Miracle-dz/UniFAR-FTUs huggingface dataset:
Long form of latent TGF-β binding protein 1 (Ltbp1L) is essential for cardiac outflow tract septation and remodeling

Latent TGF-β binding protein 1 (LTBP1) is a member of the LTBP/fibrillin family of extracellular proteins. Due to the usage of different promoters, LTBP1 exists in two major forms, long (L) and short (S), each expressed in a temporally and spatially unique fashion. Both LTBP1 molecules covalently interact with latent TGF-β and regulate its function, presumably via interaction with the extracellular matrix (ECM). To explore the in vivo role of Ltbp1 in mouse development, at the time when only the L isoform is expressed, we mutated the Ltbp1L locus by gene targeting. Ltbp1L-null animals die shortly after birth from defects in heart development, consisting of the improper septation of the cardiac outflow tract (OFT) and remodeling of the associated vessels. These cardiac anomalies present as persistent truncus arteriosus (PTA) and interrupted aortic arch (IAA), which are associated with the faulty function of cardiac neural crest cells (CNCCs). The lack of Ltbp1L in the ECM of the septating OFT and associated vessels results in altered gene expression and function of CNCCs and decreased Tgf-β activity in the OFT. This phenotype reveals a crucial role for Ltbp1L and matrix as extracellular regulators of Tgf-β activity in heart organogenesis.
Particulate and trace gas emissions from large biomass fire in North America

In this chapter we describe the results of airborne studies of smokes from 17 biomass fuel fires, including 14 prescribed fires and 3 wildfires, burned primarily in the temperate zone of North America between 34° and 49°N latitude. The prescribed fires were in forested lands and logging debris and varied in areas burned from 10 to 700 hectares (ha) (over a few hours). One of the wildfires ultimately consumed 20,000 ha and burned over a period of weeks. The larger fires produced towering columns of smoke and capping water clouds. As an indication of scale, the prescribed fires were visible only as small features in meteorological satellite imagery, but one of the wildfires studied produced a persistent, visible plume more than 1000 kilometers (km) long. Details of these fires and their fuels are given in Table 28.1. The measurements were made aboard the University of Washington's C-131A research aircraft. This twin-engined, 20,000 kilogram (kg), propeller-driven airplane carries instrumentation for measuring the size and nature of aerosol particles, trace gas concentrations, and meteorological parameters. Major portions of the aerosol system have been described by Radke (1983) and the trace gas instrumentation has been described by Hegg et al. (1987). Details concerning the analysis of data, in addition to those presented in subsequent sections, can be found in Radke et al. (1988) and Hegg et al. (1990). Our studies have focused on factors that could impact global climate through alteration of the earth's radiation balance. These include emissions of trace gases and smoke particles from biomass burning, the optical properties of the smoke, and the interaction of the smoke particles with water clouds.
Your System Gets Better Every Day You Use It: Towards Automated Continuous Experimentation

Innovation and optimization in software systems can occur from pre-development to post-deployment stages. Companies are increasingly reporting the use of experiments with customers in their systems in the post-deployment stage. Experiments with customers and users are can lead to a significant learning and return-on-investment. Experiments are used for both validation of manual hypothesis testing and feature optimization, linked to business goals. Automated experimentation refers to having the system controlling and running the experiments, opposed to having the R&D organization in control. Currently, there are no systematic approaches that combine manual hypothesis validation and optimization in automated experiments. This paper presents concepts related to automated experimentation, as controlled experiments, machine learning and software architectures for adaptation. However, this paper focuses on how architectural aspects that can contribute to support automated experimentation. A case study using an autonomous system is used to demonstrate the developed initial architecture framework. The contributions of this paper are threefold. First, it identifies software architecture qualities to support automated experimentation. Second, it develops an initial architecture framework that supports automated experiments and validates the framework with an autonomous mobile robot. Third, it identifies key research challenges that need to be addressed to support further development of automated experimentation.
Learning to Walk in 20 Minutes

We present a statistical gradient following algorithm which optimizes a control policy for bipedal walking online on a real robot. One of the distinguishing features of this system is that learning and execution occur simultaneously: there are no explicit learning trials and there is no need to model the dynamics of the robot in a simulation. Thanks in part to the mechanical design of the robot, the system is able to reliably acquire a robust policy for dynamic bipedal walking from a blank slate in less than 20 minutes. Once the robot begins walking, it quickly and continually adapts to the terrain with every step that it takes.
Seismic structure of the northeastern Japan convergent margin: A synthesis

Many studies recently made on the basis of seismic observations have revealed a detailed structure of the crust and the upper mantle beneath the northeastern Japan arc and its relationship to seismic and volcanic activity. Spatial distributions of the depths to the Conrad and the Moho discontinuities, estimated from shallow earthquake data and seismic explosion data, show that both discontinuities are deep in the middle of the land area and shallow toward the coastlines of the Japan Sea and the Pacific Ocean. The Pn velocity has a lateral variation; it is as low as ∼7.5 km/s beneath the land area, while that beneath the Japan Sea and the Pacific Ocean is 8.0–8.2 km/s. It changes abruptly at the transition zones, which are located along the coastlines. Precise structure and location of the subducted Pacific plate beneath the land area is inferred from converted or reflected seismic waves at the top or bottom of the plate. The Pacific plate is composed of a thin (∼5 km) low-velocity upper layer and a thick high-velocity lower layer, its total thickness being 80–90 km. The upper plane seismicity of the double seismic zone is confined to the thin low-velocity upper layer, which probably corresponds to the subducted former oceanic crust. The lower plane seismicity lies at the middle of the high-velocity lower layer, and the lower half of the plate below it is incapable of generating earthquakes. The shallower portion of the upper surface of the plate beneath the Pacific Ocean, along which major seismicity with low-angle thrust faultings is actually occurring, is also located by seismic observations on land and in the sea. The Pacific plate subducts at an extremely low angle of ∼5° for the first ∼25-km depth, and then the dip steepens rather abruptly to ∼30°. Normal-fault type events at the top of the plate have not been detected in the portion where the downward-bending is the largest, but have been ditected near the trench axis, where it is rather small. Tomographic inversions for seismic velocity structure clearly delineate the inclined high-velocity Pacific plate with a thickness of 80–90 km and low-velocity zones in the crust and the mantle wedge beneath active volcanoes. Seismic attenuation tomography also shows similar zones of low-Q value beneath active volcanoes, although its spatial resolution is much lower. The low-velocity zones with 2–6% velocity lows are continuously distributed from the upper crust just beneath active volcanoes to a depth of 100–150 km in the mantle wedge, and are approximately parallel to the dip of the underlying Pacific plate. These low-velocity zones probably reflect the pathway of magma ascent from a depth in the mantle wedge to the Earth's surface, corresponding to a portion of the subduction-induced secondary mantle wedge flow.
A Study of a Segmentation Technique for Dialogue Act Assignation (short paper)

A dialogue system is usually defined as a computer system that interacts with a human user to achieve a task using dialogue [5]. In these systems, the computer must know the meaning and intention of the user input, in order to give the appropriate answer. The user turns must be interpreted by the system, taking only into account the essential information, i.e, their semantics for the dialogue process and the task to be accomplished. This information is usually represented by labels called Dialogue Acts (DA) [2] which label different segments of the turn known as utterances [8]. The DA labels usually take into account the semantics of the utterance with respect to the dialogue process, but they can include semantic information related to the task the dialogue is about.
Some Results On Three-Valued Walsh Transforms from Decimations of Helleseth-Gong Sequences

The Walsh transform of two-level autocorrelation sequences has played an important role in construction of the set of sequences. For p-ary sequences, there are only two basic classes of two-level autocorrelation sequences with no subfield structures for an arbitrary odd prime p. One is the class of p-ary m-sequences and the other of p-ary Helleseth-Gong sequences. Gong, Helleseth, and Hu found many decimation numbers which yield three-valued Walsh transforms by computer search. They proved two cases and also found additional values of decimation number which yield three-valued Walsh transform. Gong, Helleseth, Hu and Li proved two more cases with new observations. In this paper, for p = 5, k = 1, n = 5 and s = 2 we proved that the decimation value d = 481 yields a three-valued Walsh transform, which is not covered in previous studies. Also we present a conjecture for p = 3 at the end of the paper.
Spectral occupancy-measurement system and mathematical models

Systematic measurements of HF spectral occupancy have been made since 1982, and mathematical models are being developed and updated as new results become available. The experimental data base has been improved by the establishment of an automatic system for spectral occupancy measurement. In particular, congestion over the entire HF spectrum is measured at least monthly, rather than only at the times of the solstices. It is important to include other parameters in the occupancy model, for example, bandwidth, geographical location and possibly antenna directivity. These problems are under consideration. >
Office Environment Syndrome Study: Part I

An indoor environment survey (temperature, relative humidity, illuminance, noise, infrasound, CO, CO2, formaldehyde, respirable dust weight, particle counts, mite allergen in carpet or chair dust, individual and total volatile organic compounds, individual and total microbiological volatile organic compounds) was conducted in 4 office buildings. A detailed self-report occupant comfort, ergonomic conditions and SBS questionnaire survey was administered to all employees, and 1,508 returns were received (72% return rate). There were few associations between specific SBS symptoms and specific environment measures were found, but total SBS symptoms were not correlated with most of the indoor environment measures. There was a significant difference in SBS reports between areas above and below 650 ppm CO2. SBS symptoms were correlated with perceived indoor environment conditions, cacosmia, overwork, migraine, allergies, and musculoskeletal complaints. SBS symptoms were not associated with negative affect, worry, or general anxiety and stress.
Corp Regulates P53 in Drosophila melanogaster via a Negative Feedback Loop

The tumor suppressor P53 is a critical mediator of the apoptotic response to DNA double-strand breaks through the transcriptional activation of pro-apoptotic genes. This mechanism is evolutionarily conserved from mammals to lower invertebrates, including Drosophila melanogaster. P53 also transcriptionally induces its primary negative regulator, Mdm2, which has not been found in Drosophila. In this study we identified the Drosophila gene companion of reaper (corp) as a gene whose overexpression promotes survival of cells with DNA damage in the soma but reduces their survival in the germline. These disparate effects are shared by p53 mutants, suggesting that Corp may be a negative regulator of P53. Confirming this supposition, we found that corp negatively regulates P53 protein level. It has been previously shown that P53 transcriptionally activates corp; thus, Corp produces a negative feedback loop on P53. We further found that Drosophila Corp shares a protein motif with vertebrate Mdm2 in a region that mediates the Mdm2:P53 physical interaction. In Corp, this motif mediates physical interaction with Drosophila P53. Our findings implicate Corp as a functional analog of vertebrate Mdm2 in flies.
Formal Concept Analysis for Information Retrieval

In this paper we describe a mechanism to improve Information Retrieval (IR) on the web. The method is based on Formal Concepts Analysis (FCA) that it is makes semantical relations during the queries, and allows a reorganizing, in the shape of a lattice of concepts, the answers provided by a search engine. We proposed for the IR an incremental algorithm based on Galois lattice. This algorithm allows a formal clustering of the data sources, and the results which it turns over are classified by order of relevance. The control of relevance is exploited in clustering, we improved the result by using ontology in field of image processing, and reformulating the user queries which make it possible to give more relevant documents. Keywords-FCA; Galois lattice; IR; Ontology; Query Reformulation)
Robot Pose Estimation in Unknown Environments by Matching 2D Range Scans

A mobile robot exploring an unknown environment has no absolute frame of reference for its position, other than features it detects through its sensors. Using distinguishable landmarks is one possible approach, but it requires solving the object recognition problem. In particular, when the robot uses two-dimensional laser range scans for localization, it is difficult to accurately detect and localize landmarks in the environment (such as corners and occlusions) from the range scans.In this paper, we develop two new iterative algorithms to register a range scan to a previous scan so as to compute relative robot positions in an unknown environment, that avoid the above problems. The first algorithm is based on matching data points with tangent directions in two scans and minimizing a distance function in order to solve the displacement between the scans. The second algorithm establishes correspondences between points in the two scans and then solves the point-to-point least-squares problem to compute the relative pose of the two scans. Our methods work in curved environments and can handle partial occlusions by rejecting outliers.
Age and biostratigraphy of Early Cambrian tuffs from SE Australia and southern China

Reassessment of faunal discoveries in the Fleurieu Peninsula, South Australia, shows that the Sellick Hill tuff is late Atdabanian or early Botomian in age and is preceded by Tommotian to Atdabanian equivalents. Previous and new sensitive high-resolution ion microprobe (SHRIMP) zircon ages from the tuff have been adjusted for Pb loss in the reference zircon, and mixture-modelling has been applied to resolve inheritance and Pb loss. The revised tuff age is now 522.0 ± 2.0 Ma (σ), 0.7% younger than the original estimate. Undocumented SHRIMP ages for zircons from a middle to upper Botomian tuff near Cymbric Vale were cited in 1994 as a single 525 ± 4 Ma population, but reprocessing using the present approach shows instead that the correct age of volcanism is 517.8 ± 2.1 Ma (σ). Reprocessed and new SHRIMP ages for zircons from tuff within Bed 5 of the Lower Cambrian Meishucun section, South China, give a revised age for the earlier Tommotian of 538.2 ± 1.5 Ma (σ). We agree with US workers that the stratotypic lowest Cambrian sequence of Newfoundland correlates within the Nemakit–Daldynian of Siberia. These results agree broadly with the Early Cambrian time scale based on zircon U–Pb isotope dilution data, but differences remain that arise more from interpretations of biostratigraphy and from the preservation and origin of the sampled zircon grains than from instrumental accuracy. In particular, the increased duration for the Tommotian indicated by our results supports notions of a more gradualistic evolution attending the origins of animal skeletons.
Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

The identification of interaction partners in protein complexes is a major goal in cell biology. Here we present a reliable affinity purification strategy to identify specific interactors that combines quantitative SILAC-based mass spectrometry with characterization of common contaminants binding to affinity matrices (bead proteomes). This strategy can be applied to affinity purification of either tagged fusion protein complexes or endogenous protein complexes, illustrated here using the well-characterized SMN complex as a model. GFP is used as the tag of choice because it shows minimal nonspecific binding to mammalian cell proteins, can be quantitatively depleted from cell extracts, and allows the integration of biochemical protein interaction data with in vivo measurements using fluorescence microscopy. Proteins binding nonspecifically to the most commonly used affinity matrices were determined using quantitative mass spectrometry, revealing important differences that affect experimental design. These data provide a specificity filter to distinguish specific protein binding partners in both quantitative and nonquantitative pull-down and immunoprecipitation experiments.
Cell Cycle and Biochemical Effects of PD 0183812

Progression through the G1 phase of the cell cycle requires phosphorylation of the retinoblastoma gene product (pRb) by the cyclin D-dependent kinases CDK4 and CDK6, whose activity can specifically be blocked by the CDK inhibitor p16INK4A. Misregulation of the pRb/cyclin D/p16INK4A pathway is one of the most common events in human cancer and has lead to the suggestion that inhibition of cyclin D-dependent kinase activity may have therapeutic value as an anticancer treatment. Through screening of a chemical library, we initially identified the [2,3-d]pyridopyrimidines as inhibitors of CDK4. Chemical modification resulted in the identification of PD 0183812 as a potent and highly selective inhibitor of both CDK4 and CDK6 kinase activity, which is competitive with ATP. Flow cytometry experiments showed that of the cell lines tested, only those expressing pRb demonstrated a G1 arrest when treated with PD 0183812. This arrest correlated in terms of incubation time and potency with a loss of pRb phosphorylation and a block in proliferation, which was reversible. These results suggest a potential use of this chemical class of compounds as therapeutic agents in the treatment of tumors with functional pRb, possessing cell cycle aberrations in other members of the pRb/cyclin D/p16INK4A pathway.
An analysis of multicast forwarding state scalability

Scalability of multicast forwarding state is likely to be a major issue facing inter-domain multicast deployment. We present a comprehensive analysis of the multicast forwarding state problem. Our goal is to understand the scaling trends of multicast forwarding state in the Internet, and to explore the intuitions that have motivated state reduction research. We conducted simulation experiments on both real and generated network topologies, with a range of parameters driven by multicast application characteristics. We found that the increase in peering among Internet backbone networks has led to more multicast forwarding state at a handful of core domains, but less state in the rest of the domains. We observed that scalability of multicast forwarding state with respect to session size follows a power law. Our findings show that distribution and concentration of multicast forwarding state in the Internet is significantly, impacted by the application characteristics. We investigated the proposals on non-branching multicast forwarding state elimination, and found substantial reduction is attainable even with very dense multicast sessions.
Association Between Ideal Cardiovascular Health and Carotid Intima‐Media Thickness: A Twin Study

Background The American Heart Association (AHA) recently developed the Cardiovascular Health Index (CVHI), a health metric consisting of 7 modifiable risk factors. The relationship of the CVHI with preclinical markers, such as carotid intima‐media thickness (CIMT) has not been assessed. Methods We examined 490 male monozygotic and dizygotic twins without overt cardiovascular disease. CIMT was measured using B‐mode ultrasonography. Each of the 7 CVHI components (blood pressure, fasting glucose, total cholesterol, body mass index, physical activity, healthy diet, and smoking) was given a point score of 0, 1, or 2 to represent poor, intermediate, or ideal health, respectively. A CVHI summation score was computed (range 0 to 14) and categorized as inadequate (0 to 4), average (5 to 9), or optimum (10 to 14) cardiovascular health. Mixed‐model regression was used to examine the association of the CVHI with CIMT. Results The mean age of the twins was 55.4 years, and 61% were monozygotic. The mean CIMT was 0.75 (±0.11) mm and the mean CVHI score was 7.7 (±2.1). There was an inverse correlation between CVHI and CIMT (Spearman r=−0.22, P<0.01). For every 5‐unit increase in overall CVHI score (indicating better cardiovascular health category), CIMT decreased by 0.045 mm (P<0.001) after adjusting for demographic variables and other confounders. Within monozygotic twin pairs, a 5‐unit increment in CVHI score was associated with a 0.05 mm lower CIMT (P<0.001). Conclusions The CVHI is independently associated with CIMT and the association is not confounded by shared genetic and other familial factors.
Information-optimal genome assembly via sparse read-overlap graphs

MOTIVATION In the context of third-generation long-read sequencing technologies, read-overlap-based approaches are expected to play a central role in the assembly step. A fundamental challenge in assembling from a read-overlap graph is that the true sequence corresponds to a Hamiltonian path on the graph, and, under most formulations, the assembly problem becomes NP-hard, restricting practical approaches to heuristics. In this work, we avoid this seemingly fundamental barrier by first setting the computational complexity issue aside, and seeking an algorithm that targets information limits In particular, we consider a basic feasibility question: when does the set of reads contain enough information to allow unambiguous reconstruction of the true sequence? RESULTS Based on insights from this information feasibility question, we present an algorithm-the Not-So-Greedy algorithm-to construct a sparse read-overlap graph. Unlike most other assembly algorithms, Not-So-Greedy comes with a performance guarantee: whenever information feasibility conditions are satisfied, the algorithm reduces the assembly problem to an Eulerian path problem on the resulting graph, and can thus be solved in linear time. In practice, this theoretical guarantee translates into assemblies of higher quality. Evaluations on both simulated reads from real genomes and a PacBio Escherichia coli K12 dataset demonstrate that Not-So-Greedy compares favorably with standard string graph approaches in terms of accuracy of the resulting read-overlap graph and contig N50. AVAILABILITY Available at github.com/samhykim/nsg CONTACT courtade@eecs.berkeley. edu or dntse@stanford.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.