Miracle-dz/UniFAR-FTUs huggingface dataset:
Overbite depth indicator and anteroposterior dysplasia indicator cephalometric norms for African Americans.

OBJECTIVES To examine normal Overbite Depth Indicator (ODI) and Anteroposterior Dysplasia Indicator (APDI) values in African Americans and to compare them with mean values from white patients. Secondary aims were to compare mean ODI and APDI values among different age, gender, and combined age-gender groups in African American patients. MATERIALS AND METHODS Lateral cephalometric radiographs of 160 African American patients (97 boys and 63 girls; age, 7 to 14 years) with normal occlusion and no history of orthodontic treatment were collected from the Bolton-Brush Growth Center. Cephalometric images were hand traced, and ODI and APDI values were assessed. Two-sample t tests were used to compare mean ODI and APDI values between African American and white patients; and between male and female African American patients. One-way analysis of variance, followed by the Tukey test, was used to compare mean ODI and APDI values among different African American age and combined age-gender groups. RESULTS Mean ODI and APDI values were significantly lower (P < .0001) in African American than white patients with normal occlusion and no history of orthodontic treatment. Mean ODI and APDI values increased with age in African American patients, and there were no significant gender differences. CONCLUSIONS The mean ODI and APDI values in 7- to 14-year-old African Americans with normal occlusion and no history of orthodontic treatment were 70.9° and 78.1°, respectively, and were significantly lower than the mean values for white patients in the same age range.
Effects of Educational Interventions on Human Papillomavirus Vaccine Acceptability: A Randomized Controlled Trial.

OBJECTIVE To estimate whether targeted educational interventions can increase human papillomavirus (HPV) vaccine acceptability and knowledge among young women. METHODS An exploratory phase of the study was conducted to determine baseline acceptance of the prophylactic HPV vaccine and barriers to acceptance. Based on the results of that phase of the study, a randomized controlled trial of women aged 12-26 at a single institution was completed. A sample size of at least 84 women in each of three study arms (control, educational handout, or educational video) was planned to detect a 20% difference in vaccine acceptability among arms. All participants completed a survey collecting data on demographics, HPV vaccine preferences, and HPV vaccine knowledge after completion of their randomization assignments. The primary outcome was HPV vaccine acceptability. The secondary outcome was HPV vaccine knowledge. RESULTS From March 2017 through August 2017, 256 women were randomized to one of three study arms: control (n=85), educational handout (n=84), or educational video (n=87). Demographics were similar between study arms. Overall, 51.7% of participants in the educational video arm reported willingness to accept the HPV vaccine compared with 33.3% and 28.2% of participants in the educational handout and control arms, respectively (P<.01). Those in the educational video and handout arms had higher median HPV vaccine knowledge scores than those in the control arm (6 and 5 vs 3, P<.01). Both interventions were reported as helpful in learning (97.7% vs 92.9%, P=.15), but the educational video arm was more likely to be helpful in deciding on vaccination (86.2% vs 70.2%, P<.01). CONCLUSION Targeted educational interventions increase HPV vaccine acceptability and knowledge among young women. Follow up studies are needed to determine whether these interventions also increase rates of vaccine uptake and series completion. CLINICAL TRIAL REGISTRATION Clinicaltrials.gov, NCT03337269.
Analyse von Translationsstarts in prokaryotischen Genomen mit Methoden des Maschinellen Lernens

Exact localization of prokaryotic translation initiation sites with automated prediction systems is still not completely solved. In this context, two approaches from the field of machine learning have been developed: The Oligo Kernel algorithm, a supervised learning method for analysis of signaling in biological sequences and TICO (Translation Initiation site COrrection), a tool for (re-)annotation of translation initiation sites with an unsupervised classification scheme.It is shown that the Oligo Kernel algorithm is well suitable for analysis of biological signals. In a case study on translation initiation sites of eubacterium Escherichia coli K-12 the high performance of the Oligo classificator is demonstrated on experimentally verified data. A visualization of the discriminative signals facilitates a biologically meaningful interpretation. For E. coli K-12 commonly known signals for translation initiation and their inherent variability can be clearly identified. Since the algorithm is flexible regarding the degree of positional smoothing it can be adapted to analysis of other biological signals.The program TICO significantly improves prediction of prokaryotic translation initiation sites as compared to previous approaches, by post-processing an initial gene annotation as obtained by a classical gene finder. The improvement of such a reannotation amounts up to 30%. The algorithm provides a visualization method allowing an intuitive presentation of the discriminative features. The program can be accessed through a web interface and is freely available as command line tool for Linux and Windows.
A Chemical Proteomic Analysis of Illudin‐Interacting Proteins

Abstract The illudin natural product family are fungal secondary metabolites with a characteristic spirocyclopropyl‐substituted fused 6,5‐bicyclic ring system. They have been extensively studied for their cytotoxicity in various tumor cell types, and semisynthetic derivatives with improved therapeutic characteristics have progressed to clinical trials. Although it is believed that this potent alkylating compound class acts mainly through DNA modification, little is known about its binding to protein sites in a cellular context. To reveal putative protein targets of the illudin family in live cancer cells, we employed a semisynthetic strategy to access a series of illudin‐based probes for activity‐based protein profiling (ABPP). While the probes largely retained potent cytotoxicity, proteomic profiling studies unraveled multiple protein hits, suggesting that illudins exert their mode of action not from addressing a specific protein target but rather from DNA modification and unselective protein binding.
Towards Migrating Security Policies along with Virtual Machines in Cloud

Multi-tenancy and elasticity are important characteristics of every cloud. Multi-tenancy can be economical; however, it raises some security concerns. For example, contender companies may have Virtual Machines (VM) on the same server and have access to the same resources. There is always the possibility that one of them tries to get access to the opponent's data. In order to address these concerns, each tenant in the cloud should be secured separately and firewalls are one of the means that can help in that regard. Firewalls also protect virtual machines from the outside threats using access control lists and policies. On the other hand, virtual machines migrate frequently in an elastic cloud and this raises another apprehension about what happens to the security policies that are associated with the migrated virtual machine. In this thesis, we primarily contribute by proposing a novel framework that coordinates the mobility of the associated security policies along with the virtual machine in Software-Defined Networks (SDN). We then design and develop a prototype application called Migration Application (MigApp), based on our framework that moves security policies and coordinates virtual machine and security policy migration. MigApp runs on top of SDN controllers and uses a distributed messaging system in order to interact with virtual machine monitor and other MigApp instances. We integrate MigApp with Floodlight controller and evaluate our work through simulations. In addition, we prepare a test-bed for security testing in clouds that are based on traditional networks. We focus on virtual machine migration and use open-source utilities to equip this test-bed. We design an architecture based on GNS3 network emulator in order to provide a distributed testing environment. We then propose a virtual machine migration framework on Oracle VirtualBox; and finally, we enrich the security aspect of framework by adding firewall rule migration and security verification mechanisms into it.
Reversible watermarking algorithm based on wavelet lifting scheme

Nowadays, digital watermarking algorithms are widely applied to ownership protection and tampering detection of digital images. In this paper, a new reversible watermarking algorithm based on wavelet lifting scheme is proposed. In the algorithm, the image is firstly divided into some no-overlapping blocks, and then is performed wavelet lifting scheme on every block, watermarking data is embedded into the image according to the attribute of the sub-band LL1 of every block In order to guarantee the security of algorithm, chaotic system is used to shuffle the position of blocks, the interesting point and usefulness of the algorithm lies in that watermarked image can be exactly restored into the original image, and the watermarking is robust to cropping. The experimental results show the effectiveness of the scheme.
Automated quantification of superficial retinal capillaries and large vessels for diabetic retinopathy on optical coherence tomographic angiography

Optical coherence tomography angiography (OCTA) is a relatively new technique with capillary‐level resolution, which has shown great potential for the diagnosis of diabetic retinopathy (DR). A fully automatic algorithm for the quantitative measurement of microcirculatory changes in sight‐threatening DR is presented. The foveal avascular zone (FAZ) segmentation was improved with a graph‐theoretic method and the large vessels and capillaries were separately identified and analyzed. The method was evaluated in healthy and diabetic eyes with various stages of retinopathy. Results showed that, compared with the healthy group, the diabetic group showed a significantly larger large vessel density, but a significantly smaller capillary density (P < .001). Circularity of FAZ was significantly smaller while nonperfusion area was significantly larger in the diabetic group. The combined variable of all image metrics reached an area under the ROC of 0.853 (95% CI, 0.784‐0.923) for mild to moderate nonproliferative DR and 0.950 (95% CI, 0.922‐0.979) for proliferative DR. Microvascular and FAZ changes with various DR stages can be accurately delineated using the developed automatic program. Quantitative metrics on OCTA serve as potential biomarkers for the staging of DR.
Distinct roles of striatal direct and indirect pathways in value-based decision making

The striatum is critically involved in value-based decision making. However, it is unclear how striatal direct and indirect pathways work together to make optimal choices in a dynamic and uncertain environment. Here, we examined the effects of selectively inactivating D1 receptor (D1R)- or D2 receptor (D2R)-expressing dorsal striatal neurons (corresponding to direct- and indirect-pathway neurons, respectively) on mouse choice behavior in a reversal task with progressively increasing reversal frequency and a dynamic two-armed bandit task. Inactivation of either D1R- or D2R-expressing striatal neurons impaired performance in both tasks, but the pattern of altered choice behavior differed between the two animal groups. A reinforcement learning model-based analysis indicated that inactivation of D1R- and D2R-expressing striatal neurons selectively impairs value-dependent action selection and value learning, respectively. Our results suggest differential contributions of striatal direct and indirect pathways to two distinct steps in value-based decision making.
Towards the automated restoration of old photographic prints: a survey

The ubiquitous fruition of cultural and artistic heritage in the field of photography requires as a first step the conversion of a huge amount of old printed material into digital form, for successive manipulation and data management. This process is particularly delicate for photographic prints, which often show the effects of aging. This paper reports a list of the principal defects that can be detected in an old photography; the different origins of them, and their different features, suggest different restoration approaches.
Role of the msaABCR Operon in Cell Wall Biosynthesis, Autolysis, Integrity, and Antibiotic Resistance in Staphylococcus aureus

Staphylococcus aureus is an important human pathogen in both community and health care settings. One of the challenges with S. aureus as a pathogen is its acquisition of antibiotic resistance. Previously, we showed that deletion of the msaABCR operon reduces cell wall thickness, resulting in decreased resistance to vancomycin in vancomycin-intermediate S. aureus (VISA). ABSTRACT Staphylococcus aureus is an important human pathogen in both community and health care settings. One of the challenges with S. aureus as a pathogen is its acquisition of antibiotic resistance. Previously, we showed that deletion of the msaABCR operon reduces cell wall thickness, resulting in decreased resistance to vancomycin in vancomycin-intermediate S. aureus (VISA). In this study, we investigated the nature of the cell wall defect in the msaABCR operon mutant in the Mu50 (VISA) and USA300 LAC methicillin-resistant Staphylococcus aureus (MRSA) strains. Results showed that msaABCR mutant cells had decreased cross-linking in both strains. This defect is typically due to increased murein hydrolase activity and/or nonspecific processing of murein hydrolases mediated by increased protease activity in mutant cells. The defect was enhanced by a decrease in teichoic acid content in the msaABCR mutant. Therefore, we propose that deletion of the msaABCR operon results in decreased peptidoglycan cross-linking, leading to increased susceptibility toward cell wall-targeting antibiotics, such as β-lactams and vancomycin. Moreover, we also observed significantly downregulated transcription of early cell wall-synthesizing genes, supporting the finding that msaABCR mutant cells have decreased peptidoglycan synthesis. More specifically, the msaABCR mutant in the USA300 LAC strain (MRSA) showed significantly reduced expression of the murA gene, whereas the msaABCR mutant in the Mu50 strain (VISA) showed significantly reduced expression of glmU, murA, and murD. Thus, we conclude that the msaABCR operon controls the balance between cell wall synthesis and cell wall hydrolysis, which is required for maintaining a robust cell wall and acquiring resistance to cell wall-targeting antibiotics, such as vancomycin and the β-lactams.
A new approach for finding the weights in neural network using graphs

This paper describes a method for obtaining the weights of a Hopfield network exploring the possibility of using graph theory. We associate each pattern going to be stored in the network with a certain basic graph and as a function of these basic graphs, we obtain a resulting graph. This graph contains the weights to be assigned to the network connections. A measure function may be defined on this graph, which can be used to classify the new patterns presented to the network during the testing process. The aim of the present research is intended to explore new specification techniques of neural networks based on graphs to be used in the optimization and simplification of network architectures and computational complexity. This methodology can be used to treat real problems in pattern recognition and speech processing. <<ETX>>
Real-Time Systems and Programming Languages - Ada, Real-Time Java and C / Real-Time POSIX, Fourth Edition

From mobile phones to microwave ovens, engine management systems to aircraft avionics systems, safety, reliability, and time-critical response are all critical factors. There is strong demand in industry for software/hardware engineers with Real-Time design and programming skills. This text focuses on the different languages (including Ada and Java) used to program real-time applications and the language constructs required to enable you to develop these critical skills.
Integrated Environmental Assessment and Management

An environmental quality standard (EQS) is a threshold value applied in regulatory monitoring for retrospective environmental risk assessment. However, an EQS may vary with time and between countries with shared water bodies, challenging coherent risk management. This study aimed to analyze the underlying reasons for changes in EQS values following a revision of previously derived EQSs for 62 substances. Relevant data were retrieved from publicly accessible databases, available literature, registration dossiers, and, in some cases, provided by manufacturers. Ecotoxicological data were assessed regarding reliability and relevance. As in previous studies, EQS derivation followed the European Union guideline. Overall, 61 annual average EQSs (AA‐EQS) and 58 maximum acceptable concentration EQSs (MAC‐EQS) were derived. Size and completeness of data sets generally increased due to the revision. AA‐EQSs increased in 13 cases and decreased in 21 cases. MAC‐EQSs increased in 22 cases and decreased in 11 cases. Most EQSs were derived using the deterministic assessment factor (AF) method. The number of substances for which EQSs were derived probabilistically by reference to the species sensitivity distribution (SSD) method increased from 2 to 5 AA‐EQSs and from 6 to 11 MAC‐EQSs. For AA‐EQS derivation, AFs were reduced in 14 cases and increased in 6 cases. For MAC‐EQS derivation, AFs were reduced in 9 cases and increased in 2 cases. Results demonstrate that the revisions did not generally lead to either lower or higher EQSs. The majority of EQSs (>93%) changed less than 10‐fold. Clearly, EQSs based on small or incomplete data sets with large AFs were more prone to considerable changes in their numeric values when revised than EQSs based on SSDs. Thus, revision can reduce uncertainty and increase robustness of an EQS. In this study, however, available data continued to be insufficient to construct SSDs for the majority of substances. This was mostly due to a lack of reliable data. Integr Environ Assess Manag 2019;15:948–960. © 2019 SETAC
Protamine‐induced condensation of peptide nanofilaments into twisted bundles with controlled helical geometry

Chiral self‐assembly of peptides is of fundamental interest in the field of biology and material science. Protamine, an alkaline biomacromolecule which is ubiquitous in fish and mammalian, plays crucial roles in directing the helical twisting of DNA. Inspired by this, we reported a bioinspired pathway to direct the hierarchical chiral self‐assembly of a short synthetic dipeptide. The peptide could self‐assemble into negatively charged chiral micelles in water that spontaneously formed a nematic liquid crystalline phase. By incorporation with protamine, the micelles condensed with the protamine into large helical bundles with precisely controlled diameter. Furthermore, to simulate the intracellular environments, we investigated macromolecular crowding on the coassembly of peptide and protamine, which leads to the formation of much thinner helical structures. The results highlight the roles of highly charged biomacromolecules and macromolecular crowding on peptide self‐assembly, which are beneficial for the practical applications of self‐assembling peptides in biomedicine and sensing.
Sexual dimorphism explains residual variance around the survival‐reproduction tradeoff in lizards: Implications for sexual conflict over life‐history evolution *

The tradeoff between survival and reproduction is a central feature of life‐history variation, but few studies have sought to explain why females of some species exhibit relatively lower survival than expected for a given level of reproductive effort (RE). Intralocus sexual conflict theory proposes that sex differences in selection on survival and RE may, by virtue of shared genes underlying these components of fitness, prevent females from optimizing this life‐history tradeoff. To test this hypothesis, we used a phylogenetically based comparative analysis of published estimates for mean annual survival and RE from females of 82 lizard species to (1) characterize the tradeoff between survival and reproduction and (2) test whether variation around this tradeoff is explained by sexual size dimorphism (SSD), a potential proxy for sexual conflict over life‐history traits. Across species, we found a strong negative correlation between mean annual survival and RE, confirming this classic life‐history tradeoff. Although residual variance around this tradeoff is unrelated to the absolute magnitude of SSD, it is strongly related to the direction of SSD. Specifically, we found that females have lower survival than expected for a given level of RE in female‐larger species, whereas they have higher survival than expected in male‐larger species. Given that female‐larger SSD is thought to reflect selection for increased fecundity, our results suggest that intralocus sexual conflict may be particularly likely to constrain female life‐history evolution in situations where increased RE is favored, but the phenotypes that facilitate this increase (e.g., body size) are constrained by antagonistic selection on males.
Ras-AKT signaling represses the phosphorylation of histone H1.5 at threonine 10 via GSK3 to promote the progression of glioma

Abstract Background Histone H1.5 has been considered as a novel cancer marker as its expression is associated with various human cancers. The objective of this study was to explore the effects of H1.5 phosphorylation in Ras-driven growth and migration of glioma cells. Methods The plasmids for expression of wide-type of Ras or RasG12V/Y40C were transfected into A172 cells. The expression levels of phosphorylated AKT and H1.5T10ph were tested by Western blot. The effects of H1.5T10ph on A172 cells growth and migration were determined by MTT, soft-agar colony formation, and transwell assay. qRT-PCR and ChIP assay were utilized to assess the role of H1.5T10ph in the transcription of Ras downstream genes. Besides, qRT-PCR and Western blot analysis were carried out to reveal the enzymes which were responsible for phosphorylating H1.5. Results H1.5T10ph was down-regulated by Ras mutation, which accompanied by the activation of AKT signaling. Ras-driven A172 cells growth and migration were inhibited when H1.5T10ph was overexpressed. Additionally, H1.5T10ph was able to regulate the transcription of Ras downstream genes, including CYR61, IGFBP3, WNT16B, NT5E, GDF15, and CARD16. Further experiments revealed that Ras-AKT signaling repressed H1.5T10ph expression through degradation of GSK3, and the degradation was dependent on MDM2 mediation. Conclusion Ras-AKT signaling driven the growth and migration of glioma cells possibly through repressing the phosphorylation of H1.5 at threonine 10. Ras-AKT activation repressed H1.5T10ph through MDM2-dependent degradation of GSK3. The findings provide a better understanding of Ras’s oncogenic functions which further suggest Ras as a therapeutic target for glioma.
A fast online learning algorithm for recurrent neural networks

The authors present arguments for a fast online training algorithm for recurrent neural networks. They present an algorithm that would require O(N/sup 3/) calculations to update the weights in one time step, which is faster than all other known online training algorithms. They formulate the derivations of this algorithm in a variational approach which has the advantage of providing a unified view of the various algorithms that were derived by a number of researchers from very different circumstances. <<ETX>>