Miracle-dz/UniFAR-FTUs huggingface dataset:
The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development

Significance Vertebrate retinal ganglion cells (RGCs) transmit all visual signals from the eye to the brain, are the pathogenic target in glaucoma, and require the Atoh7 competence factor to develop from multipotent progenitors. Atoh7 transcription is controlled by dual cis regulatory elements, including a remote shadow enhancer (SE). In humans, loss of the SE causes NCRNA disease, with congenital blindness due to optic nerve aplasia. We generated a mouse Atoh7 SE deletion model and analyzed its effects on transcription, retinal histology, and chromatin architecture. The mutant mice express 80% less Atoh7 mRNA but retain optic nerves, unlike NCRNA patients. By systematically varying dosage in a genotypic series, we show how the dual enhancers maintain robust plasticity during RGC genesis. The retinal ganglion cell (RGC) competence factor ATOH7 is dynamically expressed during retinal histogenesis. ATOH7 transcription is controlled by a promoter-adjacent primary enhancer and a remote shadow enhancer (SE). Deletion of the ATOH7 human SE causes nonsyndromic congenital retinal nonattachment (NCRNA) disease, characterized by optic nerve aplasia and total blindness. We used genome editing to model NCRNA in mice. Deletion of the murine SE reduces Atoh7 messenger RNA (mRNA) fivefold but does not recapitulate optic nerve loss; however, SEdel/knockout (KO) trans heterozygotes have thin optic nerves. By analyzing Atoh7 mRNA and protein levels, RGC development and survival, and chromatin landscape effects, we show that the SE ensures robust Atoh7 transcriptional output. Combining SE deletion and KO and wild-type alleles in a genotypic series, we determined the amount of Atoh7 needed to produce a normal complement of adult RGCs, and the secondary consequences of graded reductions in Atoh7 dosage. Together, these data reveal the workings of an evolutionary fail-safe, a duplicate enhancer mechanism that is hard-wired in the machinery of vertebrate retinal ganglion cell genesis.
Combination therapy of apo‐transferrin and thyroid hormones enhances remyelination

The current study presents two different approaches with a view to elucidating the interaction between thyroid hormones (TH) and apo‐transferrin (aTf) and their role in myelination and remyelination. First, in vitro assays were conducted to determine the single and combined effects of aTf and triiodothyronine (T3) on oligodendroglial cell lineage proliferation and oligodendrocyte (OLG) maturation in primary cultures. Results revealed higher proliferation rates upon single aTf treatment but Control values upon T3 and aTf + T3 treatments. In addition, both aTf and T3 accelerated OLG maturation, with the greatest effects being exerted by combined aTf + T3 administration in terms of both myelin basic protein (MBP) expression and morphological complexity. Second, in vivo assays were carried out to establish single and combined effects of aTf and T3, as well as TH receptor (THR) inhibitor I‐850, on remyelination following a CPZ‐induced demyelination protocol. Results showed an increase in myelin deposition and the number of mature remyelinating OLG upon single treatments, but a synergic effect upon combined aTf + T3 treatment which was prevented by THR inhibition. It may be thus concluded that combined treatment yielded the most beneficial effects on OLG maturation parameters in vitro and remyelinating capacity in vivo when compared to single treatments. These findings may help explore the development of new target molecules in the treatment of demyelinating diseases.
A Bayesian Statistical Approach to Continuous Qualification of a Bioassay

A validated bioassay is used to measure the potency of commercial lots, and as such, must be accurate, precise, and fit for its intended purpose. Regulatory expectations for a bioassay include a characterization of features, such as accuracy, precision, linearity, and range. The journey of a bioassay typically starts in a development lab, where it is initially qualified and used to support the release and stability testing of clinical lots. As a program moves through the different clinical phases, it may be optimized further, used to support process development, or transferred to new laboratories, with each activity generating additional bioassay data. Finally, the bioassay is fully validated as part of the transfer to the commercial quality control testing laboratories. In this work, rather than capturing the data from each study as a separate, independent report, it is proposed that, beginning with the qualification study, the accuracy and precision of the bioassay be continuously characterized, with each subsequent study result building upon the preceding ones. We call this approach continuous qualification. Such a proposition is naturally carried out using Bayesian statistical methods in which the historical study data is used to construct prior knowledge that is blended with the current study data. By doing so, the bioassay accuracy and precision may be assessed with high confidence well ahead of commercial manufacturing. Further, by following the total-variance approach, the method also allows for a robust construction of system suitability and control limits for potency.
Overview and Methods for the Youth Risk Behavior Surveillance System — United States, 2019

Health risk behaviors practiced during adolescence often persist into adulthood and contribute to the leading causes of morbidity and mortality in the United States. Youth health behavior data at the national, state, territorial, tribal, and local levels help monitor the effectiveness of public health interventions designed to promote adolescent health. The Youth Risk Behavior Surveillance System (YRBSS) is the largest public health surveillance system in the United States, monitoring a broad range of health-related behaviors among high school students. YRBSS includes a nationally representative Youth Risk Behavior Survey (YRBS) and separate state, local school district, territorial, and tribal school–based YRBSs. This overview report describes the surveillance system and the 2019 survey methodology, including sampling, data collection procedures, response rates, data processing, weighting, and analyses presented in this MMWR Supplement. A 2019 YRBS participation map, survey response rates, and student demographic characteristics are included. In 2019, a total of 78 YRBSs were administered to high school student populations across the United States (national and 44 states, 28 local school districts, three territories, and two tribal governments), the greatest number of participating sites with representative data since the surveillance system was established in 1991. The nine reports in this MMWR Supplement are based on national YRBS data collected during August 2018–June 2019. A full description of 2019 YRBS results and downloadable data are available (https://www.cdc.gov/healthyyouth/data/yrbs/index.htm). Efforts to improve YRBSS and related data are ongoing and include updating reliability testing for the national questionnaire, transitioning to electronic survey administration (e.g., pilot testing for a tablet platform), and exploring innovative analytic methods to stratify data by school-level socioeconomic status and geographic location. Stakeholders and public health practitioners can use YRBS data (comparable across national, state, tribal, territorial, and local jurisdictions) to estimate the prevalence of health-related behaviors among different student groups, identify student risk behaviors, monitor health behavior trends, guide public health interventions, and track progress toward national health objectives.
Neural compensation in presymptomatic hAPP mouse models of Alzheimer's disease

Largely inspired from clinical concepts like brain reserve, cognitive reserve, and neural compensation, here we review data showing how neural circuits reorganize in presymptomatic and early symptomatic hAPP mice to maintain memory intact. By informing on molecular alterations and compensatory adaptations which take place in the brain before mice show cognitive impairments, these data can help to identify ultra-early disease markers that could be targeted in a therapeutic perspective aimed at preventing rather than treating cognitive deterioration.
TATA box binding protein and ribosomal protein 4 are suitable reference genes for normalization during quantitative polymerase chain reaction study in bovine mesenchymal stem cells

Objective Quantitative polymerase chain reaction (qPCR) has been extensively used in the field of mesenchymal stem cell (MSC) research to elucidate their characteristics and clinical potential by normalization of target genes against reference genes (RGs), which are believed to be stably expressed irrespective of various experimental conditions. However, the expression of RGs is also variable depending on the experimental conditions, which may lead to false or contradictory conclusions upon normalization. Due to the current lack of information for a clear list of stable RGs in bovine MSCs, we conducted this study to identify suitable RGs in bovine MSCs. Methods The cycle threshold values of ten traditionally used RGs (18S ribosomal RNA [18S], beta-2-microglobulin [B2M], H2A histone family, member Z [H2A], peptidylprolyl isomerase A [PPIA], ribosomal protein 4 [RPL4], succinate dehydrogenase complex, subunit A [SDHA], beta actin [ACTB], glyceraldehyde-3-phosphate dehydrogenase [GAPDH], TATA box binding protein [TBP], and hypoxanthine phosphoribosyltrasnfrase1 [HPRT1]) in bovine bone marrow-derived MSCs (bBMMSCs) were validated for their stabilities using three types of RG evaluation algorithms (geNorm, Normfinder, and Bestkeeper). The effect of validated RGs was then verified by normalization of lineage-specific genes (fatty acid binding protein 4 [FABP4] and osteonectin [ON]) expressions during differentiations of bBMMSCs or POU class 5 homeobox 1 (OCT4) expression between bBMMSCs and dermal skins. Results Based on the results obtained for the three most stable RGs from geNorm (TBP, RPL4, and H2A), Normfinder (TBP, RPL4, and SDHA), and Bestkeeper (TBP, RPL4, and SDHA), it was comprehensively determined that TBP and RPL4 were the most stable RGs in bBMMSCs. However, traditional RGs were suggested to be the least stable (18S) or moderately stable (GAPDH and ACTB) in bBMMSCs. Normalization of FABP4 or ON against TBP, RPL4, and 18S presented significant differences during differentiation of bBMMSCs. However, although significantly low expression of OCT4 was detected in dermal skins compared to that in bBMMSCs when TBP and RPL4 were used in normalization, normalization against 18S exhibited no significance. Conclusion This study proposes that TBP and RPL4 were suitable as stable RGs for qPCR study in bovine MSCs.
Functions of the eukaryote-specific ribosomal protein Asc1 /RACK1 in gene-specific translational activity

Although the ribosome operates as a single molecular entity, it is composed of both ribosomal RNAs and dozens of proteins. However, the individual contributions of most ribosomal components to translational regulation are unknown. In Chapter 1, I will review the current state of knowledge related to the functions of ribosomal proteins with a focus on the RACK1 protein (Asc1 in yeast), a eukaryote-specific ribosomal protein with many proposed functions in both cellular signaling and translation. In Chapter 2, I will present evidence that the Asci protein is required for efficient translation of a specific set of mRNAs with short open reading frames (ORFs), including those that encode ribosomal proteins and nuclear-encoded mitochondrial components. Consistent with these translation defects, ASC1 mutants are unable to grow in conditions requiring full mitochondrial function. Asci -sensitive mRNAs are highly associated with the translational closed-loop complex, a group of proteins that promotes a loop-like conformation of the mRNA during translation by simultaneous interaction with the 5' and 3' ends of the mRNA molecule. In wild type cells, mRNAs that associate strongly with the translational closed-loop complex are much shorter than other ORFs. Thus, I hypothesize that the closed-loop is preferentially formed and/or stabilized on mRNAs with short ORFs, and that this process is enhanced by the presence of Asci on the small ribosomal subunit. The dependence of closed-loop formation on ORF length could also explain why short ORFs have notably higher translation efficiency than longer ORFs, a trend I observed in data collected from several eukaryotes. In Chapter 3, I will present evidence that the mammalian RACK1 protein is also required for expression of mRNAs with short ORFs and for mitochondrial function in HeLa cells, similar to my observations in yeast. These findings hint at a conserved role for the Asc1/RACK1 protein in promoting the function of the closed-loop complex and the translation of short ORFs, which encode a set of highly abundant proteins required for central metabolic functions. Chapter 4 will discuss the biochemical and cell physiological implications of these findings and suggest some avenues for future research. Thesis Supervisor: Wendy V. Gilbert Title: Associate Professor of Biology
The effect of induced blur on the Beery-Buktenica developmental test of visual-motor integration and its supplemental tests

Background The Beery-Buktenica Test of Visual-Motor Integration (Beery VMI) is a commonly used standardized test of visual-motor integration. Performance on the test is related to academic achievement, but the effect of reduced visual acuity on test results is unknown. This study determined the visual acuity demand and the spacing of the test forms for the Beery VMI and its supplemental tests and investigated the effect of induced optical blur on test results in both adults and children. Methods The overall size and critical detail size of each form and the distance between the center of each form and its adjacent crowding source were measured. The visual acuity demand and angular separation of forms were calculated. Two groups of participants (adults aged ≥18 years [n = 19] and children aged 7–12 years [n = 20]) completed four sessions in which they performed the Beery VMI and the supplemental tests under different blur conditions (habitual near correction, monocular spherical blur, binocular spherical blur and binocular astigmatic blur) in a randomized order. Results Stroke width, overall form size and box size remained constant throughout the Beery VMI, whereas these reduced with increasing difficulty for the supplemental tests. Reduced near visual acuity from simulated blur resulted in reduced mean scores for the Beery VMI and its supplemental tests, compared with habitual near vision in both adults and children. Binocular spherical blur had the most detrimental effect (p<0.001), followed by binocular astigmatic blur (p<0.001) then monocular spherical blur (p = 0.022). Conclusions In individuals with uncorrected spherical or astigmatic ametropia, reduced scores on the Beery VMI and its supplemental tests may be due to impaired near visual acuity and not reflect reduced visual-motor abilities. This highlights the importance of excluding reduced near visual acuity as a cause of reduced performance before diagnosing impairment and initiating treatment strategies for visual-motor integration.
Genotype x Environment interaction for yield and yield contributing traits in rabi sorghum

Abstract The analysis of variance for phenotypic stability revealed that the variation due to genotype x environment was considerable for all the characters studied. The significance of G x E (linear) and pooled deviation for majority of the traits suggested the importance of both linear and non-linear components in determining total genotype x environment interactions. Perusal of stability parameters revealed that eight parents were found to be average stable for grain yield. Nevertheless, it was noticed that the male parent RSV 1460 and RPOSV 3 exhibited bi value significantly greater than one, showed below average stability, which was suitable for favourable environments. Among hybrids twenty five hybrids exhibited high mean, unit regression (b i ) and least deviation from regression (S 2 d i ) and therefore they were classified as stable with average response to environments. In general, the hybrids found stable for grain yield also showed stability for two or more component characters, which indicated that the stability of various component traits might be responsible for stability of these hybrids for grain yield per plant. The best three hybrids viz., 1543A x RSV 1297, 1343A x RSV 1200 and 1343A x SPV 1359 were found to have average stability over environments for grain yield per plant with one or more stable yield contributing traits, signifying their potential for commercial exploitation for genetic improvement in rabi sorghum.
The Role of Decision Analysis in Risk Analysis: A Retrospective

In commemorating the 40th anniversary of Risk Analysis, this article takes a retrospective look at some of the ways in which decision analysis (as a “sibling field”) has contributed to the development both of the journal, and of risk analysis as a field. I begin with some early foundational papers from the first decade of the journal's history. I then review a number of papers that have applied decision analysis to risk problems over the years, including applications of related methods such as influence diagrams, multicriteria decision analysis, and risk matrices. The article then reviews some recent trends, from roughly the last five years, and concludes with observations about the parallel evolution of risk analysis and decision analysis over the decades—especially with regard to the importance of representing multiple stakeholder perspectives, and the importance of behavioral realism in decision models. Overall, the extensive literature surveyed here supports the view that the incorporation of decision‐analytic perspectives has improved the practice of risk analysis.
Harvest management affects biomass composition responses of C4 perennial bioenergy grasses in the humid subtropical USA

Elephantgrass (Pennisetum purpureum Schum.) and energycane (Saccharum spp. hybrid) are high‐yielding C4 grasses that are attractive biofuel feedstocks in the humid subtropics. Determining appropriate harvest management practices for optimal feedstock chemical composition is an important precursor to their successful use in production systems. In this research, we have investigated the effects of harvest timing and frequency on biomass nutrient, carbohydrate and lignin composition of UF1 and cv. Merkeron elephantgrasses and cv. L 79‐1002 energycane. Biomass properties under increased harvest frequency (twice per year) and delayed harvest (once per year after frost) were compared with a control (once per year prior to frost). There were no differences between elephantgrass entries in structural carbohydrates; however, elephantgrasses had greater structural hexose concentration than energycane for single‐harvest treatments (avg. 398 vs. 366 mg g−1), a trait that is preferred for biofuel production. Delayed harvest of energycane decreased structural hexose compared with the control (374 vs. 357 mg g−1) because nonstructural components accumulated in energycane stem as harvest was delayed. Frequent defoliation (2X) increased N, P, and ash concentrations (75% for N and P and 58% for ash) in harvested biomass compared with single‐harvest treatments. We conclude that multiple harvests per year increase the harvest period during which feedstock is available for processing, but they do not result in optimal feedstock composition. In contrast, extending the period of feedstock supply by delaying a single harvest to after first freeze did not negatively affect cell wall constituent properties, while it increased length of the harvest period by ~30 days in the southeast USA.
Longitudinal investigation of nasopharyngeal pneumococcal carriage in early childhood: The PATCH birth cohort study

Streptococcus pneumoniae is a common cause of infectious diseases such as pneumonia and sepsis. Its colonization is thought to be the first step in the development of invasive pneumococcal diseases. This study aimed to investigate pneumococcal colonization patterns in early childhood. A longitudinal birth cohort study was conducted for investigating nasopharyngeal colonized pneumococci at 1, 6, 12, 18, 24, and 36 months of age, particularly focusing on the serotype distribution and antimicrobial susceptibilities. Pneumococcal conjugate vaccine (PCV) effect on nasopharyngeal colonization was also assessed. During 2013–2017, 855 infants were enrolled and a total of 107 isolates were recovered from 95 infants during the first three years of life. In this period, the prevalence of pneumococcal colonization increased, with values ranging from 0.2% (2/834) at 1 month of age to 5.9% (19/323) at 36 months of age. The investigation of serotype revealed that 81.1% (73/90) belonged to the non-PCV13 serotypes–23A, 15A, 15C, and 15B. Moreover, PCV13 serotypes significantly decreased during 2014–2015, when routine PCV13 vaccination was initiated in Taiwan. PCV13 introduction may lead to the reduction in the rates of pneumococcal isolates resistant (R) to penicillin. Under conditional PCV13 vaccination, pneumococcal isolates primarily belonged to non-PCV13 serotypes. This non-PCV13 serotype replacement exhibited lower rates of penicillin R isolates, suggesting that PCV13 administration may reduce the antibiotic-nonsusceptible pneumococcal disease burden and antibiotic use.
Thermodynamic Basis for Conformational Coupling in an ATP-Binding Cassette Exporter.

ATP-binding cassette (ABC) transporters constitute one of the largest protein superfamilies and they mediate the transport diverse substrates across the membrane. The molecular mechanism for transducing the energy from ATP binding and hydrolysis into the conformational changes remains elusive. Here, we determined the thermodynamics underlying the ATP-induced global conformational switching for the ABC exporter TmrAB using temperature-resolved pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy. We show that a strong entropy-enthalpy compensation mechanism enables the closure of the nucleotide-binding domains (NBDs) over a wide temperature range. This is mechanically coupled with an outward opening of the transmembrane domains (TMDs) accompanied with an entropy gain. The conserved catalytic glutamate plays a key role in the overall energetics. Our results reveal the thermodynamic basis for the chemomechanical energy coupling in an ABC exporter and present a new strategy to explore the energetics of similar membrane protein complexes.