Miracle-dz/UniFAR-FTUs huggingface dataset:
QsdH, a Novel AHL Lactonase in the RND-Type Inner Membrane of Marine Pseudoalteromonas byunsanensis Strain 1A01261

N-acyl-homoserine lactones (AHLs) are the main quorum-sensing (QS) signals in gram-negative bacteria. AHLs trigger the expression of genes for particular biological functions when their density reaches a threshold. In this study, we identified and cloned the qsdH gene by screening a genomic library of Pseudoalteromonas byunsanensis strain 1A01261, which has AHL-degrading activity. The qsdH gene encoded a GDSL hydrolase found to be located in the N-terminus of a multidrug efflux transporter protein of the resistance-nodulation-cell division (RND) family. We further confirmed that the GDSL hydrolase, QsdH, exhibited similar AHL-degrading activity to the full-length ORF protein. QsdH was expressed and purified to process the N-terminal signal peptide yielding a 27-kDa mature protein. QsdH was capable of inactivating AHLs with an acyl chain ranging from C4 to C14 with or without 3-oxo substitution. High-performance liquid chromatography (HPLC) and electrospray ionization-mass spectrometry (ESI-MS) analyses showed that QsdH functioned as an AHL lactonase to hydrolyze the ester bond of the homoserine lactone ring of AHLs. In addition, site-directed mutagenesis demonstrated that QsdH contained oxyanion holes (Ser-Gly-Asn) in conserved blocks (I, II, and III), which had important roles in its AHL-degrading activity. Furthermore, the lactonase activity of QsdH was slightly promoted by several divalent ions. Using in silico prediction, we concluded that QsdH was located at the first periplasmic loop of the multidrug efflux transporter protein, which is essential to substrate selectivity for these efflux pumps. These findings led us to assume that the QsdH lactonase and C-terminal efflux pump might be effective in quenching QS of the P. byunsanensis strain 1A01261. Moreover, it was observed that recombinant Escherichia coli producing QsdH proteins attenuated the plant pathogenicity of Erwinia carotovora, which might have potential to control of gram-negative pathogenic bacteria.
Adaptation to Repeated Cocaine Administration in Rats

Abstract: Quantitative electroencephalogram (EEG) studies in cocaine‐dependent human patients show deficits in slow‐wave brain activity, reflected in diminished EEG power in the delta and theta frequency bands. In the present study, electrophysiological measures were monitored in 10 nonanesthetized, adult male Sprague‐Dawley rats via bipolar, epidural electrodes implanted over the somatosensory cortex. Control electrocorticograms (ECoG) were recorded twice within a two‐week interval to establish a baseline. Rats were subsequently injected daily with cocaine HCl at 15 mg/kg, i.p., for two weeks. The ECoG was recorded during a 1‐h session one day after the last injection. Total concentrations of dopamine (DA) and its metabolites were assayed in caudate nucleus (CN) and frontal cortex (FC) using HPLC/EC. Compared with controls, marked increases in DA concentrations were observed in both regions. The DA turnover decreased significantly. The power spectra, obtained by use of a fast Fourier transformation, revealed a significant decrease in slow‐wave delta frequency bands following repeated exposure to cocaine. These data are consistent with reported findings in humans that repeated exposures to cocaine result in a decrease in slow‐wave brain activity. Further studies are necessary to establish whether regional alterations in blood flow and metabolic activity may underlie such observations.
Intensified Beclin-1 Mediated by Low Expression of Mir-30a-5p Promotes Chemoresistance in Human Small Cell Lung Cancer

Background/Aims: Although small cell lung cancer (SCLC) is sensitive to initial chemotherapy, patients experience tumor recurrence and metastasis, leading to treatment failure. Autophagy as a protective pattern for cell survival in the harsh environment plays an important role in chemoresistance. However, the role of Beclin-1, a key regulator of autophagy in the drug-resistance of SCLC cells is still poorly understood. In the current study, we focused on the effect and regulation of Beclin-1 in chemoresistance of SCLC cells. Methods: We analyzed the levels of Beclin-1 in etoposide/cisplatin (EP) -resistant and -sensitive cell lines, as well as the relationship between Beclin-1 and patients’ chemosensitivity. The function of Beclin-1 in chemoresistant SCLC cells in vitro was measured by MTT, WB, colony formation and flow cytometric analysis. Further rescue experiment was performed after co-transfected with siBeclin-1 and miR-30a mimics or inhibitor. Results: Beclin-1 was upregulated in drug-resistant cells and patients with lower sensitivity to etoposide/cisplatin therapy. Downregulated Beclin-1 attenuated drug sensitivity and colony formation ability of chemoresistant cells. Moreover, inhibition of Beclin-1 resulted in a dramatic decline of autophagy and increase of apoptosis in drug-resistant cells, accompanied by a remarkable reduction in S phase and a raise in G2/M phase of cell cycle. The transfection with miR-30a-5p mimics exhibited an opposite effect. In addition, inhibition of Beclin-1 could partly reverse the effect induced by miR-30a-5p suppression in drug-sensitive cells. Conclusion: Beclin-1 regulated by miR-30a-5p plays a notable role in the drug-resistance of SCLC. Inhibition of Beclin-1 by induction of miR-30a-5p may improve the therapeutic outcome via resensitizing the drug-resistant cells to chemotherapy in SCLC.
BK channel &bgr;1-subunit deficiency exacerbates vascular fibrosis and remodelling but does not promote hypertension in high-fat fed obesity in mice

Objective: Reduced expression or increased degradation of BK (large conductance Ca2+-activated K+) channel &bgr;1-subunits has been associated with increased vascular tone and hypertension in some metabolic diseases. The contribution of BK channel function to control of blood pressure (BP), heart rate (HR) and vascular function/structure was determined in wild-type and BK channel &bgr;1-subunit knockout mice fed a high-fat or control diet. Methods and results: After 24 weeks of high-fat diet, wild-type and BK &bgr;1-knockout mice were obese, diabetic, but normotensive. High-fat-BK &bgr;1-knockout mice had decreased HR, while high-fat-wild-type mice had increased HR compared with mice on the control diet. Ganglion blockade caused a greater fall in BP and HR in mice on a high-fat diet than in mice on the control diet. &bgr;1-adrenergic receptor blockade reduced BP and HR equally in all groups. &agr;1-adrenergic receptor blockade decreased BP in high-fat-BK &bgr;1-knockout mice only. Echocardiographic evaluation revealed left ventricular hypertrophy in high-fat-BK &bgr;1-knockout mice. Although under anaesthesia, mice on a high-fat diet had higher absolute stroke volume and cardiac output, these measures were similar to control mice when adjusted for body weight. Mesenteric arteries from high-fat-BK &bgr;1-knockout mice had higher norepinephrine reactivity, greater wall thickness and collagen accumulation than high-fat-wild-type mesenteric arteries. Compared with control-wild-type mesenteric arteries, high-fat-wild-type mesenteric arteries had blunted contractile responses to a BK channel blocker, although BK &agr;-subunit (protein) and &bgr;1-subunit (mRNA) expression were unchanged. Conclusion: BK channel deficiency promotes increased sympathetic control of BP, and vascular dysfunction, remodelling and fibrosis, but does not cause hypertension in high-fat fed mice.
The Menopause Rating Scale (MRS): reliability of scores of menopausal complaints

Objective To analyze the reliability of scores of the recently developed self-administrative Menopause Rating Scale (MRS) in a follow-up investigation of a cohort after approximately one and a half years, and to look for possible reasons for variation. Method A follow-up investigation of a random sample of an initially representative survey of German women (aged 40–60), which dated back to early 1996, was performed in late 1997. A subsample of 306 women participated. The MRS scale, a self-administrative standardized questionnaire, was applied with additional, mainly health-related, questions. Results The MRS results at baseline and follow-up were significantly correlated (r = 0.60). The majority of women remained in the category ‘no or mild menopausal symptoms’. The κ statistics showed significant agreement of the various subscales (total, somatic, psychological and urogenital scales) between the two measurements. Neither age nor social factors contributed to a change of score according to a multiple regression analysis. Some, but not all, health-related variables showed a slight association with change of score, such as satisfaction with health in general and, specifically, the presence of hypertension, cardiac and gastrointestinal diseases. No overall relation to hormone replacement therapy (HRT) was found during this observation period. Conclusions The majority of women demonstrated sufficient reliability of MRS scores. Changes in the score after one and a half years were little influenced by the variables tested, except some health conditions such as cardiac disease. It should be stressed that the MRS has the benefit of being a self-administrative tool for the assessment of climacteric complaints with convenient applicability, and representative reference data have been collected in a German population.
Enhanced imaging of microcalcifications in digital breast tomosynthesis through improved image-reconstruction algorithms.

PURPOSE The authors develop a practical, iterative algorithm for image-reconstruction in undersampled tomographic systems, such as digital breast tomosynthesis (DBT). METHODS The algorithm controls image regularity by minimizing the image total p variation (TpV), a function that reduces to the total variation when p = 1.0 or the image roughness when p = 2.0. Constraints on the image, such as image positivity and estimated projection-data tolerance, are enforced by projection onto convex sets. The fact that the tomographic system is undersampled translates to the mathematical property that many widely varied resultant volumes may correspond to a given data tolerance. Thus the application of image regularity serves two purposes: (1) Reduction in the number of resultant volumes out of those allowed by fixing the data tolerance, finding the minimum image TpV for fixed data tolerance, and (2) traditional regularization, sacrificing data fidelity for higher image regularity. The present algorithm allows for this dual role of image regularity in undersampled tomography. RESULTS The proposed image-reconstruction algorithm is applied to three clinical DBT data sets. The DBT cases include one with microcalcifications and two with masses. CONCLUSIONS Results indicate that there may be a substantial advantage in using the present image-reconstruction algorithm for microcalcification imaging.
Transfer learning for rare cancer problems via Discriminative Sparse Gaussian Graphical model

Mortality prediction of rare cancer types with a small number of high-dimensional samples is a challenging task. We propose a transfer learning model where both classes in rare cancers (target task) are modeled in a joint framework by transferring knowledge from the source task. The knowledge transfer is at the data level where only “related” data points are chosen to train the target task. Moreover, both positive and negative class in training enhances the discrimination power of the proposed framework. Overall, this approach boosts the generalization performance of target task with a small number of data points. The formulation of the proposed framework is convex and expressed as a primal problem. We convert this to a dual problem and efficiently solve by alternating direction multipliers method. Our experiments with both synthetic and three real-world datasets show that our framework outperforms state-of-the-art single-task, multi-task, and transfer learning baselines.
Honesty in Accounting & Control: A Discussion of Hannan, Rankin and Towry

We provide a discussion of Hannan, Rankin and Towry (HRT) (2006) The effect of information systems on honesty in managerial reporting: A behavioral perspective. Some agency theorists have suggested that while individuals have some preference for honesty, their honesty threshold is so low that they would lie for very small payoffs. HRT's results showing a significant preference for honesty raise questions about agency theory's boundary conditions. Our discussion: provides an overview of findings on honesty and lying from the organizational research literature; summarizes management control systems research on the prevention and detection of lying; critically evaluates several aspects of HRT's predictions, design and results; and generates possible directions for future research.
Relationship Between Supervisory Working Alliance and Client Outcomes in State Vocational Rehabilitation Counseling

This study investigated the relationship between supervisory working alliance (SWA) and successful client outcomes in the state/federal vocational rehabilitation counseling system and supervision practices associated with SWA. Rehabilitation counselors (N = 166) from five randomly selected rehabilitation counseling programs participated in an electronic survey. Existence of a supervision contract, regularly scheduled contact with supervisor, and the counselors’ rating of importance of supervision were found to be positively associated with SWA among new counselors. Implications of findings for rehabilitation counselors will be discussed.
An Evaluation of the Effect of Auditory Emotional Stimuli on Interval Timing

Emotions modulate cognitive processes, including those involved in the perception of time. A number of studies have demonstrated that the emotional modulation of interval timing can be described in terms of an attentional or an arousal-based mechanism, depending on the exact task setup. In this paper, two temporal generalization experiments with auditory emotional stimuli as distractors are presented. These experiments are modeled after the work by Lui et al. ( PLoS One , 2011, 6 , e218292011) who, using visual distractors, provided evidence for an attentional account of emotion-regulated modulation of the perception of time. Experiment 1 replicates the findings of Lui et al., and thus generalizes their work to auditory stimuli. However, Experiment 2, in setup highly similar to Experiment 1, failed to find any effects of emotional modulation on interval timing. These results indicate that emotional effects on interval timing, although often reported, might not be as ubiquitous as earlier research has (implicitly) suggested.
Robust and optimal control of disturbed population dynamics

We use control theory to explore management of populations affected by disturbances and uncertainty. We consider five related topics. Chapter 2 uses linear programming to find optimal translocation strategies between wild and captive populations. To allow comparison of the solutions we classify the optimal strategy depending on which stage classes are kept in captivity. We find depending on species, that different stages are targeted when the resource available is limited. In Chapter 3 we use linear programming to create management strategies for an invading population affected by disturbance. For a sinusoidal disturbance, the final population with control is bounded between a transfer function approximation and a feedback control solution. Then we assume worst case disturbance, which creates a 2-player game. In this linear programming context, minimax≥maximin. Chapter 4 considers a 2-player linear-quadratic problem and introduces the use of disturbance attenuation into ecology. Disturbance attenuation shows how a disturbance is amplified or attenuated by the system. In Chapter 5 we consider an invading population, and we explore the effect that stochasticity has on the relationship between Allee effect and population inertia needed for successful invasion. We find that for small population densities, then demographic stochasticity dramatically reduces the likelihood of invasion and survival of the resident.
Assessment of food habits in children aged 6–12 years and the risk of caries

Food is necessary for the proper growth and development of children. The excessive intake of low-molecular carbohydrates constitutes a serious health issue, which has an unfavourable impact on the dental health status. The aim of this study was to assess the food habits in healthy children aged 6–12 years and the effect on their oral risk profile. The study included 100 children. The assessment of their nutrition was done with the help of a seven-day reproduction of the food intake and a survey used to determine their underlying food habits and preferences. The results revealed unbalanced nutrition of the children and increased intake of simple sugar, which will increase the risk of development of dental caries. The observed high levels of DMFT (number of decayed, missing and filled teeth) in 54% of the children is a logical result of the frequent intake of sugary foods and beverages for a long period of time, as this will increase the acid production by microorganisms in dental plaque, which is one of the leading etiologic factors for the development of caries. It is necessary for dentists to administer control over the carbohydrate intake and the food habits of children, as well as to encourage non-cariogenic diet in order to keep their good oral health.
A molecular phylogeography approach to biological invasions of the New World by parthenogenetic Thiarid snails

The parthenogenetic snail Melanoides tuberculata, present in tropical fresh waters of most of the Old World before 1950, has now invaded the Neotropical area. The phylogeography of this snail was studied to evaluate the pathways and number of such invasions. Because of parthenogenetic reproduction, individuals are structured into genetical clones. Within populations from both the original and invaded areas, several morphologically distinct clones (referred to as morphs) often coexist but the amount of genetic divergence among morphs is unknown. Individuals from 27 morphs and 40 populations world‐wide were sequenced at two mitochondrial genes (12S and 16S). Our phylogenetic reconstruction suggests that (i) most of the morphological variation observed in the New World predates invasion, (ii) at least six independent introductions have occurred, and (iii) invasive clones are found throughout most of the phylogenetic tree and do not come from a particular region of the area of origin. Two ideas are discussed in the light of these results. The first lies with the specificities of parthenogenesis in an invasion context. While in sexual species, independently introduced populations eventually merge into a single invasive population, in a parthenogenetic species independently introduced clones have distinct invasion dynamics and possibly exclude each other. Second, although repeated invasions in Melanoides may have an impact on indigenous molluscan faunas, their most likely effect is the world‐wide homogenization of the invasive taxon itself.
Thyroid transcription factor 1 expression is associated with outcome of patients with non-squamous non-small cell lung cancer treated with pemetrexed-based chemotherapy

Pemetrexed is an antifolate cytostatic agent targeting several folate-dependent enzymatic pathways, widely used in the treatment of locally advanced or metastatic stage non-small cell lung cancer. Aside from the non-squamous histology, there is still no available molecular biomarker predicting treatment efficacy of pemetrexed-based chemotherapy. The aim of our retrospective study was to evaluate the association of thyroid transcription factor 1 expression with outcome of a large cohort of patients with non-squamous non-small cell lung cancer treated with pemetrexed. We retrospectively analysed clinical data of 463 patients with advanced-stage non-small cell lung cancer (IIIB or IV) treated with pemetrexed-based chemotherapy. Thyroid transcription factor 1 expression was assessed using indirect immunohistochemical detection in formalin-fixed paraffin-embedded tumour tissue at the time of diagnosis. Thyroid transcription factor 1 expression was detected in the tumour tissue from 76.0% of patients, and tumours from 24.0% of patients were thyroid transcription factor 1 negative. The median progression-free survival and overall survival for patients with thyroid transcription factor 1 positive tumours were 4.8 and 11.8 months compared to 2.8 and 8.3 months for those with thyroid transcription factor 1 negative tumours (p = 0.001 and p < 0.001). The multivariable Cox proportional hazards model revealed that thyroid transcription factor 1 expression was significantly associated with progression-free survival (hazard ratio = 1.57, p < 0.001) and also with overall survival (hazard ratio = 1.73, p < 0.001). In conclusion, the results of the conducted retrospective study suggest that the thyroid transcription factor 1 expression was independently associated with progression-free survival and overall survival in patients with advanced-stage non-squamous non-small cell lung cancer treated with pemetrexed-based chemotherapy.
The Sex-Sanctioning Issue: Is it History?

A recent review of the effect of sex on courtroom outcomes suggests both that paternalism is alive and well and that the demise of gender-based leniency will emerge as the criminality of women is seen to be increasingly like that of men. This research tests these hypotheses, and a complementary hypothesis, derivedfrom the notion that sex-based differences in sanctioning are due to structural and cultural differences in the lives of male and female offenders. The hypotheses are tested with a sample of men (N =1,558) and women (N =1,365) who were convicted of the crimes of theft, forgery and drug law violations over a 16-year timespan (1965-1980). The analyses indicate that (1) the effect of sex on the decision to incarcerate can, in part, be accounted for by the pretrial release decision; and (2) with regard to the pretrial release decision, holding constant the social and cultural differences in the lives of male and female offenders significantly reduces evidence of gender-based leniency over the 16-year period.
Loss of function mutations in RP1 are responsible for retinitis pigmentosa in consanguineous familial cases

Purpose This study was undertaken to identify causal mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in consanguineous families. Methods Large consanguineous families were ascertained from the Punjab province of Pakistan. An ophthalmic examination consisting of a fundus evaluation and electroretinography (ERG) was completed, and small aliquots of blood were collected from all participating individuals. Genomic DNA was extracted from white blood cells, and a genome-wide linkage or a locus-specific exclusion analysis was completed with polymorphic short tandem repeats (STRs). Two-point logarithm of odds (LOD) scores were calculated, and all coding exons and exon–intron boundaries of RP1 were sequenced to identify the causal mutation. Results The ophthalmic examination showed that affected individuals in all families manifest cardinal symptoms of RP. Genome-wide scans localized the disease phenotype to chromosome 8q, a region harboring RP1, a gene previously implicated in the pathogenesis of RP. Sanger sequencing identified a homozygous single base deletion in exon 4: c.3697delT (p.S1233Pfs22*), a single base substitution in intron 3: c.787+1G>A (p.I263Nfs8*), a 2 bp duplication in exon 2: c. 551_552dupTA (p.Q185Yfs4*) and an 11,117 bp deletion that removes all three coding exons of RP1. These variations segregated with the disease phenotype within the respective families and were not present in ethnically matched control samples. Conclusions These results strongly suggest that these mutations in RP1 are responsible for the retinal phenotype in affected individuals of all four consanguineous families.