Miracle-dz/UniFAR-FTUs huggingface dataset:
Healthcare-associated Clostridioides difficile infection during the COVID-19 pandemic in a tertiary care hospital in Romania

Abstract Introduction. Information on healthcare-associated C.difficile infection (HA-CDI) in COVID-19 patients is limited. We aimed to assess the characteristics of HA-CDI acquired during and before the COVID-19 pandemic. Methods. We conducted a retrospective study in a tertiary care hospital, in which since March 2020 exclusively COVID-19 patients are hospitalized. We compared HA-CDI adult patients hospitalized in March 2020-February 2021 with those hospitalized during the same period in 2017–2018. Results. We found 51 cases during 2020–2021 (COVID-19 group), incidence 5.6/1000 adult discharge and 99 cases during 2017–2018 (pre-COVID-19 group), incidence 6.1/1000 adult discharge (p=0.6). The patients in COVID-19 group compared to pre-COVID-19 group were older (median age 66 vs 62 years), with similar rate of comorbidities, but with higher rate of cardiovascular diseases (62.7% vs 42.4%) and less immunosuppression (21.6% vs 55.6%), they had a higher proton pump inhibitors use (94.1% vs 32.3%), and a longer hospitalization (median 19 vs 14 days). Eighty-five (85.9%) patients in pre-COVID-19 group versus 44 (86.3%) patients in COVID-19 group received antimicrobial treatment – mainly cephalosporins (34,1%), quinolones (22,3%) and glycopeptides (21,1%) in pre-COVID-19 group and mainly cephalosporins and macrolides (63,6% each) in COVID-19 group. We found four HA-CDI-related deaths in pre-COVID-19 group and none in the COVID-19 group. Conclusions. The HA-CDI incidence in COVID-19 group did not change versus the same period of time during 2017–2018. The antibiotic use was the most important factor associated with HA-CDI. We identified a high use of broad-spectrum antibiotics despite the lack of empirical antimicrobial recommendations in COVID-19.
Exchange Rate Volatility and Sectoral Analysis of Non-Oil Export in Nigeria

Abstract The paper seeks to assess the industry-based effect of exchange rate volatility on the export of non-oil sector in Nigeria. Theoretically and empirically, volatility-trade link is ambiguous. The paper employed bound test for co-integration between exchange rate volatility and exports of non-oil products. Empirically, the results show that we can accept the hypothesis of no co-integration between volatility and export of non-oil industries in most cases. Therefore, the study concludes that the exchange rate volatility can actually produce negative effect on non-oil export industries in the short-run especially the big industries (Agriculture, food and manufacturing) but this effect does not linger into the long-run and this suggests that most of these industries have been able to develop a mechanism to cope with exchange rate volatility problem in the long-run.
Public sector innovation performance in Federation of Bosnia and Herzegovina: An exploratory factor analysis

Abstract Innovation has nowadays become the main force to cope with challenging times in the fast-changing world. The influence of public sector innovation (PSI) in resolving dynamic economical and societal challenges is undisputable. Regardless of the numerous advantages of innovation in the public sector (PS) which have been recognised worldwide, the concept of public sector innovation is still novel for the Federation of Bosnia and Herzegovina (FBiH). Moreover, there is limited empirical evidence which would facilitate the understanding of public sector innovation performance. The purpose of this paper is to identify main components of PSI performance. The primary research data was obtained through a survey with close-ended questions which was completed by the public sector institution employees in FBiH. The exploratory factor analysis (EFA) was used in order to determine the principal components of measuring public sector innovation performance. The EFA returned the factor-structures for all four suggested constructs, innovation capabilities, wider sector conditions for innovation, sources of information and the share of creative occupation, explaining between 65% and 78% of the variance of the innovation performance measurement construct. The results from the exploratory factor analysis provided a distinct estimation on the factor structure of measuring PSI. The paper has provided and analysed the first instrument in measuring public sector innovation performance in FBiH.
Contribution of metal transporters of the ABC, ZIP, and NRAMP families to manganese uptake and infective endocarditis virulence in Streptococcus sanguinis

Streptococcus sanguinis is an important cause of infective endocarditis. In strain SK36, the ABC-family manganese transporter, SsaACB, is essential for virulence. We have now identified a ZIP-family protein, TmpA, as a secondary manganese transporter. A tmpA mutant had no phenotype, but a ΔssaACB ΔtmpA mutant was far more attenuated for serum growth and somewhat more attenuated for virulence in a rabbit model than its ΔssaACB parent. The growth of both mutants was restored by supplemental manganese, but the ΔssaACB ΔtmpA mutant required twenty-fold more and accumulated less. Although ZIP-family proteins are known for zinc and iron transport, TmpA-mediated transport of either metal was minimal. In contrast to ssaACB and tmpA, which appear ubiquitous in S. sanguinis, a mntH gene encoding an NRAMP-family transporter has been identified in relatively few strains, including VMC66. As in SK36, deletion of ssaACB greatly diminished VMC66 endocarditis virulence and serum growth, and deletion of tmpA from this mutant diminished virulence further. Virulence was not significantly altered by deletion of mntH from either VMC66 or its ΔssaACB mutant. This and the accompanying paper together suggest that SsaACB is of primary importance for endocarditis virulence while secondary transporters TmpA and MntH contribute to growth under differing conditions.
Physically active lifestyle is associated with attenuation of hippocampal dysfunction in healthy older adults

Alterations in hippocampal function have been shown in older adults, expressed as changes in hippocampal activity and connectivity. While hippocampal activation during memory demands have been demonstrated to decrease with age, some older individuals present increased activity, or hyperactivity, of the hippocampus which is associated with increased neuropathology and poorer memory function. In addition, lower functional coherence between the hippocampus and core hubs of the default mode network (DMN), namely the posteromedial and medial prefrontal cortices, as well as increased local intrahippocampal connectivity, were also demonstrated in cognitively intact older adults. Aerobic exercise has been shown to elicit neuroprotective effects on hippocampal structure and vasculature in aging, and improvements in maximal aerobic capacity (MAC) have been suggested to mediate these exercise-related effects. However, how these lifestyle factors relate to hippocampal function is not clear. Fifty-two cognitively intact older adults (age 65-80) have been recruited and divided into physically active (n=29) or non-active (n=23) groups based on their aerobic activity lifestyle habits. Participants underwent resting-state as well as task-based fMRI experiments which included an associative memory encoding paradigm followed by a post-scan memory recognition test. In addition, forty-four participants also performed cardiopulmonary exercise tests to evaluate MAC. While both groups demonstrated increased anterior hippocampal activation during memory encoding, physically active lifestyle was associated with significantly lower activity level and higher memory performance in the recognition task. In addition, the physically active group also demonstrated higher functional connectivity of the anterior and posterior hippocampi with the core hubs of the DMN, and lower local intra-hippocampal connectivity within and between hemispheres. MAC was negatively associated with hippocampal activation level and demonstrated positive correlation with hippocampal-DMN connectivity. According to these findings, aerobically active lifestyle may be associated with attenuation of hippocampal dysfunction in cognitively healthy older adults.
Noise Reconstruction & Removal Network: A New Architecture to Denoise FIB-SEM Images

Recent advances in Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) allows the imaging and analysis of cellular ultrastructure at nanoscale resolution, but the collection of labels and/or noise-free data sets has several challenges, often immutable. Reasons range from time consuming manual annotations, requiring highly trained specialists, to introducing imaging artifacts from the prolonged scanning during acquisition. We propose a fully unsupervised Noise Reconstruction and Removal Network for denoising scanning electron microscopy images. The architecture, inspired by gated recurrent units, reconstructs and removes the noise by synthesizing the sequential data. At the same time the fully unsupervised training guides the network in distinguishing true signal from noise and gives comparable results to supervised architectures. We demonstrate that this new network specialized on 3D electron microscopy data sets, achieves comparable and even better results than supervised networks.
A universal, open-source, high-performance tool for automated sleep staging

The creation of a completely automated sleep-scoring system that is highly accurate, flexible, well validated, free and simple to use by anyone has yet to be accomplished. In part, this is due to the difficulty of use of existing algorithms, algorithms having been trained on too small samples, and paywall demotivation. Here we describe a novel algorithm trained and validated on +27,000 hours of polysomnographic sleep recordings across heterogeneous populations around the world. This tool offers high sleep-staging accuracy matching or exceeding human accuracy and interscorer agreement no matter the population kind. The software is easy to use, computationally low-demanding, open source, and free. Such software has the potential to facilitate broad adoption of automated sleep staging with the hope of becoming an industry standard.
Synaptic density and neuronal metabolic function measured by PET in the unilateral 6-OHDA rat model of Parkinson’s disease

Parkinson’s disease (PD) is caused by progressive neurodegeneration and characterised by motor dysfunction. Neurodegeneration of dopaminergic neurons also causes aberrations within the cortico-striato-thalamo-cortical (CSTC) circuit, which has been hypothesised to lead to non-motor symptoms such as depression. Individuals with PD have both lower synaptic density and changes in neuronal metabolic function in the basal ganglia, as measured using [11C]UCB-J and [18F]FDG positron emission tomography (PET), respectively. However, the two radioligands have not been directly compared in the same PD subject or in neurodegeneration animal models. Here, we investigate [11C]UCB-J binding and [18F]FDG uptake in the CSTC circuit following a unilateral dopaminergic lesion in rats and compare it to sham lesioned rats. Rats received either a unilateral injection of 6-hydroxydopamine (6-OHDA) or saline in the medial forebrain bundle and rostral substantia nigra (n=4/group). After three weeks, all rats underwent two PET scans using [18F]FDG, followed by [11C]UCB-J on a separate day. [18F]FDG uptake and [11C]UCB-J binding were both lower in the ipsilateral striatal regions compared to the contralateral regions. Using [11C]UCB-J, we could detect an 8.7% decrease in the ipsilateral ventral midbrain, compared to a 2.9% decrease in ventral midbrain using [18F]FDG. Differential changes between hemispheres for [11C]UCB-J and [18F]FDG outcomes were also evident in the CSTC circuit’s cortical regions, especially in the orbitofrontal cortex and medial prefrontal cortex where higher synaptic density yet lower neuronal metabolic function was observed, following lesioning. In conclusion, [11C]UCB-J and [18F]FDG PET can detect divergent changes following a dopaminergic lesion in rats, especially in cortical regions that are not directly affected by the neurotoxin. These results suggest that combined [11C]UCB-J and [18F]FDG scans could yield a better picture of the heterogeneous cerebral changes in neurodegenerative disorders.
Implicit adaptation to mirror-reversal is in the correct coordinate system but the wrong direction

Learning in visuomotor adaptation tasks is the result of both explicit and implicit processes. Explicit processes, operationalized as re-aiming an intended movement to a new goal, account for the lion’s share of learning while implicit processes, operationalized as error-dependent learning that gives rise to aftereffects, appear to be highly constrained. The limitations of implicit learning are highlighted in the mirror-reversal task, where implicit corrections act in opposition to performance. This is surprising given the mirror-reversal task has been viewed as emblematic of implicit learning. One potential confound of these studies is that both explicit and implicit processes were allowed to operate concurrently, which may interact, potentially in opposition. Therefore, we sought to further characterized implicit learning in a mirror-reversal task with a clamp design to isolate implicit learning from explicit strategies. We confirmed that implicit adaptation is in the wrong direction for mirror-reversal and operates as if the perturbation were a rotation, and only showed a moderate attenuation after three days of training. This result raised the question of whether implicit adaptation blindly operates as though perturbations were a rotation. In a separate experiment, which directly compared a mirror-reversal and a rotation, we found that implicit adaptation operates in a proper coordinate system for different perturbations: adaptation to a mirror-reversal and rotational perturbation is more consistent with Cartesian and polar coordinate systems, respectively. It remains an open question why implicit process would be flexible to the coordinate system of a perturbation but continue to be directed inappropriately. Public Significance Statement Patients with severe amnesia can improve their performance from day to day in mirror-reversal tasks. These findings led, in part, to the codification of explicit and implicit processes in classic theories regarding the taxonomy of memory systems, with motor learning resting firmly in the branch of implicit memory. However, recent evidence has shown that explicit processes also play an important role in motor learning. What’s more, these studies have found that implicit learning doesn’t operate in a useful way in the mirror-reversal task. In the present study, we further examine this puzzling behavior of implicit learning in a mirror-reversal task using a design that can isolate implicit processes from explicit strategies. We clearly showed that the implicit system adapts in the wrong direction for a mirror-reversal, acting as if the perturbation were a rotation. Surprisingly, however, we found that although adaptation is in the wrong direction, the implicit system is sensitive to a particular coordinate system. These findings further challenge the flexibility of this implicit adaptation process in motor learning.
Deciphering signatures of natural selection via deep learning

Identifying genomic regions influenced by natural selection provides fundamental insights into the genetic basis of local adaptation. We propose a deep learning-based framework, DeepGenomeScan, that can detect signatures of local adaptation. We demonstrate that DeepGenomeScan outperformed PCA and RDA-based genome scans in identifying loci underlying quantitative traits subject to complex spatial patterns of selection. Noticeably, DeepGenomeScan increases statistical power by up to 47.25% under non-linear environmental selection patterns. We applied DeepGenomeScan to a European human genetic dataset and identified some well-known genes under selection and a substantial number of clinically important genes that were not identified using existing methods.
Impact of the COVID-19 Pandemic on Consultations and Diagnoses in Gastroenterology Practices in Germany

The COVID-19 pandemic has been a major burden for healthcare systems worldwide and has caused multiple changes and problems in outpatient care. The aim of this study was to investigate the impact of the COVID-19 pandemic on consultations and diagnoses in gastroenterology practices in Germany. To this end, we retrospectively analyzed data from the Disease Analyzer database (IQVIA) using the International Classification of Diseases, 10th revision (ICD-10). We included all patients aged ≥18 years with at least one visit to one of 48 gastroenterology practices in Germany between April and September 2019 and April and September 2020. A total of 63,914 patients in the 2nd quarter of 2019, 63,701 in the 3rd quarter of 2019, 55,769 in the 2nd quarter of 2020, and 60,446 in the 3rd quarter of 2020 were included. Overall, a clear downward trend in the number of visits to gastroenterologists was observed in the 2nd quarter of 2020 compared to 2019 (−13%, p = 0.228). The decrease in consultations was particularly pronounced in patients >70 years of age (−17%, p = 0.096). This trend was evident for all gastrointestinal diagnoses except for tumors. Most notably, rates of gastrointestinal infections (−19%) or ulcers (−43%) were significantly lower in this period than in the same quarter of 2019. Reflecting the course of the pandemic, the differences between the 3rd quarter of 2020 and that of 2019 were less pronounced (−5%, p = 0.560). Our data show that the pandemic changed patients' behavior with respect to the health care system. Using the example of German gastroenterology practices, we show that the number of consultations as well as the number and range of diagnoses have changed compared to the same period in 2019.
Comparisons Between Serum Levels of Hepcidin and Leptin in Male College-Level Endurance Runners and Sprinters

Background: Hepcidin-25 is a 25 amino acid hepatokine and a key regulator of iron metabolism related to iron deficiency anemia. Recent studies have suggested that an elevated hepcidin level is correlated with low energy availability. Leptin is an appetite-suppressing adipokine and has been reported to stimulate hepcidin production in animals and cultured cells. While leptin is modulated by exercise, it is known that endurance runners and sprinters practice different types of exercise. This study investigated and compared the relationships between hepcidin and leptin levels, iron status, and body fat to understand better the risk of iron deficiency anemia in endurance runners and sprinters. Methods: Thirty-six male college track and field athletes (15 endurance runners and 21 sprinters) were recruited for this study. Dietary intake, body composition, and blood levels of ferritin, hepcidin-25, leptin, and adiponectin were measured. Correlations between hepcidin levels and ferritin, body fat, leptin, and adiponectin were evaluated using Pearson's correlation coefficient for each group. Results: The endurance runners had lower hepcidin levels and higher leptin and adiponectin levels compared with sprinters. Ferritin was positively correlated with hepcidin-25 levels in both the endurance and sprinter groups. A positive correlation was observed between hepcidin-25 and body fat or leptin levels only in sprinters. Conclusion: This is the first study investigating the relationship between blood levels of hepcidin and leptin in athletes. The positive correlation between hepcidin-25 and leptin was observed in sprinters but not endurance runners.
Cytochrome P450 Omega-Hydroxylase 4a14 Attenuates Cholestatic Liver Fibrosis

Background Cholestasis is a pathological condition involving obstruction of bile secretion and excretion that results in hepatotoxicity, inflammation, fibrosis, cirrhosis, and eventually liver failure. Common bile duct ligation (BDL) model is a well-established murine model to mimic cholestatic liver fibrosis. We previously reported that cytochrome P450 omega-hydroxylase 4a14 (Cyp4a14) plays an important role in the pathogenesis of non-alcoholic fatty liver disease (NAFLD)-related fibrosis. The goal of this study was to determine the role of Cyp4a14 in cholestatic-induced liver fibrosis. Methods C57BL/6 mice were subjected to BDL for 14 days, and Cyp4a14 mRNA and protein levels were examined and compared with those of the sham group. Cyp4a14 knockout mice and adeno-associated virus (AAV)-mediated overexpression of Cyp4a14 in C57BL/6 mice underwent BDL and liver histology, and key fibrosis markers were examined. Results Both hepatic Cyp4a14 mRNA and protein levels were markedly reduced in BDL liver compared with the time-matched sham group. Cyp4a14 gene-deficient mice aggravates whereas its overexpression alleviates BDL-induced hepatic fibrosis, which were determined by liver function, liver histology, and levels of key fibrotic markers including α-smooth muscle actin (α-SMA), transforming growth factor-β1 (TGF-β1), and collagen 1a2 (Col1a2). Conclusion Cyp4a14 exerts a contrasting role in different hepatic fibrosis models. Strategies that enhance Cyp4a14 activity may be potential strategies to cholestatic related liver fibrosis.
Spatial and Structural Factors Shape Seagrass-Associated Bacterial Communities in Singapore and Peninsular Malaysia

Plant-microbe relationships play critical roles in the functioning and health of terrestrial plants, but little is known about this relationship in marine angiosperms such as seagrasses. Here, we investigated the microbial communities associated with the seagrass Enhalus acoroides throughout Singapore and Peninsular Malaysia. At each sampling location we collected 10 individual and unconnected plants. Each plant was subsequently broken down into leaves, roots, and rhizomes. In addition to living plant parts a sediment sample was taken in close proximity to each. Using high throughput 16S rRNA gene amplicon sequencing we characterised the bacterial communities associated with each plant part and the associated sediment sample. Results indicate geographic structuring of bacterial communities, with a significant pattern of distance decay suggesting dispersal limitation is a contributing factor to the differences we see in bacterial community structure. Bacterial communities can be further differentiated by the function of the collected sample (leaf, root, and rhizome), and we identified a number of microbial indicator species that are associated with each plant part. Further analysis revealed the presence of several microbial taxa that have previously been identified as indicators of “unhealthy” or “stressed” seagrass meadows. This study addresses a current scientific gap related to the characterisation of seagrass microbiomes, and provides a foundation on which future studies can build, particularly those in the Southeast Asian seagrass biodiversity hotspot.
Total contents of major minerals in the nature yoghurt and in the yoghurts with the date powder of three dry varieties

In this paper we report on the content of major minerals (calcium, magnesium, sodium, potassium, iron and zinc) in the nature yoghurt (without sugars) and three yoghurts added with date powders. The latter’s were from three dry date varieties (Mech-Degla, Degla-Beida and Frezza). The elements determination was carried out using atomic absorption spectrometry after mineralization processing. Total mineral content showed a great difference between the yoghurt nature and yoghurts enriched by date powder fruits. In the yoghurts added with date powder, following results were found (in mg/Kg): calcium (2213.31-2938.67), sodium (783.37-959.36), potassium (725.68-771.77), magnesium (169.54-267.85), iron (9.6-11.52), zinc (1.29-7.93). Concerning the natural yoghurt the values obtained were (in mg/Kg): calcium (1950.41), Sodium (684.72), potassium (540.58), magnesium (132.16), iron (5.26), zinc (0.35). These results are in positive interrelationship with those of the rheological properties.