Miracle-dz/UniFAR-FTUs huggingface dataset:
Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts

RT-Q-PCR, and RT-PCR amplicon sequencing, provide a convenient, target-specific, high-sensitivity approach for gene expression studies and are widely used in environmental microbiology. Yet, the effectiveness and reproducibility of the reverse transcription step has not been evaluated. Therefore, we tested a combination of four commercial reverse transcriptases with two priming techniques to faithfully transcribe 16S rRNA and amoA transcripts from marine sediments. Both enzyme and priming strategy greatly affected quantification of the exact same target with differences of up to 600-fold. Furthermore, the choice of RT system significantly changed the communities recovered. For 16S rRNA, both enzyme and priming had a significant effect with enzyme having a stronger impact than priming. Inversely, for amoA only the change in priming strategy resulted in significant differences between the same sample. Specifically, more OTUs and better coverage of amoA transcripts diversity were obtained with GS priming indicating this approach was better at recovering the diversity of amoA transcripts. Moreover, sequencing of RNA mock communities revealed that, even though transcript α diversities (i.e. OTU counts within a sample) can be biased by the RT, the comparison of β diversities (i.e. differences in OTU counts between samples) is reliable as those biases are reproducible between environments. Originality-Significance Statement Is the complementary DNA (cDNA) produced after Reverse Transcription (RT) a faithful representation of the starting RNA? This is a fundamental and important question for transcriptomic-based studies in environmental microbiology that aim to quantify and/or examine the diversity of transcripts via RT approaches. Yet little is known about the reliability and reproducibility of this step. Here, we evaluated the effect of the two main components of the RT reaction – the retro transcriptase enzyme and priming strategy (gene specific vs random priming), on the quantification and diversity of cDNA. We found that both have a significant impact. We further provide evidence to enable informed choices as to the enzyme and priming combinations to improve the performance of RT-PCR approaches. Taken together, this work will improve the reliability and reproducibility of transcript-based studies in environmental microbiology.
Medical students' perspectives on the ethics of clinical reality.

INTRODUCTION Medical ethicists have pointed out that a gap exists between classroom teaching of bioethical theory and the ethics of clinical reality. Studies recommend that the teaching of bioethics should focus on everyday dilemmas in the clinical setting instead of only dramatic dilemmas and have expressed the need for more studies of how medical students perceive ethical problems in the clinical setting. This study explored themes in and types of ethical dilemmas in medical students' reflective writing in their clinical rotations. METHODS The study was a qualitative explorative analysis of group reflection texts from fourth-year medical students at Aarhus University, Denmark. RESULTS The thematic analysis of 51 group reflection texts (n = 396) revealed four key themes in the material: 1) confidentiality issues, 2) treatment options and side effects, 3) the students' role and responsibility and 4) information-giving and communication. The majority of the ethical dilemmas that the students identified were everyday dilemmas. Dramatic dilemmas were represented to a limited degree. CONCLUSIONS Students' perspectives on ethical dilemmas in the clinical setting provide a unique opportunity to integrate a variety of ethical dimensions into bioethical education and draw attention to overlooked everyday ethical dilemmas. Thus, involving the students' perspectives may be a way to bridge the gap between bioethical theory and the ethics of clinical reality. FUNDING none. TRIAL REGISTRATION not relevant.
Prognostic factors for neurological outcomes in Korean targeted temperature management recipients with return of spontaneous circulation after out-of-hospital cardiac arrests

Abstract Targeted temperature management (TTM) is recommended for comatose patients after out-of-hospital cardiac arrests (OHCAs). Even after successful TTM, several factors could influence the neuroprotective effect of TTM. The aim of this study is to identify prognostic factors associated with good neurological outcomes in TTM recipients. This study used nationwide data during 2012 to 2016 to investigate prognostic factors associated with good neurological outcomes in patients who received TTM after the return of spontaneous circulation (ROSC). Multivariate logistic regression analysis was conducted to analyse the factors that may affect the neurological outcomes in the TTM recipients. The study included 1578 eligible patients, comprising 767 with good and 811 with poor neurological outcomes. Multivariable analyses showed that OHCA in public places (OR, 1.599; 95% CI, 1.100–2.323, P = .014), initial shockable rhythms (OR, 1.721; 95% CI, 1.191–2.486, P = .004), pre-hospital ROSCs (OR, 6.748; 95% CI, 4.703–9.682, P < .001), bystander cardiopulmonary resuscitation (CPR) (OR, 1.715; 95% CI, 1.200–2.450, P = .003), and primary coronary interventions (PCIs) (OR, 2.488; 95% CI, 1.639–3.778, P < .001) were statistically significantly associated with good neurological outcomes. Whereas, increase of age (OR, 0.962; 95% CI, 0.950–0.974, P < .001) and conventional cooling (OR, 0.478; 95% CI, 0.255–0.895, P = .021) were statistically significantly associated with poor neurological outcome. This study suggests that being younger, experiencing OHCA in public places, having initial shockable rhythm, pre-hospital ROSC, and bystander CPR, implementing PCIs and applying intravascular or surface cooling devices compared to conventional cooling method could predict good neurological outcomes in post-cardiac arrest patients who received TTM.
Yield, Growth, Quality, Biochemical Characteristics and Elemental Composition of Plant Parts of Celery Leafy, Stalk and Root Types Grown in the Northern Hemisphere

Celery is one of the major nutraceutical vegetable species due to the high dietary and medicinal properties of all of its plant parts. Yield, growth and produce quality of six celery genotypes belonging to leafy (Elixir and Samurai), stalk (Atlant and Primus) or root (Egor and Dobrynya) types, as well as the distribution of biomass, sugars, mineral elements and antioxidants among the different plant parts, were assessed. Within the celery root type, cultivar Dobrynya resulted in higher yield than Egor, whereas the genotype did not significantly affect the marketable plant part production of leafy and stalk types. Leaf/petiole ratios relevant to biomass, total dissolved solids, sugars, ascorbic acid, flavonoids, antioxidant activity and ash, K, Zn, Fe, Mn, Cu and Se content were significantly affected by the celery type examined. Ash content was highest in the leaves and lowest in the roots. Celery antioxidant system was characterized by highly significant relationships between ascorbic acid, polyphenols, flavonoids, antioxidant activity and Zn. Among the celery types analyzed, the highest values of chlorophyll, Fe and Mn content as well as antioxidant activity were recorded in leaves from root genotypes, which suggests interesting nutraceutical prospects of the aforementioned plant parts for human utilization.
Diaphragm ultrasound: A novel approach to assessing pulmonary function in patients with traumatic rib fractures

BACKGROUND Rib fractures following blunt trauma are a major cause of morbidity. Various factors have been used for risk stratification for complications. Ultrasound (US) measurements of diaphragm thickness (Tdi) and related measures such as thickening fraction (TF) have been verified for use in the evaluation of diaphragm function. In healthy individuals, Tdi by US is known to have a positive and direct relationship with lung volumes including inspiratory capacity (IC). However, TF has not been previously been described in, or used to assess, pulmonary function in rib fracture patients. We examined TF and IC to elucidate the association between acute rib fractures and respiratory function. We hypothesized that TF and IC were related. Secondarily, we examined the relationship of TF in rib fractures patients, in the context of values reported for healthy controls in the literature. METHODS We prospectively enrolled adults with acute blunt traumatic rib fractures within 48 hours of admission to a level 1 trauma center. Patients requiring a chest tube or mechanical ventilation at time of consent were excluded. Inspiratory capacity was determined via incentive spirometry. Thickening fraction was determined by bedside US measurements of minimum and maximum Tdi during tidal breathing (TFtidal) or deep breathing (TFDB) was calculated (TF = [TdimaxTdi − TdiminTdi]/TdiminTdi). TFDB values were also compared with previously reported mean ± SD values of 2.04 ± 0.62 in healthy males and 1.70 ± 0.89 in females. Univariate and multivariate analyses were performed. RESULTS A total of 41 subjects (58.5% male) with a median age of 64 years (interquartile range [IQR], 53–77 years) were enrolled. Diaphragm US demonstrated a median TFtidal of 0.30 (IQR, 0.24–0.46). Median IC was 1,750 mL (IQR, 1,250–2,000 mL). As compared with previously reported controls, our mean ± SD TFDB in males 0.90 ± 0.51 and 0.88 ± 0.89 in females were significantly lower. Multivariate analysis revealed a significant inverse correlation (−0.439, p = 0.004) between TFtidal and IC, and no relationship between TFDB and IC. CONCLUSION To our knowledge, this is the first report of TF in rib fracture patients. The significant inverse association between TFtidal and IC, along with lower than normal TFDB ranges, suggests that, in the setting of rib fractures, there are alterations in the diaphragm-chest cage mechanics, whereby other muscles may play more prominent roles. LEVEL OF EVIDENCE Diagnostic tests or criteria, Level III.
Maintaining Muscle Function Across the Lifespan

Abstract Sarcopenia is a geriatric syndrome currently defined as pathological loss of muscle mass and function. Sarcopenia is not only a major contributor to loss of physical function in older adults but is also associated with increased risk of morbidity, mortality, and increased healthcare costs. As a complex and multifactorial syndrome, sarcopenia has been associated with numerous degenerative changes during the aging process, but there is building evidence for significant contributions to the development of sarcopenia from neurodegenerative changes in the peripheral nervous system. A variety of interventions have been investigated for the treatment of sarcopenia, but current management is primarily focused on nutrition and therapeutic exercise interventions. Great strides have been made to improve screening procedures and diagnostic criteria for sarcopenia, but continued optimization of diagnostic and screening strategies is needed to better identify individuals with sarcopenia or at risk of developing sarcopenia. Understanding and addressing the major drivers of sarcopenia pathogenesis will help develop therapeutics that can reduce the impact of sarcopenia on affected individuals and society.
The bronchial tree of the human embryo: an analysis of variations in the bronchial segments

A classical study has revealed the general growth of the bronchial tree and its variations up to Carnegie stage (CS) 19. In the present study, we extended the morphological analysis CS by CS until the end of the embryonic period (CS23). A total of 48 samples between CS15 and CS23 belonging to the Kyoto Collection were used to acquire imaging data by performing phase‐contrast X‐ray computed tomography. Three‐dimensionally reconstructed bronchial trees revealed the timeline of morphogenesis during the embryonic period. Structures of the trachea and lobar bronchus showed no individual difference during the analyzed stages. The right superior lobar bronchus was formed after the generation of both the right middle lobar bronchus and the left superior lobar bronchus. The speed of formation of the segmental bronchi, sub‐segmental bronchi, and further generation seemed to vary among individual samples. The distribution of the end‐branch generation among five lobes was significantly different. The median branching generation value in the right middle lobe was significantly low compared with that of the other four lobes, whereas that of the right inferior lobe was significantly larger than that of both the right and left superior lobes. Variations found between CS20 and CS23 were all described in the human adult lung, indicating that variation in the bronchial tree may well arise during the embryonic period and continue throughout life. The data provided may contribute to a better understanding of bronchial tree formation during the human embryonic period.
The early evolutionary history of sharks and shark-like fishes

The Middle Ordovician to Late Silurian represents an interval of approximately 50 million years, which has been recognised as the initial, cryptic, period in the evolutionary history of chondrichthyan fish. The fossil remains attributed to early chondrichthyans are dominated by isolated dermal scales that predate the appearance of undisputed chondrichthyan teeth and articulated skeletons in the Lower Devonian. Investigation of the inter-relationships of these scale taxa and their systematic position relative to high- ranked chondrichthyan clades has been hampered by the lack of developed scale-based classification schemes for jawed gnathostomes, coupled with the limited use of scale characters in phylogenetic studies of Palaeozoic Chondrichthyes. Here, all previously documented scale types of alleged Lower Palaeozoic chondrichthyans were examined using a combination of X-ray microtomography, SEM and Nomarski DIC optics. These were found to exhibit a set of characteristics (symmetrical trunk scales, areal crown growth and lack of hard-tissue resorption, cancellous bone and enamel) recognised as specific to the dermal skeleton of chondrichthyans among derived gnathostomes. The collected data permitted the establishment of a hierarchy of scale characters for separate taxonomic ranks, leading to the recognition of three Orders (Mongolepidida, Elegestolepida ordo nov. and Altholepida ordo nov.) of early chondrichthyans, differentiated by distinct types of scale-crown morphogenesis. A scale-based cladistic analysis of jawed gnathostomes corroborated these results by recovering a chondrichthyan clade that incorporates all examined taxa and ‘acanthodians’ with non-superpositional crown growth patterns. It is thus proposed that chondrichthyan dermoskeletal characters carry a phylogenetic signal, allowing to interpret the documented diverse types of scale morphogenesis as evidence for a major radiation of chondrichthyan lineages in the Lower Palaeozoic.
Assessing The Role Of Multi-protein Complexes In Determining Phenotype

Understanding regulatory mechanisms in complex biological systems is an important challenge, in particular to understand disease mechanisms, and to discover new therapies and drugs. In this paper, we consider the important question of cellular regulation of phenotype. Using single gene deletion data, we address the problem of linking a phenotype to underlying functional roles in the organism and provide a sound computational and statistical paradigm that can be extended to address more complex experimental settings such as multiple deletions. We apply the proposed approaches to publicly available data sets to demonstrate strong evidence for the involvement of multi-protein complexes in the phenotypes studied. Assessing the role of multi-protein complexes in determining phenotype Nolwenn Le Meur and Robert Gentleman Fred Hutchinson Cancer Center Research, Program in Computational, Biology, 1100 Fairview Avenue North M2-B876, P.O. Box 19024, Seattle, Washington, USA 98109-1024 corresponding author: Nolwenn Le Meur <nlemeur@fhcrc.org>
Photoreceptor assessment in focal laser-treated central serous chorioretinopathy using adaptive optics and fundus autofluorescence

Abstract This study analyzed cone density, cone mosaic, and fundus autofluorescence (FAF) images in patients with focal laser-treated central serous chorioretinopathy (CSC). Observational case series. Forty-two eyes of 21 patients with unilateral treated CSC and bilateral best-corrected visual acuity of 1.0 (decimal fraction) were included. FAF and cone mosaic images were obtained in all patients with an adaptive optics fundus camera. Densities were recorded at 20 points throughout the macula, and choroidal thicknesses were measured. Mean choroidal thicknesses were 419.95 ± 110.33 μm in normal eyes, 459.09 ± 90.07 μm in eyes with active CSC, and 438.61 ± 107.57 μm in treated eyes. The highest density of cones in healthy eyes was 38146 cones/mm2, with a 5.66-μm intercellular space (IS), at 700 μm temporal to the center. In eyes with treated CSC, the highest density was 32749 cones/mm2, with a 6.13-μm IS, at 500 μm nasal to the center. In all quadrants, median values of maximum cone density were significantly higher in healthy eyes (P = .02, P = .003, P = .0001, and P = .001). Three types of lesions were identified on FAF and were correlated with those on cone mosaic images. Strong correlations were detected between the presence of hypoautofluorescent lesions on the first FAF image and a greater difference between maximum values of photoreceptor density (r 2 = 0.46, P = .03), as well as between the presence of hypoautofluorescent lesions and the duration of pathology (r 2 = 0.68, P < .001). The presence of hypoautofluorescent lesions and the duration of pathology were negative prognostic factors in CSC. Laser treatment could prevent photoreceptor loss.
Prescribing for Women with Breast Cancer in Their Survivorship Phase for Menopausal Symptoms.

There were 55,000 new cases of invasive breast cancer diagnosed in the UK between 2014-2016. With around 8,000 new breast carcinoma in situ cases identified every year, this equates to 22 new cases being recorded every day (2). With treatment these women can be advised that they have an estimated 78% survival rate of ten or more years (2). Around two-thirds (65%) of women diagnosed with breast cancer in England and Wales survive their disease for twenty years or more (1). It is noteworthy that the age range 50-69 years is when the chances of breast cancer survival are highest (Figure 1).
Classification for Penicillium expansum Spoilage and Defect in Apples by Electronic Nose Combined with Chemometrics

It is crucial for the efficacy of the apple storage to apply methods like electronic nose systems for detection and prediction of spoilage or infection by Penicillium expansum. Based on the acquisition of electronic nose signals, selected sensitive feature sensors of spoilage apple and all sensors were analyzed and compared by the recognition effect. Principal component analysis (PCA), principle component analysis-discriminant analysis (PCA-DA), linear discriminant analysis (LDA), partial least squares discriminate analysis (PLS-DA) and K-nearest neighbor (KNN) were used to establish the classification model of apple with different degrees of corruption. PCA-DA has the best prediction, the accuracy of training set and prediction set was 100% and 97.22%, respectively. synergy interval (SI), genetic algorithm (GA) and competitive adaptive reweighted sampling (CARS) are three selection methods used to accurately and quickly extract appropriate feature variables, while constructing a PLS model to predict plaque area. Among them, the PLS model with unique variables was optimized by CARS method, and the best prediction result of the area of the rotten apple was obtained. The best results are as follows: Rc = 0.953, root mean square error of calibration (RMSEC) = 1.28, Rp = 0.972, root mean square error of prediction (RMSEP) = 1.01. The results demonstrated that the electronic nose has a potential application in the classification of rotten apples and the quantitative detection of spoilage area.
Whole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates

Objectives The first hospital outbreak of carbapenemase-producing Enterobacteriaceae in Slovenia occurred in 2014–2016. Whole genome sequencing was used to analyse the population of carbapenem-resistant Klebsiella pneumoniae collected in Slovenia in 2014–2017, including OXA-48 and/or NDM-1 producing strains from the outbreak. Methods A total of 32 K. pneumoniae isolates were analysed using short-read sequencing. Multi-locus sequence typing and core genome multi-locus sequence typing were used to infer genetic relatedness. Antimicrobial resistance markers, virulence factors, plasmid content and wzi types were determined. Long-read sequencing was used for six isolates for detailed analysis of plasmids and their possible transmission. Results Overall, we detected 10 different sequence types (STs), the most common being ST437 (40.6%). Isolates from the initial outbreak belonged to ST437 (12/16) and ST147 (4/16). A second outbreak of four ST15 isolates was discovered. A new ST (ST3390) and two new wzi types (wzi-556, wzi-559) were identified. blaOXA-48 was found in 17 (53.1%) isolates, blaNDM-1 in five (15.6%), and a combination of blaOXA-48/NDM-1 in seven (21.9%) isolates. Identical plasmids carrying blaOXA-48 were found in outbreak isolates sequenced with long-read sequencing technology. Conclusions Whole genome sequencing of Slovenian carbapenem-resistant K. pneumoniae isolates revealed multiple clusters of STs, two of which were involved in the first hospital outbreak of carbapenem producing K. pneumoniae in Slovenia. Transmission of the plasmid carrying blaOXA-48 between two STs was likely to have occurred. A previously unidentified second outbreak was also discovered, highlighting the importance of whole genome sequencing in detection and/or characterization of hospital outbreaks and surveillance of drug-resistant bacterial clones.
The Clinical Utility of Neuromotor Exercise as Antihypertensive Lifestyle Therapy.

Hypertension Is a Prevalent Public Health Problem The American College of Cardiology (ACC) and American Heart Association (AHA) recently redefined hypertension to a lower blood pressure (BP) threshold of 130 mm Hg for systolic BP (SBP) or 80 mm Hg for diastolic BP (DBP) than the older Joint National Commission 7 (JNC7) criteria of 140/ 90 mm Hg (1,2). Now approximately 50% of adults in the United States are classified as having hypertension. The authors of the ACC/AHA recommendations emphasized that for the approximately 35 million U.S. adults who were newly diagnosed with hypertension according to these lower BP criteria, most of them could treat their hypertension with nonpharmaceutical therapies, such as exercise, which is one of the most effective lifestyle therapies for hypertension because it lowers BP 5 to 8 mm Hg (2).