Miracle-dz/UniFAR-FTUs huggingface dataset:
Involvement of CysB and Cbl regulatory proteins in expression of the tauABCD operon and other sulfate starvation-inducible genes in Escherichia coli

Starvation for sulfate results in increased synthesis of several proteins in Escherichia coli. Among these Ssi (sulfate starvation-induced) proteins are the products of the tauABCD genes, which are required for utilization of taurine as sulfur source for growth. In this study, the role of the cbl gene in expression of tauABCD and other ssi genes was investigated. The protein encoded by cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of the genes involved in cysteine biosynthesis. Strain EC2541, which contains an internal deletion in cbl, was unable to utilize taurine and other aliphatic sulfonates as sulfur sources. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that many of the Ssi proteins were not synthesized in EC2541. Expression of a translational tauD'-'lacZ fusion required the presence of both cbl and cysB. The interactions of CysB and Cbl with the promoter region of tauABCD were studied by using gel mobility shift experiments and DNase I footprinting. CysB occupied multiple binding sites, whereas Cbl occupied only one site from 112 to 68 bp upstream of the transcription start site. Acetylserine, the inducer of transcription of CysB-regulated genes, stimulated binding of CysB but not of Cbl. Sulfate had no effect on binding of both proteins to the tauABCD promoter region. These results indicate that Cbl is a transcription factor for genes required for sulfonate-sulfur utilization and maybe for other genes whose expression is induced by sulfate starvation.
An Acoustic Model Based on Kullback-Leibler Divergence for Posterior Features

This paper investigates the use of features based on posterior probabilities of subword units such as phonemes. These features are typically transformed when used as inputs for a hidden Markov model with mixture of Gaussians as emission distribution (HMM/GMM). In this work, we introduce a novel acoustic model that avoids the Gaussian assumption and directly uses posterior features without any transformation. This model is described by a finite state machine where each state is characterized by a target distribution and the cost function associated to each state is given by the Kullback-Leibler (KL) divergence between its target distribution and the posterior features. Furthermore, hybrid HMM/ANN system can be seen as a particular case of this KL-based model where state target distributions are predefined. A recursive training algorithm to estimate the state target distributions is also presented.
Scale-invariant probabilistic latent component analysis

In this paper, we present a new method for decomposing musical spectrograms. This method is similar to shift-invariant Probabilistic Latent Component Analysis, but, when the latter works with constant Q spectrograms (i.e. with a logarithmic frequency resolution), our technique is designed to decompose standard short time Fourier transform spectrograms (i.e. with a linear frequency resolution). This makes it possible to easily reconstruct the latent signals (which can be useful for source separation).
Enriched Rehabilitative Training Promotes Improved Forelimb Motor Function and Enhanced Dendritic Growth after Focal Ischemic Injury

Chronic impairment of forelimb and digit movement is a common problem after stroke that is resistant to therapy. Previous studies have demonstrated that enrichment improves behavioral outcome after focal ischemia; however, postischemic enrichment alone is not capable of enhancing fine digit and forelimb function. Therefore, we combined environmental enrichment with daily skilled-reach training to assess the effect of intensive task-specific rehabilitation on long-term functional outcome. Rats were subjected to either endothelin-1-induced focal ischemia or sham surgery and subsequently designated to enriched-rehabilitation or standard-housing treatment groups starting 15 d after ischemia. Functional assessment of the affected forelimb at 4 and 9 weeks after treatment revealed that ischemic plus enrichment (IE) animals had improved ∼30% on the staircase-reaching task and were indistinguishable from sham animals for both latency and foot faults in a beam-traversing task. In contrast, ischemic plus standard (IS) animals remained significantly impaired on both tasks. Interestingly, both ischemic groups (IE and IS) relied on the nonaffected forelimb during upright weight-bearing movements, a pattern that persisted for the duration of the experiment. Dendritic arborization of layer V pyramidal cells within the undamaged motor cortex was examined using a Golgi–Cox procedure. IE animals showed enhanced dendritic complexity and length compared with both IS and sham groups. These results suggest that enrichment combined with task-specific rehabilitative therapy is capable of augmenting intrinsic neuronal plasticity within noninjured, functionally connected brain regions, as well as promoting enhanced functional outcome.
Human Capital and Macroeconomic Growth: Austria and Germany 1960-1997 - An Update

In an influential paper Mankiw, Romer, and Weil (1992) argue that the evidence on the international disparity in levels of per capita income and rates of growth is consistent with a standard Solow model, once it has been augmented to include human capital as an accumulable factor. In a study on Austria and Germany we augment the Solow model to allow for the accumulation of human capital. Based on a perpetual inventory estimation procedure we construct an aggregate measure of the stock of human capital of Austria and Germany by weighting workers of different schooling levels with their respective wage income. We obtain an estimate of the wage income of workers with different schooling from a Mincer type wage equation which quantifies how wages change with years of schooling. We find that the time series evidence on Austria and Germany is not consistent with a human capital augmented Solow model. Factor accumulation (broadly defined to include human capital) appears to be less (and not more) able to account for the cross-country growth performance of Austria and Germany when human capital accumulation is included in the analysis. Our results indicate that differences in technology are a driving factor in understanding cross country growth between these two neighboring countries with similar political and institutional background.
Incomplete 3D Shape Retrieval via Sparse Dictionary Learning

How to deal with missing data is one of the recurring questions in data analysis. The handling of significant missing data is a challenge. In this paper, we are interested in the problem of 3D shape retrieval where the query shape is incomplete with moderate to significant portions of the original shape missing. The key idea of our method is to grasp the basis local descriptors for each shape in the retrieved database by sparse dictionary learning and apply them in sparsely coding the local descriptors of an incomplete query. First, we present a method of computing heat kernel signatures for incomplete shapes. Next, for each shape in the database, a set of basis local descriptors, which is called a dictionary, is learned and taken as its representative. Finally, a query incomplete shape’s heat kernel signatures are respectively reconstructed by each dictionary, and the shape similarities are therefore measured by the reconstruction errors. Experimental results show that the proposed method has achieved significant improvements over previous works on retrieving non-rigid incomplete shapes.
In a Safety Net Population HPV4 Vaccine Adherence Worsens as BMI Increases

Objectives Obesity adversely inhibits antibody response to vaccination. Three doses of HPV4 may or may not provide adequate long term protection against HPV 16/18 in obese females. The aim of this study was to determine whether adherence to HPV4 vaccination in a safety net population was reduced with increasing body mass index (BMI). Methods We designed a historical prospective study evaluating the number and dates of HPV4 dosing that occurred from July 1, 2006 through October 1, 2009 by the demographic characteristics of the 10–26 year old recipient females. The defined dosing intervals were adapted from the literature and obesity categories were defined by the WHO. Results 1240 females with BMI measurements received at least one dose of HPV4; 38% were obese (class I, II and III) and 25% were overweight. Females with normal BMI received on-time triplet dosing significantly more often than did the obese class II and III females (30% vs. 18%, p<0.001). Obese class II/III females have a significant 45% less chance of completing the on-time triplet HPV4 series than normal women (OR = 0.55, 95% CI: 0.37, 0.83). Pregnancy history has a significant influence on BMI and HPV4 dosing compliance in this safety net population where 71% had been gravid. Hispanic females were less likely to complete HPV4 dosing regardless of BMI (aOR = 0.39, 95% CI: 0.16, 0.95). Conclusions Obesity, as well as gravidity and Hispanic race, are risk factors for lack of HPV4 vaccine adherence among young females in a safety net population.
Biodiversity of soil bacteria and its applications for a sustainable agriculture

Brazilian agribusiness is of great competitivity mostly due to the lack of government subsidies and the historical efforts made in research and development by the public institutes and Universities. Nevertheless the Brazilian agriculture is fundamented in the use of fertilizers and agrochemicals that needs to be imported in huge amounts to supply the Brazilian farmers. In this sense, the safety and sustainability of the Brazilian agribusiness is subjected to the supply of these inputs and to the prices prevailing on the international market. In addition, a new concern is emerging in the global society, which has increased demands for food, feed, and energy that must be provided by the agriculture, although new sustainable farming practices urge to be implemented. Natural relationships between plants and soil microbes are on the heart of the matter, with growing scientific data supporting the use of the former-potential plant-bacteria associations in large scale to increase the crop productivity and hence the production of food and energy. The total substitution of nitrogen fertilizers in soybean crops by the biological nitrogen fixation held by rhizobia corroborates the efficiency of such associations, and point out for the need to expand this and other natural mechanisms directed to provide nutrients to cereals and other nonleguminous crops. To achieve this, much effort is also needed to reach a better understanding of the mechanisms controlling plant-bacteria associations, and to develop biofertilizer formulations presenting a high efficiency under a myriad of field conditions, as those found in Brazil. Biotechnological approaches aimed to reach this goal are reviewed and discussed throughout this manuscript.
Software visualization for debugging

To illustrate these ideas, we present three visualization approaches we have explored—algorithm animation, typographic source code presentation, and interactive auralization for debugging—demonstrating the richness of software visualization media and portraying design trade-offs inherent in their use. We use a 30-minute film (designed to teach nine sorting algorithms) to demonstrate the power of algorithm animation. We show how the design and typesetting of computer program source text can enhance the program’s readability. And we show how a programming environment we created—LogoMedia—is useful for the interactive construction of visualizations during program creation and debugging. Software Vi for Debugging
Cre‐mediated recombination in cell lineages that express the progesterone receptor

Using gene‐targeting methods, a progesterone receptor Cre knockin (PR‐Cre) mouse was generated in which Cre recombinase was inserted into exon 1 of the PR gene. The insertion positions the Cre gene downstream (and under the specific control) of the endogenous PR promoter. As for heterozygotes for the progesterone receptor knockout (PRKO) mutation, mice heterozygous for the Cre knockin insertion are phenotypically indistinguishable from wildtype. Crossing the PR‐Cre with the ROSA26R reporter revealed that Cre excision activity is restricted to cells that express PR in progesterone‐responsive tissues such as the uterus, ovary, oviduct, pituitary gland, and mammary gland. Initial characterization of the PR‐Cre mouse underscores the utility of this model to precisely ablate floxed target genes specifically in cell lineages that express the PR. In the wider context of female reproductive tissue ontology, this model will be indispensable in tracing the developmental fate of cell lineages that descend from PR positive progenitors. genesis 41:58–66, 2005. © 2005 Wiley‐Liss, Inc.
Quantifying the heterogeneity of the tectonic stress field using borehole data

The heterogeneity of the tectonic stress field is a fundamental property which influences earthquake dynamics and subsurface engineering. Self‐similar scaling of stress heterogeneities is frequently assumed to explain characteristics of earthquakes such as the magnitude‐frequency relation. However, observational evidence for such scaling of the stress field heterogeneity is scarce. We analyze the local stress orientations using image logs of two closely spaced boreholes in the Coso Geothermal Field with subvertical and deviated trajectories, respectively, each spanning about 2 km in depth. Both the mean and the standard deviation of stress orientation indicators (borehole breakouts, drilling‐induced fractures, and petal‐centerline fractures) determined from each borehole agree to the limit of the resolution of our method although measurements at specific depths may not. We find that the standard deviation in these boreholes strongly depends on the interval length analyzed, generally increasing up to a wellbore log length of about 600 m and constant for longer intervals. We find the same behavior in global data from the World Stress Map. This suggests that the standard deviation of stress indicators characterizes the heterogeneity of the tectonic stress field rather than the quality of the stress measurement. A large standard deviation of a stress measurement might be an expression of strong crustal heterogeneity rather than of an unreliable stress determination. Robust characterization of stress heterogeneity requires logs that sample stress indicators along a representative sample volume of at least 1 km.
Cryptanalysis of the Full AES Using GPU-Like Special-Purpose Hardware

The block cipher Rijndael has undergone more than ten years of extensive cryptanalysis since its submission as a candidate for the Advanced Encryption Standard (AES) in April 1998. To date, most of the publicly-known cryptanalytic results are based on reduced-round variants of the AES (respectively Rijndael) algorithm. Among the few exceptions that target the full AES are the Related-Key Cryptanalysis (RKC) introduced at ASIACRYPT 2009 and attacks exploiting Time-Memory-Key (TMK) trade-offs such as demonstrated at SAC 2005. However, all these attacks are generally considered infeasible in practice due to their high complexity (i.e. 299.5 AES operations for RKC, 280 for TMK). In this paper, we evaluate the cost of cryptanalytic attacks on the full AES when using special-purpose hardware in the form of multi-core AES processors that are designed in a similar way as modern Graphics Processing Units (GPUs) such as the NVIDIA GT200b. Using today's VLSI technology would allow for the implementation of a GPU-like processor reaching a throughput of up to 1012 AES operations per second. An organization able to spend one trillion USd for designing and building a supercomputer based on such processors could theoretically break the full AES in a time frame of as little as one year when using RKC, or in merely one month when performing a TMK attack. We also analyze different time-cost trade-offs and assess the implications of progress in VLSI technology under the assumption that Moore's law will continue to hold for the next ten years. These assessments raise some concerns about the long-term security of the AES.
Minimally invasive surgery and enhanced recovery after surgery: The ideal combination?

Enhanced recovery after surgery (ERAS) and minimally invasive surgery are both in the limelight due to their potential positive effects on surgical outcome. Large randomized trials and meta‐analyses validated the use of both, laparoscopy and ERAS protocol, as individual measures. A synergistic effect of both entities might contribute to even better outcomes. This review hence assessed the literature upon up‐to‐date studies combining both methods.
Using Molecular Equivalence Numbers To Visually Explore Structural Features that Distinguish Chemical Libraries

A molecular equivalence number (meqnum) classifies a molecule with respect to a class of structural features or topological shapes such as its cyclic system or its set of functional groups. Meqnums can be used to organize molecular structures into nonoverlapping, yet highly relatable classes. We illustrate the construction of some different types of meqnums and present via examples some methods of comparing diverse chemical libraries based on meqnums. In the examples we compare a library which is a random sample from the MDL Drug Data Report (MDDR) with a library which is a random sample from the Available Chemical Directory (ACD). In our analyses, we discover some interesting features of the topological shape of a molecule and its set of functional groups that are strongly linked with compounds occurring in the MDDR but not in the ACD. We also illustrate the utility of molecular equivalence indices in delineating the structural domain over which an SAR conclusion is valid.
Replication of a Cytopathic Strain of Bovine Viral Diarrhea Virus Activates PERK and Induces Endoplasmic Reticulum Stress-Mediated Apoptosis of MDBK Cells

ABSTRACT Endoplasmic reticulum (ER) stress signaling is an adaptive cellular response to the loss of ER Ca2+ homeostasis and/or the accumulation of misfolded, unassembled, or aggregated proteins in the ER lumen. ER stress-activated signaling pathways regulate protein synthesis initiation and can also trigger apoptosis through the ER-associated caspase 12. Viruses that utilize the host cell ER as an integral part of their life cycle would be predicted to cause some level of ER stress. Bovine viral diarrhea virus (BVDV) is a positive-stranded RNA virus of the Flaviviridae family. BVDV and related flaviviruses use the host ER as the primary site of envelope glycoprotein biogenesis, genomic replication, and particle assembly. We are using a cytopathic strain of BVDV (cpBVDV) that causes cellular apoptosis as a model system to determine how virus-induced ER stress contributes to pathogenesis. We show that, in a natural infection of MDBK cells, cpBVDV activates the ER transmembrane kinase PERK (PKR-like ER kinase) and causes hyperphosphorylation of the translation initiation factor eIF2α, consistent with the induction of an ER stress response. Additionally, we show that initiation of cellular apoptosis correlates with downregulation of the antiapoptotic Bcl-2 protein, induced expression of caspase 12, and a decrease in intracellular glutathione levels. Defining the molecular stress pathways leading to cpBVDV-induced apoptosis provides the basis to study how other ER-tropic viruses, such as hepatitis C and B viruses, modulate the host cell ER stress response during the course of persistent infection.
Improve Multi Path Congestion Control Technique Using EIA

Traffic in the Internet is mainly regulated by Transmission Control Protocol and Internet Protocol, TCP/IP. A source user sends information to a destination user along a route chosen by IP routing, at a rate determined by TCP. The route chosen is typically the shortest path according to hop count or distance, and the flow rate is varied according to the level of congestion along the route, detected by information loss. In this paper, we have investigated the possibility of stable multi-path dual congestion control algorithms. These algorithms have the attractive property that they achieve desired bandwidth utilization at equilibrium. or else, increasing flow at that link would cause another to exceed the desired rate. A fluid model was given, under which the natural multipath dual algorithm is stable in the absence of propagation delays, but potentially unstable when delays are present. We then proposed a new extension to the class of dual algorithms, the controlled splitting multi-path dual algorithms, which take into consideration path diversity when evaluating source utilities. These algorithms are also globally stable in the absence of propagation delays. Furthermore, decentralized, scalable conditions for local stability were found for a controlled splitting multi-path dual algorithm with arbitrary propagation delays present. The higher the parameter p is, the closer the equilibrium point comes to that of the natural multi-path dual algorithm, but the lower gain parameters have to be in order to ensure stability. This paper presents strong theoretical support for the algorithms we propose.
PRECISION AND DEVIATION COMPARISON BETWEEN ICESAT AND ENVISAT IN TYPICAL ICE GAINING AND LOSING REGIONS OF ANTARCTICA

Abstract. This paper analyzes the precision and deviation of elevations acquired from Envisat and The Ice, Cloud and Land Elevation Satellite (ICESat) over typical ice gaining and losing regions, i.e. Lambert-Amery System (LAS) in east Antarctica, and Amundsen Sea Sector (ASS) in west Antarctica, during the same period from 2003 to 2008. We used GLA12 dataset of ICESat and Level 2 data of Envisat. Data preprocessing includes data filtering, projection transformation and track classification. Meanwhile, the slope correction is applied to Envisat data and saturation correction for ICESat data. Then the crossover analysis was used to obtain the crossing points of the ICESat tracks, Envisat tracks and ICESat-Envisat tracks separately. The two tracks we chose for cross-over analysis should be in the same campaign for ICESat (within 33 days) or the same cycle for Envisat (within 35 days). The standard deviation of a set of elevation residuals at time-coincident crossovers is calculated as the precision of each satellite while the mean value is calculated as the deviation of ICESat-Envisat. Generally, the ICESat laser altimeter gets a better precision than the Envisat radar altimeter. For Amundsen Sea Sector, the ICESat precision is found to vary from 8.9 cm to 17 cm and the Envisat precision varies from 0.81 m to 1.57 m. For LAS area, the ICESat precision is found to vary from 6.7 cm to 14.3 cm and the Envisat precision varies from 0.46 m to 0.81 m. Comparison result between Envisat and ICESat elevations shows a mean difference of 0.43 ±7.14 m for Amundsen Sea Sector and 0.53 ± 1.23 m over LAS.