Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical constraints on early blastomere packings

At very early embryonic stages, when embryos are composed of just a few cells, establishing the correct packing arrangements (contacts) between cells is essential for the proper development of the organism. As early as the 4-cell stage, the observed cellular packings in different species are distinct and, in many cases, differ from the equilibrium packings expected for simple adherent and deformable particles. It is unclear what are the specific roles that different physical parameters, such as the forces between blastomeres, their division times, orientation of cell division and embryonic confinement, play in the control of these packing configurations. Here we simulate the non-equilibrium dynamics of cells in early embryos and systematically study how these different parameters affect embryonic packings at the 4-cell stage. In the absence of embryo confinement, we find that cellular packings are not robust, with multiple packing configurations simultaneously possible and very sensitive to parameter changes. Our results indicate that the geometry of the embryo confinement determines the packing configurations at the 4-cell stage, removing degeneracy in the possible packing configurations and overriding division rules in most cases. Overall, these results indicate that physical confinement of the embryo is essential to robustly specify proper cellular arrangements at very early developmental stages. Author summary At the initial stages of embryogenesis, the precise arrangement of cells in the embryo is critical to ensure that each cell gets the right chemical and physical signals to guide the formation of the organism. Even when the embryo is made of only four cells, different species feature varying cellular arrangements: cells in mouse embryos arrange as a tetrahedron, in the nematode worm C. elegans cells make a diamond and in sea urchins cells arrange in a square configuration. How do cells in embryos of different species control their arrangements? Using computer simulations, we studied how cell divisions, physical contacts between cells and the confinement of the embryo by an eggshell affect the arrangements of cells when the embryos have only 4 cells. We find that the shape of the confining eggshell plays a key role in controlling the cell arrangements, removing unwanted arrangements and robustly specifying the proper contacts between cells. Our results highlight the important roles of embryonic confinement in establishing the proper cell-cell contacts as the embryo starts to develop.
Antibiotic susceptibility pattern of Serratia marcescens isolates from wound infections in a tertiary health institution in Calabar, Nigeria

Background: Serratia marcescens , a ubiquitous rod-shaped gram-negative bacterium is an opportunistic pathogen causing a plethora of nosocomial infections in humans including wound infections. They are identified in their ecological niches by their red pigment, prodigiosin. Information concerning these organisms in association with wound infections are sparse in our locality. This study was designed to determine the prevalence of Serratia marcescens in wound infections and their antimicrobial susceptibility profile. Methods: Wound swabs and pus were collected from the patients after receiving informed consent from them. Samples were inoculated on appropriate media and cultures were incubated at 37°C aerobically. Cultures were examined macroscopically and bacterial isolates were gram stained and microscopically examined. Pathogens were identified by their red pigment and other biochemical tests. The Kirby-Bauer disk diffusion method was used for antibiotic susceptibility testing. Results: Out of the 251 wound samples collected during the study period, 25 (9.9%) were Serratia marcescens . Males [18 (72.0%)] were more susceptible than females [7 (28.0%)], but there was no influence of gender on the rates of infection (p=0.3). The susceptibility profile of the isolates to antibiotics tested ranged between 4% and 76%. The most sensitive antibiotic was levofloxacin [19 (76%)] followed by gentamicin [17 (68%)]. All the isolates were absolutely resistant to ampicillin. Conclusion: Fluoroquinolones have shown a good activity against Serratia marcescens and should be considered as a first line antibiotic against these infections in our locality. To stay ahead in the fight against these infections, effective infection control should be practiced, antibiotic usage should be optimized and empirical treatment reduced.
Phenotypic and molecular characterization of extended spectrum β-lactamase producing Escherichia coli and Klebsiella pneumoniae isolates from various samples of animal origin from Assam, India

Extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae has become a major threat globally. Here we have characterized ESBL producing E. coli and K. pneumoniae from various sources, studied antibiogram and resistance gene profiles. Out of 385 samples, 31 (8.05%) were positive for ESBL producing E. coli. Such isolates could be recovered from 10.05, 8.33, 15.63, 6.67 and 4.35 per cent of cattle milk, curd, chicken, pork and cattle faeces samples, respectively. A total of 59 (15.32%) samples were positive for ESBL producing K. pneumoniae, which were isolated from 14.35, 6.25, 21.43 and 34.78 per cent cattle milk, chicken, beef and cattle faeces, respectively. All the 90 isolates were confirmed as ESBL producers by CDT and ESBL-E strip tests. Antibiogram revealed that 74.19% and 69.49% of the ESBL producing E. coli and K. pneumoniae isolates, respectively showed resistance to ceftizoxime, 25.81% and 23.73% to both co-trimoxazole and tetracycline, 19.35% and 25.42% to ciprofloxacin, 9.68% and 16.95% to chloramphenicol, 3.23% and 5.08% to pipercillin-tazobactam, and 3.23% and 3.39% to gentamicin. Resistance gene profiling showed blaCTX-M gene as most predominant (100%). The blaTEM gene was found in 54.84% and 55.93%, blaSHV gene in 90.32% and 77.97%, Sul 1 gene in 90.32% and 86.44% of ESBL producing E. coli and K. pneumoniae isolates, respectively. The Int1 gene was detected in 70.97% and 62.71% isolates, while qnrB gene was found in 3.23% and 10.17% of E. coli and K. pneumoniae isolates, respectively.
Variability in error-based and reward-based human motor learning is associated with entorhinal volume

Error-based and reward-based processes are critical for motor learning, and are thought to be mediated via distinct neural pathways. However, recent behavioral work in humans suggests that both learning processes are supported by cognitive strategies and that these contribute to individual differences in motor learning ability. While it has been speculated that medial temporal lobe regions may support this strategic component to learning, direct evidence is lacking. Here we first show that faster and more complete learning during error-based visuomotor adaptation is associated with better learning during reward-based shaping of reaching movements. This result suggests that strategic processes, linked to faster and better learning, drive individual differences in both error-based and reward-based motor learning. We then show that right entorhinal cortex volume was larger in good learning individuals—classified across both motor learning tasks—compared to their poorer learning counterparts. This suggests that strategic processes underlying both error- and reward-based learning are linked to neuroanatomical differences in entorhinal cortex. Significance Statement While it is widely appreciated that humans vary greatly in their motor learning abilities, little is known about the processes and neuroanatomical bases that underlie these differences. Here, using a data-driven approach, we show that individual variability in error-based and reward-based motor learning is tightly linked, and related to the use of cognitive strategies. We further show that structural differences in entorhinal cortex predict this intersubject variability in motor learning, with larger entorhinal volumes being associated with better overall error-based and reward-based learning. Together, these findings provide support for the notion that the ability to recruit strategic processes underlies intersubject variability in both error-based and reward-based learning, which itself may be linked to structural differences in medial temporal regions.
Common properties of visually-guided saccadic behavior and bottom-up attention in marmoset, macaque, and human

The saccade is a stereotypic behavior whose investigation improves our understanding of how primate brains implement precise motor control. Furthermore, saccades offer an important window into the cognitive and attentional state of the brain. Historically, saccade studies have largely relied on macaque. However, the cortical network giving rise to the saccadic command is difficult to study in macaque because relevant cortical areas lie in sulci and are difficult to access. Recently, a New World monkey – the marmoset – has garnered attention as an attractive alternative to macaque because of its smooth cortical surface, its smaller body, and its amenability to transgenic technology. However, adoption of marmoset for oculomotor research has been limited due to a lack of in-depth descriptions of marmoset saccade kinematics and their ability to perform psychophysical and cognitive tasks. Here, we directly compare free-viewing and visually-guided behavior of marmoset, macaque, and human engaged in identical tasks under similar conditions. In video free-viewing task, all species exhibited qualitatively similar saccade kinematics including saccade main sequence up to 25° in amplitude. Furthermore, the conventional bottom-up saliency model predicted gaze targets at similar rates for all species. We further verified their visually-guided behavior by training them with step and gap saccade tasks. All species showed similar gap effect and express saccades in the gap paradigm. Our results suggest that the three species have similar natural and task-guided visuomotor behavior. The marmoset can be trained on saccadic tasks and thus can serve as a model for oculomotor, attention, and cognitive research. New & noteworthy We directly compared the results of video free-viewing task and visually-guided saccade tasks (step and gap) among three different species: the marmoset, macaque and human. We found that all species exhibit qualitatively similar saccadic behavior and bottom-up saliency albeit with small differences. Our results suggest that the marmoset possesses similar neural mechanisms to macaque and human for saccadic control, and it is an appropriate model animal to study neural mechanisms for active vision and attention.
Diatom distribution in natural and impacted cut-off meanders of the Allier River, France

Parapotamal cut-off meanders from two different geological catchment regions of the Allier River, 117 km apart (upstream – metamorphic-basalt and downstream – sedimentary), differ in their degrees of infill or depth. In each region, three cut-off meanders were examined; one in each region was impacted by gravel extraction (upstream deepening) and halieutic improvement (downstream deepening), whereas the others were left in their natural state having different silt accumulations either almost cut-off from the river or less silted-up and more open to the river. The sites were monitored for one year for physical and chemical characteristics. Diatom samples collected in summer 2009 were examined along with their associated biocenosis. The two catchments, differing in geology, land-use and water quality, sheltered different diatom communities. Physical and chemical differences were recorded between up- and downstream zones of each cut-off meander due to both the influence of the groundwater (buffering the water temperature among others) and the periodic inflow from the main channel (increased oxygen saturation concentration in downstream end of the cut-off meanders, except for the impacted upstream zone which contained a lot of macrophytes). In the upstream reach (except for one site), the connection with the groundwater from the surrounding catchment, which acts as a hydro-geological reservoir, might explain the highest mineralization and water hardness recorded mainly in the upstream zone of the cut-off meander, and the presence of Pseudostaurosira subsalina (Hustedt) Morales and Thalassiosira weissflogii (Grunow) Fryxell & Hasle. For the downstream reach, in addition to up- and downstream differences, other factors came into play giving rise to different communities, for example, cattle trampling in the cut-off meander leading to the presence of hypereutrophic and polysaprobic taxa or the potential local re-emergence of mineral springs associated with brackish taxa. Moreover, the up- or downstream deepening also induced differences: the extraction of sediment nearer to the river created a system in which water input from the main channel flows in through a larger opening, inducing allochthonous processes. This increased the river's influence, creating a renewal of earlier morphological and ecological conditions, whereas the gravel extraction that modified the upstream zone increased the influence of groundwater from the surrounding catchment on this area of the site and led to water conditions independent of the main channel. Furthermore, this study has provided an important picture of the environmental variables, mechanisms and processes that drive the distribution of diatoms within the cut-off meanders along the Allier River, which can can be applied in future paleo-environmental studies.
Genetic Analysis of Some Agronomic Traits in Okra (Abelmoschus esculentus L. [Moench])

Abstract A study was carried out at the Federal University of Agriculture Abeokuta, Nigeria to determine the gene action underlying the inheritance of important agronomic traits as well as the general combining ability (GCA) and specific combining ability (SCA) of the parents and hybrids, respectively. Ten hybrids were developed by crossing five lines to two testers. The hybrids and parents were evaluated on the field in a randomised complete block design replicated three times, and data were collected on days to 50% flowering, number of branches, stem diameter, plant height, pod length, pod width, pod weight, number of pods and pod yield. The data were subjected to line by tester analysis and results showed substantial variability among the genotypes for some of the characters measured. Days to 50% flowering, number of pods and pod yield were largely under additive gene action while non-additive gene action was more important in the inheritance of plant height. Favourable GCA and SCA effects for days to 50% flowering were observed in NGB00356, NGB00326 and NGB00347 × NGB00326, respectively. The tester NGB00326 had a positive and significant GCA effect for number of pods while the highest positive SCA effect for pod yield was found in NGB00297 × NGB00326. Thus, NGB00356 and NGB00326 could be considered as sources of alleles for development of early maturing while the cross NGB00297 × NGB00326 could be exploited for high yielding okra genotypes.
Analysis of changes in hydrological cycle of a pristine mountain catchment. 1. Water balance components and snow cover

Abstract We analyse water balance, hydrological response, runoff and snow cover characteristics in the Jalovecký Creek catchment (area 22 km2, mean elevation 1500 m a.s.l.), Slovakia, in hydrological years 1989–2018 to search for changes in hydrological cycle of a mountain catchment representing hydrology of the highest part of the Western Carpathians. Daily air temperature data from two meteorological stations located in the studied mountain range (the Tatra Mountains) at higher elevations show that the study period is 0.1°C to 2.4°C warmer than the climatic standard period 1951–1980. Precipitation and snow depth data from the same stations do not allow to conclude if the study period is wetter/drier or has a decreasing snow cover. Clear trends or abrupt changes in the analysed multivariate hydrometric data time series are not obvious and the oscillations found in catchment runoff are not coherent to those found in catchment precipitation and air temperature. Several time series (flashiness index, number of flow reversals, annual and seasonal discharge maxima, runoff coefficients) indicate that hydrological cycle is more dynamic in the last years of the study period and more precipitation runs off since 2014. The snow cover characteristics and climatic conditions during the snow accumulation and melting period do not indicate pronounced changes (except the number of days with snowfall at the Kasprowy Wierch station since 2011). However, some data series (e.g. flow characteristics in March and June, annual versus summer runoff coefficients since 2014) suggest the changes in the cold period of the year.
Effect of NaCl on citrus cultivars

We investigated the effects of salinity stress-relief on the growth and mineral composition (leaf and root) of one-year-old seedlings of Cleopatra mandarin (Citrus reticulata Blanco) and Sour orange (Citrus aurantium [L]). Salinization reduced plant dry weight more in Sour orange than in Cleopatra mandarin plants, although there was no correlation between Cl and Na concentration in leaves and shoot fresh weight reduction. We observed that regulation of Na + and Cl - uptake and transport from root to shoot appear to involve different mechanisms which break down during a long period of salinization. Salinity induced a decrease in K + , Ca 2+ and total N in Cleopatra mandarin leaves and an increase in K + in Sour orange leaves. Growth of both cultivars was not recovered totally in the relief period, since relative growth rates of recovered plants were lower than for control plants after 60 days of relief.
An Alternative View to the Global Coal Trade: Complex Network Approach

Abstract The role of energy for the developmental process of nations is a known fact due to being crucial input for any phase of production of goods and services. That’s the reason why countries that are rich in energy resources also have strategic power in terms of the international trade of these resources. On the other hand, it becomes important to provide energy security for countries that are resource-poor. Although green energy has become preferred one, fossil fuel energy keeps its place as one of the most used energy resources. That's why in this study it is aimed to determine major providers and users of coal as a type of fossil fuel energy resources. It is vital to investigate the structure of global coal trade structure to determine the weaknesses and strength of supply and use of coal. Network approach provides a holistic view to the system analyzed and presents more realistic (high-degree) indicators to analyze it. In this study, global trade network of coal is analyzed from 2000 to 2017 via network analysis. Changing structure and evolution of global coal trade has been revealed via some topological parameters which are specific to complex networks such as density, clustering, assortativity/disassortativity, centrality and degree distribution.
Pleistocene glaciations and polyphyletic origins of polyploidy in an arctic cladoceran

RFLP analysis of the ND4–ND5 genes of the mtDNA genome in Daphnia middendorffiana and three closely allied species was used to investigate its origin and age. Populations of D. middendorffiana from arctic Canada were found to possess three distinct mtDNA lineages, only one of which appears unique to this species. The other two mtDNA lineages are either closely allied or identical to haplotypes in D. pulicaria, suggesting that it is the maternal parent of many clones of D. middendorffiana. Within D. pulicaria, mtDNA lineages have largely disjunct distributions, suggesting that populations of this species persisted in three glacial refugia (arctic, western, eastern) during the Pleistocene. Hybridizations between these refugial stocks and other species such as D. melanica and D. pulex likely generated many of the polyploid lineages of D. middendorffiana following the Wisconsinan glaciation. The presence of one unique mtDNA lineage in D. middendorffiana suggests that at least some of its clones are more ancient, but further studies are needed to rule out the possibility of their recent derivation from an as yet undetected sexual species. As a general result, this study suggests that polyploid cladocerans are unlikely to predate the Pleistocene.
Oviposition response of spruce budworm (Lepidoptera: Tortricidae) to host terpenes and green-leaf volatiles

A dual-choice behavioral bioassay and gas chromatography – electroantennogram detection (GC–EAD) were used to determine the effect of host terpenes and nonhost green-leaf volatiles (GLVs) on the oviposition preference of the spruce budworm, Choristoneura fumiferana (Clemens). Some emphasis was placed on assessing the ability of females to distinguish between enantiomers of chiral monoterpenes because (+)-α-pinene but not (−)-α-pinene or (±)-α-pinene had been shown previously to promote oviposition. Headspace volatiles from white spruce, Picea glauca (Moench) Voss (Pinaceae), and balsam fir, Abies balsamea (L.) Mill. (Pinaceae), were sampled using solid-phase microextraction and identified by gas chromatography – mass spectrometry with the aid of a chiral column. Females deposited significantly more egg masses on filter paper substrate treated with host monoterpenes than on controls. Contrary to expectation, substrates treated with several GLVs were also preferred over the controls. None of the GLVs or terpenes was deterrent. Females showed no significant ability in either the behavioral or the GC–EAD bioassays to distinguish between enantiomers of selected chiral monoterpenes, including α-pinene, in contrast to earlier findings. We conclude that host terpenes serve as general rather than host-specific oviposition stimuli for spruce budworm.
Response of the parameters of excess infiltration and excess storage model to land use cover change

Abstract The Loess Plateau is the main source of water in Yellow River, China. After 1980s, the Yellow river water presented a significant reduction, what caused the decrease of the Yellow river discharge had been debated in academic circles. We proceeded with runoff generation mechanisms to explain this phenomenon. We built saturation excess runoff and infiltration excess runoff generation mechanisms for rainfall–runoff simulation in Jingle sub-basin of Fen River basin on the Loess Plateau, to reveal the influence of land use change on flood processes and studied the changes of model parameters under different underlying conditions. The results showed that the runoff generation mechanism was mainly infiltration-excess overland flow, but the flood events of saturation-excess overland flow had an increasing trend because of land use cover change (the increase of forestland and grassland areas and the reduction of cultivated land). Some of the model parameters had physical significances，such as water storage capacity (WM), infiltration capacity (f), evapotranspiration (CKE), soil permeability coefficient (k) and index of storage capacity distribution curve (n) showed increasing trends, and index of infiltration capacity distribution curve (m) showed a decreasing trend. The above results proved the changes of runoff generation mechanism from the perspective of model parameters in Jingle sub-basin, which can provide a new perspective for understanding the discharge reduction in the Yellow River basin.