Miracle-dz/UniFAR-FTUs huggingface dataset:
Individual and Combined Roles of the Master Regulators AphA and LuxR in Control of the Vibrio harveyi Quorum-Sensing Regulon

ABSTRACT Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors, AphA and LuxR, coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they coregulate 77 genes. LuxR strongly controls genes at both low cell density and high cell density, suggesting that it is the major quorum-sensing regulator. In contrast, AphA is absent at high cell density and acts to fine-tune quorum-sensing gene expression at low cell density. We examined two loci as case studies of coregulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum-regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group life-styles. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell density. Thus, the asymmetric production of AphA and LuxR coupled with differences in their strengths and timing of target gene regulation generate a precise temporal pattern of gene expression.
Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205

ABSTRACT The enzymes LinBUT and LinBMI (LinB from Sphingobium japonicum UT26 and Sphingobium sp. MI1205, respectively) catalyze the hydrolytic dechlorination of β-hexachlorocyclohexane (β-HCH) and yield different products, 2,3,4,5,6-pentachlorocyclohexanol (PCHL) and 2,3,5,6-tetrachlorocyclohexane-1,4-diol (TCDL), respectively, despite their 98% identity in amino acid sequence. To reveal the structural basis of their different enzymatic properties, we performed site-directed mutagenesis and X-ray crystallographic studies of LinBMI and its seven point mutants. The mutation analysis revealed that the seven amino acid residues uniquely found in LinBMI were categorized into three groups based on the efficiency of the first-step (from β-HCH to PCHL) and second-step (from PCHL to TCDL) conversions. Crystal structure analyses of wild-type LinBMI and its seven point mutants indicated how each mutated residue contributed to the first- and second-step conversions by LinBMI. The dynamics simulation analyses of wild-type LinBMI and LinBUT revealed that the entrance of the substrate access tunnel of LinBUT was more flexible than that of LinBMI, which could lead to the different efficiencies of dehalogenation activity between these dehalogenases.
A multiple objective framework for planning accelerated life tests

We consider a framework with two conflicting objectives in the planning of ALT; i.e., meeting a desired level of statistical precision for an estimate of interest, and meeting a cost target for conducting the test. This can easily be generalized to multiple objectives with, say, precision targets for various estimates, stress limits constraint, sample size constraint, etc. In the absence of actual cost, the cost of conducting the test is related to the total test time at different stress levels, and the total sample size needed for the test. The framework is applied to planning of constant stress ALT, in which the logarithm of the lifetime follows the extreme value distribution. The proposed framework consistently leads to more cost-effective test plans without compromising the precision of the estimate, and is equally robust to misspecification of initial estimates, compared with other test plans presented in the literature.
Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii

ABSTRACT In 2004, a previously undiscovered mycobacterium resembling Mycobacterium ulcerans (the agent of Buruli ulcer) was reported in an outbreak of a lethal mycobacteriosis in a laboratory colony of the African clawed frog Xenopus tropicalis. This mycobacterium makes mycolactone and is one of several strains of M. ulcerans-like mycolactone-producing mycobacteria recovered from ectotherms around the world. Here, we describe the complete 6,399,543-bp genome of this frog pathogen (previously unofficially named “Mycobacterium liflandii”), and we show that it has undergone an intermediate degree of reductive evolution between the M. ulcerans Agy99 strain and the fish pathogen Mycobacterium marinum M strain. Like M. ulcerans Agy99, it has the pMUM mycolactone plasmid, over 200 chromosomal copies of the insertion sequence IS2404, and a high proportion of pseudogenes. However, M. liflandii has a larger genome that is closer in length, sequence, and architecture to M. marinum M than to M. ulcerans Agy99, suggesting that the M. ulcerans Agy99 strain has undergone accelerated evolution. Scrutiny of the genes specifically lost suggests that M. liflandii is a tryptophan, tyrosine, and phenylalanine auxotroph. A once-extensive M. marinum-like secondary metabolome has also been diminished through reductive evolution. Our analysis shows that M. liflandii, like M. ulcerans Agy99, has the characteristics of a niche-adapted mycobacterium but also has several distinctive features in important metabolic pathways that suggest that it is responding to different environmental pressures, supporting earlier proposals that it could be considered an M. ulcerans ecotype, hence the name M. ulcerans ecovar Liflandii.
Postnatal depression: The impact on the family

This preliminary, qualitative paper explores the impact of postnatal depression on partners and other family members. Sixty women with postnatal depresssion were asked to have a questionnaire completed and returned by their partner or close family member. Thirty (50%) questionnaires were returned, 23 (77%) of which were completed by the woman's partner. The responses revealed that postnatal depression was placing considerable extra burdens on partners and close family members, affecting social and leisure activities and causing financial problems within the family. Postnatal depression was also having an adverse effect on on the marital relationship, and a detrimental impact on partners' own mental health. Respondents highlighted the need for health care services for postnatal depression to be extended to partners and family members as well as women. The need for further research to fully assess the impact of postnatal depression on the family is discussed.
Mindfulness meditation training to reduce symptom distress in transplant patients: rationale, design, and experience with a recycled waitlist

Background Solid organ transplant recipients must take immune suppressive medications that have side effects, cause complications, and lead to distressing symptoms that reduce health-related quality of life (QOL). Mindfulness meditation has been shown to reduce these symptoms in other patient populations, and it is unlikely to interfere with the immune suppressive medication regimen. Purpose This article describes the design and rationale of a clinical trial to determine whether training in mindfulness meditation can reduce depression, anxiety and insomnia after transplantation, and summarizes baseline characteristics of the participants. Methods Transplant recipients were randomized in equal numbers to one of three arms: a Mindfulness-based Stress Reduction (MBSR) program consisting of 8 weeks of group instruction, home practice and telephone monitoring; a time and attention control Health Education program; or a waitlist arm. After serving 6 months as waitlist controls, these participants were re-randomized to MBSR or Health Education. Evaluations were obtained at baseline (prior to the active interventions), 8 weeks, 6 months, and 1 year (after randomization to MBSR or Health Education only). The primary analysis will compare composite symptom scores between MBSR and Health Education, initially or after serving in the waitlist. Subsequent analyses will compare these two groups on depression, anxiety, and insomnia symptom scales and secondary outcomes of health-related QOL, actigraphy, and health care utilization. A separate analysis, using only data collected before re-randomization, will compare short-term outcomes between the waitlist and active treatment arms. Results One hundred fifty recipients were randomized and 72% of waitlist participants (31/43) were recycled to an active intervention after 6 months. Patient characteristics were balanced across trial arms after initial and secondary randomizations. Limitations Transplant recipients are a very select population. Their adherence to the intervention and willingness to serve as waitlist controls prior to re-randomization may be atypical. Participants were not blinded to treatment and primary outcomes are self-reports. Conclusion The innovative design used in the trial enabled the waitlist group to directly contribute to the number in the primary analysis of active arms, and to also serve as an internal validation test. The trial may be a useful model for trials involving very small target populations. Clinical Trials 2009; 6: 76—89. http://ctj.sagepub. com
Gene PA2449 Is Essential for Glycine Metabolism and Pyocyanin Biosynthesis in Pseudomonas aeruginosa PAO1

ABSTRACT Many pseudomonads produce redox active compounds called phenazines that function in a variety of biological processes. Phenazines are well known for their toxicity against non-phenazine-producing organisms, which allows them to serve as crucial biocontrol agents and virulence factors during infection. As for other secondary metabolites, conditions of nutritional stress or limitation stimulate the production of phenazines, but little is known of the molecular details underlying this phenomenon. Using a combination of microarray and metabolite analyses, we demonstrate that the assimilation of glycine as a carbon source and the biosynthesis of pyocyanin in Pseudomonas aeruginosa PAO1 are both dependent on the PA2449 gene. The inactivation of the PA2449 gene was found to influence the transcription of a core set of genes encoding a glycine cleavage system, serine hydroxymethyltransferase, and serine dehydratase. PA2449 also affected the transcription of several genes that are integral in cell signaling and pyocyanin biosynthesis in P. aeruginosa PAO1. This study sheds light on the unexpected relationship between the utilization of an unfavorable carbon source and the production of pyocyanin. PA2449 is conserved among pseudomonads and might be universally involved in the assimilation of glycine among this metabolically diverse group of bacteria.
Qualidade de vida em pacientes com retinopatia diabética proliferativa

OBJECTIVE: To verify the Quality of life for the Proliferative Diabetic Retinopathy (PDR) patients. These subjects have a higher risk for severe visual loss, due to the vascular retina complications. METHODS: We evaluated the Quality of Life of 61 PDR patients, over 18 years old, who have been followed up in the Ophthalmology Clinic of the Clinical Hospital of Medicine School of Sao Paulo, Brazil. All patients data were obtained using a questionnaire of health quality of life "WHOQOL Bref - Portuguese version - 1998", and the statistical analysis was done using SPSS program. The 61 patients were classified in two groups: Group I, with 28 patients (46%), with better visual acuity (VA) of 20/200 and Group II, with 33 patients (54%), with worse or equal VA of 20/200. RESULTS: No statistical significant difference (SSD) was observed between the groups, regarding to physical domain (p= 0,255) and psychological domain (p=0,287). SSD was observed between the groups, regarding to social domain (p=0.019) and environment domain (p=0.009). CONCLUSION: Patients with poor VA can be equivalent with those with better vision in physical and psychological domains (no SSD). The SSD regarding to social and environment domains demonstrate the lack of social support for people living with severe visual loss.
Methenyl-Dephosphotetrahydromethanopterin Is a Regulatory Signal for Acclimation to Changes in Substrate Availability in Methylobacterium extorquens AM1

ABSTRACT During an environmental perturbation, the survival of a cell and its response to the perturbation depend on both the robustness and functionality of the metabolic network. The regulatory mechanisms that allow the facultative methylotrophic bacterium Methylobacterium extorquens AM1 to effect the metabolic transition from succinate to methanol growth are not well understood. Methenyl-dephosphotetrahydromethanopterin (methenyl-dH4MPT), an early intermediate during methanol metabolism, transiently accumulated 7- to 11-fold after addition of methanol to a succinate-limited culture. This accumulation partially inhibited the activity of the methylene-H4MPT dehydrogenase, MtdA, restricting carbon flux to the assimilation cycles. A strain overexpressing the gene (mch) encoding the enzyme that consumes methenyl-dH4MPT did not accumulate methenyl-dH4MPT and had a growth rate that was 2.7-fold lower than that of the wild type. This growth defect demonstrates the physiological relevance of this enzymatic regulatory mechanism during the acclimation period. Changes in metabolites and enzymatic activities were analyzed in the strain overexpressing mch. Under these conditions, the activity of the enzyme coupling formaldehyde with dH4MPT (Fae) remained constant, with concomitant formaldehyde accumulation. Release of methenyl-dH4MPT regulation did not affect the induction of the serine cycle enzyme activities immediately after methanol addition, but after 1 h, the activity of these enzymes decreased, likely due to the toxicity of formaldehyde accumulation. Our results support the hypothesis that in a changing environment, the transient accumulation of methenyl-dH4MPT and inhibition of MtdA activity are strategies that permit flexibility and acclimation of the metabolic network while preventing the accumulation of the toxic compound formaldehyde. IMPORTANCE The identification and characterization of regulatory mechanisms for methylotrophy are in the early stages. We report a nontranscriptional regulatory mechanism that was found to operate as an immediate response for acclimation during changes in substrate availability. Methenyl-dH4MPT, an early intermediate during methanol oxidation, reversibly inhibits the methylene-H4MPT dehydrogenase, MtdA, when Methylobacterium extorquens is challenged to switch from succinate to methanol growth. Bypassing this regulatory mechanism causes formaldehyde to accumulate. Fae, the enzyme catalyzing the conversion of formaldehyde to methylene-dH4MPT, was also identified as another potential regulatory target using this strategy. The results herein further our understanding of the complex regulatory network in methylotrophy and will allow us to improve metabolic engineering strategies of methylotrophs for the production of value-added products.
Genome Sequence of Strain IMCC3088, a Proteorhodopsin-Containing Marine Bacterium Belonging to the OM60/NOR5 Clade

ABSTRACT Strain IMCC3088, cultivated from the Yellow Sea, is a novel isolate belonging to the OM60/NOR5 clade and is closely related to clone OM241, Congregibacter litoralis, and strain HTCC2080. Here, the genome sequence of strain IMCC3088 is presented, showing the absence of photosynthetic gene clusters and the presence of proteorhodopsin.
Integration of Cyclic di-GMP and Quorum Sensing in the Control of vpsT and aphA in Vibrio cholerae

ABSTRACT Vibrio cholerae transitions between aquatic environmental reservoirs and infection in the gastrointestinal tracts of human hosts. The second-messenger molecule cyclic di-GMP (c-di-GMP) and quorum sensing (QS) are important signaling systems that enable V. cholerae to alternate between these distinct environments by controlling biofilm formation and virulence factor expression. Here we identify a conserved regulatory mechanism in V. cholerae that integrates c-di-GMP and QS to control the expression of two transcriptional regulators: aphA, an activator of virulence gene expression and an important regulator of the quorum-sensing pathway, and vpsT, a transcriptional activator that induces biofilm formation. Surprisingly, aphA expression was induced by c-di-GMP. Activation of both aphA and vpsT by c-di-GMP requires the transcriptional activator VpsR, which binds to c-di-GMP. The VpsR binding site at each of these promoters overlaps with the binding site of HapR, the master QS regulator at high cell densities. Our results suggest that V. cholerae combines information conveyed by QS and c-di-GMP to appropriately respond and adapt to divergent environments by modulating the expression of key transcriptional regulators.
A method for utilizing co-primary efficacy outcome measures to screen regimens for activity in two-stage Phase II clinical trials

Background Most Phase II clinical trials utilize a single primary end point to determine the promise of a regimen for future study. However, many disorders manifest themselves in complex ways. For example, migraine headaches can cause pain, auras, photophobia, and emesis. Investigators may believe that a drug is effective at reducing migraine pain and the severity of emesis during an attack. Nevertheless, they could still be interested in proceeding with the development of the drug if it is effective against only one of these symptoms. Such a study would be a candidate for a clinical trial with co-primary end points. Purpose The purpose of the article is to provide a method for designing a single arm, two-stage clinical trial with dichotomous co-primary end points of efficacy that has the ability to detect activity on either response measure with high probability when the drug is active on one or both measures, while at the same time rejecting the drug with high probability when there is little activity on both dimensions. The design enables early closure for futility and is flexible with regard to attained accrual. Methods The design is proposed in the context of cancer clinical trials with tumor response and progression-free survival (PFS) status after a certain period. Both end points are assumed to be distributed as binomial random variables, and uninteresting probabilities of success are determined from historical controls. Given the necessity of accrual flexibility, exhaustive searching algorithms to find optimum designs do not seem feasible at this time. Instead, critical values are determined for realized sample sizes using specific procedures. Then accrual windows are found to achieve a design’s desired level of significance, probability of early termination (PET), and power. Results The design is illustrated with a clinical trial that examined bevacizumab in patients with recurrent endometrial cancer. This study was negative by tumor response but positive by 6-month PFS. The procedure was compared to modified procedures in the literature, indicating that the method is competitive. Limitations Although the procedure allows investigators to construct designs with desired levels of significance and power, the PET under the null hypothesis is smaller than for single end point studies. Conclusions The impact of adding an additional end point on the sample size is often minimal, but the study gains sensitivity to activity on another dimension of treatment response. The operating characteristics are fairly robust to the level of association between the two end points. Software is available online.
Genome Sequence of Listeria monocytogenes Scott A, a Clinical Isolate from a Food-Borne Listeriosis Outbreak

ABSTRACT Listeria monocytogenes is an opportunistic food-borne pathogen and the causative agent of listeriosis in animals and humans. We present the genome sequence of Listeria monocytogenes Scott A, a widely distributed and frequently used serovar 4b clinical isolate from the 1983 listeriosis outbreak in Massachusetts.
Complete Genome Sequences of Mycobacterium tuberculosis Strains CCDC5079 and CCDC5080, Which Belong to the Beijing Family

ABSTRACT Mycobacterium tuberculosis is one of most prevalent pathogens in the world. Drug-resistant strains of this pathogen caused by the excessive use of antibiotics have long posed serious threats to public health worldwide. A broader picture of drug resistance mechanisms at the genomic level can be obtained only with large-scale comparative genomic methodology. Two closely related Beijing family isolates, one resistant to four first-line drugs (CCDC5180) and one sensitive to them (CCDC5079), were completely sequenced. These sequences will serve as valuable references for further drug resistance site identification studies and could be of great importance for developing drugs targeting these sites.
Blinding strategies in the conduct and reporting of a randomized placebo-controlled device trial

Background: Blinding is a fundamental design strengthening feature in randomized clinical trials. Blinding is particularly important in trials whose outcome measures include subjective assessment of signs and symptoms, such as trials investigating the post-thrombotic syndrome, a frequent chronic complication of deep vein thrombosis. Purpose: To determine whether strategies used to blind site investigators, research coordinators and patients were successful in a specific device trial, a multicenter trial of active versus placebo elastic compression stockings worn for 2 years to prevent post-thrombotic syndrome in patients with a first deep vein thrombosis (the SOX Trial). Methods: Patients were randomized to the active or placebo stocking intervention, which were indistinguishable in appearance at baseline. Replacement stockings were shipped directly to patients’ homes and were not worn to any of the study visits during the study. Guesstimates of treatment group assignment were completed by site investigators, research coordinators and patients at the end of study follow-up. Statistical assessments of blinding were performed using the James and Bang blinding indices. Results: Overall rates of correct responses were 10.4% for site investigators, 17.8% for research coordinators and 29.4% for patients. James blinding index values suggest that blinding was achieved for site investigators, research coordinators and patients. The treatment specific Bang blinding index values suggest that blinding was achieved for site investigators and research coordinators, but detected possible unblinding and opposite guess for patients in the active and placebo elastic compression stocking groups, respectively. Limitations: Post-study assessment of blinding, as was done for the SOX Trial, cannot distinguish between degree of blinding and hunches about an intervention’s efficacy. However, as rates of post-thrombotic syndrome along with adverse events in the SOX Trial were similar between treatment groups, it is unlikely that hunches would have interfered with our end-of-trial assessment for blinding. Conclusion: Blinding strategies used in our trial were successful overall and appeared to be most effective for site investigators and research coordinators. For patients, there may have been some degree of unblinding in the active stocking group. However, as the trial results were negative with active elastic compression stocking showing no benefit over placebo elastic compression stocking, this potential unblinding has minimal impact on the overall conclusions of the trial.