Miracle-dz/UniFAR-FTUs huggingface dataset:
Hierarchical Models for Causal Effects 1

Hierarchical models play three important roles in modeling causal effects: (i) accounting for data collection, such as in stratified and split-plot experimental designs; (ii) adjusting for unmeasured covariates, such as in panel studies; and (iii) capturing treatment effect variation, such as in subgroup analyses. Across all three areas, hierarchical models, especially Bayesian hierarchical modeling, offer substantial benefits over classical, non-hierarchical approaches. After discussing each of these topics, we explore some recent developments in the use of hierarchical models for causal inference and conclude with some thoughts on new directions for this research area. BACKGROUND ON HIERARCHICAL MODELING AND CAUSAL INFERENCE Historically, social scientists have estimated causal effects via classical, linear regression. When the data come from a simple randomized experiment, this can be a very sensible approach. However, when the data deviate from this ideal even slightly, continuing to use this approach can be problematic. For example, linear regression will yield misleading results if the researcher collects test scores at the student level but randomizes assigns the intervention at the classroom level. The goal of this approach is to use statistical methods that properly account for non-standard data structures and other features of the data collection process. Moreover, these methods can be extended to data not obtained from randomized experiments. The statistical term hierarchical modeling has two, related, meanings. First, it can refer to modeling of hierarchical data structures: for example, students within schools or, for a non-nested example, panel or time-series 1 For Emerging Trends in the Social and Behavioral Sciences, ed. Robert Scott and Stephen Kosslyn. We thank Jennifer Hill and Shira Mitchell for helpful comments and the National Science Foundation and the Institute of Education Sciences for partial support of this work. Emerging Trends in the Social and Behavioral Sciences. Edited by Robert Scott and Kosslyn. © 2015 John Wiley & Sons, Inc. ISBN 978-1-118-90077-2.
Landscape aspects of oyster reefs : fragmentation and habitat utilization

The functional value of oyster reefs is recognized in many estuarine systems, with increasing interest in oyster reef restoration for ecological function rather than for fishery production. Reefs provide structure and refuge for juvenile fish and crustaceans, and may be a locus for predator foraging. However, reef morphology influences the relative value of refuge and forage functions, and reef utilization by benthic, epibenthic, and nektonic organisms. Reef fragmentation will increase the edge to interior ratio, and may enhance use by organisms that favor edge regions, or decrease use by species requiring more interior habitat. The influence of fragmentation was examined using created intertidal oyster reefs and natural reef patches in southeastern North Carolina. Created reef treatments included a uniform circular reef, a small fragmented reef, a large fragmented reef, and reference natural reef and mudflat areas. In addition, uniform and fragmented patch reefs in two nearby tidal creeks were also sampled. All treatments were sampled immediately after construction in June 2002, and then quarterly over two years, targeting infauna, epifauna, and nekton. Effects of fragmentation on infuana were variable, with a combination of positive and negative species-specific responses. However, preferential use of large fragmented reefs over small fragmented reefs was observed for Lagodon rhomboides, Panopeus herbstii, and Geukensia demissa, suggesting that the small fragmented reefs were most likely below the patch size threshold at which edge effects become beneficial. Implications are that oyster reef fragmentation may be an important factor for restoration managers to consider when designing reefs in which increased habitat utilization is a primary goal. Although a degree of fragmentation may be beneficial for some species, once fragmentation leads to a loss of reef area below critical thresholds, degradation effects on habitat utilization could be great.
Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations

A direct attack on the protein‐folding problem has been initiated with the free energy perturbation methods of molecular dynamics. The complete conformational probability map for the alanine dipeptide is presented. This work uses the SPC model for the explicit hydration of the dipeptide. Free energy differences for the four observed minima (β, αR, αL, C 7ax ) are given, and the free energy barriers between minima are outlined.
Cross-coupled signals separation and equalization by a mirror imaged adaptive decorrelation structure

An adaptive structure for cross-coupled signals blind separation and equalization is proposed. Cross-coupled signals might occur and observed in many MIMO applications. In this paper, the output observations of reverberant/non-reverberant simplified MIMO of 2-channel cross-coupled signals are considered. The structure is based on cross-coupled adaptive FIR cancellers for signals de-correlation and two other FIR equalizers that equalize the signals against the source signal cross-coupling channels distortion. Suitable de-correlation will result signals separation while equalization is devoted for signals reshaping. This structure is shown, under certain circumstances, to estimate the source signals, with no distortion even when the transmission coupling paths between the observation sensors have low attenuation and both signals are continuous. The main issues involved in this paper are the analysis of the structure topology, system constraint and convergence of the individual adaptive transfer function to solution(s) that ensures the signals separation and equalization for reverberant or non-reverberant channels. Also, suitable adopted LMS and least squares adaptive estimation algorithms for the structure are presented.
A comparison of porp, torp, and incus homograft for ossicular reconstruction in chronic ear surgery

This report presents the results of 210 cases over a 10‐year period using PORPs, TORPs, and notched incus homografts (NIH), for ossicular reconstruction in chronic ear surgery. There were 192 adults and 18 children. The surgical technique utilized temporalis fascia in an underlay technique with canal skin covering the outer surface of the fascia. Intact canal wall mastoid‐tympanoplasty, as a one‐stage procedure, was used for most cases. Homograft nasal cartilage was placed between the Plasti‐Pore® prosthesis and the graft. Notched incus homografts were prepared prior to surgery and stored in 4% formalin. There were 149 mastoid‐tympanoplasties and 61 tympanoplasties performed. Revsion of our cases was performed in 16.6%.
Responses to dietary starch or sucrose on protein and glucose kinetics in goats fed a high-concentrate diet

Abstract Responses of whole body protein synthesis (WBPS) and glucose irreversible loss rate (ILR) were compared between dietary starch and sucrose in four male goats. Diets were fed at 1.2 times maintenance requirements of ME and CP with 30% of the ME as starch, starch plus sucrose or sucrose, twice daily. The diets consisted of 33, 32, 11 and 24% of alfalfa hay, corn, soybean meal and the carbohydrates, respectively. The WBPS and glucose ILR during 5 – 7 h after feeding were determined by an isotope dilution method of [2H5]phenylalanine, [2H2]tyrosine, [2H4]tyrosine and [13C6]glucose. Sucrose elevated ammonia nitrogen and lowered acetate concentrations in the rumen, but did not differ from starch in nitrogen retention. Glucose ILR and WBPS were similar between the carbohydrates. It was concluded that dietary sucrose would have effects similar to starch on WBPS and glucose kinetics in the absorptive state in goats fed a high-concentrate diet.
A new uncertainty decoding scheme for DNN-HMM hybrid systems with multichannel speech enhancement

Uncertainty decoding combines a probabilistic feature description with the acoustic model of a speech recognition system. For DNN-HMM hybrid systems, this can be realized by averaging the DNN outputs produced by a finite set of feature samples (drawn from an estimated probability distribution). In this article, we employ this sampling approach in combination with a multi-microphone speech enhancement system. We propose a new strategy for generating feature samples from multichannel signals, based on modeling the spatial coherence estimates between different microphone pairs as realizations of a latent random variable. From each coherence estimate, a spectral enhancement gain is computed and an enhanced feature vector is obtained, thus producing a finite set of feature samples, of which we average the respective DNN outputs. In the experimental part, this new uncertainty decoding strategy is shown to consistently improve the recognition accuracy of a DNN-HMM hybrid system for the 8-channel REVERB Challenge task.
A Study on Data Aggregation and Reliability in Managing Wireless Sensor Networks

Using data aggregation to reduce power consumption is a well studied area. In this paper we show a new result: data aggregation can also be used to increase reliability. In scenarios where status is being collected from every node (e.g. network management), one measure of reliability is the completeness (nodes included). Using some of the power savings from aggregation to increase the retransmission limit for aggregated data gives significant improvements in completeness. The contribution of this paper is in providing a detailed comparison of the completeness and energy efficiency for aggregated and non-aggregated data. Results, derived by numerical analysis and simulation, show that with data aggregation and increased retransmission limits, reliability can be substantially improved, while still saving power. These results are applicable to designing network management protocols for Wireless Sensor Networks, as well as for other scenarios where high completeness is required for network-wide data collection.
Bank liquidity creation during distress

Liquidity creation is one of banks‟ raisons d‟etre. But what happens to liquidity creation when a bank is identified as distressed by regulatory bodies and subject to interventions and receives capital injections? Does market discipline also play a role? What are the long-run effects of regulatory interventions, capital injections, and market discipline on bank performance? To address these questions, we exploit a unique dataset of German universal banks for the period 1999 - 2008. Our findings are as follows: First, regulatory interventions and capital injections are followed by lower levels of liquidity creation. We show that the probability of a decline in liquidity creation increases to up to 48 percent when such actions are taken. Second, market participants also discipline distressed banks by limiting their scope for creating liquidity. Downgrades of the Moody‟s bank financial strength rating raise the likelihood of contractions in liquidity creation to over 53 percent. Third, we present evidence that capital injections and Moody‟s rating downgrades also reduce banks‟ average asset risk. Fourth, we illustrate that there are considerable long-run effects of regulatory interventions, capital injections, and ratings downgrades. Over the five years following such disciplinary measures, banks reduce their average exposure to asset risk by 5 percentage points, and increase their capital adequacy ratio from 7.85 to 9.32 percent, whereas market shares in terms of liquidity creation decline.
Are we Overestimating the Number of Cell-Cycling Genes? The Impact of Background Models

MOTIVATION Periodic processes play fundamental roles in organisms. Prominent examples are the cell cycle and the circadian clock. Microarray array technology has enabled us to screen complete sets of transcripts for possible association with such fundamental periodic processes on a system-wide level. Frequently, quite large numbers of genes have been detected as periodically expressed. However, the small overlap between genes identified in different studies has cast some doubts on the reliability of the periodic expression detected. RESULTS In this study, comparative analysis suggests that the lacking agreement between different cell-cycle studies might be due to inadequate background models for the determination of significance. We demonstrate that the choice of background model has considerable impact on the statistical significance of periodic expression. For illustration, we reanalyzed two microarray studies of the yeast cell cycle. Our evaluation strongly indicates that the results of previous analyses might have been overoptimistic and that the use of more suitable background model promises to give more realistic results. AVAILABILITY R scripts are available on request from the corresponding author.
Bacillus subtilis RecA and its accessory factors, RecF, RecO, RecR and RecX, are required for spore resistance to DNA double-strand break

Bacillus subtilis RecA is important for spore resistance to DNA damage, even though spores contain a single non-replicating genome. We report that inactivation of RecA or its accessory factors, RecF, RecO, RecR and RecX, drastically reduce survival of mature dormant spores to ultrahigh vacuum desiccation and ionizing radiation that induce single strand (ss) DNA nicks and double-strand breaks (DSBs). The presence of non-cleavable LexA renders spores less sensitive to DSBs, and spores impaired in DSB recognition or end-processing show sensitivities to X-rays similar to wild-type. In vitro RecA cannot compete with SsbA for nucleation onto ssDNA in the presence of ATP. RecO is sufficient, at least in vitro, to overcome SsbA inhibition and stimulate RecA polymerization on SsbA-coated ssDNA. In the presence of SsbA, RecA slightly affects DNA replication in vitro, but addition of RecO facilitates RecA-mediated inhibition of DNA synthesis. We propose that repairing of the DNA lesions generates a replication stress to germinating spores, and the RecA·ssDNA filament might act by preventing potentially dangerous forms of DNA repair occurring during replication. RecA might stabilize a stalled fork or prevent or promote dissolution of reversed forks rather than its cleavage that should require end-processing.
An annotated Urdu corpus of handwritten text image and benchmarking of corpus

For linguistics related research on a language there is always a need for a large collection of database which includes all features of a language such as grammatical information, style of writing, syntax etc. Corpus provides a platform for investigation on a natural language. As compared to other languages very limited research work is done on Urdu language due to its segmentation dilemma and difficult character shape. Very less number of editable printed text data is available in Urdu language, most of the data is available in graphical or picture format. To increase Natural Language Processing research work on Urdu language there is a need for a large database which contains a range of variance in annotated Urdu handwritten as well as printed text. In our work we purpose a large database of Urdu text including 1000 handwritten text images written by 500 different writers. Each image would be four to six lines of Urdu text having 60-80 words per line the estimated number of words would be around . 35 million. Selection of words would be done from six different categories so that maximum number of distinct words can be included. Corpus would be annotated for line as well as word segmentation where a word may be an individual character or component. The corpus would be a benchmark for quantitative analysis of Handwritten Text Recognition techniques for Urdu language such as text line extraction, word segmentation and character recognition etc., and for linguistic research in Part of Speech, writer identification, dictionary etc.
Personalized Ontology-Based Query Expansion

In this paper we present a preliminary analysis of a new Google Desktop gadget aimed at defining personalised query expansions. This user friendly application is based on a dynamic local fuzzy ontology: every time that a user interacts with the gadget the ontology relationships are updated. The proposed query expansion technique takes into account past userpsilas queries and the concepts contained in relevant documents stored into the userpsilas workstation.
Tune the autocorrelation time and unleash the full power of the parallel tempering algorithm ∗

We introduce a new update scheme to systematically improve the efficiency of parallel tempering Monte Carlo simulations by taking into account the temperature dependence of autocorrelation times. In contrast to previous attempts the temperatures are not dynamically adjusted but chosen in such a way that the acceptance rate for proposed exchanges of all adjacent replica is about 50%. We show that by adapting the number of sweeps between the parallel tempering moves to the canonical autocorrelation time, the average round-trip time of a replica between the lowest and the highest temperatures is significantly decreased and, therefore, the efficiency of the parallel tempering algorithm is considerably improved. We illustrate the new algorithm with results for the two-dimensional Ising model and propose a toy model to find the optimal parameter set for the parallel tempering routine within no time.
Use of dynamic compliance for open lung positive end‐expiratory pressure titration in an experimental study

Objective: We tested whether the continuous monitoring of dynamic compliance could become a useful bedside tool for detecting the beginning of collapse of a fully recruited lung. Design: Prospective laboratory animal investigation. Setting: Clinical physiology research laboratory, University of Uppsala, Sweden. Subjects: Eight pigs submitted to repeated lung lavages. Interventions: Lung recruitment maneuver, the effect of which was confirmed by predefined oxygenation, lung mechanics, and computed tomography scan criteria, was followed by a positive end‐expiratory pressure (PEEP) reduction trial in a volume control mode with a tidal volume of 6 mL/kg. Every 10 mins, PEEP was reduced in steps of 2 cm H2O starting from 24 cm H2O. During PEEP reduction, lung collapse was defined by the maximum dynamic compliance value after which a first measurable decrease occurred. Open lung PEEP according to dynamic compliance was then defined as the level of PEEP before the point of collapse. This value was compared with oxygenation (Pao2) and CT scans. Measurements and Main Results: Pao2 and dynamic compliance were monitored continuously, whereas computed tomography scans were obtained at the end of each pressure step. Collapse defined by dynamic compliance occurred at a PEEP of 14 cm H2O. This level coincided with the oxygenation‐based collapse point when also shunt started to increase and occurred one step before the percentage of nonaerated tissue on the computed tomography exceeded 5%. Open lung PEEP was thus at 16 cm H2O, the level at which oxygenation and computed tomography scan confirmed a fully open, not yet collapsed lung condition. Conclusions: In this experimental model, the continuous monitoring of dynamic compliance identified the beginning of collapse after lung recruitment. These findings were confirmed by oxygenation and computed tomography scans. This method might become a valuable bedside tool for identifying the level of PEEP that prevents end‐expiratory collapse.
Long‐term annual surface heat and water balances over Canada and the United States South of 60°N: Reconciliation of precipitation, run‐off and temperature fields

Abstract The analysis compares the observed field of run‐off (assumed correct) with adjusted precipitation over North America (as amended by den Hartog and LeDrew over Canada) and derives the principal hydroclimatological ratios for each five‐degree latitude‐longitude square. The amended precipitation field yields values of the Budyko dry ness index close to values suggested by the vegetation distribution. The Priestley‐Taylor parameter, α, lies between unity (equilibrium) and potential (1.26) values over much of humid North America, but exceeds these values in the northwest Pacific squares, where advective heating may be the cause. Other regions of strong seasonal advective heating (e.g. the Great Plains) do not appear to influence the distribution strongly. A weighted convective forcing temperature is derived, varying from 298 K in the extreme south to below 285 K in the north. This function (and the Bowen ratio) achieve improbable values in northern Labrador‐ Ungava. The precipitation, run‐off and net .
Global description of patterns far from onset : a case study

The Cross–Newell phase diffusion equation τ(k)ΘT = −∇ · kB(k), k = ∇Θ, | k| = k, and its regularization describe patterns and defects far from onset in large aspect ratio systems with translational and rotational symmetry. In this paper we show how director field solutions of this equation can be used to describe features of global patterns. The ideas are illustrated in the context of a non-trivial case study of high Prandtl number convection in a large aspect ratio, shallow, elliptical container with heated sidewalls, for which we also have the results of simulation and experiment. © 2003 Elsevier B.V. All rights reserved.
3-D Segmentation Algorithm of Small Lung Nodules in Spiral CT Images

Computed tomography (CT) is the most sensitive imaging technique for detecting lung nodules, and is now being evaluated as a screening tool for lung cancer in several large samples studies all over the world. In this report, we describe a semiautomatic method for 3-D segmentation of lung nodules in CT images for subsequent volume assessment. The distinguishing features of our algorithm are the following. 1) The user interaction process. It allows the introduction of the knowledge of the expert in a simple and reproducible manner. 2) The adoption of the geodesic distance in a multithreshold image representation. It allows the definition of a fusion--segregation process based on both gray-level similarity and objects shape. The algorithm was validated on low-dose CT scans of small nodule phantoms (mean diameter 5.3-11 mm) and in vivo lung nodules (mean diameter 5--9.8 mm) detected in the Italung-CT screening program for lung cancer. A further test on small lung nodules of Lung Image Database Consortium (LIDC) first data set was also performed. We observed a RMS error less than 6.6% in phantoms, and the correct outlining of the nodule contour was obtained in 82/95 lung nodules of Italung-CT and in 10/12 lung nodules of LIDC first data set. The achieved results support the use of the proposed algorithm for volume measurements of lung nodules examined with low-dose CT scanning technique.