Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic diagnosis of macular diseases from OCT volume based on its two-dimensional feature map and convolutional neural network with attention mechanism

Abstract. Significance: Automatic and accurate classification of three-dimensional (3-D) retinal optical coherence tomography (OCT) images is essential for assisting ophthalmologist in the diagnosis and grading of macular diseases. Therefore, more effective OCT volume classification for automatic recognition of macular diseases is needed. Aim: For OCT volumes in which only OCT volume-level labels are known, OCT volume classifiers based on its global feature and deep learning are designed, validated, and compared with other methods. Approach: We present a general framework to classify OCT volume for automatic recognizing macular diseases. The architecture of the framework consists of three modules: B-scan feature extractor, two-dimensional (2-D) feature map generation, and volume-level classifier. Our architecture could address OCT volume classification using two 2-D image machine learning classification algorithms. Specifically, a convolutional neural network (CNN) model is trained and used as a B-scan feature extractor to construct a 2-D feature map of an OCT volume and volume-level classifiers such as support vector machine and CNN with/without attention mechanism for 2-D feature maps are described. Results: Our proposed methods are validated on the publicly available Duke dataset, which consists of 269 intermediate age-related macular degeneration (AMD) volumes and 115 normal volumes. Fivefold cross-validation was done, and average accuracy, sensitivity, and specificity of 98.17%, 99.26%, and 95.65%, respectively, are achieved. The experiments show that our methods outperform the state-of-the-art methods. Our methods are also validated on our private clinical OCT volume dataset, consisting of 448 AMD volumes and 462 diabetic macular edema volumes. Conclusions: We present a general framework of OCT volume classification based on its 2-D feature map and CNN with attention mechanism and describe its implementation schemes. Our proposed methods could classify OCT volumes automatically and effectively with high accuracy, and they are a potential practical tool for screening of ophthalmic diseases from OCT volume.
Structural network topology in limbic encephalitis is associated with amygdala enlargement, memory performance and serostatus

Limbic encephalitis (LE) forms a spectrum of autoimmune diseases involving temporal lobe epilepsy and memory impairment. Imaging features of LE are known to depend on the associated antibody and to occur on the brain network level. However, first studies investigating brain networks in LE have either focused on one distinct antibody subgroup or on distinct anatomical regions. In this study, brain graphs of 17 LE patients with autoantibodies against glutamic acid decarboxylase 65 (GAD‐LE), four LE patients with autoantibodies against leucine‐rich glioma‐inactivated 1, five LE patients with autoantibodies against contactin‐associated protein‐like 2, 26 age‐ and gender‐matched healthy control subjects, and 20 epilepsy control patients with hippocampal sclerosis were constructed based on T1‐weighted structural magnetic resonance imaging scans and diffusion tensor imaging. GAD‐LE showed significantly altered global network topology in terms of integration and segregation as compared to healthy controls and patients with hippocampal sclerosis (P < .01, analysis of variance with Tukey‐Kramer post hoc tests). Linear regression linked global network measures with amygdala volume and verbal memory performance (P < .05). Alterations of local network topology show serotype dependence in hippocampus, amygdala, insula, and various cortical regions. Our findings reveal serotype‐dependent patterns of structural connectivity and prove the relevance of in silico network measures on clinical grounds.
RAPD-PCR Analysis of Genetic Diversity of Different Colour 35 Tree Paeonia Cultivars

Random amplified polymorphic DNA (RAPD) was used to analyze the genetic polymophism of 35 tree peony cultivars derived from seven different flower colour types. Thirty four primers amplified 418 DNA fragments which included special DNA fragments from 18 cultivars. It could also be used to differentiate all cultivars being tested and the UPGMA method may be used to analyze the genetic relationship. The results showed that 35 tree peony cultivars were divided into 2 cluster groups having a similarity of 1.5, and those remaining were divided into 4 cluster groups having a similarity of 1.0. The results confirmed that the flower colour has no relationship to the genetic groups, but the tree peony cultivers come from the same place where the relationship is similar. Therefore, The genetic background has little effect on the genetic relationship.
Process Mapping and Activity-Based Costing of the Intravitreal Injection Procedure

ABSTRACT Purpose/Aim of the study To quantify the cost of performing an intravitreal injection (IVI) utilizing activity-based costing (ABC), which allocates a cost to each resource involved in a manufacturing process. Materials and Methods A prospective, observational cohort study was performed at an urban, multi-specialty ophthalmology practice affiliated with an academic institution. Fourteen patients scheduled for an IVI-only visit with a retina ophthalmologist were observed from clinic entry to exit to create a process map of time and resource utilization. Indirect costs were allocated with ABC and direct costs were estimated based on process map observations, internal accounting records, employee interviews, and nationally-reported metrics. The primary outcome measure was the cost of an IVI procedure in United States dollars. Secondary outcomes included operating income (cost subtracted from revenue) of an IVI and patient-centric time utilization for an IVI. Results The total cost of performing an IVI was $128.28; average direct material, direct labor, and overhead costs were $2.14, $97.88, and $28.26, respectively. Compared to the $104.40 reimbursement set by the Centers for Medicare and Medicaid Services for Current Procedural Terminology code 67028, this results in a negative operating income of -$23.88 (−22.87%). The median clinic resource-utilizing time to complete an IVI was 32:58 minutes (range [19:24–1:28:37]); the greatest bottleneck was physician-driven electronic health record documentation. Conclusions Our study provides an objective and accurate cost estimate of the IVI procedure and illustrates how ABC may be applied in a clinical context. Our findings suggest that IVIs may currently be undervalued by payors.
Does mitochondrial DNA replication in Chlamydomonas require a reverse transcriptase?

Among the first green algal mitochondrial DNAs (mtDNAs) to be described in great detail was that of Chlamydomonas reinhardtii (Grant & Chiang, 1980; Gray & Boer, 1988; Vahrenholz et al., 1993). It is a ~16 kb linear molecule containing fragmented rRNA genes and telomeres, arranged in an inverted-repeat orientation with 3' single-stranded overhangs (Fig. 1A). Another intriguing feature of this genome is a free-standing open reading frame (1,119 nt) encoding a reverse transcriptase-like protein (the rtl gene), which is believed to have originated from an ancient group II intron (Boer & Gray, 1988) but is no longer associated with one.
High‐resolution, relational, resonance‐based, electroencephalic mirroring (HIRREM) improves symptoms and autonomic function for insomnia: A randomized, placebo‐controlled clinical trial

Effective insomnia interventions that also address autonomic dysregulation are lacking. We evaluate high‐resolution, relational, resonance‐based, electroencephalic mirroring (HIRREM®), in a randomized, controlled clinical trial. HIRREM is a noninvasive, closed‐loop, allostatic, acoustic stimulation neurotechnology, to support self‐optimization of brain rhythms.
Isolation of bioactive components with soluble epoxide hydrolase inhibitory activity from Stachys sieboldii MiQ. by ultrasonic-assisted extraction optimized using response surface methodology

Abstract Stachys sieboldii MiQ (SSM) is an important food and medicinal herb in Korea, used to improve memory of patients with senile dementia and cardiovascular diseases. However, little information on bioactive components from SSM or standardized extraction methods for these components is available. This study isolated and purified major components from SSM for the first time, and assessed their ability to inhibit soluble epoxide hydrolase (sEH). The results showed that acteoside is the most potent inhibitor of sEH, with an IC50 of 33.5 ± 0.5 μM. Additional active components, including harpagide, tryptophan, and 8-acetate-harpagide, along with acteoside, were tentatively identified using high‐performance liquid chromatography photodiode array tandem mass spectrometry (HPLC–PDA–MS/MS) and quantified using an ultraviolet detector at 210 nm. Further, an ultrasonic-assisted extraction technique for extraction of four bioactive compounds in SSM was developed and optimized using response surface methodology (RSM). The optimal extraction conditions were: extraction time, 30.46 minutes; extraction temperature, 67.95 °C, and methanol concentration 53.85%. The prediction model of RSM was validated with laboratory experiments. The similarity between predicted and actual values was 97.84%. The extraction method is thus a rapid, environment-friendly, energy-saving method can be applied to extract bioactive components from SSM in large quantities.
Within-population variation in demography of Taraxacum officinale : season- and size-dependent survival, growth, and reproduction

1 Lefkovitch transition matrices were used to determine vital demographic rates of a natural population of Taraxacum officinale in Morgantown, WV, USA. Separate size transition matrices were calculated for each of four seasons, October-January, January-April, April-July, and July-October, to test if demographic rates vary as a function of season and if size-specific rates vary differentially among seasons. Seasondependent demography was also compared for four phenotype classes segregated by cluster analysis of leaf morphology. 2 The finite rate of increase for the entire population was largest in autumn (OctoberJanuary) and declined throughout the rest of the year. Overall, there was a small reduction in the population size. Size-specific probabilities of survival, growth and fertility varied dramatically among seasons. Sensitivity analyses showed that small individuals were particularly important to population growth from autumn to spring. Larger individuals were more important during summer. 3 Highly season-dependent demographic rates have large implications for population distribution and persistence since increased vulnerability to perturbation during particular seasons may constrain population growth and stability. Although T. officinale is a long-lived perennial, annual censuses may mask the importance of certain individuals or life history traits for maintenance of genetic variability and population viability. 4 Seasonal and annual finite rates of increase also varied as a function of phenotype class. Of two phenotype classes which had identical annual growth rates, one grew better in cool seasons while the second performed better in warm seasons. Direct competition for resources should be reduced by such inverse patterns of demography across seasons. 5 If phenotype classes are to some degree genetically determined, the differential responses observed here suggest that temporal variation in the environment could explain the maintenance of genetic diversity within populations.
Data‐driven in silico prediction of regulation heterogeneity and ATP demands of Escherichia coli in large‐scale bioreactors

Escherichia coli exposed to industrial‐scale heterogeneous mixing conditions respond to external stress by initiating short‐term metabolic and long‐term strategic transcriptional programs. In native habitats, long‐term strategies allow survival in severe stress but are of limited use in large bioreactors, where microenvironmental conditions may change right after said programs are started. Related on/off switching of genes causes additional ATP burden that may reduce the cellular capacity for producing the desired product. Here, we present an agent‐based data‐driven model linked to computational fluid dynamics, finally allowing to predict additional ATP needs of Escherichia coli K12 W3110 exposed to realistic large‐scale bioreactor conditions. The complex model describes transcriptional up‐ and downregulation dynamics of about 600 genes starting from subminute range covering 28 h. The data‐based approach was extracted from comprehensive scale‐down experiments. Simulating mixing and mass transfer conditions in a 54 m3 stirred bioreactor, 120,000 E. coli cells were tracked while fluctuating between different zones of glucose availability. It was found that cellular ATP demands rise between 30% and 45% of growth decoupled maintenance needs, which may limit the production of ATP‐intensive product formation accordingly. Furthermore, spatial analysis of individual cell transcriptional patterns reveal very heterogeneous gene amplifications with hot spots of 50%–80% messenger RNA upregulation in the upper region of the bioreactor. The phenomenon reflects the time‐delayed regulatory response of the cells that propagate through the stirred tank. After 4.2 h, cells adapt to environmental changes but still have to bear an additional 6% ATP demand.
Two-Year, Randomized, Controlled Trial of Belimumab in Lupus Nephritis.

BACKGROUND In adults with active lupus nephritis, the efficacy and safety of intravenous belimumab as compared with placebo, when added to standard therapy (mycophenolate mofetil or cyclophosphamide-azathioprine), are unknown. METHODS In a phase 3, multinational, multicenter, randomized, double-blind, placebo-controlled, 104-week trial conducted at 107 sites in 21 countries, we assigned adults with biopsy-proven, active lupus nephritis in a 1:1 ratio to receive intravenous belimumab (at a dose of 10 mg per kilogram of body weight) or matching placebo, in addition to standard therapy. The primary end point at week 104 was a primary efficacy renal response (a ratio of urinary protein to creatinine of ≤0.7, an estimated glomerular filtration rate [eGFR] that was no worse than 20% below the value before the renal flare (pre-flare value) or ≥60 ml per minute per 1.73 m2 of body-surface area, and no use of rescue therapy), and the major secondary end point was a complete renal response (a ratio of urinary protein to creatinine of <0.5, an eGFR that was no worse than 10% below the pre-flare value or ≥90 ml per minute per 1.73 m2, and no use of rescue therapy). The time to a renal-related event or death was assessed. RESULTS A total of 448 patients underwent randomization (224 to the belimumab group and 224 to the placebo group). At week 104, significantly more patients in the belimumab group than in the placebo group had a primary efficacy renal response (43% vs. 32%; odds ratio, 1.6; 95% confidence interval [CI], 1.0 to 2.3; P = 0.03) and a complete renal response (30% vs. 20%; odds ratio, 1.7; 95% CI, 1.1 to 2.7; P = 0.02). The risk of a renal-related event or death was lower among patients who received belimumab than among those who received placebo (hazard ratio, 0.51; 95% CI, 0.34 to 0.77; P = 0.001). The safety profile of belimumab was consistent with that in previous trials. CONCLUSIONS In this trial involving patients with active lupus nephritis, more patients who received belimumab plus standard therapy had a primary efficacy renal response than those who received standard therapy alone. (Funded by GlaxoSmithKline; BLISS-LN ClinicalTrials.gov number, NCT01639339.).
Identification of Key Functional Motifs of Native Amelogenin Protein for Dental Enamel Remineralisation

Dental caries or tooth decay is a preventable and multifactorial disease that affects billions of people globally and is a particular concern in younger populations. This decay arises from acid demineralisation of tooth enamel resulting in mineral loss from the subsurface. The remineralisation of early enamel carious lesions could prevent the cavitation of teeth. The enamel protein amelogenin constitutes 90% of the total enamel matrix protein in teeth and plays a key role in the biomineralisation of tooth enamel. The physiological importance of amelogenin has led to the investigation of the possible development of amelogenin-derived biomimetics against dental caries. We herein review the literature on amelogenin, its primary and secondary structure, comparison to related species, and its’ in vivo processing to bioactive peptide fragments. The key structural motifs of amelogenin that enable enamel remineralisation are discussed. The presence of several motifs in the amelogenin structure (such as polyproline, N- and C-terminal domains and C-terminal orientation) were shown to play a critical role in the formation of particle shape during remineralization. Understanding the function/structure relationships of amelogenin can aid in the rational design of synthetic polypeptides for biomineralisation, halting enamel loss and leading to improved therapies for tooth decay.
Imputing radiobiological parameters of the linear-quadratic dose-response model from a radiotherapy fractionation plan

The objective in cancer radiotherapy is to maximize tumor-kill while limiting toxic effects of radiation dose on nearby organs-at-risk (OAR). Given a fixed number of treatment sessions, planners thus face the problem of finding a dosing sequence that achieves this goal. This is called the fractionation problem, and has received steady attention over a long history in the clinical literature. Mathematical formulations of the resulting optimization problem utilize the linear-quadratic (LQ) framework to characterize radiation dose-response of tumors and OAR. This yields a nonconvex quadratically constrained quadratic program. The optimal dosing plan in this forward problem crucially depends on the parameters of the LQ model. Unfortunately, these parameters are difficult to estimate via in vitro or in vivo studies, and as such, their values are unknown to treatment planners. The clinical literature is thus replete with debates about what parameter values will make specific dosing plans effective. This paper formulates this as an inverse optimization problem. The LQ dose-response parameters appear in the objective function, the left hand side, and the right hand side of the forward problem, and none of the existing generic methods can provide an exact solution of the inverse problem. This paper exploits the structure of the problem and identifies all possible parameter values that render the given dosing plan optimal, in closed-form. This closed-form formula is applied to dosing-plans from three clinical studies published within the last two years.
Effect of Self-Controlled Practice on Neuro-Cortical Dynamics During the Processing of Visual Performance Feedback

Abstract Evidence has accumulated that learners participating in self-controlled practice can both acquire skills and process task-relevant information more effectively than those participating in externally controlled practice. However, the impact of self-controlled practice on neuro-cognitive information processing during visual performance-related feedback has received limited investigation. We expected that individuals participating in self-controlled practice would exhibit elevated neuro-cognitive information processing, as assessed via electroencephalography (EEG), compared with those engaged with externally controlled practice. Participants practiced a golf-putting task under self-controlled or externally controlled (yoked) conditions while EEG data were recorded. Results indicated that EEG theta power was maintained at an elevated level during the feedback period in the self-controlled group relative to the yoked group. The yoked group did not display increases in theta power until the time at which the ball stopped. Both groups displayed similar improvement over the course of the experiment. Correlational analyses revealed that performance improvement within each group was related differently to EEG theta power. Specifically, the self-controlled group displayed positive relationships between theta power and performance improvement, while the yoked group displayed negative relationships. These results have implications regarding the relative effectiveness of self-controlled and externally controlled practice and the instances in which they may provide the most benefit.
Chemical Constituents from Citrus changshan‐huyou and Their Anti‐Inflammatory Activities

A systematically chemical investigation of Citrus changshan‐huyou Y.B. Chang resulted in the isolation and structure determination of twelve known natural products, including limonoid, nootkatone, scoparone, β‐sitosterol, 3,3′,4′,5,6,7,8,‐heptamethoxyflavone, nobiletin, tangeretin, naringin, hesperidin, neohesperidin, 3,5‐dihydroxyphenyl β‐D‐glucoside, β‐sitosterol‐D‐glucoside. The structure modification of the most abundant compound limonin further led to eight limonoid derivatives, including epi‐limonol, epi‐limonyl acetate, and six new compounds epi‐limonol A, limonol A, limonol B, epi‐limonol B, epi‐limonol C, epi‐limonol D, which enlarged the chemical diversity of limonin related limonoids. The structures of the new limonoid derivatives were identified by extensive spectroscopic analysis. In bioassay, all the isolates, the semi‐synthetic derivatives and the previously isolated limonoids in our natural product library were subjected for anti‐inflammatory activities evaluation, and several limonoids exhibited the inhibition of TNF‐α release.
Predictors of in‐school and out‐of‐school sport injury prevention: A test of the trans‐contextual model

The current study aimed to predict secondary school students’ motivation toward sport injury prevention in “in‐school” and “out‐of‐school” contexts, and their sport injury prevention behavior at 3‐month follow‐up using the trans‐contextual model (TCM). Hong Kong secondary school students (N = 1566; mean age = 13.34 years, range = 11 to 19; female = 49.42%) were recruited. Participants were asked to complete a survey comprising previously validated scales measuring TCM constructs at baseline and a measure of sport injury prevention behavior at follow‐up three months later. Structural equation modeling (SEM) was used to examine the hypothesized paths among TCM constructs. A SEM specifying hypothesized paths among TCM variables showed acceptable fit with the data (χ2(29) = 418.55, CFI = . 93, TLI = . 90, and RMSEA = . 09, 90% CI [. 09, . 10], and SRMR = . 05). Findings supported tenets of the TCM: the effects of perceived autonomy support from PE teachers on in‐school autonomous motivation toward injury prevention, the trans‐contextual relationship between students' “in‐school” and “out‐of‐school” autonomous motivation toward injury prevention, and the effects of autonomous motivation toward injury prevention on social cognitive variables and subsequent sport injury prevention behaviors. Results supported the tenets proposed within the TCM in predicting students' “in‐school” and “out‐of‐school” autonomous motivation toward sport injury prevention. Findings underscore the potential importance of autonomy support from PE teachers in facilitating students’ sport injury prevention behaviors. Further longitudinal and intervention research is warranted to establish temporal and causal effects of TCM variables in sport injury prevention.