Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid intralacustrine evolution of an invasive pelagic three-spined stickleback (Gasterosteus aculeatus) ecotype in Lake Constance

The rapid invasion of the pelagic zone in Lake Constance by three-spined sticklebacks (Gasterosteus aculeatus) since 2012 and their subsequent drastic population growth has had stark ecosystem-wide effects, such as food-web shifts and declines in native biodiversity, including commercially important fish species. Yet, the origin of this invasive pelagic ecotype remains unclear. This study aims to determine if the pelagic ecotype arose in situ from the existing littoral population or following external colonisation, identify potential phenotypic differences between individuals from different habitats, and assess genomic signals of selection. Integrating RAD-sequencing of Lake Constance individuals and whole-genome sequence data for European outgroup populations, this study shows that the pelagic Lake Constance population likely arose recently within the lake from the littoral population, with only weak genome-wide differentiation between individuals from different habitats. This is further supported by minimal differences in meristic and morphometric traits, with shape differences only found between pelagic/inflow sticklebacks and littoral sticklebacks. Using genome scans, we identified multiple outlier loci between littoral and pelagic ecotypes across the genome, potentially suggesting early signs of sympatric speciation despite high connectivity. Furthermore, increased differentiation between pelagic and littoral sticklebacks for body shape-associated loci and the overlap of outlier loci with quantitative trait loci for ecologically relevant traits points toward a driving role of selection in this pelagic invasion. This study provides an important example of rapid ecological diversification from standing genetic variation and a rare case of littoral-pelagic ecotype divergence under high gene flow in a large oligotrophic lake. Ultimately, the results of this study will have major implications for the management of the invasive pelagic ecotype, and the entire stickleback population as a whole.
White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern

Significance This comprehensive cross-sectional study demonstrates widespread infection of WTD with SARS-CoV-2 across the State of New York. We showed cocirculation of three major SARS-CoV-2 variants of concern (VOCs; Alpha, Delta, and Gamma) in this species, long after their last detection in humans. Interestingly, the viral sequences recovered from WTD were highly divergent from SARS-CoV-2 sequences recovered from humans, suggesting rapid adaptation of the virus in WTD. The impact of these mutations on the transmissibility of the virus between WTD and from WTD to humans remains to be determined. Together, our findings indicate that WTD—the most abundant large mammal in North America—may serve as a reservoir for variant SARS-CoV-2 strains that no longer circulate in the human population.
Monitoring the Process Mean and Variance Using Individual Observations and Variable Sampling Intervals

In this paper we investigate control charts for monitoring a process to detect changes in the mean and/or variance of a normal quality variable when an individual observation is taken at each sampling point. The traditional X chart and moving range (MR) chart are evaluated. Also evaluated are the exponentially weighted moving average (EWMA) chart of the observations and the EWMA chart of the squared deviations of the observations from the target. It is shown that the combination of the X and MR charts will not detect small and moderate parameter shifts as fast as combinations involving the EWMA charts. The ability of charts to diagnose the type of parameter shift produced by a special cause is also investigated. It is shown that combinations involving the EWMA charts are just as effective at diagnosing the type of parameter shift as the traditional combination of the X and MR charts. The effect of adding the variable sampling interval (VSI) feature is also evaluated for some of the combinations of charts. The VSI feature allows the sampling interval to be varied as a function of the values of the statistics being plotted. It is shown that adding the VSI feature to the combinations of charts results in very substantial reductions in the expected time required to detect shifts in process parameters.
Metabolic costs of walking and arm reaching in persons with mild multiple sclerosis

Movement slowness is a common and disruptive symptom of multiple sclerosis (MS). A potential cause is that individuals with MS slow down to conserve energy as a behavioral adjustment to heightened metabolic costs of movement. To investigate this prospect, we measured the metabolic costs of both walking and seated arm reaching at five speeds in persons with mild MS (pwMS; n = 13; 46.0 ± 7.7yrs) and sex- and age-matched controls (HCs; n = 13; 45.8 ± 7.8yrs). Notably, the cohort of pwMS was highly mobile and no individuals required a cane or aid when walking. We found that the net metabolic power of walking was approximately 20% higher for pwMS across all speeds (p = 0.0185). In contrast, we found no differences in the gross costs of reaching between pwMS and HCs (p = 0.492). Collectively, our results suggest that abnormal slowness of movement in MS – particularly reaching – is not the consequence of heightened effort costs alone. Our findings are consistent with the possibility that demyelination of reward regions of the central nervous system in MS disrupt the dopamine-mediated impetus to move more quickly and thereby prompt slower movements. NEW & NOTEWORTHY Individuals with multiple sclerosis (MS) often move more slowly than those without the disease. A possible cause is that movements in MS are more energetically expensive and slowing is an adaptation to conserve metabolic resources. Here, we find that while walking is more costly for persons with MS, arm reaching movements are not. These results bring into question the driving force of movement slowness in MS and implicate other motor-related networks contributing to slowing.
Habitat use differences mediate anthropogenic threat exposure in white sturgeon

Understanding intraspecific variation in habitat use, particularly of long-lived fishes across multiple life history stages, is core to improved conservation management. Here, we present results from a synthesis of acoustic telemetry data for sub-adult and adult white sturgeon (Acipenser transmontanus) from 2010 to 2017 in the San Francisco Estuary and Sacramento River ecosystems. We focused primarily on uncovering spatial patterns of inferred habitat occupancy across life stages, and on linking habitat use to extant anthropogenic threats. We found substantial differences in habitat use across individuals and over time that was related to fish size classes defined relative to the slot limit (102-152 cm) used to regulate recreational fishing. However, differences in habitat use were not explained by fish sex or water year flow conditions. We also estimated indices of overall exposure for two major threats: capture by anglers and habitat modification. Fish of harvestable size were detected less often than others in areas where many are caught. Future monitoring and management of white sturgeon might benefit from examining multiple phases of white sturgeon life history. For example, additional tracking studies could improve our understanding of juvenile habitat use, adult survival rates, patterns of anadromy, and cross-basin habitat utilization.
Improved genome editing by an engineered CRISPR-Cas12a

CRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded DNA (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated genome editing, we first used structure-guided engineering to generate variants of Lachnospiraceae bacterium Cas12a (LbCas12a) that selectively disrupt trans-activity. The resulting engineered mutant with the biggest differential between cis- and trans-DNase activity in vitro showed minimal genome editing activity in human cells, motivating a second set of experiments using directed evolution to generate additional mutants with robust genome editing activity. Notably, these engineered and evolved mutants had enhanced ability to induce homology-directed repair (HDR) editing by 2-18-fold depending on the genomic locus. Finally, we found that a site-specific reversion mutation produced improved Cas12a (iCas12a) variants with superior genome editing efficiency at genomic sites that are difficult to edit using wild-type Cas12a. This strategy of coupled rational engineering and directed evolution establishes a pipeline for creating improved genome editing tools by combining structural insights with randomization and selection. The availability of experimental and predicted structures of other CRISPR-Cas enzymes will enable this strategy to be applied to improve the efficacy of other genome editing proteins.
OPT3 Transports Copper to the Phloem, Mediates Shoot-to-Root Copper Signaling and Crosstalk Between Copper and Iron Homeostasis in A. thaliana

Copper and iron are essential micronutrients but are toxic when accumulating in cells in excess. Thus, their uptake by roots is tightly regulated. While plants sense and respond to local copper availability, the systemic regulation of copper uptake has not been documented. By contrast, both local and systemic control for iron uptake has been reported. Iron abundance in the phloem has been suggested to act systemically, regulating the expression of iron uptake genes in the root. Consistently, shoot-to-root iron signaling is disrupted in A. thaliana mutants lacking the phloem companion cell-localized iron transporter, AtOPT3: opt3 mutants overaccumulate iron in leaves while constitutively upregulating iron deficiency-responsive genes in roots. We report that AtOPT3 transports copper and mediates its delivery from source leaves to sinks including young leaves and developing embryos. Consequently, the opt3 mutant accumulates less copper in the phloem, is sensitive to copper deficiency, and mounts transcriptional copper deficiency response in roots. Copper rescues these defects. Notably, feeding the opt3 mutant with copper or iron via the phloem in leaves downregulates the expression of both copper and iron-deficiency marker genes in roots, suggesting that copper and iron can substitute each other’s function in the phloem in shoot-to-root communication. One-sentence summary AtOPT3 loads copper and iron into the phloem companion cells, for subsequent distribution to sink tissues and systemic signaling of copper and iron deficiency.
Long-range alteration of the physical environment mediates cooperation between Pseudomonas aeruginosa swarming colonies

Pseudomonas aeruginosa makes and secretes massive amounts of rhamnolipid surfactants that enable swarming motility over biogel surfaces. But how this rhamnolipids interact with biogels to assist swarming remains unclear. Here I use a combination of optical techniques across scales and genetically-engineered strains to demonstrate that rhamnolipids can induce agar gel swelling over distances > 10,000x the body size of an individual cell. The swelling front is on the micrometric scale, and is easily visible using shadowgraphy. Rhamnolipid transport is not restricted to the surface of the gel, but occurs through the whole thickness of the plate and, consequently, the spreading dynamics depends on the local thickness. Surprisingly, rhamnolipids can cross the whole gel and induce swelling on the opposite side of a two-face Petri dish. The swelling front delimits an area where the mechanical properties of the surface properties are modified: water wets the surface more easily, which increases the motility of individual bacteria and enables collective motility. A genetically-engineered mutant unable to secrete rhamnolipids (DrhlA), and therefore unable to swarm, is rescued from afar with rhamnolipids produced by a remote colony. These results exemplify the remarkable capacity of bacteria to change the physical environment around them and its ecological consequences. Significance statement Living organisms have the ability to interact mechanically with their environment. Pseudomonas aeruginosa, a motile bacterium, can spread collectively on biogels, a behavior called swarming. Rhamnolipids, surfactant molecules P. aeruginosa make and secrete, are required for swarming. Here, I demonstrate rhamnolipids not only physically alter the biogel in the vicinity of the secreting cells, but also over distances much greater than the bacterial cell size, through gel swelling. This long-distance physical alteration can even rescue a remote colony which would not produce rhamnolipids. This work illustrates the remarkable ability of bacteria to change the mechanical property of the world surrounding them.
Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni

The outer membrane factor CmeC of the efflux machinery CmeABC plays an important role in conferring antibiotic and bile resistance to Campylobacter jejuni. Curiously, the protein is N-glycosylated, with the glycans playing a key role in the effective function of this system. In this work we have employed atomistic equilibrium molecular dynamics simulations of CmeC in a representative model of the C. jejuni outer membrane to characterise the dynamics of the protein and its associated glycans. We show that the glycans are more conformationally labile than had previously been thought. The extracellular loops of CmeC visit the open and closed states freely suggesting the absence of a gating mechanism on this side, while the narrow periplasmic entrance remains tightly closed, regulated via coordination to solvated cations. We identify several cation binding sites on the interior surface of the protein. Additionally, we used steered molecular dynamics simulations to elucidate translocation pathways for a bile acid and a macrolide antibiotic. These, and additional equilibrium simulations suggest that the anionic bile acid utilises multivalent cations to climb the ladder of acidic residues that line the interior surface of the protein.
Receding contact problem for a coated layer and a half-plane loaded by a rigid cylindrical stamp

In this study, the frictionless contact problem between a coated layer and a half-plane is considered when they are pressed by a rigid cylindrical stamp. Upon loading, two unknown contact widths and contact pressures occur on the contact areas the advanced contact area between the stamp and the coating; and the receding contact area between the layer and the half-plane. This problem is reduced to two singular integral equations by using the Fourier transform and applying the boundary conditions of the problem. The numerical solution of the system of singular integral equations is obtained by applying the Gauss–Chebyshev integration formulas.
Field Instruction: A Relational Model to Promote A Positive Professional Identity for Social Work Students

ABSTRACT The development of a social work professional identity is an element of social work education. It is not clear how students in social work programs develop this identity; its development seems to be dependent on the integration of various learning experiences and exposure to curriculum content in the classroom, and in the fieldwork assignments. Teachers and field instructors play important roles in this process. In this paper, the authors argue that a positive professional social work identity can be fostered through the relationship with instructors in fieldwork supervision. Using Kohut’s theory of Self Psychology, the authors present a model that highlights the application of the concept of self-object needs to the field instructor-student relationship. One of the central premises of his theory is that individuals from childhood and throughout adulthood internalize the experiences provided by self-objects to meet the emotional needs of the self. The authors propose that field instructors provide self-object experiences that can sustain and foster the development of a positive professional identity for social work students in training. The application of this model underscores students’ affective changes associated with students’ professional development in social work programs.
Eddy fluxes in baroclinic turbulence

The eddy heat flux generated by the statistically equilibrated baroclinic instability of a uniform, horizontal temperature gradient is studied using a two- mode quasigeostrophic model. An overview of the dependence of the eddy diffusivity of heat D[tau] on the planetary potential vorticity gradient [beta], the bottom friction [kappa], the deformation radius [lambda], the vertical shear of the large-scale flow 2U and the domain size L is provided at 70 numerical simulations with [beta]=0 (f-plane) and 110 simulations with [beta] ! = 0 ([beta]-plane). Strong, axisymmetric, well-separated baroclinic vortices dominate the equilibrated barotropic vorticity and temperature fields of f-plane turbulence. The heat flux arises from a systematic northward (southward) migration of anti-cyclonic (cyclonic) eddies with warm (cold) fluid trapped in the cores. Zonal jets form spontaneously on the [beta]-plane, and stationary, isotropic, jet-scale eddies align within the strong eastward-flowing regions of the jets. In both studies, the vortices and jets give rise to a strong anti-correlation between the barotropic vorticity [zeta] and the temperature field [tau]. The baroclinic mode is also an important contributor to dissipation by bottom friction and energizes the barotropic mode at scales larger than [lambda]. This in part explains why previous parameterizations for the eddy heat flux based on Kolmogorovian cascade theories are found to be unreliable. In a separate study, temperature and salinity profiles obtained with expendable conductivity, temperature and depth (XCTD) probes within Drake Passage, Southern Ocean are used to analyze the turbulent diapycnal eddy diffusivity [kappa][rho] to a depth of 1000 meters. The Polar Front separates two dynamically different regions with strong, surface-intensified mixing north of the Front. South of the Polar Front mixing is weaker and peaks at a depth of approximately 500 m, near the local temperature maximum. Peak values of [kappa][rho] are found to exceed 10^-3 m^2 s^-1. Wind-driven near-inertial waves, mesoscale eddies and thermohaline intrusions are discussed as possible factors contributing to observed mixing patterns
In the memory of Nancy Tagi Sagafi-nejad - former Associate Editor of CCJ Nancy Gail Black Sagafi-nejad

The relationship between sustainable supply chain management practices and companies’ performances has been the subject of many research studies in the past few years. Some authors showed that sustainable supply chain management doesn’t contribute to the financial performance, while others found the opposite. This research paper is fully in line with this debate and aims to investigate the relationship between the financial performance and the supply chain’s sustainability of Moroccan industrial companies listed on the stock exchange and belonging to three different sectors. A statistical analysis was carried out using the database of Vigeo Eiris, an international environmental, social and corporate governance research and rating agency founded in 2002, and companies’ annual reports. Results show that sustainable relationships with partners in the upstream supply chain impact the financial performance of companies in different ways, depending on the characteristics of each sector. The findings of this research have financial, ecological and social implications as they can help companies understand the importance of having an efficient supply chain while being environmentally and socially responsible.
Recreational fishing fight times are not correlated with physiological status of blue sharks ( Prionace glauca ) in the Northwestern Atlantic

Sharks, like other fish, react to capture and handling stress with more exaggerated physiological responses than most other vertebrates, and the potential consequences of their capture include both sub-lethal and lethal effects. , are of in both in commercial and and while the capture response of sharks in commercial has been comparably well-studied, there is a relative lack of information regarding the influence of handling and capture on the species in the recreational Our analysis of blood-based biomarkers, such as lactate, pH, and plasma electrolytes, sampled from twenty blue sharks captured in the recreational suggests that over the short hook times (time on the line) characteristic of the fishery, blue sharks do not fight to the point of blood acidosis and are likely able to withstand capture and handling in a catch-and-release setting. We did note an inverse relationship between shark total length and blood glucose levels, suggesting the possi-bility that smaller individuals may be more susceptible to capture stress, but this variation may also reflect other metabolic factors or an ontogenetic shift in diet. We discuss these findings within the context of the recreational fishery, including priorities for angler education.
Correlation and path coefficient analysis for yield and yield attributing traits in advanced bread wheat ( Triticum aestivum L.) Lines

Knowledge of nature and magnitude of genetic variability among genotypes, mutual association between yield and attributing traits is important for effective selection in plant-breeding program. Ninety advanced bread wheat lines along with four standard checks viz . HD-2967, NW-5054, DBW-187 and HD–2733 were evaluated at Main experimental station of Acharya Narendra Dev University of Agriculture and Technology, Ayodhya (U.P.) in augmented block design in Rabi 2020 to evaluate the correlation of yield and yield attributing traits and determine the direct and indirect effects of yield attributing traits on grain yield. Analysis of variance showed significant differences among the tested genotypes for all the majority of agro-morphological characters under study which clearly indicates high variability among the tested advanced bread wheat lines. Grain yield had highly significant and positive correlation with biological yield per plant, harvest index (%), days to maturity, days to 50% flowering, plant height and tillers/plant. Maximum positive direct effect on grain yield per hectare was exerted by biological yield per plant followed harvest index, days to 50% flowering and plant height. Selection based on these traits could be more effective to maximize grain yield. Path analysis showed that maximum positive direct effect on grain yield per hectare was exerted by biological yield per plant followed harvest index, days to 50% flowering and plant height. This implies the true relationship between these traits and grain yield. Consequently, these traits should be considered as important selection criteria in future breeding program for the development high yielding wheat varieties.