Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of the polymerase chain reaction for diagnosis of chancroid

The published nucleotide sequences of the 16S rRNA gene of Haemophilus ducreyi were used to develop primer sets and probes for the diagnosis of chancroid by polymerase chain reaction (PCR) DNA amplification. One set of broad specificity primers yielded a 303-bp PCR product from all bacteria tested. Two 16-base probes internal to this sequence were species specific for H. ducreyi when tested with 12 species of the families Pasteurellaceae and Enterobacteriaceae. The two probes in combination with the broad specificity primers were 100% sensitive with 51 strains of H. ducreyi isolated from six continents over a 15-year period. The direct detection of H. ducreyi from 100 clinical specimens by PCR showed a sensitivity of 83 to 98% and a specificity of 51 to 67%, depending on the number of amplification cycles.
Selectivity of the Renal Collecting Duct Water Channel Aquaporin-3*

Aquaporin-3 (AQP3) is a water channel found in the basolateral cell membrane of principal cells of the renal collecting tubule as well as in other epithelia. To examine the selectivity of AQP3, the permeability to water (Pf), urea (Pur), and glycerol (Pgly) of Xenopus oocytes injected with cRNA encoding AQP3 was measured. Oocytes injected with cRNA encoding either human or rat aquaporin-1 (AQP1) were used as controls. Although both aquaporins permit water flow across the cell membrane, only AQP3 was permeable to glycerol and urea (Pgly > Pur). The uptake of glycerol into oocytes expressing AQP3 was linear up to 165 mM. For AQP3 the Arrhenius energy of activation for Pf was 3 kcal/mol, whereas for Pgly and Pur it was >12 kcal/mol. The sulfhydryl reagent p-chloromercuriphenylsulfonate (1 mM) abolished Pf of AQP3, whereas it did not affect Pgly. In addition, phloretin (0.1 mM) inhibited Pf of AQP3 by 35%, whereas it did not alter Pgly or Pur. We conclude that water does not share the same pathway with glycerol or urea in AQP3 and that this aquaporin, therefore, forms a water-selective channel.
Prion-Like Domains in Phagobiota

Prions are molecules characterized by self-propagation, which can undergo a conformational switch leading to the creation of new prions. Prion proteins have originally been associated with the development of mammalian pathologies; however, recently they have been shown to contribute to the environmental adaptation in a variety of prokaryotic and eukaryotic organisms. Bacteriophages are widespread and represent the important regulators of microbiota homeostasis and have been shown to be diverse across various bacterial families. Here, we examined whether bacteriophages contain prion-like proteins and whether these prion-like protein domains are involved in the regulation of homeostasis. We used a computational algorithm, prion-like amino acid composition, to detect prion-like domains in 370,617 publicly available bacteriophage protein sequences, which resulted in the identification of 5040 putative prions. We analyzed a set of these prion-like proteins, and observed regularities in their distribution across different phage families, associated with their interactions with the bacterial host cells. We found that prion-like domains could be found across all phages of various groups of bacteria and archaea. The results obtained in this study indicate that bacteriophage prion-like proteins are predominantly involved in the interactions between bacteriophages and bacterial cell, such as those associated with the attachment and penetration of bacteriophage in the cell, and the release of the phage progeny. These data allow the identification of phage prion-like proteins as novel regulators of the interactions between bacteriophages and bacterial cells.
The Dark Side of Online Participation: Exploring Non- and Negative Participation

In this contribution, we differentiate the meaning of online participation based on a qualitative study (focus groups, online communities) with 96 individuals from a broad range of social backgrounds in Germany. Our contribution is twofold: First and in line with other recent research, we posit and show that online participation and non-participation can be active or passive. Especially the forms of active non-participation and passive participation are noteworthy because they challenge existing notions of participation as a voluntary active act of engagement. Second, we argue that the "dark sides" or socially undesired forms of online participation need to be taken into account more strongly. Such a critical perspective can question the often enthusiastic and strongly positive twist prevalent in the discourse around online participation.
Assessment of farmer-oriented agricultural extension intervention in Iran

ABSTRACT Purpose: The main purpose of this study was to determine the characteristics of farmer-oriented policies as regards the Iranian agricultural extension system. Methodology: To fulfill this objective, a Delphi technique was utilized. The study used a series of three steps, engaging a panel of experts on farmer-oriented policies of agricultural extension system. Finding: The characteristics of farmer-oriented policies in agricultural extension system were classified into six categories including: need-based programs, proper interaction among stakeholders, decentralization and higher stakeholders’ participation, enabling stakeholders with emphasis on smallholder farmers, market-oriented programs and integrated policies. The findings indicated that ‘enabling farmers to solve their technical problems’ and ‘engaging farmers in planning, executing and evaluating of the programs’ had the highest percentage of agreement. Theoretical implication: From a theoretical point of view, the finding of this research has introduced six categories as characteristics of a farmer-oriented policy that could have practical implications for agricultural extension system in Iran. Also, this paper proposes a framework for future studies in the field of farmer-oriented policies in agricultural extension system. Practical implications: Recognizing the characteristics of farmer-oriented intervention of agricultural extension shows that targeted extension approaches are needed to pay attention to these characteristics in various stages of planning, delivering and evaluation of extension programs. Originality/value: This paper provides a comprehensive list of characteristics of farmer-oriented policies of agricultural extension that can be helpful for agricultural policy-makers in devising programs of extension services.
Posttraumatic syringomyelia: predisposing factors

Posttraumatic spinal cord cavitation (syrinx) and progressive myelopathy associated with a posttraumatic syrinx (PTS) have been recognized for many years. Predisposing factors for PTS have not been well defined. All symptomatic PTS patients ( n = 58) treated at the University of Toronto neurosurgical units over 30 years were analysed retrospectively to discover risk factors for the development of PTS. There were 46 males and 12 females (mean age 42.2 years); 28 patients had cervical (CSCI), and 30 had thoracic and lumbar spinal cord injuries (TLSCI). Neurological deficit was complete in 40 (69%) compared with 43% complete injuries in the concurrent spinal and injury (SCI) population in general ( p = 0.0003). Onset of PTS was earlier with: increasing age ( p < 0.02), cervical and thoracic levels of injury ( p < 0.007 and p < 0.02, respectively, compared with lumbar injuries), dislocated fractures ( p < 0.003) and spinal surgery ( p < 0.001) and, marginally, with complete SCI ( p = 0.06). Mean time to onset of PTS appears to have decreased in recent years ( p < 0.0001). PTS follows complete spinal cord injury (SCI) more often than incomplete and is frequently associated with arachnoiditis. Onset is earlier with increasing age, cervical and thoracic levels compared with lumbar, displaced fractures and spinal instrumentation without decompression. A group of SCI patients who are at greater risk of developing early PTS is thus identified, facilitating cost-effective follow-up.
The Characterization of Two New Clusters of Duplicated Genes Suggests a ‘Lego’ Organization of the Yeast Saccharomyces cerevisiae Chromosomes

The systematic sequencing of 42 485 bp of yeast chromosome VII (nucleotides 377948 to 420432) has revealed the presence of 27 putative open reading frames (ORFs) coding for proteins of at least 100 amino acids. The degree of redundancy observed is elevated since five of the 27 ORFs are duplications of a previously identified gene. These duplicated copies may be classified in two types of cluster organization. The first type includes genes sharing a significant level of identity in the amino acid sequences of their predicted protein product. They are recovered on two different chromosomes, transcribed in the same orientation and the distance between them is conserved. The second type of cluster is based on one gene unit tandemly repeated. This duplication is itself repeated elsewhere in the genome. The level of nucleic acid identity is high within the coding sequence and the non‐coding region between the two repeats. In addition, the basic gene unit is recovered many times in the genome and is a component of a multigene family of unknown function. These organizations in clusters of genes suggest a ‘Lego organization’ of the yeast chromosomes, as recently proposed for the genome of plants (Moore, 1995). The sequence is deposited in the Yeast Genome Databank under Accession Number from Z72562 to Z72586. © 1997 John Wiley & Sons, Ltd.
Effects of Nitrate Application on Amaranthus powellii Wats : II. Stomatal Response to Vapor Pressure Difference is Consistent with Optimization of Stomatal Conductance.

The hypothesis of optimal stomatal conductance predicts conductance should vary with changes of the vapor pressure difference between leaf and air (VPD) to keep the partial derivative of transpiration rate (E) with respect to assimilation rate (A) constant ( partial differentialE/ partial differentialA = lambda). Stomatal conductance of Amaranthus powellii Wats. decreased strongly with increasing VPD for leaves with high total leaf nitrogen concentrations; whereas, it decreased slightly with increasing VPD for leaves with low leaf nitrogen concentrations. The calculated value of partial differentialE/ partial differentialA was constant for leaves with high leaf nitrogen concentrations but was not constant for leaves with low leaf nitrogen concentrations. However, the predicted values of stomatal conductance, transpiration rate, and assimilation rate for a constant lambda = 220 moles H(2)O/mole CO(2) and the measured values fit the y = x line for all nitrate treatments. These data extend the experimental support for the optimal water use efficiency hypothesis for a C(4) plant grown under different nitrate concentrations.
Automatic Measurement of Renal Volume in Children Using 99mTc Dimercaptosuccinic Acid SPECT: Normal Ranges With Body Weight

Objective: The purpose of this study was to automate volume measurement of pediatric kidneys using Technetium-99m-dimercaptosuccinic acid (99mTc DMSA) SPECT. Assessment of renal size is essential in making an accurate clinical diagnosis and in evaluating normal and abnormal renal growth. Existing techniques for measuring renal length and volume are often observer-dependent and are limited by interobserver variability. Materials and Methods: An automated method using 99mTc DMSA SPECT was developed to measure renal length, volume, and 2D/3D split renal functions. An adaptive threshold was used for segmentation of renal images. To improve measurement accuracy of renal volumes, a boundary-weighted integration and a linear correction from phantom experiments were applied. Using the new automated software, we evaluated 620 normal kidneys in 310 patients aged 1 to 21 years. Results: In all, 99.4% of renal volume measurement was inter-/intraobserver reproducible without manual intervention. Correlations between renal size (volume and length) and growth parameters (age and body weight) were evaluated by nonlinear regression modeling. Body weight was found to be the best predictor of kidney volume and length (P < 0.0001). Normal ranges were established according to body weight. Conclusions: Automatic renal volume measurement with 99mTc DMSA SPECT demonstrates high observer reproducibility, and it is useful for achieving accurate assessment of renal growth using sequential measurements. The renal growth models generated by this study will aid physicians in evaluating and monitoring renal growth.
Pharmacokinetics of mirodenafil, a new erectogenic, and its metabolite, SK3541, in rats: involvement of CYP1A1/2, 2B1/2, 2D subfamily, and 3A1/2 for the metabolism of both mirodenafil and SK3541.

PURPOSE This study was performed to find which types of hepatic CYP isoforms are responsible for the metabolism of mirodenafil (a new erectogenic) and one of its metabolite, SK3541, using various hepatic CYP inducers and inhibitors in rats. METHODS Mirodenafil at a dose of 20 mg/kg was administered intravenously to control rats and rats pretreated with various CYP inducers and inhibitors. The disappearance of SK3541 was also measured in vitro hepatic microsomes of rats with and without CYP inducer and inhibitors. RESULTS Compared to controls, in rats pretreated with 3-methylcholanthrene, orphenadrine, and dexamethasone (main inducers of CYP1A1/2, 2B1/2, and 3A1/2, respectively), the non-renal clearances (CLNRs) of mirodenafil were significantly faster (by 39.4%, 59.3%, and 63.9%, respectively). However, compared to controls, in rats pretreated with quinine and troleandomycin (main inhibitors of CYP2D subfamily and 3A1/2, respectively), the CLNRs of mirodenafil were significantly slower (by 36.1% and 33.2%, respectively). In rat hepatic microsomes spiked with furafylline, quinine, and troleandomycin (main inhibitors of CYP1A2, 2D subfamily, and 3A1/2, respectively), the intrinsic clearances (CLints) for the disappearance of SK3541 were significantly slower (by 18.4%, 35.3%, and 51.5%, respectively) than controls. Also in rat hepatic microsomes pretreated with orphenadrine (a main inducer of CYP2B1/2), the CLint for the disappearance of SK3541 was significantly faster (by 55.5%) than controls. CONCLUSIONS The above data suggest that hepatic CYP1A1/2, 2B1/2, 2D subfamily, and 3A1/2 are involved in the metabolism of both mirodenafil and SK3541 in rats.
Physical Activity, Overweight, and Perceptions of Neighborhood Environments Among Portuguese Girls.

BACKGROUND The purpose of this study was 1) to compare physical activity levels according to body-mass index; 2) to determine which, if any, neighborhood perceived attributes were related to overweight. METHODS The sample comprised 610 girls age 14.7 ± 1.6 y. Girls were grouped into normal weight and overweight. Environmental variables and physical activity were assessed by questionnaire. RESULTS No significant differences were found in physical activity levels between normal weight and overweight girls. Logistic regression analysis revealed that girls who agreed that "there is so much traffic on the streets that it makes it unpleasant to walk in the neighborhood" were more likely to be overweight (OR = 1.78; 95% CI 1.10 to 2.89). CONCLUSION The study found no relationship between perceptions of the environment and overweight among Portuguese girls, except for perceptions of security for walking in the neighborhood.
EFFECT OF RANIBIZUMAB RETREATMENT FREQUENCY ON NEUROSENSORY RETINAL VOLUME IN NEOVASCULAR AMD

Purpose: To determine the characteristics of patients with neovascular age-related macular degeneration who show initial anatomic improvements on optical coherence tomography in response to treatment with ranibizumab, but who subsequently regress toward their anatomic baseline. Methods: Data from 50 consecutive patients, receiving ranibizumab therapy for neovascular age-related macular degeneration, were collected. Raw StratusOCT images were analyzed using custom software (“OCTOR”). Changes in volume of neurosensory retina at months 1, 3, and 6 were calculated. Baseline demographic and morphologic characteristics were compared. Results: Forty-two patients (84%) showed a reduction in total retinal volume 1 month after initial treatment with ranibizumab. Of the patients that initially showed a reduction, 16 (38%) maintained this reduction through month 6, whereas 26 patients (62%) demonstrated a subsequent increase in retinal volume. Patients who maintained a reduction in edema received 3.75 ± 1.18 injections of ranibizumab versus 2.96 ± 1.34 injections for patients who did not (P = 0.049). Regression of initial anatomic improvements was associated with worsening of visual acuity (r = 0.599, P = 0.002). Conclusion: Patients receiving fewer injections of ranibizumab appeared less likely to maintain anatomic improvements achieved following commencement of ranibizumab therapy; regression of these improvements was associated with deterioration in visual acuity.
Image super-resolution via weighted random forest

This paper proposes a novel learning-based image super-resolution via a weighted random forest model (SWRF). The proposed method uses the LR-HR training data to train a random forest model. The underlying idea of this approach is to use several decision trees to classify the training data based on a simple splitting threshold value at each class. A linear regression model is learnt to map the relationship between LR and HR patches. During the up-sampling process, to obtain a more robust super-resolved HR image, instead of averaging the linear regression models from different trees, a biased weighting vector is learnt to adaptively super-resolve the LR image. Furthermore, we improve this proposed image super-resolution method via a weighted random forest model with rotation (SWRF-f) to further improve the super-resolution quality. Sufficient experimental results prove that the proposed approach can achieve the state-of-the-art super-resolution performance with reduced computation time.
Corticofugal axons from adjacent ‘barrel’ columns of rat somatosensory cortex: cortical and thalamic terminal patterns

The cortical representations of the vibrissae of the rat form a matrix in which each whisker has its own area of cortex, called a ‘barrel’. The afferent pathways from the periphery travel first to the trigeminal nuclei and thence via the ventroposteromedial thalamus (VPM) to the cortical barrels have been described in detail. We have studied the output from barrels by filling adjacent areas of the primary somatosensory cortex (SI) with either Phaseolus vulgaris leucoagglutinin (PHA‐L) or biotinylated dextran amine (BDA) and demonstrating the course and terminations of the axons that arise within the barrel fields. The method not only dramatically illustrates the previously described corticothalamic pathway to VPM but also demonstrates a strict topography in the cortical afferents to the thalamic reticular nucleus (RT). Cells supplying the RT projection are found below the barrels in layer IV. Connections to the posterior thalamus, on the other hand, have no discernible topography and are derived from cortical areas surrounding the barrels. Thus the outputs of these ‘septal’ areas return to the region from which they receive thalamic input. The corticocortical connections are also visible in the same material. Contralateral cortical connections arise from the cells of the septa between barrels. The projections to secondary somatosensory area (SII) are mirror images of the barrel pattern in SI with rather more overlap but nonetheless a recognisable topography.
Infant growth restriction is associated with distinct patterns of DNA methylation in human placentas

The placenta acts not only as a conduit of nutrient and waste exchange between mother and developing fetus, but also functions as a regulator of the intrauterine environment. Recent work has identified changes in the expression of candidate genes, often through epigenetic alteration, which alter the placenta's function and impact fetal growth. In this study, we used the Illumina Infinium HumanMethylation27 BeadChip array to examine genome-wide DNA methylation patterns in 206 term human placentas. Semi-supervised recursively partitioned mixture modeling was implemented to identify specific patterns of placental DNA methylation that could differentially classify intrauterine growth restriction (IUGR) and small for gestational age (SGA) placentas from appropriate for gestational age (AGA) placentas, and these associations were validated in a masked testing series of samples. Our work demonstrates that patterns of DNA methylation in human placenta are reliably and significantly associated with infant growth and serve as a proof of principle that methylation status in the human term placenta can function as a marker for the intrauterine environment, and could potentially play a critical functional role in fetal development.
Characterization and quantification of porcine circulating endothelial cells

Endothelial damage is a critical step in the development of (xeno) transplantation‐related and cardiovascular pathology. In humans, the amount of circulating endothelial cells (CEC) correlates to disease intensity and functions as a valuable damage marker. While (xeno) transplantation and cardiovascular research is regularly performed in porcine models, the paucity of antibodies against porcine endothelium epitopes hinders the use of CEC as damage marker.
Hsp31 Is a Stress Response Chaperone That Intervenes in the Protein Misfolding Process*

Background: Hsp31 is a multifunctional cellular stress response protein. Results: Hsp31 is a stress-inducible chaperone that has substoichiometric activity on a wide spectrum of substrates, including prions and the non-physiological client, α-synuclein. Conclusion: Hsp31 protects cells from α-synuclein-mediated toxicity via chaperone activity and independently from enzymatic activity and autophagy. Significance: This is the first characterization of the early acting and wide ranging chaperone activity of Hsp31. The Saccharomyces cerevisiae heat shock protein Hsp31 is a stress-inducible homodimeric protein that is involved in diauxic shift reprogramming and has glyoxalase activity. We show that substoichiometric concentrations of Hsp31 can abrogate aggregation of a broad array of substrates in vitro. Hsp31 also modulates the aggregation of α-synuclein (αSyn), a target of the chaperone activity of human DJ-1, an Hsp31 homolog. We demonstrate that Hsp31 is able to suppress the in vitro fibrillization or aggregation of αSyn, citrate synthase and insulin. Chaperone activity was also observed in vivo because constitutive overexpression of Hsp31 reduced the incidence of αSyn cytoplasmic foci, and yeast cells were rescued from αSyn-generated proteotoxicity upon Hsp31 overexpression. Moreover, we showed that Hsp31 protein levels are increased by H2O2, in the diauxic phase of normal growth conditions, and in cells under αSyn-mediated proteotoxic stress. We show that Hsp31 chaperone activity and not the methylglyoxalase activity or the autophagy pathway drives the protective effects. We also demonstrate reduced aggregation of the Sup35 prion domain, PrD-Sup35, as visualized by fluorescent protein fusions. In addition, Hsp31 acts on its substrates prior to the formation of large aggregates because Hsp31 does not mutually localize with prion aggregates, and it prevents the formation of detectable in vitro αSyn fibrils. These studies establish that the protective role of Hsp31 against cellular stress is achieved by chaperone activity that intervenes early in the protein misfolding process and is effective on a wide spectrum of substrate proteins, including αSyn and prion proteins.