Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of bacterial communities of riverbank sediments contaminated with polycyclic aromatic hydrocarbons

PAHs are common toxic pollutants that persist in the environment. PAHs have low solubility in water and tend to attach to organic matter and particles in water, soils and sediments. High concentrations of PAHs are found in a variety of ecosystems, especially where anthropogenic pollution is increased. PAHs pose risks to aquatic biota and are linked to deformities and cancer in humans, fish, and benthic organisms. Aerobic bioremediation of PAHs is a common approach successfully implemented in soils, waters and sediments. Yet other organisms including algae, fungi and plants are also suitable for bioremediation. On the other hand, anaerobic biodegradation of PAHs is limited and less research has been dedicated to this type of degradation. Nevertheless, anaerobic biodegradation of PAHs can occur under nitrate or sulfate reducing conditions. Bioremediation of contaminated soils and sediments with PAHs can be simple, costeffective and ex situ and in situ. More research is needed to fully understand mechanisms of bacterial metabolism in degradation of PAHs. 1 Selected portions of this chapter were included (granted copyright permission) in the following publication: Johnston C, Johnston GP. Rajesh Arora (Ed.). 2012; Bioremediation of polycyclic aromatic hydrocarbons, in Microbial Biotechnology: Energy and Environment, CAB International, Wallingford, UK), 279-296 pp. Dr. Carl Johnston was responsible for fungal degradation and phytoremediation sections, as well as final editorial changes and final revision. I wrote the following sections: general description of PAHs, sources of PAHs, exposure of PAHs, PAHs in aquatic environments, aerobic remediation (composting and landfarming), microbial degradation (algal and bacterial) and anaerobic degradation.
Frequency of heterotic hybrids in relation to parental genetic divergence and general combining ability in blackgram [Vigna mungo (L.) Hepper]

An investigation was carried out to test the predictability of frequency of heterotic hybrids based on parental gca effects and genetic diversity in blackgram. The 40 F1s effected using 10 lines and 4 testers were evaluated along with their parents for 10 productivity per set raits. The overall gca status (high and low) of each parent and overall sca and heterotic status (high and low) of each hybrid across 10 traits were determined. Based on overall gca status and genetic divergence of parents, the hybrids were grouped into different classes. The hybrids involving parents contrasting for overall gca status and/or those involving parents with intermediate genetic divergence were more frequently heterotic than those involving comparable gca status and with extreme genetic divergence. It is hence, desirable to involve parents with intermediate genetic divergence and contrasting gca effects to recover higher frequencies of heterotic hybrids for productivity per se traits in blackgram.
Strain features of pneumococcal isolates in the pre- and post-PCV10 era in Pakistan

Pakistan is amongst the four countries with the highest number of pneumococcal deaths. While the PCV10 vaccine was introduced in Pakistan in October 2012, data regarding the impact of the vaccine on the population dynamics of Streptococcus pneumoniae in Pakistan remain obscure. Using whole genome sequencing of 190 isolates (nasopharyngeal carriage=75, disease=113, unknown sites=2) collected between 2002 and 2020, this study presents characteristics of pneumococcal strains in Pakistan in the pre- and post-vaccine era. The isolates were characterized on the basis of serotype distribution, genetic lineages (or Global Pneumococcal Sequence Cluster, GPSC) and antibiotic resistance. A high level of diversity in serotype and genetic lineages of pneumococci was observed in Pakistan. Among 190 isolates, we identified 54 serotypes, 67 GPSCs and 116 sequence types (STs) including 23 new STs. The most prevalent GPSCs and their associated serotypes in nasopharyngeal carriage were GPSC54 (expressing serotype 9V), GPSC5 (15A and 7B, and serogroup 24), GPSC25 (15B/15C), GPSC67 (18C) and GPSC376 (6A and 6D). Similarly, among 113 disease-causing isolates, the most prevalent GPSC/serotype combinations were GPSC2 (serotype 1), GPSC10 (serotypes 14, 10A, 19A and 19F), GPSC43 (serotypes 13, 11A, 23B, 35A and 9V), GPSC67 (serotypes 18A and 18C) and GPSC642 (serotype 11A). Of the 190 isolates, the highest levels of resistance were observed against penicillin (58.9 %, n=122), erythromycin (29.5 %, n=56), clindamycin (13.2 %, n=25), co-trimoxazole (94.2 %, n=179) and tetracycline/doxycycline (53.2 %, n=101). A higher proportion of disease-causing isolates were multidrug resistant as compared to carriage isolates (54 % vs 25 %). Our data suggest limited coverage of PCV10 in nasopharyngeal (21.6 %, 16/74) as well as disease-causing (38.1 %, 16/42) isolates among children ≤5 years old; however, higher valent vaccine PCV13 would increase the coverage rates to 33.8 % in nasopharyngeal and 54.8 % in disease-causing isolates, whereas PCV24/25 would offer the highest coverage rates. Owing to the diversity of serotypes observed during the post-vaccine period, the suggested inclusion of serotype in future vaccine formulations will require investigations with larger data sets with an extended temporal window. This article contains data hosted by Microreact.
Bimodal Pollination Systems in Andean Melastomataceae Involving Birds, Bats, and Rodents

Floral adaptation to a single most effective functional pollinator group leads to specialized pollination syndromes. However, adaptations allowing for pollination by two functional groups (bimodal pollination systems) remain a rarely investigated conundrum. We tested whether floral scent and nectar traits of species visited by two functional pollinator groups indicate specialization on either of the two pollinator groups or adaptations of both (bimodal systems). We studied pollination biology in four species of Meriania (Melastomataceae) in the Ecuadorian Andes. Pollinator observations and exclusion experiments showed that each species was effectively pollinated by two functional groups (hummingbirds/bats, hummingbirds/rodents, flowerpiercers/rodents), nectar composition followed known bird preferences, and scent profiles gave mixed support for specialization on bats and rodents. Our results suggest that nectar-rewarding Meriania species have evolved stable bimodal pollination strategies with parallel adaptations to two functional pollinator groups. The discovery of rodent pollination is particularly important given its rarity outside of South Africa.
Cross-Species Comparative DNA Methylation Reveals Novel Insights into Complex Trait Genetics among Cattle, Sheep, and Goats

Abstract The cross-species characterization of evolutionary changes in the functional genome can facilitate the translation of genetic findings across species and the interpretation of the evolutionary basis underlying complex phenotypes. Yet, this has not been fully explored between cattle, sheep, goats, and other mammals. Here, we systematically characterized the evolutionary dynamics of DNA methylation and gene expression in 3 somatic tissues (i.e. brain, liver, and skeletal muscle) and sperm across 7 mammalian species, including 3 ruminant livestock species (cattle, sheep, and goats), humans, pigs, mice, and dogs, by generating and integrating 160 DNA methylation and transcriptomic data sets. We demonstrate dynamic changes of DNA hypomethylated regions and hypermethylated regions in tissue-type manner across cattle, sheep, and goats. Specifically, based on the phylo-epigenetic model of DNA methylome, we identified a total of 25,074 hypomethylated region extension events specific to cattle, which participated in rewiring tissue-specific regulatory network. Furthermore, by integrating genome-wide association studies of 50 cattle traits, we provided novel insights into the genetic and evolutionary basis of complex phenotypes in cattle. Overall, our study provides a valuable resource for exploring the evolutionary dynamics of the functional genome and highlights the importance of cross-species characterization of multiomics data sets for the evolutionary interpretation of complex phenotypes in cattle livestock.
A new Middle Miocene selachian assemblage (Chondrichthyes, Elasmobranchii) from the Central Paratethys (Nyirád, Hungary): implications for temporal turnover and biogeography

Abstract A new Middle Miocene (Langhian - early Serravallian) assemblage with shark and ray teeth from Nyirád (Hungary, Transdanubia, Veszprém County) consists of nine families, with 15 different species. The assemblage shares many common genera with other Middle Miocene assemblages in the Paratethys (Notorynchus, Carcharias, Otodus, Cosmopolitodus, Hemipristis, Galeocerdo, Carcharhinus, and Aetobatus), and reflects a subtropical climate and a close connection with the Mediterranean Sea. However, a detailed faunal compilation of Miocene selachians reveals that several taxa that were still present in the Mediterranean or lived in the Paratethys during the Lower Miocene disappeared or became very rare by the Middle Miocene in the Central Paratethys (e.g., Isistius, Centrophorus, Mitsukurina, Carcharoides, Parotodus, Alopias). The taxa that went locally extinct in the Paratethys are mainly represented by deep-water or pelagic forms. Their disappearance is most probably related to the gradual separation of the Paratethys from the Mediterranean. The common presence of some large, rather pelagic sharks (e.g., Otodus, Cosmopolitodus) in the Central Paratethys during the Middle Miocene is explained here by the widespread occurrence of their potential prey represented by marine mammals (e.g., whales and dolphins).
Modelling and upscaling of shallow compaction in basins

Heterogeneous fine-grained sediments at shallow burial (< 1000m) below the seafloor can often experience large strain of mechanical compaction and variable degrees of overpressure in their pore space as a result of disequilibrium dissipation of pore fluid. Shallow overpressure can pose significant risks to economics and safety of hydrocarbon production and may impact on hydrocarbon generation deep in a basin and hydrocarbon migration to traps during basin evolution. However, when basin modelling ignores the heterogeneity of sediments, large strain deformation and fluid flow conditions at smaller lengthand/or time-scales than those at basin scales, it can lead to incorrect prediction of sediment compaction, and hence the mass of the sediment column, the magnitude of pore pressure and its distribution at shallow burials, and consequently can impact on the simulation of basin evolution. In this thesis, the necessity of considering large-strain consolidation in modelling shallow compaction is demonstrated, and a one-dimensional large-strain numerical simulator, based on one of Gibson’s consolidation models and suitable for basin modelling, is developed and verified. An analytical upscaling technique is also developed for determining the effective compressible parameters and permeability for horizontally layered systems of certain compaction characteristics. They are used subsequently to analyse parametrically the compaction behaviours of the layered systems and to calculate effective coefficients for the systems, with results showing that fine-scale simulation is required when considering the effect of fluid-structure interaction. However, the large strain model over-predicts the pressure of the Ursa region, Gulf of Mexico, based on information from the Integrated Ocean Drilling Program (IODP). An analysis indicates that horizontal fluid flow, or lateral motion of mass transport processes, may explain the over prediction. The limitation of a 1D model is further discussed thereafter both in fluid flow and mechanical deformation. With strong applicability and fundamentality, the Modified Cam Clay model is adopted in 2D research, and related verification is provided. Modified Cam Clay can show elastic and elastic-plastic properties in basin evolution. Heterogeneous Modified Cam Clay materials can be upscaled to a homogenous anisotropic elastic material in elastic deformation and a homogenous Modified Cam Clay material in elastic-plastic deformation, however, the upscaled parameters vary with the effective stress. The value of the upscaling is demonstrated by modelling the evolution of a simplified North Africa basin model.
Conodonts in Ordovician biostratigraphy

The long time interval after Pander's (1856) original conodont study can in terms of Ordovician conodont biostratigraphical research be subdivided into three periods, namely the Pioneer Period (1856–1955), the Transition Period (1955–1971) and the Modern Period (1971-Recent). During the pre-1920s, the few published conodont investigations were restricted to Europe and North America and were not concerned about the potential use of conodonts as guide fossils. Although primarily of taxonomic nature, the pioneer studies by Branson & Mehl, Stauffer and Furnish during the 1930s represent the beginning of the use of conodonts in Ordovician biostratigraphy. However, no formal zones were introduced until Lindstrom (1955) proposed four conodont zones in the Lower Ordovician of Sweden, which marks the end of the Pioneer Period. Because Lindstrom's zone classification was not followed by similar work outside Baltoscandia, the time interval up to the late 1960s can be regarded as a Transition Period. A milestone symposium volume, entitled ‘Symposium on Conodont Biostratigraphy’ and published in 1971, summarized much new information on Ordovician conodont biostratigraphy and is taken as the beginning of the Modern Period of Ordovician conodont biostratigraphy. In this volume, the Baltoscandic Ordovician was subdivided into named conodont zones, whereas the North American Ordovician succession was classified into a series of lettered or numbered faunas. Although most of the latter did not receive zone names until 1984, this classification has been used widely in North America. The Middle and Upper Ordovician Baltoscandic zone classification, which was largely based on evolutionary species changes in lineages and hence includes phylozones, has subsequently undergone only minor changes and has been used slightly modified also in some other regions, such as New Zealand, China and eastern North America. The great importance of conodonts in Ordovician biostratigraphy is shown by the fact that conodonts are used for the definition of two of the seven global stages, and seven of the 20 stage slices, now recognized within this system.
Orthodontic tooth movement after periodontal regeneration of intrabony defects

The prevalence of intrabony defects in patients with advanced periodontitis stages III and IV is high. These patients usually need both periodontal treatment and orthodontic therapy, including tooth movement through bone defects, to improve masticatory function, aesthetics, and overall quality of life. Clinical practice guidelines recommend periodontal regenerative surgical interventions to resolve these defects and propose initiating orthodontic tooth movement (OTM) once periodontal therapy goals have been met. Surgical interventions using various regenerative technologies like barrier membranes and enamel matrix proteins, combined or not with bone replacement grafts, have proven effective in regenerating lost periodontal tissues. However, the combination of periodontal and orthodontic treatments requires consideration of how periodontal regenerative therapies influence OTM. Studies suggest that regenerated bone may differ in density, composition, vascularity, and cellular activity, potentially affecting the speed and efficiency of OTM, and potential root resorption of moved teeth. Understanding the sequence and timing of implementing OTM after regenerative periodontal interventions is crucial due to their interlinked processes of bone resorption and formation. This narrative review aims to uncover scientific evidence regarding these combined treatments, examining the impacts of different regenerative technologies on OTM and delineating their advantages, limitations, and best practices.
Influence of microscale weak zones on bulk strength

Shear zones have different rheological properties than the surrounding rocks, indicating that the bulk strength of regions containing shear zone networks cannot be determined by considering the host rock rheology alone. We demonstrate the value of this concept at the microscale. We first consider the phase arrangements in naturally deformed rocks and document that weak phases exhibit little interconnection within a microstructure. Rather, three‐dimensional weak zones, analogous to viscous shear zones, can interconnect or bridge weak phases. These zones typically form at high stress sites, comprise multiple minerals, and deform by mechanisms independent of those in the surrounding minerals. The presence of weak zones strongly affects the bulk strength of the rock, disproportionate to the mode of the weak zones. For example, the development of 1% mode of a weak zone at a high stress site can reduce the bulk strength of the rock nearly an order of magnitude. Calculation of the bulk strength of the rock by some averaging algorithm of the deformation mechanisms operating outside the weak zones will overestimate strength. Instead, accurate calculations and predictions of bulk strength require accounting for the presence and geometry of weak zones. For this reason, we advocate use of the scale‐independent conceptual rheological model of interconnected weak zones or layers rather than that of interconnected weak phases. More generally, the way forward in improving quantification of the mechanical properties of the lithosphere requires recognizing and explicitly accounting for the spatial and temporal distribution of deformation mechanisms operating throughout a rock.
New ant (Hymenoptera: Formicidae) records for Ecuador deposited at the Carl Rettenmeyer ant collection in the QCAZ Museum

Here we report 3,221 ant specimens from >150 ant species, deposited in the Carl Rettenmeyer ant collection, in the QCAZ Museun, Entomology section, of the Pontifical Catholic University of Ecuador. This material was originally collected at Limoncocha (currently Sucumbios Province, Ecuador), between 1968‐1973, by Dr. Carl Rettenmeyer and collaborators. Twenty five ant species in this list are reported for Ecuador for the first time. Given the size and age of this collection, it constitutes the biggest and oldest ant collection for any Ecuadorian locality inside the country.
GENETIC ENHANCEMENT OF SEMI-EXOTIC MAIZE GERMPLASM

ABSTRACT - The characterization of 26 populations with varying levels of exotic germplasm was conducted in two environments representing distinct locations and planting seasons. The whole set was identified by five subsets: I ≡ local adapted germplasm; II ≡ exotic derived from tropical germplasm; III ≡ semi-exotic derived from tropical germplasm; IV ≡ semi-exotic derived from varying proportion of tropical and temperate germplasm; and V ≡ semi-exotic derived from temperate germplasm. In the experiment eI (Anhembi, SP; three replications) the mean yield (EW - ear weight, t ha-1) for the five sets were 9.49, 8.88, 9.11, 8.68 and 8.51; which are equivalent to 79.5, 74.4, 76.3, 72.7 and 71.3 in percent of the hybrid check. Means for other traits (E10 – weight of ten ears, EL – ear length, ED – ear diameter, and TB – tassel branch number) were also shown. In the experiment eII (Piracicaba, SP; no replications), the following traits were evaluated: EW, GW (grain weight), GR (grain yield ratio), MF (days to male flowering), and SW (specific weight). A low correlation (0.220) was observed for EW between environments. In general, the populations under study presented a fairly good potential to be used in breeding programs. Key words: exotic germplasm, population improvement, Zea mays. SOBRELEVACAO DO VALOR GENETICO DE GERMOPLASMA SEMIEXOTICO DE MILHO RESUMO - A caracterizacao de 26 populacoes com varios niveis de germoplasma exotico foi conduzida em dois ambientes, representando locais e epocas de plantio distintas. O conjunto total foi identificado por cinco subconjun-tos: I ≡ germoplasma local adaptado; II ≡ exotico derivado de germoplasma tropical; III ≡ semiexotico derivado de germoplasma tropical; IV ≡ semiexotico derivado de variadas proporcoes de germoplasma tropical e temperado; e V ≡ semiexotico derivado de germoplasma temperado. No experimento eI (Anhembi, SP; tres repeticoes), as medias de producao (EW – peso de espigas, t ha-1) para os cinco subconjuntos foram 9,49, 8,88, 9,11, 8,68 e 8,51, que sao equivalentes a 79,5%, 74,4%, 76,3%, 72,7% e 71,3% da media da testemunha. As medias de outros caracteres (E10 – peso de 10 espigas, EL – comprimento da espiga, ED – diâmetro da espiga e TB – numero de ramificacoes do pendao) tambem foram apresentadas. No experimento eII (Piracicaba, SP; sem repeticao), foram avaliados os caracteres: EW; GW (peso de graos); GR (rendimento de graos); MF (dias para florescimento masculino); e SW (peso especifico). Uma baixa correlacao (0.220) foi observada para EW entre ambientes. As populacoes avaliadas apresentam bom potencial para serem usadas em programas de melhoramento. Palavras chave: germoplasma exotico, melhoramento de populacoes, Zea mays.
JM3D&JM3D-LLM: Elevating 3D Understanding with Joint Multi-modal Cues

The rising importance of 3D understanding, pivotal in computer vision, autonomous driving, and robotics, is evident. However, a prevailing trend, which straightforwardly resorted to transferring 2D alignment strategies to the 3D domain, encounters three distinct challenges: (1) Information Degradation: This arises from the alignment of 3D data with mere single-view 2D images and generic texts, neglecting the need for multi-view images and detailed subcategory texts. (2) Insufficient Synergy: These strategies align 3D representations to image and text features individually, hampering the overall optimization for 3D models. (3) Underutilization: The fine-grained information inherent in the learned representations is often not fully exploited, indicating a potential loss in detail. To address these issues, we introduce JM3D, a comprehensive approach integrating point cloud, text, and image. Key contributions include the Structured Multimodal Organizer (SMO), enriching vision-language representation with multiple views and hierarchical text, and the Joint Multi-modal Alignment (JMA), combining language understanding with visual representation. Our advanced model, JM3D-LLM, marries 3D representation with large language models via efficient fine-tuning. Evaluations on ModelNet40 and ScanObjectNN establish JM3D's superiority. The superior performance of JM3D-LLM further underscores the effectiveness of our representation transfer approach. Our code and models are available at https://github.com/Mr-Neko/JM3D.
On strong growth conditions for weighted spaces of entire functions

We characterize the inclusion relations between weighted classes of entire functions with rapid decreasing growth and study strong growth comparison relations between given weights. In our considerations first we focus on weights defined in terms of the so-called associated weight function where the weight(system) is based on a given sequence. Then the abstract weight function case is reduced to the weight sequence setting by using the so-called associated weight sequence. Finally, we compare weighted entire function spaces defined in terms of so-called dilatation-type and exponential-type weight systems.