Miracle-dz/UniFAR-FTUs huggingface dataset:
Linked Common Polymorphisms in the Gelatinase A Promoter Are Associated with Diminished Transcriptional Response to Estrogen and Genetic Fitness*

Gelatinase A (matrix metalloproteinase-2) plays a prominent role in multiple biologic processes. Prior studies have established critical roles for gelatinase A transcriptional regulation by defined enhancer elements. To determine possible functional single nucleotide polymorphisms within these elements, we determined the single nucleotide polymorphism distribution within 1,665 bp of the gelatinase A 5′-flanking region, using a healthy homogeneous Caucasian study group of 463 individuals. Among the polymorphisms detected, a G → A transition at bp –1575 was located immediately 5′ to a half-palindromic potential estrogen receptor binding site. In estrogen receptor-positive MCF-7 cells the –1575G allele functioned as an enhancer, whereas the –1575A allele reduced transcription activity significantly. Gel shift assays confirmed that the differences in allelic expression affected binding of the estrogen receptor-α to this region. Cotransfection experiments with an estrogen receptor-α expression vector in MDA-MB-231 cells, which do not constitutively express an estrogen receptor, revealed that estrogen receptor is absolutely required for enhancing activity. Allelic distribution analysis indicated that a previously reported C → T transition within an Sp1 binding site at –1306 was in linkage disequilibrium with the –1575G → A transition. Luciferase reporter studies of the linked variant –1575A –1306T allele versus the wild type –1575G –1306C allele demonstrated an additive reduction in estrogen-dependent reporter activity. The frequency of the –1575G → A transition deviated significantly from the expected Hardy-Weinberg distribution in two independently assembled study populations consisting of healthy adult blood donors and newborns of Caucasian origin, both with a calculated 21% reduction in genetic fitness. Gelatinase A is a known estrogen-responsive gene and the demonstration of a loss of function polymorphism within an operational estrogen receptor binding site associated with a decrease in genetic fitness underscores the biologic significance of promoter polymorphism analyses.
Unsupervised Approaches to Sequence Tagging , Morphology Induction , and Lexical Resource Acquisition

We consider unsupervised approaches to three types of problems involving the prediction of natural language information at or below the level of words: sequence labeling (including part-of-speech tagging); decomposition (morphological analysis and segmentation); and lexical resource acquisition (building dictionaries to encode linguistic knowledge about words within and across languages). We highlight the strengths and weaknesses of these approaches, including the extent of labeled data/resources assumed as input, the robustness of modeling techniques to linguistic variation, and the semantic richness of the output relative to the input.
Optimizing Every Operation in a Write-optimized File System

File systems that employ write-optimized dictionaries (WODs) can perform random-writes, metadata updates, and recursive directory traversals orders of magnitude faster than conventional file systems. However, previous WOD-based file systems have not obtained all of these performance gains without sacrificing performance on other operations, such as file deletion, file or directory renaming, or sequential writes. Using three techniques, late-binding journaling, zoning, and range deletion, we show that there is no fundamental trade-off in write-optimization. These dramatic improvements can be retained while matching conventional file systems on all other operations. BetrFS 0.2 delivers order-of-magnitude better performance than conventional file systems on directory scans and small random writes and matches the performance of conventional file systems on rename, delete, and sequential I/O. For example, BetrFS 0.2 performs directory scans 2.2× faster, and small random writes over two orders of magnitude faster, than the fastest conventional file system. But unlike BetrFS 0.1, it renames and deletes files commensurate with conventional file systems and performs large sequential I/O at nearly disk bandwidth. The performance benefits of these techniques extend to applications as well. BetrFS 0.2 continues to outperform conventional file systems on many applications, such as as rsync, git-diff, and tar, but improves git-clone performance by 35% over BetrFS 0.1, yielding performance comparable to other file systems.
Non-sparse Multiple Kernel Learning

Approaches to multiple kernel learning (MKL) employ l1-norm constraints on the mixing coefficients to promote sparse kernel combinations. When features encode orthogonal characterizations of a problem, sparseness may lead to discarding useful information and may thus result in poor generalization p erformance. We study non-sparse multiple kernel learning by imposing an l2-norm constraint on the mixing coefficients. Empirically, l2-MKL proves robust against noisy and redundant feature sets and significantly improves the promoter de t ction rate compared to l1-norm and canonical MKL on large scales.
Contribution of developmental changes in energy metabolism to excitation-contraction coupling of a ventricular cell: A simulation study

In fetal guinea pigs, ventricular cells have higher anaerobic glycolytic capacity and lower mitochondrial enzyme activity. Here, we implemented developmental changes in glycolytic enzyme activity, concentrations of glycogen, and total creatine in late embryonic and adult ventricular cell models. We then simulated the effects of hypoxic conditions on dynamic changes in contractile force and ATP concentration. Our model demonstrates that fetal ventricular cells maintain ATP for longer periods of time than adult ventricular cells. This is consistent with reported dynamics of ventricular cells under hypoxic conditions.
Subjective Probabilities and Short‐Term Economic Forecasts: An Empirical Investigation

Subjective probabilities for one‐week forecasts of five series (F.T. Share Index, dollar–sterling rate and three oil price series) were obtained from a panel of BP personnel in 18 successive weeks. Two kinds of form were completed on alternate weeks by each subject, one requiring probabilities of given percentage changes (A) and one requiring percentiles (B). Average results for 23 participants show a bias towards central values on both forms, smaller on A than B. The main feature shown by analysis of variance was marked variation between participants, consistent over series and forms, and not associated with discipline or professional interest. On a logarithmic scoring rule the average performance was the same on the two forms, but subjects with smallest central bias scored slightly better on Form B. Subjective distribution shapes showed no consistent pattern.
Traffic and Sprawl: Evidence from U.S. Commuting, 1985 To 1997*

Author(s): Crane, RD; Chatman, DG | Abstract: The consequences of sprawl for travel behavior remain unclear. Theory suggests at least two possible commuting outcomes. As jobs decentralize and central employment areas congest, workers might shorten their commutes in time and distance by relocating to the suburbs. Or, the average commute could grow if residential choice is relatively inelastic with respect to job location, amenity explanations for residential and job location dominate, or as dual-worker households in polycentric labor markets become the norm. Evidence on these questions is surprisingly rare and dated. For data on individual travel behavior, we use the American Housing Survey, a detailed individual-level panel survey for most major metropolitan areas of the U.S. for several years between 1985 and 1997. Commute distance is regressed on a reduced form travel demand model, including U.S. Bureau of Economic Analysis measures of metro-wide employment deconcentration at the one-digit SIC industry level. The model specification conforms to urban form theory, the model estimation uses panel techniques, and the potential endogeneity of wages and land costs -- as compensations for commute costs -- is addressed statistically. We find that the more suburbanized is employment -- that is, the more sprawl -- the shorter the average commute. There are strong differences by industry, however, that may reflect a combination of industry agglomeration effects, differential job location stability by industry, and historical transitions.
Scalable Blocking for Privacy Preserving Record Linkage

When dealing with sensitive and personal user data, the process of record linkage raises privacy issues. Thus, privacy preserving record linkage has emerged with the goal of identifying matching records across multiple data sources while preserving the privacy of the individuals they describe. The task is very resource demanding, considering the abundance of available data, which, in addition, are often dirty. Blocking techniques are deployed prior to matching to prune out unlikely to match candidate records so as to reduce processing time. However, when scaling to large datasets, such methods often result in quality loss. To this end, we propose Multi-Sampling Transitive Closure for Encrypted Fields (MS-TCEF), a novel privacy preserving blocking technique based on the use of reference sets. Our new method effectively prunes records based on redundant assignments to blocks, providing better fault-tolerance and maintaining result quality while scaling linearly with respect to the dataset size. We provide a theoretical analysis on the method's complexity and show how it outperforms state-of-the-art privacy preserving blocking techniques with respect to both recall and processing cost.
Disk M Dwarf Luminosity Function From HST Star Counts

We study a sample of 257 Galactic disk M dwarfs (8 12 (M<0.25 \ms), decreasing by a factor \gsim 3 by M_V~14 (M~0.14\ms). This decrease in the LF is in good agreement with the ground-based photometric study of nearby stars by Stobie et al. (1989), and in mild conflict with the most recent LF measurements based on local parallax stars by Reid et al. (1995). The local LF of the faint Galactic disk stars can be transformed into a local mass function using an empirical mass-M_V relation. The mass function can be represented analytically over the mass range 0.1\ms<M<1.6\ms by \log(\phi)=-1.35-1.34\log(M/\ms)-1.85 [\log(M/\ms)]^2 where \phi is the number density per logarithmic unit of mass. The total column density of M stars is only \Sigma_M=11.8\pm 1.8\ms\pc^{-2}, implying a total `observed' disk column density of \Sigma_\obs~=39\ms\pc^{-2}, lower than previously believed, and also lower than all estimates with which we are familiar of the dynamically inferred mass of the disk. The measured scale length for the M-star disk is 3.0\pm 0.4 kpc. The optical depth to microlensing toward the LMC by the observed stars in the Milky Way disk is \tau~1x10^{-8}, compared to the observed optical depth found in ongoing experiments \tau_\obs~ 10^{-7}. The M-stars show evidence for a population with characteristics intermediate between thin disk and spheroid populations. Approximating what may be a continuum of populations by two separate component, we find characteristic exponential scale heights of ~210 pc and ~740 pc.
Frontal face recognition from video via rank-aware multiple measurement vector recovery

The Sparse Classification approach for image based face recognition assumes that each test sample can be expressed as a linear combination of training samples of the correct class. We propose a video based face recognition approach based on the same assumption. Our formulation requires solving a low-rank row-sparse Multiple Measurement Vector (MMV) recovery problem. Such a row-sparse MMV matrix is low rank as well. Since low rank row sparse MMV recovery is not a well-studied problem, we propose a novel algorithm to solve such it. The experimental evaluation is carried on the VidTIMIT database. The proposed method yields better results than state-of-the-art methods in video based frontal face recognition.
Repair of O6-methylguanine adducts in human telomeric G-quadruplex DNA by O6-alkylguanine-DNA alkyltransferase

O6-alkylguanine-DNA alkyltransferase (AGT) is a single-cycle DNA repair enzyme that removes pro-mutagenic O6-alkylguanine adducts from DNA. Its functions with short single-stranded and duplex substrates have been characterized, but its ability to act on other DNA structures remains poorly understood. Here, we examine the functions of this enzyme on O6-methylguanine (6mG) adducts in the four-stranded structure of the human telomeric G-quadruplex. On a folded 22-nt G-quadruplex substrate, binding saturated at 2 AGT:DNA, significantly less than the ∼5 AGT:DNA found with linear single-stranded DNAs of similar length, and less than the value found with the telomere sequence under conditions that inhibit quadruplex formation (4 AGT:DNA). Despite these differences, AGT repaired 6mG adducts located within folded G-quadruplexes, at rates that were comparable to those found for a duplex DNA substrate under analogous conditions. Repair was kinetically biphasic with the amplitudes of rapid and slow phases dependent on the position of the adduct within the G-quadruplex: in general, adducts located in the top or bottom tetrads of a quadruplex stack exhibited more rapid-phase repair than did adducts located in the inner tetrad. This distinction may reflect differences in the conformational dynamics of 6mG residues in G-quadruplex DNAs.
Direct Manipulation Interfaces

Direct manipulation has been lauded as a good form of interface design, and some interfaces that have this property have been well received by users. In this article we seek a cognitive account of both the advantages and disadvantages of direct manipulation interfaces. We identify two underlying phenomena that give rise to the feeling of directness. One deals with the information processing distance between the user's intentions and the facilities provided by the machine. Reduction of this distance makes the interface feel direct by reducing the effort required of the user to accomplish goals. The second phenomenon concerns the relation between the input and output vocabularies of the interface language. In particular, direct manipulation requires that the system provide representations of objects that behave as if they are the objects themselves. This provides the feeling of directness of manipulation.
Secondary-storage confidence computation for conjunctive queries with inequalities

This paper investigates the problem of efficiently computing the confidences of distinct tuples in the answers to conjunctive queries with inequalities (<) on tuple-independent probabilistic databases. This problem is fundamental to probabilistic databases and was recently stated open. Our contributions are of both theoretical and practical importance. We define a class of tractable queries with inequalities, and generalize existing results on #P-hardness of query evaluation, now in the presence of inequalities. For the tractable queries, we introduce a confidence computation technique based on efficient compilation of the lineage of the query answer into Ordered Binary Decision Diagrams (OBDDs), whose sizes are linear in the number of variables of the lineage. We implemented a secondary-storage variant of our technique in PostgreSQL. This variant does not need to materialize the OBDD, but computes, in one scan over the lineage, the probabilities of OBDD fragments and combines them on the fly. Experiments with probabilistic TPC-H data show up to two orders of magnitude improvements when compared with state-of-the-art approaches.
Channel Estimation and Data Equalization in Frequency-Selective MIMO Systems with One-Bit Quantization

This paper addresses channel estimation and data equalization on frequency-selective 1-bit quantized Multiple Input-Multiple Output (MIMO) systems. No joint processing or Channel State Information is assumed at the transmitter, and therefore our findings are also applicable to the uplink of Multi-User MIMO systems. System models for both Orthogonal Division Frequency Multiplexing (OFDM) and single-carrier schemes are developed. A Cram\'er-Rao Lower Bound for the estimation problems is derived. The two nonlinear algorithms Expectation Maximization (EM) and Generalized Approximate Message Passing (GAMP) are adapted to the problems, and a linear method based on the Bussgang theorem is proposed. In the OFDM case, the linear method enables subcarrier-wise estimation, greatly reducing computational complexity. Simulations are carried out to compare the algorithms with different settings. The results turn out to be close to the Cram\'er-Rao bound in the low Signal to Noise Ratio (SNR) region. The OFDM setting is more suitable for the nonlinear algorithms, and that the linear methods incur a performance loss with respect to the nonlinear approaches. In the relevant low and medium SNR regions, the loss amounts to 2-3 dB and might well be justified in exchange for the reduced computational effort, especially in Massive MIMO settings.
Stability of a localized and greedy routing algorithm

In this work, we study the problem of routing packets between undifferentiated sources and sinks in a network modeled by a multigraph. We consider a distributed and local algorithm that transmits packets hop by hop in the network and study its behavior. At each step, a node transmits its queued packets to its neighbors in order to optimize a local gradient. This protocol is greedy since it does not require to record the history about the past actions, and localized since nodes only need information about their neighborhood. A transmission protocol is stable if the number of packets in the network does not diverge. To prove the stability, it is sufficient to prove that the number of packets stored in the network remains bounded as soon as the sources inject a flow that another method could have exhausted. The localized and greedy protocol considered has been shown to be stable in some specific cases related to the arrival rate of the packets. We investigate its stability in a more general context and therefore reinforce results from the literature that worked for differentiated suboptimal flows. We show that, to prove the stability of this protocol, it is sufficient to prove the intuitive following conjecture: roughly, if the protocol is stable when all sources inject the maximum number of packets at each turn and no packets are lost, then the protocol is stable whatever be the behavior of the network (i.e., when less packets are injected and some of them may be lost).
The Impact of Police Work-Family Conflict on Turnover Intentions: The Roles of Organizational Support and Job Burnout

Work-family conflict is always considered to have a positive influence on job burnout and turnover intentions. But things may be different for Chinese police, who may be less likely to leave their job because of their firm beliefs and higher welfare. Considering this, we use Beijing police as the sample of our research, and explore the impact of work-family conflict on turnover intentions under the roles of organizational support and job burnout. By analyzing 316 valid questionnaires surveyed from the Beijing public security system, we get the following conclusions: work-family conflict and job burnout have a significant and positive correlation with turnover intentions; job burnout plays a partial mediating role in the relationship between work-family conflict and turnover intentions; organizational support plays a moderating role between work-family conflict and job burnout.
A Qualitative Study of Domain Specific Languages for Model Driven Security

In Model-Driven development, software system design is represented through models which are created using general purpose modeling languages e.g., UML. Later on system artifacts are automatically generated from these models. Model-Driven Security is a specialization of Model-Driven paradigm towards the domain of security, where security objectives are modeled along the system models and security infrastructures are directly generated from these models. Currently available general purpose modeling languages like UML do not have capability to model the security objectives along the system models. Over the past decade, many researchers are trying to address these limitations of the general purpose modeling languages and come up with several Domain Specific Modeling Languages for Model Driven Security. In this study, a comparative study is presented regarding the security Domain Specific Modeling Languages presented by the most prominent researchers for the development of secure system. A success criteria has been defined and these DSLs are critically analyzed based on it to obtain the qualitative results.
Toward a climate-depend paradigm of ammonia emission & deposition

Existing descriptions of bi-directional ammonia (NH3) land–atmosphere exchange incorporate temperature and moisture controls, and are beginning to be used in regional chemical transport models. However, such models have typically applied simpler emission factors to upscale the main NH3 emission terms. While this approach has successfully simulated the main spatial patterns on local to global scales, it fails to address the environment- and climate-dependence of emissions. To handle these issues, we outline the basis for a new modelling paradigm where both NH3 emissions and deposition are calculated online according to diurnal, seasonal and spatial differences in meteorology. We show how measurements reveal a strong, but complex pattern of climatic dependence, which is increasingly being characterized using ground-based NH3 monitoring and satellite observations, while advances in process-based modelling are illustrated for agricultural and natural sources, including a global application for seabird colonies. A future architecture for NH3 emission–deposition modelling is proposed that integrates the spatio-temporal interactions, and provides the necessary foundation to assess the consequences of climate change. Based on available measurements, a first empirical estimate suggests that 5°C warming would increase emissions by 42 per cent (28–67%). Together with increased anthropogenic activity, global NH3 emissions may increase from 65 (45–85) Tg N in 2008 to reach 132 (89–179) Tg by 2100.
Asymmetric Segregation of Numb in Retinal Development and the Influence of the Pigmented Epithelium

Asymmetric segregation of cell-fate determinants during cytokinesis plays an important part in controlling cell-fate choice in invertebrates. During Drosophila neurogenesis, for example, asymmetric segregation of the Numb protein, which inhibits Notch signaling, is necessary for the two daughter cells of a division to have different fates. In vertebrates, the role of asymmetric segregation of cell-fate determinants is uncertain, and the way the process might be regulated is unknown. We have studied the orientation of cell divisions and the distribution of Numb in the developing rat retina. We show that, whereas most retinal neuroepithelial cells divide with their mitotic spindles oriented parallel to the plane of the neuroepithelium, a substantial minority divides with their spindles oriented perpendicularly. The proportion of these vertically dividing cells changes during development, peaking around the day of birth. Numb appears to be inherited only by the apical daughter cell when a neuroepithelial cell divides vertically. Similarly, in dissociated cell cultures, some retinal neuroepithelial cells divide asymmetrically and distribute Numb to only one of the two daughter cells, suggesting that the dissociated cells can retain their polarity in vitro. Using retinal explant cultures, we find that the retinal pigment epithelium apparently promotes vertical divisions in the neural retina. To our knowledge, this is the first evidence that asymmetric segregation of cell-fate determinants may contribute to cell diversification in the mammalian retina and that an epithelium controls this process by influencing the plane of division in the adjacent neural retina.