Miracle-dz/UniFAR-FTUs huggingface dataset:
Multivisceral Resection for Locally Advanced Rectal Cancer: Prognostic Factors Influencing Outcome

Aims: To assess outcome in patients with locally advanced rectal cancer undergoing multivisceral resection. Methods: Retrospective study of 30 consecutive patients (mean age 67.8 years) with primary locally advanced rectal cancer undergoing en bloc multivisceral resection of the organs involved with curative intent between 1998 and 2010. Overall survival, local and distal recurrence, and disease-free survival were analyzed by the Kaplan–Meier method. Risk factors for clinical outcome were obtained using a Cox multivariate model. Results: Postoperative complications occurred in 76.7% of patients and the in-hospital mortality rate was 10%. The median follow-up was 28.8 months. A total of 19 patients died at follow-up. Of the 11 patients who were alive, 7 were free of disease. In the multivariate analysis, lymph node involvement, stage II, and lymph vascular invasion were significantly associated with survival, and stage III showed a strong trend towards significance. Suture dehiscence (peritonitis and intra-abdominal abscess) showed a significant trend towards a higher local recurrence. Lymph vascular invasion was associated with a higher distant recurrence. Conclusion: Lymph node involvement was associated with worse survival, whereas stage II and absence of lymph vascular invasion were associated with a better survival. Lymph vascular invasion was associated with a higher distant recurrence.
A text-to-speech system based entirely on rules

When reading a text a native speaker pronounces most words correctly even if they are unknown to him. During this process he makes use of his knowledge of the language, the semantic content and the syntax. However, if we take away all information except the spelling and some pronunciation rules on the word level, the task would be more difficult. This is basically the case in our text-to-speech synthesis system containing neither semantic and syntactic analysis nor a word or morpheme dictionary. At the conference the function of our present synthesis system will be discussed. The result shows that such a system might well be based on rules rather than on an extensive dictionary. Furthermore a useful tool in speech synthesis work is described (i.e. a programming language).
Acetabular reconstruction with impaction bone grafting and cemented polyethylene socket in total hip revision arthroplasty

Background and aims: Bone deficiency in revision total hip arthroplasty is a challenge to the surgeon. One option for restoration of the bone stock is impaction bone grafting and use of a cemented socket. The aim of this study was to evaluate the mid-term clinical outcome of impaction bone grafting and cemented socket revisions. Material and methods: A total of 59 patients (60 hips) underwent revision arthroplasty with impaction bone grafting and application of a cemented socket on the acetabular side in the Turku University Hospital from 1999 to 2004. The study end-point was re-revision for any reason. The cumulative percentages for survival were followed and estimated with Kaplan–Meier curves. Associations between occurrence of re-revision and potential risk factors were analyzed with logistic regression. Results were quantified by odd ratios and 95% confidence intervals. The mean age of the patients was 69 years (33% male). A total of 3% of the patients had a class I Paprosky acetabular defect, 38% had class II, and 55% had class III. Results: The overall survival rate was 73%. The mean follow-up time was 7 years. The most common reason for re-revision was aseptic loosening of the acetabular component (13 patients, 81% of re-revisions). Cox’s regression analysis did not identify any risk factors for re-revision. Conclusion: Our results were inferior compared to some previous studies. Impaction bone grafting of acetabular defects in revision total hip arthroplasty may not always provide a reliable bone stock in long-term.
Fecal Bacteroidales Diversity and Decay in Response to Variations in Temperature and Salinity

ABSTRACT Bacteroidales are attractive as water quality indicators because of their potential to discern sources of fecal pollution, and it is presumed that these bacteria do not multiply outside their host organisms. The persistence of a fecal Bacteroidales marker was monitored over 14 days in river water microcosms that varied in temperature from 10°C to 30°C and salinity from 0‰ to 30‰ by quantitative PCR (qPCR). Decay rates were estimated and compared to the results of other studies examining the survival and persistence of Bacteroidales markers by converting decay rates from other studies to a common decay rate unit. The log-linear decay rates estimated in this work ranged from −0.18 to −1.31 ln(C T /C 0) day−1, where C T is the threshold cycle and C 0 is the concentration of cells at time zero, which is comparable to findings in previous studies. Salinity had a positive effect on Bacteroidales marker persistence, while decay was more rapid at higher temperatures. Comparison of 16S rRNA gene clone libraries generated from microcosm samples indicated that most of the operational taxonomic unit (OTU) and phylogenetic diversity was found within samples and not between samples, indicating at least qualitatively that diverse lineages persist and likely have similar survival characteristics under most of the conditions examined. It was noted that the samples at higher salinities also had the smallest amount of diversity between samples as well as the lowest decay rates. This research also highlights the need for a repository of raw survival and persistence data if more sophisticated models of decay are to be employed and compared between different studies.
High and Low Temperatures Differently Affect Infection Density and Vertical Transmission of Male-Killing Spiroplasma Symbionts in Drosophila Hosts

ABSTRACT We investigated the vertical transmission, reproductive phenotype, and infection density of a male-killing Spiroplasma symbiont in two Drosophila species under physiological high and low temperatures through successive host generations. In both the native host Drosophila nebulosa and the nonnative host Drosophila melanogaster, the symbiont infection and the male-killing phenotype were stably maintained at 25°C, rapidly lost at 18°C, and gradually lost at 28°C. In the nonnative host, both the high and low temperatures significantly suppressed the infection density of the spiroplasma. In the native host, by contrast, the low temperature suppressed the infection density of the spiroplasma whereas the high temperature had little effect on the infection density. These results suggested that the low temperature suppresses both the infection density and the vertical transmission of the spiroplasma whereas the high temperature suppresses the vertical transmission preferentially. The spiroplasma density was consistently higher in the native host than in the nonnative host, suggesting that the host genotype may affect the infection density of the symbiont. The temperature- and genotype-dependent instability of the symbiont infection highlights a complex genotype-by-genotype-by-environment interaction and may be relevant to the low infection frequencies of the male-killing spiroplasmas in natural Drosophila populations.
Improvement of the Representation of Bifidobacteria in Fecal Microbiota Metagenomic Libraries by Application of the cpn60 Universal Primer Cocktail

ABSTRACT Actinobacteria, particularly bifidobacteria, are widely observed to be underrepresented in metagenomic studies of microbial communities. We have compared human fecal microbiota clone libraries based on 16S rRNA and cpn60 PCR products. Taxonomic profiles were similar except that the cpn60 libraries contained large numbers of bifidobacterial sequences.
Impact of Body Mass Index on Complications and Survival after Surgery for Esophageal and Gastro-Esophageal-Junction Cancer

Background and Aims: The impact of body mass index on complications and survival in patients undergoing esophagectomy has been extensively studied with conflicting results. In this study, we assess the impact of body mass index on complications and survival following surgery for esophageal and gastro-esophageal-junction cancer in a Danish population. Material and Methods: We identified 285 consecutive patients, who underwent curative-intended treatment for esophageal and gastro-esophageal-junction cancer in the period 2003–2010. We manually reviewed the electronic medical records of all patients included in the study. Body mass index was calculated as weight in kilograms divided by height in meters squared. We grouped patients according to their body mass index, using the World Health Organization definition, as underweight (body mass index < 18.5 kg/m2), normal weight (body mass index: 18.5–24.9 kg/m2), overweight (body mass index: 25–29.9 kg/m2), and obese (body mass index ⩽ 30 kg/m2). Results: Median age at surgery was 65 years (range: 27–84 years), of which 207 (72.6%) were males. Patients with the lowest body mass index and the obese patients seemed to have a higher frequency of minor complications. Anastomotic leakage occurred in less than 10% of the patients and was equally distributed across the groups as was the other major complications. There were no differences in the 1-, 2-, or 5-year survival rates between the four body mass index groups after adjustment for possible confounders. Five-year survival rates for the four body mass index groups were 31.8%, 28.7%, 27.9%, and 26.1%, respectively. Conclusion: Body mass index over 30 or under 18.5 does not seem to affect survival rates or the presence of serious postoperative complications following esophagectomy in patients with esophageal and gastro-esophageal-junction cancers not receiving neoadjuvant oncological treatment.
Cofactor Trapping, a New Method To Produce Flavin Mononucleotide

ABSTRACT We have purified flavin mononucleotide (FMN) from a flavoprotein-overexpressing Escherichia coli strain by cofactor trapping. This approach uses an overexpressed flavoprotein to trap FMN, which is thus removed from the cascade regulating FMN production in E. coli. This, in turn, allows the isolation of highly pure FMN.
Text-independent speaker identification from a large linguistically unconstrained time-spaced data base

A very large data base consisting of over thirty-six hours of linguistically unconstrained extemporaneous speech, from seventeen speakers, recorded over a period of more than three months, was analyzed to determine the effectiveness of long-term average features for speaker identification. The results were strongly dependent on the voiced speech averaging interval, or L v . Monotonic increases in the probability of correct identification were obtained as L v increased, even with substantial time periods between successive sessions. Speaker identification performance in open tests improved if features with small between-class to within-class variance ratios were eliminated. For L v corresponding to approximately thirty-nine seconds of speech, true text-independent results (no linguistic constraints embedded into the data base) of 98.05% for speaker identification were obtained.
Mobile technologies and the holistic management of chronic diseases

Ageing populations and unhealthy lifestyles have led to some chronic conditions such as diabetes and heart disease reaching epidemic proportions in many developed nations. This paper explores the potential of mobile technologies to improve this situation. The pervasive nature of these technologies can contribute holistically across the whole spectrum of chronic care ranging from public information access and awareness, through monitoring and treatment of chronic disease, to support for patient carers. A related study to determine the perceptions of healthcare providers to m-health confirmed the view that attitudes were likely to be more important barriers to progress than technology. A key finding concerned the importance of seamless and integrated m-health processes across the spectrum of chronic disease management.
Overproduction of Exopolysaccharides by an Escherichia coli K-12 rpoS Mutant in Response to Osmotic Stress

ABSTRACT The yjbEFGH operon is implicated in the production of an exopolysaccharide of an unknown function and is induced by osmotic stress and negatively regulated by the general stress response sigma factor RpoS. Despite the obvious importance of RpoS, negative selection for rpoS has been reported to take place in starved cultures, suggesting an adaptive occurrence allowing the overexpression of RpoD-dependent uptake and nutrient-scavenging systems. The trade-off of the RpoS-dependent functions for improved nutrient utilization abilities makes the bacterium more sensitive to environmental stressors, e.g., osmotic stress. In this work, we addressed the hypothesis that overinduction of genes in rpoS-deficient strains indicates their essentiality. Using DNA microarrays, real-time PCR, and transcriptional fusions, we show that genes of the wca operon, implicated in the production of the colanic acid exopolysaccharide, previously shown to be induced by osmotic stress, are also negatively controlled by RpoS. Both exopolysaccharides in the synthesis of which yjb and wca are involved are overproduced in an rpoS mutant during osmotic stress. We also show that both operons are essential in an rpoS-deficient strain but not in the wild type; promoters of both operons are constitutively active in yjb rpoS mutants; this strain produces extremely mucoid colonies, forms long filaments, and exhibits a reduced growth capability. In addition, the wca rpoS mutant's growth is inhibited by osmotic stress. These results indicate that although induced in the wild type, both operons are much more valuable for an rpoS-deficient strain, suggesting that the overproduction of both exopolysaccharides is an adaptive action.
Flexibility-Rigidity Coordination of the Dense Exopolysaccharide Matrix in Terrestrial Cyanobacteria Acclimated to Periodic Desiccation

ABSTRACT A dense exopolysaccharide (EPS) matrix is crucial for cyanobacterial survival in terrestrial xeric environments, in which cyanobacteria undergo frequent expansion and shrinkage processes during environmental desiccation-rehydration cycles. However, it is unclear how terrestrial cyanobacteria coordinate the structural dynamics of the EPS matrix upon expansion and shrinkage to avoid potential mechanical stress while benefiting from the matrix. In the present study, we sought to answer this question by investigating the gene expression, protein dynamics, enzymatic characteristics, and biological roles of WspA, an abundantly secreted protein, in the representative terrestrial cyanobacterium Nostoc flagelliforme. The results demonstrated that WspA is a novel β-galactosidase that facilitates softening of the EPS matrix by breaking the polysaccharide backbone under substantial moisture or facilitates the thickening and relinkage of the broken matrix during the drying process, and thus these regulations are well correlated with moisture availability or desiccation-rehydration cycles. This coordination of flexibility and rigidity of the cyanobacterial extracellular matrix may contribute to a favorable balance of cell growth and stress resistance in xeric environments. IMPORTANCE How the exopolysaccharide matrix is dynamically coordinated by exoproteins to cope with frequent expansion and shrinkage processes in terrestrial colonial cyanobacteria remains unclear. Here we elucidated the biochemical identity and biological roles of a dominant exoprotein in these regulation processes. Our study thus gained insight into this regulative mechanism in cyanobacteria to combat periodic desiccation. In addition, the filamentous drought-adapted cyanobacterium Nostoc flagelliforme serves as an ideal model for us to explore this issue in this study.
Detection of the Emerging Shiga Toxin-Producing Escherichia coli O26:H11/H− Sequence Type 29 (ST29) Clone in Human Patients and Healthy Cattle in Switzerland

ABSTRACT Shiga toxin-producing Escherichia coli O26:H11/H− strains showing the characteristics of the emerging human-pathogenic ST29 clone (stx 2a + only, eae +, plasmid gene profile hlyA + etpD +) were detected from human patients and healthy cattle, indicating a possible reservoir. Sheep also appear to shed strains related to the new pathogenic clone O26:H11/H− (ST29, stx 1a + only, eae +, plasmid gene profile hlyA + etpD +).
Blind Super Resolution of Real-Life Video Sequences

Super resolution (SR) for real-life video sequences is a challenging problem due to complex nature of the motion fields. In this paper, a novel blind SR method is proposed to improve the spatial resolution of video sequences, while the overall point spread function of the imaging system, motion fields, and noise statistics are unknown. To estimate the blur(s), first, a nonuniform interpolation SR method is utilized to upsample the frames, and then, the blur(s) is(are) estimated through a multiscale process. The blur estimation process is initially performed on a few emphasized edges and gradually on more edges as the iterations continue. Also for faster convergence, the blur is estimated in the filter domain rather than the pixel domain. The high-resolution frames are estimated using a cost function that has the fidelity and regularization terms of type Huber-Markov random field to preserve edges and fine details. The fidelity term is adaptively weighted at each iteration using a masking operation to suppress artifacts due to inaccurate motions. Very promising results are obtained for real-life videos containing detailed structures, complex motions, fast-moving objects, deformable regions, or severe brightness changes. The proposed method outperforms the state of the art in all performed experiments through both subjective and objective evaluations. The results are available online at http://lyle.smu. edu/~rajand/Video_SR/.
Frequency-axis warping to improve automatic word recognition

Frequency normalization of talkers remains a problem in word recognition, especially where new talkers cannot be asked to provide samples (of their vowels, for example) in advance. Several methods were investigated; for each, parameters were derived by calculating their effect on formant histograms derived from casual speech. Methods tried were a) uniform multiplication of frequencies ("stretching" the vocal tract); b) "stretching" each formant region by a different amount; c) combined shift and stretch (affine mapping); d) different affine mappings for different formants (this includes warping each formant as a function of its range); e) warping each formant non-linearly as a function of its distribution. Experiments show that parameters derived from casual speech improve vowel recognition markedly, and that method e) appears strongest.
Recombinant human interleukin 10 in the treatment of patients with mild to moderately active Crohn's disease

Abstract Background & Aims: Interleukin 10 (IL-10) is an anti-inflammatory, immunomodulatory cytokine that regulates mucosal inflammation. This study evaluated the safety, tolerance, and efficacy of recombinant human IL-10 (rhuIL-10) for mild to moderately active Crohn's disease. Methods: We conducted a 24-week multicenter, prospective, randomized, double-blind, placebo-controlled, and sequential-escalating-dose study. Ninetyfive patients with Crohn's Disease Activity Index of 200–350, not presently undergoing corticosteroid, mesalamine, or immunosuppressive therapy, were treated with subcutaneous rhuIL-10 (1, 5, 10, or 20 μg/kg) or placebo once daily for 28 consecutive days. Patients were followed up for 20 weeks after treatment. Evaluation of safety and tolerance was the first objective, and efficacy was the second objective. Results: Adverse effects were dose-related, mild-to-moderate in severity, and reversible. Asymptomatic and reversible anemia and thrombocytopenia were observed at higher doses. No withdrawal or delayed adverse effects were evident during 20 weeks of follow-up. At the end of treatment (day 29), intent-to-treat analysis showed that 23.5% (confidence interval [CI], 6.8%–49.9%) of patients receiving 5 μg/kg rhuIL-10 experienced clinical remission and endoscopic improvement; 0% (CI, 0%–14.8%) of patients in the placebo group did. Higher doses of recombinant human IL-10 were less effective than 5 μg/kg. No rhuIL-10 serum accumulation and no antibody against IL-10 were detected after 4 weeks. Conclusions: Subcutaneous rhuIL-10 administered daily for 28 days to patients with mild to moderately active Crohn's disease is safe, well-tolerated, and shows clinical and endoscopic improvement. GASTROENTEROLOGY 2000;119:1473-1482
Identification and Characterization of the Asperthecin Gene Cluster of Aspergillus nidulans

ABSTRACT The sequencing of Aspergillus genomes has revealed that the products of a large number of secondary metabolism pathways have not yet been identified. This is probably because many secondary metabolite gene clusters are not expressed under normal laboratory culture conditions. It is, therefore, important to discover conditions or regulatory factors that can induce the expression of these genes. We report that the deletion of sumO, the gene that encodes the small ubiquitin-like protein SUMO in A. nidulans, caused a dramatic increase in the production of the secondary metabolite asperthecin and a decrease in the synthesis of austinol/dehydroaustinol and sterigmatocystin. The overproduction of asperthecin in the sumO deletion mutant has allowed us, through a series of targeted deletions, to identify the genes required for asperthecin synthesis. The asperthecin biosynthesis genes are clustered and include genes encoding an iterative type I polyketide synthase, a hydrolase, and a monooxygenase. The identification of these genes allows us to propose a biosynthetic pathway for asperthecin.
Serratia marcescens Quinoprotein Glucose Dehydrogenase Activity Mediates Medium Acidification and Inhibition of Prodigiosin Production by Glucose

ABSTRACT Serratia marcescens is a model organism for the study of secondary metabolites. The biologically active pigment prodigiosin (2-methyl-3-pentyl-6-methoxyprodiginine), like many other secondary metabolites, is inhibited by growth in glucose-rich medium. Whereas previous studies indicated that this inhibitory effect was pH dependent and did not require cyclic AMP (cAMP), there is no information on the genes involved in mediating this phenomenon. Here we used transposon mutagenesis to identify genes involved in the inhibition of prodigiosin by glucose. Multiple genetic loci involved in quinoprotein glucose dehydrogenase (GDH) activity were found to be required for glucose inhibition of prodigiosin production, including pyrroloquinoline quinone and ubiquinone biosynthetic genes. Upon assessing whether the enzymatic products of GDH activity were involved in the inhibitory effect, we observed that d-glucono-1,5-lactone and d-gluconic acid, but not d-gluconate, were able to inhibit prodigiosin production. These data support a model in which the oxidation of d-glucose by quinoprotein GDH initiates a reduction in pH that inhibits prodigiosin production through transcriptional control of the prodigiosin biosynthetic operon, providing new insight into the genetic pathways that control prodigiosin production. Strains generated in this report may be useful in large-scale production of secondary metabolites.