Miracle-dz/UniFAR-FTUs huggingface dataset:
Procalcitonin as a marker of Gram-negative bloodstream infections in hematological patients with febrile neutropenia

Abstract The aim of this study was to explore the predictive value of procalcitonin (PCT) in Gram-negative bloodstream infections (BSIs) in hematological patients with febrile neutropenia. A total of 1466 samples (396 blood culture (BC)-positive, 1052 BC-negative, and 18 contaminated specimens) were included, comprising 268 Gram-negative, 88 Gram-positive, 19 fungal, and 21 polymicrobial BSIs. Median PCT value (0.72 ng/mL; IQR: 0.23–3.87) was significantly higher in Gram-negative than Gram-positive (0.34 ng/mL; IQR: 0.14–2.23; p < .01), or fungal (0.27 ng/mL; IQR: 0.13–0.40; p < .01) BSIs. In mono-microbial BSIs, the best PCT cutoff distinguishing Gram-negative BSIs from all other fever causes was 0.56 ng/ml, with a specificity of 76.8%. PCT levels were significantly higher in BSIs from multidrug-resistant (MDR) Gram-negative strains than from non-MDR (p < .01). This study confirms that elevated PCT may predict Gram-negative BSIs in hematological patients with febrile neutropenia, and demonstrates higher PCT levels in MDR Gram-negative BSIs in these patients.
Differences in the path to exit the ribosome across the three domains of life

Recent advances in biological imaging have led to a surge of fine-resolution structures of the ribosome from diverse organisms. Comparing these structures, especially the exit tunnel, to characterize the key similarities and differences across species is essential for various important applications, such as designing antibiotic drugs and understanding the intricate details of translation dynamics. Here, we compile and compare 20 fine-resolution cryo-EM and X-ray crystallography structures of the ribosome recently obtained from all three domains of life (bacteria, archaea and eukarya). We first show that a hierarchical clustering of tunnel shapes closely reflects the species phylogeny. Then, by analyzing the ribosomal RNAs and proteins localized near the tunnel, we explain the observed geometric variations and show direct association between the conservations of the geometry, structure, and sequence. We find that the tunnel is more conserved in its upper part, from the polypeptide transferase center to the constriction site. In the lower part, tunnels are significantly narrower in eukaryotes than in bacteria, and we provide evidence for the existence of a second constriction site in eukaryotic tunnels. We also show that ribosomal RNA and protein sequences are more likely to be conserved closer to the tunnel, as is the presence of positively charged amino acids. Overall, our comparative analysis shows how the geometric and biophysical properties of the exit tunnel play an important role in ensuring proper transit of the nascent polypeptide chain, and may explain the differences observed in several co-translational processes across species.
Isolation of Desulfovibrio spp. from human gut microbiota using a next‐generation sequencing directed culture method

Desulfovibrio spp. is predominant member of sulphate‐reducing bacteria in human gut microbiota. Previous studies indicated that the isolation of Desulfovibrio strains from human faecal samples is very important to study the roles of human intestinal Desulfovibrio spp. in maintaining healthy states or causing diseases, as well as defining their biological characteristics. However, there are very few reports describing the isolation of Desulfovibrio spp. from human faecal samples. In this study, faecal samples were inoculated into various media containing different components. The enriched culture communities were identified using 16S rRNA gene high‐throughput sequencing analysis, enabling us to identify the specific components that enable the enrichment of Desulfovibrio. Using this information, we developed five specific media and identified an effective enrichment medium that produced the highest relative abundance of Desulfovibrio in communities cultured from four faecal samples (26·5, 73·5, 44·7 and 77·6% respectively). In addition, the major non‐Desulfovibrio genera were identified. Finally, three species of Desulfovibrio, D. desulfuricans, D. piger and D. legallii were isolated, representing the first time that has D. legallii been isolated from a human gastrointestinal source.
Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters

Discrete morphological data have been widely used to study species evolution, but the use of quantitative (or continuous) morphological characters is less common. Here, we implement a Bayesian method to estimate species divergence times using quantitative characters. Quantitative character evolution is modelled using Brownian diffusion with character correlation and accounting for character variation within populations. Through simulations, we demonstrate that ignoring the population variation (or population “noise”) and the correlation among characters leads to biased estimates of divergence times and rate, especially if the correlation and population noise are strong. We apply our new method to the analysis of quantitative characters (cranium landmarks) and molecular data from carnivoran mammals. Our results show that time estimates are affected by whether the correlations and population noise are accounted for or ignored in the analysis. The estimates are also affected by the type of data analysed, with analyses of morphological characters only, molecular data only, or a combination of both; showing noticeable differences among the time estimates. Rate variation of morphological characters among the carnivoran species appears to be very high, with Bayesian model selection indicating that the independent-rates model fits the morphological data better than the autocorrelated-rates model. We suggest that using morphological continuous characters, together with molecular data, can bring a new perspective to the study of species evolution. Our new model is implemented in the MCMCtree computer program for Bayesian inference of divergence times. [Bayesian inference, continuous morphological characters, geometric morphometrics, Procrustes alignment, molecular clock, divergence times, phylogeny]
The effect of music on mood, motivation, and exercise among patients in a cardiac rehabilitation program: A pilot study.

AIM Exploring the effect of music on mood, motivation, and exercise performance among patients with phase III cardiac rehabilitation. BACKGROUND Cardiac rehabilitation programs address risk factors associated with heart health following acute heart issues or cardiac surgery. In phase III, patients are involved in cardiac health maintenance. Exercise is a major component. Motivating patients to engage in exercise and remain in the program has been problematic. Evidence suggests that music could enhance patient involvement in exercise activities. METHOD A quasi-experimental design was used in this pilot study. A convenience sample of 17 phase III cardiac rehabilitation patients participated. Data were collected on: mood, motivation, and exercise. Participants responded to the Brief Mood Introspection Scale, a 5-point visual analog scale, and an investigator-designed questionnaire on motivation. Treadmill data (speed, distance, and time) were also collected. RESULTS At baseline participants scored high on mood, motivation to exercise, and fondness for music. Little change occurred over the 9 week period. Participants in this study walked further, on average, than individuals of the same age. CONCLUSION Music appears to maintain patients' positive moods, motivate them to exercise and help them to continue rehabilitation efforts. Over time music may encourage patients to walk a further distance.
Surgical site infections and the microbiome: An updated perspective

Abstract Objective: To address 3 questions: What are the origins of bacteria causing surgical site infections (SSIs)? Is there evidence that the offending bacteria are present at the incision site when surgery begins? What are the estimates of the proportion of SSIs that can be prevented with perioperative control of the microbiome? Design: Review of the literature, examining recognized sources of bacteria causing surgical site infections. Methods: Specifically, I examined the impact of improved control of the microbiome of the skin and nares on reducing SSIs. The initial effort was to examine the reduction of SSIs linked solely to preoperative skin preparation regimens and to either topical nasal antibiotics or pre- and postoperative nasal antiseptic regimens. To corroborate the concept of the importance of the microbiome, a review of studies showing the relationship of SSIs and marker organisms (eg, Propionobacterium acnes) present at the incision sites was performed. The relationships of SSIs to the microbiome of the skin and nares were summarized. Results: Depending on key assumptions, ∼70%–95% of all SSIs arise from the microbiome of the patients’ skin or nares. Data from the studies of marker organisms suggest that the infecting bacteria are present at the incision site at the time of surgery. Conclusions: Almost all SSIs arise from the patient’s microbiome. The occurrence of SSIs can be viewed as a perioperative failure to control the microbiome.
Ligase 3–mediated end‐joining maintains genome stability of human embryonic stem cells

Maintenance of human embryonic stem cells (hESCs) with stable genome is important for their future use in cell replacement therapy and disease modeling. Our understanding of the mechanisms maintaining genomic stability of hESC and our ability to modulate them is essential in preventing unwanted mutation accumulation during their in vitro cultivation. In this study, we show the DNA damage response mechanism in hESCs is composed of known, yet unlikely components. Clustered oxidative base damage is converted into DNA double‐strand breaks (DSBs) by base excision repair (BER) and then quickly repaired by ligase (Lig)3‐mediated end‐joining (EJ). If there is further induction of clustered oxidative base damage by irradiation, then BER‐mediated DSBs become essential in triggering the checkpoint response in hESCs. hESCs limit the mutagenic potential of Lig3–mediated EJ by DNA break end protection involving p53 binding protein 1 (53BP1), which results in fast and error‐free microhomology‐mediated repair and a low mutant frequency in hESCs. DSBs in hESCs are also repaired via homologous recombination (HR); however, DSB overload, together with massive end protection by 53BP1, triggers competition between error‐free HR and mutagenic nonhomologous EJ. —Kohutova, A. , Raška, J., Kruta, M. , Seneklova, M. , Barta, T. , Fojtik, P., Jurakova, T. , Walter, C. A. , Hampl, A. , Dvorak, P., Rotrekl, V. Ligase 3–mediated end‐joining maintains genome stability of human embryonic stem cells. FASEB J. 33, 6778–6788 (2019). www.fasebj. org
Antiangiogenic Actions of Vascular Endothelial Growth Factor-A165b, an Inhibitory Isoform of Vascular Endothelial Growth Factor-A, in Human Obesity

Background— Experimental studies suggest that visceral adiposity and adipose tissue dysfunction play a central role in obesity-related cardiometabolic complications. Impaired angiogenesis in fat has been implicated in the development of adipose tissue hypoxia, capillary rarefaction, inflammation, and metabolic dysregulation, but pathophysiological mechanisms remain unknown. In this study, we examined the role of a novel antiangiogenic isoform of vascular endothelial growth factor-A (VEGF-A), VEGF-A165b, in human obesity. Methods and Results— We biopsied paired subcutaneous and visceral adipose tissue in 40 obese subjects (body mass index, 45±8 kg/m2; age, 45±11 years) during bariatric surgery and characterized depot-specific adipose tissue angiogenic capacity using an established ex vivo assay. Visceral adipose tissue exhibited significantly blunted angiogenic growth compared with subcutaneous fat (P<0.001) that was associated with marked tissue upregulation of VEGF-A165b (P=0.004). The extent of VEGF-A165b expression correlated negatively with angiogenic growth (r=−0.6, P=0.006). Although recombinant VEGF-A165b significantly impaired angiogenesis, targeted inhibition of VEGF-A165b with neutralizing antibody stimulated fat pad neovascularization and restored VEGF receptor activation. Blood levels of VEGF-A165b were significantly higher in obese subjects compared with lean control subjects (P=0.02), and surgical weight loss induced a marked decline in serumVEGF-A165b (P=0.003). Conclusions— We demonstrate that impaired adipose tissue angiogenesis is associated with overexpression of a novel antiangiogenic factor, VEGF-A165b, that may play a pathogenic role in human adiposopathy. Moreover, systemic upregulation of VEGF-A165b in circulating blood may have wider-ranging implications beyond the adipose milieu. VEGF-A165b may represent a novel area of investigation to gain further understanding of mechanisms that modulate the cardiometabolic consequences of obesity.
Deep Submicron EGFET Based on Transistor Association Technique for Chemical Sensing

Extended-gate field-effect transistor (EGFET) is an electronic interface originally developed as a substitute for an ion-sensitive field-effect transistor (ISFET). Although the literature shows that commercial off-the-shelf components are widely used for biosensor fabrication, studies on electronic interfaces are still scarce (e.g., noise processes, scaling). Therefore, the incorporation of a custom EGFET can lead to biosensors with optimized performance. In this paper, the design and characterization of a transistor association (TA)-based EGFET was investigated. Prototypes were manufactured using a 130 nm standard complementary metal-oxide semiconductor (CMOS) process and compared with devices presented in recent literature. A DC equivalence with the counterpart involving a single equivalent transistor was observed. Experimental results showed a power consumption of 24.99 mW at 1.2 V supply voltage with a minimum die area of 0.685 × 1.2 mm2. The higher aspect ratio devices required a proportionally increased die area and power consumption. Conversely, the input-referred noise showed an opposite trend with a minimum of 176.4 nVrms over the 0.1 to 10 Hz frequency band for a higher aspect ratio. EGFET as a pH sensor presented further validation of the design with an average voltage sensitivity of 50.3 mV/pH, a maximum current sensitivity of 15.71 mA1/2/pH, a linearity higher than 99.9%, and the possibility of operating at a lower noise level with a compact design and a low complexity.
c‐Jun expression after cerebral hyperstimulation differs between rats and marmosets

Immediate early genes (IEGs) are a fundamental element in the way we respond and adapt to a variety of stimuli. We have recently reported that IEG response, as measured by c‐Fos expression, is different between rodents and primates. Here, we further extend this analysis by assessing the expression of c‐Jun, one of the main complements of c‐Fos, under the same stimulation protocol. For this, we investigated the immunohistochemical expression of c‐Jun (and compared with that previously shown for c‐Fos) after stimulation with pentylenetetrazol in the cingulate gyrus, motor cortex, piriform cortex, inferior temporal cortex, and visual cortex of rats and marmosets (Callithrix jacchus), both male and female. Overall the immunohistochemical expression of c‐Jun was more intense but remained elevated for a shorter duration in marmosets as compared to rats. These results are in contrast to what we had previously shown for c‐Fos. Furthermore, in terms of the temporal profile, c‐Fos and c‐Jun expression occurred in a complementary manner in rats—the peak of c‐Fos expression coincided with low levels of c‐jun expression—and in a superimposed manner in marmosets—the peak of c‐Fos expression coincided with the peak of c‐Jun expression. Since Fos proteins may form dimers with Jun proteins and together control late gene expressions in the cell nucleus, this different expression profile between primates and rodents may bear meaningful impact for how the nervous system reacts and adapts to stimulation.
Women’s Smoking: Relationships Among Emotional Labor, Occupational Stress, and Health Promotion

Call centers in Korea have been found to be operated mainly by women, and they experience high levels of job-related stress. Compared with the general population, the prevalence of smoking among women in Korea’s call centers is strikingly high. Little attention has been paid to the associations between smoking behavior and their emotional labor, occupational stress, and health-promotion behaviors. For this cross-sectional study, a paper-based survey was conducted in a sample of female employees in a credit card call center (N = 309). Among the participants, about 20% (n = 62) were current smokers. Smokers were less engaged in health-promotion behaviors than nonsmokers, and occupational stress was negatively associated with health-promoting behaviors in nonsmokers, but not in smokers. Smokers may use cigarettes as a way of alleviating the emotional burden of their work.
Home Blood Pressure Variability as Cardiovascular Risk Factor in the Population of Ohasama

Blood pressure variability based on office measurement predicts outcome in selected patients. We explored whether novel indices of blood pressure variability derived from the self-measured home blood pressure predicted outcome in a general population. We monitored mortality and stroke in 2421 Ohasama residents (Iwate Prefecture, Japan). At enrollment (1988–1995), participants (mean age, 58.6 years; 60.9% women; 27.1% treated) measured their blood pressure at home, using an oscillometric device. In multivariable-adjusted Cox models, we assessed the independent predictive value of the within-subject mean systolic blood pressure (SBP) and corresponding variability as estimated by variability independent of the mean, difference between maximum and minimum blood pressure, and average real variability. Over 12.0 years (median), 412 participants died, 139 of cardiovascular causes, and 223 had a stroke. In models including morning SBP, variability independent of the mean and average real variability (median, 26 readings) predicted total and cardiovascular mortality in all of the participants (P⩽0.044); variability independent of the mean predicted cardiovascular mortality in treated (P=0.014) but not in untreated (P=0.23) participants; and morning maximum and minimum blood pressure did not predict any end point (P≥0.085). In models already including evening SBP, only variability independent of the mean predicted cardiovascular mortality in all and in untreated participants (P⩽0.046). The R 2 statistics, a measure for the incremental risk explained by adding blood pressure variability to models already including SBP and covariables, ranged from <0.01% to 0.88%. In a general population, new indices of blood pressure variability derived from home blood pressure did not incrementally predict outcome over and beyond mean SBP.
Chronic Rhinosinusitis in Cystic Fibrosis: Diagnosis and Medical Management

Chronic rhinosinusitis (CRS) is nearly ubiquitous in patients with cystic fibrosis (CF). CF CRS is a challenging entity to define, diagnose, and treat, as patients often have severe refractory sinus disease in addition to complex medical comorbidities. The purpose of this article is to review the literature on the medical management of CF CRS and determine how to best identify, diagnose, and manage CF CRS. Ultimately, the treatment of these patients requires a multi-disciplinary approach involving the pulmonologist and otolaryngologist.
Evaluation of Serum microRNAs in Patients with Diabetic Kidney Disease: A Nested Case-Controlled Study and Bioinformatics Analysis

Background Diabetic kidney disease (DKD) can result in end-stage kidney disease and renal failure. This study aimed to examine the expression of serum microRNAs (miRNAs), miR-20a, miR-99b, miR-122-5p, and miR-486-5p, and to use bioinformatics data to investigate the pathways involved in DKD. Material/Methods Serum miRNAs were obtained from 25 healthy volunteers, 50 patients with non-complicated type 2 diabetes mellitus (T2DM), and 42 patients with T2DM and DKD. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression of serum miRNAs. Specificity and sensitivity of the association between serum miRNAs in DKD were evaluated by analysis of the receiver operating characteristic (ROC) area under the curve (AUC). Serum miRNAs and clinical parameters of the patients were compared. Bioinformatics data analysis accessed the miRNA targets involved in the pathways related to the pathogenesis of DKD. Results Serum levels of miR-99b and miR-122 significantly increased, and mir-20a and miR-486 decreased in the DKD group compared with healthy controls. Serum levels of miR-20a, miR-99b, miR-486-5p, and miR-122-5p were significantly correlated with albuminuria, estimated glomerular filtration rate (eGFR), blood glucose and lipid profiles. ROC curve analysis showed that diagnostic accuracy of serum levels of miR-99b for DKD was superior to miR-486-5p, miR-122-5p, and miR-20a, resulting in AUCs of 0.895, 0.853, 0.80, and 0.697, respectively. These four miRNAs regulate several genes affecting oxidative stress, inflammation, and apoptosis. Conclusions Serum miR-99b, miR-486-5p, miR-122-5p, and miR-20a were differentially expressed in patients with T2DM and DKD and should be evaluated further as potential biomarkers for DKD.
Pre-Stroke Frailty Is Independently Associated With Post-Stroke Cognition: A Cross-Sectional Study

Abstract Objective: Post-stroke cognitive impairment is common, but mechanisms and risk factors are poorly understood. Frailty may be an important risk factor for cognitive impairment after stroke. We investigated the association between pre-stroke frailty and acute post-stoke cognition. Methods: We studied consecutively admitted acute stroke patients in a single urban teaching hospital during three recruitment waves between May 2016 and December 2017. Cognition was assessed using the Mini-Montreal Cognitive Assessment (min=0; max=12). A Frailty Index was used to generate frailty scores for each patient (min=0; max=100). Clinical and demographic information were collected, including pre-stroke cognition, delirium, and stroke-severity. We conducted univariate and multiple-linear regression analyses with covariates forced in (covariates included were: age, sex, stroke severity, stroke-type, pre-stroke cognitive impairment, delirium, previous stroke/transient ischemic attack) to investigate the association between pre-stroke frailty and post-stroke cognition. Results: Complete data were available for 154 stroke patients. Mean age was 68 years (SD=11; range=32–97); 93 (60%) were male. Median mini-Montreal Cognitive Assessment score was 8 (IQR=4–12). Mean Frailty Index score was 18 (SD=11). Pre-stroke cognitive impairment was apparent in 13/154 (8%) patients. Pre-stroke frailty was significantly associated with lower post-stroke cognition (Standardized-Beta=−0.40; p<0.001) and this association was independent of covariates (Unstandardized-Beta=−0.05; p=0.005). Additional significant variables in the multiple regression model were age (Unstandardized-Beta=−0.05; p=0.002), delirium (Unstandardized-Beta=−2.81; p<0.001), pre-stroke cognitive impairment (Unstandardized-Beta=−2.28; p=0.001), and stroke-severity (Unstandardized-Beta=−0.20; p<0.001). Conclusions: Pre-stroke frailty may be a moderator of post-stroke cognition, independent of other well-established post-stroke cognitive impairment risk factors. (JINS, 2019, 25, 501–506)