Miracle-dz/UniFAR-FTUs huggingface dataset:
Combinatorial roles for BMPs and Endothelin 1 in patterning the dorsal-ventral axis of the craniofacial skeleton

Bone morphogenetic proteins (BMPs) play crucial roles in craniofacial development but little is known about their interactions with other signals, such as Endothelin 1 (Edn1) and Jagged/Notch, which pattern the dorsal-ventral (DV) axis of the pharyngeal arches. Here, we use transgenic zebrafish to monitor and perturb BMP signaling during arch formation. With a BMP-responsive transgene, Tg(Bre:GFP), we show active BMP signaling in neural crest (NC)-derived skeletal precursors of the ventral arches, and in surrounding epithelia. Loss-of-function studies using a heat shock-inducible, dominant-negative BMP receptor 1a [Tg(hs70I:dnBmpr1a-GFP)] to bypass early roles show that BMP signaling is required for ventral arch development just after NC migration, the same stages at which we detect Tg(Bre:GFP). Inhibition of BMP signaling at these stages reduces expression of the ventral signal Edn1, as well as ventral-specific genes such as hand2 and dlx6a in the arches, and expands expression of the dorsal signal jag1b. This results in a loss or reduction of ventral and intermediate skeletal elements and a mis-shapen dorsal arch skeleton. Conversely, ectopic BMP causes dorsal expansion of ventral-specific gene expression and corresponding reductions/transformations of dorsal cartilages. Soon after NC migration, BMP is required to induce Edn1 and overexpression of either signal partially rescues ventral skeletal defects in embryos deficient for the other. However, once arch primordia are established the effects of BMPs become restricted to more ventral and anterior (palate) domains, which do not depend on Edn1. This suggests that BMPs act upstream and in parallel to Edn1 to promote ventral fates in the arches during early DV patterning, but later acquire distinct roles that further subdivide the identities of NC cells to pattern the craniofacial skeleton.
Chinese Word Sense Disambiguation Based on Lexical Semantic Ontology

This paper describes preliminary works of word sense disambiguation on Chinese verbs using the information derived from lexical semantic ontology (LSO). In spite of sophisticated methods, simple algorithm is employed to underline the characters of the features chosen from LSO data. Several groups of tests are designed to find different effects of the features and other aspects. Some promising results are gotten from the prime tests on nine Chinese ambiguous verbs. The results show what informative features the LSO provides and the potential improving ways.
Posttranscriptional Control of the Expression and Function of Diacylglycerol Acyltransferase-1 in Mouse Adipocytes*

Acyl-CoA:diacylglycerol acyltransferase-1 (DGAT1) catalyzes the final step of triglyceride synthesis in mammalian cells. Data obtained from DGAT1-knockout mice have indicated that this enzyme plays an important role in energy homeostasis. We investigated the regulation of the expression and function of DGAT1 in mouse 3T3-L1 cell as a model for mammalian adipocytes. We demonstrated that the DGAT1 protein level increased by ∼90-fold following differentiation of 3T3-L1 into mature adipocytes, a change that was accompanied by ∼7-fold increase in DGAT1 mRNA. On the other hand, forced overexpression of DGAT1 mRNA by >20-fold via a recombinant adenovirus only resulted in ∼2-fold increase in DGAT1 protein in mature adipocytes and little increase in preadipocytes. These results indicated that gene expression of DGAT1 in adipocytes is subjected to rigorous posttranscriptional regulation, which is modulated significantly by the differentiation status of 3T3-L1 cells. Protein stability is not a significant factor in the control of DGAT1 expression. The steady-state levels of DGAT1 were unaffected by blockage of proteolytic pathways by ALLN. However, translational control was suggested by sequence analysis of the 5′-untranslated region of human DGAT1 (hDGAT1) mRNA. We found that the level of DGAT1 activity was predominantly a function of the steady-state level of DGAT1 protein. No significant functional changes were observed when the conserved tyrosine phosphorylation site in hDGAT1 was mutated by a single base pair substitution. Despite only a ∼2-fold increase in DGAT1 protein caused by recombinant viral transduction, a proportionate increase in cellular triglyceride synthesis resulted without affecting the triglyceride lipolysis rate, leading to >2-fold increase in intracellular triglyceride accumulation. No change in adipocyte morphology or in the expression levels of lipoprotein lipase, proxisomal proliferation-activating receptor-γ, and aP2 was evident secondary to DGAT1 overexpression at different stages in 3T3-L1 differentiation. These data suggest that dysregulation of DGAT1 may play a role in the development of obesity, and manipulation of the steady-state level of DGAT1 protein may offer a potential means to treat or prevent obesity.
Personal and Contextual Contributors to Young Children's Activity-Based Perceived Self-Efficacy

This study investigated personal and contextual influences to young children's perceived self-efficacy (SE) in social and independent learning situations. The participants were children (n = 24) 6–8 years old from four Finnish elementary school classrooms. First, teachers from each classroom were asked to rate their students’ social competence (SC). Second, the participants were videotaped in 45 social and 15 independent learning situations, and later interviewed about their SE perceptions using video-stimulated recall. Participants with higher SE demonstrated more stable perceptions and greater involvement in social learning situations. However, a statistically significant relationship between perceived SE and SC was not found. Participants also identified 4 factors promoting perceived SE: positive emotional states, mastery experiences, personal strategic behavior, and contextual support.
Integrating logic retiming and register placement

Retiming relocates registers in a circuit to shorten the clock cycle time. In deep sub-micron era, conventional pre-layout retiming cannot work properly because of dominant interconnection delay that is not available before layout. Although some retiming algorithms incorporating interconnection delay have been proposed, layout information is still not utilized effectively nor efficiently. Retiming and layout is combined for the first time in this paper. We present heuristics for two key problems: interconnection delay estimation and post-retiming incremental placement. An efficient retiming algorithm incorporating interconnection delay is also proposed. Experimental results show that on the average we can improve the circuit speed by 5.4% targeted toward a 0.52 /spl mu/m CMOS technology. Scaling down the technology to 0.1 /spl mu/m, as much as 25.6% improvement have been achieved.
AC-WAR: Architecting the Cache Hierarchy to Improve the Lifetime of a Non-Volatile Endurance-Limited Main Memory

This work shows how by adapting replacement policies in contemporary cache hierarchies it is possible to extend the lifespan of a write endurance-limited main memory by almost one order of magnitude. The inception of this idea is that during cache residency 1) blocks are modified in a bimodal way: either most of the content of the block is modified or most of the content of the block never changes, and 2) in most applications, the majority of blocks are only slightly modified. When those facts are considered by the cache replacement algorithms, it is possible to significantly reduce the number of bit-flips per write-back to main memory. Our proposal favors the off-chip eviction of slightly modified blocks according to an adaptive replacement algorithm that operates coordinately in L2 and L3. This way it is possible to improve significantly system memory lifetime, with negligible performance degradation. We found that using a few bits per block to track changes in cache blocks with respect to the main memory content is enough. With a slightly modified sectored LRU and a simple cache performance predictor it is possible to achieve a simple implementation with minimal cost in area and no impact on cache access time. On average, our proposal increases the memory lifetime obtained with an LRU policy up to 10 times (10×) and 15 times (15×) when combined with other memory centric techniques. In both cases, the performance degradation could be considered negligible.
The Glass Ceiling Effect

The popular notion of glass ceiling effects implies that gender (or other) disadvantages are stronger at the top of the hierarchy than at lower levels and that these disadvantages become worse later in a person's career. We define four specific criteria that must be met to conclude that a glass ceiling exists. Using random effects models and data from the Panel Study of Income Dynamics, we examine gender and race inequalities at the 25th, 50th, and 75th percentiles of white male earnings. We find evidence of a glass ceiling for women, but racial inequalities among men do not follow a similar pattern. Thus, we should not describe all systems of differential work rewards as "glass ceilings. " They appear to be a distinctively gender phenomenon.
Effects of lithium on cognitive performance: a meta-analysis.

BACKGROUND Cognitive impairment is underrecognized among patients with bipolar disorder and may represent not only effects of the illness but also adverse effects of its treatments. Among these, lithium is the best-studied mood stabilizer. As its cognitive effects are mixed and not well-known, we assessed reported effects of lithium on cognitive performance. DATA SOURCES MEDLINE, PsycINFO, and EMBASE databases (1950 to December 2008) were queried with the keywords lithium, cognit*, neurocognit*, neuropsych*, psycholog*, attention, concentration, processing speed, memory, executive, and learning. Database searches were supplemented with bibliographic cross-referencing by hand. The literature search was conducted independently by 2 authors (A.P.W. and T.S.W.) during August and September 2008, and questions about appropriate inclusion or exclusion were resolved between them by consensus. STUDY SELECTION Of 586 reports initially identified as being of potential interest, 12, involving 539 subjects, met our inclusion criteria: (1) cognitive performance compared between subjects taking lithium and comparable subjects not taking lithium; comparability was assured by: (2) patients with the same affective disorder diagnoses in euthymic or remitted status or healthy volunteers; (3) groups of similar age and sex; (4) similar intelligence, education, or occupation; (5) similar distribution of other concurrent psychotropic drugs; and (6) cognitive abilities (outcomes) assessed with performance-based measures. DATA EXTRACTION Standardized mean-difference effect size (ES), corrected for small-sample bias (Hedges' g), was computed for cognitive tasks in each study. ES estimates were transformed so that positive values indicate poorer performance by lithium-treated subjects. Infrequently, when means and standard deviations were not provided, ES was estimated from reported values of t, F, or z tests. For analysis, similar neurocognitive tests were grouped a priori based on the cognitive domains they aimed to assess. DATA SYNTHESIS We identified 12 studies involving 276 lithium-treated and 263 similar or the same subjects, lithium-free. Lithium was taken for a mean duration of 3.9 years by affective disorder patients and 2.5 weeks by healthy volunteers, yielding a mean daily trough serum concentration of 0.80 mEq/L. Overall, lithium treatment was associated with small but significant impairment in immediate verbal learning and memory (ES = 0.24; 95% CI, 0.05-0.43) and creativity (ES = 0.33; 95% CI, 0.02-0.64), whereas delayed verbal memory, visual memory, attention, executive function, processing speed, and psychomotor performance were not significantly affected. Selectively, among the 326 affective-disorder patients, in addition to these overall impairments, long-term lithium treatment also was associated with even greater impairment in psychomotor performance (ES = 0.62; 95% CI, 0.27-0.97), with no evidence of cognitive improvements. CONCLUSIONS Lithium treatment appears to have only few and minor negative effects on cognition.
The bounded disorder access method

A new key associative access method, called the bounded disorder method, is described. The method uses a combination of hashing and tree indexing. The method has very good random access performance, being comparable to the best hashing methods if its small index is stored entirely in main memory. The method's advantage compared with hashing is that range searches are possible while searching only a portion of the file proportional to the size of the range. It is possible to control index size by controlling node size. Node size can be increased without increasing the amount of data transferred during a random probe. Further, increasing node size has only a minor effect on key sequential access performance. Even quite large nodes, so long as they can be read into memory in their entirety, have good key sequential performance. The bounded disorder method is the only one of the methods employing large nodes that can cope well with arbitrary key distributions. These properties make the bounded disorder method a good choice as the only access method of a data base system.
Event based heterogeneous sensors fusion for public place surveillance

In the context of public place surveillance, the evaluation of available technologies shows that the security bottleneck isn't the surveillance hardware, but rather the real-time analysis and correlation of data provided by various sensors. Also, there is an evident lack of global threat management policy. In this paper, we present an implementation of an event based inference technology called complex event processing, which allows fusion of information generated by heterogeneous sensors supporting the goal of providing a global situational view for public place surveillance. We also present a description logic paradigm to support a non programmer in the situation modeling task. An example of panic crowd detection in an airport illustrates the complete process.
Surface Immobilizable Chelator for Label-free Electrical Detection of Pyrophosphatew Chemcomm

A new pyrophosphate (PPi) chelator was designed for surface-sensitive electrical detection of biomolecular reactions. This article describes the synthesis of the PPi-selective receptor, its surface immobilization and application to label-free electrical detection on a silicon-based field-effect transistor (FET) sensor. Nucleotide incorporation reactions, catalyzed by DNA and RNA polymerases, are critically important in the biological processes of living systems. Their common byproduct, pyro-phosphate (PPi), is a negatively charged small molecule typically detected using optical techniques, such as chemi-luminescence. 1 Label-free electrical monitoring of biochemical reactions offers several advantages including increased port-ability and improved integration. 2 The former advantage is due to the elimination of bulky optical measurement components and the latter is due to the ability to fabricate many individually addressable electronic devices at micro-or nanoscale. Scalable semiconductor manufacturing techniques can be adapted to produce dense, highly reproducible sensor arrays to process samples and signals in a highly parallel fashion. We are developing an electrical signal detection platform capable of detecting DNA synthesis reactions by making use of the intrinsic physicochemical properties of PPi. Here we report the synthesis of a PPi-selective receptor, its surface immobilization and application to label-free electrical detection on a field-effect transistor (FET) device. Various optical PPi detection technologies have been developed. Among these, luciferase-based PPi detection has been used for bacterial detection and DNA sequencing applications. 1 Non-enzymatic PPi detection technologies have also been reported. 3,4 These include fluorescence-and absorption-based detection using PPi chelators, which can detect submicromolar PPi in bulk solution. One class of chelators is designed such that they can bind to indicator dyes, where PPi is detected either colorimetrically 5 or fluorescently 6 when dye molecules are displaced from chelator by PPi binding. Extending chelation-based sensing to surface-sensitive electrical detection requires a chelator compatible with surface immobilization and selective to the target analyte. Surface capture of PPi signaling molecules is expected to enhance the sensitivity of field-effect devices to PPi in a process that we call ''signal immobilization''. The negatively-charged PPi molecules are expected to decrease the number of positively charged carriers in a p-type field-effect transistor (FET) sensor functionalized with such a chelator, resulting in a decrease in threshold voltage. In order to test this ''signal immobilization'' concept, we designed a new chelator with three functional components: a binding site, a linker, and a handle. The binding site selectively captures PPi from solution, while the linker between the binding site and handle …
Young Children’s Inductive Generalizations About Social Categories: When Is Gender Essential?

Two experiments investigated 3- to 5-year-olds’ inductive generalizations about social categories. In Experiment 1, participants were shown pictures of children contrasting in appearance and either gender or classmate status, and were asked to generalize either biological properties or behaviors. Contrary to expectations, performance did not differ for chance for gender, but children generalized on the basis of appearance more than classmate status. Experiment 2 further examined children’s use of gender for inductive inferences. Children were asked to generalize either stereotyped behaviors (stereotype condition) or novel behaviors (neutral condition) and novel biological properties (both conditions). In the stereotype condition, children generalized both behaviors and biological properties on the basis of gender more than appearance, but, in the neutral condition, children’s performance usually did not differ from chance. The implications of these results for essentialism, similarity-based induction, and cognitive variability are discussed.
The Complete Nucleotide Sequence of the Human Immunoglobulin Heavy Chain Variable Region Locus

The complete nucleotide sequence of the 957-kb DNA of the human immunoglobulin heavy chain variable (VH) region locus was determined and 43 novel VH segments were identified. The region contains 123 VH segments classifiable into seven different families, of which 79 are pseudogenes. Of the 44 VH segments with an open reading frame, 39 are expressed as heavy chain proteins and 1 as mRNA, while the remaining 4 are not found in immunoglobulin cDNAs. Combinatorial diversity of VH region was calculated to be ∼6,000. Conservation of the promoter and recombination signal sequences was observed to be higher in functional VH segments than in pseudogenes. Phylogenetic analysis of 114 VH segments clearly showed clustering of the VH segments of each family. However, an independent branch in the tree contained a single VH, V4-44.1P, sharing similar levels of homology to human VH families and to those of other vertebrates. Comparison between different copies of homologous units that appear repeatedly across the locus clearly demonstrates that dynamic DNA reorganization of the locus took place at least eight times between 133 and 10 million years ago. One nonimmunoglobulin gene of unknown function was identified in the intergenic region.
Effect of the BRCA2 CTRD domain on RAD51 filaments analyzed by an ensemble of single molecule techniques

Homologous recombination is essential for the preservation of genome stability, thereby preventing cancer. The recombination protein RAD51 drives DNA strand exchange, which requires the assembly, rearrangement and disassembly of a RAD51 filament on DNA, coupled to ATP binding and hydrolysis. This process is facilitated and controlled by recombination mediators and accessory factors. Here, we have employed a range of single molecule techniques to determine the influence of the C-terminal RAD51 interaction domain (CTRD) of the breast cancer tumor suppressor BRCA2 on intrinsic aspects of RAD51-DNA interactions. We show that at high concentration the CTRD entangles RAD51 filaments and reduces RAD51 filament formation in a concentration dependent manner. It does not affect the rate of filament disassembly measured as the loss of fluorescent signal due to intrinsic RAD51 protein dissociation from double-stranded DNA (dsDNA). We conclude that, outside the context of the full-length protein, the CTRD does not reduce RAD51 dissociation kinetics, but instead hinders filament formation on dsDNA. The CTRDs mode of action is most likely sequestration of multiple RAD51 molecules thereby rendering them inactive for filament formation on dsDNA.
Incorporating hardware and software features into a prediction model for processor‐system throughput

The cycle‐accurate simulation is a method for design space study of a processor system before it goes for the hardware implementation. Even though the simulations provide precise results about the system performance, the simulation times are exorbitantly high for practical systems. Therefore, an alternative is to use experimentally‐ developed models that tend to be faster than the aforementioned simulations. This is an extension to our previous work done in the area of neural network models for assessing the processor system throughput. In addition to hardware‐related parameters, the current work includes multiple software‐related parameters to better represent the dynamic behavior of programs. Consequently, the model provides higher accuracy estimates of a widely used performance metric (instructions per cycle) when tested with industry standard CPU benchmark programs. Potential uses of the model are compiler design and computer architecture research and teaching. © 2015 Wiley Periodicals, Inc. Comput Appl Eng Educ 24:169–179, 2016; View this article online at wileyonlinelibrary.com/journal/cae; DOI 10.1002/cae.21681.
Does “authority” mean quality? predicting expert quality ratings of Web documents

For many topics, the World Wide Web contains hundreds or thousands of relevant documents of widely varying quality. Users face a daunting challenge in identifying a small subset of documents worthy of their attention. Link analysis algorithms have received much interest recently, in large part for their potential to identify high quality items. We report here on an experimental evaluation of this potential. We evaluated a number of link and content-based algorithms using a dataset of web documents rated for quality by human topic experts. Link-based metrics did a good job of picking out high-quality items. Precision at 5 is about 0.75, and precision at 10 is about 0.55; this is in a dataset where 0.32 of all documents were of high quality. Surprisingly, a simple content-based metric performed nearly as well; ranking documents by the total number of pages on their containing site.