Miracle-dz/UniFAR-FTUs huggingface dataset:
Myeloid Zinc Finger 1 (Mzf1) Differentially Modulates Murine Cardiogenesis by Interacting with an Nkx2.5 Cardiac Enhancer

Vertebrate heart development is strictly regulated by temporal and spatial expression of growth and transcription factors (TFs). We analyzed nine TFs, selected by in silico analysis of an Nkx2.5 enhancer, for their ability to transactivate the respective enhancer element that drives, specifically, expression of genes in cardiac progenitor cells (CPCs). Mzf1 showed significant activity in reporter assays and bound directly to the Nkx2.5 cardiac enhancer (Nkx2.5 CE) during murine ES cell differentiation. While Mzf1 is established as a hematopoietic TF, its ability to regulate cardiogenesis is completely unknown. Mzf1 expression was significantly enriched in CPCs from in vitro differentiated ES cells and in mouse embryonic hearts. To examine the effect of Mzf1 overexpression on CPC formation, we generated a double transgenic, inducible, tetOMzf1-Nkx2.5 CE eGFP ES line. During in vitro differentiation an early and continuous Mzf1 overexpression inhibited CPC formation and cardiac gene expression. A late Mzf1 overexpression, coincident with a second physiological peak of Mzf1 expression, resulted in enhanced cardiogenesis. These findings implicate a novel, temporal-specific role of Mzf1 in embryonic heart development. Thereby we add another piece of puzzle in understanding the complex mechanisms of vertebrate cardiac development and progenitor cell differentiation. Consequently, this knowledge will be of critical importance to guide efficient cardiac regenerative strategies and to gain further insights into the molecular basis of congenital heart malformations.
Eurographics/ Acm Siggraph Symposium on Computer Animation (2007) Controlling Individual Agents in High-density Crowd Simulation

Permission to make digital or hard copies of part or all of this wor k for per sonal or classr oom use is granted without fee provided that copies are not made or distributed for commer cial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this wor k owned by other s than ACM must be honored. Abstracting with cr edit is permitted. To copy other wise, to republish, to post on ser ver s, or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from Permissions Dept, ACM Abstract Simulating the motion of realistic, large, dense crowds of autonomous agents is still a challenge for the computer graphics community. Typical approaches either resemble particle simulations (where agents lack orientation controls) or are conservative in the range of human motion possible (agents lack psychological state and aren't allowed to 'push' each other). Our HiDAC system (for High-Density Autonomous Crowds) focuses on the problem of simulating the local motion and global wayfinding behaviors of crowds moving in a natural manner within dynamically changing virtual environments. By applying a combination of psychological and geometrical rules with a social and physical forces model, HiDAC exhibits a wide variety of emergent behaviors from agent line formation to pushing behavior and its consequences; relative to the current situation, personalities of the individuals and perceived social density.
The CDC 6600 Project

This article is an account of the development of the Control Data 6600 computer first developed in 1964. Of historical interest is the design team approach adopted by Control Data in which a small staff of engineers was isolated from the main operations of the company. Some review is made of the design process as well as the unique features of the machine. The article also includes some comments in retrospect about the results of certain of the initial design objectives.
Free-text input vs menu selection: exploring the difference with a tutorial dialogue system.

We describe the in-class evaluation of two versions of a tutorial dialogue system with 338 volunteers from a first-year undergraduate health-sciences class. One version uses supervised machine-learning techniques to classify student free-text responses; the other requires students to select their preferred response from a series of options (menu-based). Our results indicate that both the free-text and menu-based tutors produced significant gains on immediate post-test scores compared to a control group. In addition, there was no significant difference in performance between students in the free-text and menu-based conditions. We note specific analysis work still to do as part of this research and speculate briefly on the potential for using tutorial dialogue systems in real class settings.
Adaptive routing in k-ary n-cube multicomputers

Wormhole routing makes the communication latency insensitive of the network diameter and reduces the buffer size of each router. It has been widely adopted in many new generation distributed memory multiprocessor systems (DMMPs). The concept of virtual system is invented for deadlock-free routing design. Using a great deal of virtual channels is quite expensive to be implemented in practice and is not limitless. In this paper experimental results are given to evaluate the tradeoff between network congestion delay and throughput. Some results show that the congestion delay does not reduce visibly when the number of virtual channels is greater than that of internal channels by 2. A reasonable number of virtual channels can be derived from the results. A virtual networks system using only four virtual networks, two virtual channels in each direction, is presented. It shows that the minimum number of virtual networks to support a partially adaptive, minimal and deadlock free routing in k-ary n-cubes is just four. It uses only four virtual networks but can get a high degree of adaptiveness and high traffic capacity. Simulation results are presented to verify the performance.
The ICSI Meeting Project: Resources and Research

This paper provides a progress report on ICSI s Meeting Project, including both the data collected and annotated as part of the pro-ject, as well as the research lines such materials support. We include a general description of the official ICSI Meeting Corpus , as currently available through the Linguistic Data Consortium, discuss some of the existing and planned annotations which augment the basic transcripts provided there, and describe several research efforts that make use of these materials. The corpus supports wide-ranging efforts, from low-level processing of the audio signal (including automatic speech transcription, speaker tracking, and work on far-field acoustics) to higher-level analyses of meeting structure, content, and interactions (such as topic and sentence segmentation, and automatic detection of dialogue acts and meeting hot spots ).
Thalamic afferents influence cortical progenitors via ephrin A5-EphA4 interactions

The phenotype of excitatory cerebral cortex neurons is specified at the progenitor level, orchestrated by various intrinsic and extrinsic factors. Here, we provide evidence for a subcortical contribution to cortical progenitor regulation by thalamic axons via ephrin A5-EphA4 interactions. Ephrin A5 is expressed by thalamic axons and represents a high-affinity ligand for EphA4 receptors detected in cortical precursors. Recombinant ephrin A5-Fc protein, as well as ephrin A ligand-expressing, thalamic axons affect the output of cortical progenitor division in vitro. Ephrin A5-deficient mice show an altered division mode of radial glial cells (RGCs) accompanied by increased numbers of intermediate progenitor cells (IPCs) and an elevated neuronal production for the deep cortical layers at E13.5. In turn, at E16.5 the pool of IPCs is diminished, accompanied by reduced rates of generated neurons destined for the upper cortical layers. This correlates with extended infragranular layers at the expense of superficial cortical layers in adult ephrin A5-deficient and EphA4-deficient mice. We suggest that ephrin A5 ligands imported by invading thalamic axons interact with EphA4-expressing RGCs, thereby contributing to the fine-tuning of IPC generation and thus the proper neuronal output for cortical layers. Summary: Eph/ephrin signalling between thalamic axons and cortical progenitors regulates neurogenesis the mouse cortex, providing evidence for extra-cortical control of this process.
Real-time 3D indoor localization

We present real time indoor localization in the multi-story building using 3D particle filter. Filtration takes place in three dimensional space. Presented method incorporates information from inertial sensors, Wi-Fi signal strength, barometric and building data. We also describe additional methods for determining final locations. Algorithm was tested in multi-story office building and results show that it performs better than particle filters running in two dimensional spaces. Furthermore we propose novel incorporation of floor detection algorithm into particle filter.
Aberrant Splicing of tau Pre-mRNA Caused by Intronic Mutations Associated with the Inherited Dementia Frontotemporal Dementia with Parkinsonism Linked to Chromosome 17

ABSTRACT Frontotemporal dementia accounts for a significant fraction of dementia cases. Frontotemporal dementia with parkinsonism linked to chromosome 17 is associated with either exonic or intronic mutations in the tau gene. This highlights the involvement of aberrant pre-mRNA splicing in the pathogenesis of neurodegenerative disorders. Little is known about the molecular mechanisms of the splicing defects underlying these diseases. To establish a model system for studying the role of pre-mRNA splicing in neurodegenerative diseases, we have constructed a tau minigene that reproduces tau alternative splicing in both cultured cells and in vitro biochemical assays. We demonstrate that mutations in a nonconserved intronic region of the human tau gene lead to increased splicing between exon 10 and exon 11. Systematic biochemical analyses indicate the importance of U1 snRNP and, to a lesser extent, U6 snRNP in differentially recognizing wild-type versus intron mutant tau pre-mRNAs. Gel mobility shift assays with purified U1 snRNP and oligonucleotide-directed RNase H cleavage experiments support the idea that the intronic mutations destabilize a stem-loop structure that sequesters the 5′ splice site downstream of exon 10 in tau pre-mRNA, leading to increases in U1 snRNP binding and in splicing between exon 10 and exon 11. Thus, mutations in nonconserved intronic regions that increase rather than decrease alternative splicing can be an important pathogenic mechanism for the development of human diseases.
Translating an Adolescent Smoking Cessation Program Into Policy and Practice in an Australian Context

Although Australia's restrictive tobacco control policies have made it an international leader in reducing smoking prevalence, and only 7% of teens smoke weekly, cessation efforts are still needed among adolescents. Of the campaigns and programs implemented in Australia to reduce this problem among adolescents, most have provided only abstinence messages and few have been effectively evaluated and translated into policy and practice. This article describes the translation of a harm minimization cessation program for teens, the Smoking Cessation for Youth Project (SCYP), derived from an approach developed with adults. In addition, the article describes the unique sociopolitical context of Australia in which the SCYP program was developed and the significant conceptual, contextual, and methodological factors that enabled and limited this program's effective implementation and translation.
Disease Biomarkers in Cerebrospinal Fluid of Patients with First-Onset Psychosis

Background Psychosis is a severe mental condition that is characterized by a loss of contact with reality and is typically associated with hallucinations and delusional beliefs. There are numerous psychiatric conditions that present with psychotic symptoms, most importantly schizophrenia, bipolar affective disorder, and some forms of severe depression referred to as psychotic depression. The pathological mechanisms resulting in psychotic symptoms are not understood, nor is it understood whether the various psychotic illnesses are the result of similar biochemical disturbances. The identification of biological markers (so-called biomarkers) of psychosis is a fundamental step towards a better understanding of the pathogenesis of psychosis and holds the potential for more objective testing methods. Methods and Findings Surface-enhanced laser desorption ionization mass spectrometry was employed to profile proteins and peptides in a total of 179 cerebrospinal fluid samples (58 schizophrenia patients, 16 patients with depression, five patients with obsessive-compulsive disorder, ten patients with Alzheimer disease, and 90 controls). Our results show a highly significant differential distribution of samples from healthy volunteers away from drug-naïve patients with first-onset paranoid schizophrenia. The key alterations were the up-regulation of a 40-amino acid VGF-derived peptide, the down-regulation of transthyretin at ~4 kDa, and a peptide cluster at ~6,800–7,300 Da (which is likely to be influenced by the doubly charged ions of the transthyretin protein cluster). These schizophrenia-specific protein/peptide changes were replicated in an independent sample set. Both experiments achieved a specificity of 95% and a sensitivity of 80% or 88% in the initial study and in a subsequent validation study, respectively. Conclusions Our results suggest that the application of modern proteomics techniques, particularly mass spectrometric approaches, holds the potential to advance the understanding of the biochemical basis of psychiatric disorders and may in turn allow for the development of diagnostics and improved therapeutics. Further studies are required to validate the clinical effectiveness and disease specificity of the identified biomarkers.
Inferring the structural properties of eddies in the log layer from spectral statistics

The structure of near-wall layers has been the subject of much research over many years, with conceptual descriptions of the Attached Eddy Hypothesis (AEH, henceforth) by Townsend (1980) and Perry & Chong (1982) being key historical fix points. The fact that major efforts have continued unabated over the past two to three decades reflects the exceptional structural complexity of near-wall layers awaiting insight, as well as new opportunities to investigate open questions as a consequence of outstandingly high-quality experimental and DNS data emerging over the past decade (Marusic et al. (2013); Smits et al. (2011); Hultmark et al. (2013); Rosenberg et al. (2013); Jiménez & Hoyas (2008); Lee & Moser (2015)). In particular, the availability of massive amounts of spatially and temporally fully-resolved raw DNS data for fairly high Reynolds numbers has opened new routes to investigating many statistical and structural properties of near-wall layers, with the objective of unravelling a variety of scale-interaction processes.
Ultraviolet and yellow reflectance but not fluorescence is important for visual discrimination of conspecifics by Heliconius erato

ABSTRACT Toxic Heliconius butterflies have yellow hindwing bars that – unlike those of their closest relatives – reflect ultraviolet (UV) and long wavelength light, and also fluoresce. The pigment in the yellow scales is 3-hydroxy-dl-kynurenine (3-OHK), which is found in the hair and scales of a variety of animals. In other butterflies like pierids with color schemes characterized by independent sources of variation in UV and human-visible yellow/orange, behavioral experiments have generally implicated the UV component as most relevant to mate choice. This has not been addressed in Heliconius butterflies, where variation exists in analogous color components, but moreover where fluorescence due to 3-OHK could also contribute to yellow wing coloration. In addition, the potential cost due to predator visibility is largely unknown for the analogous well-studied pierid butterfly species. In field studies with butterfly paper models, we show that both UV and 3-OHK yellow act as signals for H. erato when compared with models lacking UV or resembling ancestral Eueides yellow, respectively, but attack rates by birds do not differ significantly between the models. Furthermore, measurement of the quantum yield and reflectance spectra of 3-OHK indicates that fluorescence does not contribute to the visual signal under broad-spectrum illumination. Our results suggest that the use of 3-OHK pigmentation instead of ancestral yellow was driven by sexual selection rather than predation. Highlighted Article: Heliconius butterflies use a co-opted yellow pigment for conspecific communication, which predators find similarly aposematic compared with the ancestral yellow pigments used by non-Heliconius mimics.
Altering Toluene 4-Monooxygenase by Active-Site Engineering for the Synthesis of 3-Methoxycatechol, Methoxyhydroquinone, and Methylhydroquinone

ABSTRACT Wild-type toluene 4-monooxygenase (T4MO) of Pseudomonas mendocina KR1 oxidizes toluene to p-cresol (96%) and oxidizes benzene sequentially to phenol, to catechol, and to 1,2,3-trihydroxybenzene. In this study T4MO was found to oxidize o-cresol to 3-methylcatechol (91%) and methylhydroquinone (9%), to oxidize m-cresol and p-cresol to 4-methylcatechol (100%), and to oxidize o-methoxyphenol to 4-methoxyresorcinol (87%), 3-methoxycatechol (11%), and methoxyhydroquinone (2%). Apparent V max values of 6.6 ± 0.9 to 10.7 ± 0.1 nmol/min/ mg of protein were obtained for o-, m-, and p-cresol oxidation by wild-type T4MO, which are comparable to the toluene oxidation rate (15.1 ± 0.8 nmol/min/mg of protein). After these new reactions were discovered, saturation mutagenesis was performed near the diiron catalytic center at positions I100, G103, and A107 of the alpha subunit of the hydroxylase (TmoA) based on directed evolution of the related toluene o-monooxygenase of Burkholderia cepacia G4 (K. A. Canada, S. Iwashita, H. Shim, and T. K. Wood, J. Bacteriol. 184 :344-349, 2002) and a previously reported T4MO G103L regiospecific mutant (K. H. Mitchell, J. M. Studts, and B. G. Fox, Biochemistry 41 :3176-3188, 2002). By using o-cresol and o-methoxyphenol as model substrates, regiospecific mutants of T4MO were created; for example, TmoA variant G103A/A107S produced 3-methylcatechol (98%) from o-cresol twofold faster and produced 3-methoxycatechol (82%) from 1 mM o-methoxyphenol seven times faster than the wild-type T4MO (1.5 ± 0.2 versus 0.21 ± 0.01 nmol/min/mg of protein). Variant I100L produced 3-methoxycatechol from o-methoxyphenol four times faster than wild-type T4MO, and G103S/A107T produced methylhydroquinone (92%) from o-cresol fourfold faster than wild-type T4MO and there was 10 times more in terms of the percentage of the product. Variant G103S produced 40-fold more methoxyhydroquinone from o-methoxyphenol than the wild-type enzyme produced (80 versus 2%) and produced methylhydroquinone (80%) from o-cresol. Hence, the regiospecific oxidation of o-methoxyphenol and o-cresol was changed for significant synthesis of 3-methoxycatechol, methoxyhydroquinone, 3-methylcatechol, and methylhydroquinone. The enzyme variants also demonstrated altered monohydroxylation regiospecificity for toluene; for example, G103S/A107G formed 82% o-cresol, so saturation mutagenesis converted T4MO into an ortho-hydroxylating enzyme. Furthermore, G103S/A107T formed 100% p-cresol from toluene; hence, a better para-hydroxylating enzyme than wild-type T4MO was formed. Structure homology modeling suggested that hydrogen bonding interactions of the hydroxyl groups of altered residues S103, S107, and T107 influence the regiospecificity of the oxygenase reaction.
System for Event Summary Notifications : Preliminary Operational Results at SDG & E

Modern power systems may include a variety of technologies configured to monitor electrical and physical parameters. Such monitoring systems provide a wealth of information regarding the health and operation of systems. Normally, these measurements are uniform and behave in a consistent manner through time. Areas of interest in these measurements, possibly indicating that a mechanical system is failing, are rare. The volume of these data can be overwhelming to operators attempting to identify these areas of interest. Automated identification of anomalous events offloads the job of continuous monitoring from the operators and allows them to focus their attention elsewhere. In this paper, we describe a frequency-domain statistical anomaly detector recently installed at San Diego Gas & Electric to collect streamed measurements and process them to produce event summary notifications. Simultaneous monitoring of multiple stations enables geographic, time, and frequency correlation of events. We further discuss results of operating this system at San Diego Gas & Electric.
Supply Chain Coordination Using Returns Policy with Sales Rebate and Penalty under Effort and Price Dependent Demand

A supply chain is two or more parties linked by a flow of goods, information, and funds. When one or more parties of the supply chain try to optimize their own profits, system performance may be hurt. In the standard newsvendor setting, both the returns policy and the sales rebate and penalty (SRP) are coordination contracts that provide incentives to all of the supply chain's members so that the decentralized supply chain behaves nearly or exactly the same as the integrated one. When demand is influenced by the retail price and retailer sales effort, each of the returns policy and the SRP contract no longer coordinates on its own. To solve this problem, we employ a new model combined the returns policy with the SRP contract. By analyzing we find that a properly designed returns policy with SRP achieves coordination and a win-win outcome.
An activating gucy2c mutation causes impaired contractility and fluid stagnation in the small bowel

Abstract Objective: Familial GUCY2C diarrhoea syndrome (FGDS) is caused by an activating mutation in the GUCY2C gene encoding the receptor guanylate cyclase C in enterocytes. Activation leads to increased secretion of fluid into the intestinal lumen. Twenty percent of the patients have increased risk of Crohn’s disease and intestinal obstruction (CD, 20%) and the condition resembles irritable bowel syndrome with diarrhoea. We aimed to describe fluid content, contractility, peristaltic activity and bowel wall thickness in the intestine in fasting FGDS patients, using ultrasound, with healthy volunteers serving as controls. Methods: Twenty-three patients with FGDS and 22 healthy controls (HC) were examined with a Logiq E9 scanner in a fasting state. Bowel wall thickness was measured and fluid-filled small bowel loops were counted using three-dimensional (3D) magnetic positioning navigation. The HC ingested 500 ml PEG solution, an electrolyte balanced, non-absorbable solution, in order to investigate the contractions of the small bowel. Results: The fasting 23 FGDS patients had significantly higher number of fluid-filled small bowel segments compared to 22 fasting HC, p < 0.001. A high number of non-occlusive contractions in the ileum was observed, which was significant when compared to HC after ingesting PEG solution, p < 0.016. An increase in intestinal wall thickness or other signs of CD were not observed. Conclusions: FGDS is characterised by multiple, fluid-filled small bowel loops with incomplete contractions and fluid stagnation in fasting state. These findings may play a role in the increased risk of bowel obstruction as well as IBS-like symptoms observed in these patients.