Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of a swallowing disturbance questionnaire for detecting dysphagia in patients with Parkinson's disease

Underreporting of swallowing disturbances by Parkinson's disease (PD) patients may lead to delay in diagnosis and treatment, alerting the physician to an existing dysphagia only after the first episode of aspiration pneumonia. We developed and validated a swallowing disturbance questionnaire (SDQ) for PD patients and compared its findings to an objective assessment. Fifty‐seven PD patients (mean age 69 ± 10 years) participated in this study. Each patient was queried about experiencing swallowing disturbances and asked to complete a self‐reported 15‐item “yes/no” questionnaire on swallowing disturbances (24 replied “no”). All study patients underwent a physical/clinical swallowing evaluation by a speech pathologist and an otolaryngologist. The 33 patients who complained of swallowing disturbances also underwent fiberoptic endoscopyic evaluation of swallowing (FEES). According to the ROC test, the “optimal” score (where the sensitivity and specificity curves cross) is 11 (sensitivity 80.5%, specificity 81.3%). Using the SDQ questionnaire substantially reduced Type I errors (specifically, an existing swallowing problem missed by the selected cutoff point). On the basis of the SDQ assessment alone, 12 of the 24 (50%) noncomplaining patients would have been referred to further evaluation that they otherwise would not have undergone. The SDQ emerged as a validated tool to detect early dysphagia in PD patients. © 2007 Movement Disorder Society
5α-Reductase Type 1 Deficiency or Inhibition Predisposes to Insulin Resistance, Hepatic Steatosis, and Liver Fibrosis in Rodents

5α-Reductase type 1 (5αR1) catalyses A-ring reduction of androgens and glucocorticoids in liver, potentially influencing hepatic manifestations of the metabolic syndrome. Male mice, homozygous for a disrupted 5αR1 allele (5αR1 knockout [KO] mice), were studied after metabolic (high-fat diet) and fibrotic (carbon tetrachloride [CCl4]) challenge. The effect of the 5α-reductase inhibitor finasteride on metabolism was investigated in male obese Zucker rats. While eating a high-fat diet, male 5αR1-KO mice demonstrated greater mean weight gain (21.6 ± 1.4 vs 16.2 ± 2.4 g), hyperinsulinemia (insulin area under the curve during glucose tolerance test 609 ± 103 vs. 313 ± 66 ng ⋅ mL−1 ⋅ min), and hepatic steatosis (liver triglycerides 136.1 ± 17.0 vs. 89.3 ± 12.1 μmol ⋅ g−1). mRNA transcript profiles in liver were consistent with decreased fatty acid β-oxidation and increased triglyceride storage. 5αR1-KO male mice were more susceptible to fibrosis after CCl4 administration (37% increase in collagen staining). The nonselective 5α-reductase inhibitor finasteride induced hyperinsulinemia and hepatic steatosis (10.6 ± 1.2 vs. 7.0 ± 1.0 μmol ⋅ g−1) in obese male Zucker rats, both intact and castrated. 5αR1 deficiency induces insulin resistance and hepatic steatosis, consistent with the intrahepatic accumulation of glucocorticoids, and predisposes to hepatic fibrosis. Hepatic steatosis is independent of androgens in rats. Variations in 5αR1 activity in obesity and with nonselective 5α-reductase inhibition in men with prostate disease may have important consequences for the onset and progression of metabolic liver disease.
Drug safety evaluation of roflumilast for the treatment of COPD: a meta-analysis

ABSTRACT Introduction: Roflumilast is the only phosphodiesterase 4 inhibitor approved for the treatment of COPD patients with chronic cough and sputum, and a history of exacerbations, but the compliance to treatment is reduced by poorly tolerated adverse events (AEs). Areas covered: The synthesis of clinical evidences indicates that roflumilast 500μg once-daily increased the risk of AEs, with no impact on the risk of serious AEs (SAEs), compared with placebo. Gastrointestinal AEs were common in patients treated with roflumilast, that may also induce headache, backpain and insomnia. Roflumilast protects against COPD related AEs. The frequency of very SAEs was rare but greater in patients treated with roflumilast than placebo, although factors other than the study drug were related with these SAEs. Expert opinion: The safety profile of roflumilast administered in combination with further drugs for the treatment of COPD should be investigated through specifically designed RCTs, and the post-marketing surveillance might help to characterize the real risk of very SAEs. Roflumilast may provide more benefit than harm in patients at high risk of severe exacerbations, and the therapy discontinuation may be reduced by a correct education of patients on the generally transient and mild-to-moderate nature of gastrointestinal AEs induced by this drug.
The Arabidopsis PEX12 Gene Is Required for Peroxisome Biogenesis and Is Essential for Development1[w]

Peroxisomes perform diverse and vital functions in eukaryotes, and abnormalities in peroxisomal function lead to severe developmental disorders in humans. Peroxisomes are also involved in a wide array of physiological and metabolic functions unique to plants, yet many aspects of this important organelle are poorly understood. In yeast and mammals, various steps in peroxisome biogenesis require the function of peroxin (PEX) proteins, among which PEX12 is a RING finger peroxisomal membrane protein involved in the import of matrix proteins. To investigate the role of PEX12 in plants, we identified a T-DNA knockout allele of PEX12 and generated partial loss-of-function pex12 mutants using RNA interference. We show that pex12 null mutants are developmentally arrested during early embryogenesis, and that the embryo-lethal phenotype can be rescued by overexpression of the PEX12-cyan fluorescent protein fusion protein, which targets to the peroxisome. Using virus-induced gene-silencing techniques, we demonstrate that peroxisomal number and fluorescence of the yellow fluorescent protein-peroxisome targeting signal type 1 protein are greatly reduced when PEX12 is silenced. RNA interference plants with partial reduction of the PEX12 transcript exhibit impaired peroxisome biogenesis and function, inhibition of plant growth, and reduced fertility. Our work provides evidence that the Arabidopsis (Arabidopsis thaliana) PEX12 protein is required for peroxisome biogenesis and plays an essential role throughout plant development.
CD4+CD25+ regulatory T cells in patients with Behçet's disease.

OBJECTIVE To investigate whether the CD4+CD25+ regulatory T cell (Treg) population, which plays important role in autoimmune diseases is related to the pathophysiology of Behçet's disease (BD). METHODS Forty-two patients with BD (20 patients in active disease) fulfilling the criteria of the International Study Group of BD. Twenty age-matched healthy controls were studied. We analyzed CD4+CD25+/high T cells and the mRNA expression of Foxp3, cytotoxic T lymphocyte-associated antigen 4 (CTLA-4), and transforming growth factor beta (TGF-beta) in BD. We have studied the ability of CD4+CD25+ (Treg) to regulate proliferation of CD4+CD25- T cells during active BD stage. RESULTS Active BD patients had significantly higher CD4+CD25+/high T cells, as compared with BD in the remission stage, and healthy controls. There was no significant differences in the CD4+ CD25+/high T cells expression between healthy controls and remission BD. In active BD, mRNA for Forkhead box p3 (Foxp3) and cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) were highly expressed when compared to remission BD and healthy controls. There was no differences in the mRNA expression for TGF-beta in active BD, remission BD and healthy controls. Functionally, CD4+CD25+/high T cells in active BD were impaired in their proliferative responses and could suppress the proliferation of their CD4+CD25- counterparts. CONCLUSION These data demonstrate that CD4+CD25+ Treg cells, with the potential to regulate suppression of effector T cells, were increased in the peripheral circulation of active BD patients. The role of CD4+CD25+/high T cells in the regulatory process of the inflammation in active BD, could be taken in account.
Does an expressed sequence tag (EST) library of Salsola iberica (tumbleweed) help to understand plant responses to environmental stresses?

Weeds play an important role in agriculture and molecular techniques are useful to help understand traits that contribute to weediness and weeds’ interactions with the environment. A total of 377 expressed sequence tags (ESTs) from a modest library were arranged into 227 unique fragments and 61 contigs, which consisted of two or more ESTs. From blastx results, we mapped and annotated unigenes using the gene ontology vocabulary according to biological process, cellular component and molecular function. These were then compared to a reference set of Arabidopsis thaliana sequences for statistically significant over- or underrepresented genes. The sequences were also compared against multiple protein databases for similarity of functional domains. Overall, the S. iberica sequences showed high similarity to response to stress, which included salt-induced proteins, betaine aldehydehyde dehydrogenase and calcium binding proteins. Only a modest number of transcripts were sequenced; however, the results presented here demonstrate the metabolic versatility of S. iberica in sub-optimal conditions that are likely to contribute to its cosmopolitan distribution. Here we propose that an EST library of an economically important weed species could be used to understand the weed’s interactions with the environment.
Investigation on the bioactivity of culturable endophytic and epiphytic bacteria associated with ethnomedicinal plants.

INTRODUCTION The growing need for the bioactive compounds of ethnomedicinal plants for the treatment of diseases has resulted in exploitation of medicinal plants. The present investigation aimed to study the diversity of endophytic and epiphytic bacteria associated with ethnomedicinal plants and to explore their potential as source of bioactive compounds. METHODOLOGY Characterization of culturable endophytic and epiphytic bacteria associated with 11 ethnomedicinal plants and their potential as natural antioxidants was assessed through free radical scavenging activity, total phenolics, total flavonoids, metal ion chelation, and antagonistic activity. Genetic screening to assess the potential of endophytes and epiphytes to synthesize bioactive compounds was achieved by screening for the presence of the non-ribosomal peptide synthetase (NRPS) gene. RESULT The frequently isolated endophytic bacterium recovered was Bacillus sp. Antioxidative property of the bacterial extracts revealed endophytes with potent antioxidant activity and better antagonistic activity as compared to epiphytes. Genetic screening revealed the presence of the NRPS gene in seven plant-associated bacteria, indicating the production of natural products. CONCLUSIONS The study indicated the extracts of bacterial endophytes associated with ethnomedicinal plants as good sources of natural products with potential application in oxidative stress. The isolates could be used as new bioactive agents.
Computed Critiquing Integrated into Daily Clinical Practice Affects Physicians’ Behavior

Summary Objective: We developed AsthmaCritic, a non-inquisitive critiquing system integrated with the general practitioners’ electronic medical records. The system is based on the guidelines for asthma and chronic obstructive pulmonary disease (COPD) as issued by the Dutch College of General Practitioners. This paper assesses the effect of AsthmaCritic on monitoring and treatment of asthma and COPD by Dutch general practitioners in daily practice. Methods: A randomized clinical trial in 32 practices (40 Dutch general practitioners) using electronic patient records. An intervention group was given the use of AsthmaCritic, a control group continued working in the usual manner. Both groups had the disposal of the asthma and COPD guidelines routinely distributed by the Dutch College of General Practitioners. We measured the average number of contacts, FEV1 (forced ex-piratory volume), and peak-flow measurements per asthma/COPD patient per practice; and, the average number of antihistamine, cromoglycate, deptropine, and oral bronchodilator prescriptions per asthma/COPD patient per practice. Results: The number of contacts increased in the age group of 12-39 years. The number of FEV1, peak-flow measurements, and the ratio of coded measurements increased, whereas the number of cromoglycate prescriptions decreased in the age group of 12-39 years. Conclusions: Our study shows that the guideline-based critiquing system AsthmaCritic changed the manner in which the physicians monitored their patients and, to a lesser extent, their treatment behavior. In addition, the physicians changed their data-recording habits.
Cargo Selectivity of the ERGIC‐53/MCFD2 Transport Receptor Complex

Exit of soluble secretory proteins from the endoplasmic reticulum (ER) can occur by receptor‐mediated export as exemplified by blood coagulation factors V and VIII. Their efficient secretion requires the membrane lectin ER Golgi intermediate compartment protein‐53 (ERGIC‐53) and its soluble luminal interaction partner multiple coagulation factor deficiency protein 2 (MCFD2), which form a cargo receptor complex in the early secretory pathway. ERGIC‐53 also interacts with the two lysosomal glycoproteins cathepsin Z and cathepsin C. Here, we tested the subunit interdependence and cargo selectivity of ERGIC‐53 and MCFD2 by short interference RNA‐based knockdown. In the absence of ERGIC‐53, MCFD2 was secreted, whereas knocking down MCFD2 had no effect on the localization of ERGIC‐53. Cargo binding properties of the ERGIC‐53/MCFD2 complex were analyzed in vivo using yellow fluorescent protein fragment complementation. We found that MCFD2 is dispensable for the binding of cathepsin Z and cathepsin C to ERGIC‐53. The results indicate that ERGIC‐53 can bind cargo glycoproteins in an MCFD2‐independent fashion and suggest that MCFD2 is a recruitment factor for blood coagulation factors V and VIII.
Viability and Isolation of Marine Bacteria by Dilution Culture: Theory, Procedures, and Initial Results

Dilution culture, a method for growing the typical small bacteria from natural aquatic assemblages, has been developed. Each of 11 experimental trials of the technique was successful. Populations are measured, diluted to a small and known number of cells, inoculated into unamended sterilized seawater, and examined three times for the presence of 104 or more cells per ml over a 9-week interval. Mean viability for assemblage members is obtained from the frequency of growth, and many of the cultures produced are pure. Statistical formulations for determining viability and the frequency of pure culture production are derived. Formulations for associated errors are derived as well. Computer simulations of experiments agreed with computed values within the expected error, which verified the formulations. These led to strategies for optimizing viability determinations and pure culture production. Viabilities were usually between 2 and 60% and decreased with >5 mg of amino acids per liter as carbon. In view of difficulties in growing marine oligobacteria, these high values are noteworthy. Significant differences in population characteristics during growth, observed by high-resolution flow cytometry, suggested substantial population diversity. Growth of total populations as well as of cytometry-resolved subpopulations sometimes were truncated at levels of near 104 cells per ml, showing that viable cells could escape detection. Viability is therefore defined as the ability to grow to that population; true viabilities could be even higher. Doubling times, based on whole populations as well as individual subpopulations, were in the 1-day to 1-week range. Data were examined for changes in viability with dilution suggesting cell-cell interactions, but none could be confirmed. The frequency of pure culture production can be adjusted by inoculum size if the viability is known. These apparently pure cultures produced retained the size and apparent DNA-content characteristic of the bulk of the organisms in the parent seawater. Three cultures are now available, two of which have been carried for 3 years. The method is thus seen as a useful step for improving our understanding of typical aquatic organisms.
Experimental comparison of single-pixel imaging algorithms

Single-pixel imaging (SPI) is a novel technique that captures 2D images using a photodiode, instead of conventional 2D array sensors. SPI has high signal-to-noise ratio, wide spectral range, low cost, and robustness to light scattering. Various algorithms have been proposed for SPI reconstruction, including linear correlation methods, the alternating projection (AP) method, and compressive sensing (CS) based methods. However, there has been no comprehensive review discussing respective advantages, which is important for SPI's further applications and development. In this paper, we review and compare these algorithms in a unified reconstruction framework. We also propose two other SPI algorithms, including a conjugate gradient descent (CGD) based method and a Poisson maximum-likelihood-based method. Both simulations and experiments validate the following conclusions: to obtain comparable reconstruction accuracy, the CS-based total variation (TV) regularization method requires the fewest measurements and consumes the least running time for small-scale reconstruction, the CGD and AP methods run fastest in large-scale cases, and the TV and AP methods are the most robust to measurement noise. In a word, there are trade-offs in capture efficiency, computational complexity, and robustness to noise among different SPI algorithms. We have released our source code for non-commercial use.
Polyphase sequences with good correlation properties

Design of sequences with good auto and crosscorrelation properties is one of the main tasks in several applications, including multi-user radar, sonar, and communications. In this paper we describe a new construction of polyphase sequences with optimal correlation properties. The construction includes, as special cases, a family of finite chirps and two previously proposed families of communications sequences. The main tool used in the construction is the finite Zak transform. The construction suggests several further generalizations that can be obtained by operating exclusively on subgroups of the permutation group.
Coherence Among Climate Signals, Precipitation, and Groundwater

Climate signals may affect groundwater level at different time scales in different geographical regions, and those patterns or time scales can be estimated using coherence analysis. This study shows that the synthesis effort required to search for patterns at the physical geography scale is possible, and this approach should be applicable in other regions of the world. The relations between climate signals, Southern Oscillation Index, Pacific Decadal Oscillation, North Atlantic Oscillation, North Pacific Pattern (SOI, PDO, NAO, and NP), precipitation, and groundwater level in three geographical areas of Wisconsin are examined using a three‐tiered coherence analysis. In the high frequency band (<4−1 cycles/year), there is a significant coherence between four climate signals and groundwater level in all three areas. In the low frequency band (>8−1 to ≤23−1 cycles/year), we found significant coherence between the SOI and NP signals and groundwater level in the forested area, characterized by shallow wells constructed in sand and gravel aquifers. In the high frequency band, there is significant coherence between the four climate signals and precipitation in all three areas. In the low frequency band, the four climate signals have effect on precipitation in the agricultural area, and SOI and NP have effect on precipitation in the forested and driftless areas. Precipitation affects groundwater level in all three areas, and in high, low and intermediate frequency bands. In the agricultural area, deeper aquifers and a more complex hydrostratigraphy and land use dilute the effect of precipitation on groundwater level for interdecadal frequencies.
The good governance indicators of the millennium challenge account

This paper assesses the validity of the perception-based governance indicators used by the US Millennium Challenge Account (MCA) for aid allocation decisions. By conducting Explanatory and Confirmatory Factor Analysis of data from 1996 to 2009, we find that although the MCA purports to measure seven distinct dimensions of governance, only two discrete underlying dimensions, the ‘participatory dimension of governance’ and the ‘overall quality of governance,’ can be identified. Our results also show that some of the doubts that have been raised concerning the validity of perception-based governance indicators are less warranted when the indicators are applied exclusively to developing countries.
Species-specific DNA probes for the identification of African trypanosomes in tsetse flies

SUMMARY We have obtained 5 specific DNA probes for African trypanosomes of the subgenera Trypanozoon and Nannomonas. Each probe consists of one repeat unit of the major repetitive DNA (satellite DNA) of each species or intra-specific group. One probe hybridized with all members of subgenus Trypanozoon (except T. equiperdum which was not tested). In subgenus Nannomonas, one probe recognized T. simiae, but 3 probes were needed to identify all stocks of T. congolense available. Each of the 3 latter probes recognized trypanosomes from one of the 3 major groups of T. congolense previously defined by isoenzyme characterization, i.e. savannah, forest and Kenya coast types. As few as 100 trypanosomes could be unequivocally identified by dot blot hybridization and individual trypanosomes could be identified by in situ hybridization. We show how this simple methodology can be used in the field for the identification of immature and mature trypanosome infections in tsetse.
Conformational alterations in the ermC transcript in vivo during induction.

ermC is an inducible antibiotic resistance gene from Staphylococcus aureus, one of several whose expression is regulated at the level of mRNA secondary structure. During induction of ermC, the inhibition of a ribosome active in translation of a short leader peptide by low levels of antibiotic belonging to the macrolide‐lincosamide‐streptogramin b family is believed to cause a rearrangement in mRNA secondary structure. The resultant conformational isomerization unmasks the methylase ribosome binding site and initiator Met codon, causing increased translation of the ermC transcript. Expression of ermC can also be demonstrated in Bacillus subtilis carrying plasmid pE194. To probe the ermC transcript in vivo during induction, ermC was transferred to B. subtilis by transformation and the resultant transformants were treated with dimethyl sulfate which reacts with N‐1 of adenine and N‐3 of cytosine residues in a manner that is sensitive to secondary structure. The bases modified in vivo were detected by primer extension with reverse transcriptase using total cellular RNA as template and a complementary ermC‐specific oligonucleotide as primer. Physical evidence was obtained for the secondary structural rearrangements predicted by the ermC regulatory model. Additionally, physical evidence was obtained demonstrating that during induction, the stalled ribosome protects codons 9 and 10 of the leader peptide from modification by dimethyl sulfate, in agreement with genetic data obtained previously that identified the integrity of codons 5‐9 as critical for induction of ermC by erythromycin.