Molecular identification and subtyping of Blastocystis sp. in hospital patients in Central China

Blastocystis is a common enteric protist that inhabits the gastrointestinal tract of approximately 1 billion people worldwide. In this study, a total of 1,070 patients from two hospitals in Zhengzhou, Central China were enrolled to know molecular characteristics of Blastocystis sp. The microorganism was identified and subtyped with a PCR amplification and sequencing of the small subunit ribosomal deoxyribonucleic acid (SSU-rDNA). The overall minimum prevalence of Blastocystis sp. in participants was 3.1% (33/1070). Although there were no significant differences on Blastocystis sp. infections among study sites, age groups, and gender, the higher infection was observed in the patients with gastrointestinal diseases (8.8%, 15/170). Sequence analysis of the 33 isolates revealed three known subtypes, such as ST1 (n = 7), ST3 (n = 23), and ST7 (n = 3). Among them, ST3 was the dominant subtype being detected in 23 isolates (69.7%), followed by ST1 (21.2%, 7/33) and ST7 (9.1%, 3/33). The phylogenetic analysis demonstrated that three subtypes (ST1, ST3 and ST7) were clustered with their reference sequences with good bootstrap support. The subtype determination of Blastocystis sp. isolates by the phylogenetic analysis was well supported by online platform. The present study provides the first molecular report of Blastocystis sp. infections in hospital patients in Central China.     

A framework for feature extraction from hospital medical data with applications in risk prediction

Background

Feature engineering is a time consuming component of predictive modeling. We propose a versatile platform to automatically extract features for risk prediction, based on a pre-defined and extensible entity schema. The extraction is independent of disease type or risk prediction task. We contrast auto-extracted features to baselines generated from the Elixhauser comorbidities.

Results

Hospital medical records was transformed to event sequences, to which filters were applied to extract feature sets capturing diversity in temporal scales and data types. The features were evaluated on a readmission prediction task, comparing with baseline feature sets generated from the Elixhauser comorbidities. The prediction model was through logistic regression with elastic net regularization. Predictions horizons of 1, 2, 3, 6, 12 months were considered for four diverse diseases: diabetes, COPD, mental disorders and pneumonia, with derivation and validation cohorts defined on non-overlapping data-collection periods.For unplanned readmissions, auto-extracted feature set using socio-demographic information and medical records, outperformed baselines derived from the socio-demographic information and Elixhauser comorbidities, over 20 settings (5 prediction horizons over 4 diseases). In particular over 30-day prediction, the AUCs are: COPD—baseline: 0.60 (95% CI: 0.57, 0.63), auto-extracted: 0.67 (0.64, 0.70); diabetes—baseline: 0.60 (0.58, 0.63), auto-extracted: 0.67 (0.64, 0.69); mental disorders—baseline: 0.57 (0.54, 0.60), auto-extracted: 0.69 (0.64,0.70); pneumonia—baseline: 0.61 (0.59, 0.63), auto-extracted: 0.70 (0.67, 0.72).

Conclusions

The advantages of auto-extracted standard features from complex medical records, in a disease and task agnostic manner were demonstrated. Auto-extracted features have good predictive power over multiple time horizons. Such feature sets have potential to form the foundation of complex automated analytic tasks.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0425-8) contains supplementary material, which is available to authorized users.     

Testing for dependence between failure time and visit compliance with interval-censored data

Interval-censored failure-time data arise when subjects miss prescheduled visits at which the failure is to be assessed. The resulting intervals in which the failure is known to have occurred are overlapping. Most approaches to the analysis of these data assume that the visit-compliance process is ignorable with respect to likelihood analysis of the failure-time distribution. While this assumption offers considerable simplification, it is not always plausible. Here we test for dependence between the failure- and visit-compliance processes, applicable to studies in which data collection continues after the occurrence of the failure. We do not make any of the assumptions made by previous authors about the joint distribution of the visit-compliance process, a covariate process, and the failure time. Instead, we consider conditional models of the true failure history given the current visit compliance at each visit time, allowing for correlation across visit times. Because failure status is not known at some visit times due to missed visits, only models of the observed failure history given current visit compliance are estimable. We describe how the parameters from these models can be used to test for a negative association and how bounds on unestimable parameters provided by the observed data are needed additionally to infer a positive association. We illustrate the method with data from an AIDS study and we investigate the power of the test through a simulation study.     

Concordance of cancer drug therapy information derived from routinely collected hospital admissions data and the Systemic Anti-Cancer Therapy (SACT) dataset,for older women diagnosed with early invasive breast cancer in England

BackgroundEvaluating uptake of oncological treatments, and subsequent outcomes, depends on data sources containing accurate and complete information about cancer drug therapy (CDT). This study aimed to evaluate the consistency of CDT information in the Hospital Episode Statistics Admitted Patient Care (HES-APC) and Systemic Anti-Cancer Therapy (SACT) datasets for early invasive breast cancer (EIBC).MethodsThe study included women (50 + years) diagnosed with EIBC in England from 2014 to 2019 who had surgery within six months of diagnosis. Concordance of CDT recorded in HES-APC (identified using OPCS codes) and SACT was evaluated at both patient-level and cycle-level. Factors associated with CDT use captured only in HES-APC were assessed using statistical models.ResultsThe cohort contained 129,326 women with EIBC. Overall concordance between SACT and HES-APC on CDT use was 94 %. Concordance increased over the study period (91–96 %), and there was wide variation across NHS trusts (lowest decile of trusts had concordance≤77 %; highest decile≥99 %). Among women receiving CDT, 9 % (n = 2781/31693) of use was not captured in SACT; incompleteness was worst (18 %=47/259) among women aged 80 + and those diagnosed in 2014 (21%=1121/5401). OPCS codes in HES-APC were good at identifying patient-level and cycle-level use of trastuzumab or FEC chemotherapy (fluorouracil, epirubicin, cyclophosphamide), with 89 % and 93 % concordance with SACT respectively (patient-level agreement). Among cycles of solely oral CDT recorded in SACT, only 24 % were captured in HES-APC, compared to 71 % for intravenous/subcutaneous CDT.ConclusionsCombining information in HES-APC and SACT provides a more complete picture of CDT treatment in women aged 50 + receiving surgery for EIBC than using either data source alone. HES-APC may have particular value in identifying CDT use among older women, those diagnosed less recently, and in NHS trusts with low SACT data returns.     

The International Atomic Energy Agency action plan on radiation protection of patients and staff in interventional procedures: Achieving change in practice

IntroductionThe International Atomic Energy Agency (IAEA) organized the 3rd international conference on radiation protection (RP) of patients in December 2017. This paper presents the conclusions on the interventional procedures (IP) session.Material and methodsThe IAEA conference was conducted as a series of plenary sessions followed by various thematic sessions. “Radiation protection of patients and staff in interventional procedures” session keynote speakers presented information on: 1) Risk management of skin injuries, 2) Occupational radiation risks and 3) RP for paediatric patients. Then, a summary of the session-related papers was presented by a rapporteur, followed by an open question-and-answer discussion.ResultsSixty-seven percent (67%) of papers came from Europe. Forty-four percent (44%) were patient studies, 44% were occupational and 12% were combined studies. Occupational studies were mostly on eye lens dosimetry. The rest were on scattered radiation measurements and dose tracking. The majority of patient studies related to patient exposure with only one study on paediatric patients. Automatic patient dose reporting is considered as a first step for dose optimization. Despite efforts, paediatric IP radiation dose data are still scarce. The keynote speakers outlined recent achievements but also challenges in the field. Forecasting technology, task-specific targeted education from educators familiar with the clinical situation, more accurate estimation of lens doses and improved identification of high-risk professional groups are some of the areas they focused on.ConclusionsManufacturers play an important role in making patients safer. Low dose technologies are still expensive and manufacturers should make these affordable in less resourced countries. Automatic patient dose reporting and real-time skin dose map are important for dose optimization. Clinical audit and better QA processes together with more studies on the impact of lens opacities in clinical practice and on paediatric patients are needed.     

A pilot study on the effect of advance care planning implementation on healthcare utilisation and satisfaction in patients with advanced heart failure

BackgroundPatients with advanced heart failure may benefit from palliative care, including advance care planning (ACP). ACP, which can include referral back to the general practitioner (GP), may prevent unbeneficial hospital admissions and interventional/surgical procedures that are not in accordance with the patient’s personal goals of care.AimTo implement ACP in patients with advanced heart failure and explore the effect of ACP on healthcare utilisation as well as the satisfaction of patients and cardiologists.MethodsIn this pilot study, we enrolled 30 patients with New York Heart Association class III/IV heart failure who had had at least one unplanned hospital admission in the previous year because of heart failure. A structured ACP conversation was held and documented by the treating physician. Primary outcome was the number of visits to the emergency department and/or admissions within 3 months after the ACP conversation. Secondary endpoints were the satisfaction of patients and cardiologists as established by using a five-point Likert scale.ResultsMedian age of the patients was 81 years (range 33–94). Twenty-seven ACP documents could be analysed (90%). Twenty-one patients (78%) did not want to be readmitted to the hospital and subsequently none of them were readmitted during follow-up. Twenty-two patients (81%) discontinued all hospital care. All patients who died during follow-up (n = 12, 40%) died at home. Most patients and cardiologists indicated that they would recommend the intervention to others (80% and 92% respectively).ConclusionACP, and subsequent out-of-hospital care by the GP, was shown to be applicable in the present study of patients with advanced heart failure and evident palliative care needs. Patients and cardiologists were satisfied with this intervention.     

Disturbance of circadian rhythms in analgosedated intensive care unit patients with and without craniocerebral injury

Melatonin, cortisol, heart rate, blood pressure, spontaneous motor activity, and body temperature follow stable circadian rhythms in healthy individuals. These circadian rhythms may be influenced or impaired by the loss of external zeitgebers during analgosedation, critical illness, continuous therapeutic intervention in the intensive care unit (ICU), and cerebral injury. This prospective, observational, clinical study examined 24 critically ill analgo-sedated patients, 13 patients following surgery, trauma, or acute respiratory distress (ICU), and 11 patients with acute severe brain injury following trauma or cerebral hemorrhage (CCI). Blood samples for the determination of melatonin and cortisol were obtained from each patient at 2 h intervals for 24 h beginning at 18:00 h on day 1 and ending 16:00 h on day 2. Blood pressure, heart rate, body temperature, and spontaneous motor activity were monitored continuously. Level of sedation was assessed using the Ramsey Sedation Scale. The severity of illness was assessed using the APACHE-II-score. The time series data were analyzed by rhythm analysis with the Chronos-Fit program, using partial Fourier series with up to six harmonics. The 24 h profiles of all parameters from both groups of patients were greatly disturbed/abolished compared to the well-known rhythmic 24 h patterns in healthy controls. These rhythm disturbances were more pronounced in patients with brain injury. The results of this study provide evidence for a pronounced disturbance of the physiological temporal organization in ICU patients. The relative contribution of analgosedation and/or brain injury, however, is a point of future investigation.     

Structural and functional analysis of perforin mutations in association with clinical data of familial hemophagocytic lymphohistiocytosis type 2 (FHL2) patients

Perforin plays a key role in the immune system via pore formation at the target cell membrane in the elimination of virus‐infected and transformed cells. A vast number of observed mutations in perforin impair this mechanism resulting in a rare but fatal disease, familial hemophagocytic lymphohistiocytosis type 2 (FHL2). Here we report a comprehensive in silico structural analysis of a collection of 76 missense perforin mutations based on a proposed pore model. In our model, perforin monomers oligomerize having cyclic symmetry in consistent with previously found experimental constraints yet having flexibility in the size of the pore and the number of monomers involved. Clusters of the mutations on the model map to three distinct functional regions of the perforin. Calculated stability (free energy) changes show that the mutations mainly destabilize the protein structure, interestingly however, A91V polymorphism, leads to a more stable one. Structural characteristics of mutations help explain the severe functional consequences on perforin deficient patients. Our study provides a structural approach to the mutation effects on the perforin oligomerization and impaired cytotoxic function in FHL2 patients.     

The interplay among psychopathology,personal resources,context‐related factors and real‐life functioning in schizophrenia: stability in relationships after 4 years and differences in network structure between recovered and non‐recovered patients

Improving real‐life functioning is the main goal of the most advanced integrated treatment programs in people with schizophrenia. The Italian Network for Research on Psychoses previously explored, by using network analysis, the interplay among illness‐related variables, personal resources, context‐related factors and real‐life functioning in a large sample of patients with schizophrenia. The same research network has now completed a 4‐year follow‐up of the original sample. In the present study, we used network analysis to test whether the pattern of relationships among all variables investigated at baseline was similar at follow‐up. In addition, we compared the network structure of patients who were classified as recovered at follow‐up versus those who did not recover. Six hundred eighteen subjects recruited at baseline could be assessed in the follow‐up study. The network structure did not change significantly from baseline to follow‐up, and the overall strength of the connections among variables increased slightly, but not significantly. Functional capacity and everyday life skills had a high betweenness and closeness in the network at follow‐up, as they had at baseline, while psychopathological variables remained more peripheral. The network structure and connectivity of non‐recovered patients were similar to those observed in the whole sample, but very different from those in recovered subjects, in which we found few connections only. These data strongly suggest that tightly coupled symptoms/dysfunctions tend to maintain each other's activation, contributing to poor outcome in schizophrenia. Early and integrated treatment plans, targeting variables with high centrality, might prevent the emergence of self‐reinforcing networks of symptoms and dysfunctions in people with schizophrenia.     

The relationship between 8-oxo-7,8-dihydro-2'-deoxyguanosine level and extent of cytosine methylation in leukocytes DNA of healthy subjects and in patients with colon adenomas and carcinomas

It has been known for a long time that DNA hypomethylation occurs in many human cancers and precancerous conditions. However, the mechanisms of hypomethylation are largely unknown. It is possible that endogenous 8-oxo-7,8-dihydroguanine (8-oxoGua) level may be linked to aberrant DNA methylation of adjacent cytosine and in this way influences carcinogenesis. Therefore, the aim of the present study was to assess a possible link between 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) background level and 5-methylcytosine content in DNA from human leukocytes of healthy subjects (n = 105) as well as in patients with colon adenomas (n = 39) and carcinomas (n = 50).

Our results demonstrated statistically significant negative correlation between background level of 8-oxodG and 5-methylcytosine content in DNA isolated from leukocytes of healthy donors (r = −0.3436, p = 0.0003). The mean content of 5-methylcytosine was significantly lower, while 8-oxodG level was significantly higher in leukocytes DNA of patients with colon adenomas and carcinomas in comparison with healthy subjects. The mean values for 5-methylcytosine were: 3.59 ± 0.173% (healthy subjects), 3.38 ± 0.128% (patients with adenomas), 3.40 ± 0.208% (colon cancer patients). The mean values of 8-oxodG in DNA were, respectively: 4.67 ± 1.276, 5.72 ± 1.787, 5.76 ± 1.884 8-oxodG per 10⁶ dG molecules. DNA from affected tissue (colon) suffered from significant, about 10% reduction in cytosine methylation in comparison with leukocytes of the paired subjects.

Our work provides the first in vivo evidence suggesting that increased levels of 8-oxodG in DNA may lead to carcinogenesis not only via mispair/mutagenic potential of the modified base but also through its ability to influence gene expression by affecting DNA methylation.