Miracle-dz/UniFAR-FTUs huggingface dataset:
Disentangling Brain Graphs: A Note on the Conflation of Network and Connectivity Analyses

Understanding the human brain remains the holy grail in biomedical science, and arguably in all of the sciences. Our brains represent the most complex systems in the world (and some contend the universe) comprising nearly 100 billion neurons with septillions of possible connections between them. The structure of these connections engenders an efficient hierarchical system capable of consciousness, as well as complex thoughts, feelings, and behaviors. Brain connectivity and network analyses have exploded over the last decade due to their potential in helping us understand both normal and abnormal brain function. Functional connectivity (FC) analysis examines functional associations between time series pairs in specified brain voxels or regions. Brain network analysis serves as a distinct subfield of connectivity analysis, in which associations are quantified for all time series pairs to create an interconnected representation of the brain (a brain network), which allows studying its systemic properties. While connectivity analyses underlie network analyses, the subtle distinction between the two research areas has generally been overlooked in the literature, with them often being referred to synonymously. However, developing more useful analytic methods and allowing for more precise biological interpretations require distinguishing these two complementary domains.
Understanding Plant Cellulose Synthases through a Comprehensive Investigation of the Cellulose Synthase Family Sequences

The development of cellulose as an organizing structure in the plant cell wall was a key event in both the initial colonization and the subsequent domination of the terrestrial ecosystem by vascular plants. A wealth of experimental data has demonstrated the complicated genetic interactions required to form the large synthetic complex that synthesizes cellulose. However, these results are lacking an extensive analysis of the evolution, specialization, and regulation of the proteins that compose this complex. Here we perform an in-depth analysis of the sequences in the cellulose synthase (CesA) family. We investigate the phylogeny of the CesA family, with emphasis on evolutionary specialization. We define specialized clades and identify the class-specific regions within the CesA sequence that may explain this specialization. We investigate changes in regulation of CesAs by looking at the conservation of proposed phosphorylation sites. We investigate the conservation of sites where mutations have been documented that impair CesA function, and compare these sites to those observed in the closest cellulose synthase-like (Csl) families to better understand what regions may separate the CesAs from other Csls. Finally we identify two positions with strong conservation of the aromatic trait, but lacking conservation of amino acid identity, which may represent residues important for positioning the sugar substrate for catalysis. These analyses provide useful tools for understanding characterized mutations and post-translational modifications, and for informing further experiments to probe CesA assembly, regulation, and function through site-directed mutagenesis or domain swapping experiments.
Learning Fine-Grained Knowledge about Contingent Relations between Everyday Events

Much of the user-generated content on social media is provided by ordinary people telling stories about their daily lives. We develop and test a novel method for learning fine-grained common-sense knowledge from these stories about contingent (causal and conditional) relationships between everyday events. This type of knowledge is useful for text and story understanding, information extraction, question answering, and text summarization. We test and compare different methods for learning contingency relation, and compare what is learned from topic-sorted story collections vs. general-domain stories. Our experiments show that using topic-specific datasets enables learning finer-grained knowledge about events and results in significant improvement over the baselines. An evaluation on Amazon Mechanical Turk shows 82% of the relations between events that we learn from topic-sorted stories are judged as contingent.
Dietary cholesterol-oxidation products accumulate in serum and liver in apolipoprotein E-deficient mice, but do not accelerate atherosclerosis

There are conflicting reports regarding the effect of dietary cholesterol-oxidation products (oxysterols) on the development of atherosclerosis in experimental animals. To address this issue, apolipoprotein (Apo) E-deficient mice were fed a purified diet (AIN-93) or the same purified diet containing 0·2 g cholesterol or 0·2 g oxysterols/kg. The dietary oxysterols had no significant effect on the serum lipid levels. Although all of the diet-derived oxysterols (cholest-5-en-3β,7α-diol, cholest-5-en-3β,7β-diol, cholestan-5α,6α-epoxy-3β-ol, cholestan-5β,6β-epoxy-3β-ol, cholestan-3β, 5α, 6β-triol, cholest-5-en-3β-ol-7-one and cholest-5-en-3β, 25-diol) accumulated in the serum and liver, only cholest-5-en-3β-ol-7-one and cholestan-3β, 5α, 6β-triol accumulated significantly (P<0·05) in the aorta. The oxysterol diet did not result in elevation of the aortic cholesterol level or the lesion volume in the aortic valve. These present results indicate that exogenous oxysterols do not promote the development of atherosclerosis in ApoE-deficient mice.
The Balance between Recombination Enzymes and Accessory Replicative Helicases in Facilitating Genome Duplication

Accessory replicative helicases aid the primary replicative helicase in duplicating protein-bound DNA, especially transcribed DNA. Recombination enzymes also aid genome duplication by facilitating the repair of DNA lesions via strand exchange and also processing of blocked fork DNA to generate structures onto which the replisome can be reloaded. There is significant interplay between accessory helicases and recombination enzymes in both bacteria and lower eukaryotes but how these replication repair systems interact to ensure efficient genome duplication remains unclear. Here, we demonstrate that the DNA content defects of Escherichia coli cells lacking the strand exchange protein RecA are driven primarily by conflicts between replication and transcription, as is the case in cells lacking the accessory helicase Rep. However, in contrast to Rep, neither RecA nor RecBCD, the helicase/exonuclease that loads RecA onto dsDNA ends, is important for maintaining rapid chromosome duplication. Furthermore, RecA and RecBCD together can sustain viability in the absence of accessory replicative helicases but only when transcriptional barriers to replication are suppressed by an RNA polymerase mutation. Our data indicate that the minimisation of replisome pausing by accessory helicases has a more significant impact on successful completion of chromosome duplication than recombination-directed fork repair.
China’s Core Competences Advantage in a Multipolar World

Societal traditions have a decisive impact on cognition and cognitive biases, and thus on the foundations of core competences, including (natural) science and (natural) science-based innovation. The increasing global multi-polarity means that the centuries old dominance of the Occidental Tradition is waning, and the other societal traditions, including the Sino Tradition, will gain ground. Chinese companies will have an advantage over their Occidental counterparts, because Chinese companies can search for core competences and thus competitive advantages based on the different aspects of Occidental Tradition, Sino Tradition and the combination of the two. Occidental companies are limited to the different aspects of the Occidental Tradition. Thus, Chinese companies have a core competences advantage in a multipolar world.
Option Hedging in thePresence of Jump

We examine Schweizer's (1991) locally risk-minimizing (LRM) hedge approach for hedging a European call in the case when the stock price follows a Poisson jump di usion process with lognormally distributed jump sizes. In contrast to Merton's (1976) hedging strategy where di usion risk is perfectly hedged while jump risk remains un-hedged, the locally risk-minimizing strategy hedges both di usion risk as well as jump risk partly. The hedge ratio consists of a di usion component and a jump component. The value of the LRM hedge portfolio is equal to the (discounted) expected terminal payo of the option weighted with a so-called minimal martingale density. It is a weighted sum of Black/Scholes values where some weights may be negative. The latter property is due to our result that the minimal martingale density is negative with positive probability if, e.g., the market price of risk is positive. However, introducing a single call does not admit arbitrage opportunities if its value is smaller than the underlying stock price and larger than the Black/Scholes value based on the di usion volatility. We relate the LRM approach to the so-called locally variance-minimizing (LVM) hedging strategy in Bates' (1991) systematic jump risk model. By numerical analysis we nd that the LRM and LVM hedge ratios are less sensitive to changes in the stock price than delta hedging strategies in the models of Merton, Black/Scholes, and Bates. If the expected jump size is signi cantly di erent from zero and positive (negative), then the LRM and LVM hedge ratios are substantially larger (smaller) than e.g. Merton's for out-of-the-money (in-the-money) calls. Moreover, the worst case behaviour of the LRM strategy and LVM strategy are substantially better: The 99%-, 95%-, as well as the 90%-quantile of the total hedging costs are signi cantly lower than for the alternative strategies.
Control of Scar Tissue Formation in the Cornea: Strategies in Clinical and Corneal Tissue Engineering

Corneal structure is highly organized and unified in architecture with structural and functional integration which mediates transparency and vision. Disease and injury are the second most common cause of blindness affecting over 10 million people worldwide. Ninety percent of blindness is permanent due to scarring and vascularization. Scarring caused via fibrotic cellular responses, heals the tissue, but fails to restore transparency. Controlling keratocyte activation and differentiation are key for the inhibition and prevention of fibrosis. Ophthalmic surgery techniques are continually developing to preserve and restore vision but corneal regression and scarring are often detrimental side effects and long term continuous follow up studies are lacking or discouraging. Appropriate corneal models may lead to a reduced need for corneal transplantation as presently there are insufficient numbers or suitable tissue to meet demand. Synthetic optical materials are under development for keratoprothesis although clinical use is limited due to implantation complications and high rejection rates. Tissue engineered corneas offer an alternative which more closely mimic the morphological, physiological and biomechanical properties of native corneas. However, replication of the native collagen fiber organization and retaining the phenotype of stromal cells which prevent scar-like tissue formation remains a challenge. Careful manipulation of culture environments are under investigation to determine a suitable environment that simulates native ECM organization and stimulates keratocyte migration and generation.
Management and Training of Dairy Personnel with Emphasis on Team Work and Performance

It is well known that transition cow diseases negatively affect reproductive performance; thus, profitability and welfare of dairy herds. Prevention of diseases at the herd level requires a constant effort and effective coordination of the total system (animals, environment, nutrition, and personnel). Substantial knowledge exists to prevent many diseases or conditions; however, it must be translated into on-farm applications or practices to have a meaningful effect at the herd level. Reproductive data of dairy herds throughout the United States showed that more than 73% of the variation in pregnancy risk (between bottom 10% and top 10% of herds) was due to management practices and/or environment. Fully trained and competent workers know what to do and how to do it, and have the skills and abilities to do the work. However, competent workers will often fail to perform when conflict or lack of satisfaction, motivation, and/or communication occur; resulting in lower work performance which affects the overall herd productivity. Frequent assessment of performance, educational needs, and training of dairy personnel should be top priorities for dairy operations to achieve a consistent and efficient herd performance over time. Practicing veterinarians regularly visit their clients and are ideally placed to identify at-risk dairy herds likely to benefit from personnel training (e.g., calving management), conflict management, and development of preventive SOPs.
Testate amoebae as palaeohydrological proxies in sürmene ağaçbaşi yaylasi peatland (northeast Turkey)

Testate amoebae are unicellular micro-organisms whose hydrological sensitivity and good preservation in peats make them valuable proxies for past peatland surface wetness, and therefore climate. Previous testate amoebae transfer functions have been spatially restricted with no studies from Asia. To derive a transfer function, a sequence of samples was extracted from an ombrotrophic peatland in Turkey and amoebae counted. The internal structure of the data was explored using principal components analysis and relationships with the environmental data tested by redundancy analyses. Transfer function models were developed using a variety of techniques. As in other regions, depth to water table is the most important control on amoebae community composition. Transfer function performance was initially poor, primarily due to the inclusion of samples from areas of the site that had been heavily affected by peat cutting and had distinctly different amoebae communities. Model performance is improved by selective sample exclusion, reducing jack-knifed root mean square error of prediction to 7.1 cm. The model was tested using an initial palaeoecological data-set. Overlap with the training set was limited, although a hydrological reconstruction using this model produces similar results to a transfer function derived from northern European peatlands. This study provides the first testate amoebae transfer function from Asia and demonstrates that hydrological preferences of many of the key taxa are consistent across a large area of the Northern Hemisphere. The transfer function will allow detailed palaeoclimate reconstruction from this peatland, adding to our knowledge of Holocene climatic change in southwest Asia.
How and why criteria defining moderators and mediators differ between the Baron & Kenny and MacArthur approaches.

OBJECTIVE In recognition of the increasingly important role of moderators and mediators in clinical research, clear definitions are sought of the two terms to avoid inconsistent, ambiguous, and possibly misleading results across clinical research studies. DESIGN The criteria used to define moderators and mediators proposed by the Baron & Kenny approach, which have been long used in social/behavioral research, are directly compared to the criteria proposed by the recent MacArthur approach, which modified the Baron & Kenny criteria. RESULTS After clarifying the differences in criteria between approaches, the rationale for the modifications is clarified and the implications for the design and interpretation of future studies considered. CONCLUSIONS Researchers may find modifications introduced in the MacArthur approach more appropriate to their research objectives, particularly if their research might have a direct influence on decision making.
Evaluation of Existing GaAs MIM-Capacitor Processes for Use with High-Voltage GaN MMIC Technologies

In this paper several existing industrial GaAs MIMcapacitor processes were evaluated regarding their suitability for use with high-voltage GaN MMIC technologies. These processes were tested using different time domain voltage stress methods from which lifetime estimations based on the linear field model were calculated. In addition the influence of electrode geometries and dielectric thicknesses on capacitor performance was investigated. Furthermore early device failures were correlated with defects detected on MIM bottom electrodes, these defects being identified by automated inspection
A theory of clock synchronization

We consider the problem of clock synchronization in a system with uncertain message delays and clocks with bounded drift. To analyze this classical problem, we introduce the concept of synchronization graphs, and show that the tightest achievable synchronization at any given execution is characterized by the distances in the synchronization graph for that execution. Synchronization graphs are derived from information which is locally available for computation at the processors (local time of events and system specification), and can therefore be used by distributed algorithms. Using synchronization graphs, we obtain the first optimal on-line distributed algorithms for external clock synchronization, where the task of all processors is to estimate the reading of the local clock of a distinguished processor. The algorithms are optimal for all executions, rather than only for worst cases. The algorithm for systems with arbitrarily drifting clocks has high overhead; we prove that this phenomenon is unavoidable, namely any optimal general algorithm for external synchronization has unbounded space complexity. For systems with drift-free clocks (i.e., clocks that run at the rate of real time), we present a particularly simple and efficient algorithm. We also present results for internal synchronization, where the task of the processors in the system is to generate a synchronized "tick. " Our approach is robust in the sense it encompasses various system models, such as point-to-point or broadcast channels, communication links that may lose, duplicate and re-order messages, and crashing processors. In addition, synchronization graphs can be used to detect corrupted information. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Edge detection based JND model for digital watermarking

In the watermarking schemes, Just Noticeable Distortion (JND) model provides an efficient method to keep the balance between watermark's imperceptibility and robustness. Traditional JND models are not as perfect as they should be. Edge detection, which extracts content features well, improves the performance of JND models. In this paper we explore the reasons and simulate JND models based on edge detection either in spatial domain or in DCT domain. The experiment results show that JND models based on edge detection in DCT domain have better performance than those in spatial domain.
Gauge Optimization and Duality

Gauge functions significantly generalize the notion of a norm, and gauge optimization, as defined by [R. M. Freund, Math. Programming, 38 (1987), pp. 47--67], seeks the element of a convex set that is minimal with respect to a gauge function. This conceptually simple problem can be used to model a remarkable array of useful problems, including a special case of conic optimization, and related problems that arise in machine learning and signal processing. The gauge structure of these problems allows for a special kind of duality framework. This paper explores the duality framework proposed by Freund, and proposes a particular form of the problem that exposes some useful properties of the gauge optimization framework (such as the variational properties of its value function), and yet maintains most of the generality of the abstract form of gauge optimization.
Test case prioritization for regression testing of service-oriented business applications

Regression testing assures the quality of modified service-oriented business applications against unintended changes. However, a typical regression test suite is large in size. Earlier execution of those test cases that may detect failures is attractive. Many existing prioritization techniques order test cases according to their respective coverage of program statements in a previous version of the application. On the other hand, industrial service-oriented business applications are typically written in orchestration languages such as WS-BPEL and integrated with workflow steps and web services via XPath and WSDL. Faults in these artifacts may cause the application to extract wrong data from messages, leading to failures in service compositions. Surprisingly, current regression testing research hardly considers these artifacts. We propose a multilevel coverage model to capture the business process, XPath, and WSDL from the perspective of regression testing. We develop a family of test case prioritization techniques atop the model. Empirical results show that our techniques can achieve significantly higher rates of fault detection than existing techniques.
Technicolor Racism or Caricature Assassination? Satirizing White Anxiety About the Obama Presidency

ABSTRACT Using the theory of iconography, this article deconstructs the “Politics of Fear” caricature of Barack and Michelle Obama, featured on the cover of The New Yorker magazine, to investigate White imagination about the couple's socio-cultural identities. Published before the 2008 Democratic nominating convention, the caricature set the couple within the Oval Office and depicted Barack in an Arab-style tunic bumping fists with an armed Angela Davis-esque Michelle dressed in fatigues. We examine defenses of the image as satire against anti-Obama caricatures. We also examine original and secondary survey data to uncover the determinants of support for the caricature. We argue that the caricature gave a unifying visual form to disparate trepidations about the Americanness and religious identity of the Obamas. Our article concludes by situating the controversy over the cover alongside longstanding suspicions by Whites that Barack Obama has deceived Americans about his religious identity and loyalty to American ideals.
Pre-clinical assessment of memantine as a potential therapeutic agent for the treatment of Down syndrome

Down syndrome (DS) is the most common genetically defined cause of intellectual disabilities and the Ts65Dn mouse is the most researched mouse model for DS. Three major alterations in hippocampal synaptic plasticity have been described in Ts65Dn mice: 1) reduced long-term potentiation (LTP) in the CA1; 2) almost complete absence of LTP in the dentate gyrus; and 3) increased long-term depression (LTD) in the CA1 region. At present, the mechanisms underlying these changes in synaptic plasticity are not well understood. However, there are several human chromosome 21 encoded proteins that are predicted to directly or indirectly impact NMDA receptor function or NMDA-mediated signaling. Given the key role of NMDA receptors in synaptic plasticity and learning and memory, the studies described here may help provide a mechanistic basis for previous electrophysiological and behavioral studies in the Ts65Dn mouse. In this study, we found that the Ts65Dn mouse displays pharmacological responses consistent with a dysfunction in molecular pathways coupled to the gating of NMDA receptors. In particular, the Ts65Dn mouse displayed a