Miracle-dz/UniFAR-FTUs huggingface dataset:
Proof Complexity Meets Algebra

We analyze how the standard reductions between constraint satisfaction problems affect their proof complexity. We show that, for the most studied propositional, algebraic, and semialgebraic proof systems, the classical constructions of pp-interpretability, homomorphic equivalence, and addition of constants to a core preserve the proof complexity of the CSP. As a result, for those proof systems, the classes of constraint languages for which small unsatisfiability certificates exist can be characterized algebraically. We illustrate our results by a gap theorem saying that a constraint language either has resolution refutations of constant width or does not have bounded-depth Frege refutations of subexponential size. The former holds exactly for the widely studied class of constraint languages of bounded width. This class is also known to coincide with the class of languages with refutations of sublinear degree in Sums of Squares and Polynomial Calculus over the real field, for which we provide alternative proofs. We then ask for the existence of a natural proof system with good behavior with respect to reductions and simultaneously small-size refutations beyond bounded width. We give an example of such a proof system by showing that bounded-degree Lovász-Schrijver satisfies both requirements. Finally, building on the known lower bounds, we demonstrate the applicability of the method of reducibilities and construct new explicit hard instances of the graph three-coloring problem for all studied proof systems.
The DtxR Regulon of Corynebacterium glutamicum

ABSTRACT Previous studies with Corynebacterium diphtheriae and Mycobacterium species revealed that the transcriptional regulator DtxR and its ortholog IdeR play a central role in the control of iron metabolism. In the present work, we used genome-based approaches to determine the DtxR regulon of Corynebacterium glutamicum, a nonpathogenic relative of C. diphtheriae. First, global gene expression of a dtxR deletion mutant was compared with that of the wild type using DNA microarrays. Second, we used a computer-based approach to identify 117 putative DtxR binding sites in the C. glutamicum genome. In the third step, 74 of the corresponding genome regions were amplified by PCR, 51 of which were shifted by the DtxR protein. Finally, we analyzed which of the genes preceded by a functional DtxR binding site showed altered mRNA levels in the transcriptome comparison. Fifty-one genes organized in 27 putative operons displayed an increased mRNA level in the ΔdtxR mutant and thus are presumably repressed by DtxR. The majority of these genes are obviously involved in iron acquisition, three encode transcriptional regulators, e.g., the recently identified repressor of iron proteins RipA, and the others encode proteins of diverse or unknown functions. Thirteen genes showed a decreased mRNA level in the ΔdtxR mutant and thus might be activated by DtxR. This group included the suf operon, whose products are involved in the formation and repair of iron-sulfur clusters, and several genes for transcriptional regulators. Our results clearly establish DtxR as the master regulator of iron-dependent gene expression in C. glutamicum.
Effect of Aspect Ratio and The Maximum Relative Camber on Hydrodynamic Performance of A Vertical Double-Curved Otter Board

As an important accessory of Antarctic krill fishing gear, otter board has the effect of providing net horizontal expansion. To study the effects of aspect ratio and maximum relative camber on the hydrodynamic performance of Antarctic krill otter board, provide theoretical basis for the design and optimization of the otter board, the hydrodynamic performance parameters were analysed by flume model experiments. The results show: with the increase of aspect ratio, Clmax and Kmax show an upward trend; when the maximum relative camber is less than or equal to 10%, the value of ∝0 fluctuates around 20°. When the maximum relative camber is greater than 10%, ∝0 decreases gradually in the range of 32.5° to 22.5°; K∝0 increases firstly and then decreases. With the increase of maximum relative camber, Clmax shows an upward trend; Kmax shows a downward trend; when the aspect ratio is less than or equal to 2.0, ∝0 shows an upward trend in the range of 20° to 32.5°, and when the aspect ratio is greater than 2.0, the value shows a fluctuating trend around 20°. K∝0 fluctuates and there is no obvious principle.
Limbic-cortical neuronal damage and the pathophysiology of schizophrenia.

Neurobiological studies of patients with schizophrenia suggest that abnormalities of both anatomy and function occur in limbic-cortical structures. An anatomical circuit links the functioning of the ventral striatum (i.e., nucleus accumbens) with the hippocampus and other limbic-cortical structures where neurobiological abnormalities have been found. In animals, lesions of limbic-cortical neurons cause decreases in glutamatergic input to the nucleus accumbens and are also associated with decreases in presynaptic dopamine release, increases in the density of D2-like dopamine receptors, and insensitivity to the actions of dopamine antagonists such as haloperidol. These experiments suggest a plausible pathophysiology of schizophrenia, in that schizophrenic symptoms may be caused by an abnormal dopaminergic state brought about by a primary limbic-cortical lesion and deficits in glutamatergic inputs to the ventral striatum.
Phase Structure of Hot and/or Dense QCD with the Schwinger-Dyson Equation

We investigate the phase structure of hot and/or dense QCD using the Schwinger-Dyson equation (SDE) with the improved ladder approximation in the Landau gauge. We show that the phase transition from the two-flavor color superconducting (2SC) phase to the quarkgluon plasma (QGP) phase is of second order, and that the scaling properties of the Majorana mass gap and the diquark condensate are consistent with mean field scaling. We examine the effect of the antiquark contribution and find that setting the antiquark Majorana mass equal to the quark one is a good approximation in the medium density region. We also study the effect of the Debye screening mass of the gluon and find that ignoring it causes the critical lines to move to the region of higher temperature and higher chemical potential.
SELF‐ATTRIBUTED SEASONALITY OF MOOD AND BEHAVIOR: A REPORT FROM THE NETHERLANDS STUDY OF DEPRESSION AND ANXIETY

Seasonal changes in mood and behavior are considered to be common in the general population and in patients with psychiatric disorders. However, in several studies this seasonality could not be demonstrated. The present study examined self‐attributed seasonality of depressive symptoms among patients with a lifetime diagnosis of a depressive disorder (D), an anxiety disorder (A), a comorbid depressive and anxiety disorder (DA), and healthy controls (HC).
System level verification of video and image processing specifications

A formal verification method is presented to verify the loop ordering of a high level transformed description against its original specification. The verification is done in an automatic way and its complexity is independent on the sizes of the loops bounds. Any practical structure of loop nests can be handled. The method is especially suited for applications in the area of speech, image and video processing, front-end telecom and numerical computing systems which exhibit many loops and complex multi-dimensional signals. The efficiency of the approach is demonstrated on several realistic examples.
Thermal limits across life stages do not predict contemporary geographic distributions

Rapid and ongoing climate change is causing a complete redistribution of life on Earth. To predict species’ geographic responses to climate change, it is critical that we establish the role of species’ thermal tolerances in shaping their climatic envelopes. Using experimentally-derived measures of thermal limits and a database of georeferenced occurrence records, we test whether thermal limits can predict the hottest and coldest temperatures experienced within the geographic distributions of 13 North American odonate species. We measure thermal limits in both odonate larvae and adults to account for potential life stage-related differences. Lastly, we use a time-calibrated phylogeny of North American odonates to estimate the effects of evolutionary history on the relationship between species’ thermal and climatic limits. We find that, even after accounting for ontogenetic differences and phylogeny, thermal limits do not translate into climatic limits. Further, we determine that species’ thermal limits are constrained by phylogeny, while climatic limits appear to have evolved free from phylogenetic associations. This suggests that the evolvability of odonates’ thermal limits is limited and that currently, species are in disequilibrium with their environment. Additionally, other traits or processes, such as biotic interactions, are potentially shaping odonates’ geographic distributions. In the face of climate change, odonates are unlikely to adapt to novel environmental conditions and thus will likely have to continue to shift their geographic distributions in order to track their ancestral thermal niches. Further, purely climate-based models will likely be insufficient for predicting odonates’ geographic responses to climate change.
Using Multiple Regression Models to Understand the Influence of Geologic History, Topography, Island Size, Isolation and Dispersability on Plant Community Assemblage in the Western Aleutian Islands

Those Aleutian islands which are historically free of predators, such as Buldir Island (pictured above), are often densely populated with burrowing, crevice and surface nesting seabird colonies. The hillside behind the cabins has many thousands of Storm-Petrel burrows, and an associated lush vegetation. Introduction: Island groups are often subject to habitat filters and dissimilar dispersal sources, and as a result may reflect dissimilar plant assemblages between islands. Though the Aleutian Islands have likely acted as a route for plant dispersal across the North Pacific, many continental endemics have colonized the islands but have not dispersed over the chain as a whole (Talbot, 1994). Typically, North American endemic plant species represent an increasing proportion of the flora with closer proximity to the Alaskan mainland, while Asian endemics increase in proportion towards Kamchatka (Lindroth, 1961). Using plant species occurrence data across the Western Aleutian Islands, we may examine the impact of several barriers to dispersal and flora assemblage.
Anticancer Effect of a Novel Proteasome Inhibitor, YSY01A, via G2/M Arrest in PC-3M Cells in vitro and in vivo

YSY01A is a new tripeptideboronic acid and an analog of PS341. However, YSY01A's antitumor effects and mechanism have not yet been elucidated. This study demonstrates that YSY01A inhibited proteasome activity by combining with the chymotrypsin-like (CT-L) site (β5i/β5), the post-glutamyl peptide hydrolase (PGPH) site (β1i/β1) and the trypsin-like (T-L) site (β2i/β2) in special fluorgonic substrates and proteasome probe tests. We explored the anticancer effect using methyl thiazolyltetrazolium (MTT) or sulforhodamine B (SRB), and PC-3M cells were sensitive to YSY01A among the four cancer cell types tested. The YSY01A antiproliferative effect was stronger than that of PS341. In vivo, YSY01A (1.25, 2.25, and 3.25 mg/kg) inhibited PC-3M cell xenograft tumor growth, and the tumor volume inhibition rate was approximately 40% to 60%. YSY01A arrested PC-3M cells in the G2/M phase of the cell cycle by flow cytometry (FCM). Many proteins related to the cell cycle were analyzed using western blot, and YSY01A was shown to increase p21, p27, cyclinB1, P-cdc2 (tyr15) and wee1 protein expression in both cells and tumor tissue in a concentration-dependent manner. YSY01A, a proteasome inhibitor, exerts anticancer effects on PC-3M cells in vitro and in vivo. The mechanism of the YSY01A-mediated antitumor effect is that the cell cycle is arrested at the G2/M stage. This study suggests that YSY01A may be a novel therapeutic agent for prostate cancer.
Screening for Down syndrome

Abstract Screening for Down Syndrome was initially only related to maternal age and has successively developed by introducing biochemical markers and algorithms to estimate the risk for particularly trisomy 21 and 18. We now have a long experience of screening with four biochemical markers, alpha-fetoprotein, total hCG, unconjugated estriol and free β-hCG during the second trimester. Screening is now moving towards screening in the first trimester using a combination of ultrasound (Nuchal Translucency) and the maternal serum biochemical markers free β-hCG and Pregnancy Associated Plasma Protein-A (PAPP-A). This has become known as the combined test. Several maternal and pregnancy factors which can influence the concentrations of biochemical markers are discussed. The possibilities of screening for other aneuploidies in the first trimester and an outline of recent methods to improve overall screening performance are highlighted and the review will suggest some possible options for the future in which Cell Free DNA techniques may become part of an improved overall screening strategy. In conclusion it is emphasized that the time has come to invert the Pyramid of Antenatal Care to focus on the 11–13 week assessment.
Dynamic association of the ULK1 complex with omegasomes during autophagy induction

Summary Induction of autophagy requires the ULK1 protein kinase complex and the Vps34 lipid kinase complex. PtdIns3P synthesised by Vps34 accumulates in omegasomes, membrane extensions of the ER within which some autophagosomes form. The ULK1 complex is thought to target autophagosomes independently of PtdIns3P, and its functional relationship to omegasomes is unclear. Here we show that the ULK1 complex colocalises with omegasomes in a PtdIns3P-dependent way. Live-cell imaging of Atg13 (a ULK1 complex component), omegasomes and LC3 establishes and annotates for the first time a complete sequence of steps leading to autophagosome formation, as follows. Upon starvation, the ULK1 complex forms puncta associated with the ER and sporadically with mitochondria. If PtdIns3P is available, these puncta become omegasomes. Subsequently, the ULK1 complex exits omegasomes and autophagosomes bud off. If PtdIns3P is unavailable, ULK1 puncta are greatly reduced in number and duration. Atg13 contains a region with affinity for acidic phospholipids, required for translocation to punctate structures and autophagy progression.
The Exposure Assessment in Current Time Study: Implementation, Feasibility, and Acceptability of Real-Time Data Collection in a Community Cohort of Illicit Drug Users

Objective. We describe the study design and evaluate the implementation, feasibility, and acceptability of an ecological momentary assessment (EMA) study of illicit drug users. Design. Four sequential field trials targeting observation of 30 individuals followed for a four week period. Participants. Participants were recruited from an ongoing community-cohort of current or former injection drug users. Of 113 individuals enrolled, 109 completed study procedures during four trials conducted from November 2008 to May 2013. Methods. Hand-held electronic diaries used in the initial trials were transitioned to a smartphone platform for the final trial with identical data collection. Random-prompts delivered five times daily assessed participant location, activity, mood, and social context. Event-contingent data collection involved participant self-reports of illicit drug use and craving. Main Outcome Measures. Feasibility measures included participant retention, days of followup, random-prompt response rates, and device loss rate. Acceptability was evaluated from an end-of-trial questionnaire. Sociodemographic, behavioral, clinical, and trial characteristics were evaluated as correlates of weekly random-prompt response rates ≥80% using logistic regression with generalized estimating equations. Results. Study participants were a median of 48.5 years old, 90% African American, 52% male, and 59% HIV-infected with limited income and educational attainment. During a median followup of 28 days, 78% of 11,181 random-prompts delivered were answered (mean of 2.8 responses daily), while 2,798 participant-initiated events were reported (30% drug use events; 70% craving events). Self-reported acceptability to study procedures was uniformly favorable. Device loss was rare (only 1 lost device every 190 person-days of observation). Higher educational attainment was consistently associated with a higher response rate to random-prompts, while an association of HIV infection with lower response rates was not observed after accounting for differences in trial recruitment procedures. Conclusion. Near real-time EMA data collection in the field is feasible and acceptable among community-dwelling illicit drug users. These data provide the basis for future studies of EMA-informed interventions to prevent drug relapse and improve HIV treatment outcomes in this population.
Random matrices meet machine learning: A large dimensional analysis of LS-SVM

This article proposes a performance analysis of kernel least squares support vector machines (LS-SVMs) based on a random matrix approach, in the regime where both the dimension of data p and their number n grow large at the same rate. Under a two-class Gaussian mixture model for the input data, we prove that the LS-SVM decision function is asymptotically normal with means and covariances shown to depend explicitly on the derivatives of the kernel function. This provides improved understanding along with new insights into the internal workings of SVM-type methods for large datasets.
Epigenetic changes induced by reactive oxygen species in hepatocellular carcinoma: methylation of the E-cadherin promoter.

BACKGROUND & AIMS In addition to genetic alterations, epigenetic changes underlie tumor progression and metastasis. Promoter methylation can silence tumor suppressor genes, and reactive oxygen species (ROS) promote DNA damage, although the relationship between ROS and epigenetic changes in cancer cells is not clear. We sought to determine whether ROS promote hypermethylation of the promoter region of E-cadherin, a regulator of the epithelial-to-mesenchymal transition, in hepatocellular carcinoma (HCC) cells. METHODS HCC cells were exposed to H(2)O(2) or stably transfected to express Snail, a transcription factor that down-regulates E-cadherin expression. E-cadherin and Snail expression levels were examined by real-time reverse-transcriptase polymerase chain reaction and immunoblot analyses. The methylation status of E-cadherin was examined by methyl-specific polymerase chain reaction, bisulfite sequencing, and chromatin immunoprecipitation. The interactions between Snail, histone deacetylase 1, and DNA methyltransferase 1 were assessed by immunoprecipitation/immunoblot and immunofluorescence analyses. ROS-induced stress, E-cadherin expression, Snail expression, and E-cadherin promoter methylation were confirmed in HCC tissues by immunoblot, immunohistochemistry, and methyl-specific polymerase chain reaction analyses. RESULTS We demonstrated that ROS induce hypermethylation of the E-cadherin promoter by increasing Snail expression. Snail induced DNA methylation of the E-cadherin promoter by recruiting histone deacetylase 1 and DNA methyltransferase 1. In human HCC tissues, we observed a correlation among ROS induction, E-cadherin down-regulation, Snail up-regulation, and E-cadherin promoter methylation. CONCLUSIONS These findings provide novel mechanistic insights into epigenetic modulations induced by ROS in the process of carcinogenesis. They are potentially relevant to understanding the activity of ROS in silencing various tumor suppressor genes and in subsequent tumor progression and metastasis.
Semi-Automatic Schema Integration in Clio

Schema integration is the problem of finding a unified representation, called the integrated schema, from a set of source schemas that are related to each other. The relationships between the source schemas can be represented via correspondences between schema elements or via some other forms of schema mappings such as constraints or views. The integrated schema can be viewed as a means for dealing with the heterogeneity in the source schemas, by providing a standard representation of the data. Schema integration has received much of attention in the research literature [1, 2, 6, 8, 10] and still remains a challenge in practice. Existing approaches require substantial amount of human feedback during the integration process and moreover, the outcome of these approaches is a single integrated schema. In general, however, there can be multiple possible schemas that integrate data in different ways and each may be valuable in a given scenario.
Subspace Clustering Based Tag Sharing for Inductive Tag Matrix Refinement with Complex Errors

Annotating images with tags is useful for indexing and retrieving images. However, many available annotation data include missing or inaccurate annotations. In this paper, we propose an image annotation framework which sequentially performs tag completion and refinement. We utilize the subspace property of data via sparse subspace clustering for tag completion. Then we propose a novel matrix completion model for tag refinement, integrating visual correlation, semantic correlation and the novelly studied property of complex errors. The proposed method outperforms the state-of-the-art approaches on multiple benchmark datasets even when they contain certain levels of annotation noise.
The Complexity of Decentralized Control of Markov Decision Processes

We consider decentralized control of Markov decision processes and give complexity bounds on the worst-case running time for algorithms that find optimal solutions. Generalizations of both the fully observable case and the partially observable case that allow for decentralized control are described. For even two agents, the finite-horizon problems corresponding to both of these models are hard for nondeterministic exponential time. These complexity results illustrate a fundamental difference between centralized and decentralized control of Markov decision processes. In contrast to the problems involving centralized control, the problems we considerprovably do not admit polynomial-time algorithms. Furthermore, assuming EXP ? NEXP, the problems require superexponential time to solve in the worst case.