Miracle-dz/UniFAR-FTUs huggingface dataset:
A PTK7/Ror2 Co-Receptor Complex Affects Xenopus Neural Crest Migration

Neural crest cells are a highly migratory pluripotent cell population that generates a wide array of different cell types and failure in their migration can result in severe birth defects and malformation syndromes. Neural crest migration is controlled by various means including chemotaxis, repellent guidance cues and cell-cell interaction. Non-canonical Wnt PCP (planar cell polarity) signaling has previously been shown to control cell-contact mediated neural crest cell guidance. PTK7 (protein tyrosine kinase 7) is a transmembrane pseudokinase and a known regulator of Wnt/PCP signaling, which is expressed in Xenopus neural crest cells and required for their migration. PTK7 functions as a Wnt co-receptor; however, it remains unclear by which means PTK7 affects neural crest migration. Expressing fluorescently labeled proteins in Xenopus neural crest cells we find that PTK7 co-localizes with the Ror2 Wnt-receptor. Further, co-immunoprecipitation experiments demonstrate that PTK7 interacts with Ror2. The PTK7/Ror2 interaction is likely relevant for neural crest migration, because Ror2 expression can rescue the PTK7 loss of function migration defect. Live cell imaging of explanted neural crest cells shows that PTK7 loss of function affects the formation of cell protrusions as well as cell motility. Co-expression of Ror2 can rescue these defects. In vivo analysis demonstrates that a kinase dead Ror2 mutant cannot rescue PTK7 loss of function. Thus, our data suggest that Ror2 can substitute for PTK7 and that the signaling function of its kinase domain is required for this effect.
Solution properties of γ‐crystallins: Compact structure and low frictional ratio are conserved properties of diverse γ‐crystallins

γ‐crystallins are highly specialized proteins of the vertebrate eye lens where they survive without turnover under high molecular crowding while maintaining transparency. They share a tightly folded structural template but there are striking differences among species. Their amino acid compositions are unusual. Even in mammals, γ‐crystallins have high contents of sulfur‐containing methionine and cysteine, but this reaches extremes in fish γM‐crystallins with up to 15% Met. In addition, fish γM‐crystallins do not conserve the paired tryptophan residues found in each domain in mammalian γ‐crystallins and in the related β‐crystallins. To gain insight into important, evolutionarily conserved properties and functionality of γ‐crystallins, zebrafish (Danio rerio) γM2b and γM7 were compared with mouse γS and human γD. For all four proteins, far UV CD spectra showed the expected β‐sheet secondary structure. Like the mammalian proteins, γM7 was highly soluble but γM2b was much less so. The heat and denaturant stability of both fish proteins was lower than either mammalian protein. The ability of full‐length and truncated versions of human αB‐crystallin to retard aggregation of the heat denatured proteins also showed differences. However, when solution behavior was investigated by sedimentation velocity experiments, the diverse γ‐crystallins showed remarkably similar hydrodynamic properties with low frictional ratios and partial specific volumes. The solution behavior of γ‐crystallins, with highly compact structures suited for the densely packed environment of the lens, seems to be highly conserved and appears largely independent of amino acid composition.
Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes

The tandem duplication random loss operation (TDRL) is an important genome rearrangement operation in metazoan mitochondrial genomes. A TDRL consists of a duplication of a contiguous set of genes in tandem followed by a random loss of one copy of each duplicated gene. This paper presents an analysis of the combinatorics of TDRLs on circular genomes, e.g., the mitochondrial genome. In particular, results on TDRLs for circular genomes and their linear representatives are established. Moreover, the distance between gene orders with respect to linear TDRLs and circular TDRLs is studied. An analysis of the available animal mitochondrial gene orders shows the practical relevance of the theoretical results.
Dynamic stability of a foam lamella flowing through a periodically constricted tube

Experimental studies of foam flow in two dimensional, water-wet, porous medium micro-models reveal the importance of the capillary pressure of the medium upon the existence of foam in a given porous medium. Preformed foam injected into a dry medium simply cannot enter until it breaks and the released liquid imbibes into the small pores. This coalescence process increases the medium liquid saturation and reduces the capillary pressure according to a typical Leverett function. Upon reaching high enough liquid saturation, foam then flows into the micro-model. On the other hand, if foam is injected into a previously surfactant solution saturated medium, it immediately flows to a steady state. It has also been observed in studies of foam flow in partially liquid saturated bead packs and sand packs that breakage occurs if the gas superficial velocity is increased sufficiently. For a porous medium with a given permeability and saturation (and corresponding capillary pressure) there is a critical gas velocity above which lamellae rupture. Similarly, if the capillary pressure is increased at a given velocity of flow, lamellae will rupture. Others have measured this critical capillary pressure of foam coalescence for bead packs of permeabilities ranging from 72 to 8970 . mu.m/sup 2/ andmore » various surfactant formulations. This paper introduces a hydrodynamic theory that explains the foam breakage phenomena described above by analyzing the stability of a single foam lamella flowing through a periodically constricted sinusoidal pore. « less
Low Complexity Detection Algorithm for Low PAPR Interleaving Based NOMA Schemes

In this paper, a low PAPR interleaving based non-orthogonal multiple access (NoMA) scheme is introduced. By utilizing the property of DFT spread OFDM (DFT-s-OFDM), the peak-to-average power ratio (PAPR) can be reduced compared with existing NoMA schemes without sacrificing achievable data rates. Meanwhile, a low-complexity detection algorithm is also proposed on top of the elementary signal estimator (ESE) with the joint Gaussian distribution assumption, which can maintain good detection performance with moderate detection complexity. Simulation results, including PAPR and BLER performance, show that the proposed scheme can provide good performance with lower PAPR, which is suitable for mMTC scenario for 5G.
Know your farmer: Ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars

Bark and ambrosia beetles are highly specialized weevils (Curculionidae) that have established diverse symbioses with fungi, most often from the order Ophiostomatales (Ascomycota, Sordariomycetes). The two types of beetles are distinguished by their feeding habits and intimacy of interactions with their symbiotic fungi. The tree tissue diet of bark beetles is facilitated by fungi, while ambrosia beetles feed solely on fungi that they farm. The farming life history strategy requires domestication of a fungus, which the beetles consume as their sole food source. Ambrosia beetles in the subfamily Platypodinae originated in the mid‐Cretaceous (119–88 Ma) and are the oldest known group of farming insects. However, attempts to resolve phylogenetic relationships and the timing of domestication events for fungal cultivars have been largely inconclusive. We sequenced the genomes of 12 ambrosia beetle fungal cultivars and bark beetle associates, including the devastating laurel wilt pathogen, Raffaelea lauricola, to estimate a robust phylogeny of the Ophiostomatales. We find evidence for contemporaneous diversification of the beetles and their associated fungi, followed by three independent domestication events of the ambrosia fungi genus Raffaelea. We estimate the first domestication of an Ophiostomatales fungus occurred ~86 Ma, 25 million years earlier than prior estimates and in close agreement with the estimated age of farming in the Platypodinae (96 Ma). Comparisons of the timing of fungal domestication events with the timing of beetle radiations support the hypothesis that the first large beetle radiations may have spread domesticated “ambrosia” fungi to other fungi‐associated beetle groups, perhaps facilitating the evolution of new farming lineages.
A Pilot Trial of a Computerized Renal Template Note to Improve Resident Knowledge and Documentation of Kidney Disease

Summary Background: Kidney disease is under-documented in physician notes. The use of template-guided notes may improve physician recognition of kidney disease early in training. Objective: The objective of this study was to determine whether a computerized inpatient renal template note with clinical decision support improves resident knowledge and documentation of kidney disease. Methods: In this prospective study, first year medical residents were encouraged to use the renal template note for documentation over a one-month period. The renal template note included an option for classification of acute kidney injury (AKI) and chronic kidney disease (CKD) categories with a link to standard classifications. Pre- and post-knowledge of AKI and CKD categories was tested with a quiz and surveys of resident experience with the intervention were conducted. Appropriate AKI and/or CKD classification was determined in 100 renal template notes and 112 comparable historical internal medicine resident progress notes from approximately one year prior. Results: 2,435 inpatient encounters amongst 15 residents who participated were documented using the renal template note. A significantly higher percent of residents correctly staged earlier stage CKD (CKD3) using the renal template note compared to historical notes (9/46 vs. 0/33, p<0.01). Documentation of AKI and more advanced CKD stages (CKD4 and 5) did not improve. Knowledge based on quiz scores increased modestly but was not significant. The renal template note was well received by residents and was perceived as helping improve knowledge and documentation of kidney disease. Conclusions: The renal template note significantly improved staging of earlier stage CKD (CKD3) with a modest but non-significant improvement in resident knowledge. Given the importance of early recognition and treatment of CKD, future studies should focus on teaching early recognition using template notes with supplemental educational interventions. Citation: Shirazian S, Wang R, Moledina D, Liberman V, Zeidan J, Strand D, Mattana J. A pilot trial of a computerized renal template note to improve resident knowledge and documentation of kidney disease. Appl Clin Inf 2013; 4: 528–540 http://dx.doi. org/10.4338/ACI-2013-07-RA-0048
Hypercapnia Accelerates Adipogenesis: A Novel Role of High CO2 in Exacerbating Obesity

Abstract Obesity is a major risk factor for the development of obstructive sleep apnea (OSA) and obesity hypoventilation syndrome (OHS), which manifest as intermittent hypercapnia and sustained plus intermittent hypercapnia, respectively. In this study, we investigated whether CO2 affects adipocyte differentiation (adipogenesis) and maturation (hypertrophy). Human visceral or subcutaneous preadipocytes were grown to confluence and then induced to differentiate to adipocytes under hypocapnia, normocapnia, and hypercapnia with or without hypoxia. Adipogenesis was also induced under intermittent or sustained hypercapnia. Differentiated adipocytes were maintained to maturity under normocapnia or hypercapnia. Our main findings are as follows: (1) hypercapnia accelerated adipogenesis in visceral and subcutaneous preadipocytes, whereas hypocapnia inhibited adipogenesis; (2) hypercapnia did not affect adipocyte hypertrophy; (3) hypercapnia‐accelerated adipogenesis was independent of extracellular acidosis, oxygen concentration, or either intermittent or sustained exposure to high CO2; and (4) the mechanisms underlying hypercapnia‐accelerated adipogenesis involved increased production of cyclic adenosine monophosphate (cAMP) via soluble adenylyl cyclase, leading to the activation of protein kinase A and exchanger protein directly activated by cAMP, which, in turn, activated proadipogenic transcription factors, such as cAMP response element binding protein, CCAAT/enhancer binding protein &bgr;, and peroxisome proliferator‐activated receptor &ggr;. This study reveals a novel role of high CO2 in promoting adipogenesis, which provides mechanistic clues to a pathoetiological interaction between OSA/OHS and obesity. Our data suggest a vicious cycle of disease progression via the following mechanism: OSA/OHS → hypoventilation → hypercapnia → increased adipogenesis → increased fat mass → exacerbated OSA/OHS.
Visualisation of Native Surfaces by Two-Step Molding

One of the most important tasks of microscopy is to provide information about structures in their natural state. Since most life science microscopy procedures require fixation, dehydration, drying, and sectioning, diverse artefacts are unavoidable. It is also possible to dehydrate the water content of a specimen by freeze-drying. However, even relatively stable surface structures are changed during such treatments. Methods of liquid substitution and freezing-substitution show good results for biological specimens with a waxy solid coverage (Ensikat and Barthlott, 1993) and soft specimens in a mechanically deformed state (Gorb et al., 2000). However, all these methods have certain restrictions for some types of specimens. For example, there are numerous biological surfaces covered with secretory fluids. Some specimens bear solid waxy coverings, which can be partly dissolved and washed out in organic solvents, such as ethanol, acetone, or propylenoxide. Often one would like to visualise dynamic processes (growth, deformation, or crystallisation) under environmental conditions, but at the high resolution in the SEM.
TASI lectures on black holes in string theory

This is a write-up of introductory lectures on black holes in string theory given at TASI-99. Topics discussed include: Black holes, thermodynamics and the Bekenstein-Hawking entropy, the information problem; supergravity actions, conserved quantum numbers, supersymmetry and BPS states, units and duality, dimensional reduction, solution-generating; extremal M-branes and D-branes, smearing, probe actions, nonextremal branes, the Gregory-Laflamme instability; breakdown of supergravity and the Correspondence Principle, limits in parameter space, singularity resolution; making black holes with branes, intersection-ology, explicit d=5,4 examples; string/brane computations of extremal black hole entropy in d=5,4, rotation, fractionation; non-extremality and entropy, the link to BTZ black holes, Hawking radiation and absorption cross-sections in the string/brane and supergravity pictures.
Well-Being and Resilience in Children With Speech and Language Disorders.

Purpose Children with speech and language disorders are at risk in relation to psychological and social well-being. The aim of this study was to understand the experiences of these children from their own perspectives focusing on risks to their well-being and protective indicators that may promote resilience. Method Eleven 9- to 12-year-old children (4 boys and 7 girls) were recruited using purposeful sampling. One participant presented with a speech sound disorder, 1 presented with both a speech and language disorder, and 9 with language disorders. All were receiving additional educational supports. Narrative inquiry, a qualitative design, was employed. Data were generated in home and school settings using multiple semi-structured interviews with each child over a 6-month period. A total of 59 interviews were conducted. The data were analyzed to identify themes in relation to potential risk factors to well-being and protective strategies. Results Potential risk factors in relation to well-being were communication impairment and disability, difficulties with relationships, and concern about academic achievement. Potential protective strategies were hope, agency, and positive relationships. Conclusion This study highlights the importance of listening to children's narratives so that those at risk in relation to well-being can be identified. Conceptualization of well-being and resilience within an ecological framework may enable identification of protective strategies at both individual and environmental levels that can be strengthened to mitigate negative experiences.
Object Tracking in Satellite Videos by Fusing the Kernel Correlation Filter and the Three-Frame-Difference Algorithm

Object tracking is a popular topic in the field of computer vision. The detailed spatial information provided by a very high resolution remote sensing sensor makes it possible to track targets of interest in satellite videos. In recent years, correlation filters have yielded promising results. However, in terms of dealing with object tracking in satellite videos, the kernel correlation filter (KCF) tracker achieves poor results due to the fact that the size of each target is too small compared with the entire image, and the target and the background are very similar. Therefore, in this letter, we propose a new object tracking method for satellite videos by fusing the KCF tracker and a three-frame-difference algorithm. A specific strategy is proposed herein for taking advantage of the KCF tracker and the three-frame-difference algorithm to build a strong tracker. We evaluate the proposed method in three satellite videos and show its superiority to other state-of-the-art tracking methods.
Non-axisymmetric Magnetic Flux Transport in the Sun

The solar magnetic field drives a wide range of phenomena, from sunspots to flares and coronal mass ejections. This field is maintained against ohmic dissipation by means of a hydromagnetic dynamo. In recent years, evidence has accumulated in support of a particular family of dynamo models, Babcock-Leighton models, where the surface fields play a key role. Specifically, the surface transport of magnetic flux coming from emerged regions regenerates the global dipole field, which is the source of the subsurface toroidal field for the next cycle. Many global dynamo models rely on the approximation of axial symmetry. In this thesis, we explore the consequences of relaxing this assumption. Relaxing it on the the surface, we find that the large-scale converging flows around active regions affect the strength of the global dipole. This may contribute to the variability of the solar cycle and provides a saturation mechanism. Relaxing the assumption beneath the surface, we find that the subsurface azimuthal field of the Sun is strongly axisymmetric.
EFFECT OF FLY ASH ON THE DURABILITY OF AIR-ENTRAINED CONCRETE

Concretes containing fly ash were evaluated to establish the effect of fly ash on freeze-thaw resistance, resistance to deicer scaling, and chloride-ion penetration. The effects of low-temperature curing and moisture availability during curing were also evaluated. These tests indicated that the freeze-thaw resistance of air-entrained concrete was reduced by the use of certain fly ashes when cured at low temperature. For other conditions there was no significant influence of fly ash. Deicer scaling resistance tests showed that air-entrained concrete without fly ash generally performed somewhat better than concrete fly ash, regardless of the type of curing provided. Air-entrained concretes made with some fly ashes were as resistant to chloride-ion penetration as air-entrained concrete without fly ash. The class of fly ash did not significantly influence the degree of chloride-ion penetration.
Balloon pulmonary angioplasty for inoperable patients with chronic thromboembolic disease

Symptomatic patients with residual pulmonary perfusion defects or vascular lesions but no pulmonary hypertension at rest are diagnosed with chronic thromboembolic disease (CTED). Balloon pulmonary angioplasty (BPA) is an emerging treatment for patients with inoperable chronic thromboembolic pulmonary hypertension (CTEPH), but data regarding the safety and efficacy of BPA in patients with CTED are lacking. We report a prospective series of ten consecutive patients with CTED who underwent 35 BPA interventions (median of four per patient) at two German institutions. All patients underwent a comprehensive diagnostic workup at baseline and 24 weeks after their last intervention. BPA was safe, with one pulmonary vascular injury and subsequent self-limiting pulmonary bleeding as the only complication (2.9% of the interventions, 10% of the patients). After the procedures, World Health Organization functional class, 6-min walking distance, pulmonary vascular resistance, and pulmonary arterial compliance improved, and NT-proBNP concentrations declined in 9/10 patients. BPA may be a new treatment option for carefully selected patients with CTED. A larger, prospective, international registry is required to confirm these results.
High-speed superresolution imaging of the proteins in fission yeast clathrin-mediated endocytic actin patches

High-speed superresolution localization microscopy shows that actin filaments assemble in two zones in Schizosaccharomyces pombe actin patches, one around the base of the membrane invagination and another ~200 nm deeper into the cytoplasm. Both zones of actin filaments are important for elongation of the endocytic tubule and membrane scission
Corporate Governance and the Information Content of Insider Trades

Most corporate governance research focuses on the behavior of chief executive officers, board members, institutional shareholders, and other similar parties. Little research focuses on the impact of executives whose primary responsibility is to enforce and shape corporate governance inside the firm. This study examines the role of the general counsel (GC) in mitigating informed trading by corporate insiders. We find that insider trading profits and the predictive ability of insider trades for future operating performance are generally higher when insiders trade within firm‐imposed restricted trade windows. However, when GC approval is required to execute a trade, insiders’ trading profits and the predictive ability of insider trades for future operating performance are substantively lower. Thus, when given the authority, it appears the GC can effectively limit the extent to which corporate insiders use their private information to extract rents from shareholders.
A Comprehensive Database for Antarctic Iceberg Tracking Using Scatterometer Data

This paper describes the development of, and the methodology for, a new, consolidated Brigham Young University (BYU)/National Ice Center (NIC) Antarctic iceberg tracking database. The new database combines daily positional data from the original BYU daily iceberg tracking database derived from scatterometers, and the NIC's weekly Antarctic iceberg tracking database derived mostly from optical and infrared sensors. Interpolation methods and statistical analyses of iceberg locations are discussed. A new, automated method of using positional data and scatterometer backscatter images to estimate sizes and rotational patterns of icebergs is also developed. This information is included in the new database.