PeerJ Preprints: Respiratory Medicinehttps://peerj.com/preprints/index.atom?journal=peerj&subject=6700Respiratory Medicine articles published in PeerJ PreprintsVariant analysis of RNA sequences in severe equine asthmahttps://peerj.com/preprints/34912018-08-292018-08-29Laurence TessierOlivier CôtéDorothee Bienzle
Background. Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants or potential relevance to the pathogenesis of asthma. Methods. RNA-Seq data were generated from endobronchial biopsies collected from 6 asthmatic and 7 non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for sequence variant calling was performed with Picard tools and Genome Analysis Toolkit (GATK). Sequence variants were called and filtered using GATK and Ensembl Variant Effect Predictor (VEP) tools, and two RNA-Seq predicted sequence variants were investigated with both PCR and Sanger sequencing. Supplementary analysis of novel sequence variant selection with VEP was based on a score of <0.01 predicted with Sorting Intolerant From Tolerant (SIFT) software, missense nature, location within the protein coding sequence and presence in all asthmatic individuals. For select variants, effect on protein function was assessed with Polymorphism Phenotyping (PolyPhen) 2 and Screening for Non-Acceptable Polymorphism (SNAP) 2 software. Sequences were aligned and 3D protein structures predicted with Geneious software. Difference in allele frequency between the groups was assessed using a Pearson's Chi-squared test with Yates' continuity correction, and difference in genotype frequency was calculated using the Fisher's exact test for count data. Results. RNA-Seq variant calling and filtering correctly identified substitution variants in PACRG and RTTN. Sanger sequencing confirmed that the PACRG substitution was appropriately identified in all 26 samples while the RTTN substitution was identified correctly in 24 of 26 samples. These variants of uncertain significance had substitutions that were predicted to result in loss of function and to be non-neutral. Amino acid substitutions projected no change of hydrophobicity and isoelectric point in PACRG, and a change in both for RTTN. For PACRG, no difference in allele frequency between the two groups was detected but a higher proportion of asthmatic horses had the altered RTTN allele compared to non-asthmatic animals. Discussion. RNA-Seq was sensitive and specific for calling gene sequence variants in this disease model. Even moderate coverage (<10-20 cpm) yielded correct identification in 92% of samples, suggesting RNA-Seq may be suitable to detect sequence variants in low coverage samples. The impact of amino acid alterations in PACRG and RTTN proteins, and possible association of the sequence variants with asthma, is of uncertain significance, but their role in ciliary function may be of future interest.
Background. Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants or potential relevance to the pathogenesis of asthma. Methods. RNA-Seq data were generated from endobronchial biopsies collected from 6 asthmatic and 7 non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for sequence variant calling was performed with Picard tools and Genome Analysis Toolkit (GATK). Sequence variants were called and filtered using GATK and Ensembl Variant Effect Predictor (VEP) tools, and two RNA-Seq predicted sequence variants were investigated with both PCR and Sanger sequencing. Supplementary analysis of novel sequence variant selection with VEP was based on a score of <0.01 predicted with Sorting Intolerant From Tolerant (SIFT) software, missense nature, location within the protein coding sequence and presence in all asthmatic individuals. For select variants, effect on protein function was assessed with Polymorphism Phenotyping (PolyPhen) 2 and Screening for Non-Acceptable Polymorphism (SNAP) 2 software. Sequences were aligned and 3D protein structures predicted with Geneious software. Difference in allele frequency between the groups was assessed using a Pearson's Chi-squared test with Yates' continuity correction, and difference in genotype frequency was calculated using the Fisher's exact test for count data. Results. RNA-Seq variant calling and filtering correctly identified substitution variants in PACRG and RTTN. Sanger sequencing confirmed that the PACRG substitution was appropriately identified in all 26 samples while the RTTN substitution was identified correctly in 24 of 26 samples. These variants of uncertain significance had substitutions that were predicted to result in loss of function and to be non-neutral. Amino acid substitutions projected no change of hydrophobicity and isoelectric point in PACRG, and a change in both for RTTN. For PACRG, no difference in allele frequency between the two groups was detected but a higher proportion of asthmatic horses had the altered RTTN allele compared to non-asthmatic animals. Discussion. RNA-Seq was sensitive and specific for calling gene sequence variants in this disease model. Even moderate coverage (<10-20 cpm) yielded correct identification in 92% of samples, suggesting RNA-Seq may be suitable to detect sequence variants in low coverage samples. The impact of amino acid alterations in PACRG and RTTN proteins, and possible association of the sequence variants with asthma, is of uncertain significance, but their role in ciliary function may be of future interest.The laryngeal tie-forward procedure to alleviate aspiration of feed caused by hypoplasia of the soft palate of an adult marehttps://peerj.com/preprints/266382018-03-072018-03-07José R CastroJim Schumacher
Background
An adult mare, presented to the University of Tennessee’s Veterinary MedicalCenter because of chronic, persistent coughing and abnormal respiratory noise,was found, during endoscopic examination of its nasopharynx and larynx, to havehypoplasia of the caudal fourth of its soft palate and an aryepiglottic fold entrapment.The mare had developed chronic discharge of feed from the nares after the aryepiglotticfold entrapment was relieved with a laser, using endoscopic guidance.
Methods
The mare received a laryngeal tie forward procedure to ameliorate discharge of feedfrom the nares by decreasing the gap between the apex of the epiglottis and thesoft palate.
Results
The distance between the epiglottis and the soft palate appeared to have beenreduced during endoscopic examination of the nasopharynx, and the horse nolonger experienced discharge of feed from the nares or persistent coughing. Thehorse continued to produce abnormal respiratory noise but was able to be usedfor trail riding.
Discussion
The tie-forward procedure should be considered as a treatment to ameliorate signs of hypoplastic soft palate in horses, if the palatal defect is short.
BackgroundAn adult mare, presented to the University of Tennessee’s Veterinary MedicalCenter because of chronic, persistent coughing and abnormal respiratory noise,was found, during endoscopic examination of its nasopharynx and larynx, to havehypoplasia of the caudal fourth of its soft palate and an aryepiglottic fold entrapment.The mare had developed chronic discharge of feed from the nares after the aryepiglotticfold entrapment was relieved with a laser, using endoscopic guidance.MethodsThe mare received a laryngeal tie forward procedure to ameliorate discharge of feedfrom the nares by decreasing the gap between the apex of the epiglottis and thesoft palate.ResultsThe distance between the epiglottis and the soft palate appeared to have beenreduced during endoscopic examination of the nasopharynx, and the horse nolonger experienced discharge of feed from the nares or persistent coughing. Thehorse continued to produce abnormal respiratory noise but was able to be usedfor trail riding.DiscussionThe tie-forward procedure should be considered as a treatment to ameliorate signs of hypoplastic soft palate in horses, if the palatal defect is short.Drop-out from the tuberculosis contact investigation cascade in a routine public health setting in urban Uganda: A prospective, multi-center studyhttps://peerj.com/preprints/33132017-10-032017-10-03Mari Armstrong-HoughPatricia TurimumahoroAmanda MeyerEmmanuel OchomDiana BabiryeIrene AyakakaDavid MarkJoseph GgitaAdithya CattamanchiDavid DowdyFrank MugabeElizabeth FairJessica HabererAchilles KatambaJ. Lucian Davis
Setting Seven public tuberculosis (TB) units in Kampala, Uganda, where Uganda’s national TB program recently introduced household contact investigation, as recommended by 2012 guidelines from WHO.
Objective To apply a cascade analysis to implementation of household contact investigation in a programmatic setting. Design Prospective, multi-center observational study.
Methods We constructed a cascade for household contact investigation to describe the proportions of: 1) index patient households recruited; 2) index patient households visited; 3) contacts screened for TB; and 4) contacts completing evaluation for, and diagnosed with, active TB.
Results 338 (33%) of 1022 consecutive index TB patients were eligible for contact investigation. Lay health workers scheduled home visits for 207 (61%) index patients and completed 104 (50%). Among 287 eligible contacts, they screened 256 (89%) for symptoms or risk factors for TB. 131 (51%) had an indication for further TB evaluation. These included 59 (45%) with symptoms alone, 58 (44%) children <5, and 14 (11%) with HIV. Among 131 contacts found to be symptomatic or at risk, 26 (20%) contacts completed evaluation, including five (19%) diagnosed with and treated for active TB, for an overall yield of 1.7%. The cumulative conditional probability of completing the entire cascade was 5%.
Conclusion Major opportunities exist for improving the effectiveness and yield of TB contact investigation by increasing the proportion of index households completing screening visits by lay health workers and the proportion of at-risk contacts completing TB evaluation.
Setting Seven public tuberculosis (TB) units in Kampala, Uganda, where Uganda’s national TB program recently introduced household contact investigation, as recommended by 2012 guidelines from WHO.Objective To apply a cascade analysis to implementation of household contact investigation in a programmatic setting. Design Prospective, multi-center observational study.Methods We constructed a cascade for household contact investigation to describe the proportions of: 1) index patient households recruited; 2) index patient households visited; 3) contacts screened for TB; and 4) contacts completing evaluation for, and diagnosed with, active TB.Results 338 (33%) of 1022 consecutive index TB patients were eligible for contact investigation. Lay health workers scheduled home visits for 207 (61%) index patients and completed 104 (50%). Among 287 eligible contacts, they screened 256 (89%) for symptoms or risk factors for TB. 131 (51%) had an indication for further TB evaluation. These included 59 (45%) with symptoms alone, 58 (44%) children <5, and 14 (11%) with HIV. Among 131 contacts found to be symptomatic or at risk, 26 (20%) contacts completed evaluation, including five (19%) diagnosed with and treated for active TB, for an overall yield of 1.7%. The cumulative conditional probability of completing the entire cascade was 5%.Conclusion Major opportunities exist for improving the effectiveness and yield of TB contact investigation by increasing the proportion of index households completing screening visits by lay health workers and the proportion of at-risk contacts completing TB evaluation.Short-term effect of reduction in forced vital capacity after diving exposurehttps://peerj.com/preprints/30272017-08-112017-08-11Hua Cheng
To discuss whether there is relationship between short-term and long-time attenuation effects of ventilation caused by diving activity. The ventilation observed before and after hyperbaric exposure for 20min by case-control experiments. Participants of the experimental group (EG) stayed for 20min under 12-m underwater and the control group (CG) stayed in hyperbaric chamber under pressure of 2.2ATA. Immediate effects of pulmonary ventilation detected by the Spirometer and compared by paired T test to reveal the different caused by environmental pressure. The Vital Capacity (VC) rises while the Minute Ventilation (MV), Maximal Voluntary Ventilation (MVV) decreases after the exposure for 20min in both groups. The Forced Vital Capacity (FVC) is detected decreased significantly in EG (t=1.21, P =0.25) while it slightly increased in CG (t=-0.42, P =0.68).The ratio of Forced Expiratory Volume in one second to VC (FEV1.0/VC %) increase in EG (t=-0.73, P=0.48) while decrease in CG (t=0.42, P=0.17). The Ratio of FEV1.0 to FVC (FEV1.0 %) values increase obviously in EG (t=-1.48, P =0.16) and a bit in CG (t=-0.23, P =0.82). High pressure is the common factor in both groups that leads the changes in the same trend in VC, MV and MVV. Extra factors as immersion effect, loading of diving equipment and low temperature underwater, would encounter EG participants. Instant reduced effects of FVC under diving exposure in the study are quite consistent with the long-term cumulative effect of professional divers in previous research, which illustrated even small depth of short-range diving exercise have definite influences on ventilation.
To discuss whether there is relationship between short-term and long-time attenuation effects of ventilation caused by diving activity. The ventilation observed before and after hyperbaric exposure for 20min by case-control experiments. Participants of the experimental group (EG) stayed for 20min under 12-m underwater and the control group (CG) stayed in hyperbaric chamber under pressure of 2.2ATA. Immediate effects of pulmonary ventilation detected by the Spirometer and compared by paired T test to reveal the different caused by environmental pressure. The Vital Capacity (VC) rises while the Minute Ventilation (MV), Maximal Voluntary Ventilation (MVV) decreases after the exposure for 20min in both groups. The Forced Vital Capacity (FVC) is detected decreased significantly in EG (t=1.21, P =0.25) while it slightly increased in CG (t=-0.42, P =0.68).The ratio of Forced Expiratory Volume in one second to VC (FEV1.0/VC %) increase in EG (t=-0.73, P=0.48) while decrease in CG (t=0.42, P=0.17). The Ratio of FEV1.0 to FVC (FEV1.0 %) values increase obviously in EG (t=-1.48, P =0.16) and a bit in CG (t=-0.23, P =0.82). High pressure is the common factor in both groups that leads the changes in the same trend in VC, MV and MVV. Extra factors as immersion effect, loading of diving equipment and low temperature underwater, would encounter EG participants. Instant reduced effects of FVC under diving exposure in the study are quite consistent with the long-term cumulative effect of professional divers in previous research, which illustrated even small depth of short-range diving exercise have definite influences on ventilation.Why respiratory viruses or bacteria have the highest probability to be deposited in the respiratory tract in flu seasonshttps://peerj.com/preprints/22372017-08-092017-08-09Aleksandr N Ishmatov
Objective:
In this study the main aspects of influenza transmission via fine and ultrafine bioaerosols were considered. Here, we aimed to estimate the impact of the different environment conditions on the deposition rate of the infectious bioaerosols in the respiratory tract.
Background:
The latest researches show the infected people generate the fine and ultrafine infectious bioaerosols with submicron particles/droplets (size below 1 µm). The airborne transmission of these particles/droplets in the environment is effective. It is considered the deposition of submicron particles in the respiratory tract (RT) has very low probability. But most studies examined the aerosol deposition in RT under normal environmental conditions and did not paid attention to the affecting the different environmental factors.
Methods:
We review the problems of epidemiology of respiratory infections and aspects of airborne transmission/spread of infectious agents. We contrast these approaches with known data from next areas: inhalation toxicology, respiratory drug delivery and physics of heat and mass transfer in the airways.
Results:
Based on the conducted analysis, we propose the next main concepts:
1 Breathing cool air leads to the supersaturation of air in RT;
2 the air supersaturation leads to the intensive condensational growth(CG) of inhaled viruses or bacteria in RT;
3 CG leads to the intensive and dramatically growth of deposition rate of viruses or bacteria in RT.
We have shown:
a) Under normal conditions of inhaled air (T>20˚C; Relatively Humidity, RH=60%) there is no transition in supersaturated condition in RT and CG is insignificant and probability of virus deposition on epithelium of RT is low – no more than 20%.
b) Breathing cool/cold air of T<+15˚C and RH of [30..60]% leads to the supersaturation in the airways and it can dramatically increase the deposition rate of inhaled bioaerosols in RT(up to 96%).
c) With an increase in RH of inhaled air the supersaturation in RT occurs even at warm temperature of inhaled air (for inhaled air of T<20°C and RH>70% ; T<25°C and RH>90%). Which also indicates the deposition rate of bioaerosols in RT under these conditions is high.
Conclusion:
Under specific environmental conditions (when flu seasons) the processes of supersaturation in the RT can be observed. These results indicate the high probability of virus deposition on epithelium of RT and correspond to influenza and seasonal respiratory infections in temperate and tropical climates.
We believe the effect of supersaturation in the airways can be the key to understanding of ‘the age-old epidemiologic mystery of influenza seasonality in the different climatic conditions’.
Objective:In this study the main aspects of influenza transmission via fine and ultrafine bioaerosols were considered. Here, we aimed to estimate the impact of the different environment conditions on the deposition rate of the infectious bioaerosols in the respiratory tract.Background:The latest researches show the infected people generate the fine and ultrafine infectious bioaerosols with submicron particles/droplets (size below 1 µm). The airborne transmission of these particles/droplets in the environment is effective. It is considered the deposition of submicron particles in the respiratory tract (RT) has very low probability. But most studies examined the aerosol deposition in RT under normal environmental conditions and did not paid attention to the affecting the different environmental factors.Methods: We review the problems of epidemiology of respiratory infections and aspects of airborne transmission/spread of infectious agents. We contrast these approaches with known data from next areas: inhalation toxicology, respiratory drug delivery and physics of heat and mass transfer in the airways.Results:Based on the conducted analysis, we propose the next main concepts:1 Breathing cool air leads to the supersaturation of air in RT;2 the air supersaturation leads to the intensive condensational growth(CG) of inhaled viruses or bacteria in RT;3 CG leads to the intensive and dramatically growth of deposition rate of viruses or bacteria in RT.We have shown:a) Under normal conditions of inhaled air (T>20˚C; Relatively Humidity, RH=60%) there is no transition in supersaturated condition in RT and CG is insignificant and probability of virus deposition on epithelium of RT is low – no more than 20%.b) Breathing cool/cold air of T<+15˚C and RH of [30..60]% leads to the supersaturation in the airways and it can dramatically increase the deposition rate of inhaled bioaerosols in RT(up to 96%).c) With an increase in RH of inhaled air the supersaturation in RT occurs even at warm temperature of inhaled air (for inhaled air of T<20°C and RH>70% ; T<25°C and RH>90%). Which also indicates the deposition rate of bioaerosols in RT under these conditions is high.Conclusion: Under specific environmental conditions (when flu seasons) the processes of supersaturation in the RT can be observed. These results indicate the high probability of virus deposition on epithelium of RT and correspond to influenza and seasonal respiratory infections in temperate and tropical climates.We believe the effect of supersaturation in the airways can be the key to understanding of ‘the age-old epidemiologic mystery of influenza seasonality in the different climatic conditions’.On the connection between supersaturation in the upper airways and «humid-rainy» and «cold-dry» seasonal patterns of influenzahttps://peerj.com/preprints/28592017-08-092017-08-09Aleksandr N Ishmatov
We have originally shown for the first time the two different climatic patterns of seasonality of influenza and common colds have an only one common “link”. It is the effect of supersaturation and condensational growth in the upper airways which occurs under specific environmental conditions when flu seasons take place in the tropical/subtropical and temperate regions.
We have found that under climatic conditions which are peculiar to the seasonal patterns of influenza and common colds (“humid-rainy” and “cold-dry”) the effect of supersaturation and condensational growth may be additional factor/reason leading to the next:
- dramatic rise of deposition rate of infectious agents from inhaled air in the upper airways;
- additional acidification of epithelial lining fluid in the local areas of the respiratory tract, and, as a result, may lead to destructive impacts on host cells and weakening of the defense mechanisms of the airways;
- additional affecting on the critical local cooling and reducing (as a consequence) the antiviral immune response of the airway epithelial cells.
Thus, the effect of supersaturation and condensational growth in the upper airways can act as a common trigger for influenza, common colds and other respiratory infection in both mid-latitudes and in the tropics/subtropics.
We have originally shown for the first time the two different climatic patterns of seasonality of influenza and common colds have an only one common “link”. It is the effect of supersaturation and condensational growth in the upper airways which occurs under specific environmental conditions when flu seasons take place in the tropical/subtropical and temperate regions.We have found that under climatic conditions which are peculiar to the seasonal patterns of influenza and common colds (“humid-rainy” and “cold-dry”) the effect of supersaturation and condensational growth may be additional factor/reason leading to the next:- dramatic rise of deposition rate of infectious agents from inhaled air in the upper airways;- additional acidification of epithelial lining fluid in the local areas of the respiratory tract, and, as a result, may lead to destructive impacts on host cells and weakening of the defense mechanisms of the airways;- additional affecting on the critical local cooling and reducing (as a consequence) the antiviral immune response of the airway epithelial cells.Thus, the effect of supersaturation and condensational growth in the upper airways can act as a common trigger for influenza, common colds and other respiratory infection in both mid-latitudes and in the tropics/subtropics.From raw ion mobility measurements to disease classification: a comparison of analysis processeshttps://peerj.com/preprints/12942015-08-112015-08-11Salome HorschDominik KopczynskiJörg Ingo BaumbachJörg RahnenführerSven Rahmann
Ion mobility spectrometry (IMS) is a technology for the detection of volatile compounds in the air of exhaled breath that is increasingly used in medical applications. One major goal is to classify patients into disease groups, for example diseased versus healthy, from simple breath samples. Raw IMS measurements are data matrices in which peak regions representing the compounds have to be identified and quantified. A typical analysis process consists of pre-processing and peak detection in single experiments, peak clustering to obtain consensus peaks across several experiments, and classification of samples based on the resulting multivariate peak intensities. Recently several automated algorithms for peak detection and peak clustering have been introduced, in order to overcome the current need for human-based analysis that is slow, subjective and sometimes not reproducible. We present an unbiased comparison of a multitude of combinations of peak processing and multivariate classification algorithms on a disease dataset. The specific combination of the algorithms for the different analysis steps determines the classification accuracy, with the encouraging result that certain fully-automated combinations perform even better than current manual approaches.
Ion mobility spectrometry (IMS) is a technology for the detection of volatile compounds in the air of exhaled breath that is increasingly used in medical applications. One major goal is to classify patients into disease groups, for example diseased versus healthy, from simple breath samples. Raw IMS measurements are data matrices in which peak regions representing the compounds have to be identified and quantified. A typical analysis process consists of pre-processing and peak detection in single experiments, peak clustering to obtain consensus peaks across several experiments, and classification of samples based on the resulting multivariate peak intensities. Recently several automated algorithms for peak detection and peak clustering have been introduced, in order to overcome the current need for human-based analysis that is slow, subjective and sometimes not reproducible. We present an unbiased comparison of a multitude of combinations of peak processing and multivariate classification algorithms on a disease dataset. The specific combination of the algorithms for the different analysis steps determines the classification accuracy, with the encouraging result that certain fully-automated combinations perform even better than current manual approaches.Metabolic syndrome in hospitalized patients with chronic obstructive pulmonary diseasehttps://peerj.com/preprints/10222015-05-012015-05-01Evgeni MekovYanina SlavovaAdelina TsakovaMarianka GenovaDimitar KostadinovDelcho MinchevDora Marinova
The metabolic syndrome (MS) affects 21-53% of patients with chronic obstructive pulmonary disease (COPD) with a higher prevalence in the early stages of COPD, with results being highly variable between studies. MS may also correlate with disease characteristics. The aim of the study is to examine the prevalence of MS and its correlation with comorbidities and COPD characteristics in patients with COPD admitted for exacerbation. 152 patients with COPD admitted for exacerbation were studied for presence of MS. All of them were also assessed for vitamin D status and diabetes mellitus type 2 (DM). Data were gathered for smoking status and exacerbations during the last year. All patients completed CAT (COPD assessment test) and mMRC (Modified Medical Research Council Dyspnea scale) questionnaires and underwent spirometry. Duration of current hospital stay was recorded. 25% of patients have MS. 23,1% of the male and 29,5% of the female patients have MS (p>0.05). The prevalence of MS in this study is significantly lower when compared to a national representative study (44,6% in subjects over 45 years). 69,1% of all patients and 97,4% from MS patients have arterial hypertension. The presence of MS is associated with significantly worse cough and sleep (1st and 7th CAT questions; p=0.002 and p=0.001 respectively) and higher total CAT score (p=0.017). Average BMI is 27,31. None of the patients have MS and BMI <25. There is a correlation between the presence of MS and DM (p=0.008) and with the number of exacerbations in the last year (p=0.015). There is no correlation between the presence of MS and the pulmonary function. This study among hospitalized COPD patients finds comparable but relatively low prevalence of MS (25%) compared to previously published data (21-53%) and lower prevalence compared to general population (44,6%). MS may impact natural course and the number of exacerbations of COPD. Having in mind that MS is more common in the early stages and decreases with COPD progression, the COPD patients admitted for exacerbation may be considered as having advanced COPD.
The metabolic syndrome (MS) affects 21-53% of patients with chronic obstructive pulmonary disease (COPD) with a higher prevalence in the early stages of COPD, with results being highly variable between studies. MS may also correlate with disease characteristics. The aim of the study is to examine the prevalence of MS and its correlation with comorbidities and COPD characteristics in patients with COPD admitted for exacerbation. 152 patients with COPD admitted for exacerbation were studied for presence of MS. All of them were also assessed for vitamin D status and diabetes mellitus type 2 (DM). Data were gathered for smoking status and exacerbations during the last year. All patients completed CAT (COPD assessment test) and mMRC (Modified Medical Research Council Dyspnea scale) questionnaires and underwent spirometry. Duration of current hospital stay was recorded. 25% of patients have MS. 23,1% of the male and 29,5% of the female patients have MS (p>0.05). The prevalence of MS in this study is significantly lower when compared to a national representative study (44,6% in subjects over 45 years). 69,1% of all patients and 97,4% from MS patients have arterial hypertension. The presence of MS is associated with significantly worse cough and sleep (1st and 7th CAT questions; p=0.002 and p=0.001 respectively) and higher total CAT score (p=0.017). Average BMI is 27,31. None of the patients have MS and BMI <25. There is a correlation between the presence of MS and DM (p=0.008) and with the number of exacerbations in the last year (p=0.015). There is no correlation between the presence of MS and the pulmonary function. This study among hospitalized COPD patients finds comparable but relatively low prevalence of MS (25%) compared to previously published data (21-53%) and lower prevalence compared to general population (44,6%). MS may impact natural course and the number of exacerbations of COPD. Having in mind that MS is more common in the early stages and decreases with COPD progression, the COPD patients admitted for exacerbation may be considered as having advanced COPD.Diabetes mellitus type 2 in hospitalized patients with chronic obstructive pulmonary diseasehttps://peerj.com/preprints/9392015-03-312015-03-31Evgeni MekovYanina SlavovaMarianka GenovaAdelina TsakovaDimitar KostadinovDelcho MinchevDora Marinova
Diabetes mellitus (DM) affects 2-37% of patients with chronic obstructive pulmonary disease (COPD), with results being highly variable between studies. DM may also correlate with disease characteristics.The aim of this study was to examine the prevalence of DM and its correlation with comorbidities and COPD characteristics in patients with COPD admitted for exacerbation. 152 patients were studied for presence of DM. All of them were also assessed for vitamin D status and metabolic syndrome (MS). Data were gathered for smoking status and exacerbations during the last year. All patients completed CAT (COPD assessment test) and mMRC (Modified Medical Research Council Dyspnea scale) questionnaires and underwent spirometry. Duration of current hospital stay was recorded. 13.2% (20/152) of patients are taking medications for DM. Additional 21.7% (33/152) have newly discovered DM and 30.9% (47/152) have prediabetes. Only 34.2% of the studied patients do not have DM or prediabetes. 37% (40/108) of males have DM vs. 29,5% (13/44) of females (p=0.379). The prevalence of DM in this study is significantly higher when compared to an unselected Bulgarian population (12,8% in subjects over 45 years). 91% of patients with newly discovered diabetes had glycated hemoglobin (HbA1c)≥6,5% suggesting prolonged hyperglycemia. There is a correlation between the presence of DM and MS (p=0.008). The presence of DM is associated with more severe exacerbations (hospitalizations) during the previous year (p=0.003) and a longer hospital stay (p=0.006). DM is not associated with reduced quality of life and worse pulmonary function. The patients with COPD admitted for exacerbation are at great risk for impaired glucose metabolism which is associated with worse COPD characteristics. The majority of the patients in this study are unaware of having DM.
Diabetes mellitus (DM) affects 2-37% of patients with chronic obstructive pulmonary disease (COPD), with results being highly variable between studies. DM may also correlate with disease characteristics.The aim of this study was to examine the prevalence of DM and its correlation with comorbidities and COPD characteristics in patients with COPD admitted for exacerbation. 152 patients were studied for presence of DM. All of them were also assessed for vitamin D status and metabolic syndrome (MS). Data were gathered for smoking status and exacerbations during the last year. All patients completed CAT (COPD assessment test) and mMRC (Modified Medical Research Council Dyspnea scale) questionnaires and underwent spirometry. Duration of current hospital stay was recorded. 13.2% (20/152) of patients are taking medications for DM. Additional 21.7% (33/152) have newly discovered DM and 30.9% (47/152) have prediabetes. Only 34.2% of the studied patients do not have DM or prediabetes. 37% (40/108) of males have DM vs. 29,5% (13/44) of females (p=0.379). The prevalence of DM in this study is significantly higher when compared to an unselected Bulgarian population (12,8% in subjects over 45 years). 91% of patients with newly discovered diabetes had glycated hemoglobin (HbA1c)≥6,5% suggesting prolonged hyperglycemia. There is a correlation between the presence of DM and MS (p=0.008). The presence of DM is associated with more severe exacerbations (hospitalizations) during the previous year (p=0.003) and a longer hospital stay (p=0.006). DM is not associated with reduced quality of life and worse pulmonary function. The patients with COPD admitted for exacerbation are at great risk for impaired glucose metabolism which is associated with worse COPD characteristics. The majority of the patients in this study are unaware of having DM.Temporal profiling of the bacterial and fungal communities in ΔF508 adult cysticfibrosis sputumhttps://peerj.com/preprints/637v12014-11-262014-11-26Andrew NelsonAudrey PerryChristopher J StewartClare V LanyonJohn D PerryStephen J BourkeAnthony De SoyzaStephen P Cummings
Aims: The purpose of this study was to analyse the bacterial and fungal turnover in the lungs of cystic fibrosis patients who were ΔF508 homo- and hetero-zygotes. Further to this we wanted to identify the effects that Intravenous (IV) antibiotic perturbations had on the community and most importantly, whether exacerbations in these patients could be attributed to microbial species or communities. Methods: A total of 149 samples were collected from 18 adult CF patients attending a clinic at the RVI hospital, Newcastle upon Tyne. The samples were subject to DNA extraction followed by bacterial and fungal community DGGE analysis as well as qPCR analysis of the bacterial load. Results: We have found that bacterial and fungal communities present in the CF lung are not different when patients are suffering an exacerbation. Further to this, we have found that bacterial communities in the CF lung are disturbed by IV antibiotic administration and cause increased species turnover. We have shown that fungal taxa are capable of chronically colonising the CF lung. Conclusions: Our study adds further evidence to the assertion that changes in bacterial communities are not the cause of CF exacerbations. However, we were able to demonstrate that acquisition of new bacterial taxa was strongly associated with exacerbations in one patient. This study is the first to illustrate that fungi can persist in the CF lung but are not associated with clinical status.
Aims: The purpose of this study was to analyse the bacterial and fungal turnover in the lungs of cystic fibrosis patients who were ΔF508 homo- and hetero-zygotes. Further to this we wanted to identify the effects that Intravenous (IV) antibiotic perturbations had on the community and most importantly, whether exacerbations in these patients could be attributed to microbial species or communities. Methods: A total of 149 samples were collected from 18 adult CF patients attending a clinic at the RVI hospital, Newcastle upon Tyne. The samples were subject to DNA extraction followed by bacterial and fungal community DGGE analysis as well as qPCR analysis of the bacterial load. Results: We have found that bacterial and fungal communities present in the CF lung are not different when patients are suffering an exacerbation. Further to this, we have found that bacterial communities in the CF lung are disturbed by IV antibiotic administration and cause increased species turnover. We have shown that fungal taxa are capable of chronically colonising the CF lung. Conclusions: Our study adds further evidence to the assertion that changes in bacterial communities are not the cause of CF exacerbations. However, we were able to demonstrate that acquisition of new bacterial taxa was strongly associated with exacerbations in one patient. This study is the first to illustrate that fungi can persist in the CF lung but are not associated with clinical status.