Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Biphenyl Dioxygenase Sequences and Activities Encoded by the Metagenomes of Highly Polychlorobiphenyl-Contaminated Soils

ABSTRACT Total extracted DNA from two heavily polychlorobiphenyl-contaminated soils was analyzed with respect to biphenyl dioxygenase sequences and activities. This was done by PCR amplification and cloning of a DNA segment encoding the active site of the enzyme. The translated sequences obtained fell into three similarity clusters (I to III). Sequence identities were high within but moderate or low between the clusters. Members of clusters I and II showed high sequence similarities with well-known biphenyl dioxygenases. Cluster III showed low (43%) sequence identity with a biphenyl dioxygenase from Rhodococcus jostii RHA1. Amplicons from the three clusters were used to reconstitute and express complete biphenyl dioxygenase operons. In most cases, the resulting hybrid dioxygenases were detected in cell extracts of the recombinant hosts. At least 83% of these enzymes were catalytically active. Several amino acid exchanges were identified that critically affected activity. Chlorobiphenyl turnover by the enzymes containing the prototype sequences of clusters I and II was characterized with 10 congeners that were major, minor, or not constituents of the contaminated soils. No direct correlations were observed between on-site concentrations and rates of productive dioxygenations of these chlorobiphenyls. The prototype enzymes displayed markedly different substrate and product ranges. The cluster II dioxygenase possessed a broader substrate spectrum toward the assayed congeners, whereas the cluster I enzyme was superior in the attack of ortho-chlorinated aromatic rings. These results demonstrate the feasibility of the applied approach to functionally characterize dioxygenase activities of soil metagenomes via amplification of incomplete genes.
Coded modulation using superimposed binary codes

In this correspondence, we investigate in a comprehensive fashion a one-layer coding/shaping scheme resembling a perfectly cooperated multiple-access system. At the transmitter, binary data are encoded by either single-level or multilevel codes. The coded bits are first randomly interleaved and then entered into a signal mapper. At each time, the signal mapper accepts as input multiple binary digits and delivers as output an amplitude signal, where the input are first independently mapped into 2-PAM signals (possibly having different amplitudes) and then superimposed to form the output. The receiver consists of an iterative decoding/demapping algorithm with an entropy-based stopping criterion. In the special cases when all the 2-PAM signals have equal amplitudes, based on an irregular trellis, we propose an optimal soft-input-soft-output (SISO) demapping algorithm with quadratic rather than exponential complexity. In the general cases, when multilevel codes are employed, we propose power-allocation strategies to facilitate the iterative decoding/dempaping algorithm. Using the unequal power-allocations and the Gaussian-approximation-based suboptimal demapping algorithm (with linear complexity), coded modulation with high bandwidth efficiency can be implemented.
Dynamic hyperinflation during activities of daily living in COPD patients

The objective of this study was to investigate whether some activities of daily living (ADLs) usually related to dyspnea sensation in patients with chronic obstructive pulmonary disease (COPD) are associated with dynamic lung hyperinflation (DH) and whether the use of simple energy conservation techniques (ECTs) might reduce this possible hyperinflation. Eighteen patients (mean age: 65.8 ± 9.8 years) with moderate-to-severe COPD performed six ADLs (walking on a treadmill, storing pots, walking 56 meters carrying a 5-kilogram weight, climbing stairs, simulating taking a shower, and putting on shoes) and had their inspiratory capacity (IC) measured before and after each task. The patients were moderately obstructed with forced expiratory volume in 1 second (FEV1): 1.4 ± 0.4 L (50% ± 12.4); FEV1/forced vital capacity: 0.4 ± 8.1; residual volume/total lung capacity: 52.7 ± 10.2, and a reduction in IC was seen after all six activities (p < 0.05): (1) going upstairs, 170 mL; (2) walking 56 meters carrying 5 kilogram weight, 150 mL; (3) walking on a treadmill without and with ECT, respectively, 230 mL and 235 mL; (4) storing pots without and with ECT, respectively, 170 mL and 128 mL; (5) taking a shower without and with ECT, respectively, 172 mL and 118 mL; and (6) putting on shoes without and with ECT, respectively, 210 mL and 78 mL). Patients with moderate to severe COPD develop DH after performing common ADLs involving the upper and lower limbs. Simple ECTs may avoid DH in some of these ADLs.
Symmetric Boolean functions depending on an odd number of variables with maximum algebraic immunity

To resist algebraic attacks, Boolean functions should possess high algebraic immunity. In 2003, Courtois and Meier showed that the algebraic immunity of an n-variable Boolean function is upper bounded by /spl lceil/n/2/spl rceil/. And then several papers studied how to find symmetric Boolean functions with maximum algebraic immunity. In this correspondence, we prove that for each odd n, there is exactly one trivially balanced n-variable symmetric Boolean function achieving the maximum algebraic immunity.
A Binary Communication Channel With Memory Based on a Finite Queue

A model for a binary additive noise communication channel with memory is introduced. The channel noise process, which is generated according to a ball sampling mechanism involving a queue of finite length M, is a stationary ergodic Mth-order Markov source. The channel properties are analyzed and several of its statistical and information-theoretical quantities (e.g., block transition distribution, autocorrelation function (ACF), capacity, and error exponent) are derived in either closed or easily computable form in terms of its four parameters. The capacity of the queue-based channel (QBC) is also analytically and numerically compared for a variety of channel conditions with the capacity of other binary models, such as the well-known Gilbert-Elliott channel (GEC), the Fritchman channel, and the finite-memory contagion channel. We also investigate the modeling of the traditional GEC using this QBC model. The QBC parameters are estimated by minimizing the Kullback-Leibler divergence rate between the probability of noise sequences generated by the GEC and the QBC, while maintaining identical bit-error rates (BER) and correlation coefficients. The accuracy of fitting the GEC via the QBC is evaluated in terms of ACF, channel capacity, and error exponent. Numerical results indicate that the QBC provides a good approximation of the GEC for various channel conditions; it thus offers an interesting alternative to the GEC while remaining mathematically tractable.
The Cryptococcus neoformans Capsule: a Sword and a Shield

SUMMARY The human fungal pathogen Cryptococcus neoformans is characterized by its ability to induce a distinct polysaccharide capsule in response to a number of host-specific environmental stimuli. The induction of capsule is a complex biological process encompassing regulation at multiple steps, including the biosynthesis, transport, and maintenance of the polysaccharide at the cell surface. By precisely regulating the composition of its cell surface and secreted polysaccharides, C. neoformans has developed intricate ways to establish chronic infection and dormancy in the human host. The plasticity of the capsule structure in response to various host conditions also underscores the complex relationship between host and parasite. Much of this precise regulation of capsule is achieved through the transcriptional responses of multiple conserved signaling pathways that have been coopted to regulate this C. neoformans-specific virulence-associated phenotype. This review focuses on specific host stimuli that trigger the activation of the signal transduction cascades and on the downstream transcriptional responses that are required for robust encapsulation around the cell.
Economic Vulnerability, Discrimination, and Hurricane Katrina: Health Among Black Katrina Survivors in Eastern New Orleans

BACKGROUND : Few works have viewed disaster relief in the context of socioeconomic disparity and racial inequality before Katrina. OBJECTIVE : By using the vulnerable-populations conceptual framework, our study aimed to investigate the relationship among economic vulnerability, perceived discrimination, and health outcomes among 69 Black Katrina survivors in Eastern New Orleans. STUDY DESIGN : A mixed-method approach, including survey and focus groups, was applied to collect data. RESULTS : Our findings suggested that a higher level of perceived racial discrimination during Katrina and financial strain post-Katrina were associated with more posttraumatic stress disorder (PTSD) symptoms; support provided by network members served to enhance mental and physical health. Compared with Black males, female survivors reported more PTSD symptoms and worse mental health. CONCLUSIONS : It is imperative for nursing scholars and public policies to directly address the intricacies of race, class, and gender inequality to deliver interventions tailored to meet the unique needs of vulnerable populations. J Am Psychiatr Nurses Assoc, 2007; 13(5), 257-266. DOI: 10.1177/1078390307307260
Data-driven generation of pronunciation dictionaries in the German Verbmobil project: discussion of experimental results

In the framework of the German Verbmobil project we developed a procedure for the automatic, data-driven generation of pronunciation dictionaries for speech recognition systems. In most recognizers, only simple dictionaries containing the canonical pronunciation form are used. They represent the correct pronunciation, but in most cases the canonical pronunciation does not match the actual realization of the word. To solve this problem we chose an approach to derive pronunciation variants automatically from a speech database. The training algorithm is based on a canonical dictionary which is compiled into a graph representation in a first stage. Pronunciation variants are then learned from a training sample consisting of speech signal and its orthographic transcription. The authors focus on the experimental results obtained in the Verbmobil framework and introduce methods to evaluate pronunciation dictionaries generated by the training procedure.
Extraction of pitch information in noisy speech using wavelet transform with aliasing compensation

Although many wavelet-based pitch detection methods have been proposed in the literature, there still remains a need to investigate new wavelet-based methods for more accurate and more robust pitch determination. In this paper, an improved wavelet-based method is developed for extraction of pitch information in noisy speech. At each decomposition in the wavelet transform, an aliasing compensation algorithm is applied to approximate and detail signals, in which the distortion of aliasing due to downsampling and upsampling operations of the wavelet transform is eliminated. In addition, this paper utilizes the concept of spatial correlation function used in signal denoising to improve the performance of pitch detection in a noisy environment. It is shown in various experimental results that this new type of method has a considerable performance improvement compared with other conventional methods and wavelet-based methods.
Immunobiology of Human Cytomegalovirus: from Bench to Bedside

SUMMARY Following primary infection, human cytomegalovirus (HCMV) establishes lifelong latency and periodically reactivates without causing symptoms in healthy individuals. In the absence of an adequate host-derived immune response, this fine balance of permitting viral reactivation without causing pathogenesis is disrupted, and HCMV can subsequently cause invasive disease and an array of damaging indirect immunological effects. Over the last decade, our knowledge of the immune response to HCMV infection in healthy virus carriers and diseased individuals has allowed us to translate these findings to develop better diagnostic tools and therapeutic strategies. The application of these emerging technologies in the clinical setting is likely to provide opportunities for better management of patients with HCMV-associated diseases.
The impact of non-health attributes of care on patients' choice of GP

After completing a structured evaluation of their general practitioner (GP) in terms of non-health factors, 128 people who had visited their GP in the past six months for treatment of a minor condition were administered a discrete choice experiment (DCE) designed to evaluate their preferences for non-health attributes of care within a general practice consultation. SAS and SYSTAT were used to analyse responses. Trust, legitimation, recognition of and support for emotional distress, dignity, reassurance and information (whether it is asked for or not), were the attributes respondents valued most highly. In general, participants were unwilling to change GPs.
Microbial Translocation in the Pathogenesis of HIV Infection and AIDS

SUMMARY In pathogenic simian immunodeficiency virus (SIV) and human immunodeficiency virus (HIV) infections, the translocation of microbial products from the gastrointestinal (GI) tract to portal and systemic circulation has been proposed as a major driver of the chronic immune activation that is associated with disease progression. Consistently, microbial translocation is not present in nonpathogenic SIV infections of natural host species. In vivo studies demonstrated that HIV/SIV-associated microbial translocation results from a series of immunopathological events occurring at the GI mucosa: (i) early and severe mucosal CD4+ depletion, (ii) mucosal immune hyperactivation/persistent inflammation; (iii) damage to the integrity of the intestinal epithelium with enterocyte apoptosis and tight junction disruption; and (iv) subverted the gut microbiome, with a predominance of opportunistic bacteria. Direct in situ evidence of microbial translocation has been provided for SIV-infected rhesus macaques showing translocated microbial products in the intestinal lamina propria and distant sites. While the mechanisms by which microbial translocation causes immune activation remain controversial, a key pathogenic event appears to be innate immunity activation via Toll-like receptors and other pathogen recognition receptors. Accumulating clinical observations suggest that microbial translocation might affect HIV disease progression, response to therapy, and non-AIDS comorbidities. Given its detrimental effect on overall immunity, several interventions to prevent/block microbial translocation are currently under investigation as novel therapeutic agents for HIV/AIDS.
Double affine projection algorithm-based speech enhancement algorithm

A symmetric feedback implementation scheme for two microphones speech enhancement is presented. We consider the coupling systems modeled as a linear time-invariant finite impulse response (FIR) filter and propose a new recursive-based adaptive filter solution to enhance the noisy speech. The optimum filter weight adaptation is based on a double affine projection algorithm (DAPA). This approach can be extended for a subclass of signal separations where the direct link is stronger than the interference link in both channels. A comparative study with other adaptive algorithms shows the superiority of the DAPA in performance improvement.
Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

SUMMARY The epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generate in silico results for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.
Concurrent Chemoradiotherapy with Weekly Paclitaxel for Locally Advanced Non-small Cell Lung Cancer

Purpose: Concurrent chemoradiotherapy (CCRT) is the standard treatment for locally advanced non-small cell lung cancer (NSCLC). Paclitaxel is an active agent against NSCLC and it has a radiosensitizing effect. We investigated the efficacy and toxicity of weekly paclitaxel administration along with concurrent radiotherapy for treating locally advanced and locally recurrent NSCLC. Materials and Methods: Twenty-five previously untreated stage III or locally recurrent NSCLC patients received weekly paclitaxel (60 mg/m) and concurrent radiotherapy. Chemotherapy was given on days 1, 8, 15 and 22. Concurrent radiotherapy at 1.5 Gy was given twice a day to a total dose of 54 Gy in 3.5 weeks. After the completion of CCRT, consolidation chemotherapy was delivered if possible. Results: The overall response rate was 72% with one complete response and 17 partial responses. The median overall survival was 16 months with a 2 year survival rate and a 5 year survival rate of 38% and 24%, respectively. The rate of grade ≥3 radiation pneumonitis was 16% (4 patients) and 2 patients were died from the pneumonitis. The rate of grade 3 radiation esophagitis was 12% (3 patients) and the hematologic toxicities were not significant. Conclusion: Weekly paclitaxel with concurrent radiotherapy is effective for treating locally advanced and locally recurrent NSCLC, but radiation pneumonitis is the major toxicity and this is potentially fatal. (J Lung Cancer 2009;8(1):8 󰠏12)
Human Infections and Detection of Plasmodium knowlesi

SUMMARY Plasmodium knowlesi is a malaria parasite that is found in nature in long-tailed and pig-tailed macaques. Naturally acquired human infections were thought to be extremely rare until a large focus of human infections was reported in 2004 in Sarawak, Malaysian Borneo. Human infections have since been described throughout Southeast Asia, and P. knowlesi is now recognized as the fifth species of Plasmodium causing malaria in humans. The molecular, entomological, and epidemiological data indicate that human infections with P. knowlesi are not newly emergent and that knowlesi malaria is primarily a zoonosis. Human infections were undiagnosed until molecular detection methods that could distinguish P. knowlesi from the morphologically similar human malaria parasite P. malariae became available. P. knowlesi infections cause a spectrum of disease and are potentially fatal, but if detected early enough, infections in humans are readily treatable. In this review on knowlesi malaria, we describe the early studies on P. knowlesi and focus on the epidemiology, diagnosis, clinical aspects, and treatment of knowlesi malaria. We also discuss the gaps in our knowledge and the challenges that lie ahead in studying the epidemiology and pathogenesis of knowlesi malaria and in the prevention and control of this zoonotic infection.
Pertussis: Microbiology, Disease, Treatment, and Prevention

SUMMARY Pertussis is a severe respiratory infection caused by Bordetella pertussis, and in 2008, pertussis was associated with an estimated 16 million cases and 195,000 deaths globally. Sizeable outbreaks of pertussis have been reported over the past 5 years, and disease reemergence has been the focus of international attention to develop a deeper understanding of pathogen virulence and genetic evolution of B. pertussis strains. During the past 20 years, the scientific community has recognized pertussis among adults as well as infants and children. Increased recognition that older children and adolescents are at risk for disease and may transmit B. pertussis to younger siblings has underscored the need to better understand the role of innate, humoral, and cell-mediated immunity, including the role of waning immunity. Although recognition of adult pertussis has increased in tandem with a better understanding of B. pertussis pathogenesis, pertussis in neonates and adults can manifest with atypical clinical presentations. Such disease patterns make pertussis recognition difficult and lead to delays in treatment. Ongoing research using newer tools for molecular analysis holds promise for improved understanding of pertussis epidemiology, bacterial pathogenesis, bioinformatics, and immunology. Together, these advances provide a foundation for the development of new-generation diagnostics, therapeutics, and vaccines.
Intestinal Carriage of Carbapenemase-Producing Organisms: Current Status of Surveillance Methods

SUMMARY Carbapenemases have become a significant mechanism for broad-spectrum β-lactam resistance in Enterobacteriaceae and other Gram-negative bacteria such as Pseudomonas and Acinetobacter spp. Intestinal carriage of carbapenemase-producing organisms (CPOs) is an important source of transmission. Isolation of carriers is one strategy that can be used to limit the spread of these bacteria. In this review, we critically examine the clinical performance, advantages, and disadvantages of methods available for the detection of intestinal carriage of CPOs. Culture-based methods (Centers for Disease Control and Prevention [CDC] protocols, chromogenic media, specialized agars, and double-disk synergy tests) for detecting carriage of CPOs are convenient due to their ready availability and low cost, but their limited sensitivity and long turnaround time may not always be optimal for infection control practices. Contemporary nucleic acid amplification techniques (NAATs) such as real-time PCR, hybridization assays, loop-mediated isothermal amplification (LAMP), or a combined culture and NAAT approach may provide fast results and/or added sensitivity and specificity compared with culture-based methods. Infection control practitioners and clinical microbiologists should be aware of the strengths and limitations of available methods to determine the most suitable approach for their medical facility to fit their infection control needs.