Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuroprotective and anti‐inflammatory effects of morin in a murine model of Parkinson's disease

Parkinson's disease (PD) is one of the most common neurodegenerative disorders and is characterized by loss of dopaminergic neurons in the substantia nigra (SN). Although the causes of PD are not understood, evidence suggests that oxidative stress, mitochondrial dysfunction, and inflammation are associated with its pathogenesis. Morin (3,5,7,2′,4′‐pentahydroxyflavone) is a flavonol found in wine and many herbs and fruits. Previous studies have suggested that morin prevents oxidative damage and inflammation and ameliorates mitochondrial dysfunction. The present study describes the neuroprotective effects of morin in a 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP)‐induced mouse model of PD, and we report the results of our investigation into its neuroprotective mechanism in primary neurons and astrocytes. In the mouse model, morin pretreatment ameliorated motor dysfunction, protected against dopaminergic neuronal losses in SN and striatum, and alleviated MPTP‐induced astrocyte activation. In vitro studies revealed that morin protected primary cultured neurons against 1‐methyl‐4‐phenylpyridine (MPP+)‐mediated reactive oxygen species production and mitochondrial membrane potential (MMP) disruption. In addition, morin effectively reduced MPP+‐induced astroglial activation and nuclear translocation of nuclear factor‐κB in primary cultured astrocytes. These results indicate that morin acts via multiple neuroprotective mechanisms in our mouse model and suggest that morin be viewed as a potential treatment and preventative for PD. © 2016 Wiley Periodicals, Inc.
Good spaced seeds for homology search

Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma, Tromp and Li (2002) discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed. Our numerical computation shows that the ranks of spaced seeds (based on sensitivity) change with the sequences similarity. Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search in DNA genomic sequences. We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences.
IMPRES: integrated monitoring for processor reliability and security

Security and reliability in processor based systems are concerns requiring adroit solutions. Security is often compromised by code injection attacks, jeopardizing even 'trusted software'. Reliability is of concern where unintended code is executed in modern processors with ever smaller feature sizes and low voltage swings causing bit flips. Countermeasures by software-only approaches increase code size by large amounts and therefore significantly reduce performance. Hardware assisted approaches add extensive amounts of hardware monitors and thus incur unacceptably high hardware cost. This paper presents a novel hardware/software technique at the granularity of micro-instructions to reduce overheads considerably. Experiments show that our technique incurs an additional hardware overhead of 0.91% and clock period increase of 0.06%. Average clock cycle and code size overheads are just 11.9% and 10.6% for five industry standard application benchmarks. These overheads are far smaller than have been previously encountered
The MMSR bilingual and crosschannel corpora for speaker recognition research and evaluation

Abstract : We describe efforts to create corpora to support and evaluate systems that meet the challenge of speaker recognition in the face of both channel and language variation. In addition to addressing ongoing evaluation of speaker recognition systems, these corpora are aimed at the bilingual and crosschannel dimensions. We report on specific data collection efforts at the Linguistic Data Consortium, the 2004 speaker recognition evaluation program organized by the National Institute of Standards and Technology (NIST), and the research ongoing at the US Federal Bureau of Investigation and MIT Lincoln Laboratory. We cover the design and requirements, the collections and evaluation integrating discussions of the data preparation, research, technology development and evaluation on a grand scale.
STATISTICAL APPROACH TO BIOLOGICAL RANDOM SEQUENCE GENERATION

Simulations of originally existent biological sequences are helpful for computational analysis and manipulations, rather than wet lab experiments, considerably reducing the cost and time associated with traditional wet lab experiments. The basic idea is to compare the results of a run on real data to many runs on random data. This paper discusses the need for random biological sequence analysis and an alternative for generating biological random sequences. A novel random generation algorithm which uses the statistical distributions to generate numbers and to map these numbers into biological random sequences is conceived. Algorithm for generating random sequences with normal and binomial distributions is implemented; random sequences with tandem repeats, GC base control and nucleotide position control are also incorporated by modifying this algorithm. The newly proposed algorithm and all the mentioned features are also implemented as a platform independent tool named Biolets which can be freely downloaded from the web site http://sooryakiran.com/products_biolets. html.
Expression and Distribution of Carboxypeptidase B in the Hippocampal Subregions of Normal and Alzheimer’s Disease Brain

Earlier neurochemical studies suggested that human brain carboxypeptidase B may play a significant role in the degradation of amyloid-β1-42 in the brain. Using an immunohistochemical technique we report here on the neuronal expression and distribution of this enzyme in the segments (CA1a, CA1b and CA1c) of the CA1 subfield and in area CA4 of the hippocampus in normal and Alzheimer’s disease brain samples. Its distribution was compared with the appearance of neurofibrillary tangles in the same brain sample. For immunohistochemical localization of carboxypeptidase B, a specific C14-module antibody was applied, together with the Gallyas silver impregnation technique for the demonstration of neurofibrillary tangles. The results revealed that, in the control samples, most of the immunoreactivity appeared in segment CA1a in the pyramidal cells, less in segment CA1b and least in segment CA1c. In the Alzheimer’s disease samples, there was no particular immunostaining in the neurons, but, a large number of silver-impregnated degenerated neurons appeared. The results support the suggestion that carboxypeptidase B may play a significant role in elimination of the intracellular accumulation and toxicity of amyloid-β in the human brain and thereby protect the neurons from degeneration.
Normalization of Voltage-Sensitive Dye Signal with Functional Activity Measures

In general, signal amplitude in optical imaging is normalized using the well-established ΔF/F method, where functional activity is divided by the total fluorescent light flux. This measure is used both directly, as a measure of population activity, and indirectly, to quantify spatial and spatiotemporal activity patterns. Despite its ubiquitous use, the stability and accuracy of this measure has not been validated for voltage-sensitive dye imaging of mammalian neocortex in vivo. In this report, we find that this normalization can introduce dynamic biases. In particular, the ΔF/F is influenced by dye staining quality, and the ratio is also unstable over the course of experiments. As methods to record and analyze optical imaging signals become more precise, such biases can have an increasingly pernicious impact on the accuracy of findings, especially in the comparison of cytoarchitechtonic areas, in area-of-activation measurements, and in plasticity or developmental experiments. These dynamic biases of the ΔF/F method may, to an extent, be mitigated by a novel method of normalization, ΔF/ΔFepileptiform. This normalization uses as a reference the measured activity of epileptiform spikes elicited by global disinhibition with bicuculline methiodide. Since this normalization is based on a functional measure, i.e. the signal amplitude of “hypersynchronized” bursts of activity in the cortical network, it is less influenced by staining of non-functional elements. We demonstrate that such a functional measure can better represent the amplitude of population mass action, and discuss alternative functional normalizations based on the amplitude of synchronized spontaneous sleep-like activity. These findings demonstrate that the traditional ΔF/F normalization of voltage-sensitive dye signals can introduce pernicious inaccuracies in the quantification of neural population activity. They further suggest that normalization-independent metrics such as waveform propagation patterns, oscillations in single detectors, and phase relationships between detector pairs may better capture the biological information which is obtained by high-sensitivity imaging.
The scope for joint household / commercial collections : a case study

Although commercial and household wastes are compositionally similar, common UK practice is for separate collections. This paper uses vehicle routeing and scheduling software to predict the benefits of allowing household and commercial waste to be collected together by a common vehicle fleet. This was compared in a case study where collections were made from over 25,000 households on an alternate weekly basis and from 577 commercial premises having one or more collections each week. Modelled joint collections reduced vehicle mileage by up to 9.8%, equating to an annual savings of around £36,800 and a carbon equivalent savings of 2688kg per annum. The modelled benefits were greatest when a common starting time (6am) was adopted for the commercial and household collections. The modelled rounds were estimated to have sufficient time and vehicle capacity available to allow an additional 50% of commercial waste to be collected, equating to 35.8 tonnes per week.
Morphokinetic Characteristics and Developmental Potential of In Vitro Cultured Embryos from Natural Cycles in Patients with Poor Ovarian Response

Background. Patients with poor ovarian response to ovarian hyperstimulation represent an interesting group for studying the impact of embryo cleavage irregularities on clinical outcome since all embryos, regardless of their quality, are usually transferred to the uterus. The aim of our study was to follow the morphokinetics of fertilized oocytes from natural cycles in poor responders. Methods. Zygotes from 53 cycles were cultured in vitro for 3 days. The morphokinetics of their development and transfer outcomes were retrospectively analyzed for the normally and irregularly cleaved embryos. Results. Of all embryos, 30.2% had single and 20.8% multiple cleavage irregularities with the following prevalence: developmental arrest 30.2%, direct cleavage to more than two cells 24.5%, chaotic cleavage 13.2%, and reverse cleavage 11.3%. These embryos had longer pronuclear phases, first cytokinesis, second embryo cell cycles, and less synchronized divisions. The transfer of normally developing embryos resulted in an implantation rate of 30.8% and a delivery rate of 23.1%, but irregularly cleaved embryos did not implant. Conclusions. The use of time-lapse microscopy in poor responder patients identified embryos with cleavage abnormalities that are related with no or extremely low implantation potential. Gained information about embryo quality is important for counselling patients about their expectations.
Letter knowledge in parent–child conversations: differences between families differing in socio-economic status

When formal literacy instruction begins, around the age of 5 or 6, children from families low in socioeconomic status (SES) tend to be less prepared than children from families of higher SES. The goal of our study is to explore one route through which SES may influence children's early literacy skills: informal conversations about letters. The study builds on previous studies (Robins and Treiman, 2009; Robins et al., 2012, 2014) of parent–child conversations that show how U. S. parents and their young children talk about writing and provide preliminary evidence about similarities and differences in parent–child conversations as a function of SES. Focusing on parents and children aged three to five, we conducted five separate analyses of these conversations, asking whether and how family SES influences the previously established patterns. Although we found talk about letters in both upper and lower SES families, there were differences in the nature of these conversations. The proportion of letter talk utterances that were questions was lower in lower SES families and, of all the letter names that lower SES families talked about, more of them were uttered in isolation rather than in sequences. Lower SES families were especially likely to associate letters with the child's name, and they placed more emphasis on sequences in alphabetic order. We found no SES differences in the factors that influenced use of particular letter names (monograms), but there were SES differences in two-letter sequences (digrams). Focusing on the alphabet and on associations between the child's name and the letters within it may help to interest the child in literacy activities, but they many not be very informative about the relationship between letters and words in general. Understanding the patterns in parent–child conversations about letters is an important first step for exploring their contribution to children's early literacy skills and school readiness.
Privacy-preserving anonymization of set-valued data

In this paper we study the problem of protecting privacy in the publication of set-valued data. Consider a collection of transactional data that contains detailed information about items bought together by individuals. Even after removing all personal characteristics of the buyer, which can serve as links to his identity, the publication of such data is still subject to privacy attacks from adversaries who have partial knowledge about the set. Unlike most previous works, we do not distinguish data as sensitive and non-sensitive, but we consider them both as potential quasi-identifiers and potential sensitive data, depending on the point of view of the adversary. We define a new version of the k-anonymity guarantee, the km-anonymity, to limit the effects of the data dimensionality and we propose efficient algorithms to transform the database. Our anonymization model relies on generalization instead of suppression, which is the most common practice in related works on such data. We develop an algorithm which finds the optimal solution, however, at a high cost which makes it inapplicable for large, realistic problems. Then, we propose two greedy heuristics, which scale much better and in most of the cases find a solution close to the optimal. The proposed algorithms are experimentally evaluated using real datasets.
Simple wind energy controller for an expanded operating range

Small-scale stand-alone wind energy systems are an important alternative source of electrical energy, finding applications in locations where conventional generation is not practical. Unfortunately, most of these systems do not capture power at every wind speed-especially low wind speeds which are low in power but can be very common. To address this problem, the authors have proposed a power electronic converter, designed for efficiency, simplicity and ruggedness. A simple feed forward technique is presented using discrete components and minimal sensors. Test data are presented, indicating that the technique eliminates the standard "cut-in" wind speed and expands the operating range of a wind turbine.
Dual Requirement of Cytokine and Activation Receptor Triggering for Cytotoxic Control of Murine Cytomegalovirus by NK Cells

Natural killer (NK) cells play a critical role in controlling murine cytomegalovirus (MCMV) and can mediate both cytokine production and direct cytotoxicity. The NK cell activation receptor, Ly49H, is responsible for genetic resistance to MCMV in C57BL/6 mice. Recognition of the viral m157 protein by Ly49H is sufficient for effective control of MCMV infection. Additionally, during the host response to infection, distinct immune and non-immune cells elaborate a variety of pleiotropic cytokines which have the potential to impact viral pathogenesis, NK cells, and other immune functions, both directly and indirectly. While the effects of various immune deficiencies have been examined for general antiviral phenotypes, their direct effects on Ly49H-dependent MCMV control are poorly understood. To specifically interrogate Ly49H-dependent functions, herein we employed an in vivo viral competition approach to show Ly49H-dependent MCMV control is specifically mediated through cytotoxicity but not IFNγ production. Whereas m157 induced Ly49H-dependent degranulation, efficient cytotoxicity also required either IL-12 or type I interferon (IFN-I) which acted directly on NK cells to produce granzyme B. These studies demonstrate that both of these distinct NK cell-intrinsic mechanisms are integrated for optimal viral control by NK cells.
Parsing expression grammars made practical

Parsing Expression Grammars (PEGs) define languages by specifying a recursive-descent parser that recognises them. The PEG formalism exhibits desirable properties, such as closure under composition, built-in disambiguation, unification of syntactic and lexical concerns, and closely matching programmer intuition. Unfortunately, state of the art PEG parsers struggle with left-recursive grammar rules, which are not supported by the original definition of the formalism and can lead to infinite recursion under naive implementations. Likewise, support for associativity and explicit precedence is spotty. To remedy these issues, we introduce Autumn, a general purpose PEG library that supports left-recursion, left and right associativity and precedence rules, and does so efficiently. Furthermore, we identify infix and postfix operators as a major source of inefficiency in left-recursive PEG parsers and show how to tackle this problem. We also explore the extensibility of the PEG paradigm by showing how one can easily introduce new parsing operators and how our parser accommodates custom memoization and error handling strategies. We compare our parser to both state of the art and battle-tested PEG and CFG parsers, such as Rats! , Parboiled and ANTLR.
Kinematic, Dynamic Modeling and Remote Control of a Robotic Machine

In this paper, a robotic machine with 3 degrees of freedom (DOF) is proposed. First, the geometric structure of the 3-DOF parallel robot is presented; in the mechanism, a fourth kinematic link -a passive link connecting the base center to the moving platform center -is introduced. This last link is used to constrain the motion of the moving platform to only 3-DOF. Then, the kinematic and dynamic models are developed. With the models, a web-based remote control approach is then applied. The 3-DOF parallel robot can be used as a machine tool for the purpose of polishing, deburring and milling, etc. Finally, an experiment to demonstrate the proposed 3-DOF structure is set up, and some conclusions are given by the end.
Structural basis for the recognition–evasion arms race between Tomato mosaic virus and the resistance gene Tm-1

Significance The Red Queen hypothesis proposes that host defense genes evolve to counter the adverse effects of rapidly evolving invasive viruses. Although 3D structures of host–viral protein complexes have provided great insights into the molecular conflicts between them, a single structure represents only an evolutionary snapshot. Here we present the atomic details of the step-by-step arms race between tomato mosaic virus replication protein and the host inhibitor protein Tm-1, in which host recognition of a viral molecule, viral adaptive evasion of the recognition, host counteradaptation, and viral counter-counteradaptation are depicted by determination of the complex structures of Tm-1 variants and the viral protein and by biochemical analyses and molecular dynamics simulations of the interactions between these proteins. The tomato mosaic virus (ToMV) resistance gene Tm-1 encodes a protein that shows no sequence homology to functionally characterized proteins. Tm-1 binds ToMV replication proteins and thereby inhibits replication complex formation. ToMV mutants that overcome this resistance have amino acid substitutions in the helicase domain of the replication proteins (ToMV-Hel). A small region of Tm-1 in the genome of the wild tomato Solanum habrochaites has been under positive selection during its antagonistic coevolution with ToMV. Here we report crystal structures for the N-terminal inhibitory domains of Tm-1 and a natural Tm-1 variant with an I91-to-T substitution that has a greater ability to inhibit ToMV RNA replication and their complexes with ToMV-Hel. Each complex contains a Tm-1 dimer and two ToMV-Hel monomers with the interfaces between Tm-1 and ToMV-Hel bridged by ATP. Residues in ToMV-Hel and Tm-1 involved in antagonistic coevolution are found at the interface. The structural differences between ToMV-Hel in its free form and in complex with Tm-1 suggest that Tm-1 affects nucleoside triphosphatase activity of ToMV-Hel, and this effect was confirmed experimentally. Molecular dynamics simulations of complexes formed by Tm-1 with ToMV-Hel variants showed how the amino acid changes in ToMV-Hel impair the interaction with Tm-1 to overcome the resistance. With these findings, together with the biochemical properties of the interactions between ToMV-Hel and Tm-1 variants and effects of the mutations in the polymorphic residues of Tm-1, an atomic view of a step-by-step coevolutionary arms race between a plant resistance protein and a viral protein emerges.
Taking the Operant Paradigm into the Field: Associative Learning in Wild Great Tits

Associative learning is essential for resource acquisition, predator avoidance and reproduction in a wide diversity of species, and is therefore a key target for evolutionary and comparative cognition research. Automated operant devices can greatly enhance the study of associative learning and yet their use has been mainly restricted to laboratory conditions. We developed a portable, weatherproof, battery-operated operant device and conducted the first fully automated colour-associative learning experiment using free-ranging individuals in the wild. We used the device to run a colour discrimination task in a monitored population of tits (Paridae). Over two winter months, 80 individuals from four species recorded a total of 5,128 trials. Great tits (Parus major) were more likely than other species to visit the devices and engage in trials, but there were no sex or personality biases in the sample of great tits landing at the devices and registering key pecks. Juveniles were more likely than adults to visit the devices and to register trials. Individuals that were successful at solving a novel technical problem in captivity (lever-pulling) learned faster than non-solvers when at the operant devices in the wild, suggesting cross-contextual consistency in learning performance in very different tasks. There was no significant effect of personality or sex on learning rate, but juveniles’ choice accuracy tended to improve at a faster rate than adults. We discuss how customisable automated operant devices, such as the one described here, could prove to be a powerful tool in evolutionary ecology studies of cognitive traits, especially among inquisitive species such as great tits.