Miracle-dz/UniFAR-FTUs huggingface dataset:
A Highly Conserved Poc1 Protein Characterized in Embryos of the Hydrozoan Clytia hemisphaerica: Localization and Functional Studies

Poc1 (Protein of Centriole 1) proteins are highly conserved WD40 domain-containing centriole components, well characterized in the alga Chlamydomonas, the ciliated protazoan Tetrahymena, the insect Drosophila and in vertebrate cells including Xenopus and zebrafish embryos. Functions and localizations related to the centriole and ciliary axoneme have been demonstrated for Poc1 in a range of species. The vertebrate Poc1 protein has also been reported to show an additional association with mitochondria, including enrichment in the specialized “germ plasm” region of Xenopus oocytes. We have identified and characterized a highly conserved Poc1 protein in the cnidarian Clytia hemisphaerica. Clytia Poc1 mRNA was found to be strongly expressed in eggs and early embryos, showing a punctate perinuclear localization in young oocytes. Fluorescence-tagged Poc1 proteins expressed in developing embryos showed strong localization to centrioles, including basal bodies. Anti-human Poc1 antibodies decorated mitochondria in Clytia, as reported in human cells, but failed to recognise endogenous or fluorescent-tagged Clytia Poc1. Injection of specific morpholino oligonucleotides into Clytia eggs prior to fertilization to repress Poc1 mRNA translation interfered with cell division from the blastula stage, likely corresponding to when neosynthesis normally takes over from maternally supplied protein. Cell cycle lengthening and arrest were observed, phenotypes consistent with an impaired centriolar biogenesis or function. The specificity of the defects could be demonstrated by injection of synthetic Poc1 mRNA, which restored normal development. We conclude that in Clytia embryos, Poc1 has an essentially centriolar localization and function.
CD8 Epitope Escape and Reversion in Acute HCV Infection

In the setting of acute hepatitis C virus (HCV) infection, robust HCV-specific CD8+ cytotoxic T lymphocyte (CTL) responses are associated with initial control of viremia. Despite these responses, 70–80% of individuals develop persistent infection. Although viral escape from CD8 responses has been illustrated in the chimpanzee model of HCV infection, the effect of CD8 selection pressure on viral evolution and containment in acute HCV infection in humans remains unclear. Here, we examined viral evolution in an immunodominant human histocompatibility leukocyte antigen (HLA)-B8–restricted NS3 epitope in subjects with acute HCV infection. Development of mutations within the epitope coincided with loss of strong ex vivo tetramer and interferon γ enzyme-linked immunospot responses, and endogenous expression of variant NS3 sequences suggested that the selected mutations altered processing and presentation of the variant epitope. Analysis of NS3 sequences from 30 additional chronic HCV-infected subjects revealed a strong association between sequence variation within this region and expression of HLA-B8, supporting reproducible allele-specific selection pressures at the population level. Interestingly, transmission of an HLA-B8–associated escape mutation to an HLA-B8 negative subject resulted in rapid reversion of the mutation. Together, these data indicate that viral escape from CD8+ T cell responses occurs during human HCV infection and that acute immune selection pressure is of sufficient magnitude to influence HCV evolution.
Buzzwords in Females’ Ears? The Use of Buzz Songs in the Communication of Nightingales (Luscinia megarhynchos)

Differences in individual male birds’ singing may serve as honest indicators of male quality in male-male competition and female mate choice. This has been shown e.g. for overall song output and repertoire size in many bird species. More recently, differences in structural song characteristics such as the performance of physically challenging song components were analysed in this regard. Here we show that buzz elements in the song of nightingales (Luscinia megarhynchos) hold the potential to serve as indicators of male quality and may therefore serve a communicative function. Buzzes were produced with considerable differences between males. The body weight of the males was correlated with one measure of these buzzes, namely the repetition rate of the buzz subunits, and individuals with larger repertoires sang buzzes at higher subunit-rates. A model of buzz performance constraints suggested that buzzes were sung with different proficiencies. In playback experiments, female nightingales showed more active behaviour when hearing buzz songs. The results support the idea that performance differences in the acoustic fine structure of song components are used in the communication of a large repertoire species such as the nightingale.
Satellite-Based Spatiotemporal Trends in PM2.5 Concentrations: China, 2004–2013

Background Three decades of rapid economic development is causing severe and widespread PM2.5 (particulate matter ≤ 2.5 μm) pollution in China. However, research on the health impacts of PM2.5 exposure has been hindered by limited historical PM2.5 concentration data. Objectives We estimated ambient PM2.5 concentrations from 2004 to 2013 in China at 0.1° resolution using the most recent satellite data and evaluated model performance with available ground observations. Methods We developed a two-stage spatial statistical model using the Moderate Resolution Imaging Spectroradiometer (MODIS) Collection 6 aerosol optical depth (AOD) and assimilated meteorology, land use data, and PM2.5 concentrations from China’s recently established ground monitoring network. An inverse variance weighting (IVW) approach was developed to combine MODIS Dark Target and Deep Blue AOD to optimize data coverage. We evaluated model-predicted PM2.5 concentrations from 2004 to early 2014 using ground observations. Results The overall model cross-validation R2 and relative prediction error were 0.79 and 35.6%, respectively. Validation beyond the model year (2013) indicated that it accurately predicted PM2.5 concentrations with little bias at the monthly (R2 = 0.73, regression slope = 0.91) and seasonal (R2 = 0.79, regression slope = 0.92) levels. Seasonal variations revealed that winter was the most polluted season and that summer was the cleanest season. Analysis of predicted PM2.5 levels showed a mean annual increase of 1.97 μg/m3 between 2004 and 2007 and a decrease of 0.46 μg/m3 between 2008 and 2013. Conclusions Our satellite-driven model can provide reliable historical PM2.5 estimates in China at a resolution comparable to those used in epidemiologic studies on the health effects of long-term PM2.5 exposure in North America. This data source can potentially advance research on PM2.5 health effects in China. Citation Ma Z, Hu X, Sayer AM, Levy R, Zhang Q, Xue Y, Tong S, Bi J, Huang L, Liu Y. 2016. Satellite-based spatiotemporal trends in PM2.5 concentrations: China, 2004–2013. Environ Health Perspect 124:184–192; http://dx.doi. org/10.1289/ehp.1409481
Butyrated ManNAc analog improves protein expression in Chinese hamster ovary cells

The chemical additive sodium butyrate (NaBu) has been applied in cell culture media as a direct and convenient method to increase the protein expression in Chinese hamster ovary (CHO) and other mammalian cells. In this study, we examined an alternative chemical additive, 1,3,4‐O‐Bu3ManNAc, for its effect on recombinant protein production in CHO. Supplementation with 1,3,4‐O‐Bu3ManNAc for two stable CHO cell lines, expressing human erythropoietin or IgG, enhanced protein expression for both products with negligible impact on cell growth, viability, glucose utilization, and lactate accumulation. In contrast, sodium butyrate treatment resulted in a ∼20% decrease in maximal viable cell density and ∼30% decrease in cell viability at the end of cell cultures compared to untreated or 1,3,4‐O‐Bu3ManNAc treated CHO cell lines for both products. While NaBu treatment enhanced product yields more than the 1,3,4‐O‐Bu3ManNAc treatment, the NaBu treated cells also exhibited higher levels of caspase 3 positive cells using microscopy analysis. Furthermore, the mRNA levels of four cell apoptosis genes (Cul2, BAK, BAX, and BCL2L11) were up‐regulated more in sodium butyrate treated wild‐type, erythropoietin, or IgG expressing CHO‐K1 cell lines while most of the mRNA levels of apoptosis genes in 1,3,4‐O‐Bu3ManNAc treated cell lines remained equal or increased only slightly compared to the levels in untreated CHO cell lines. Finally, lectin blot analysis revealed that the 1,3,4‐O‐Bu3ManNAc‐treated cells displayed higher relative sialylation levels on recombinant EPO, consistent with the effect of the ManNAc component of this additive, compared to control while NaBu treatment led to lower sialylation levels than control, or 1,3,4‐O‐Bu3ManNAc‐treatment. These findings demonstrate that 1,3,4‐O‐Bu3ManNAc has fewer negative effects on cell cytotoxicity and apoptosis, perhaps as a result of a more deliberate uptake and release of the butyrate compounds, while simultaneously increasing the expression of multiple recombinant proteins, and improving the glycosylation characteristics when applied at comparable molarity levels to NaBu. Thus, 1,3,4‐O‐Bu3ManNAc represents a highly promising media additive alternative in cell culture for improving protein yields without sacrificing cell mass and product quality in future bioproduction processes.
Probiotics: A Promising Role in Dental Health

Probiotics have a role in maintaining oral health through interaction with oral microbiome, thus contributing to healthy microbial equilibrium. The nature and composition of any individual microbiome impacts the general health, being a major contributor to oral health. The emergence of drug resistance and the side effects of available antimicrobials have restricted their use in an array of prophylactic options. Indeed, some new strategies to prevent oral diseases are based on manipulating oral microbiota, which is provided by probiotics. Currently, no sufficient substantial evidence exists to support the use of probiotics to prevent, treat or manage oral cavity diseases. At present, probiotic use did not cause adverse effects or increased risks of caries or periodontal diseases. This implicates no strong evidence against treatment using probiotics. In this review, we try to explore the use of probiotics in prevention, treatment and management of some oral cavity diseases and the possibilities of developing designer probiotics for the next generation of oral and throat complimentary healthcare.
A Novel Task for the Investigation of Action Acquisition

We present a behavioural task designed for the investigation of how novel instrumental actions are discovered and learnt. The task consists of free movement with a manipulandum, during which the full range of possible movements can be explored by the participant and recorded. A subset of these movements, the ‘target’, is set to trigger a reinforcing signal. The task is to discover what movements of the manipulandum evoke the reinforcement signal. Targets can be defined in spatial, temporal, or kinematic terms, can be a combination of these aspects, or can represent the concatenation of actions into a larger gesture. The task allows the study of how the specific elements of behaviour which cause the reinforcing signal are identified, refined and stored by the participant. The task provides a paradigm where the exploratory motive drives learning and as such we view it as in the tradition of Thorndike [1]. Most importantly it allows for repeated measures, since when a novel action is acquired the criterion for triggering reinforcement can be changed requiring a new action to be discovered. Here, we present data using both humans and rats as subjects, showing that our task is easily scalable in difficulty, adaptable across species, and produces a rich set of behavioural measures offering new and valuable insight into the action learning process.
Catching Worms, Trojan Horses and PUPs: Unsupervised Detection of Silent Delivery Campaigns

The growing commoditization of the underground economy has given rise to malware delivery networks, which charge fees for quickly delivering malware or unwanted software to a large number of hosts. To provide this service, a key method is the orchestration of silent delivery campaigns, which involve a group of downloaders that receive remote commands and that deliver their payloads without any user interaction. These campaigns have not been characterized systematically, unlike other aspects of malware delivery networks. Moreover, silent delivery campaigns can evade detection by relying on inconspicuous downloaders on the client side and on disposable domain names on the server side. We describe Beewolf, a system for detecting silent delivery campaigns from Internet-wide records of download events. The key observation behind our system is that the downloaders involved in these campaigns frequently retrieve payloads in lockstep. Beewolf identifies such locksteps in an unsupervised and deterministic manner. By exploiting novel techniques and empirical observations, Beewolf can operate on streaming data. We utilize Beewolf to study silent delivery campaigns at scale, on a data set of 33.3 million download events. This investigation yields novel findings, e.g. malware distributed through compromised software update channels, a substantial overlap between the delivery ecosystems for malware and unwanted software, and several types of business relationships within these ecosystems. Beewolf achieves over 92% true positives and fewer than 5% false positives. Moreover, Beewolf can detect suspicious downloaders a median of 165 days ahead of existing anti-virus products and payload-hosting domains a median of 196 days ahead of existing blacklists.
Coupling proofs are probabilistic product programs

Couplings are a powerful mathematical tool for reasoning about pairs of probabilistic processes. Recent developments in formal verification identify a close connection between couplings and pRHL, a relational program logic motivated by applications to provable security, enabling formal construction of couplings from the probability theory literature. However, existing work using pRHL merely shows existence of a coupling and does not give a way to prove quantitative properties about the coupling, needed to reason about mixing and convergence of probabilistic processes. Furthermore, pRHL is inherently incomplete, and is not able to capture some advanced forms of couplings such as shift couplings. We address both problems as follows. First, we define an extension of pRHL, called x-pRHL, which explicitly constructs the coupling in a pRHL derivation in the form of a probabilistic product program that simulates two correlated runs of the original program. Existing verification tools for probabilistic programs can then be directly applied to the probabilistic product to prove quantitative properties of the coupling. Second, we equip x-pRHL with a new rule for while loops, where reasoning can freely mix synchronized and unsynchronized loop iterations. Our proof rule can capture examples of shift couplings, and the logic is relatively complete for deterministic programs. We show soundness of x-PRHL and use it to analyze two classes of examples. First, we verify rapid mixing using different tools from coupling: standard coupling, shift coupling, and path coupling, a compositional principle for combining local couplings into a global coupling. Second, we verify (approximate) equivalence between a source and an optimized program for several instances of loop optimizations from the literature.
Evaluation of Endocrine Late Complications in Childhood Acute Lymphoblastic Leukemia Survivors: A Report of a Single-Center Experience and Review of the Literature

Objective: Improvement in long-term survival in patients with acute lymphoblastic leukemia (ALL) in childhood has led to the need for monitorization of treatment-related morbidity and mortality. In the current study, we aimed to evaluate endocrine side effects of treatment in ALL survivors who were in remission for at least 2 years. Materials and Methods: Sixty patients diagnosed with ALL, who were in remission for at least 2 years, were cross-sectionally evaluated for long-term endocrine complications. Results: The median age of the patients at the time of diagnosis, at the time of chemotherapy completion, and at the time of the study was 5 years (minimum-maximum: 1.7-13), 8 years (minimum-maximum: 4.25-16), and 11.7 years (minimum-maximum: 7-22), respectively, and median follow-up time was 4 years (minimum-maximum: 2-10.1). At least one complication was observed in 81.6% of patients. Vitamin D insufficiency/deficiency (46.6%), overweight/obesity (33.3%), and dyslipidemia (23.3%) were the three most frequent endocrine complications. Other complications seen in our patients were hyperparathyroidism secondary to vitamin D deficiency (15%), insulin resistance (11.7%), hypertension (8.3%), short stature (6.7%), thyroid function abnormality (5%), precocious puberty (3.3%), and decreased bone mineral density (1.7%). There were no statistically significant correlations between endocrine complications and age, sex, and radiotherapy, except vitamin D insufficiency/deficiency, which was significantly more frequent in pubertal ALL survivors compared to prepubertal ALL survivors (57.5% and 25%, respectively, p=0.011). Conclusion: A high frequency of endocrine complications was observed in the current study. The high frequency of late effects necessitates long-term surveillance of this population to better understand the incidence of late-occurring events and the defining of high-risk features that can facilitate developing intervention strategies for early detection and prevention.
Guidelines for Diagnosis and Management of Beta-Thalassemia Intermedia

Beta-thalassemia intermedia (β-TI) is a genetic variant of beta-thalassemias with a clinical disorder whose severity falls between thalassemia minor and thalassemia major. Different genetic defects are involved in this disorder and, based on severity of disease, clinical complications like skeletal deformities and growth retardation, splenomegaly, extramedullary hematopoiesis, heart failure, and endocrine disorders may be present in untreated patients. Precise diagnosis and management are essential in these patients for prevention of later clinical complications. Diagnosis of TI is based on clinical and laboratory data. There are some treatment strategies like modulation of gamma-globulin chain production with hydroxyurea or other drugs, transfusion, splenectomy, and stem cell transplantation. Iron chelation therapy is also needed in many of these patients even if they are not transfused. The aim of this manuscript is to review the clinical manifestations, complications, genetic defects, and unmet treatments needs in TI.
Structural persistence of three dimensional autonomous formations

Built upon a recently developed theoretical framework, we consider some practical issues raised in multi-agent formation control in three dimensional space. We introduce the partial equilibrium problem, which is associated with unsafe control of a formation in practical 3-dimensional applications. We define structurally persistent graphs, a class of persistent graphs free of any partial equi- librium problem. In real deployment of control of multi-agent systems, forma- tions with underlying structurally persistent graphs are of interest. We study the connections between the allocation of degrees of freedom (DOFs) across agents and the characteristics of persistence and/or structural persistence of a directed graph. We also show how to transfer degrees of freedom between agents, when the formation changes with new agent(s) added, to preserve persistence and/or structural persistence
Origin of the plasticity in bulk amorphous alloys

Unlike the dislocation-based plasticity in crystalline metals, which can be readily explained by their crystal structure and the presence of defects, the nature of the plasticity in amorphous alloys is not completely understood. Experiments have shown that the plasticity in amorphous alloys is strongly dependent on their atomic packing density. This study, based on the combination of experimental and computational techniques, examines the origin of the plasticity in amorphous alloys considering characteristics of the inherent atomic-scale structure as defined by short-range ordered (SRO) clusters. The role of various SRO atomic clusters in creating free volume during shear deformation is discussed. We report that the plasticity exhibited by amorphous alloys is very sensitive to the characteristics of the atomic packing state, which can be described by various SRO atomic structures and quantified by the effective activation energy for crystallization.
Universal Power Law Behavior of the AC Conductivity Versus Frequency of Agglomerate Morphologies in Conductive Carbon Nanotube-Reinforced Epoxy Networks

The Jonscher universal power law for ac conductivity versus frequency (f = ω/2π) in the dispersion region was tested for a multiwall carbon nanotube/epoxy nanocomposite. The effect of changes in agglomerate morphology on the fitting parameters A and n in the equation σac = Aωn was investigated. Changing nanotube agglomerate morphology was tracked by optical microscopy through curing. Evolving morphology was compared alongside ac conductivity obtained via a broadband dielectric spectrometer to elucidate possible physical meaning of the universal power law in the context of this system. The −logA/n was unaffected by changes in agglomerate morphology affected during cure, yet connected with each other in their dependence on temperature. For this system, the relationship between the fitting parameters in the universal dynamic response equation remains empirical at this stage with regard to biphasic “texture” or morphology within such a network. Electrical conductivity σ versus frequency ω for a composite consisting of agglomerated multiwalled carbon nanotubes dispersed throughout a cured epoxy matrix was discovered to follow the empirical universal dynamic response equation of Jonscher. The frequency behavior of the exponent n is discussed in terms of underlying morphology throughout which charge carriers migrate. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 1918–1923
Unsupervised Learning of Deep Feature Representation for Clustering Egocentric Actions

Popularity of wearable cameras in life logging, law enforcement, assistive vision and other similar applications is leading to explosion in generation of egocentric video content. First person action recognition is an important aspect of automatic analysis of such videos. Annotating such videos is hard, not only because of obvious scalability constraints, but also because of privacy issues often associated with egocentric videos. This motivates the use of unsupervised methods for egocentric video analysis. In this work, we propose a robust and generic unsupervised approach for first person action clustering. Unlike the contemporary approaches, our technique is neither limited to any particular class of action nor requires priors such as pre-training, fine-tuning, etc. We learn time sequenced visual and flow features from an array of weak feature extractors based on convolutional and LSTM autoencoder networks. We demonstrate that clustering of such features leads to the discovery of semantically meaningful actions present in the video. We validate our approach on four disparate public egocentric actions datasets amounting to approximately 50 hours of videos. We show that our approach surpasses the supervised state of the art accuracies without using the action labels.