing the merger of two distinct genomes in a single hybrid organism, is an important process in plant evolution and a valuable tool in breeding programs. Newly established hybrids often experience massive genomic perturbations, including karyotype reshuffling and gene expression modifications. These phenomena may be asymmetric with respect to the two progenitors, with one of the parental genomes being “dominant. ” Such “genome dominance” can manifest in several ways, including biased homoeolog gene expression and expression level dominance. Here we employed a k‐mer–based approach to study gene expression in reciprocal Festuca pratensis Huds. × Lolium multiflorum Lam. allopolyploid grasses. Our study revealed significantly more genes where expression mimicked that of the Lolium parent compared with the Festuca parent. This genome dominance was heritable to successive generation and its direction was only slightly modified by environmental conditions and plant age. Our results suggest that Lolium genome dominance was at least partially caused by its more efficient trans‐acting gene expression regulatory factors. Unraveling the mechanisms responsible for propagation of parent‐specific traits in hybrid crops contributes to our understanding of allopolyploid genome evolution and opens a way to targeted breeding strategies.
Tackling the challenges of evolutionary forest research with multidata approaches

Many forest tree species have characteristics that make the study of their evolutionary ecology complex. For example, they are long‐lived and thus have long generation times, and their often large, complex genomes have hampered establishing genomic resources. One way to tackle this challenge is to access multiple complementary data sources and analytical approaches when attempting to infer patterns of adaptive evolution. In the cover article of this issue of Molecular Ecology, Depardieu et al. (2021) combine large amounts of environmental, genomic, dendrochronological, and gene expression data in a common garden to explore the polygenic basis of drought resistance in white spruce (Picea glauca), a long‐lived conifer. They identify candidate genes involved in growth and resistance to extreme drought events and show how multiple data sets may deliver complementary evidence to circumvent the manifold challenges of the research field.