Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymorphism in biomineral nanoparticles

Biomineralisation is the process by which living things produce hard mineral tissues with unique physical properties. The study of this process can help us produce biomimetic materials, reproducing such properties, with the study of nucleation and crystallisation of the materials being particularly important. I have used molecular simulation techniques to help gain a greater understanding of these processes, focussing particularly on identifying the conformations and solid phases available to nanoparticles of two biomineral compounds. The bones and teeth of mammals are made largely of calcium phosphates. I have used metadynamics to study nanoparticles of tricalcium phosphate (TCP) and have identified high and lower order configurations. To facilitate this work I reviewed the extant empirical potentials for calcium phosphate systems, selecting the most appropriate for TCP. Calcium carbonate, found in examples throughout the animal kingdom, has three crystalline polymorphs relevant to biomineralisation: calcite, aragonite and vaterite. While nanoparticles of calcite have been extensively studied the other polymorphs have been neglected to date. In this work I present a technique for predicting crystalline morphologies for all three polymorphs across a range of sizes, and compare the energetic ordering. In water the energetic ordering of the nanoparticles is heavily dependent on nanoparticle size. Furthermore, I present work calculating the surface enthalpies of a variety of calcium carbonate surfaces, many of which are negative. It appears that entropic penalty of ordered water is key to understanding the stability of nanocrystals. Also presented is an application of the nudged elastic band method to study transitions between nanoparticle crystal conformations. Between all three crystal polymorphs the nanoparticles passed through an amorphous region of phase space. These results have also been used to evaluate order parameters for use in metadynamics simulations.
Quadrocopter performance benchmarking using optimal control

A numerical method for computing quadrocopter maneuvers between two states is presented. Computed maneuvers satisfy Pontryagin's minimum principle with respect to time-optimality. First, in order to obtain the structure of time-optimal maneuvers, we apply the minimum principle to a first-principles, two-dimensional quadrotor model. Then we present a numerical algorithm that enables the computation of maneuvers for arbitrary initial and final states. The developed method is used to compute a set of maneuvers, which are discussed and demonstrated experimentally in the ETH Zurich Flying Machine Arena testbed.
Activating Transcription Factor 3-mediated Chemo-intervention with Cancer Chemokines in a Noncanonical Pathway under Endoplasmic Reticulum Stress*

Background: Cancer-favoring ER stress responses drive proinflammatory programs including cancer chemokine production. Results: ER stress-induced cancer chemokines are regulated by preventive exposure to a natural flavone apigenin via ATF3. Conclusion: ATF3 epigenetically suppresses expression of EGR-1, a noncanonical proinflammatory transcriptional modulator crucial to cancer chemokine induction. Significance: ATF3-mediated chemokine suppression implicates a novel chemo-intervention with ER stress response-related tumorigenesis. The cell-protective features of the endoplasmic reticulum (ER) stress response are chronically activated in vigorously growing malignant tumor cells, which provide cellular growth advantages over the adverse microenvironment including chemotherapy. As an intervention with ER stress responses in the intestinal cancer cells, preventive exposure to flavone apigenin potentiated superinduction of a regulatory transcription factor, activating transcription factor 3 (ATF3), which is also known to be an integral player coordinating ER stress response-related gene expression. ATF3 superinduction was due to increased turnover of ATF3 transcript via stabilization with HuR protein in the cancer cells under ER stress. Moreover, enhanced ATF3 caused inhibitory action against ER stress-induced cancer chemokines that are potent mediators determining the survival and metastatic potential of epithelial cancer cells. Although enhanced ATF3 was a negative regulator of the well known proinflammatory transcription factor NF-κB, blocking of NF-κB signaling did not affect ER stress-induced chemokine expression. Instead, immediately expressed transcription factor early growth response protein 1 (EGR-1) was positively involved in cancer chemokine induction by ER stressors. ER stress-induced EGR-1 and subsequent chemokine production were repressed by ATF3. Mechanistically, ATF3 directly interacted with and recruited HDAC1 protein, which led to epigenetic suppression of EGR-1 expression and subsequent chemokine production. Conclusively, superinduced ATF3 attenuated ER stress-induced cancer chemokine expression by epigenetically interfering with induction of EGR-1, a transcriptional modulator crucial to cancer chemokine production. Thus, these results suggest a potent therapeutic intervention of ER stress response-related cancer-favoring events by ATF3.
Chalcone derivatives as potential antifungal agents: Synthesis, and antifungal activity

Much research has been carried out with the aim to discover the therapeutic values of chalcone derivatives. Chalcones possess wide range of pharmacological activity such as antibacterial, antimalarial, antiprotozoal, antitubercular, anticancer, and antifungal agents etc. The presence of reactive α,β-unsaturated keto group in chalcones is found to be responsible for their biological activity. The rapid developments of resistance to antifungal agents, led to design, and synthesize the new antifungal agents. The derivatives of chalcones were prepared using Claisen-Schmidt condensation scheme with appropriate tetralone and aldehyde derivatives. Ten derivatives were synthesized and were biologically screened for antifungal activity. The newly synthesized derivatives of chalcone showed antifungal activity against fungal species, Microsporum gypseum. The results so obtained were superior or comparable to ketoconazole. It was observed that none of the compounds tested showed positive results for fungi Candida albicans nor against fungi Aspergillus niger. Chalcone derivatives showed inhibitory effect against M. gypseum species of fungus. It was found that among the chalcone derivatives so synthesized, two of them, that is, 4-chloro derivative, and unsubstituted derivative of chalcone showed antifungal activity superior to ketoconazole. Thus, these can be the potential new molecule as antifungal agent.
Automatic Reproducible Crash Detection

Crash reproduction, which spends much time of developers in reading and understanding source code, is a crucial yet time-consuming task in program debugging. To reduce the time and resource cost, automatic techniques of test generation have been proposed. These techniques aim to automatically generate test cases to reproduce the scenario of a crashed project. Unfortunately, due to the lack of a detailed comprehension of the source code, a generated test case may fail in reproducing an expected crash. In this paper, we propose an automatic approach to reproducible bug detection. This approach predicts whether a crash is difficult to reproduce or not via training a classifier based on historical reproducible crash data. If a crash is difficult to reproduce, it is better to assign the crash to a developer, instead of using an automatic technique of test generation. Our work can help to prioritize crashes and to save the cost of developers. Preliminary experiments show that our approach effectively detects reproducible crashes via evaluating 45 crashes.
Efficient Recognition of Authentic Dynamic Facial Expressions on the Feedtum Database

In order to allow for fast recognition of a user's affective state we discuss innovative holistic and self organizing approaches for efficient facial expression analysis. The feature set is thereby formed by global descriptors and MPEG based DCT coefficients. In view of subsequent classification we compare modeling by pseudo multidimensional hidden Markov models and support vector machines. Within the latter case super-vectors are constructed based on sequential floating search methods. Extensive test-runs as a proof of concept are carried out on our publicly available FEEDTUM database consisting of elicited spontaneous emotions of 18 subjects within the MPEG-4 emotion-set plus added neutrality. Maximum recognition performance reaches the benchmark-rate gained by a human perception test with 20 test-persons and manifest the effectiveness of the introduced novel concepts
Individual quality and carotenoid-based plumage ornaments in male red bishops (Euplectes orix): plumage is not all that counts

Males in many bird species develop elaborate carotenoid-based plumage ornaments that play an important role as signals of individual quality in intra- or intersexual selection. In the present study, we investigated which of several factors related to male condition and health affect the brightness and coloration of the carotenoid-based orange-red breeding plumage in males of the red bishop (Euplectes orix), a polygynous and sexually dimorphic weaverbird species. The study revealed a very complex pattern, with the relationships between plumage traits and both heterophil-to-lymphocyte ratio and blood parasite load varying considerably among seasons, suggesting a strong influence of environmental conditions. Furthermore, overall condition of males strongly affected the association pattern between plumage traits and other factors, with males in bad condition being forced to allocate resources away from plumage elaboration to body maintenance or the enhancement of immune functions, whereas males in good condition can afford to invest in plumage ornamentation without obvious detrimental effects on health. Thus, females cannot rely on plumage characteristics alone to gather information on male quality, but have to assess additional traits that advertise general male health status. Perhaps surprisingly, testosterone levels were not related to male plumage characteristics.
MCMC genome rearrangement

MOTIVATION As more and more genomes have been sequenced, genomic data is rapidly accumulating. Genome-wide mutations are believed more neutral than local mutations such as substitutions, insertions and deletions, therefore phylogenetic investigations based on inversions, transpositions and inverted transpositions are less biased by the hypothesis on neutral evolution. Although efficient algorithms exist for obtaining the inversion distance of two signed permutations, there is no reliable algorithm when both inversions and transpositions are considered. Moreover, different type of mutations happen with different rates, and it is not clear how to weight them in a distance based approach. RESULTS We introduce a Markov Chain Monte Carlo method to genome rearrangement based on a stochastic model of evolution, which can estimate the number of different evolutionary events needed to sort a signed permutation. The performance of the method was tested on simulated data, and the estimated numbers of different types of mutations were reliable. Human and Drosophila mitochondrial data were also analysed with the new method. The mixing time of the Markov Chain is short both in terms of CPU times and number of proposals. AVAILABILITY The source code in C is available on request from the author.
Parity logging with reserved space: towards efficient updates and recovery in erasure-coded clustered storage

Many modern storage systems adopt erasure coding to provide data availability guarantees with low redundancy. Log-based storage is often used to append new data rather than overwrite existing data so as to achieve high update efficiency, but introduces significant I/O overhead during recovery due to reassembling updates from data and parity chunks. We propose parity logging with reserved space, which comprises two key design features: (1) it takes a hybrid of in-place data updates and log-based parity updates to balance the costs of updates and recovery, and (2) it keeps parity updates in a reserved space next to the parity chunk to mitigate disk seeks. We further propose a workload-aware scheme to dynamically predict and adjust the reserved space size. We prototype an erasure-coded clustered storage system called CodFS, and conduct testbed experiments on different update schemes under synthetic and real-world workloads. We show that our proposed update scheme achieves high update and recovery performance, which cannot be simultaneously achieved by pure in-place or log-based update schemes.
Aspectual influences on early tense comprehension

This study investigated the ASPECT FIRST HYPOTHESIS which claims that children initially use verbal morphology to mark aspect and not tense. Experiment 1 tested 46 two- and three-year-old children's comprehension of tense as it is marked in the auxiliary system using a sentence-to-scene matching task. Children were presented with multiple performances of the same event and asked where a character is V'ing, was V'ing and is gonna V. Results showed that even the two-year-old children could successfully understand tense in this experiment. Experiment 2 changed the information available in the scenes by varying whether or not the past-time event reached its completion point. Thirty-six two-, three- and four-year-old children participated. The results showed that the two-year-olds could only successfully understand past and present auxiliaries when past-time information in the scenes was co-extensive with completion information in the scenes. This result suggests that these children may be making a grammatical aspect (perfective/imperfective) judgment and not a tense (past/present) judgment, or at least, that grammatical aspect influences tense interpretation for these children.
Model of adaptive RAN formation for heterogeneous mobile network

It is expected that extensive deployment of small cells (SCs) in LTE networks will take place in the near future, especially in dense urban zones. In this paper, we propose a new model of 3-tier heterogeneous radio access network (RAN) based on adaptive structure synthesis method with a combination of deterministic and stochastic geometry. Results show the improvement of peak data rates and energy efficiency depending on load scenarios.
Signal and interference statistics of a CDMA system with feedback power control

A feedback power control approach that allows power commands to be updated at a higher rate than the rate of multipath fading is investigated. The signal and interference statistics as received at the base stations after power control are obtained for a simulated direct-sequence code-division multiple-access (CDMA) system, which includes multiple base stations with diversity receivers and a large number of power-controlled users continuously moving at various speeds. It is shown that often-used analyses based on perfect average power control lead to optimistic capacity results (by 25% to 60%) because interference is underestimated by 1 to 2 dB. <<ETX>>
Modeling Around-the-Clock Price Discovery for Cross-Listed Stocks Using State Space Methods

U.S. trading in non-U.S. stocks has grown dramatically. Around the clock, these stocks trade in the home market, in the U.S. market, and, potentially, in both markets simultaneously. We develop a general methodology based on a state space model to study 24-hour price discovery in a multiple-markets setting. As opposed to the standard variance ratio approach, this model deals naturally with (1) simultaneous quotes in an overlap, (2) missing observations in a nonoverlap, (3) noise due to transitory microstructure effects, and (4) contemporaneous correlation in returns due to market-wide factors. We apply our model to Dutch stocks, cross-listed in the United States. Our findings suggest a minor role for the New York Stock Exchange in price discovery for Dutch shares, in spite of its nontrivial and growing market share.
Na+/Ca2+ Exchanger Maintains Ionic Homeostasis in the Peri-Infarct Area

Background and Purpose— A prominent feature of cerebral ischemia is the excessive intracellular accumulation of both Na+ and Ca2+ ions, which results in subsequent cell death. The plasma membrane Na+/Ca2+ exchanger (NCX), regulates the distribution of these ions acting either in the forward mode or in its reverse mode and it can play a critical role in brain ischemia. However, it is unclear whether the activity of NCX leads to detrimental or beneficial effects. Methods— Extracellular field potentials and whole-cell patch clamp recordings were obtained from rat corticostriatal brain-slice preparations in the peri-infarct area 24 hours after the permanent middle cerebral artery occlusion. Ischemia was induced in rats by permanents middle cerebral artery occlusion. Results— Bepridil, an inhibitor of NCX, reduced in a concentration-dependent manner (IC50=68 &mgr;mol/L) the field potential amplitude recorded from the peri-infarct area of corticostriatal slices. Conversely, no change was observed in sham-operated animals. The effect of bepridil was mimicked by 5-(N-4-chlorobenzyl)-2′,4′-dimethylbenzamil (CB-DMB) (IC50=6 &mgr;mol/L), a more selective inhibitor of NCX. In whole-cell patch clamp experiments, bepridil and CB-DMB caused an inward current in spiny neurons recorded from the peri-infarct area but not in the same cells recorded from controls. Interestingly, cholinergic interneurons recorded from the striatal peri-infarct area did not develop an inward current after the application of NCX inhibitors, suggesting that the electrophysiological alterations induced by NCX inhibition are cell-type specific. Bepridil and CB-DMB also induced a suppression of excitatory synaptic currents in most of spiny neurons recorded from the peri-infarct area. This effect was not coupled to a significant change of paired-pulse facilitation suggesting a postsynaptic site of action. Conclusions— Our data indicate that NCX plays a critical role in the maintenance of ionic homeostasis in the peri-infarct area.
Mini Review Article

Modeling the Mycobacterium tuberculosis granuloma – the critical battlefield in host immunity and disease Granulomas are the hallmark of Mycobacterium tuberculosis (M.tb) infection and thus sit at the center of tuberculosis (TB) immunopathogenesis. TB can result from either early progression of a primary granuloma during the infection process or reactivation of an established granuloma in a latently infected person. Granulomas are compact, organized aggregates of immune cells consisting of blood-derived infected and uninfected macrophages, foamy macrophages, epithelioid cells (uniquely differentiated macrophages), and multinucleated giant cells (Langerhans cells) surrounded by a ring of lymphocytes. The granuloma's main function is to localize and contain M.tb while concentrating the immune response to a limited area. However, complete eradication does not occur since M.tb has its own strategies to persist within the granuloma and to reactivate and escape under certain conditions. Thus M.tb-containing granulomas represent a unique battlefield for dictating both the host immune and bacterial response. The architecture, composition, function, and maintenance of granulomas are key aspects to study since they are expected to have a profound influence on M.tb physiology in this niche. Granulomas are not only present in mycobacterial infections; they can be found in many other infectious and non-infectious diseases and play a crucial role in immunity and disease. Here we review the models currently available to study the granulomatous response to M.tb.
A Carbon Nanoparticle Lymphatic Tracer Protected Parathyroid Glands During Radical Thyroidectomy for Papillary Thyroid Non-Microcarcinoma

The study assessed the role of an activated carbon nanoparticle lymphatic tracer in reducing unintentional damage to the parathyroid glands during thyroidectomy for papillary thyroid non-microcarcinoma diagnosed intraoperatively by cryosections. A total of 103 patients with papillary thyroid non-microcarcinomas diagnosed by intraoperative cryosection were randomly assigned to receive routine radical thyroidectomy or radical thyroidectomy following administration of activated carbon nanoparticle lymphatic tracer to the contralateral thyroid, at the department of Thyroid Surgery, Sun Yat-sen Memorial Hospital (Guangzhou, China), between January 2012 and May 2013. The success of level VI lymphadenectomy and postoperative parathyroid function were compared. Administration of the activated carbon nanoparticle lymphatic tracer did not affect the frequency of recovered lymph nodes containing metastases; however, it did significantly reduce the incidence of permanent and transient hypoparathyroidism from 2 to 0 and 18 to 6, and reduced the mean recovery time for transient hypoparathyroidism from 57.0 days to 22.3 days. Administration of activated carbon nanoparticles to the contralateral thyroid after intraoperative cryosections did not contribute to lymphadenectomy for papillary thyroid non-microcarcinoma, but significantly protected parathyroid functions. This approach could decrease the morbidity of radical thyroidectomy and the occurrence of hypoparathyroidism.
Ku70 Is Required for DNA Repair but Not for T Cell Antigen Receptor Gene Recombination In Vivo

Ku is a complex of two proteins, Ku70 and Ku80, and functions as a heterodimer to bind DNA double-strand breaks (DSB) and activate DNA-dependent protein kinase. The role of the Ku70 subunit in DNA DSB repair, hypersensitivity to ionizing radiation, and V(D)J recombination was examined in mice that lack Ku70 (Ku70 −/−). Like Ku80 −/− mice, Ku70 −/− mice showed a profound deficiency in DNA DSB repair and were proportional dwarfs. Surprisingly, in contrast to Ku80−/− mice in which both T and B lymphocyte development were arrested at an early stage, lack of Ku70 was compatible with T cell receptor gene recombination and the development of mature CD4+CD8− and CD4−CD8+ T cells. Our data shows, for the first time, that Ku70 plays an essential role in DNA DSB repair, but is not required for TCR V(D)J recombination. These results suggest that distinct but overlapping repair pathways may mediate DNA DSB repair and V(D)J recombination.