Miracle-dz/UniFAR-FTUs huggingface dataset:
Power spectrum blind sampling using optimal multicoset sampling patterns in the MSE sense

We consider the design of a multicoset sampling pattern to be used in power spectrum blind sampling (PSBS). The criterion for the PSBS pattern design that we propose is based on the minimization of the mean square error of the power spectrum estimate. The design framework appears as a constrained optimization problem, whose complexity increases with the pattern length. We solve such a constrained optimization problem in terms of nonlinear integer programming by using exhaustive search.
How microbes utilize host ubiquitination

Activity, abundance and localization of eukaryotic proteins can be regulated through covalent attachment of ubiquitin and ubiquitin‐like moieties. Ubiquitination is important in various aspects of immunity. Pathogens utilize host ubiquitination for the suppression of immune signalling and reprogramming host processes to promote microbial life. They deliver so‐called effector molecules into host cells, which functionally or structurally resemble components of the host ubiquitination machinery utilizing this enzymatic process or they secrete molecules to inhibit ubiquitin‐mediated degradation. Since prokaryotic pathogens lack a classical ubiquitination system, effector mimicry of components of the ubiquitin machinery could be achieved through gene flow. Horizontal gene transfer allows pathogenic bacteria to access ubiquitination enzymes from a potential host, while lateral gene transfer recruits components from another pathogen providing spread within the microbial community. Additionally, convergent evolution can shape bacterial proteins to acquire ubiquitination functions.
Symmetry assessment by finite expansion: Application to forensic fingerprints

Common image features have too poor information for identification of forensic images of fingerprints, where only a small area of the finger is imaged and hence a small amount of key points are available. Noise, nonlinear deformation, and unknown rotation are additional issues that complicate identification of forensic fingerprints. We propose a feature extraction method which describes image information around key points: Symmetry Assessment by Finite Expansion (SAFE). The feature set has built-in quality estimates as well as a rotation invariance property. The theory is developed for continuous space, allowing compensation for features directly in the feature space when images undergo such rotation without actually rotating them. Experiments supporting that use of these features improves identification of forensic fingerprint images of the public NIST SD27 database are presented. Performance of matching orientation information in a neighborhood of core points has an EER of 24% with these features alone, without using minutiae constellations, in contrast to 36% when using minutiae alone. Rank-20 CMC is 58%, which is lower than 67% when using notably more manually collected minutiae information.
Molecular attenuation of vaccinia virus: mutant generation and animal characterization

These studies demonstrated that the inbred BALB/c mouse strain can be optimized for the assessment of vaccinia virus virulence, growth, and spread from the site of inoculation and immune protection from a lethal vaccinia virus challenge. The studies established that manipulation of the vaccinia virus genome generated mutants exhibiting a wide range of attenuated phenotypes. The nine NYCBH vaccinia virus mutants had intracranial 50% lethal doses that ranged from 2 to greater than 7 log10 units. The decreased neurovirulence was due to decreased replication in brain tissue. Three mutants had a decreased ability to disseminate to the lungs, brains, livers, and spleens of mice after intranasal infection. One mutant had a decreased transmission from mice infected by tail scarification to naive cage mates. Although the mutants, with one exception, grew to wild-type titers in cell culture, they showed a growth potential on the scarified skin of mice that was dramatically different from that of the wild-type virus. Consequently, all of the mutants had significantly compromised immunogenicities at low virus immunization doses compared with that of the wild-type virus. Conversely, at high immunization doses most mutants could induce an immune response similar to that of the wild-type virus. Three Wyeth vaccine strain mutants were also studied. Whereas the thymidine kinase, ribonucleotide reductase, and hemagglutinin mutants had a reduced virulence (50% lethal dose), only the thymidine kinase mutant retained its immunogenicity.
Multiscale modeling of brain dynamics: from single neurons and networks to mathematical tools

The extreme complexity of the brain naturally requires mathematical modeling approaches on a large variety of scales; the spectrum ranges from single neuron dynamics over the behavior of groups of neurons to neuronal network activity. Thus, the connection between the microscopic scale (single neuron activity) to macroscopic behavior (emergent behavior of the collective dynamics) and vice versa is a key to understand the brain in its complexity. In this work, we attempt a review of a wide range of approaches, ranging from the modeling of single neuron dynamics to machine learning. The models include biophysical as well as data‐driven phenomenological models. The discussed models include Hodgkin–Huxley, FitzHugh–Nagumo, coupled oscillators (Kuramoto oscillators, Rössler oscillators, and the Hindmarsh–Rose neuron), Integrate and Fire, networks of neurons, and neural field equations. In addition to the mathematical models, important mathematical methods in multiscale modeling and reconstruction of the causal connectivity are sketched. The methods include linear and nonlinear tools from statistics, data analysis, and time series analysis up to differential equations, dynamical systems, and bifurcation theory, including Granger causal connectivity analysis, phase synchronization connectivity analysis, principal component analysis (PCA), independent component analysis (ICA), and manifold learning algorithms such as ISOMAP, and diffusion maps and equation‐free techniques. WIREs Syst Biol Med 2016, 8:438–458. doi: 10.1002/wsbm.1348
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria.

Riboswitches that sense S-adenosylmethionine (SAM) are widely distributed throughout a variety of bacterial lineages. Four classes of SAM-binding riboswitches have been reported to date, constituting the most diverse collection of riboswitch classes that sense the same compound. Three of these classes, termed SAM-I, SAM-II, and SAM-III represent unique structures that form distinct binding pockets for the ligand. SAM-IV riboswitches carry different conserved sequence and structural features compared to other SAM riboswitches, but nucleotides and substructures corresponding to the ligand binding pocket are identical to SAM-I aptamers. In this article, we describe a fifth class of SAM binding aptamer, which we have termed SAM-V. SAM-V was discovered by analyzing GC-rich intergenic regions preceding metabolic genes in the marine alpha-proteobacterium "Candidatus Pelagibacter ubique. " Although the motif is nearly unrepresented in cultured bacteria whose genomes have been completely sequenced, SAM-V is prevalent in marine metagenomic sequences. The consensus sequence and structure of SAM-V show some similarities to that of the SAM-II riboswitch, and it is likely that the two aptamers form similar ligand binding pockets. In addition, we identified numerous examples of a tandem SAM-II/SAM-V aptamer architecture. In this arrangement, the SAM-II aptamer is always positioned 5' of the SAM-V aptamer and the SAM-II aptamer is followed by a predicted intrinsic transcription terminator stem. The SAM-V aptamer, however, appears to use a ribosome binding site occlusion mechanism for genetic regulation. This tandem riboswitch arrangement exhibits an architecture that can potentially control both the transcriptional and translational stages of gene expression.
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009

The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest freely available information system containing a huge amount of biochemical and molecular information on all classified enzymes as well as software tools for querying the database and calculating molecular properties. The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. The data in BRENDA are manually curated from more than 79 000 primary literature references. Each entry is clearly linked to a literature reference, the origin organism and, where available, to the protein sequence of the enzyme protein. A new search option provides the access to protein-specific data. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are additional databases created by continuously improved text-mining procedures. These databases ought to provide a complete survey on enzyme data of the literature collection of PubMed. The web service via a SOAP (Simple Object Access Protocol) interface for access to the BRENDA data has been further enhanced.
Outcomes of cataract surgery in diabetic patients: results of the Pan American Collaborative Retina Study Group.

PURPOSE This study was designed to evaluate the visual and anatomical outcomes after cataract surgery in diabetic patients with different intraoperative therapeutic strategies. METHODS The research design comprised of a multicentric, retrospective, interventional study conducted at 6 centers in Argentina, Brazil, Costa Rica, Puerto Rico, Spain, and Venezuela. We included 138 diabetic patients with at least 6-month follow-up following phacoemulsification and intraocular lens implantation. Best-corrected visual acuity (BCVA) and central subfield thickness were collected at baseline and at 1-, 2-, 3-, and 6-month follow-up. Of these, 42 cases were not treated with any intraoperative coadjuvant medication (Group 1), 59 patients received intraoperative bevacizumab (Group 2) and 37 patients received intraoperative triamcinolone (4 mg/0.1 ml) (Group 3). RESULTS The mean logMAR [± standard deviation (SD)] BCVA improved from 0.82 (± 0.43) at baseline, to 0.14 (± 0.23) at 6-month follow-up (p<0.001) in Group 1; from 0.80 (± 0.48) to 0.54 (± 0.45) (p<0.001) in Group 2; and from 1.0 (± 0.40) to 0.46 (± 0.34) (p<0.001) in Group 3. The mean central subfield thickness increased from 263.57 µm (± 35.7) at baseline to 274.57 µm (± 48.7) at 6-month follow-up (p=0.088) in Group 1; from 316.02 µm (± 100.4) to 339.56 µm (± 145.3) (p=0.184) in Group 2; and from 259.18 µm (± 97.9) to 282.21 µm (± 87.24) (p=0.044) in Group 3. CONCLUSION Diabetic patients may significantly benefit from cataract surgery. This study provides evidence to support the use of intravitreal triamcinolone or bevacizumab at the time of cataract surgery in cases with pre-existent diabetic macular edema or moderate-severe non-proliferative diabetic retinopathy.
The role of blood flow in glaucoma

The arterial supply to the eye arises primarily from the ophthalmic artery (OA), which is the first branch of the internal carotid artery (ICA) and is approximately 0.5 mm in diameter. The OA branches into the central retinal artery (CRA) and one to five posterior ciliary trunks which divide into multiple branches forming separate groups of the main posterior ciliary arteries (PCA). The PCA branches into arteries supplying the outer retina, choroid, and retrobulbar tissues. The main PCAs further divide into several short posterior ciliary arteries (SPCA) before or after piercing the sclera. The CRA penetrates the optic nerve approximately 15 mm behind the eye globe, courses adjacent to the central retinal vein (CRV), passes through the lamina cribrosa (LC) and branches into four major arterioles supplying the inner retinal layers. The venous drainage of the retina, choroid and optic nerve is mainly through the CRV and the ophthalmic veins (OV). The CRV and OV are major tributaries to the cavernous sinus, which ultimately drains into the internal jugular veins (IJV) at the base of the skull. The vascular beds supplying the eye are typically divided into three groups: the retinal, choroidal, and retrobulbar vascular beds. The retinal vascular bed is supplied by the CRA, drained by the CRV, and nourishes the inner two-thirds of the retina. The choroidal vascular bed is supplied by the PCA, drained by the OV, and nourishes the deep outer retinal layer. The retrobulbar vascular bed is supplied by the PCA and branches of the CRA, drained by the CRV, and nourishes the superficial nerve fiber layer, the pre-laminar (or pro-laminar) region, the laminar region, and the retrolaminar region. 18. The role of blood flow in glaucoma
A scalable architecture for maintaining packet latency measurements

Latency has become an important metric for network monitoring since the emergence of new latency-sensitive applications (e.g., algorithmic trading and high-performance computing). In this paper, to provide latency measurements at both finer (e.g., packet) as well as flexible (e.g., flow subsets) levels of granularity, we propose an architecture called MAPLE that essentially stores packet-level latencies in routers and allows network operators to query the latency of arbitrary traffic sub-populations. MAPLE is built using a scalable data structure called SVBF with small storage needs.
Multinomial tree models for assessing the status of the reference in studies of the accuracy of tools for binary classification

Studies that evaluate the accuracy of binary classification tools are needed. Such studies provide 2 × 2 cross-classifications of test outcomes and the categories according to an unquestionable reference (or gold standard). However, sometimes a suboptimal reliability reference is employed. Several methods have been proposed to deal with studies where the observations are cross-classified with an imperfect reference. These methods require that the status of the reference, as a gold standard or as an imperfect reference, is known. In this paper a procedure for determining whether it is appropriate to maintain the assumption that the reference is a gold standard or an imperfect reference, is proposed. This procedure fits two nested multinomial tree models, and assesses and compares their absolute and incremental fit. Its implementation requires the availability of the results of several independent studies. These should be carried out using similar designs to provide frequencies of cross-classification between a test and the reference under investigation. The procedure is applied in two examples with real data.
Refractive, Topographic, and Aberrometric Results at 2-Year Follow-Up for Accelerated Corneal Cross-Link for Progressive Keratoconus

Purpose. To report the visual, refractive, and corneal topography and wavefront aberration results of accelerated corneal cross-linking (CXL) during a 24-month follow-up. Methods. Forty-seven eyes underwent riboflavin-ultraviolet A-induced accelerated CXL treatment (30 mW/cm2 with a total dose of 7.2 joules/cm2). Uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), spherical and cylindrical values, keratometry (K) measurements (K steep, K flat, K avg, and K apex), central corneal thickness, and anterior corneal aberrometric analyses including total wavefront error (WFE), total high order aberration (HOA), astigmatism, trefoil, coma, quadrafoil, secondary astigmatism, and spherical aberration were evaluated. Results. The mean UDVA and CDVA were significantly improved at 1 (p = 0.003 and p = 0.004, resp.) and 2 years after treatment (p = 0.001 and p = 0.001, resp.). The mean K steep, K flat, K average, and K apex values were significantly lower than baseline at 12 months (p = 0.008, p = 0.024, p = 0.001, and p = 0.014, resp.) and 24 months (p = 0.014, p = 0.017, p = 0.001, and p = 0.012, resp.). Corneal thickness showed a significant decrease at 1 month. Total HOA and coma decreased significantly at the 12-month (p = 0.001 and p = 0.009, resp.) and 24-month visits (p = 0.001 and p = 0.007, resp.). Conclusion. Accelerated CXL (30 mW/cm2) was found to be effective in improving UDVA, CDVA, corneal topography readings, total HOA, and coma aberrations during the 24-month follow-up.
Compressible Flow Phenomena at Inception of Lateral Density Currents Fed by Collapsing Gas‐Particle Mixtures

Many geological flows are sourced by falling gas‐particle mixtures, such as during collapse of lava domes, and impulsive eruptive jets, and sustained columns, and rock falls. The transition from vertical to lateral flow is complex due to the range of coupling between particles of different sizes and densities and the carrier gas, and due to the potential for compressible flow phenomena. We use multiphase modeling to explore these dynamics. In mixtures with small particles, and with subsonic speeds, particles follow the gas such that outgoing lateral flows have similar particle concentration and speed as the vertical flows. Large particles concentrate immediately upon impact and move laterally away as granular flows overridden by a high‐speed jet of expelled gas. When a falling flow is supersonic, a bow shock develops above the impact zone, and this produces a zone of high pressure from which lateral flows emerge as overpressured wall jets. The jets form complex structures as the mixtures expand and accelerate and then recompress through a recompression zone that mimics a Mach disk shock in ideal gas jets. In mixtures with moderate to high ratios of fine to coarse particles, the latter tend to follow fine particles through the expansion‐recompression flow fields because of particle‐particle drag. Expansion within the flow fields can lead to locally reduced gas pressure that could enhance substrate erosion in natural flows. The recompression zones form at distances, and have peak pressures, that are roughly proportional to the Mach numbers of impacting flows.
A System Design Methodology Based on a Formal Computational Model

The modern electronic system design has become extremely complex due to the increasing demand of higher performance and improved functionality. In this paper, we address this problem with a system design methodology which is based on functional language and uses skeletons for design exploration. Transformational design method is also introduced during various design exploration stages. The final design is synthesized into a VHDL and C model which can be further implemented.
Oxidative Stress in Chagas Disease

There is growing evidence to suggest that chagasic myocardia are exposed to sustained oxidative stress induced injuries that may contribute to disease progression. Trypanosoma cruzi invasion- and replication-mediated cellular injuries and immune-mediated cytotoxic reactions are the common source of reactive oxygen species (ROS) during acute infection. Mitochondria are proposed to be the major source of ROS in chronic chagasic hearts. However, it has not been established yet, whether mitochondrial dysfunction is a causative factor in chagasic cardiomyopathy or a consequence of other pathological events. A better understanding of oxidative stress in relation to cardiac tissue damage would be useful in the evaluation of its true role in the pathogenesis of Chagas disease and other heart diseases. In this review, we discuss the evidence for increased oxidative stress in chagasic disease, with emphasis on mitochondrial abnormalities, and its role in sustaining oxidative stress in myocardium.
The Reionization History and Early Metal Enrichment Inferred from the Gamma-Ray Burst Rate

Based on the gamma-ray burst event rate at redshifts of 4 ≤ z ≤ 12, which is assessed by the spectral peak energy-to-luminosity relation recently found by Yonetoku et al., we observationally derive the star formation rate (SFR) for Population III (Pop. III) stars in a high-redshift universe. As a result, we find that Pop. III stars could form continuously at 4 ≤ z ≤ 12. Using the derived Pop. III SFR, we attempt to estimate the ultraviolet (UV) photon emission rate at 7 ≤ z ≤ 12 in which redshift range no observational information has been hitherto obtained on ionizing radiation intensity. We find that the UV emissivity at 7 ≤ z ≤ 12 can make a noticeable contribution to the early reionization. The maximal emissivity is higher than the level required to keep ionizing the intergalactic matter (IGM) at 7 ≤ z ≤ 12. However, if the escape fraction of ionizing photons from Pop. III objects is smaller than 10%, then the IGM can be neutralized at some redshift, which may lead to the double reionization. As for the enrichment, the ejection of all metals synthesized in Pop. III objects is marginally consistent with the IGM metallicity, although the confinement of metals in Pop. III objects can reduce the enrichment significantly.
A case study of API redesign for improved usability

As software grows more complex, software developers' productivity is increasingly defined by their ability to effectively reuse code. Even APIs (application programming interfaces) and other code explicitly intended for reuse are often difficult and time consuming for developers to use. This paper describes the user-centered design and evaluation process we evolved in redesigning SAP's BRFplus - a business rules engine, whose API was created for platform development, but which is now also increasingly being used by application developers - even though it was not initially designed with their specific needs in mind. Our API redesign attempts to take both the initial as well as the new emergent user requirements into account. A usability evaluation of our proposed changes to the API suggests that our user-centered design process was successful in helping to create an API that significantly improved users' productivity and better matches the different users' needs.
Welfare receipt and substance-abuse treatment among low-income mothers: the impact of welfare reform.

OBJECTIVES We explored changing relations between substance use, welfare receipt, and substance-abuse treatment among low-income mothers before and after welfare reform. METHODS We examined annual data from mothers aged 18 to 49 years in the 1990-2001 National Household Survey of Drug Abuse and the 2002 National Survey of Drug Use and Health. Logistic regression was used to examine determinants of treatment receipt. RESULTS Among low-income, substance-using mothers, the proportion receiving cash assistance declined from 54% in 1996 to 38% in 2001. The decline was much smaller (37% to 31%) among low-income mothers who did not use illicit substances. Low-income, substance-using mothers who received cash assistance were much more likely than other low-income, substance-using mothers to receive treatment services. Among 2002 National Survey of Drug Use and Health respondents deemed "in need" of substance-abuse treatment, welfare recipients were significantly more likely than nonrecipients to receive such services (adjusted odds ratio=2.31; P<.05). Controlling for other factors, welfare receipt was associated with higher prevalence of illicit drug use. Such use declined among both welfare recipients and other mothers between 1990 and 2001. CONCLUSIONS Welfare is a major access point to identify and serve low-income mothers with substance-use disorders, but it reaches a smaller proportion of illicit drug users than it did prereform. Declining welfare receipt among low-income mothers with substance abuse disorders poses a new challenge in serving this population.