Miracle-dz/UniFAR-FTUs huggingface dataset:
Egg envelopes of Armadillidium vulgare (Latreille, 1804) (Crustacea, Isopoda Oniscidea): Ultrastructure and lectins binding

The ultrastructural study carried out on (a) oocytes of Armadillidium vulgare during vitellogenesis, (b) mature eggs taken from the ovaries during the parturial moult of the posterior half of the body, and (c) fertilized eggs collected within a few hours of their release into the brood pouch, has clearly demonstrated that before the fertilization the chorion is the only envelope present in the egg of oniscidean isopods. In the mature eggs, the chorion appears as a uniformly electron‐dense lamina, about 0.4–0.5 µm thick, which does not show any specialized area. A second envelope, described by other authors as vitelline envelope, is formed above the oolemma only right after fertilization and appears separated from the chorion by a space full of liquid. The ways in which the genesis of this envelope is realized are not yet clear; it could be interpreted rather as a fertilization membrane. The investigations carried out with the aid of a battery of FITC‐lectins have highlighted the presence at the chorion surface of unfertilized eggs of various saccharide residues distributed in uniform way. No significant change was observed in the pattern of lectins binding to the chorion of eggs taken from the brood pouch, thus demonstrating how, after the fertilization, no significant rearrangement in the distribution of saccharide residues present on the egg surface occurs in A. vulgare. The ways in which, therefore, the recognition, the binding and the entry of the peculiar sperm of oniscidean isopods into the egg occur, still remain all to be deciphered. Microsc. Res. Tech. 79:792–798, 2016. © 2016 Wiley Periodicals, Inc.
Software Diversity for Improved Network Security: Optimal Distribution of Software-Based Shared Vulnerabilities

Firms, and other agencies, tend to adopt widely used software to gain economic benefits of scale, which can lead to a software monoculture. This can, in turn, involve the risk of correlated computer systems failure as all systems on the network are exposed to the same software-based vulnerabilities. Software diversity has been introduced as a strategy for disrupting such a monoculture and ultimately decreasing the risk of correlated failure. Nevertheless, common vulnerabilities can be shared by different software products. We thus expand software diversity research here and consider shared vulnerabilities between different software alternatives. We develop a combinatorial optimization model of software diversity on a network in an effort to identify the optimal software distribution that best improves network security. We also develop a simulation model of virus propagation based on the susceptible-infected-susceptible model. This model allows calculation of the epidemic threshold, a measure of network re.
The Initial Study of Term Vector Generation Methods for News Summarization

In this paper, I present initial study of new term vector generation methods. The Random Manhattan Indexing and the Skip-gram model were introduced as novel techniques of term vector generation with interesting features. The purpose of this study is to determine whether the methods are suitable for the Summec: A Summarization Engine for Czech. The Summec already use Heuristic, TF-IDF and Latent Semantic Analysis methods for news article summarization. I test quality of generated vectors on the Summec’s evaluation set and compare them with existing summarization methods. The novel summarization meth-ods perform by 2 % worse than the LSA method. The evaluation set contains 50 newspaper articles, each annotated by 15 persons. The ROUGE toolkit is used to compare generated summaries with the human references. The above-mentioned evaluation set and the Summec demo are available online at http://nlp.ite. tul.cz/sumarizace.
Fine-tuning Tumor Immunity with Integrin Trans-regulation

Cantor and colleagues created an α4(S988A) integrin-bearing mouse, which precludes PKA-mediated α4 phosphorylation, and showed that manipulating the signaling properties of α4 integrins can selectively enhance T-cell entry, but not myeloid-cell entry, into B16 melanomas, thereby limiting tumor growth. Inefficient T-cell homing to tissues limits adoptive T-cell immunotherapy of solid tumors. αLβ2 and α4β1 integrins mediate trafficking of T cells into tissues via engagement of ICAM-1 and VCAM-1, respectively. Inhibiting protein kinase A (PKA)–mediated phosphorylation of α4 integrin in cells results in an increase in αLβ2-mediated migration on mixed ICAM-1–VCAM-1 substrates in vitro, a phenomenon termed “integrin trans-regulation. ” Here, we created an α4(S988A)-bearing mouse, which precludes PKA-mediated α4 phosphorylation, to examine the effect of integrin trans-regulation in vivo. The α4(S988A) mouse exhibited a dramatic and selective increase in migration of lymphocytes, but not myeloid cells, to sites of inflammation. Importantly, we found that the α4(S988A) mice exhibited a marked increase in T-cell entry into and reduced growth of B16 melanomas, consistent with antitumor roles of infiltrating T cells and progrowth functions of tumor-associated macrophages. Thus, increased α4 trans-regulation of αLβ2 integrin function biases leukocyte emigration toward lymphocytes relative to myeloid cells and enhances tumor immunity. Cancer Immunol Res; 3(6); 661–7. ©2015 AACR.
Gallic acid attenuates calcium calmodulin‐dependent kinase II‐induced apoptosis in spontaneously hypertensive rats

Hypertension causes cardiac hypertrophy and leads to heart failure. Apoptotic cells are common in hypertensive hearts. Ca2+/calmodulin‐dependent protein kinase II (CaMKII) is associated with apoptosis. We recently demonstrated that gallic acid reduces nitric oxide synthase inhibition‐induced hypertension. Gallic acid is a trihydroxybenzoic acid and has been shown to have beneficial effects, such as anti‐cancer, anti‐calcification and anti‐oxidant activity. The purpose of this study was to determine whether gallic acid regulates cardiac hypertrophy and apoptosis in essential hypertension. Gallic acid significantly lowered systolic and diastolic blood pressure in spontaneously hypertensive rats (SHRs). Wheat germ agglutinin (WGA) and H&E staining revealed that gallic acid reduced cardiac enlargement in SHRs. Gallic acid treatment decreased cardiac hypertrophy marker genes, including atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP), in SHRs. The four isoforms, α, β, δ and γ, of CaMKII were increased in SHRs and were significantly reduced by gallic acid administration. Gallic acid reduced cleaved caspase‐3 protein as well as bax, p53 and p300 mRNA levels in SHRs. CaMKII δ overexpression induced bax and p53 expression, which was attenuated by gallic acid treatment in H9c2 cells. Gallic acid treatment reduced DNA fragmentation and the TUNEL positive cells induced by angiotensin II. Taken together, gallic acid could be a novel therapeutic for the treatment of hypertension through suppression of CaMKII δ‐induced apoptosis.
Advanced text authorship detection methods and their application to biblical texts

Authorship attribution has a range of applications in a growing number of fields such as forensic evidence, plagiarism detection, email filtering, and web information management. In this study, three attribution techniques are extended, tested on a corpus of English texts, and applied to a book in the New Testament of disputed authorship. The word recurrence interval based method compares standard deviations of the number of words between successive occurrences of a keyword both graphically and with chi-squared tests. The trigram Markov method compares the probabilities of the occurrence of words conditional on the preceding two words to determine the similarity between texts. The third method extracts stylometric measures such as the frequency of occurrence of function words and from these constructs text classification models using multiple discriminant analysis. The effectiveness of these techniques is compared. The accuracy of the results obtained by some of these extended methods is higher than many of the current state of the art approaches. Statistical evidence is presented about the authorship of the selected book from the New Testament.
4-Phenylbutyrate Attenuates the ER Stress Response and Cyclic AMP Accumulation in DYT1 Dystonia Cell Models

Dystonia is a neurological disorder in which sustained muscle contractions induce twisting and repetitive movements or abnormal posturing. DYT1 early-onset primary dystonia is the most common form of hereditary dystonia and is caused by deletion of a glutamic acid residue (302/303) near the carboxyl-terminus of encoded torsinA. TorsinA is localized primarily within the contiguous lumen of the endoplasmic reticulum (ER) and nuclear envelope (NE), and is hypothesized to function as a molecular chaperone and an important regulator of the ER stress-signaling pathway, but how the mutation in torsinA causes disease remains unclear. Multiple lines of evidence suggest that the clinical symptoms of dystonia result from abnormalities in dopamine (DA) signaling, and possibly involving its down-stream effector adenylate cyclase that produces the second messenger cyclic adenosine-3′, 5′-monophosphate (cAMP). Here we find that mutation in torsinA induces ER stress, and inhibits the cyclic adenosine-3′, 5′-monophosphate (cAMP) response to the adenylate cyclase agonist forskolin. Both defective mechanins are corrected by the small molecule 4-phenylbutyrate (4-PBA) that alleviates ER stress. Our results link torsinA, the ER-stress-response, and cAMP-dependent signaling, and suggest 4-PBA could also be used in dystonia treatment. Other pharmacological agents known to modulate the cAMP cascade, and ER stress may also be therapeutic in dystonia patients and can be tested in the models described here, thus supplementing current efforts centered on the dopamine pathway.
Encoding many channels on the same frequency through radio vorticity: first experimental test

We have shown experimentally, in a real-world setting, that it is possible to use two beams of incoherent radio waves, transmitted on the same frequency but encoded in two different orbital angular momentum states, to simultaneously transmit two independent radio channels. This novel radio technique allows the implementation of, in principle, an infinite number of channels in a given, fixed bandwidth, even without using polarization, multiport or dense coding techniques. This paves the way for innovative techniques in radio science and entirely new paradigms in radio communication protocols that might offer a solution to the problem of radio-band congestion.
Vocalization in caterpillars: a novel sound-producing mechanism for insects

ABSTRACT Insects have evolved a great diversity of sound-producing mechanisms largely attributable to their hardened exoskeleton, which can be rubbed, vibrated or tapped against different substrates to produce acoustic signals. However, sound production by forced air, while common in vertebrates, is poorly understood in insects. We report on a caterpillar that ‘vocalizes’ by forcing air into and out of its gut. When disturbed, larvae of the Nessus sphinx hawkmoth (Sphingidae: Amphion floridensis) produce sound trains comprising a stereotyped pattern of long (370 ms) followed by multiple short-duration (23 ms) units. Sounds are emitted from the oral cavity, as confirmed by close-up videos and comparing sound amplitudes at different body regions. Numerical models using measurements of the caterpillar foregut were constructed to test hypotheses explaining sound production. We propose that sound is generated by ring vortices created as air flows through the orifice between two foregut chambers (crop and oesophagus), a mechanism analogous to a whistling kettle. As air flows past the orifice, certain sound frequencies are amplified by a Helmholtz resonator effect of the oesophagus chamber. Long sound units occur during inflation, while short sound units occur during deflation. Several other insects have been reported to produce sounds by forced air, but the aeroacoustic mechanisms of such sounds remain elusive. Our results provide evidence for this mechanism by showing that caterpillars employ mechanisms similar to rocket engines to produce sounds. Highlighted Article: Caterpillars have evolved a novel mechanism of sound production, analogous to vocalization in vertebrates, to ‘shout’ at predators.
DeepDemosaicking: Adaptive Image Demosaicking via Multiple Deep Fully Convolutional Networks

Convolutional neural networks are currently the state-of-the-art solution for a wide range of image processing tasks. Their deep architecture extracts low- and high-level features from images, thus improving the model’s performance. In this paper, we propose a method for image demosaicking based on deep convolutional neural networks. Demosaicking is the task of reproducing full color images from incomplete images formed from overlaid color filter arrays on image sensors found in digital cameras. Instead of producing the output image directly, the proposed method divides the demosaicking task into an initial demosaicking step and a refinement step. The initial step produces a rough demosaicked image containing unwanted color artifacts. The refinement step then reduces these color artifacts using deep residual estimation and multi-model fusion producing a higher quality image. Experimental results show that the proposed method outperforms several existing and state-of-the-art methods in terms of both the subjective and objective evaluations.
Computational Investigation of Ligand Binding to the Peripheral Site in CYP3A4: Conformational Dynamics and Inhibitor Discovery

Human cytochrome P450 3A4 (CYP3A4) is a major drug-metabolizing enzyme responsible for the metabolism of ∼50% of clinically used drugs and is often involved in drug-drug interactions. It exhibits atypical binding and kinetic behavior toward many ligands. Binding of ligands to CYP3A4 is a complex process. Recent studies from both crystallography and biochemistry suggested the existence of a peripheral ligand-binding site at the enzyme surface. However, the stability of the ligand bound at this peripheral site and the possibility of discovering new CYP3A4 ligands based on this site remain unclear. In this study, we employed a combination of molecular docking, multiparalleled molecular dynamics (MD) simulations, virtual screening, and experimental bioassay to investigate these issues. Our results revealed that the binding mode of progesterone (PGS), a substrate of CYP3A4, in the crystal structure was not stable and underwent a significant conformational change. Through Glide docking and MD refinement, it was found that PGS was able to stably bind at the peripheral site via contacts with Phe215, Phe219, Phe220, and Asp214. On the basis of the refined peripheral site, virtual screening was then performed against the Enamine database. A total of three compounds were finally found to have inhibitory activity against CYP3A4 in both human liver microsome and recombinant human CYP3A4 enzyme assays, one of which showed potent inhibitory activity with IC50 lower than 1 μM and two of which exhibited moderate inhibitory activity with IC50 values lower than 10 μM. The findings not only presented the dynamic behavior of PGS at the peripheral site but also demonstrated the first indication of discovering CYP3A4 inhibitors based on the peripheral site.
Electrical Detection of Pneumococcus through the Nanoparticle Decoration Method

A simple method of nanoparticle decoration can be used in the detection of pneumococcus. After the pneumococcal bacteria were captured by an antibody (pneumococcal C-polysaccharide (PnC) antibody) between the interdigitated electrodes, the gold nanoparticles conjugated with the PnC antibodies were let to bind onto an outer membrane of the bacteria. Upon successfully dense decoration, the bacteria surface will become conductive owing to the metal nanoparticles, and a distinctive conductance change between the electrodes can be observed. Since this success ratio, or the probability of the conductance change, reflects the concentration of the analyte, a number of repeated measurements can be used in the quantification of the bacteria. In this way, we have successfully detected S. pneumoniae in the range of 10–108 CFU/mL. The limit of detection in this work is lower than that in the commercial detection kit. We hope that the nanoparticle decoration method will play a role in the facile detection of various bacteria.
Dynamic memory disambiguation in the presence of out-of-order store issuing

With the help of the memory dependence predictor the instruction scheduler can speculatively issue load instructions at the earliest possible time without causing significant amounts of memory order violations. For maximum performance, the scheduler must also allow full out-of-order issuing of store instructions since any superfluous ordering of stores results in false memory dependencies which adversely affect the timely issuing of dependent loads. Unfortunately, simple techniques of detecting memory order violations do not work well when store instructions issue out-of-order since they yield many false memory order violations. By using a novel memory order violation detection mechanism that is employed in the retire logic of the processor and delaying the checking for memory order violations, we are able to allow full out-of-order issuing of store instructions without causing false memory order violations. In addition, our mechanism can take advantage of data value redundancy. We present an implementation of our technique using the store set memory dependence predictor. An out-of-order superscalar processor that uses our technique delivers an IPC which is within 100, 96 and 85% of a processor equipped with an ideal memory disambiguator at issue widths of 8, 16 and 32 instructions respectively.
Effects of a Continuous Care Model on Patients’ Knowledge and Health-Related Quality of Life in Systemic Lupus Erythematosus

Purpose: The purpose of this study was to evaluate the effects of applying the continuous care model (CCM) on the knowledge level and health-related quality of life (HRQoL) of systemic lupus erythematosus (SLE) patients and their perceptions of family awareness about the disease. Design: The Continuous Care Model (CCM) was implemented for 3 months on 34 SLE patients, in a pretest–posttest quasiexperimental design. Methods: Two sets of questionnaires were designed for knowledge assessment. HRQoL was assessed by SF-36 questionnaires. Analysis was by paired t test and one-way ANOVA. Findings: The continuous care model significantly improved patients’ knowledge level and their perceptions of their family members’ awareness of their disease. HRQoL status in SLE patients was poorer than the general population in six of eight SF-36 scales (p < .05), except for Bodily Pain and Mental Health. Postintervention scores showed improvement in six SF-36 scales (p < .001), except for Bodily Pain and Social Functioning. Conclusions: Our results underlined the advantages of applying the CCM as a comprehensive method of self-care in SLE. Clinical Relevance: Despite many improvements in SLE care, the patients’ quality of life is still much affected by SLE. Implementation of the CCM could lead to improvement in the knowledge and HRQoL of SLE patients.
Estimation of temporospatial boundary conditions using a particle swarm optimisation technique

In this paper, we present an inverse solver for the estimation of the temporospatial heat transfer coefficients (HTCs) without using prior information of the thermal boundary conditions. The particle swarm optimisation (PSO) method has been introduced to recover the unknown HTC function obtained during immersion quenching. The HTC obtained on the surfaces of a cylindrical work piece is aimed to estimate by using cooling curves recorded internal thermocouples. The fitness function to be minimised by the PSO approach is defined by the deviation of the measured and the calculated cooling curves. The PSO algorithm has been parallelised and implemented on the graphics processing unit (GPU) architecture. The method is tested and evaluated by using hypothetical HTC function on a 2D axis symmetrical heat transfer model. The proposed approach provide significant acceleration of computation and accurate estimation.
Silicon Nanomaterials for Biosensing and Bioimaging Analysis

Biochemical analysis in reliable, low-toxicity, and real-time manners are essentially important for exploring and unraveling biological events and related mechanisms. Silicon nanomaterial-based sensors and probes have potentiality to satisfy the above-mentioned requirements. Herein, we present an overview of the recent significant improvement in large-scale and facile synthesis of high-quality silicon nanomaterials and the research progress of biosensing and bioimaging analysis based on silicon nanomaterials. We especially illustrate the advanced applications of silicon nanomaterials in the field of ultrasensitive biomolecular detection and dynamic biological imaging analysis, with a focus on real-time and long-term detection. In the final section of this review, we discuss the major challenges and promising development in this domain.
The association between serum uric acid and blood pressure in different age groups in a healthy Chinese cohort

Abstract High serum uric acid (sUA) has been reported to be a risk factor for hypertension however, whether this is the case for all age groups is not clear. We examined the association between sUA concentrations and systolic and diastolic blood pressure (SBP and DBP) in different age groups in a cohort of healthy Chinese participants. A total of 1082 healthy participants aged from 41 to 70 years were included. sUA concentration was measured by the uricase-peroxidase method. SBP and DBP were assessed using mercury sphygmomanometry. Hypertension was defined as SBP ≥140 mm Hg or DBP ≥90 mm Hg. Hyperuricemia (HUA) was defined as sUA concentration of >7 mg/dL in men and >6 mg/dL in women. The association between sUA concentration and SBP and DBP was examined using Pearson's correlation test, multivariate linear regression, and logistic regression analysis. The prevalence of hypertension and HUA increased with age (P < .001). Hypertension was more common in participants that had HUA than in those that did not (38.95% vs 30.16%, P = .02). Higher sUA was significantly associated with higher SBP and DBP in the 41- to 50-year-old participants (SBP, &bgr; = 0.35, P < .001; DBP, &bgr; = .29, P < .001; after adjustment for age, sex, total cholesterol, estimated glomerular filtration rate, and fasting plasma glucose). HUA was also a risk factor for hypertension in this age group (odds ratio 1.425, 95% confidence interval, 1.217–1.668, P < .001). There was no association between sUA concentration and SBP and DBP in the other age groups. In this population of healthy Chinese participants, sUA concentration was positively associated with hypertension only in the 41- to 50-year-old group. Lowering uric acid in this age group may help to reduce the incidence of hypertension.
A Biocompatible Near-Infrared 3D Tracking System

A fundamental challenge in soft-tissue surgery is that target tissue moves and deforms, becomes occluded by blood or other tissue, and is difficult to differentiate from surrounding tissue. We developed small biocompatible near-infrared fluorescent (NIRF) markers with a novel fused plenoptic and NIR camera tracking system, enabling 3D tracking of tools and target tissue while overcoming blood and tissue occlusion in the uncontrolled, rapidly changing surgical environment. In this work, we present the tracking system and marker design and compare tracking accuracies to standard optical tracking methods using robotic experiments. At speeds of 1 mm/s, we observe tracking accuracies of 1.61 mm, degrading only to 1.71 mm when the markers are covered in blood and tissue.