Miracle-dz/UniFAR-FTUs huggingface dataset:
Alternative Assembly of Qβ Virus Like Particles

Qβ virus like particles (VLPs) are versatile platforms for grafting functional groups for vaccine development. The structure of Qβ VLPs at atomic detail are critical for design of more effective vaccines. While the structures of native Qβ VLPs have been determined previously, the structure of VLPs assembled from a recombinantly expressed Qβ coat protein, which are extensively used as platforms have not been studied. We sought to determine the crystal structures of VLPs assembled from recombinantly expressed Qβ coat protein of wild type and two mutants: A38K and A38K/A40C/D102C. The structures of Qβ VLPs assembled from recombinantly expressed Qβ coat proteins showed that VLPs can be assembled both in T=1 and T=3 symmetry.
Self-Reported Medication Use among Pregnant and Breastfeeding Women during the COVID-19 Pandemic: A Cross-Sectional Study in Five European Countries

Insight into the epidemiology of perinatal medication use during the COVID-19 pandemic is scarce. Therefore, a cross-sectional study using an anonymous web survey was performed in Ireland, Norway, Switzerland, The Netherlands, and United Kingdom (UK) to investigate the prevalence and type of medications used by pregnant and breast-feeding women during the first pandemic wave. Factors associated with medication use were estimated by logistic regression. In total, 8378 women participated (i.e., 3666 pregnant and 4712 breastfeeding women). Most responses were collected in Norway (34%) and The Netherlands (28%), followed by Switzerland (19%), Ireland (17%) and UK (2%). Participants were more often professionally active and more often had a higher educational level compared to the general birthing population in each country. Overall, approximately 60% of women reported having used at least 1 medication in the preceding 3 months. Daily and occasional use was reported by 34% and 42% of pregnant and 29% and 44% of breastfeeding women. The most prevalent ATC (Anatomical Therapeutic Chemical) categories were the nervous system, the respiratory system, the alimentary tract/metabolism, and the musculo-skeletal system. Paracetamol, ibuprofen, antacids, and cetirizine were the most frequently used medications. The rate of antibacterial use was lower than previously reported. Having a chronic illness, country, maternal age, SARS-CoV-2 testing, professional status and time since delivery were associated with medication use. In conclusion, perinatal medication use was highly prevalent during the first pandemic wave, underlining the importance of maintaining counseling efforts on medication use, even in times of disrupted healthcare services and/or limited resources.
The temporal and contextual stability of activity levels in hippocampal CA1 cells

Recent long-term optical imaging studies have demonstrated that the activity levels of hippocampal neurons in a familiar environment change on a daily to weekly basis. However, it is unclear whether there is any time-invariant property in the cells’ neural representations. In this study, using miniature fluorescence microscopy, we measured the neural activity of the mouse hippocampus in four different environments every 3 days. Although the activity level of hippocampal neurons fluctuated greatly in each environment across days, we found a significant correlation between the activity levels for different days, and the correlation was higher for averaged activity levels across multiple environments. When the number of environments used for averaging was increased, a higher activity correlation was observed. Furthermore, the number of environments in which a cell showed activity was preserved. Cells that showed place cell activity in many environments had greater spatial information content, and thus carried a higher amount of information about the current position. In contrast, cells that were active only in a small number of environments provided sparse representation for the environment. These results suggest that each cell has not only an inherent activity level but also play a characteristic role in the coding of space. Significance Statement Recent studies have revealed that place cell activity in the hippocampal CA1 cells exhibit instability on a daily to weekly scale. However, it is unclear whether there is any invariant property in the activity of the cells. In this study, we found that, although the activity level of CA1 neurons fluctuated greatly in one environment, the mean activity level across multiple environments was more stable. Furthermore, the number of environments in which a cell showed activity was preserved over time. These results suggest that even though the spatial code changes dynamically, each cell has an inherent activity level and plays a characteristic role in spatial coding.
Towards Understanding the Source of Brine Mineralization in Southeast Nigeria: Evidence from High-Resolution Airborne Magnetic and Gravity Data

Investigation into understanding the genesis of brines in southeast Nigeria was carried out utilizing high-resolution potential field (HRPF) data. This study reveals that igneous intrusions and associated hydrothermal fluids are responsible for brine generation. The obtained result of the analytic signal revealed the locations and spatial distribution of short- and long-wavelength geologic structures associated with igneous intrusions. The low pass filtering, upward continuation, and 2D modelling procedures showed key synclinal structures which coincided well with the location of brine fields. The results showed that salt ponds are common in the neighborhood of igneous intrusions. To validate this finding, a conceptual model describing igneous-related hydrothermal circulation systems that are driven by convective cells of the hydrothermal fluid and overburden loads was generated. This model fits reasonably well into the overall stratigraphic and geologic framework of the study area.
Machine Learning in Prostate MRI for Prostate Cancer: Current Status and Future Opportunities

Advances in our understanding of the role of magnetic resonance imaging (MRI) for the detection of prostate cancer have enabled its integration into clinical routines in the past two decades. The Prostate Imaging Reporting and Data System (PI-RADS) is an established imaging-based scoring system that scores the probability of clinically significant prostate cancer on MRI to guide management. Image fusion technology allows one to combine the superior soft tissue contrast resolution of MRI, with real-time anatomical depiction using ultrasound or computed tomography. This allows the accurate mapping of prostate cancer for targeted biopsy and treatment. Machine learning provides vast opportunities for automated organ and lesion depiction that could increase the reproducibility of PI-RADS categorisation, and improve co-registration across imaging modalities to enhance diagnostic and treatment methods that can then be individualised based on clinical risk of malignancy. In this article, we provide a comprehensive and contemporary review of advancements, and share insights into new opportunities in this field.
Early onset of severe lymphopenia during definitive radiotherapy correlates with mean body dose and predicts poor survival in cervical cancer

BACKGROUND: Lymphopenia during definitive radiotherapy (RT) has been shown to reduce survival in patients with cervical cancer. However, there are few studies on the significance of onset time of lymphopenia during RT in patients with cervical cancer. OBJECTIVE: This study aimed to exam the prognostic significance of early onset of severe lymphopenia (EOSL) during definitive RT in patients with cervical cancer. METHODS: Newly diagnosed cervical cancer patients treated with definitive RT from January 2015 to December 2019 were eligible for this retrospective study. EOSL was defined as first onset of grade 3–4 lymphopenia ⩽ 3 weeks from the start of RT. Mean body dose (MBD) was the mean radiation dose absorbed by the body during the whole course of external beam RT (EBRT) and was directly obtained from the dose volume histogram (DVH) of the EBRT planning. Logistic regression analysis and restricted cubic spline (RCS) models were applied to assess relationships between clinicopathological factors and EOSL. Survival analysis was performed using Kaplan-Meier curves and log-rank test. A COX regression model was developed to predict overall survival (OS). RESULTS: A total of 104 patients were included and 59.6% had EOSL. MBD (P= 0.04), concurrent cisplatin (P= 0.011), and pre-RT absolute lymphocyte count (ALC) (P= 0.001) were associated with EOSL. A linear relationship (P for non-linearity = 0.803) between MBD and risk of EOSL was found. Patients with EOSL had decreased OS (2-yr 75.1% vs 91.1%, P= 0.021) and progression-free survival (PFS) (2-yr 71.2% vs 83.7%, P= 0.071). An OS prediction COX model was developed with C-index of 0.835 and AUC of 0.872. CONCLUSIONS: EOSL during definitive RT correlates with MBD and predicts poor survival in patients with cervical cancer.
Real-Time Detection of Full-Scale Forest Fire Smoke Based on Deep Convolution Neural Network

To reduce the loss induced by forest fires, it is very important to detect the forest fire smoke in real time so that early and timely warning can be issued. Machine vision and image processing technology is widely used for detecting forest fire smoke. However, most of the traditional image detection algorithms require manual extraction of image features and, thus, are not real-time. This paper evaluates the effectiveness of using the deep convolutional neural network to detect forest fire smoke in real time. Several target detection deep convolutional neural network algorithms evaluated include the EfficientDet (EfficientDet: Scalable and Efficient Object Detection), Faster R-CNN (Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks), YOLOv3 (You Only Look Once V3), and SSD (Single Shot MultiBox Detector) advanced CNN (Convolutional Neural Networks) model. The YOLOv3 showed a detection speed up to 27 FPS, indicating it is a real-time smoke detector. By comparing these algorithms with the current existing forest fire smoke detection algorithms, it can be found that the deep convolutional neural network algorithms result in better smoke detection accuracy. In particular, the EfficientDet algorithm achieves an average detection accuracy of 95.7%, which is the best real-time forest fire smoke detection among the evaluated algorithms.
Epidemiology and laboratory diagnosis of very virulent infectious bursal disease virus in vaccinated chickens in Khartoum, Sudan

Background: Infectious Bursal Disease (IBD, Gumboro disease) has become more severe than in early outbreaks in the 1980s. The present research aims to study the epidemiology of IBD in Khartoum state and compare some commonly used laboratory techniques for diagnosis. Method: We collected epidemiological data from 30 farms that showed signs suggestive of IBD, estimated the morbidity and mortality rates, and interviewed the owners about the type and the doses of the used vaccines. We collected bursas of Fabricius for virus assays and histopathology. Samples positive in the agar gel immunodiffusion (AGID) test were inoculated onto chicken embryo fibroblast cell culture and embryonated chicken eggs. Twenty-two-day-old chicks were infected experimentally with three selected isolates, and morbidity and mortality rates were compared. Results: The results showed that 70% of outbreaks occurred between 6 and 8 weeks of age, and the mean mortality rate was 51%. Epidemiologic, clinical, gross, and histopathological findings were characteristic of the severe disease caused by the very virulent IBDvirus (vvIBDV). The farms that used intermediate or the intermediate plus vaccines had lowered mortality compared with the farms that used intermediate vaccines. The AGID was found more sensitive than the counter-immuno-electrophoresis (CIEP) since it detected 83.4% of the IBDV antigen in the samples while the CIEP detected 66.7% of the samples. The reverse transcriptase polymerase chain reaction (RT-PCR) was found to be rapid, specific, and was more sensitive detecting 100% of the tested samples. Virus isolation in embryonated eggs and cell culture was not successful. Conclusion: A vvIBDV is responsible for the recent outbreaks of the disease in Sudan, resulting in a mean high mortality rate of 51%, even in vaccinated flocks. The RT-PCR and AGID are the best methods for laboratory confirmation.
Silver Nanoparticles Alter Microtubule Arrangement, Dynamics and Stress Phytohormone Levels

The superior properties of silver nanoparticles (AgNPs) has resulted in their broad utilization worldwide, but also the risk of irreversible environment infestation. The plant cuticle and cell wall can trap a large part of the nanoparticles and thus protect the internal cell structures, where the cytoskeleton, for example, reacts very quickly to the threat, and defense signaling is subsequently triggered. We therefore used not only wild-type Arabidopsis seedlings, but also the glabra 1 mutant, which has a different composition of the cuticle. Both lines had GFP-labeled microtubules (MTs), allowing us to observe their arrangement. To quantify MT dynamics, we developed a new microscopic method based on the FRAP technique. The number and growth rate of MTs decreased significantly after AgNPs, similarly in both lines. However, the layer above the plasma membrane thickened significantly in wild-type plants. The levels of three major stress phytohormone derivatives—jasmonic, abscisic, and salicylic acids—after AgNP (with concomitant Ag+) treatment increased significantly (particularly in mutant plants) and to some extent resembled the plant response after mechanical stress. The profile of phytohormones helped us to estimate the mechanism of response to AgNPs and also to understand the broader physiological context of the observed changes in MT structure and dynamics.
Feminist Worlding and World Cinema: The Case of Małgorzata Szumowska

This article discusses the concept of worlding in the cinema of Małgorzata Szumowska. Informed by philosophical theory of worlding and worldliness, by thinkers such as Martin Heidegger, Hannah Arendt, and Gayatri Spivak, and the film theory of cinematic worlds, proposed by Daniel Yacavone, the project examines the function of cinematic world building and its potential connection to World Cinema and feminist filmmaking. Close analysis of Szumowska’s film The Other Lamb (2019) traces the role of monstration and mise en scène in creating emancipatory cinema.
Taking territory seriously in a fluid, topologically varied world: reflections in the wake of the populist turn and the COVID-19 pandemic

This article is published as part of the Geografiska Annaler: Series B, Human Geography special issue based on the Vega symposium: ‘Bounded spaces in question: X-raying the persistence of regions and territories, edited by Anssi Paasi. ABSTRACT A concern with territory may seem anachronistic in the face of the interconnected, fluid, topologically complex political-geographic landscape of the twenty-first century. Yet in many places borders are hardening, the movement of people is becoming more limited, and state nationalism is gaining ground. The recent rise of populist-nationalist movements and the responses to the spread of SARS-CoV-2 around the world are illustrative of conflicting political and social dynamics that are simultaneously reinforcing and challenging dominant territorial ideas and assumptions. Coming to grips with this state of affairs demands an increasingly sophisticated engagement with the concept of territory–one that treats territory as a shifting, yet sticky, element of a complex system that is constantly being remade through the interplay of material circumstances and ideological dispositions.
Accessory phase perspectives for ore-forming processes and magmatic sulphide exploration in the Labrador Trough, northern Québec, Canada

The compositions of resistant indicator minerals are diagnostic of their original host environment. They may be used to fingerprint different types of mineral deposit as well as vector towards them. We have characterised the composition of apatite and Fe-Ti oxides in variably-mineralised mafic-ultramafic rock units of the Montagnais Sill Complex in the Labrador Trough to assess their suitability for vectoring magmatic sulphide occurrences. Two broad types of apatite were identified: (i) fluoro- to hydroxy-apatite (Cl/[Cl+F] < 0.2); and (ii) chloro- to hydroxy apatite (Cl/[Cl+F] > 0.5). The former reflects variable degrees of degassing and Cl-loss during Rayleigh fractionation and is not indicative of Ni-Cu-mineralisation or host rock. The latter exists only in sulphidic olivine cumulate units and thus, may be used to vector similar rock types in the Labrador Trough. Ilmenite is the dominant oxide, except for the upper parts of differentiated gabbroic sills in which titanomagnetite is dominant. Magnetite occurs only as a secondary phase in serpentinised olivine cumulates and is not discriminative for magmatic sulphides. Ilmenite and titanomagnetite in the sulphidic olivine-bearing units have characteristically high Mg (~ 1,000-10,000 ppm), Cr (~ 100-1,000 ppm), Ni (~ 10-1,000 ppm), and Cu (~ 1-10,000 ppm) concentrations relative to those from other rock units. Their composition is consistent with Fe-Ti oxides derived from evolved sulphide melts in ultramafic-hosted Ni-Cu-(PGE) sulphide deposits and thus may be used to vector towards similar magmatic sulphide occurrences in the Labrador Trough.
Comparison of Bacterial Community Structure in PM2.5 within Broiler Houses under Different Rearing Systems in China

Background: In intensive poultry farming, high concentrations of indoor particulate matter (PM) impact production performance and welfare. In this study, PM2.5 level and bacterial community diversity were investigated in a multilayer cage house rearing system (CH) and a net flooring house rearing system (FH) during different growth stages to clarify the effects of the rearing systems on the diversity of airborne bacteria and help improve health management. Methods: The IC and high-throughput sequencing were used for ion composition and bacterial diversity analysis of PM2.5 collected from CH and FH. Results: The concentrations of NH3, CO2 and PM2.5 in CH were significantly lower than FH (p < 0.001) in both middle and late rearing stages. PM concentrations gradually increased with broiler growth only in FH. The water-soluble ions of PM2.5 samples had no significant difference between the two systems (p > 0.05). Firmicutes, Actinobacteria and Proteobacteria were the most abundant phyla in both the atmosphere and the broiler houses, but the composition was significantly different. The bacterial community in the broiler houses had strong correlations with temperature, humidity and PM of extremely high concentrations. Ions had stronger correlations with microbial community structure. Conclusions: The superiority of CH in environmental control over FH indicates that improved techniques in environmental control and breeding management can greatly reduce farming air pollution and improve the health management of broiler houses.
Using high-resolution global climate models from the PRIMAVERA project to create a European winter windstorm event set

Abstract. PRIMAVERA was a European Union Horizon 2020 project whose primary aim was to generate advanced and well-evaluated high-resolution global climate model datasets, for the beneﬁt of governments, business and society in general. Following consultation with members of the insurance industry, we have used a PRIMAVERA multi-model ensemble to generate a European winter windstorm event set for use in insurance risk analysis, containing approximately 1300 years of windstorm data. To create the storm footprints for the event set, the storms in the PRIMAVERA models are identified through tracking. A method is developed to separate the winds from storms occurring in the domain at the same time. The wind footprints are bias corrected and converted to 3-s gusts onto a uniform grid using quantile mapping. The distribution of the number of model storms per season as a function of estimated loss is consistent with re-analysis, as are the total losses per season, and the additional event set data greatly reduces uncertainty on return period magnitudes. The event set also reproduces the temporally clustered nature of European windstorms. Since the event set is generated from global climate models, it can help to quantify the non-linear relationship between large-scale climate indices such as the North Atlantic Oscillation (NAO) and windstorm damage. Although we find only a moderate positive correlation between extended winter NAO and storm damage in northern European countries (consistent with re-analysis), there is a large change in risk of extreme seasons between negative and positive NAO states. The intensities of the most severe storms in the event set are, however, sensitive to the gust conversion/bias correction method used, so care should be taken when interpreting the expected damages for very long return periods.
The effectiveness and safety of pulmonary autograft as living tissue in Ross procedure: a systematic review

Background Reports on effectiveness and safety after the implant of pulmonary autograft (PA) living tissue in Ross procedure, to treat both congenital and acquired disease of the aortic valve and left ventricular outflow tract (LVOT), show variable durability results. We undertake a quantitative systematic review of evidence on outcome after the Ross procedure with the aim to improve insight into outcome and potential determinants. Methods A systematic search of reports published from October 1979 to January 2021 was conducted (PubMed, Ovid Medline, Ovid Embase and Cochrane library) reporting outcomes after the Ross procedure in patients with diseased aortic valve with or without LVOT. Inclusion criteria were observational studies reporting on mortality and/or morbidity after autograft aortic valve or root replacement, completeness of follow-up >90%, and study size n≥30. Forty articles meeting the inclusion criteria were allocated to two categories: pediatric patient series and young adult patient series. Results were tabulated for a clearer presentation. Results A total of 342 studies were evaluated of which forty studies were included in the final analysis as per the eligibility criteria. A total of 8,468 patients were included (7,796 in pediatric cohort and young adult series and 672 in pediatric series). Late mortality rates were remarkably low alongside similar age-matched mortality with the general population in young adults. There were differences in implantation techniques as regard the variability in stress and the somatic growth that recorded conflicting outcomes regarding the miniroot vs the subcoronary approach. Discussion The adaptability of lung autograft to allow for both stress variability and somatic growth make it an ideal conduit for Ross’s operation. The use of the miniroot technique over subcoronary implantation for better adaptability to withstand varying degrees of stress is perhaps more applicable to different patient subgroups.