Miracle-dz/UniFAR-FTUs huggingface dataset:
Type Batched Program Reduction

Given a program with a property of interest, program reduction searches for a smaller program that preserves the property and is easier to understand. Domain agnostic program reducers can reduce programs of multiple languages without extra domain knowledge. Despite their reusability, they may still take hours to run, hindering productivity and scalability. This paper proposes type batched program reduction, which uses machine learning to suggest portions of a program, or batches, that are most likely to be advantageous to reduce at a particular point in the reduction. We also extend this to jointly reduce multiple portions of a program at once, improving the performance further. Suggesting an appropriate order for removing batches from a program along with their potential simultaneous removal enables our reducer to outperform the state of the art reducers in reduction time over a set of large programs from multiple programming languages. This work lays foundations for further improvements in ML guided program reduction.
OLFF-Net: Robust Registration of 3D Point Cloud based on Overlapped Local Feature Fusion

Recent advance in high-accuracy sensors has made point cloud become the main data format to characterize the three-dimensional world. Since the sensor can only scan and capture the 3D data within a limited field of view, an alignment algorithm is needed to generate the complete 3D scene. Point cloud registration is the solution for alignment problem that aims to estimate the transformation matrix between two frames of different point cloud sets. In this paper, we propose a neural network called OLFF-Net to achieve robust registration of 3D point clouds based on overlapped local feature fusion, which focuses on extracting rotational-invariant local features while providing enough information to achieve accurate alignment. Extensive experiments on representative datasets indicate that the framework can largely outperform competing methods with an average improvement of 16.82% in the metrics over the compared methods. More importantly, it shows significant generalization capability and can be widely applied to point cloud data with multiple complex structures.
Tetracycline transactivator overexpression in keratinocytes triggers a TRPV1 primary sensory neuron-dependent neuropathic itch

Mouse models that combine tetracycline-controlled gene expression systems and conditional genetic activation can tightly regulate transgene expression in discrete cell types and tissues. However, the commonly used Tet-Off variant, tetracycline transactivator (tTA), when overexpressed and fully active, can lead to developmental lethality, disease, or more subtle behavioral phenotypes. Here we describe a profound itch phenotype in mice expressing a genetically encoded tTA that is conditionally activated within the Phox2a lineage. Phox2a; tTA mice develop intense, localized scratching and regional skin lesions that can be controlled by the tTA inhibitor, doxycycline. As gabapentin, but not morphine, relieved the scratching, we consider this phenotype to result from chronic neuropathic itch, not pain. In contrast to the Phox2a lineage, mice with tTA activated within the Phox2b lineage, which has many similar areas of recombination within the nervous system, did not recapitulate the scratching phenotype. In Phox2a-Cre mice, but not Phox2b-Cre, intense Cre-dependent reporter expression was found in skin keratinocytes which formed the area at which skin lesions developed. Most interestingly, repeated topical application of the DREADD agonist, CNO, which chronically induced Gi signaling in Phox2a-keratinocytes, completely reversed the localized scratching and skin lesions. Furthermore, ablation of TRPV1-expressing, primary afferent neurons reduced the scratching with a time course comparable to that produced by Gi-DREADD inhibition. These temporal properties suggest that the neuropathic itch condition arises not only from localized keratinocyte activation of peripheral nerves but also from a persistent, gabapentin-sensitive state of central sensitization.
A rigorous and versatile statistical test for correlations between time series

In disciplines from biology to climate science, a routine task is to compute a correlation between a pair of time series, and determine whether the correlation is statistically significant (i.e. unlikely under the null hypothesis that the time series are independent). This problem is challenging because time series typically exhibit autocorrelation, which cannot be properly analyzed with the standard iid-oriented statistical tests. Although there are well-known parametric tests for time series, these are designed for linear correlation statistics and thus not suitable for the increasingly popular nonlinear correlation statistics. Among nonparametric tests, the conditions that guarantee correct false positive rates are either restrictive or unclear. Here we describe the truncated time-shift (TTS) test, a nonparametric procedure to test for dependence between two time series. We prove that this test is valid as long as one of the time series is stationary, a minimally restrictive requirement among current tests. The TTS test is versatile because it can be used with any correlation statistic. Using synthetic data, we demonstrate that this test performs correctly even while other tests suffer high false positive rates. In simulation examples, simple guidelines for parameter choices allow high statistical power to be achieved with sufficient data. We apply the test to data sets from climatology, animal behavior and microbiome science, verifying previously discovered dependence relationships and detecting additional relationships.
Impact of environmental factors on calling behavior in midshipman fish across ocean basins

Chorusing is widespread across the animal kingdom. Animal calling behavior is often driven by phenological and environmental factors such as seasonality, lunar period, and temperature. Now, in the Anthropocene, factors such as increased anthropogenic noise levels are also affecting calling behavior. Many fish call in choruses to attract mates, but the dynamics that drive fish calling behavior have rarely been studied in the field. We investigated how seasonality, lunar period, ambient noise, and temperature influenced the calling behavior of two species of toadfish, the plainfin midshipman (Porichthys notatus) and putatively, the Atlantic midshipman (Porichthys plectrodon). Acoustic recordings from a two-year period in twelve different locations, spanning two ocean basins showed that midshipman chorus presence was driven by seasonality and lunar period. Furthermore, chorus frequency increased with increasing temperature. Chorus levels were strongly influenced by seasonality and increased somewhat with increasing noise levels. Taken together, these results indicate that midshipman calling behavior was strongly influenced by interacting environmental conditions. Understanding the various impacts of each driver will facilitate predictions of changes in midshipman calling due to future changes in environmental conditions.
Incorporating photosynthetic acclimation improves stomatal optimisation models

Stomatal opening in plant leaves is regulated through a balance of carbon and water exchange under different environmental conditions. Accurate estimation of stomatal regulation is crucial for understanding how plants respond to changing environmental conditions, particularly under climate change. A new generation of optimality-based modelling schemes determines instantaneous stomatal responses from a balance of trade-offs between carbon gains and hydraulic costs, but most such schemes do not account for biochemical acclimation in response to drought. Here, we compare the performance of seven instantaneous stomatal optimisation models with and without accounting for photosynthetic acclimation. Using experimental data from 38 plant species, we found that accounting for photosynthetic acclimation improves the prediction of carbon assimilation in a majority of the tested models. Non-stomatal mechanisms contributed significantly to the reduction of photosynthesis under drought conditions in all tested models. Drought effects on photosynthesis could not accurately be explained by the hydraulic impairment functions embedded in the stomatal models alone, indicating that photosynthetic acclimation must be considered to improve estimates of carbon assimilation during drought. Summary Statement Accounting for photosynthetic acclimation improves the predictions of carbon assimilation in all the stomatal optimization models evaluated. The influence of drought on photosynthesis cannot be fully explained by the hydraulic impairment function of the stomatal models alone.
Atomic-level architecture of Caulobacter crescentus flagellar filaments provide evidence for multi-flagellin filament stabilization

Flagella are dynamic, ion-powered machines with assembly pathways that are optimized for efficient flagella production. In bacteria, dozens of genes are coordinated at specific times in the cell lifecycle to generate each component of the flagellum. This is the case for Caulobacter crescentus, but little is known about why this species encodes six different flagellin genes. Furthermore, little is known about the benefits multi-flagellin species possess over single flagellin species, if any, or what molecular properties allow for multi-flagellin filaments to assemble. Here we present an in-depth analysis of several single flagellin filaments from C. crescentus, including an extremely well-resolved structure of a bacterial flagellar filament. We highlight key molecular interactions that differ between each bacterial strain and speculate how these interactions may alleviate or impose helical strain on the overall architecture of the filament. We detail conserved residues within the flagellin subunit that allow for the synthesis of multi-flagellin filaments. We further comment on how these molecular differences impact bacterial motility and highlight how no single flagellin filament achieves wild-type levels of motility, suggesting C. crescentus has evolved to produce a filament optimized for motility comprised of six flagellins. Finally, we highlight an ordered arrangement of glycosylation sites on the surface of the filaments and speculate how these sites may protect the β-hairpin located on the surface exposed domain of the flagellin subunit.
The VanS sensor histidine kinase from type-B VRE recognizes vancomycin directly

Vancomycin-resistant enterococci (VRE) are among the most common causes of nosocomial infections, which can be challenging to treat. VRE have acquired a suite of resistance genes that function together to confer resistance to vancomycin. Expression of the resistance phenotype is controlled by the VanRS two-component system. This system senses the presence of the antibiotic, and responds by initiating transcription of resistance genes. VanS is a transmembrane sensor histidine kinase, and plays a fundamental role in antibiotic resistance by detecting vancomycin and then transducing this signal to VanR. Despite the critical role played by VanS, fundamental questions remain about its function, and in particular about how it senses vancomycin. Here, we focus on purified VanRS systems from the two most clinically prevalent forms of VRE, types A and B. We show that in a native-like membrane environment, the enzymatic activities of type-A VanS are insensitive to vancomycin, suggesting that the protein functions by an indirect mechanism that detects a downstream consequence of antibiotic activity. In contrast, the autokinase activity of type-B VanS is strongly stimulated by vancomycin. We additionally demonstrate that this effect is mediated by a direct physical interaction between the antibiotic and the type-B VanS protein, and localize the interacting region to the protein’s periplasmic domain. This represents the first time that a direct sensing mechanism has been confirmed for any VanS protein. Significance Statement When vancomycin-resistant enterococci (VRE) sense the presence of vancomycin, they remodel their cell walls to block antibiotic binding. This resistance phenotype is controlled by the VanS protein, a sensor histidine kinase that senses the antibiotic and signals for transcription of resistance genes. However, the mechanism by which VanS detects the antibiotic has remained unclear. Here, we show that VanS proteins from the two most common types of VRE use very different sensing mechanisms. Vancomycin does not alter the signaling activity of VanS from type-A VRE, suggesting an indirect sensing mechanism; in contrast, VanS from type-B VRE is activated by direct binding of the antibiotic. Such mechanistic insights will likely prove useful in circumventing vancomycin resistance.
Increasing adult neurogenesis protects mice from epilepsy

Neurogenesis occurs in the adult brain in the hippocampal dentate gyrus, an area that contains neurons which are vulnerable to insults and injury, such as severe seizures. Previous studies showed that increasing adult neurogenesis reduced neuronal damage after these seizures. Because the damage typically is followed by chronic life-long seizures (epilepsy), we asked if increasing adult neurogenesis would prevent epilepsy. Adult neurogenesis was selectively increased by deleting the pro-apoptotic gene Bax from Nestin-expressing progenitors. Tamoxifen was administered at 6 weeks of age to conditionally delete Bax in Nestin-CreERT2Baxfl/fl mice. Six weeks after tamoxifen administration, severe seizures (status epilepticus; SE) were induced by injection of the convulsant pilocarpine. Mice with increased adult neurogenesis exhibited fewer chronic seizures. Postictal depression was reduced also. These results were primarily female mice, possibly because they were the more affected by Bax deletion than males, consistent with sex differences in Bax in development. The female mice with enhanced adult neurogenesis also showed less neuronal loss of hilar mossy cells and hilar somatostatin-expressing neurons than wild type females or males, which is notable because these two cell types are implicated in epileptogenesis. The results suggest that increasing adult neurogenesis in the normal adult brain can reduce experimental epilepsy, and the effect shows a striking sex difference. The results are surprising in light of past studies showing that suppressing adult-born neurons can also reduce chronic seizures.
Threat expectation does not improve perceptual discrimination despite causing heightened priority processing in the frontoparietal network

Threat cues have been widely shown to elicit increased sensory and attentional neural processing. However, whether this enhanced recruitment leads to measurable behavioral improvements in perception is still in question. Here we adjudicate between two opposing theories: that threat cues do or do not enhance perceptual sensitivity. We created threat stimuli by pairing one direction of motion in a random dot kinematogram with an aversive sound. While in the MRI scanner, 46 subjects (both men and women) completed a cued (threat/safe/neutral) perceptual decision-making task where they indicated the perceived motion direction of each moving dots stimulus. We found strong evidence that threat cues did not increase perceptual sensitivity compared to safe and neutral cues. This lack of improvement in perceptual decision-making ability occurred despite the threat cue resulting in widespread increases in frontoparietal BOLD activity, as well as increased connectivity between the right insula and the frontoparietal network. These results call into question the intuitive claim that expectation automatically enhances our perception of threat, and highlight the role of the frontoparietal network in prioritizing the processing of threat-related environmental cues. Significance Statement Threatening information receives enhanced priority processing in the brain. Evidence of increased neural activity to threat has fostered the current view that such selective processing leads to a boost in perception, suggesting that motivationally relevant top-down effects can directly change what we see. In the real world, danger is often preceded by an environmental cue that predicts its imminent approach. Here we used an aversive conditioning paradigm to test whether threat cues can change subjects’ ability to visually distinguish between threat and safe stimuli. Our results provide strong evidence for the lack of an effect of threat expectation on perceptual sensitivity, supporting the theory that perception is impenetrable by top-down cognitive influences despite robust neural attentional priority.
Cycles and Optimistic Stability in Graphs: The Role of Competition, Veto Players and Moderators

Abstract This article provides sufficient conditions for existence of a non-empty optimistic stable standard of behaviour (OSSB) in directed graphs. Graphs which are completely connected by single-player arcs for each player always admit a (non-unique) OSSB. More specifically, a loop is broken by adding a single-player move to some appropriately chosen default position. If there are nodes with a decision cycle over the move to the successor node, introducing veto players ensures that an OSSB exists which assigns a non-empty solution to every vertex along the equilibrium path.
Degradable and Antidegradable Qubit Channels

Degradable and Antidegradable Qubit Channels Connor Paul-Paddock Advisor: University of Guelph, 2016 Dr. Bei Zeng Dr. Rejesh Periera This thesis investigates a characterization for the set of antidegradable qubit channels. The characterization comes from a correspondence between the antidegradability of a channel, and the symmetric extendibility of the Choi operator. Using an inequality intended to describe the set of bipartite qubit states which admit symmetric extension, we demonstrate that it additionally provides a condition to characterize the set of antidegradable qubit channels. Using the characterization we investigate the antidegradability of qubit channels with respect to the rank of the Choi matrix. We also apply the antidegradability criterion to the qubit amplitude damping and qubit depolarizing channel. We end by discussing degradable and antidegradable channels in terms of their channel capacities and the applications of these results to investigating phenomena such as super-additive coherent information and superactivation.
Microlocal analysis of imaging operators for effective common offset seismic reconstruction

The elliptic Radon transform (eRT) integrates functions over ellipses in 2D and ellipsoids of revolution in 3D. It thus serves as a model for linearized seismic imaging under the common offset scanning geometry where sources and receivers are offset by a constant vector. As an inversion formula of eRT is unknown we propose certain imaging operators (generalized backprojection operators) which allow to reconstruct some singularities of the searched-for reflectivity function from seismic measurements. We calculate and analyze the principal symbols of these imaging operators as pseudo-differential operators to understand how they map, emphasize or de-emphasize singularities. We use this information to develop local reconstruction operators that reconstruct relatively independently of depth and offset. Numerical examples illustrate the theoretical findings.
A global convergent outlier robust adaptive predictor for MIMO Hammerstein models

The paper considers the outlier‐robust recursive stochastic approximation algorithm for adaptive prediction of multiple‐input multiple‐output (MIMO) Hammerstein model with a static nonlinear block in polynomial form and a linear block is output error (OE) model. It is assumed that there is a priori information about a distribution class to which a real disturbance belongs. Within the framework of these assumptions, the main contributions of this paper are: (i) for MIMO Hammerstein OE model, the stochastic approximation algorithm, based on robust statistics (in the sense of Huber), is derived; (ii) scalar gain of algorithm is exactly determined using the Laplace function; and (iii) a global convergence of robust adaptive predictor is proved. The proof is based on martingale theory and generalized strictly positive real conditions. Practical behavior of algorithm was illustrated by simulations. Copyright © 2016 John Wiley & Sons, Ltd.
Harmonic Resonances of Planet and Moon Orbits - From the Titius-Bode Law to Self-Organizing Systems

The geometric arrangement of planet and moon orbits into a regularly spaced pattern of distances is the result of a self-organizing system. The positive feedback mechanism that operates a self-organizing system is accomplished by harmonic orbit resonances, leading to long-term stable planet and moon orbits in solar or stellar systems. The distance pattern of planets was originally described by the empirical Titius-Bode law, and by a generalized version with a constant geometric progression factor (corresponding to logarithmic spacing). We find that the orbital periods $T_i$ and planet distances $R_i$ from the Sun are not consistent with logarithmic spacing, but rather follow the quantized scaling $(R_{i+1}/R_i) = (T_{i+1}/T_i)^{2/3} = (H_{i+1}/H_i)^{2/3}$, where the harmonic ratios are given by five dominant resonances, namely $(H_{i+1} : H_{i}) = (3:2), (5:3), (2:1), (5:2), (3:1)$. We find that the orbital period ratios tend to follow the quantized harmonic ratios in increasing order. We apply this harmonic orbit resonance model to the planets and moons in our solar system, and to the exo-planets of 55 Cnc and HD 10180 planetary systems. The model allows us a prediction of missing planets in each planetary system, based on the quasi-regular self-organizing pattern of harmonic orbit resonance zones. We predict 7 (and 4) missing exo-planets around the star 55 Cnc (and HD 10180). The accuracy of the predicted planet and moon distances amounts to a few percents. All analyzed systems are found to have $\approx 10$ resonant zones that can be occupied with planets (or moons) in long-term stable orbits.
FORECASTING ANALYSIS OF PHARMACEUTICALS AND MEDICAL DEVICES IN A CATEGORY NEEDED IN 2011

Forecasting of pharmaceuticals and medical devices are an effort to estimate the needs of pharmaceuticals and medical devices in hospital. Pharmaceuticals and medical devices of class A based on ABC analysis represents a small amount in stock but has the largest inventory value. This study aimed to determine the exact forecasting that used to estimate the needs of pharmaceuticals and medical devices in class A in the Pharmacy Department Immanuel Hospital Bandung. This research was a descriptive study with retrospective data collection. Forecasting analysis of pharmaceuticals and medical devices needed used the average of last period, seasonal variation, and seasonal index with trend adjustment in 2011. Forecasting analysis was calculated based on consumtion of pharmaceuticals and medical devices in 2008-2010. Accuracy of forecasting methods were determined by the smallest value of mean absolute deviation (MAD) and mean squared error (MSE). The results from 24 samples of pharmaceuticals and medical devices in class A showed that there were 12 samples (50%) with the smallest MAD for seasonal index with trend adjustment method, 8 samples (66.67%) with the smallest MAD values for average of last period method, and 4 samples (16.67%) with the smallest MAD for seasonal variation method. According to MSE, there were 14 samples (58.33%) with the smallest MSE value for the seasonal index with trend adjustment method, 8 samples (66.67%) with the smallest MSE value for the average of last period method, and 2 samples (8, 33%) with the smallest MSE for seasonal variation method. It can be concluded that seasonal index with trend adjustment analysis was better compared the method of seasonal variation and the average of last period to forecasting needs of pharmaceuticals and medical devices in A category. Keywords :seasonal index with trend adjustment, ABC Analysis, Immanuel Hospital Bandung