Miracle-dz/UniFAR-FTUs huggingface dataset:
A revised SNP-based barcoding scheme for typing Mycobacterium tuberculosis complex isolates

ABSTRACT The development of whole-genome sequencing technologies is gradually leading to a more detailed description of the population structure of the Mycobacterium tuberculosis complex (MTBC). In this study, we correlated previously published classifications on a collection of more than 10,000 genomes and proposed a new, comprehensive nomenclature that unifies the existing ones. In total, we identified 169 lineages and sublineages of M. tuberculosis/M. africanum and 9 animal-adapted species. For the purpose of organizing these genotypes in a more streamlined manner, we stratified them into five hierarchical levels. To represent the classification and compare it with the reference, we compiled a confirmatory data set of 670 high-quality isolates, which includes all genotypes and species of MTBC, and this confirmatory data set can serve as a basis for further studies. We proposed a set of 213 robust barcoding single-nucleotide polymorphisms and a suitable workflow for reliable differentiation of genotypes and species within the complex. This work integrates the results of all the major systematized studies to date to provide an understanding of the global diversity of the MTBC population structure. The results of this work may ultimately help to reliably determine the pathogen genotype and associate it with traits that reflect its prevalence, virulence, vaccination, and treatment efficiency, as well as to reliably find natural features revealed during its spread. IMPORTANCE Through years of research into the Mycobacterium tuberculosis complex (MTBC), a number of ambiguous phylogenetic classifications have emerged, which often overlap with one another. In the present study, we have combined all major studies on MTBC classification and inferred a unified, most complete to date classification and accompanying SNP barcodes. Through years of research into the Mycobacterium tuberculosis complex (MTBC), a number of ambiguous phylogenetic classifications have emerged, which often overlap with one another. In the present study, we have combined all major studies on MTBC classification and inferred a unified, most complete to date classification and accompanying SNP barcodes.
Increased PDGFRB and NF-κB signaling caused by highly prevalent somatic mutations in intracranial aneurysms

Intracranial aneurysms (IAs) are a high-risk factor for life-threatening subarachnoid hemorrhage. Their etiology, however, remains mostly unknown at present. We conducted screening for sporadic somatic mutations in 65 IA tissues (54 saccular and 11 fusiform aneurysms) and paired blood samples by whole-exome and targeted deep sequencing. We identified sporadic mutations in multiple signaling genes and examined their impact on downstream signaling pathways and gene expression in vitro and an arterial dilatation model in mice in vivo. We identified 16 genes that were mutated in at least one IA case and found that these mutations were highly prevalent (92%: 60 of 65 IAs) among all IA cases examined. In particular, mutations in six genes (PDGFRB, AHNAK, OBSCN, RBM10, CACNA1E, and OR5P3), many of which are linked to NF-κB signaling, were found in both fusiform and saccular IAs at a high prevalence (43% of all IA cases examined). We found that mutant PDGFRBs constitutively activated ERK and NF-κB signaling, enhanced cell motility, and induced inflammation-related gene expression in vitro. Spatial transcriptomics also detected similar changes in vessels from patients with IA. Furthermore, virus-mediated overexpression of a mutant PDGFRB induced a fusiform-like dilatation of the basilar artery in mice, which was blocked by systemic administration of the tyrosine kinase inhibitor sunitinib. Collectively, this study reveals a high prevalence of somatic mutations in NF-κB signaling pathway–related genes in both fusiform and saccular IAs and opens a new avenue of research for developing pharmacological interventions. Description Somatic mutations in multiple NF-κB signaling–related genes are identified in both saccular and fusiform intracranial aneurysms. Editor’s summary Although somatic PDGFRB mutations have been identified in some forms of intracranial aneurysms (IAs), their prevalence in other types of IAs and underlying pathogenic mechanisms are not well understood. In this study by Shima and colleagues, they find PDGFRB and NF-κB signaling are increased in IAs from patients with fusiform and saccular aneurysms, despite their different presentations. In vitro and in vivo experiments demonstrated this aberrant signaling could be attenuated by the tyrosine kinase inhibitor sunitnib, which limited pathological vessel remodeling. These results suggest that modulation of PDGFRB and NF-κB signaling may be a viable therapeutic strategy for the treatment of IAs. —Allison Williams
Long-Term Changes in a Pygmy Cormorant Microcarbo pygmaeus Wintering Population in Southern Bulgaria

Abstract. Waterbirds are declining globally due to different threats that affect their abundance and shift both their breeding and wintering ranges. Cormorants disperse over vast distances during winter and are suitable indicators of the impacts of human-wildlife interactions and abiotic factors. During wintering periods, Pygmy Cormorants Microcarbo pygmaeus use regular roosts where they overnight on suitable perches, a refuge from adverse weather conditions and disturbances. Our study aimed to determine the wintering population size of the Pygmy Cormorant and its dynamics across 23-years (1996–2019) at seven roosting sites in the Maritsa River valley, Southern Bulgaria. This is a critical site for the species conservation where 3065–8180 birds are wintering annually. The wintering Pygmy Cormorant population showed a tendency to increase between 1996 and 2019 (λ = 1.03 ± 0.001). Each year Pygmy Cormorants were most abundant in December (mean ± SE, 2609 ± 185 individuals), while the lowest numbers were recorded in March (1207 ± 106). Pygmy Cormorants aggregated to roost between 4:00 PM and 5:30 PM throughout the study. The area of wintering foraging habitat of the Pygmy Cormorant increased significantly across all roosting sites in the study period from 2675.97 ha to 22564.35 ha. The number of Pygmy Cormorants at the roost was positively affected by the drop in the daily air mean temperatures and the decrease of the day length. Despite the global population increase, the Pygmy Cormorant faces a high risk of human-induced mortality during wintering and is thus regionally classified as endangered.
Status and Distribution of Alligator Snapping Turtles (Macrochelys temminckii) in Northern Louisiana

Abstract - The Alligator Snapping Turtle (Macrochelys temminckii) is a species of conservation concern across its range due to past commercial harvest for consumption. Northern Louisiana was originally surveyed in the 1980s, but the survey data were not compiled and published. After almost 40 years, we resurveyed the region to validate the historic data as well as provide current data on the distribution of Alligator Snapping Turtles. From the 1980s, we provide demographic data for 300 Alligator Snapping Turtles collected from 17 Louisiana parishes. From 2018–2020, we captured and measured 62 Alligator Snapping Turtles from 19 trapping sites. We recommend continued surveying and monitoring efforts in Louisiana to track populations during the post-commercial–harvest period.
Post-Fledging Survival and Dispersal of the White-Throated Dipper Cinclus cinclus

Abstract. The post-fledging period is still an understudied stage of avian life cycle, even in the case of otherwise frequently studied species. The general breeding biology of the White-throated Dipper is known well, but only a few studies have focused on survival and dispersal during the post-fledging period. In this study we report on results revealed by radio-telemetry, a method which has not been used in the species to date. Nestlings (37 individuals from 9 nests) in a mountain population of central Slovakia were radio-tagged on the mean expected fledging age (22 days post-hatch) and monitored daily until death, disappearance or reaching independence. Only 22–32% (depending on the handling of uncertain data) of fledglings survived the first 12 days post-fledging. Predation was the most frequently suspected cause of death. The daily survival rate was markedly lower during the first two days after fledging (0.717–0.758) than later (0.914–0.941). The daily movement distance remained stable during the first week post-fledging and increased around the age of reaching independence (c. 12 days post-fledging). On the other hand, the distance from the natal nest and the within-brood distance (length of river occupied by fledglings from the same nest) increased gradually since fledging. We propose that in our study population the low post-fledging survival could be potentially balanced by frequent renesting and/or double-brooding, timing of which corresponds well with the age of reaching independence when juvenile birds disperse outside the natal territory.
Variation in Relative Abundance, Population Structure, and Body Size of the Suwannee Alligator Snapping Turtle (Macrochelys suwanniensis) in the Suwannee River

Abstract - Geological processes influence water chemistry and biological productivity along the Suwannee River and divide the mainstem of the river into 6 distinct ecological reaches (ERs) in Florida. Because of these distinctions, we hypothesized that the Macrochelys suwanniensis (Suwannee Alligator Snapping Turtle) population varies among ERs. During 2011–2013, we sampled two 5-km sites in each ER to investigate spatial variation in relative abundance, sex ratio, size-class distribution, and body size of M. suwanniensis. Capture rates and male body sizes were greater in the middle ERs than in the upstream and downstream ERs. Sex ratios were male-skewed only in the middle ERs. Additional research is needed to understand the ecological drivers of M. suwanniensis population dynamics in this river.
Home Range and Habitat Use of Translocated Alligator Snapping Turtles (Macrochelys temminckii) in an Extensive River System

Abstract - Macrochelys temminckii (Alligator Snapping Turtle) occurs at low densities in the Choctawhatchee River system in Florida. Translocation could help bolster the population, but its effectiveness for this species is not well studied. We released 9 adults into a cutoff of the Choctawhatchee River and radio-tracked them from Sept 2017 to May 2019 to monitor movements and habitat use. Turtles had significantly larger home-range distances than previously reported (12,882.8 ± 8781.5 m for males and 10,621.6 ± 6020.4 m for females), but all established a home range overlapping with 1 or more individuals. On several occasions turtles were found together, suggesting interaction and potential mating opportunities. This study suggests that translocation may be an effective strategy for augmenting populations of this species.
Distribution Patterns and Factors Influencing Relative Abundance of the Alligator Snapping Turtle (Macrochelys temminckii) in Mississippi

Abstract - Macrochelys temminckii (Alligator Snapping Turtle) was recently proposed as a threatened species under the US Endangered Species Act due to current and projected future declining populations range wide. Despite a presumed statewide distribution in Mississippi, the Alligator Snapping Turtle had been documented in only 32 of 82 counties between 1857 and 2012, thus leaving a substantial gap in our knowledge of this species' distribution. Therefore, we collected credible records from museums, literature, and the general public, as well as directly assessed the current distribution and relative abundance of the Alligator Snapping Turtle in all major river systems (i.e., Pascagoula, Pearl, Tombigbee, and Mississippi river drainages) in Mississippi. From 2017 to 2021, we systematically trapped 77 sites across the state totaling 839 captures of 787 individual Alligator Snapping Turtles over the course of 4750 trap nights. State-wide catch per unit effort (CPUE) averaged 0.177, with the Big Black River (0.348) and Tombigbee River (0.028) drainages having the highest and lowest average CPUE, respectively. In Mississippi, CPUE was positively correlated with greater surrounding wetland area and river size, and negatively correlated with terrain ruggedness. This survey, along with the collaboration of other biologists and the public, verified an additional 189 locality records in 56 counties, with Alligator Snapping Turtle presence reconfirmed at 29 of 30 historical localities. Currently, it appears that there have been no local extirpations of the species in Mississippi, and state-wide CPUE was higher than those of the surrounding states.
The growth and composition of branching populations

A single-type general branching population develops by individuals reproducing according to i.i. d. point processes on R +, interpreted as the individuals' ages. Such a population can be measured or counted in many different ways: those born, those alive or in some sub-phase of life, for example. Special choices of reproduction point process and counting yield the classical Galton–Watson or Bellman–Harris process. This reasonably self-contained survey paper discusses the exponential growth of such populations, in the supercritical case, and the asymptotic stability of composition according to very general ways of counting. The outcome is a strict definition of a stable population in exponential growth, as a probability space, a margin of which is the well-known stable age distribution.
Nesting Behavior and Ecology in a Captive Population of Alligator Snapping Turtles (Macrochelys temminckii)

Abstract - We investigated nesting behavior and terrestrial activity in a captive population of Macrochelys temminckii (Alligator Snapping Turtle) housed outdoors in semi-natural environmental conditions in Oklahoma. The nesting season lasted from 12 May to 15 June 2012, and turtles were most active between the hours 2300–0300. Nesting duration averaged 182.5 min. Over 50% of nest construction time was spent excavating the cavity, whereas covering the eggs accounted for ∼28% of the total duration. Individual females averaged 25 non-nesting emergences before successfully depositing eggs. Terrestrial activity was positively correlated with increasing average nighttime temperature. We found thermal profiles generated by temperature data loggers affixed to females useful for studying terrestrial activity during nesting.
Using Local Ecological Knowledge to Document Distribution and Temporal Patterns of Macrochelys temminckii in Texas

Abstract - Long-term studies on long-lived species are rare, as is the case for the Alligator Snapping Turtle (Macrochelys temminckii). Here, we developed a database of historical accounts drawing spatial and temporal data from local ecological knowledge (LEK) and non-LEK sources. Across all sources, we compiled 215 spatial and 263 temporal records. To test applicability of LEK, we conducted field surveys at sites selected based on LEK accounts, non-LEK accounts, and habitat. Our surveys yielded occupancy rates of 66.7%, 68.8%, and 40%, respectively, while detectability models estimated proportion of occupied sites to be 58–77%. Catch per unit effort did not vary when compared to previous assessments in Texas. Turtles were most active from February to September. Incorporation of LEK when developing study designs will ultimately enhance communication between researchers and local experts.
What tests and measures accurately diagnose persisting post-concussive symptoms in children, adolescents and adults following sport-related concussion? A systematic review

Objective To determine what tests and measures accurately diagnose persisting post-concussive symptoms (PPCS) in children, adolescents and adults following sport-related concussion (SRC). Design A systematic literature review. Data sources MEDLINE, Embase, PsycINFO, Cochrane Central Register of Controlled Trials, CINAHL and SPORTDiscus through March 2022. Eligibility criteria Original, empirical, peer-reviewed findings (cohort studies, case-control studies, cross-sectional studies and case series) published in English and focused on SRC. Studies needed to compare individuals with PPCS to a comparison group or their own baseline prior to concussion, on tests or measures potentially affected by concussion or associated with PPCS. Results: Of 3298 records screened, 26 articles were included in the qualitative synthesis, including 1016 participants with concussion and 531 in comparison groups; 7 studies involved adults, 8 involved children and adolescents and 11 spanned both age groups. No studies focused on diagnostic accuracy. Studies were heterogeneous in participant characteristics, definitions of concussion and PPCS, timing of assessment and the tests and measures examined. Some studies found differences between individuals with PPCS and comparison groups or their own pre-injury assessments, but definitive conclusions were not possible because most studies had small convenience samples, cross-sectional designs and were rated high risk of bias. Conclusion The diagnosis of PPCS continues to rely on symptom report, preferably using standardised symptom rating scales. The existing research does not indicate that any other specific tool or measure has satisfactory accuracy for clinical diagnosis. Future research drawing on prospective, longitudinal cohort studies could help inform clinical practice.
On the Davison Convolution of Arithmetical Functions

Abstract The Davison convolution of arithmetical functions f and g is defined by where K is a complex-valued function on the set of all ordered pairs (n, d) such that n is a positive integer and d is a positive divisor of n. In this paper we shall consider the arithmetical equations f(r) = g, f(r) = fg, f o g = h in f and the congruence (f o g)(n) = 0 (mod n), where f(r) is the iterate of f with respect to the Davison convolution.
Rough set theory based object-oriented classification of high resolution remotely sensed imagery

Object-oriented classification has been paid more attention in the field of remote sensing.In this paper,a novel object-oriented algorithm based on rough set theory is proposed to classify different objects extracted from high-resolution remotely sensed imagery.The method consists of three steps.Firstly,image segmentation is achieved by watershed transform based on phase congruency gradient and foreground marking to extract image objects.Secondly,texture vector of each object is obtained by Gabor wavelet,and clustering rules is further formed based on the knowledge reduction theory.Finally,according to the restriction of the preliminary clustering result derived from spectral feature of objects,the ultimate classification is achieved referring to the rules.Meanwhile,a new technique to discretize continuous interval-valued attributes is developed,which is very suitable for the object-oriented classification,because the rough set is inadequate for dealing with continuous attributes.The experiments demonstrate that the proposed method can achieve better results and better accuracies.
Closeness Centrality on Uncertain Graphs

Centrality is a family of metrics for characterizing the importance of a vertex in a graph. Although a large number of centrality metrics have been proposed, a majority of them ignores uncertainty in graph data. In this article, we formulate closeness centrality on uncertain graphs and define the batch closeness centrality evaluation problem that computes the closeness centrality of a subset of vertices in an uncertain graph. We develop three algorithms, MS-BCC, MG-BCC, and MGMS-BCC, based on sampling to approximate the closeness centrality of the specified vertices. All these algorithms require to perform breadth-first searches (BFS) starting from the specified vertices on a large number of sampled possible worlds of the uncertain graph. To improve the efficiency of the algorithms, we exploit operation-level parallelism of the BFS traversals and simultaneously execute the shared sequences of operations in the breadth-first searches. Parallelization is realized at different levels in these algorithms. The experimental results show that the proposed algorithms can efficiently and accurately approximate the closeness centrality of the given vertices. MGMS-BCC is faster than both MS-BCC and MG-BCC because it avoids more repeated executions of the shared operation sequences in the BFS traversals.
Deep learning–based vortex decomposition and switching based on fiber vector eigenmodes

Abstract Structured optical fields, such as cylindrical vector (CV) and orbital angular momentum (OAM) modes, have attracted considerable attention due to their polarization singularities and helical phase wavefront structure. However, one of the most critical challenges is still the intelligent generation or precise control of these modes. Here, we demonstrate the first simulation and experimental realization of decomposing the CV and OAM modes by reconstructing the multi-view images of projected intensity distribution. Assisted by the deep learning–based stochastic parallel gradient descent (SPGD) algorithm, the modal coefficients and optical field distributions can be retrieved in 1.32 s within an average error of 0.416 % showing high efficiency and accuracy. Especially, the interference pattern and quarter-wave plate are exploited to confirm the phase and distinguish elliptical or circular polarization direction, respectively. The generated donut modes are experimentally decomposed in the CV and OAM modes, where purity of CV modes reaches 99.5 %. Finally, fast switching vortex modes is achieved by electrically driving the polarization controller to deliver diverse CV modes. Our findings may provide a convenient way to characterize and deepen the understanding of CV or OAM modes in view of modal proportions, which is expected of latent applied value on information coding and quantum computation.
Evaluation of spatial resolution in image acquisition by optical flatbed scanners for radiochromic film dosimetry

Introduction: Radiochromic films are two-dimensional dosimeters that do not require developing and give values of absorbed dose with accuracy and precision. Since this dosimeter colours directly after irradiation, it can be digitized with commercial optical flatbed scanners to obtain a calibration curve that links blackening of the film with dose. Although the film has an intrinsic high spatial resolution, the scanner determines the actual resolution of this dosimeter, in particular the “dot per inch” (dpi) parameter. The present study investigates the effective spatial resolution of a scanner used for Gafchromic® XR-QA2 film (designed for radiology Quality Assurance) analysis. Material and methods: The quantitative evaluation of the resolution was performed with the Modulation Transfer Function (MTF) method, comparing the nominal resolution with the experimental one. The analysis was performed with two procedures. First, the 1951 USAF resolution test chart, a tool that tests the performance of optical devices, was used. Secondly, a combined system of mammography X-ray tube, XR-QA2 film and a bar pattern object was used. In both cases the MTF method has been applied and the results were compared. Results: The USAF and the film images have been acquired with increasing dpi and a standard protocol for radiochromic analysis, to evaluate horizontal and vertical and resolution. The effective resolution corresponds to the value of the MTF at 50%. In both cases and for both procedures, it was verified that, starting from a dpi value, the effective resolution saturates. Conclusion: The study found that, for dosimetric applications, the dpi of the scanner have to be adjusted to a reasonable value because, if too high, it requires high scanning and computational time without providing additional information.