Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecology of Anti-Biofilm Agents II: Bacteriophage Exploitation and Biocontrol of Biofilm Bacteria

Bacteriophages are the viruses of bacteria. In the guise of phage therapy they have been used for decades to successfully treat what are probable biofilm-containing chronic bacterial infections. More recently, phage treatment or biocontrol of biofilm bacteria has been brought back to the laboratory for more rigorous assessment as well as towards the use of phages to combat environmental biofilms, ones other than those directly associated with bacterial infections. Considered in a companion article is the inherent ecological utility of bacteriophages versus antibiotics as anti-biofilm agents. Discussed here is a model for phage ecological interaction with bacteria as they may occur across biofilm-containing ecosystems. Specifically, to the extent that individual bacterial types are not highly abundant within biofilm-containing environments, then phage exploitation of those bacteria may represent a “Feast-or-famine” existence in which infection of highly localized concentrations of phage-sensitive bacteria alternate with treacherous searches by the resulting phage progeny virions for new concentrations of phage-sensitive bacteria to infect. An updated synopsis of the literature concerning laboratory testing of phage use to combat bacterial biofilms is then provided along with tips on how “Ecologically” such phage-mediated biofilm control can be modified to more reliably achieve anti-biofilm efficacy.
Biological variability of fecal calprotectin in patients referred for colonoscopy without colonic inflammation or neoplasm

OBJECTIVE:Fecal calprotectin concentration in stool has recently been proposed as a marker of colonic neoplasm and inflammation, but the intraindividual day-to-day variability has so far received little attention.The present study was undertaken to determine the biological variability of fecal calprotectin in patients referred for colonoscopy.METHODS:A prospective design was applied. In each of 14 consecutive patients submitted for colonoscopy, eight stool samples were collected before the endoscopy. A detailed questionnaire was used. Calprotectin was measured by quantitative enzyme-linked immunoassay, and standard deviation for the within-patient variability was estimated from one-way analysis of variance.RESULTS:In absence of colonic neoplasm and inflammation, two populations of patients emerged: one (36%) with remarkably low and stable fecal calprotectin values all within the recommended cut-off of 50 μg/g, and one (64%) with labile values also beyond this limit. In this latter group, fecal calprotectin was 70 μg/g (mean) (single tests ranged from 9 to 461), and SD within patients was 52 μg/g, showing considerable day-to-day variation. History, concurrent diseases, or findings at colonoscopy could not explain labile values. A similar pattern was observed for spot variation in one stool sample from healthy volunteers, suggesting that factors other than disease contribute to the significant intraindividual biological variation of fecal calprotectin.CONCLUSIONS:Day-to-day variation of fecal calprotectin is considerable in patients without colonic inflammation or neoplasm, for whom the pattern of stabile low fecal calprotectin may seem to be a valid negative predictor. The origin and pattern of fecal calprotectin excretion deserve further attention.
A Community Perspective on Changes in Health Related to Diarrhea in Northeastern Brazil

Background Diarrhea is a major cause of death in children in developing countries. However, in Brazil, diarrhea-related morbidity and mortality have declined over the past decades. Objective To explore community perspectives in Brazil on changes in health related to diarrhea and factors that may have contributed to these changes. Methods This qualitative study included 12 focus group sessions held with 50 mothers and 42 grandmothers in the state of Ceará. Results Most grandmothers reported having lost at least one child to diarrhea, and all participants had witnessed children dying from diarrhea in the past. The participants saw a clear decline in diarrhea over the past 20 years. They felt that this was due to social, economic, and cultural progress. The participants also considered government-supported outreach programs very important for health improvement. Conclusions Knowledge of diarrhea and its causes in the community is broad, but many traditional beliefs about the illness still prevail. The Brazilian experience is an example of the critical effect that policies to promote income redistribution and universal access to education, health, water supply, and sanitation services may have on the reduction of undernutrition and diarrhea among children.
Recommending questions using the mdl-based tree cut model

The paper is concerned with the problem of question recommendation. Specifically, given a question as query, we are to retrieve and rank other questions according to their likelihood of being good recommendations of the queried question. A good recommendation provides alternative aspects around users' interest. We tackle the problem of question recommendation in two steps: first represent questions as graphs of topic terms, and then rank recommendations on the basis of the graphs. We formalize both steps as the tree-cutting problems and then employ the MDL (Minimum Description Length) for selecting the best cuts. Experiments have been conducted with the real questions posted at Yahoo! Answers. The questions are about two domains, 'travel' and 'computers & internet'. Experimental results indicate that the use of the MDL-based tree cut model can significantly outperform the baseline methods of word-based VSM or phrase-based VSM. The results also show that the use of the MDL-based tree cut model is essential to our approach.
Effect of Acute and Chronic Administration of Carbamazepine on Cisplatin-Induced Hyperalgesia in Rats

Background Cisplatin is an effective antineoplastic drug used extensively in the treatment of malignancies. It induces painful peripheral neuropathy at high doses. Objectives The aim of this study was to investigate the effect of carbamazepine (CBZ) on cisplatin-induced peripheral neuropathic pain by using the tail-flick test. Materials and Methods The study was performed using male Wistar rats weighing 180–200 g. Neuropathic pain was induced by intraperitoneal (IP) administration of cisplatin (5 mg/kg). The effect of oral (PO) CBZ administration (5, 10, and 15 mg/kg) on cisplatin-induced pain was assessed using the tail-flick test. Results Our results showed that cisplatin (5 mg/kg, IP) induced egregious pain (P < 0.01) on day 15. Acute administration of CBZ (5, 10, and 15 mg/kg, PO) caused significant (P < 0.05) increase in tail-flick time latency in a dose-dependent manner, in comparison with that observed in the control group. Furthermore, chronic administration of CBZ (5, 10, and 15 mg/kg, PO) increased (P < 0.05) the pain threshold on days 5 and 10. The analgesic effect of morphine (5 mg/kg, IP) was greater than that after acute CBZ administration (5, 10, and 15 mg/kg, PO). Conclusions Our results showed that both acute and chronic CBZ administration attenuated cisplatin-induced pain. We suggest that CBZ can be used clinically for alleviating cisplatin-induced neuropathic pain in cancer patients, without any limitations such as tolerance to analgesic effect.
Modelling of thrust force for worn drill bits characterised by cutting edge radius in drilling carbon fibre–reinforced plastic/Ti-6Al-4V alloy stacks

Wear rates are rapid when drilling carbon fibre–reinforced plastics/Ti-6Al-4V alloy stacks because of their distinct mechanical properties. Tool wear leads to a high thrust force, thereby reducing the quality of the drilled holes. This article develops a novel mechanistic model for carbon fibre–reinforced plastics/Ti-6Al-4V stacks, which is characterised by the cutting edge radius, to predict the variation of the thrust force when drilling with worn drill bits. Drilling experiments with varying feed rates were performed using carbide twist drill bits. The thrust force and drill edge profile were measured to calibrate and validate the presented model. The edge radius increases with both the cutting distance and number of drilled holes at varying feed rates. It was found that the growth rate of the edge radius increased with the feed rate with identical cutting distances, whereas it decreased slightly with the feed rate when the number of drilled holes was identical. Tool wear reduces the equivalent rake angle of the drill edge, resulting in higher thrust force. The maximum thrust force increases almost linearly with the edge radius of worn drills for both materials. The predicted thrust force curves are in very good agreement with the measured curves during the entire process. Average absolute errors of the maximum thrust force for carbon fibre–reinforced plastics and Ti-6Al-4V alloy are 3.24% and 1.88%, respectively.
A New Mobile Phone-Based Tool for Assessing Energy and Certain Food Intakes in Young Children: A Validation Study

Background Childhood obesity is an increasing health problem globally. Obesity may be established already at pre-school age. Further research in this area requires accurate and easy-to-use methods for assessing the intake of energy and foods. Traditional methods have limited accuracy, and place large demands on the study participants and researchers. Mobile phones offer possibilities for methodological advancements in this area since they are readily available, enable instant digitalization of collected data, and also contain a camera to photograph pre- and post-meal food items. We have recently developed a new tool for assessing energy and food intake in children using mobile phones called the Tool for Energy Balance in Children (TECH). Objective The main aims of our study are to (1) compare energy intake by means of TECH with total energy expenditure (TEE) measured using a criterion method, the doubly labeled water (DLW) method, and (2) to compare intakes of fruits and berries, vegetables, juice, and sweetened beverages assessed by means of TECH with intakes obtained using a Web-based food frequency questionnaire (KidMeal-Q) in 3 year olds. Methods In this study, 30 Swedish 3 year olds were included. Energy intake using TECH was compared to TEE measured using the DLW method. Intakes of vegetables, fruits and berries, juice, as well as sweetened beverages were assessed using TECH and compared to the corresponding intakes assessed using KidMeal-Q. Wilcoxon matched pairs test, Spearman rank order correlations, and the Bland-Altman procedure were applied. Results The mean energy intake, assessed by TECH, was 5400 kJ/24h (SD 1500). This value was not significantly different (P=.23) from TEE (5070 kJ/24h, SD 600). However, the limits of agreement (2 standard deviations) in the Bland-Altman plot for energy intake estimated using TECH compared to TEE were wide (2990 kJ/24h), and TECH overestimated high and underestimated low energy intakes. The Bland-Altman plots for foods showed similar patterns. The mean intakes of vegetables, fruits and berries, juice, and sweetened beverages estimated using TECH were not significantly different from the corresponding intakes estimated using KidMeal-Q. Moderate but statistically significant correlations (ρ=.42-.46, P=.01-.02) between TECH and KidMeal-Q were observed for intakes of vegetables, fruits and berries, and juice, but not for sweetened beverages. Conclusion We found that one day of recordings using TECH was not able to accurately estimate intakes of energy or certain foods in 3 year old children.
Nepalese retroflex stops: a static palatography study of inter- and intra-speaker variability

Abstract Retroflex sounds are classically defined as produced with the tongue tip curled backward and often in contact behind the alveolar ridge ([1], [2], [3]). The sounds, however, present a great inter-language, inter- and intra-speaker articulatory variation. Retroflex stops in Nepali, an Indo-Aryan language spoken in Nepal, are produced with the tongue tip with no backward curling movement at the alveolar ridge ([4],[5]). For Pokharel [5], this is not a real type of retroflexion, but rather is apico-alveolar with no backward curling of the tongue tip. The aim of this study is to experimentally verify Pokharel’s statement and the originality is to go beyond this claim. We wish to verify whether there is any co-articulation effect while producing the retroflex in different vocalic contexts. We use the direct palatography method to determine the place of articulation. Our articulatory data reveal an important articulatory inter and intra speaker variability. The majority of the retroflex stops realized in our study are sub-apico-post-alveolar in the case of back vowels and apico-alveolar in the case of the front vowels. Index terms : retroflex, retraction, Nepali, apical, alveolar, palatograms, linguograms.
Early Steps in Proanthocyanidin Biosynthesis in the Model Legume Medicago truncatula1[W][OA]

Oligomeric proanthocyanidins (PAs) composed primarily of epicatechin units accumulate in the seed coats of the model legume Medicago truncatula, reaching maximal levels at around 20 d after pollination. Genes encoding the single Medicago anthocyanidin synthase (ANS; EC 1.14.11.19) and leucoanthocyanidin reductase (LAR; EC 1.17.1.3) were cloned and the corresponding enzymes functionally identified. Recombinant MtANS converted leucocyanidin to cyanidin, and, more efficiently, dihydroquercetin to the flavonol quercetin. Levels of transcripts encoding dihydroflavonol reductase, ANS, and anthocyanidin reductase (ANR), the enzyme responsible for conversion of anthocyanidin to (−)-epicatechin, paralleled the accumulation of PAs in developing seeds, whereas LAR transcripts appeared to be more transiently expressed. LAR, ANS, and ANR proteins were localized to the cytosol in transfected tobacco (Nicotiana tabacum) leaves. Antisense down-regulation of ANS in M. truncatula resulted in reduced anthocyanin and PA levels, but had no impact on flavonol levels. Transgenic tobacco plants constitutively overexpressing MtLAR showed reduced anthocyanin content, but no catechin or increased levels of PAs were detected either in leaves or in flowers. Our results confirm previously ascribed in vivo functions for ANS and ANR. However, the apparent lack of catechin in M. truncatula PAs, the poor correlation between LAR expression and PA accumulation, and the lack of production of catechin monomers or oligomers in transgenic plants overexpressing MtLAR question the role of MtLAR in PA biosynthesis in Medicago.
Experimental strategies for microRNA target identification

MicroRNAs (miRNAs) are important regulators of eukaryotic gene expression in most biological processes. They act by guiding the RNAi-induced silencing complex (RISC) to partially complementary sequences in target mRNAs to suppress gene expression by a combination of translation inhibition and mRNA decay. The commonly accepted mechanism of miRNA targeting in animals involves an interaction between the 5′-end of the miRNA called the ‘seed region’ and the 3′ untranslated region (3′-UTR) of the mRNA. Many target prediction algorithms are based around such a model, though increasing evidence demonstrates that targeting can also be mediated through sites other than the 3′-UTR and that seed region base pairing is not always required. The power and validity of such in silico data can be therefore hindered by the simplified rules used to represent targeting interactions. Experimentation is essential to identify genuine miRNA targets, however many experimental modalities exist and their limitations need to be understood. This review summarizes and critiques the existing experimental techniques for miRNA target identification.
Neural correlates of visualizations of concrete and abstract words in preschool children: a developmental embodied approach

The neural correlates of visualization underlying word comprehension were examined in preschool children. On each trial, a concrete or abstract word was delivered binaurally (part 1: post-auditory visualization), followed by a four-picture array (a target plus three distractors; part 2: matching visualization). Children were to select the picture matching the word they heard in part 1. Event-related potentials (ERPs) locked to each stimulus presentation and task interval were averaged over sets of trials of increasing word abstractness. ERP time-course during both parts of the task showed that early activity (i.e., <300 ms) was predominant in response to concrete words, while activity in response to abstract words became evident only at intermediate (i.e., 300–699 ms) and late (i.e., 700–1000 ms) ERP intervals. Specifically, ERP topography showed that while early activity during post-auditory visualization was linked to left temporo-parietal areas for concrete words, early activity during matching visualization occurred mostly in occipito-parietal areas for concrete words, but more anteriorly in centro-parietal areas for abstract words. In intermediate ERPs, post-auditory visualization coincided with parieto-occipital and parieto-frontal activity in response to both concrete and abstract words, while in matching visualization a parieto-central activity was common to both types of words. In the late ERPs for both types of words, the post-auditory visualization involved right-hemispheric activity following a “post-anterior” pathway sequence: occipital, parietal, and temporal areas; conversely, matching visualization involved left-hemispheric activity following an “ant-posterior” pathway sequence: frontal, temporal, parietal, and occipital areas. These results suggest that, similarly, for concrete and abstract words, meaning in young children depends on variably complex visualization processes integrating visuo-auditory experiences and supramodal embodying representations.
Triangular systolic array with reduced latency for QR-decomposition of complex matrices

The novel CORDIC-based architecture of the triangular systolic array for QRD of large size complex matrices is presented. The proposed architecture relies on QRD using a three angle complex rotation approach that provides significant reduction of latency (systolic operation time) and makes the QRD in such a way that the upper triangular matrix R has only real diagonal elements
“It's my secret”: Barriers to paediatric HIV treatment in a poor rural South African setting

In South Africa, a third of children born are exposed to HIV, while fewer undergo an HIV confirmatory test. Anti-retroviral therapy (ART) coverage among children remains low-despite roll-out of the national ART programme in South Africa in 2004. This study sought to understand critical barriers to seeking HIV-related care for children in rural South Africa. Data presented in this article derive from community-based qualitative research in poor rural villages in north-east South Africa; this includes 21 in-depth interviews in 2008 among caregivers of children identified as HIV-positive in 2007 from a randomly selected community-based sample. Using NVIVO 8, data were coded and analysed, using a constant comparative method to identify themes and their repetitions and variations. Structural barriers leading to poor access to health care, and social and systems barriers, all influenced paediatric HIV treatment seeking. Of concern was the expressed need to maintain secrecy regarding a child's HIV status to avoid stigma and discrimination, and misconceptions regarding the course of HIV disease in children; this led to a delay in seeking appropriate care. These barriers need to be addressed, including through focused awareness campaigns, improved access to health care and interventions to address rural poverty and development at both household and community levels. In addition, training of health care professionals to improve their attitudes and practice may be necessary. However, this study only provides the perspective of the caregivers; further studies with health care providers are needed to gain a fuller picture for appropriate policy and practice guidance.
Query reformulation with constraints

Let Σ<inf>1</inf>, Σ<inf>2</inf> be two schemas, which may overlap, <i>C</i> be a set of constraints on the joint schema Σ<inf>1</inf> ∪ Σ<inf>2</inf>, and <i>q</i><inf>1</inf> be a Σ<inf>1</inf>-query. An <b>(equivalent) reformulation</b> of <i>q</i><inf>1</inf> in the presence of <i>C</i> is a Σ<inf>2</inf>-query, <i>q</i><inf>2</inf>, such that <i>q</i><inf>2</inf> gives the same answers as <i>q</i><inf>1</inf> on any Σ<inf>1</inf> ∪ Σ<inf>2</inf>-database instance that satisfies <i>C</i>. In general, there may exist multiple such reformulations and choosing among them may require, for example, a cost model.
7-Glutathione-pyrrole and 7-cysteine-pyrrole are potential carcinogenic metabolites of pyrrolizidine alkaloids

ABSTRACT Many pyrrolizidine alkaloids (PAs) are hepatotoxic, genotoxic, and carcinogenic phytochemicals. Metabolism of PAs in vivo generates four (±)-6,7-dihydro-7-hydroxy-1-hydroxymethyl-5H-pyrrolizine (DHP)-DNA adducts that have been proposed to be responsible for PA-induced liver tumor formation in rats. In this present study, we determined that the same set of DHP-DNA adducts was formed upon the incubation of 7-glutathione-DHP and 7-cysteine-DHP with cultured human hepatocarcinoma HepG2 cells. These results suggest that 7-glutathione-DHP and 7-cysteine-DHP are reactive metabolites of PAs that can bind to cellular DNA to form DHP-DNA adducts in HepG2 cells, and can potentially initiate liver tumor formation.
Effect of different non-chloride sodium sources on the performance of heat-stressed broiler chickens

1. One hundred and eighty 1-d-old broiler chicks were used to evaluate the effect upon broiler performance during severely hot summer months of three different sodium salts: sodium bicarbonate (NaHCO3), sodium carbonate (Na2CO3) and sodium sulphate (Na2SO4), in starter and finisher diets having an identical electrolyte balance (DEB) of 250 mEq/kg. 2. The non-chloride sodium salts were added to contribute the same amount of sodium and were substituted at the expense of builder's sand in the basal diets containing common salt (NaCl) as Na and Cl source. 3. Each diet was fed to three experimental units having 15 chicks each until 42 d of age. Severe heat-stress conditions, maintained in the rearing room, were indicated by high average weekly room temperature (minimum 29·3°C; maximum 38·0°C). 4. Diets containing sodium salts gave better body weight gain, feed intake and feed to gain ratio than the control diet. Sodium salts also enhanced water intake as well as water to feed intake ratio. This effect was more pronounced in broilers fed NaHCO3 supplement (with NaCl in the basal diets). 5. The increased water intake resulted in lower body temperature in heat-stressed birds fed NaHCO3 supplemented diet than in birds fed other sodium salts. A lower mortality rate was noted with NaHCO3 (15·15%), Na2CO3 (13·64%) and Na2SO4 (15·15%) supplements than with the control (33·33%) treatment. 6. Better carcase and parts yield were observed in sodium supplemented broilers. Sodium salts reduced the alkalotic pH and enhanced the blood sodium content, which ultimately improved the blood electrolyte balance and overall performance of heat-stressed broilers. 7. Supplementing broiler diets with sodium salts improved the live performance of heat-stressed broilers and better productive performance was noted with NaHCO3 than other sodium supplements.