Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomewide identification of target genes of histone methyltransferase dG9a during Drosophila embryogenesis

Post‐translational modification of the histone plays important roles in epigenetic regulation of various biological processes. Among the identified histone methyltransferases (HMTases), G9a is a histone H3 Lys 9 (H3K9)‐specific example active in euchromatic regions. Drosophila G9a (dG9a) has been reported to feature H3K9 dimethylation activity in vivo. Here, we show that the time required for hatching of a homozygous dG9a null mutant and heteroallelic combination of dG9a null mutants is delayed, suggesting that dG9a is at least partially responsible for progression of embryogenesis. Immunocytochemical analyses of the wild‐type and the dG9a null mutant flies indicated that dG9a localizes in cytoplasm up to nuclear division cycle 7 where it is likely responsible for di‐methylation of nucleosome‐free H3K9. From cycles 8–11, dG9a moves into the nucleus and is responsible for di‐methylating H3K9 in nucleosomes. RNA‐sequence analysis utilizing early wild‐type and dG9a mutant embryos showed that dG9a down‐regulates expression of genes responsible for embryogenesis. RNA fluorescent in situ hybridization analysis further showed temporal and spatial expression patterns of these mRNAs did not significantly change in the dG9a mutant. These results indicate that dG9a controls transcription levels of some zygotic genes without changing temporal and spatial expression patterns of the transcripts of these genes.
Flexible reference trace reduction for VM simulations

The unmanageably large size of reference traces has spurred the development of sophisticated trace reduction techniques. In this article we present two new algorithms for trace reduction: Safely Allowed Drop (SAD) and Optimal LRU Reduction (OLR). Both achieve high reduction factors and guarantee exact simulations for common replacement policies and for memories larger than a user-defined threshold. In particular, simulation on OLR-reduced traces is accurate for the LRU replacement algorithm, while simulation on SAD-reduced traces is accurate for the LRU and OPT algorithms. Both policies can easily be modified and extended to maintain timing information, thus allowing for exact simulation of the Working Set and VMIN policies. OLR also satisfies an optimality property: for a given original trace and chosen memory size, it produces the shortest possible reduced trace that has the same LRU behavior as the original for a memory of at least the chosen size. We present a proof of this optimality of OLR, and show that SAD, while not optimal, yields nearly optimal performance in practice.Our approach has multiple applications, especially in simulating virtual memory systems; many page replacement algorithms are similar to LRU in that more recently referenced pages are likely to be resident. For several replacement algorithms in the literature, SAD- and OLR-reduced traces yield exact simulations. For many other algorithms, our trace reduction eliminates information that matters little: we present extensive measurements to show that the error for simulations of the clock and segq (segmented queue) replacement policies (the most common LRU approximations) is under 3% for the vast majority of memory sizes. In nearly all cases, the error is much smaller than that incurred by the well-known stack deletion technique.SAD and OLR have many desirable properties. In practice, they achieve reduction factors up to several orders of magnitude. The reduction translates to both storage savings and simulation speedups. Both techniques require little memory and perform a single forward traversal of the original trace, making them suitable for online trace reduction. Neither requires that the simulator be modified to accept the reduced trace.
Small genome symbiont underlies cuticle hardness in beetles

Significance Beetles are successful in the terrestrial ecosystem, which is attributable to, at least partly, their highly sclerotized exoskeleton. Here, we report a bacterial symbiont extremely specialized for underpinning the beetle’s hardness. The ancient endosymbiont Nardonella associated with weevils has an extremely small genome devoted to a single biological function, tyrosine provisioning, which is needed for insect’s cuticle formation and hardening. Notably, only the final step reaction of the tyrosine synthesis pathway is complemented by host-encoded aminotransferases up-regulated in the bacteriome, highlighting a highly focused aspect of the host–symbiont metabolic integrity. Both symbiont suppression by an antibiotic and RNA interference of the host aminotransferases induce reddish and soft weevils, verifying the pivotal role of the symbiosis for the beetle’s hardness. Beetles, representing the majority of the insect species diversity, are characterized by thick and hard cuticle, which plays important roles for their environmental adaptation and underpins their inordinate diversity and prosperity. Here, we report a bacterial endosymbiont extremely specialized for sustaining beetle’s cuticle formation. Many weevils are associated with a γ-proteobacterial endosymbiont lineage Nardonella, whose evolutionary origin is estimated as older than 100 million years, but its functional aspect has been elusive. Sequencing of Nardonella genomes from diverse weevils unveiled drastic size reduction to 0.2 Mb, in which minimal complete gene sets for bacterial replication, transcription, and translation were present but almost all of the other metabolic pathway genes were missing. Notably, the only metabolic pathway retained in the Nardonella genomes was the tyrosine synthesis pathway, identifying tyrosine provisioning as Nardonella’s sole biological role. Weevils are armored with hard cuticle, tyrosine is the principal precursor for cuticle formation, and experimental suppression of Nardonella resulted in emergence of reddish and soft weevils with low tyrosine titer, confirming the importance of Nardonella-mediated tyrosine production for host’s cuticle formation and hardening. Notably, Nardonella’s tyrosine synthesis pathway was incomplete, lacking the final step transaminase gene. RNA sequencing identified host’s aminotransferase genes up-regulated in the bacteriome. RNA interference targeting the aminotransferase genes induced reddish and soft weevils with low tyrosine titer, verifying host’s final step regulation of the tyrosine synthesis pathway. Our finding highlights an impressively intimate and focused aspect of the host–symbiont metabolic integrity via streamlined evolution for a single biological function of ecological relevance.
Tips in biliary stone removal using endoscopic papillary large balloon dilation

The use of limited endoscopic sphincterotomy with large balloon dilation (ESLBD) has recently been shown to be useful for removal of large common bile duct stones in a dilated bile duct. The technique can reduce the need of mechanical lithotripsy, risk of adverse events and costs of the procedure. The aim of the review is to provide an overview in the current status of ESLBD with particular focus on the technical aspects of the technique for bile duct stone removal.
Maternal complications and neonatal outcome in Arab women of a fast developing country

Objective: The objective of the study was to examine maternal complications that occur during the third trimester and their neonatal outcome in Arab women residing in Qatar. Design: This is a prospective hospital-based study. Setting: The survey was carried out in women's hospital. Materials and Methods: The study was based on the log book of the women's hospital, from which we recruited women in their third trimester of pregnancy between the first week of January 2010 and April 2011. Of the 1 824 Arab women who were approached to participate in the study, 1 432 (78.5%) consented. Face-to-face interviews were conducted with the pregnant women in the third trimester attending routine antenatal clinics at a women's hospital. The questionnaire covered variables related to sociodemographic factors, family history, medical history, maternal complications, and neonatal outcome. Medical records of the patients were referred to collect the clinical variables. Results: Of the pregnant women studied, 39.8% were less than 30 years of age. The risk of maternal complications was higher in housewives (60.8%) and women with a low monthly household income (38.2%). Most of the pregnant women (77.6%) had antenatal care. Normal delivery (69.7%) was more common in expatriate Arab women, whereas caesarean was more prevalent in Qatari women (22.2%). Women aged 35 years or older had a significantly higher risk of maternal complications such as gestational diabetes (20.8% vs 13.4%; P < 0.01), gestational hypertension (21.6% vs 15.2%; P = 0.003), and ante-partum hemorrhage (17.9% vs 13.7%; P = 0.042) than younger women. Gestational diabetes increased the risk of caesarean delivery (25.1%) and macrosomia (42.3%). The frequency of caesarean delivery (22.1%) was higher in women with gestational hypertension. Neonatal complications such as Apgar score (<7) 1 minute (33.1% vs 21.2%; P < 0.001), 5 minutes (13.1% vs 8.2%; P = 0.005), and congenital anomalies (2.9% vs 0.9%; P = 0.007) were significantly higher in newborns of older women. Low birth weight (11.1%) and Apgar 1st minute < 7 rate (28.2%) were higher in newborns of mothers with ante-partum hemorrhage. Conclusion: The study findings revealed that maternal complications such as gestational diabetes, gestational hypertension, ante-partum hemorrhage, and maternal anemia were significantly higher in older pregnant women. Similarly, neonatal complications were higher in the newborns of older women. Gestational hypertension was the leading maternal complication observed in Arab women.
Multi-Contact Locomotion Using a Contact Graph with Feasibility Predictors

Multi-contact locomotion that uses both the hands and feet in a complex environment remains a challenging problem in computer animation. To address this problem, we present a contact graph, which is a motion graph augmented by learned feasibility predictors, namely contact spaces and an occupancy estimator, for a motion clip in each graph node. By estimating the feasibilities of candidate contact points that can be reached by modifying a motion clip, the predictors allow us to find contact points that are likely to be valid and natural before attempting to generate the actual motion for the contact points. The contact graph thus enables the efficient generation of multi-contact motion in two steps: planning contact points to the goal and then generating the whole-body motion. We demonstrate the effectiveness of our method by creating several climbing motions in complex and cluttered environments by using only a small number of motion samples.
Automatically reducing and bounding geometric complexity by using images

Large and complex 3D models are required for computer-aided design, architectural visualizations, flight simulation, and many types of virtual environments. Often, it is not possible to render all the geometry of these complex scenes at interactive rates, even with high-end computer graphics systems. This has led to extensive work in 3D model simplification methods. We have been investigating dynamically replacing portions of 3D models with images. This approach is similar to the old stage trick of draping cloth backgrounds in order to generate the illusion of presence in a scene too complex to actually construct on stage. An image (or backdrop) once created, can be rendered in time independent of the geometric complexity it represents. Consequently, significant frame rate increases can be achieved at the expense of storage space and visual quality. Properly handling these last two tradeoffs is crucial to a fast rendering system. In this dissertation, we present a preprocessing and run-time algorithm for creating a constant-frame-rate rendering system that replaces selected geometry with images enhanced with depth at each pixel. First, we describe the preprocessing algorithm to automatically bound the geometric complexity of arbitrary 3D models by using images. Second, we explore two general approaches to displaying images, surrounded by geometry, at run time. Third, we present a system tailored to architectural models.
Statistical Syntax-Directed Translation with Extended Domain of Locality

In syntax-directed translation, the source-language input is first parsed into a parse-tree, which is then recursively converted into a string in the target-language. We model this conversion by an extended tree-to-string transducer that has multi-level trees on the source-side, which gives our system more expressive power and flexibility. We also define a direct probability model and use a linear-time dynamic programming algorithm to search for the best derivation. The model is then extended to the general log-linear frame-work in order to incorporate other features like n-gram language models. We devise a simple-yet-effective algorithm to generate non-duplicate k-best translations for n-gram rescoring. Preliminary experiments on English-to-Chinese translation show a significant improvement in terms of translation quality compared to a state-of-the- art phrase-based system.
Compartmentalized PDE4A5 Signaling Impairs Hippocampal Synaptic Plasticity and Long-Term Memory

Alterations in cAMP signaling are thought to contribute to neurocognitive and neuropsychiatric disorders. Members of the cAMP-specific phosphodiesterase 4 (PDE4) family, which contains >25 different isoforms, play a key role in determining spatial cAMP degradation so as to orchestrate compartmentalized cAMP signaling in cells. Each isoform binds to a different set of protein complexes through its unique N-terminal domain, thereby leading to targeted degradation of cAMP in specific intracellular compartments. However, the functional role of specific compartmentalized PDE4 isoforms has not been examined in vivo. Here, we show that increasing protein levels of the PDE4A5 isoform in mouse hippocampal excitatory neurons impairs a long-lasting form of hippocampal synaptic plasticity and attenuates hippocampus-dependent long-term memories without affecting anxiety. In contrast, viral expression of a truncated version of PDE4A5, which lacks the unique N-terminal targeting domain, does not affect long-term memory. Further, overexpression of the PDE4A1 isoform, which targets a different subset of signalosomes, leaves memory undisturbed. Fluorescence resonance energy transfer sensor-based cAMP measurements reveal that the full-length PDE4A5, in contrast to the truncated form, hampers forskolin-mediated increases in neuronal cAMP levels. Our study indicates that the unique N-terminal localization domain of PDE4A5 is essential for the targeting of specific cAMP-dependent signaling underlying synaptic plasticity and memory. The development of compounds to disrupt the compartmentalization of individual PDE4 isoforms by targeting their unique N-terminal domains may provide a fruitful approach to prevent cognitive deficits in neuropsychiatric and neurocognitive disorders that are associated with alterations in cAMP signaling. SIGNIFICANCE STATEMENT Neurons exhibit localized signaling processes that enable biochemical cascades to be activated selectively in specific subcellular compartments. The phosphodiesterase 4 (PDE4) family coordinates the degradation of cAMP, leading to the local attenuation of cAMP-dependent signaling pathways. Sleep deprivation leads to increased hippocampal expression of the PDE4A5 isoform. Here, we explored whether PDE4A5 overexpression mimics behavioral and synaptic plasticity phenotypes associated with sleep deprivation. Viral expression of PDE4A5 in hippocampal neurons impairs long-term potentiation and attenuates the formation of hippocampus-dependent long-term memories. Our findings suggest that PDE4A5 is a molecular constraint on cognitive processes and may contribute to the development of novel therapeutic approaches to prevent cognitive deficits in neuropsychiatric and neurocognitive disorders that are associated with alterations in cAMP signaling.
An evolutionary lagrangian method for the 0/1 multiple knapsack problem

We propose a new evolutionary approach to solve the 0/1 multiple knapsack problem. We approach the problem from a new viewpoint different from traditional methods. The most remarkable feature is the Lagrangian method. Lagrange multipliers transform the problem, keeping the optimality as well as decreasing the complexity. However, it is not easy to find Lagrange multipliers nearest to the constraints of the problem. We propose an evolution strategy to find the optimal Lagrange multipliers. Also, we improve the evolution strategy by adjusting its objective function properly. We show the efficiency of the proposed methods by the experiments. We make comparisons with existing general approach on well-known benchmark data.
Cognitive‐nigrostriatal relationships in de novo, drug‐naïve Parkinson's disease patients: A [I‐123]FP‐CIT SPECT study

To unveil cognitive‐nigrostriatal correlations in Parkinson's disease (PD), 30 de novo, drug‐naïve PD patients and 15 patients with essential tremor (Controls, CTR) underwent a neuropsychological (NPS) battery and brain SPECT with [I‐123]Ioflupane, as a biomarker of nigrostriatal function. Automatic extraction of uptake at caudate and putamen level was conducted through the BasGan software, also allowing partial volume effect correction. Because of the multicollinearity among neuropsychological tests and among SPECT variables, factor analysis was applied to 16 neuropsychological scores; moreover, the four SPECT variables were merged into a mean SPECT value (mSPECT). Factor analysis identified four NPS factors: a dys‐executive (NPS‐EX), a visuospatial (NPS‐VS), a verbal memory (NPS‐VM), and a “mixed” (NPD‐MIX) factor. In PD group, there were inverse correlations between UPDRS‐III score and both NPS‐VS (P < 0.01) and mSPECT (P < 0.05), and a direct correlation between mSPECT and NPS‐EX (P < 0.05). Post hoc analysis showed a direct correlation between NPS‐EX and caudate uptake in both hemispheres (P < 0.05). Moreover, inverse correlations were found between UPDRS‐III and, respectively, putamen uptake in the less affected hemisphere (P < 0.01), and putamen and caudate uptake in the more affected hemisphere (P < 0.05). In CTR, no correlation was found between mSPECT and either NPS or GDS values. Nigro‐caudate function affects executive capabilities in PD but not in CTR, which appears to be unrelated to the disease motor severity at its onset. Instead, PD motor severity is related to nigro‐putaminal impairment and visuospatial dysfunction. The role of these data as predictive features of cognitive decline and eventually dementia remains to be established in longitudinal studies. © 2010 Movement Disorder Society
Network simulation via hybrid system modeling: a time-stepped approach

The ever increasing complexity of networks dramatically increases the challenges faced by service providers to analyze network behavior and (re)provision resources to support multiple complex distributed applications. Accurate and scalable simulation tools are pivotal to this cause. The recently proposed hybrid systems model for data communication networks shows promise in achieving performance characteristics comparable to fluid models while retaining the accuracy of discrete models. Using the hybrid systems paradigm, this paper provides contributions to the modeling of TCP behavior and the analysis/simulation of data communication networks based on these models. An important distinguishing feature of our simulation framework is a faithful accounting of link propagation delays which has been ignored in previous work for the sake of simplicity. Other salient aspects of the work include a new finite state machine model for a drop-tail queue, a new model for fast recovery/fast retransmit mode, a revised sending rate model, and an embedded time-out mode transition mechanism all of which employ a time-stepped solution method to solve the hybrid system network models. Our simulation results are consistent with well-known packet based simulators such as ns-2, thus demonstrating the accuracy of our hybrid model. Our future efforts will be directed towards studying and improving the computational performance of hybrid model based simulations.
Link Sensing-Adaptive Passive Object Localization in Wireless Sensor Networks

The passive object localization (POL) problem in wireless sensor networks aims to determine the location of a target without any device attached for receiving or transmitting signal. This problem is challenging as there is very limited information available for deriving the target location. By combining the diffraction and scattering models, we propose a link sensing adaptive approach to POL, which first decides the target position attribute based on the signal strength and then localizes the target in different modes. We conduct rigorous localizability analyses and design a unit localization area scheme to achieve a higher level of localization accuracy. The efficacy of the proposed method is evaluated through comprehensive experiments in real life network environments.
Living well in the Neuropolis

This paper is about the relationship between cities and brains: it charts the back-and-forth between the hectic, stressful lives of urban citizens, and a psychological and neurobiological literature that claims to make such stress both visible and knowable. But beyond such genealogical labour, the paper also asks: what can a sociology concerned with the effects of ‘biosocial’ agencies take from a scientific literature on the urban brain? What might sociology even contribute to that literature, in its turn? To investigate these possibilities, the paper centres on the emergence and description of what it calls ‘the Neuropolis’ – a term it deploys to hold together both an intellectual and scientific figure and a real, physical enclosure. The Neuropolis is an image of the city embedded in neuropsychological concepts and histories, but it also describes an embodied set of (sometimes pathological) relations and effects that take places between cities and the people who live in them. At the heart of the paper is an argument that finding a way to thread these phenomena together might open up new paths for thinking about ‘good’ life in the contemporary city. Pushing at this claim, the paper argues that mapping the relations, histories, spaces, and people held together by this term is a vital task for the future of urban sociology.
Secure multiparty computation of approximations

Approximation algorithms can sometimes provide efficient solutions when no efficient exact computation is known. In particular, approximations are often useful in a distributed setting where the inputs are held by different parties and may be extremely large. Furthermore, for some applications, the parties want to compute a function of their inputs securely without revealing more information than necessary. In this work, we study the question of simultaneously addressing the above efficiency and security concerns via what we call secure approximations.We start by extending standard definitions of secure (exact) computation to the setting of secure approximations. Our definitions guarantee that no additional information is revealed by the approximation beyond what follows from the output of the function being approximated. We then study the complexity of specific secure approximation problems. In particular, we obtain a sublinear-communication protocol for securely approximating the Hamming distance and a polynomial-time protocol for securely approximating the permanent and related #P-hard problems.
Numerical solution of stiff differential equations via Haar wavelets

A simple and effective algorithm based on Haar wavelets is proposed to the solution of stiff problems in this article. It can integrate the stiff equation with very accurate results for any length of time. The simulation result shows that the single-term Haar wavelet method is better than the improved Runge–Kutta–Fehlberg method, while the terms of both expansions are the same.