Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictors of time to death among cervical cancer patients at Tikur Anbesa specialized hospital from 2014 to 2019: A survival analysis

Background Cervical cancer (CC) is the 4th most prevalent cancer among females globally. In Ethiopia, around 7,095 new CC cases are diagnosed every year and it is the second common cause of cancer deaths in women. There is limited evidence on survival status as well as about predictors of time to death among CC patients in Ethiopia. Thus, this study investigated the five-year survival status and predictors of time to death among CC patients who had been admitted at Tikur Anbesa specialized Hospital (TASH) from 2014–2019. Methods Facility-based, retrospective-cohort study was conducted at Tikur Anbesa specialized Hospital among 348 patients from June 2014 to June 2019. A systematic random sampling method was employed to select the study participants. Data were extracted from the patient card, and through phone calls. The data was collected using the android version CS-Entry tool. Data was analyzed by SPSS version 23. Kaplan and Meier’s method was used to estimate survival functions and Cox-proportional hazard regression analysis was carried out in order to identify the independent predictors of time to death. Results The overall incidence of death was 31 per 100 person-years of follow up. The median (IQR) follow-up time of the entire cohorts was 18.55 (8.96–49.65) months. The independent predictors for time to death included; age older than 50 years [AHR: 1.4; 95% CI: 1.1–1.9], late stage of CC at diagnosis [AHR: 2.2; 95% CI: 1.7–2.9], No CC treatment [AHR: 2.1; 95% CI: 1.5–3.1] and HIV positive [AHR: 2.3; 95% CI: 1.4–3.8]. Conclusion and recommendation The death rate of CC patients was high. The significant predictors associated with shorten time to death of CC patients were older age, advanced cancer stage at diagnosis, HIV infection and not receiving cancer treatment. Therefore, improving early detection and initiation of treatment for all CC patients is necessary in order to improve patient’s survival status. The government needs to strengthen the routine CC screening programs to address high-risk women such as elderly and HIV positive women in Ethiopia.
Identification of HIV Rapid Mutations Using Differences in Nucleotide Distribution over Time

Mutation is the driving force of species evolution, which may change the genetic information of organisms and obtain selective competitive advantages to adapt to environmental changes. It may change the structure or function of translated proteins, and cause abnormal cell operation, a variety of diseases and even cancer. Therefore, it is particularly important to identify gene regions with high mutations. Mutations will cause changes in nucleotide distribution, which can be characterized by natural vectors globally. Based on natural vectors, we propose a mathematical formula for measuring the difference in nucleotide distribution over time to investigate the mutations of human immunodeficiency virus. The studied dataset is from public databases and includes gene sequences from twenty HIV-infected patients. The results show that the mutation rate of the nine major genes or gene segment regions in the genome exhibits discrepancy during the infected period, and the Env gene has the fastest mutation rate. We deduce that the peak of virus mutation has a close temporal relationship with viral divergence and diversity. The mutation study of HIV is of great significance to clinical diagnosis and drug design.
Incidence and Predictors of Mortality among Preterm Neonates Admitted to the Neonatal Intensive Care Unit at Debre Markos Referral Hospital, Northwest Ethiopia

Background Prematurity is the most frequent cause of neonatal death and the second leading cause of under-five mortality. Preterm related complications accounts for 35 % of neonatal deaths within the first week after birth. So far, most studies done in Ethiopia have focused on estimating the prevalence and determinant factors of premature neonatal death. The current study aimed to assess the incidence and predictors of mortality among preterm neonates admitted to neonatal intensive care unit at Debre Markos Referral Hospital. Methods An institution-based retrospective follow up study was conducted among premature neonates admitted to Neonatal Intensive Care Unit at Debre Markos Referral Hospital from July 2019 to October 2019. Around 498 patients were selected randomly. A multivariable cox proportional hazards model was fitted to identify predictors of mortality. Results A total of 498 preterm babies were followed, and the mean age for follow up at the time of admission to NICU was 15 hours ± 38 SD. Death rate in preterm was estimated to be 27.11% (95% CI: 23.3%, 31.1%). Preterm neonates with gestational age of less than 32 weeks (AHR=1.51; 95% CI: 1.02, 2.24), respiratory distress syndrome (AHR=1.49; 95% CI: 1.03, 2.17), perinatal asphyxia (AHR=1.74, 95% CI: 1.01, 2.76) and congenital malformation (AHR=3.38, 95% CI: 1.21, 8.77) were statistically significant predictors of mortality among preterms. Conclusion The incidence of death in preterm neonates is relatively low. Gestational age less than 32 weeks, perinatal asphyxia, respiratory distress syndrome and congenital malformation were found as predictors.
Human Transcriptome Array Analysis Identifies CDR2 as a Novel Suppressed Gene for Kawasaki Disease

Kawasaki disease (KD) is a febrile childhood vasculitis that involves the coronary arteries. Most previous studies have focused on the genes activated in the acute phase of KD. However, in this study, we focused on suppressed genes in the acute stage of KD and identified novel targets with clinical significance and potential prognostic value for KD patients. We enrolled 18 patients with KD, 18 healthy controls (HC), and 18 febrile controls (FC) for human transcriptome array analysis. Another 19 healthy controls, 20 febrile controls, and 31 patients with KD were recruited for RT-PCR validation of target mRNA expressions. The results of Human Transcriptome Array (HTA) 2.0 showed 461 genes that were significantly higher in KD and then normalized after IVIG, as well as 99 suppressed genes in KD. Furthermore, we identified the four genes in KD with the most downregulation, including BCL11B, DUSP2, DDX24, and CDR2, as well as the upregulation of their expression following IVIG administration. The mRNA expression of CDR2 by qRT-PCR was the most compatible with the pattern of the HTA2.0 results. Furthermore, we found higher DDX24 mRNA expression in KD patients with CAL when compared to those without CAL 3 weeks after IVIG administration. In summary, activated gene expression represented a majority in the immune response of KD. In this study, we identified CDR2 as a novel suppressed gene for Kawasaki disease via human transcriptome array analysis and DDX24 associated with CAL formation, which may contribute to further understanding of CAL pathogenesis in KD.
The integration of mHealth technologies in telemedicine during the COVID-19 era: A cross-sectional study

Telemedicine is a rapidly expanding field of medicine and an alternative method for delivering quality medical care to patients’ fingertips. With the COVID-19 pandemic, there has been an increase in the use of telemedicine to connect patients and healthcare providers, which has been made possible by mobile health (mHealth) applications. The goal of this study was to compare the satisfaction of patients with telemedicine among mHealth users and non-users. This was a survey-based study that included outpatients from Abu Dhabi. The association between patient satisfaction with telemedicine and use of mHealth technologies was described using regression models. This study included a total of 515 completed responses. The use of mHealth application was significantly associated with ease of booking telemedicine appointments (OR 2.61, 95% CI 1.63–4.18; P < .001), perception of similarity of quality of care between telemedicine consultations and in-person visits (OR 1.81, 95% CI 1.26–2.61; P = .001), and preference for using telemedicine applications over in-person visits during the COVID-19 pandemic (OR 1.74, 95% CI 1.12–2.72; P = .015). Our study results support that the use of mHealth applications is associated with increased patient satisfaction with telemedicine appointments.
Multipole-moment effects in ion–molecule reactions at low temperatures: part II – charge–quadrupole-interaction-induced suppression of the He+ + N2 reaction at collision energies below kB·10 K

We report on an experimental and theoretical investigation of the He+ + N2 reaction at collision energies in the range between 0 and kB·10 K. The reaction is studied within the orbit of a highly excited Rydberg electron after merging a beam of He Rydberg atoms (He(n), n is the principal quantum number), with a supersonic beam of ground-state N2 molecules using a surface-electrode Rydberg–Stark decelerator and deflector. The collision energy Ecoll is varied by changing the velocity of the He(n) atoms for a fixed velocity of the N2 beam and the relative yields of the ionic reaction products N+ and N2+ are monitored in a time-of-flight mass spectrometer. We observe a reduction of the total reaction-product yield of ∼30% as Ecoll is reduced from ≈kB·10 K to zero. An adiabatic capture model is used to calculate the rotational-state-dependent interaction potentials experienced by the N2 molecules in the electric field of the He+ ion and the corresponding collision-energy-dependent capture rate coefficients. The total collision-energy-dependent capture rate coefficient is then determined by summing over the contributions of the N2 rotational states populated at the 7.0 K rotational temperature of the supersonic beam. The measured and calculated rate coefficients are in good agreement, which enables us to attribute the observed reduction of the reaction rate at low collision energies to the negative quadrupole moment, Qzz, of the N2 molecules. The effect of the sign of the quadrupole moment is illustrated by calculations of the rotational-state-dependent capture rate coefficients for ion–molecule reactions involving N2 (negative Qzz value) and H2 (positive Qzz value) for |J, M〉 rotational states with J ≤ 5 (M is the quantum number associated with the projection of the rotational angular momentum vector J⃑ on the collision axis). With decreasing value of |M|, J⃑ gradually aligns perpendicularly to the collision axis, leading to increasingly repulsive (attractive) interaction potentials for diatomic molecules with positive (negative) Qzz values and to reaction rate coefficients that decrease (increase) with decreasing collision energies.
A Comparative Study of the Triglycerides/HDL Ratio and Pseudocholinesterase Levels in Patients with Bladder Cancer

Background: Lipid alterations may serve as potential tumour biomarkers. The ratio of triglycerides to HDL cholesterol (TG/HDL ratio) is associated with various cancers. Pseudocholinesterase (PChE) activity, involved in TG hydrolysis, plays an important role in the metabolism of lipoprotein. There is scarce data assessing the reliability of both the TG/HDL ratio and PChE levels in correctly classifying patients suffering from bladder cancer. Methods: Three hundred and ninety-six patients undergoing cystoscopy or transurethral resection of the bladder (TURB), broken into two major groups, i.e., patients with histologically confirmed, non-metastatic bladder cancer (n = 208) and without bladder cancer (no bladder cancer, n = 188), formed the study population. The last group was split into two subgroups consisting of a cohort of patients never suffering from bladder cancer but with other bladder diseases (no CaBD, n = 100) and another cohort formed by patients characterised by eradicated bladder cancer after TURB with no recurrence during a three-month follow-up (previous bladder cancer, n = 88). Pieces of information by both metabolic derangement (the presence of type 2 diabetes mellitus), hypertension and lipid profile were retrieved from patient records upon entry to the study. Sensitivity, specificity, areas under the ROC (AUROC) of the TG/HDL ratio, and PChE levels were used in diagnostic decision making. Results: The TG/HDL ratio as well as PChE concentrations of bladder cancer patients were significantly different when compared to those with previous bladder cancer and the no CaBD patients (p = 0.023 and 0.0004, respectively). There was an independent role of both the TG/HDL ratio and PChE levels in predicting the presence of bladder cancer (OR: 1.22 and 0.99, respectively), but the reliability of the TG/HDL ratio (AUROC: 0.587) was superior to that of PChE levels (AUROC: 0.374). The AUROC of a new parameter resulting from the combination of the TG/HDL ratio with PChE levels showed a further increment in the discriminant power of the bladder cancer presence (0.6298), interestingly with a negative predictive value (89%) according to the Bayesian approach. The cut-off of the TG/HDL ratio, the main marker of the present study that better distinguishes bladder cancer from no bladder cancer patients, was 2.147. Discussion and Conclusions: The reliability of the TG/HDL ratio is based on the fact that this parameter likely mirrors the insulin resistance (IR) underlying bladder cancer patients. Furthermore, PChE levels evidence both IR and the associated non-alcoholic fatty liver disease. The TG/HDL ratio and PChE levels as well as their combined use could help physicians to assess/confirm the presence of this very common cancer, where early detection is important to ensure the best therapeutical approach.
Absence, loss-of-function, or inhibition of Escherichia coli AcrB does not increase expression of other efflux pump genes supporting the discovery of AcrB inhibitors as antibiotic adjuvants

Abstract Objectives To determine whether expression of efflux pumps and antibiotic susceptibility are altered in Escherichia coli in response to efflux inhibition. Methods The promoter regions of nine efflux pump genes (acrAB, acrD, acrEF, emrAB, macAB, cusCFBA, mdtK, mdtABC, mdfA) were fused to gfp in pMW82 and fluorescence from each reporter construct was used as a measure of the transcriptional response to conditions in which AcrB was inhibited, absent or made non-functional. Expression was also determined by RT-qPCR. Drug susceptibility of efflux pump mutants with missense mutations known or predicted to cause loss of function of the encoded efflux pump was investigated. Results Data from the GFP reporter constructs revealed that no increased expression of the tested efflux pump genes was observed when AcrB was absent, made non-functional, or inhibited by an efflux pump inhibitor/competitive substrate, such as PAβN or chlorpromazine. This was confirmed by RT-qPCR for PAβN and chlorpromazine; however, a small but significant increase in macB gene expression was seen when acrB is deleted. Efflux inhibitors only synergized with antibiotics in the presence of a functional AcrB. When AcrB was absent or non-functional, there was no impact on MICs when other efflux pumps were also made non-functional. Conclusions Absence, loss-of-function, or inhibition of E. coli AcrB did not significantly increase expression of other efflux pump genes, which suggests there is no compensatory mechanism to overcome efflux inhibition and supports the discovery of inhibitors of AcrB as antibiotic adjuvants.
Prediction of Time Series Gene Expression and Structural Analysis of Gene Regulatory Networks Using Recurrent Neural Networks

Methods for time series prediction and classification of gene regulatory networks (GRNs) from gene expression data have been treated separately so far. The recent emergence of attention-based recurrent neural network (RNN) models boosted the interpretability of RNN parameters, making them appealing for the understanding of gene interactions. In this work, we generated synthetic time series gene expression data from a range of archetypal GRNs and we relied on a dual attention RNN to predict the gene temporal dynamics. We show that the prediction is extremely accurate for GRNs with different architectures. Next, we focused on the attention mechanism of the RNN and, using tools from graph theory, we found that its graph properties allow one to hierarchically distinguish different architectures of the GRN. We show that the GRN responded differently to the addition of noise in the prediction by the RNN and we related the noise response to the analysis of the attention mechanism. In conclusion, this work provides a way to understand and exploit the attention mechanism of RNNs and it paves the way to RNN-based methods for time series prediction and inference of GRNs from gene expression data.
Characterization of the complete chloroplast genome of Brassica oleracea var. italica and phylogenetic relationships in Brassicaceae

Broccoli (Brassica oleracea var. italica) is an important B. oleracea cultivar, with high economic and agronomic value. However, comparative genome analyses are still needed to clarify variation among cultivars and phylogenetic relationships within the family Brassicaceae. Herein, the complete chloroplast (cp) genome of broccoli was generated by Illumina sequencing platform to provide basic information for genetic studies and to establish phylogenetic relationships within Brassicaceae. The whole genome was 153,364 bp, including two inverted repeat (IR) regions of 26,197 bp each, separated by a small single copy (SSC) region of 17,834 bp and a large single copy (LSC) region of 83,136 bp. The total GC content of the entire chloroplast genome accounts for 36%, while the GC content in each region of SSC,LSC, and IR accounts for 29.1%, 34.15% and 42.35%, respectively. The genome harbored 133 genes, including 88 protein-coding genes, 37 tRNAs, and 8 rRNAs, with 17 duplicates in IRs. The most abundant amino acid was leucine and the least abundant was cysteine. Codon usage analyses revealed a bias for A/T-ending codons. A total of 35 repeat sequences and 92 simple sequence repeats were detected, and the SC-IR boundary regions were variable between the seven cp genomes. A phylogenetic analysis suggested that broccoli is closely related to Brassica oleracea var. italica MH388764.1, Brassica oleracea var. italica MH388765.1, and Brassica oleracea NC_0441167. 1. Our results are expected to be useful for further species identification, population genetics analyses, and biological research on broccoli.
Hypertonic saline jet nebulization breathing treatments produce a predictable quantity of aerosolized sodium chloride for inhalation

Purpose The amount of sodium chloride (NaCl) that escapes a nebulizer cup, intended for patient inhalation, during a 5-min hypertonic saline jet nebulization (HSJN) breathing treatment is apparently unknown in the pure and applied scientific literature. This study aimed to address this void by focusing on NaCl mass changes prior to and after a typical HSJN breathing treatment using an ordinary household, medical-grade air compressor. Research methods Saline solutions of varying concentrations were nebulized to room air for 5 min. Pre- and post-nebulization NaCl concentrations were determined from measured conductivities via calibration curve. The resulting data were used to quantify NaCl mass changed from the beginning and end of a typical HSJN breathing treatment. Main findings Conductivity was a reliable metric in NaCl concentrations ranging from 2.10 × 10-1 to 8.16 × 10-3 M. Pre- and post-nebulization NaCl mass differences of 19–114 mg linearly correlated with saline concentration (wt%). The resulting trendline data reasonably predict how much NaCl is available for patient inhalation during a typical HSJN breathing treatment. Linearity in the data suggests that factors such as colligative properties (e.g., osmolarity) have a minimal influence on the amount of NaCl that escapes the nebulizer cup. Conclusions These results are the first to quantify how much NaCl escapes a nebulizer cup during a typical HSJN breathing treatment. Furthermore, the results represent a key starting point upon which future studies can be built to explore additional airflow rates, kinetics, and temperature effects. Collectively, these findings will play a critical role in ascertaining the mechanism of action in hypertonic saline breathing treatments.
Clinical Outcome of Discordant Empirical Therapy and Risk Factors Associated to Treatment Failure in Children Hospitalized for Urinary Tract Infections

With the spread of antibiotic resistance in pediatric urinary tract infections (UTIs), more patients are likely to be started empirically on antibiotics to which pathogens are later found to be resistant (discordant therapy). However, in-vivo effectiveness may be different from in-vitro susceptibility. Aims of this study were to describe clinical outcomes of discordant empirical treatments in pediatric UTIs and to investigate risk factors associated to treatment failure. This observational, retrospective study was conducted on children hospitalized for febrile UTIs with positive urine culture and started on discordant empirical therapy. Failure rates of discordant treatments and associated risk factors were investigated. A total of 142/1600 (8.9%) patients were treated with inadequate empirical antibiotics. Clinical failure was observed in 67/142 (47.2%) patients, with no fatal events. Higher failure rates were observed for combinations of penicillin and beta-lactamase inhibitors (57.1%). Significant risk factors for failure of discordant treatment were history of recurrent UTIs (95% CI: 1.13–9.98, OR: 3.23, p < 0.05), recent use of antibiotics (95% CI: 1.46–21.82, OR: 5.02, p < 0.01), infections caused by Pseudomonas aeruginosa (95% CI: 1.85–62.10, OR: 7.30, p < 0.05), and empirical treatment with combinations of penicillin and beta-lactamase inhibitors (95% CI: 0.94–4.03, OR: 1.94, p = 0.05). This study showed that discordant empirical treatments may still be effective in more than half of pediatric UTIs. Clinical effectiveness varies between different discordant antibiotics in pediatric UTIs, and patients presenting risk factors for treatment failure may need a differentiated empirical approach.
De‐escalation of five‐year adjuvant endocrine therapy in patients with estrogen receptor‐low positive (immunohistochemistry staining 1%‐10%) breast cancer: Propensity‐matched analysis from a prospectively maintained cohort

The standard 5 years of endocrine therapy has demonstrated additional benefits compared with short‐term (2‐3 years) treatment in patients with estrogen receptor (ER)‐positive breast cancer; however, data specific to ER‐low positive breast cancer (1%‐10% by immunohistochemistry) are limited, and it is unclear whether long‐term treatment is still necessary for this subgroup.