Disease category-specific annotation of variants using an ensemble learning framework.

Understanding the impact of non-coding sequence variants on complex diseases is an essential problem. We present a novel ensemble learning framework-CASAVA, to predict genomic loci in terms of disease category-specific risk. Using disease-associated variants identified by GWAS as training data, and diverse sequencing-based genomics and epigenomics profiles as features, CASAVA provides risk prediction of 24 major categories of diseases throughout the human genome. Our studies showed that CASAVA scores at a genomic locus provide a reasonable prediction of the disease-specific and disease category-specific risk prediction for non-coding variants located within the locus. Taking MHC2TA and immune system diseases as an example, we demonstrate the potential of CASAVA in revealing variant-disease associations. A website (http://zhanglabtools.org/CASAVA) has been built to facilitate easily access to CASAVA scores.

Delineation of the bacterial composition in exogenous endophthalmitis using 16S rDNA sequencing.

PURPOSE: To determine the bacterial spectrum of exogenous endophthalmitis of different origins, namely, posttraumatic, postcataract surgery, filtering bleb-associated, and intravitreal treatment-related endophthalmitis, using the 16S rDNA sequencing method. METHODS: Aqueous humor or vitreous humor samples were collected from 24 endophthalmitis patients. Traditional cultivation and 16S rDNA sequencing were conducted with these samples. Three senile cataract controls and one intraocular irrigating solution were used as sequencing control. RESULTS: Eleven of the 24 samples (45.8%) obtained positive bacterial cultivation, and each sample positive for only one species. The 11 culture-positive species could all be identified in their corresponding sequencing results, but only four strains being the top one pathogen in the sequencing. A total of 567 species were isolated using 16S rDNA sequencing, with the top five species being Pseudomonas sp., Staphylococcus epidermidis, Staphylococcus sp., Streptococcus sp., and Enterococcus faecalis. The dominant bacterial strains varied among the different endophthalmitis categories but with no significant difference in the overall bacterial spectrum. Bacterial atlas containing Pseudomonas, Streptococcus, Staphylococcus, Actinomycetales_unclassified, Thermus, and Janibacter was shared by the four categories. Aqueous humor bacterial profile showed a higher overlap with contaminating bacteria from the environment. CONCLUSIONS: 16S rDNA sequencing is more efficient for endophthalmitis pathogen screening than the traditional cultivation method in terms of positive detection rate and the number of bacteria identified. But the risk of environmental contamination exists when using 16S rDNA sequencing method for endophthalmitis diagnosis. Different categories of endophthalmitis displayed diversified bacterial composition.

Investigation of the EHV-1 Genotype (N752, D752, and H752) in Swabs Collected From Equids With Respiratory and Neurological Disease and Abortion From the United States (2019-2022).

Contemporary data on equine herpesvirus-1 (EHV-1) genotype (non-neuropathogenic or N752, neuropathogenic or D752 and new variant or H752) in clinically diseased equids is important in order to determine the frequency of these genotypes and their association with disease expression. A total of 297 EHV-1 qPCR-positive swabs collected from 2019 to 2022 from horses with respiratory disease (EHV-1), neurological disease (equine herpesvirus-1 myeloencephalopathy [EHM]) and abortion were tested for the three different EHV-1 genotypes (N752, D752 and H752) using qPCR allelic discrimination assays. All submissions originated from the United States and included 257 EHV-1 cases, 35 EHM cases and 5 cases of abortion. EHV-1 qPCR-positive cases were predominantly seen during winter and spring. N752 was the predominant genotype detected in EHV-1 cases (87.5%), EHM cases (74.3%) and abortions (80%). D752 was detected less frequently in EHV-1 cases (9.3%) and EHM cases (25.7%), while H752 was only detected in EHV-1 cases (3.1%). While the N752 genotype has remained the predominant genotype affecting horses with respiratory disease and abortion, it has also become a leading genotype in cases of EHM, when compared to historical data. The new H752 genotype, first reported in the United States in 2021, has remained confined to a cluster of geographically and temporally related outbreaks and the data showed no emerging spread of H752 since it was first reported. While the monitoring of EHV-1 genotypes is important from a diagnostic and epidemiological standpoint, it may also help establish medical interventions and preventive protocols to reduce the risk of severe complications associated with EHV-1 infection.

Association of ABO blood group with respiratory disease hospitalization and severe outcomes: a retrospective cohort study in blood donors.

OBJECTIVES: Environmental, socioeconomic, and genetic factors all are associated with respiratory diseases. We aimed to investigate the association between the ABO blood group and the susceptibility to respiratory diseases. METHODS: We constructed a retrospective cohort study of blood donors in Shaanxi, China between January 1, 2012, and December 31, 2018, to investigate the impacts of the ABO blood group on the risk of hospitalization due to respiratory diseases. RESULTS: Of 1,686,263 enrolled participants (680,788 females), 26,597 were admitted to the hospital for respiratory diseases. Compared with blood group O, blood groups A, B, and AB all demonstrated a higher risk for diseases of the upper respiratory tract (International Classification of Diseases, Tenth Revision: J30-J39) (ARR (Adjusted relative risk) 1.139, 95% confidence interval [1.106-1.225]; 1.095 [1.019-1.177]; 1.178 [1.067-1.30], respectively). Conversely, blood group A was found to have a lower risk (0.86 [0.747-0.991]) for influenza (J09-J11) and blood group B had a lower risk for pneumonia (J12-J18) (0.911 [0.851-0.976]) than blood group O. The duration of hospitalization was significantly different across the blood groups in J09-J11 and J30-J39 (P <0.05). CONCLUSION: The blood group appears to be a prognostic factor in differentiating the occurrence of specific respiratory diseases and duration.

Temporal patterns of hospital readmissions according to disease category for patients after elective colorectal surgery.

RATIONALE: The aim of this study was to identify temporal readmission patterns according to baseline disease categories to provide opportunities for targeted interventions. METHODS: Retrospective analysis of consecutive adult (≥18 years) patients who underwent elective colorectal resections (2011-2017) at Mayo Clinic Rochester, MN. A prospective administrative database including patient demographics, procedure characteristics, discharge information and specifics on 30-day readmissions (to index facility) including timing and reasons was utilized. The ICD-9 codes were regrouped into the main pathologies Cancer, Crohn's disease (CD)/chronic ulcerative colitis (CUC), and diverticular disease. RESULTS: In total, 521 (7.2%) out of 7245 patients undergoing inpatient colorectal surgery were readmitted. In all increments of time from discharge (0-2 days: 31.3% of all readmissions, 3-7 days: 32.4% of all readmissions, 8-14 days: 18% of all readmissions, and 15-30 days: 18.3% of all readmissions), reasons for readmission differed significantly (all P < 0.001). Across all disease categories, early readmissions (within 2 days of discharge) were most likely due to ileus/obstruction (53.4% of early readmissions), whereas with 42.5%, infection was the most common cause for late readmissions (>7 days). Patients with home discharge were more likely to be readmitted earlier within the 30-day observation period (P = 0.099), whereas patients with a longer length of index hospital stay (>7 days) were readmitted later (P = 0.080). CONCLUSIONS: Reasons for readmission appear to be universal across different disease categories. Targeted educational and collaborative measures may help to mitigate the burden of hospital readmissions to index facilities.

Factors associated with localization of tuberculosis disease among patients in a high burden country: A health facility-based comparative study in Ethiopia.

INTRODUCTION: In contrast to most tuberculosis (TB) high burden countries, Ethiopia has for a long time reported a very high percentage of extra pulmonary TB (EPTB), which is also reflected in population based estimations reported by the World Health Organization (WHO). Particularly a steadily higher proportion of cervical tuberculous lymphadenitis (TBLN) has been described. Here we identify clinical and demographic factors associated with anatomic site of the TB disease. METHOD: A health facility based comparative study was conducted among TBLN and PTB patients who visited selected health facilities in Ethiopia during 2016 and 2017. Associated risk factors were identified through a multivariate logistic regression model using R-studio. RESULT: A total of 1,890 study participants, 427 TBLN and 1,463 PTB patients, were included. The mean age of TBLN patients (29 years ± 14.4 SD) was lower than that of PTB cases (36 years ± 15.0 SD). There were slightly more women diagnosed with TBLN (51.1%) while nearly 6 out of 10 male patients were diagnosed with PTB (58.9%). Most significantly, younger age groups (<15 Years) were more likely to develop cervical TBLN than older people (>56 years), with an AOR of 9.76 (95% CI: 4.87, 19.56). The odds of cervical TBLN among women [1.69 (1.30, 2.20)] was higher than that for men. In addition, adjusted estimates suggested that, compared with PTB, renal diseases [3.41 (1.29, 9.02)] and the presence of other concomitant chronic illness [1.61 (1.23, 2.09)] had a significant association with TBLN. CONCLUSION: Generally, the risk of developing a particular form of TB disease is usually associated with demographic and medical history of an infected individual. Hence, the current symptom based screening, which primarily rely on chronic cough in many countries, may lead to missing significant portions of TBLN cases.

[Study of clinical application of manipulations of filiform needles to promote qi by data mining technique].

OBJECTIVE: To analyze the diseases and effects of the manipulations to promote qi by filiform needles, with the help of data mining technique. METHODS: Literature about different manipulations to promote qi by filiform needles in recent 60 years was collected in China National Knowledge Infrastructure(CNKI). Then databases were established to mine the relativities among the diseases, subjects, acupoints selection law,routes and directions of meridian qi and effects. RESULTS: ①Total 489 articles were included. The basic manipulations with the frequency of 630 were on the top. The auxiliary and four methods of Feijingzouqi respectively appeared 70 times. The diseases in the internal medicine were treated with the basic and auxiliary methods of the higher frequencies, 311 and 44 times separately. While the four methods of Feijingzouqi were mostly used in the surgical area, 37 timestotally. ②The diseases treated from high to low by lifting, thrusting and twirling represented retention of urine, sequelae of stroke, pain in waist and lower limbs, of which the effect for retention of urine was better than those of the other two, and the lifting and thrusting method was superior to twirling. ③As for the auxiliary methods, 25 times were found about vibration needling; 18 times, twisting. The highest frequency of 6 times for the vibration needling was on the sequelae of stroke; while 4 times for the twisting, stranguria. ④As to the four methods of Feijingzouqi, Cangguitanxue was most frequently applied, and its highest frequency of 18 was on bi syndrome. CONCLUSIONS: Manipulations to promote qi by filiform needles are crucial to achieving the effects of acupuncture. The basic methods are widely used in clinic and have been seen good efficacy. While the auxiliary means assist to promote qi to stimulate the body,among which the four methods of Feijingzouqi are mainly to smooth the meridians and drive qi of patients with surgical diseases and take meridian blocking the priority.