Miracle-dz/UniFAR-FTUs huggingface dataset:
Tag jumps illuminated – reducing sequence‐to‐sample misidentifications in metabarcoding studies

Metabarcoding of environmental samples on second‐generation sequencing platforms has rapidly become a valuable tool for ecological studies. A fundamental assumption of this approach is the reliance on being able to track tagged amplicons back to the samples from which they originated. In this study, we address the problem of sequences in metabarcoding sequencing outputs with false combinations of used tags (tag jumps). Unless these sequences can be identified and excluded from downstream analyses, tag jumps creating sequences with false, but already used tag combinations, can cause incorrect assignment of sequences to samples and artificially inflate diversity. In this study, we document and investigate tag jumping in metabarcoding studies on Illumina sequencing platforms by amplifying mixed‐template extracts obtained from bat droppings and leech gut contents with tagged generic arthropod and mammal primers, respectively. We found that an average of 2.6% and 2.1% of sequences had tag combinations, which could be explained by tag jumping in the leech and bat diet study, respectively. We suggest that tag jumping can happen during blunt‐ending of pools of tagged amplicons during library build and as a consequence of chimera formation during bulk amplification of tagged amplicons during library index PCR. We argue that tag jumping and contamination between libraries represents a considerable challenge for Illumina‐based metabarcoding studies, and suggest measures to avoid false assignment of tag jumping‐derived sequences to samples.
Pulmonary response to inhaled antigen: neuroimmune interactions promote the recruitment of dendritic cells to the lung and the cellular immune response to inhaled antigen.

Dendritic cells (DCs) play a critical role in capturing and presenting inhaled antigens to T lymphocytes. We report that pulmonary DCs in the Lewis rat are normally located in the lung in immediate proximity to nerve fibers that contain immunoreactive substance P (SP). Functionally, pulmonary DCs bound 125I-SP and displayed increased motility in vitro in response to graded concentrations of SP. However, SP had no effect on the accessory cell activities of DCs. To examine the role of neural influences on the pulmonary immune response to inhaled antigen, Lewis rats were pretreated with capsaicin (CAP), which damages small nerves and depletes neuropeptide stores, and then challenged intratracheally (i.t.) with hen egg lysozyme (HEL). The number and antigen-presenting cell activities of pulmonary DCs in the CAP-treated rats were comparable to those of controls up to day 14. T lymphocytes harvested from the regional lymph nodes draining the lung were effectively sensitized to HEL in both groups. However, when CAP-treated rats sensitized to HEL i.t. at day 0 were rechallenged with HEL i.t. at day 14, the lungs showed decreased numbers of OX-6+ DCs and diminished pulmonary lymphoid infiltrates compared with controls. We suggest that CAP interferes with a neural-mediated response that contributes to the accumulation of inflammatory cells during the efferent limb of the pulmonary-cell-mediated immune response in vivo.
Measles vaccination in HIV-infected children: systematic review and meta-analysis of safety and immunogenicity.

BACKGROUND Measles control may be more challenging in regions with a high prevalence of HIV infection. HIV-infected children are likely to derive particular benefit from measles vaccines because of an increased risk of severe illness. However, HIV infection can impair vaccine effectiveness and may increase the risk of serious adverse events after receipt of live vaccines. We conducted a systematic review to assess the safety and immunogenicity of measles vaccine in HIV-infected children. METHODS The authors searched 8 databases through 12 February 2009 and reference lists. Study selection and data extraction were conducted in duplicate. Meta-analysis was conducted when appropriate. RESULTS Thirty-nine studies published from 1987 through 2008 were included. In 19 studies with information about measles vaccine safety, more than half reported no serious adverse events. Among HIV-infected children, 59% (95% confidence intervals [CI], 46-71%) were seropositive after receiving standard-titer measles vaccine at 6 months (1 study), comparable to the proportion of seropositive HIV-infected children vaccinated at 9 (8 studies) and 12 months (10 studies). Among HIV-exposed but uninfected and HIV-unexposed children, the proportion of seropositive children increased with increasing age at vaccination. Fewer HIV-infected children were protected after vaccination at 12 months than HIV-exposed but uninfected children (relative risk, 0.61; 95% CI, .50-.73). CONCLUSIONS Measles vaccines appear to be safe in HIV-infected children, but the evidence is limited. When the burden of measles is high, measles vaccination at 6 months of age is likely to benefit children of HIV-infected women, regardless of the child's HIV infection status.
Credit usage, payment behavior, and the accuracy of consumer credit files

Through intensive interviews, examination of credit reports, and rescoring of corrected credit files, the researchers consider household characteristics, major life events, financial resources, and payment habits as they study the integrity of credit-bureau data, vulnerability to error, and results of disputes filed with the major credit bureaus. Credit usage and management are found to vary widely within demographic groups. Vulnerability to error and outcomes of disputes depend primarily on the credit record itself. Consumers with moderate credit scores are more likely than those with very high or low scores to see significant improvement in their records when errors are corrected.
Molecular dynamics study of a calmodulin‐like protein with an IQ peptide: Spontaneous refolding of the protein around the peptide

The Calmodulin (CaM) is a small (16.7 kDa), highly acidic protein that is crucial to all eukaryotes by serving as a prototypical calcium sensor. In the present study, we investigated, through molecular dynamics simulations, the dynamics of a complex between the Mlc1p protein, which is a CaM‐like protein, and the IQ4 peptide. This protein‐peptide interaction is of high importance because IQ motifs are widely distributed among different kinds of CaM‐binding proteins. The Mlc1p‐IQ4 complex, which had been resolved by crystallography to 2.1 Å, confers to a Ca+2‐independent stable structure. During the simulations, the complex undergoes a complicated modulation process, which involves bending of the angles between the α‐helices of the protein, breaking of the α‐helical structure of the IQ4 peptide into two sections, and formation of new contact points between the protein and the peptide. The dynamics of the process consist of fast sub picosecond events and much slower ones that take a few nanoseconds to completion. Our study expands the information embedded in the crystal structure of the Mlc1p‐IQ4 complex by describing its dynamic behavior as it evolves from the crystal structure to a form stable in solution. The article shows that careful application of molecular dynamics simulations can be used for extending the structural information presented by the crystal structure, thereby revealing the dynamic configuration of the protein in its physiological environment. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Improvement of the functions of osteoblasts seeded on modified poly(D,L-lactic acid) with poly(aspartic acid).

One of the challenges in the field of tissue engineering is the development of biomaterial/cell interactions. For the purposes of the present study, two molecular weights of poly(aspartic acid) (PASP) were used to modify poly(D,L-lactic acid) (PDLLA) films in order to enhance their cell affinity. The properties of the PDLLA-modified surfaces and the controls were investigated by water contact angle measurement and electron spectroscopy for chemical analysis (ESCA). These data reflect the change in the biocompatibility of modified PDLLA surfaces. Then rat osteoblasts were seeded onto these modified surfaces and on controls to examine their effects on cell adhesion and proliferation. Cell morphologies on these surfaces were studied by scanning electron microscopy (SEM), and cell viability was evaluated with a MTT assay. In addition, differentiated cell function was assessed by measuring alkaline phosphatase (ALP) activity. The results suggest that PASP-modified surfaces may enhance the interactions between osteoblasts and PDLLA films.
Efficacy of 1,3‐diacylglycerol as a fat emulsifier in low‐density diet for broilers

&NA; An experiment was conducted to study the effects of dietary supplementation of 1,3‐diacylglycerol (DAG) as an emulsifier in a low‐density diet on growth performance, nutrient digestibility, blood characteristics, and meat quality in broilers. A total of 480 1‐day‐old male 308 Ross broiler chicks were randomly allocated into 1 of the following 5 treatments: Control, fed a basal diet (CON), basal diet minus 100 kcal ME diet (LE), T1 (LE + 0.075% 1,3‐DAG), T2 (LE + 0.10% 1,3‐DAG), and T3 (LE + 0.15% 1,3‐DAG). The supplementation of low energy diet to broilers reduced (P < 0.05) feed intake compared to CON diet during wk 1 of the experiment. The supplementation of LE diet with 0.075, 0.10, and 0.15% 1,3‐DAG linearly increased (P = 0.09) body weight gain (BWG) and decreased (P = 0.08) feed intake (FI) during wk 1. During wk 2 to 3 and overall (0 to 5 wk), there was linear increase (P < 0.05) in BWG and decrease in feed conversion ratio (FCR) in LE diet supplemented with graded levels of emulsifier. The LE diet reduced (P < 0.05) dry matter (DM) and energy digestibility (P = 0.07) compared with CON diet. Supplementing energy‐reduced diet with different levels of 1,3‐DAG linearly increased (P < 0.05) DM, and energy digestibility, but no significant differences were observed in blood profiles, meat quality (except drip loss) of broilers. In conclusion, DAG positively affected growth performances and nutrient digestibility in broilers. However, meat quality and serum profiles were unaffected in broilers fed an energy‐reduced diet supplemented with DAG.
Parental attitudes and postoperative problems related to paediatric day stay tonsillectomy.

AIM To assess the difficulties parents have caring for a child at home after day stay tonsillectomy. METHOD Parents of fifty two children who had day stay tonsillectomy or adenotonsillectomy were questioned by telephone the following morning and 10 to 14 days following surgery about difficulties they had experienced following discharge from the unit. RESULTS The following morning six parents (12%) found the pain difficult to manage with paracetamol and in nine children (17%) the fluid intake was poor. The patient's general practitioner was consulted for advice by fifteen parents (30%) during the postoperative period. Psychological problems were experienced by four children (8%). The majority of parents had few problems and felt comfortable caring for the child at home following surgery. CONCLUSIONS While most parents were happy caring for the child at home some parents had difficulties particularly with pain relief and ensuring adequate fluid intake. Communication links and support for these parents need to be improved. Surgical and anaesthetic techniques to reduce postoperative discomfort also need to be explored.
An adaptive differential codebook using M-PSK constellations for slowly varying channels

We propose an adaptive scheme of a differential codebook for temporally correlated channels. The codeword entries of the proposed codebook are selected among the set of M-PSK constellations and the values of M proposed in this paper are 8, 16, or 32. Firstly, we analyze mathematically how the optimal spherical cap radius of the proposed codebook is tracked. Then, we explain how to implement the proposed differential equal-gain codebook practically. Among the candidate differential codebooks designed for various temporal correlation coefficients, the proper codebook can be chosen (or switched) according to the temporal correlation coefficients of wireless channels. We assume that the correlation coefficients of the channels are known to the receiver and the properly (or optimally) chosen differential codebook can show the best system throughput performance. Monte-Carlo simulations demonstrate that the achievable throughput performance employing the proposed codebook is always superior to those of the differential codebooks employing M-PSK constellations and non-adaptive differential codebooks with the same amount of feedback information.
Observation of inverted cubic phase in hydrated dioleoylphosphatidylethanolamine membranes.

We report the observation of an inverted cubic phase in aqueous dispersions of 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) by small-angle X-ray diffraction. DOPE is a paradigm in the study of nonlamellar phases in biological systems: it exhibits a well-known phase transition from the lamellar (L alpha) to the inverted hexagonal phase (HII) as the temperature is raised. The transition is observed to occur rapidly when a DOPE dispersion is heated from 2 degrees C, where the L alpha phase is stable, to 15 degrees C, where the HII phase is stable. We report on the induction of a crystallographically well-defined cubic lattice that is slowly formed when the lipid dispersion is rapidly cycled between -5 and 15 degrees C hundreds of times. Once formed, the cubic lattice is stable at 4 degrees C for several weeks and exhibits the same remarkable metastability that characterizes other cubic phases in lipid-water systems. X-ray diffraction indicates that the cubic lattice is most consistent with either the Pn3m or Pn3 space group. Tests of lipid purity after induction of the cubic indicate the lipid is at least 98% pure. The cubic lattice can be destroyed and the system reset by cycling the specimen several times between -30 and 2 degrees C. The kinetics of the formation of the cubic are dependent on the thermal history of the sample, overall water concentration, and the extreme temperatures of the cycle. (ABSTRACT TRUNCATED AT 250 WORDS)
Depression in patients with Parkinson's disease

Parkinson's disease (PD) is a disabling neurodegenerative condition commonly complicated by the existence of comorbid depression. The prevalence rates of depression in this patient group have been reported to be as high as 40%. Currently, depression in PD is undertreated; there have been few controlled clinical trials of antidepressants in this patient group. Patients with PD are usually elderly and often administered a range of medication, therefore the choice of antidepressant must be undertaken with care. Tricyclic antidepressants (TCAs) have been studied in patients with PD and comorbid depression; however, the risk of anticholinergic side‐effects means that their use is largely avoided. Selective serotonin reuptake inhibitors have comparable efficacy to the TCAs and a better tolerability profile in patients with depression; they are rapidly being considered as first‐line therapy for PD patients with depression. Clinical studies in this patient group are warranted. This article reviews the characteristics of comorbid depression in patients with PD and discusses the treatment options available. Copyright © 1999 John Wiley & Sons, Ltd.
Fuzzy-associative-memory-based knowledge construction with an application to a human-machine interface

A fuzzy knowledge construction method is proposed for application to human-machine interfaces. This paper considers a human movement estimation system to be one of the interfaces. This estimation system transforms human physical movements into qualitative linguistic labels. For example, the degrees of magnitude and speed of the physical movement are represented by qualitative words. It is difficult to construct the transformation knowledge because the relation between the movements and the labels is fuzzy. This paper proposes a method of constructing the knowledge. This proposed method uses a fuzzy associative memory organizing units system and is applied to estimating human sports movements. Experimental results show that the proposed method is suitable for application to human-machine interfaces.
The Combination of Acoustic Rhinometry, Rhinoresistometry and Flow Simulation in Noses before and after Turbinate Surgery: A Model Study

Background: Especially to young examiners, the interpretation of rhinometric findings seems to be difficult. In order to understand rhinometric assessments precisely, knowledge of airflow behavior in the nose is necessary. We therefore investigated the influence of nasal concha surgery on acoustic rhinometry and rhinoresistometry in a model. Method: Six nose models were examined with acoustic rhinometry and rhinoresistometry, each of these models with its lateral wall altered to represent various conditions after nasal concha surgery. Besides, all models were rinsed with water and the flow was visualized for observation. Results and Conclusions: The normal nose presented an even flow distribution over the entire nasal cavity. After nasal concha resection, though, an unfavorable flow course and a strong increase in turbulence were seen. Additionally, flow resistance decreased considerably. In the model with general lateral wall hyperplasia, reduction of the inferior and even of the middle nasal concha showed good functional results. The model revealed a good correlation between the result of flow observation and findings in acoustic rhinometry and rhinoresistometry. Both methods complement one another in their diagnostic outcome.
The Paradox of Citizenship in American Politics: Ideals and Reality

In the concept of the aesthetic formation of knowledge and its as soon as possible and success-oriented application, insights and profits without the reference to the arguments developed around 1900. The main investigation also includes the period between the entry into force and the presentation in its current version. Their function as part of the literary portrayal and narrative technique.
Comparison of a rebound and an applanation tonometer for measuring intraocular pressure in normal rabbits.

OBJECTIVE To compare intraocular pressure (IOP) measurements made on healthy adult rabbits without the effect of tranquilizers using the new applanation tonometer, Tono-Pen Avia(®), and the rebound tonometer Tonovet(®). METHODS Intraocular pressure was measured throughout the day (6:00, 9:00, 12:00, 15:00, and 18:00 h) in 38 adult New Zealand White rabbits (76 eyes). The animals were 20 males and 18 females, with a mean weight of 3.5 kg and an average age of 6 months. A complete ocular exam (including Schirmer tear test, fluorescein staining, slit-lamp biomicroscopy, and direct ophthalmoscopy) was performed on all animals at the beginning of the trial. Rebound tonometry was performed, and after 10 min, anesthetic drops were instilled and applanation tonometry was carried out. IOP values obtained using the two techniques were analyzed statistically. RESULTS The mean IOP was 9.51 ± 2.62 mmHg with Tonovet(®), and 15.44 ± 2.16 mmHg with the Tono-Pen Avia(®). Significant differences between measurements with the two tonometers were observed (P < 0.001). The linear regression equation describing the relationship between the two tonometers was y = 0.4923x + 10.754 (y = Tonovet(®) and x = Tono-Pen Avia(®)). High IOPs were recorded in the early measurements (6:00), but the average IOPs from both devices were statistically similar throughout the day (P = 0.086). The correlation coefficient was r(2) = 0.357. No significant difference in IOP regarding gender was observed. CONCLUSION The Tono-Pen Avia(®) recorded higher levels of IOP compared with the Tonovet(®). Early in the day, the IOP of rabbits was higher than later in the day, regardless of the tonometer used.
A Thrombomodulin Gene Polymorphism (C1418T) Is Associated with Early Outcomes in Patients Undergoing Coronary Artery Bypass Graft Surgery with a Conventional Cardiopulmonary Bypass during Hospitalization

Background: Thrombomodulin (TM) is a type of cell membrane-bound anticoagulant protein cofactor in the thrombin-mediated activation of protein C. Previous evidence has shown an association between TM polymorphisms and systemic inflammation. Conventional cardiopulmonary bypass (CPB), beating-heart CPB, and off-pump techniques have been widely used in cardiac surgery. However, these techniques may also cause systemic inflammatory responses in the patients. Whether TM polymorphisms are associated with systemic inflammation after cardiac surgery is still unclear. Methods: We analyzed the TM gene C1418T polymorphisms in 347 patients who underwent coronary artery bridge graft (CABG) surgery using allele-specific primers in a PCR assay. The clinical data during the hospital stay were collected and tested for correlations with the TM gene C1418T polymorphisms. Results: We separated the patients into two groups based on their TM C1418T genotype (CC genotype group and CT/TT genotype group). The days spent in an intensive care unit (ICU) and the incidence of fever in the ICU were significantly lower in the beating-heart CPB and off-pump groups than in the conventional CPB group. Additionally, the TM gene C1418T polymorphisms did not affect the early outcomes in patients in the beating-heart CPB and off-pump groups. Interestingly, in the conventional CPB group, patients with the CC genotype had a lower rate of fever, shorter duration of fever, and delay of ICU when compared with the CT/TT genotype. Conclusion: Surgeons may use a patient’s TM gene C1418T polymorphism to predict the strength of systemic inflammation and speculate on early outcomes during hospitalization before conventional CPB is performed.
Toxicological evaluation of aqueous extract of Aloe ferox Mill. in loperamide-induced constipated rats

Aloe ferox Mill. is a widely used medicinal plant in South Africa for the treatment of many ailments including constipation. The present study evaluated the toxicological effect of aqueous leaf extract of the herb at 50, 100 and 200 mg/kg body weight for 7 days on the haematological parameters as well as liver and kidney function indices in loperamide—induced constipated rats. The extract did not cause any significant (p > 0.05) effect on the kidney and liver—body weight ratio as well as the kidney function indices including serum levels of creatinine, uric acid, urea, calcium and potassium ions at all the dosages investigated. Whereas the serum levels of total protein, albumin, bilirubin and gamma glutamyl trasferase (GGT) were not affected, the elevated activities of alkaline phosphatase (ALP), alanine transaminase (ALT) and aspartate transaminase (AST) in the untreated constipated animals were normalized following treatment with extract. The data obtained with respect to the haematological analysis indicated that the extracts had no significant (p > 0.05) effect on the haematological parameters with the exception of lymphocyte count which was increased in the untreated constipated rats. This was however attenuated after administering the herb. The available evidence in this study suggests that A. ferox may be safe as an oral remedy for constipation. Generally, the effect of the extract compared favourably well with senokot, a recommended drug for the treatment of constipation.