Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent Cis-Trans Coevolution Driven by the Emergence of A Novel Gene in Drosophila

Young, or newly evolved, genes arise ubiquitously across the tree of life, and can rapidly acquire novel functions that influence a diverse array of biological processes1. Previous work identified a young regulatory gene in Drosophila, Zeus, which diverged rapidly from its parent Caf40 and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the Drosophila melanogaster genome2. However, the way in which new DNA-binding proteins acquire and coevolve with their targets in the genome is not understood. Here, by comparing Zeus ChIP-seq data from D. melanogaster and D. simulans to the ancestral Caf40 binding events from D. yakuba, a species that diverged before the duplication event, we find a dynamic pattern in which Zeus binding rapidly co-evolved with a previously unknown DNA motif under the influence of positive selection. Interestingly, while both copies of Zeus acquired targets at male-biased and testis-specific genes, D. melanogaster and D. simulans proteins have specialized binding on different chromosomes, a pattern echoed in the evolution of the associated motif. Our results suggest that evolution of young regulatory genes can be coupled to substantial rewiring of the transcriptional networks into which they integrate, even over short evolutionary timescales. Our results thus uncover dynamic, genome-wide evolutionary processes associated with new genes.
Neonatal stress augments the hypoxic chemoreflex of adult male rats by increasing AMPA receptor‐mediated modulation

• What is the central question of this study? Early life exposure to stress augments the hypoxic chemoreflex of adult male rats. This effect predisposes to respiratory instability during sleep. We used pharmacological and neuroanatomical approaches to determine whether a change in glutamatergic neurotransmission contributes to this abnormal respiratory phenotype. • What is the main finding and its importance? We initially showed that neonatal stress augments sensitivity to an AMPA/kainate receptor antagonist. Results from autoradiography experiments support this observation because they demonstrate that neonatal stress increases expression of AMPA receptors in key regions that regulate breathing. Region‐specific changes in brain‐derived neurotrophic factor expression may contribute to these changes in glutamatergic neurotransmission. These results bring new insight into the pathophysiology of sleep‐disordered breathing.
Cholesterol efflux and atheroprotection: advancing the concept of reverse cholesterol transport.

High-density lipoprotein (HDL) has been proposed to have several antiatherosclerotic properties, including the ability to mediate macrophage cholesterol efflux, antioxidant capacity, antiinflammatory properties, nitric oxide–promoting activity, and ability to transport proteins with their own intrinsic biological activities.1 HDL particles are critical acceptors of cholesterol from lipid-laden macrophages and thereby participate in the maintenance of net cholesterol balance in the arterial wall and in the reduction of proinflammatory responses by arterial cholesterol-loaded macrophages. The pathways that regulate HDL-mediated macrophage cholesterol efflux and disposition of cholesterol involve cell membrane–bound transporters, plasma lipid acceptors, plasma proteins and enzymes, and hepatic cellular receptors (Figure 1). From the earliest proposed concept for HDL-mediated cholesterol efflux,2,3 the concentration of the cholesterol content in HDL particles has been considered a surrogate measurement for the efficiency of the “reverse cholesterol transport” (RCT) process; however, macrophage-derived cholesterol represents a minor component of the cholesterol transported by HDL particles.4–7 One important pathway for cholesterol-mediated efflux from macrophage foam cells involves interaction between the ATP-binding cassette transporter A1 (ABCA1) and cholesterol-deficient and phospholipid-depleted apolipoprotein (apo) A-I complexes (pre-β migrating HDL or very small HDL [HDL-VS]; Figure 2). 1,8 Subsequently, the ATP-binding cassette transporter G1 (ABCG1) mediates macrophage cholesterol efflux through interactions (Figure 3) with spherical, cholesterol-containing α-HDL particles (small HDL [HDL-S], medium HDL [HDL-M], large HDL [HDL-L], and very large (HDL-VL). 1 In contrast, the scavenger receptor class B type I (SR-BI) is a multifunctional receptor that mediates bidirectional lipid transport in the macrophage, which is dependent on the content of cholesterol in lipid-laden macrophages. A more established role for SR-BI in cholesterol trafficking involves selective uptake of cholesteryl esters from mature HDL by the liver. Recent studies suggest that polymorphisms in SR-BI contribute to the functional capacity of this cholesterol …
The Case of "Missing Causal Genes" and the Practice of Medicine: A Sherlock Holmes Approach of Deductive Reasoning.

The practice of medicine is an exceedingly gratifying privilege, a notion that is commonly shared among the physicians. Also commonly understood but often not expressed is the humbling nature of this practice. Seldom, if ever, we know the true answers to our patients’ questions. Yet, we adeptly offer explanations, commonly based on the group data, and yet the essence of the practice of medicine is recognizing the uniqueness of the individual and his/her disease. To quote Sir William Osler, the father of western medicine, “the good physician treats the disease; the great physician treats the patient who has the disease. ” Still, our answers typically gratify the patients and perhaps give the physicians an incontrovertibly false sense of being omniscient. The landscape of the practice of medicine has been recently enriched with the entry of the medical genetics. The impetus provided by the recent elucidation of the genetic causes of single-gene cardiovascular diseases has ushered in clinical applications of the molecular genetic discoveries and along with it our exuberance about genetic-based diagnosis, risk stratification, prevention, and treatment. Molecular Genetic testing is now routinely performed as part of the medical evaluation of patients with medical conditions commonly recognized as single-gene diseases, such as inherited cardiomyopathies and arrhythmic syndromes.1–3 It is also being advocated for risk stratification of patients with complex phenotypes, albeit its validity remains unsettled. Along with these advances, the need to educate and train the practicing physicians in understanding the fundamentals of genetics and their applications to the practice of medicine are increasingly recognized.4 Despite the remarkable progress in elucidation of genetic causes of cardiovascular diseases during the past 25 years, the causal genes in ≈30% to 50% of various single-gene cardiovascular diseases, including hereditary cardiomyopathies and arrhythmic syndromes, have yet-to-be identified (Figure). The common causal …
Synaptic Targeting of N-Type Calcium Channels in Hippocampal Neurons

N-type calcium (Ca2+) channels play a critical role in synaptic function, but the mechanisms responsible for their targeting in neurons are poorly understood. N-type channels are formed by an α1B (CaV2.2) pore-forming subunit associated with β and α2δ auxiliary subunits. By expressing epitope-tagged recombinant α1B subunits in rat hippocampal neuronal cultures, we demonstrate here that synaptic targeting of N-type channels depends on neuronal contacts and synapse formation. We also establish that the C-terminal 163 aa (2177–2339) of the α1B-1 (CaV2.2a) splice variant contain sequences that are both necessary and sufficient for synaptic targeting. By site-directed mutagenesis, we demonstrate that postsynaptic density-95/discs large/zona occludens-1 and Src homology 3 domain-binding motifs located within this region of the α1B subunit (Maximov et al., 1999) act as synergistic synaptic targeting signals. We also show that the recombinant modular adaptor proteins Mint1 and CASK colocalize with N-type channels in synapses. We found that the α1B-2(CaV2.2b) splice variant is restricted to soma and dendrites and postulated that somatodendritic and axonal/presynaptic isoforms of N-type channels are generated via alternative splicing of α1B C termini. These data lead us to propose that during synaptogenesis, the α1B-1 (CaV2.2a) splice variant of the N-type Ca2+ channel pore-forming subunit is recruited to presynaptic locations by means of interactions with modular adaptor proteins Mint1 and CASK. Our results provide a novel insight into the molecular mechanisms responsible for targeting of Ca2+ channels and other synaptic proteins in neurons.
Illinois Math Solver: Math Reasoning on the Web

There has been a recent interest in understanding text to perform mathematical reasoning. In particular, most of these efforts have focussed on automatically solving school level math word problems. In order to make advancements in this area accessible to people, as well as to facilitate this line of research, we release the ILLINOIS MATH SOLVER, a web based tool that supports performing mathematical reasoning. ILLINOIS MATH SOLVER can answer a wide range of mathematics questions, ranging from compositional operation questions like “What is the result when 6 is divided by the sum of 7 and 5 ? ” to elementary school level math word problems, like “I bought 6 apples. I ate 3 of them. How many do I have left ? ”. The web based demo can be used as a tutoring tool for elementary school students, since it not only outputs the final result, but also the mathematical expression to compute it. The tool will allow researchers to understand the capabilities and limitations of a state of the art arithmetic problem solver, and also enable crowd based data acquisition for mathematical reasoning. The system is currently online at https://cogcomp.cs. illinois. edu/page/demo_view/Math.
Development of spatial receptive-field organization and orientation selectivity in kitten striate cortex.

The functional organization of the receptive field of neurons in striate cortex of kittens from 8 days to 3 mo of age was studied by extracellular recordings. A quantitative dual-stimulus technique was used, which allowed for analysis of both enhancement and suppression zones in the receptive field. Furthermore the development of orientation selectivity was studied quantitatively in the same cells. Already in the youngest kittens the receptive fields were spatially organized like adult fields, with a central zone and adjacent flanks that responded in opposite manner to the light stimulus. The relative suppression in the subzones was as strong as in adult cells. Both simple and complex cells were found from 8 days. The receptive fields were like magnified adult fields. The width of the dominant discharge-field zone and the distance between the positions giving maximum discharge and maximum suppression decreased with age in the same proportions. The decrease could be explained by a corresponding decrease of the receptive-field-center size of retinal ganglion cells. Forty percent of the cells were orientation selective before 2 wk, and the fraction increased to 94% at 4 wk. Cells whose responses could be attenuated to at least half of the maximal response by changes of slit orientation were termed orientation selective. The half-width of the orientation-tuning curves narrowed during the first 5 wk, and this change was most marked in simple cells. The ability of the cells to discriminate between orientations in statistical terms was weak in the youngest kittens due to a large response variability, and showed a more pronounced development than the half-width did. The orientation-tuning curves were fitted by an exponential function, which showed the shape to be adultlike in all age groups. Two kittens were dark reared until recording at 1 mo of age. The spatial receptive-field organization and the orientation selectivity in these kittens were similar to normal-reared kittens at 1 mo. The responsivity of the cells of the dark-reared kittens was lower, and the latency before firing was longer than in the normal-reared kittens of the same age, and these response properties were more similar to those in 1- to 2-wk-old normal kittens. Our results indicate that the spatial organization of the receptive field is innate in most cells and that visual experience is unnecessary for the organization to be maintained and for the receptive-field width to mature during the first month postnatally. (ABSTRACT TRUNCATED AT 400 WORDS)
Synthesis and Photocatalytic Performance of Novel Visible-Light-Driven Bi2WO6 Photocatalyst via a Reverse Microemulsion Process

The novel visible-light-driven Bi2WO6 photocatalyst with orthorhombic structures was synthesized via a reverse microemulsion method. The as-prepared Bi2WO6 samples were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM). The photocatalytic activity of the Bi2WO6 powders was determined by degradation of methyl orange molecules in water under visible light irradiation (λ>400nm). The results revealed that the particle and crystallite sizes of the Bi2WO6 powders significantly depended on the synthesis temperature of the reverse microemulsion solutions. The photocatalytic tests indicated that the synthesis temperature also can significantly affect the visible light driven photocatalytic activities.
Dielectric, Piezoelectric, and Elastic Properties of Cement‐Based Piezoelectric Ceramic Composites

The material properties, including piezoelectric, dielectric, and elastic properties of cement-based piezoelectric ceramic composites are measured in our study. Different kinds of diphase composite models are proposed to explain the material properties. The modified cube model with chemical reaction is adopted because of the chemical reaction existing between lead zirconate titanate (PZT) ceramic particles and cement grains. The experimental results match the model very well. Moreover, the influence of volume fraction of PZT ceramic on the material properties of composites is also discussed in detail. The results show that the material properties of cement-based piezoelectric ceramic composite can be tuned to a compatible value to match the requirement of structure materials, i.e. concrete.
The impact of broadcasting on the spread of opinions in social media conversations

We extend our earlier work by focusing on broadcasting opinions (one-to-many interactions) alongside narrowcasts (one-to-one interactions) in social media conversations taking explicitly into consideration the behavioral characteristics of agents and the properties of the underlying network. In particular, we construct a generalized model for the spread of influence through broadcast and narrowcast interactions on social media discussion sites, and implement an agent-based model to develop insights regarding the effects of broadcasting. Our preliminary experiments show that increased broadcasting (in terms of frequency, depth, and number of broadcasters) increases homogeneity in an evolving scale-free network.
Dimensionality reduction via representation and affinity learning

Because graphs are crucial in modeling the data distribution or structure, graph-based dimensionality reduction methods have been widely employed in many machine learning and pattern recognition applications. However, in most existing graph-based dimensionality reduction techniques, the graph is usually specified empirically or learned from raw data, which may deteriorate their performances. In this paper, we propose a novel algorithm named Dimensionality Reduction via Representation and Affinity Learning (DRRAL), which adaptively constructs graph and learns the projection matrix for dimensionality reduction. Our algorithm takes noise and different local structure of each sample into account. Moreover, an efficient optimization strategy based on the iterative updating Augmented Lagrange Multiplier (ALM) and eigenvectors is developed to solve the proposed DRRAL. Extensive experimental results on five databases are carried out to verify the feasibility and effectiveness of proposed approach.
Automated Assessment of Physical-motion Tasks for Military Integrative Training

We describe the performance assessment component of the BASE-IT system, a real-time monitoring system of performance of U.S. Marines during training exercises for urban warfare. This automated component measures how well Marines are following procedures and staying safe, by tracking where they are and where they are looking. Such monitoring of physical motion is a relatively new application of computer technology with implications for instruction in physical education, choreography, and police work.
A review of melt extrusion additive manufacturing processes: II. Materials, dimensional accuracy, and surface roughness

Purpose – The purpose of this paper is to critically review the literature related to dimensional accuracy and surface roughness for fused deposition modeling and similar extrusion-based additive manufacturing or rapid prototyping processes. Design/methodology/approach – A systematic review of the literature was carried out by focusing on the relationship between process and product design parameters and the dimensional and surface properties of finished parts. Methods for evaluating these performance parameters are also reviewed. Findings – Fused deposition modeling® and related processes are the most widely used polymer rapid prototyping processes. For many applications, resolution, dimensional accuracy and surface roughness are among the most important properties in final parts. The influence of feedstock properties and system design on dimensional accuracy and resolution is reviewed. Thermal warping and shrinkage are often major sources of dimensional error in finished parts. This phenomenon is explor.
Analysis of Feature Selection Algorithms on Classification: A Survey

1. INTRODUCTIONmining is a process of knowledge discovery. The KDD is an automated process of knowledge discovery from the original data. The KDD consists of many steps like data cleaning, data integration, data selection, data transformation, data mining, pattern evaluation and knowledge representation. Among the steps the data selection is very much important to select the relevant feature and remove the irrelevant attributes. Classification is one of the datamining techniques used to discover the unknown class. The different classification methods in data mining are Bayesian classification (Statistical classifier), Decision tree induction, and Rule based classification (IF THEN Rule), Classification using Back propagation (Neural network algorithm), Support vector machine, Classification using Association Rule, k-nearest neighbor classifiers, casebased reasoning classifiers, Rough set approach, Genetic algorithm, Fuzzy set approach.
Estimation of forest parameters using 3D satellite data

Accurate data about the forest are needed both in climate research and forest management planning. This thesis focuses on using different types of three-dimensional (3D) satellite data sources to accurately estimate forest variables, primarily above-ground biomass (AGB) and tree height (H). Different satellite sensors have been used and compared, and depending on the sensors, the acquired satellite images have been processed in different ways to create 3D surface models. The three main processing alternatives have been stereogrammetry, radargrammetry and interferometry. The surface models were used together with digital terrain models from airborne laser scanning, to take the difference between the two in order to create canopy height models. The models have been built and evaluated on data from two test sites: Krycklan located in northern Sweden (Lat. 64°N, Long. 19°E) and Remningstorp in southern Sweden (Lat. 58°N, Long. 13°E). The included studies have shown that 3D satellite data are efficient to use for accurate estimations of AGB and H at stand-level. Moreover, the optical stereogrammetric models can play a role in the boreal region, but to obtain accurate estimations they are dependent on rather high resolution, along-track data with pixel sizes smaller than 10 m. Radargrammetry applies stereogrammetry to radar images, which can be taken regardless of atmospheric conditions, time of day, or season. Data from TerraSAR X were used and AGB and H could be estimated with 22.9% and 7.7% root mean square error (RMSE), respectively, at stand-level. Interferometry was applied to data from the TanDEM-X mission and this technique was superior to stereogrammetric and radargrammetric techniques, where AGB and H could be estimated with 14.4% and 4.1% RMSE, respectively, at stand-level. The first three studies in this thesis used empirical approaches and in contrast to this, the last two studies employed the two-level model (TLM), which has been developed with semi-empirical modeling based on simplified physical reasoning. The TLM also used TanDEM-X data and this showed potential for even more accurate predictions of forest related variables. To conclude, this thesis shows the potential of 3D satellite data as a highly reliable and a widely applicable remote sensing data source for estimation of forest parameters.
Microstructure evolution of SnPb and SnAg/Cu BGA solder joints during thermal aging

The microstructures and performances of eutectic SnPb and near eutectic SnAg/Cu solder joints on the Au/Ni/Cu substrates of ball-grid-array (BGA) socket were evaluated and compared after reflow and thermal aging treatments at 150 and 170/spl deg/C The growth rate of intermetallic (IM) layer was characterized and analyzed using SEM and EDS line scan techniques. Ball shear tests were used to determine the failure shear stresses of the joints. It is found that the lead-free SnAg/Cu alloy has a faster IM growth rate during reflow, compared to the eutectic SnPb. In solid-state aging, however, a faster growth rate is found for the interfacial IM layer with SnPb solder than for the lead-free alloy of which no clear IM growth after aging at 150 and 170/spl deg/C for 735 hours. In addition, significant phase coalescence was found in the aged SnPb solder joints. Spheroidization and coalescence of Ag-rich phases in the eutectic regions were also observed for the aged lead-free SnAg/Cu solder joints. From the ball shear test results, the failure shear stresses decrease as aging time increases for the SnPb and SnAg/Cu joints aged at both 150 and 170/spl deg/C excepting an initial increase of the failure shear stresses for the SnAg/Cu solder joints aged at 4-6 hours. Also, the decrease of the failure shear stresses is leveled around aging time of 20 hours up to the maximum aging time in the study for SnPb aged at 150/spl deg/C and SnAg/Cu aged at 150 and 170/spl deg/C. However, generally, better high temperature performances were observed for the lead-free SnAg/Cu solder joints compared to the eutectic SnPb joints.