Miracle-dz/UniFAR-FTUs huggingface dataset:
Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits

The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.
Chlamydia sp. in free-ranging populations of hawks (Buteo sp.) in Northern California

Chlamydiaceae bacteria include a large range of vertebrate hosts. Chlamydial organisms in raptors have been poorly studied. Previous reports have shown controversial prevalence in freeranging raptorial populations. In addition, avian chlamydiosis by Chlamydia psittaci strain G has been reported in Buteo species in Northern California. The objective of this study was to estimate the prevalence of Chlamydia sp. in free-ranging populations of hawks (Buteo sp.) from Northern California. We also compared Chlamydia sp. status with species (red-tailed hawks and Swainson’s hawks), age (juvenile and adult), sex (male and female), season (summer, fall, winter, spring), and bird geographic range (resident, medium-distance migrant, long-distance migrant). A total of 297 free-ranging Buteo sp. were sampled for swabs and whole blood. Conjunctiva, choana and cloaca were sampled with a single swab for qPCR analysis. Positive samples were sequenced based on the ompA gene and compared by high resolution melt analysis with all known C. psittaci strains (A-G, E/B, M56, WC), and C. pneumoniae. Aliquots from the plasma samples were sent to commercial laboratories in order to perform serology for IgM using the elementary body agglutination test (EBA; n=78) and for IgY using the indirect immunofluorescent assay (IFA; n=51). The overall prevalence of Chlamydiaceae in free-ranging Buteo species sampled in nine counties of Northern California was 1.37% (4/291) via qPCR analysis of multi-mucosal site swabs. An atypical chlamydial organism was detected by qPCR which was not identical to any C. psittaci known strain or C. pneumoniae. However, the most similar sequence was to the mammalian C. psittaci strain M56. None of the samples were positive for either serologic test. Due to the lack of antibody titers in any sample, it is possible that this chlamydial sequence is from a mammalian prey item passing through the gastrointestinal tract. Further studies will be required to identify this bacterium and its impact in the health of wild Buteo populations in Northern California.
Smallholder Farmers Perception of Climate Change and Variability Impactand Their Adaptation Strategies in the Upper and Lower Niger River BasinDevelopment Authority Areas, Nigeria

The work attempted to analyze vulnerabilities and adaptation responses of smallholder farmers in the Upper and Lower Niger River Basin Development Authority areas (U & LNRBDA). Qualitative data was used in this study. The qualitative data was collected using questionnaire method. One thousand and two hundred questionnaires (1200) were administered out of which one thousand and one hundred and twenty-four (1124) were returned for analysis. The research findings revealed that there is high level of climate change awareness in the study area. A significant number of the smallholder farmers attested to the fact that they were aware of the changing climate-increasing temperatures, unpredictable, erratic, heavy and increasing rainfall, late onset and early retreat of rains. This is validated by the various empirical studies in the region. Smallholder farmers in the study areas really possess knowledge of the impacts of climate change and variability which helped them to cope with climate change and variability. They were able to identify their areas of vulnerability and appropriate adaptation options in their own capacity. It is recommended that the government needs to build on their capacity, knowledge and practices to enhance resilience of the smallholder farmers and for sustainability of adaptation strategies to climate change and variability.
Profiling of Aeromagnetic Data Interpretation using the Eye Tracker

Summary Interpretation of geoscientific data is a difficult and sometimes an impossible task. The interpretation process involves the interplay between what are obviously or objectively noticeable phenomena in observations and what interpreters bring (i.e. subjectivity) to the interpretation in regards to presuppositions and expectations. As a first step towards understanding subjectivity and human biases in interpretation, our study focuses on quantitative profiling of the behaviour of interpreters. Whilst the data is being observed, we use an eye tracker that captures eye gaze information associated with the visualization of the data. The specific aims of this study include the analysis of: (1) target spotting accuracy and efficiency between interpreters with different levels of experience and different geoscience expertise; (2) the impact of commonly used enhancement tools for data interpretation. A preliminary experiment was conducted using an aeromagnetic dataset from Ontario, Canada, and the 1st order vertical derivative (1VD) of the corresponding data, to characterise the observation patterns in free viewing and target spotting accuracy for specific geological features (faults, granitoid intrusions, kimberlite pipes). The results showed: some distinct observation patterns between experienced and inexperienced interpreters; and the impact of the 1VD enhanced data in interpretation. The study outcomes may impact on a wide range of geoscientific activities including: risk management in decision making for the mining industry; education and training of geoscientists; and the development of enhancement tools for geoscientific data.
Phytoplankton observations in offshore Norwegian coastal waters between 62°N and 69°N - I. Variation in time of the spring diatom maximum 1968-71

BRAARUD, T. and NYGAARD, I. 1978. Phytoplankton observations in offshore Norwegian coastal waters between 62' N and 69" N. I. Variation in time of the spring diatom maximum 1968-71. FiskDir. Sh-r. Ser. HavUnde~s. , 16: 489-505. An attenlpt was made to trace yearly fluctuations in the timing of the spring diatom maximum along the Norwegian west coast, 62" N-69" N. Quantitative data on the diatonl population at 281 stations with 0 m samples and 120 stations with additional san~ples from the 10, 20 and 30 m levels, collected in March-April during the four years 1968-71, were used. A delay of about three weeks from the southern to the northern part of the area, as previously observed, was again established. The years 1970 and 1971 were years with an early ~l~aximum while 1969 was a definitely late year within the whole area. The time variatiorl in 1968-71 recorded in the Tr~ndelag and Helgeland subareas, showed trends different from those of the neighbour areas. The phytoplankton data were not adequate for a detailed analysis of the factors responsible for the timing of the maximum each year in the respective parts of the investigated area.
The Current Status of Palliative Care, Hospice, and End-of-Life Health Care Utilization in Patients With Malignant Ureteral Obstruction

Abstract Introduction: Malignant ureteral obstruction is associated with a poor prognosis, with a median survival of 3 to 7 months. These patients are ideal candidates for concurrent palliative care services, consistent with American Society of Clinical Oncology guidelines. We aimed to characterize palliative care, hospice, and end-of-life health care utilization in patients with malignant ureteral obstruction. Methods: Patients ≥ 18 years old at our institution and diagnosed with malignant ureteral obstruction between May 2014 and August 2020 were retrospectively identified and pertinent data extracted. Palliative care, hospice, and end-of-life health care utilization was described, and factors associated with each were assessed with logistic regression models. Overall survival was assessed with Cox proportional hazard regression models. Results: One hundred fifteen patients qualified for analysis; 39.1% (45/115) utilized palliative care and spent a median of 12.5 days (IQR 3-52 days) on nonhospice palliative care. On adjusted analysis Black ethnicity (aOR 3.44, 95% CI: 1.08-10.94) was associated with palliative care utilization. Of the patients, 53.9% (62/115) utilized hospice. The median time from hospice initiation to death was 12 days (IQR 5-23 days). On adjusted analysis, prior extirpative surgery (aOR 3.63, 95% CI 1.01-13.05) and palliative care utilization (aOR 4.38, 95% CI 1.70-11.31) were associated with hospice utilization. Median survival following diagnosis was 141 days (IQR 37.5-442.5). Of the patients, 43.0% (37/86) had high end-of-life health care utilization. On multivariable analysis, only hospice (aOR 0.03, 95% CI 0.01-0.14) was associated with less end-of-life health care utilization. Conclusions: Palliative care is underutilized in malignant ureteral obstruction. Hospice, but not palliative care utilization, was associated with decreased end-of-life health care utilization.
Développement d'une plateforme de microscopie en imagerie de fluorescence en temps de vie (FLIM) et de nanoparticules plasmoniques fluorescentes

v Table des matières . vii Liste des symboles et abréviations . xiii Remerciements . xv Introduction . 1 Chapitre 1 : Théorie . 5 1.1 La photoluminescence . 5 1.1.1 L’excitation/absorption . 6 1.1.2 L’état excité . 7 1.1.3 L’émission . 7 1.1.4. Temps de vie de fluorescence et rendement quantique . 9 1.1.5 Spectroscopie de fluorescence . 10 1.2 La plasmonique . 12 1.2. 1 Les métaux . 13 1.2. 2 La taille . 14 1.2. 3 La forme. 15 1.2. 4 Le couplage plasmonique . 16 1.3 La fluorescence augmentée par les métaux . 17 1.4 La microscopie . 20 1.4. 1 Microscopie optique. 20 1.4. 1.1 Microscopie à champ clair . 21 1.4. 1.2 Microscopie à champ sombre . 21 1.4. 1.3 Microscopie de fluorescence . 22 1.4. 1.4 Microscopie confocale à balayage laser . 24 1.4. 1.5 Microscopie d’imagerie en temps de vie de fluorescence (FLIM) . 25 1.4. 1.6 Résolution de la microscopie optique . 26 1.4. 2 Microscopie électronique . 27
Temperature control after successful resuscitation from cardiac arrest in adults

Background Out-of-hospital cardiac arrest (OHCA) is the third leading cause of death in Europe, and results in a high burden of disability for patients and their families. 1 When the heart stops, the body and brain cells quickly deplete of oxygen. Without intervention, brain damage occurs rapidly, and death is inevitable. Unfortunately, the prognosis for OHCA remains poor, even when return of spontane-ous circulation (ROSC) is achieved. Only a few (less than 10%) OHCA patients can be discharged from the hospital, and only two thirds of these are discharged with a good neurological outcome to lead an independent life. 1 Reperfusion injury starts immediately following ROSC. Multiple pathophysiological cascades lead to reactive astrogliosis and microglia activation, and neuronal death by necrosis and apoptosis. This is one of the key components of what has been described as ‘post resuscitation syndrome’. 2 Mild hypothermia in the range of 32 to 34 8 C was shown to mitigate these different pathophysiological cascades simultaneously, efﬁciently limiting brain cell damage. 3 Numerous animal studies conﬁrmed the bene-ﬁcial effect of mild hypothermia. 4 In 2002, two landmark randomised clinical trials (RCT) in patients after cardiac arrest with shockable rhythm showed improved neurological outcomes following treatment with mild hypo-thermia in the range of 32 to 34 8 C compared with no temperature control. 5,6 As a result of these studies, in 2005, the European Resuscitation Council (ERC) guidelines recommended the use of mild hypothermia in
Designing an early selection morphological traits index for reproductive efficiency in Pura Raza Española mares

Abstract The low rate of reproductive efficiency in horses may be linked to the equine industry’s practice of maintaining breeding stock that stands out for its athletic or morphological performance but exhibits poor reproductive efficiency. In this study, the age at first foaling, age at last foaling, interval between first and second foaling, average interval between foaling, foaling number and reproductive efficiency, and their relationship with the morphological records in 19,758 Pura Raza Española (PRE) mares were analyzed. After a partial least squares analysis height at withers, lateral hock angle, dorsal-sternal diameter, perimeter of anterior cannon bone, angle of shoulder, thoracic perimeter, hip-stifle distance, and angle of croup were the most important traits related with reproductive traits in PRE mares. A multivariate animal model with both morphological and reproductive traits was applied, including age, geographical area, coat color, and average stud size in the decade of the mare’s first foaling. The results indicate that reproductive selection is feasible, and is enhanced by the use of morphological traits, given the moderate to high magnitudes of heritability values in both types of traits, which oscillated between 0.1 (interval between first and second foaling) and 0.95 (height at withers). The resulting genetic parameters were used to develop a series of selection indexes based on morphological or morphological and reproductive combination traits to improve reproductive efficiency traits in PRE mares and thus compute the expected genetic response (EGR) for the different strategies. The increase in EGR, when comparing EGR using only reproductive traits as selection criteria vs. using a combined index of both morphological and reproductive traits, oscillated between 4.0% for the age at first foaling to 46.8% for the interval between first and second foaling. In addition, two precocity indexes showed positive EGR when the age at last foaling and the interval between first and second foaling, both with and without morphological traits, were used as selection criteria. Therefore, this analysis reveals that the preselection of reproductive traits based on morphological traits is possible in PRE mares. Ultimately, this knowledge will help breeders achieve genetic progress in reproductive traits, leading to healthier and more successful breeding outcomes in horses.
Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation

SUMMARY The microbial community inhabiting the human colon, referred to as the gut microbiota, is mostly composed of bacterial species that, through extensive metabolic networking, degrade and ferment components of food and human secretions. The taxonomic composition of the microbiota has been extensively investigated in metagenomic studies that have also revealed details of molecular processes by which common components of the human diet are metabolized by specific members of the microbiota. Most studies of the gut microbiota aim to detect deviations in microbiota composition in patients relative to controls in the hope of showing that some diseases and conditions are due to or exacerbated by alterations to the gut microbiota. The aim of this review is to consider the gut microbiota in relation to the evolution of Homo sapiens which was heavily influenced by the consumption of a nutrient-dense non-arboreal diet, limited gut storage capacity, and acquisition of skills relating to mastering fire, cooking, and cultivation of cereal crops. The review delves into the past to gain an appreciation of what is important in the present. A holistic view of “healthy” microbiota function is proposed based on the evolutionary pathway shared by humans and gut microbes.
Stereotactic radiotherapy in previously treated lung cancers—what are the risks?

Patients affected by intra-thoracic recurrences of primary or secondary lung malignancies after the first course of definitive radiotherapy (RT) have limited therapeutic options, and they are often treated with palliative intent. Re-irradiation with stereotactic radiotherapy (SRT) represents an appealing approach, due to the optimized dose distribution that allows for high-dose delivery with better sparing of organs at risk; however, toxicity still represents an issue, even with dose-fractionation risk-adapted approaches. This review aims to analyze clinical data and dosimetric parameters related to stereotactic re-irradiation, mainly focusing on the toxicity profile, whose risk often limits the adoption of this technique in clinical practice.
High-density ear-EEG for understanding ear-centered EEG

Background. Mobile ear-EEG provides the opportunity to record EEG unobtrusively in everyday life. However, in real-life, the EEG data quickly becomes difficult to interpret, as the neural signal is contaminated by other, non-neural signal contributions. Due to the small number of electrodes in ear-EEG devices, the interpretation of the EEG becomes even more difficult. For meaningful and reliable ear-EEG, it is crucial that the brain signals we wish to record in real life are well-understood and that we make optimal use of the available electrodes. Their placement should be guided by prior knowledge about the characteristics of the signal of interest. Objective. We want to understand the signal we record with ear-EEG and make recommendations on how to optimally place a limited number of electrodes. Approach. We built a high-density ear-EEG with 31 channels spaced densely around one ear. We used it to record four auditory event-related potentials (ERPs): the mismatch negativity, the P300, the N100 and the N400. With this data, we gain an understanding of how different stages of auditory processing are reflected in ear-EEG. We investigate the electrode configurations that carry the most information and use a mass univariate ERP analysis to identify the optimal channel configuration. We additionally use a multivariate approach to investigate the added value of multi-channel recordings. Main results. We find significant condition differences for all ERPs. The different ERPs vary considerably in their spatial extent and different electrode positions are necessary to optimally capture each component. In the multivariate analysis, we find that the investigation of the ERPs benefits strongly from multi-channel ear-EEG. Significance. Our work emphasizes the importance of a strong theoretical and practical background when building and using ear-EEG. We provide recommendations on finding the optimal electrode positions. These results will guide future research employing ear-EEG in real-life scenarios.
Genomic analysis of lineage-specific transmission of multidrug resistance tuberculosis in China

ABSTRACT Objectives We investigated the genetic diversities and lineage-specific transmission dynamics of multidrug-resistant tuberculosis (MDR-TB), with the goal of determining the potential factors driving the MDR epidemics in China. Methods We curated a large nationwide Mycobacterium tuberculosis (M. tuberculosis) whole genome sequence data set, including 1313 MDR strains. We reconstructed the phylogeny and mapped the transmission networks of MDR-TB across China using Bayesian inference. To identify drug-resistance variants linked to enhanced transmissibility, we employed ordinary least-squares (OLS) regression analysis. Result The majority of MDR-TB strains in China belong to lineage 2.2. 1. Transmission chain analysis has indicated that the repeated and frequent transmission of L2.2. 1 plays a central role in the establishment of MDR epidemic in China, but no occurrence of a large predominant MDR outbreak was detected. Using OLS regression, the most common single nucleotide polymorphisms (SNPs) associated with resistance to isoniazid (katG_p.Ser315Thr and katG_p.Ser315Asn) and rifampicin (rpoB_p.Ser450Leu, rpoB_p.His445Tyr, rpoB_p.His445Arg, rpoB_p.His445Asp, and rpoB_p.His445Asn) were more likely to be found in L2 clustered strains. Several putative compensatory mutations in rpoA, rpoC, and katG were significantly associated with clustering. The eastern, central, and southern regions of China had a high level of connectivity for the migration of L2 MDR strains throughout the country. The skyline plot showed distinct population size expansion dynamics for MDR-TB lineages in China. Conclusion MDR-TB epidemic in China is predominantly driven by the spread of highly transmissible Beijing strains. A range of drug-resistance mutations of L2 MDR-TB strains displayed minimal fitness costs and may facilitate their transmission.
A Mechanism for the Origin of Specifically Oriented Textures in Development with Special Reference to Nitella Wall Texture

Many oriented growth phenomena, including the elongation of the Nitella internode, are based upon oriented or textured cell wall structure. In many cases the ordered textures are not present in the earliest stages of cell development but appear later. In Nitella lateral cell (leaf) development the first appearance of transverse wall texture (detected in polarized light) approximately coincides with a transverse stretching of the cell and its wall. This oriented stretching appears not to have its origin in a pre-existing texture but rather to be the result of a particular distribution of wall expansion rates. The relation between rates and oriented distortions is studied as a general phenomenon. The form these rate variations must take to provide longitudinal, transverse, or isotropic distortion is derived. Model devices made of rubber membranes, where expansion rate is varied by reinforcement of the rubber, generate distortions (textures in the rubber) of the type predicted. In the course of development it is possible that imbalances in expansion rate based on gradients (of metabolites, pH, light, etc.) bring on, through strain orientation, the initial alignment of originally randomly oriented fibrous ultrastructures, such as microfibrils of the cell wall or cytoplasmic microtubules.