Miracle-dz/UniFAR-FTUs huggingface dataset:
Thermophilic bacterial communities in hot composts as revealed by most probable number counts and molecular (16S rDNA) methods

Thermogenic composts are known to host a variety of thermophilic micro-organisms that were recently investigated by cultural means and identified as Thermus thermophilus, Bacillus spp. , and Hydrogenobacter spp. In this paper, we present a classical, cultural enumeration of thermophilic populations on the one hand, and a molecular investigation of the bacterial community by restriction enzyme analyses of a clone library of bacterial 16S rRNA genes on the other hand. Bacterial diversity, revealed by the clone analyses of four samples, was shown to undergo a dramatic change between the young (13–18-day) and the old (39–41-day) samples, possibly linked to the general decrease in temperature and the physicochemical evolution of organic matter during the composting process. Among the 200 clones investigated, 69 clones could be identified as Thermus thermophilus and thermophilic Bacillus spp. These results proved both taxa to be among the dominant bacterial populations at the highest temperatures reached by thermogenic composts.
Do Introduced Grasses Improve Forage Production on the Northern Mixed Prairie

Abstract Relative benefit of introducing forage species to the Northern Great Plains have been examined with contradictory conclusions. In most cases, studies were either confounded by time of establishment or treatments were not randomized and lacked independence. We examined aboveground net primary production (ANPP) in northern mixed prairie using a randomized complete block design with four treatments: crested wheatgrass (Agropyron cristatum [L.] Gaertn.), Russian wildrye (Psathyrostachys juncea [Fisch.] Nevski), a native control that was not harvested, and a harvested native. The experiment was conducted in a Stipa–Agropyron–Bouteloua site and a Stipa–Bouteloua site over 13 yr and 12 yr, respectively. The data were analyzed by sampling period (Stipa–Agropyron–Bouteloua: 1, 1994 to 1997; 2, 1998 to 2001; 3, 2002 to 2006; and Stipa–Bouteloua: 1, 1995 to 1998; 2, 1999 to 2002; 3, 2003 to 2006). ANPP among treatments was influenced (P < 0.05) by site and its interaction with treatment and sampling period (1 to 3). ANPP from the native-control, harvested-native, crested wheatgrass, and Russian wildrye treatments was 220.9, 183.9, 300.8, and 189.6 g · m–2 (SEM = 11.2), respectively, in the Stipa–Agropyron–Bouteloua site and 122.9, 98.2, 216.3, and 115.9 g · m–2 (SEM = 12.0), respectively, in the Stipa–Bouteloua site. Mean ANPP (SEM) within each sampling period (1 to 3) was 186.4 (9.1), 135.4 (5.8), and 263.9 (8.8) g · m–2 in the Stipa–Agropyron–Bouteloua site, respectively, and 124.5 (6.4), 138.6 (6.1), and 151.3 (10.5) g · m–2 in the Stipa–Bouteloua site, respectively. Russian wildrye in the Stipa–Bouteloua site and crested wheatgrass in both sites was relatively more productive in the first period after establishment than in subsequent years. The study confirms the relative ANPP advantage of crested wheatgrass over native on the Stipa–Bouteloua site but not on the Stipa–Agropyron–Bouteloua site, whereas Russian wildrye exhibited no ANPP advantage over the native on either site.
Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments†

Abstract Multipartite viruses have two or more genome segments, and package different segments into different particle types. Although multipartition is thought to have a cost for virus transmission, its benefits are not clear. Recent experimental work has shown that the equilibrium frequency of viral genome segments, the setpoint genome formula (SGF), can be unbalanced and host-species dependent. These observations have reinvigorated the hypothesis that changes in genome-segment frequencies can lead to changes in virus-gene expression that might be adaptive. Here we explore this hypothesis by developing models of bipartite virus infection, leading to a threefold contribution. First, we show that the SGF depends on the cellular multiplicity of infection (MOI), when the requirements for infection clash with optimizing the SGF for virus-particle yield per cell. Second, we find that convergence on the SGF is very rapid, often occurring within a few cellular rounds of infection. Low and intermediate MOIs lead to faster convergence on the SGF. For low MOIs, this effect occurs because of the requirements for infection, whereas for intermediate MOIs this effect is also due to the high levels of variation generated in the genome formula (GF). Third, we explored the conditions under which a bipartite virus could outcompete a monopartite one. As the heterogeneity between environments and specificity of gene-expression requirements for each environment increased, the bipartite virus was more likely to outcompete the monopartite virus. Under some conditions, changes in the GF helped to exclude the monopartite competitor, highlighting the versatility of the GF. Our results show the inextricable relationship between MOI and the SGF, and suggest that under some conditions, the cost of multipartition can be outweighed by its benefits for the rapid tuning of viral gene expression.
Quality evaluation of living and postmortem Chinese mitten crabs (Eriocheir sinensis)

Abstract Total volatile basic nitrogen (TVBN), biogenic amine, total viable count (TVC), volatile compounds, and sensory evaluation were conducted to assess the quality of Chinese Mitten Crabs (Eriocheir sinensis) at living, zero, 2, 5, 10, 15, and 24 hr postmortem. The sensory evaluation found a noticeable odor of spoilage becoming evident 10 hr postmortem. The TVBN value increased and then decreased as time increased, reaching 23.67 mg N/100 g at 24 hr postmortem. Although biogenic amines were detected at 5 hr postmortem, by 24 hr postmortem these had not reached dangerous levels of toxicity. The initial TVC (6.06 Log CFU/g) of the living crab samples was relatively high and climbed further postmortem, reaching 10.00 Log CFU/g 24 hr postmortem. Trimethylamine was detected in the living sample in belly meat and 2 hr postmortem in crab roe and reached 8.33 µg/g in the roe 24 hr postmortem. Indole was detected at 0 hr (belly meat) and 10 hr (crab roe) postmortem, but did not change significantly during the observation period. Sulfur‐containing compounds were detected 5 hr after death and gradually increased over the observation period. Most indicators showed major changes at 5 hr and 10 hr postmortem. By 10 hr postmortem, the crab had entered the putrefaction stage and was thus no longer safe for consumption.
A Small-Sized Population of Human Umbilical Cord Blood-Derived Mesenchymal Stem Cells Shows High Stemness Properties and Therapeutic Benefit

Mesenchymal stem cells (MSCs) represent a promising means to promote tissue regeneration. However, the heterogeneity of MSCs impedes their use for regenerative medicine. Further investigation of this phenotype is required to develop cell therapies with improved clinical efficacy. Here, a small-sized population of human umbilical cord blood-derived MSCs (UCB-MSCs) was isolated using a filter and centrifuge system to analyze its stem cell characteristics. Consequently, this population showed higher cell growth and lower senescence. Additionally, it exhibited diverse stem cell properties including differentiation, stemness, and adhesion, as compared to those of the population before isolation. Using cell surface protein array or sorting analysis, both EGFR and CD49f were identified as markers associated with the small-sized population. Accordingly, suppression of these surface proteins abolished the superior characteristics of this population. Moreover, compared to that with large or nonisolated populations, the small-sized population showed greater therapeutic efficacy by promoting the engraftment potential of infused cells and reducing lung damage in an emphysema mouse model. Therefore, the isolation of this small-sized population of UCB-MSCs could be a simple and effective way to enhance the efficacy of cell therapy.
Unoccupied aerial system enabled functional modeling of maize height reveals dynamic expression of loci

Abstract Unoccupied aerial systems (UAS) were used to phenotype growth trajectories of inbred maize populations under field conditions. Three recombinant inbred line populations were surveyed on a weekly basis collecting RGB images across two irrigation regimens (irrigated and non‐irrigated/rain fed). Plant height, estimated by the 95th percentile (P95) height from UAS generated 3D point clouds, exceeded 70% correlation (r) to manual ground truth measurements and 51% of experimental variance was explained by genetics. The Weibull sigmoidal function accurately modeled plant growth (R 2: >99%; RMSE: <4 cm) from P95 genetic means. The mean asymptote was strongly correlated (r 2 = 0.66–0.77) with terminal plant height. Maximum absolute growth rates (mm/day) were weakly correlated with height and flowering time. The average inflection point ranged from 57 to 60 days after sowing (DAS) and was correlated with flowering time (r 2 = 0.45–0.68). Functional growth parameters (asymptote, inflection point, growth rate) alone identified 34 genetic loci, each explaining 3–15% of total genetic variation. Plant height was estimated at one‐day intervals to 85 DAS, identifying 58 unique temporal quantitative trait loci (QTL) locations. Genomic hotspots on chromosomes 1 and 3 indicated chromosomal regions associated with functional growth trajectories influencing flowering time, growth rate, and terminal growth. Temporal QTL demonstrated unique dynamic expression patterns not previously observable, and no QTL were significantly expressed throughout the entire growing season. UAS technologies improved phenotypic selection accuracy and permitted monitoring traits on a temporal scale previously infeasible using manual measurements, furthering understanding of crop development and biological trajectories.
Polystichum perpusillum (sect. Haplopolystichum, Dryopteridaceae), a New Fern Species from Guizhou, China

Polystichum perpusillum L.B. Zhang & H. He, a new fern species of Polystichum sect. Haplopolystichum (Dryopteridaceae), is described and illustrated from the entrance to a karst cave in southern Guizhou, China. A phylogenetic analysis based on the chloroplast trnL-F sequences shows that it is phylogenetically isolated in the section with no close relatives. Morphologically, it is similar to P. minutissimum, but P. perpusillum has an acute lamina apex, up to 12 pairs of pinnae per lamina, and deltoid-ovate or ovate-lanceolate rachis scales, while P. minutissimum has a round lamina apex, 5–8 pairs of pinnae per lamina, and subulate or linear rachis scales. Polystichum perpusillum has a granulate sculpture with Verrucae on its perispore, a sculpture rare in the genus. The species is considered to be critically endangered.
Prevalence and Risk Factors of Urinary Incontinence in Frail Elderly Females

Background/Purpose. Urinary incontinence (UI) is an important geriatric health problem, and it is linked to frailty syndrome. We had conducted a study to detect the prevalence and risk factors of UI and its effect on quality of life (QOL) among frail elderly females living in Cairo, Egypt. Methods. We carried out a cross-sectional study on 130 frail elderly females sixty years and older, attending Ain Shams Geriatrics Hospital, Cairo, Egypt. Each patient gave oral consent and then was subjected to history taking, full clinical examination, diagnosis of frailty (clinical frailty scale), assessment of UI by the Arabic version of International Consultation on Incontinence Questionnaire-Urinary Incontinence Short Form (ICIQ-UI SF), assessment of QOL by using the Arabic version of Incontinence Impact Questionnaire Short Form (IIQ-7 SF), and complete urine analysis. Results. The prevalence of UI among the studied population was 80%. Mixed UI was the most prevalent type. UI was significantly associated with older age, functional impairment, multiparity, osteoarthritis, stroke, vaginal prolapse, and laxative use. All IIQ-7 subscales were higher (worse health-related QOL) for women with mixed UI. Conclusion. Urinary incontinence is prevalent in frail elderly females. Mixed UI, compared with other types, has a significant negative impact on all domains of quality of life.
Host population density and body mass as determinants of species richness in parasite communities: comparative analyses of directly transmitted nematodes of mammals

Epidemiological theory predicts positive correlations between host population density or body mass and species richness among parasite communities. Here I test these predictions by a comparative study of communities of directly transmitted mammalian parasites, gastrointestinal strongylid nematodes. I use data from 45 species of mammals, representing examination of 17 200 individual hosts. The variable studied was the average number of gastrointestinal strongylid nematode species per host population, and three different methods were used to obtain estimates of parasite species richness that are unbiased by number of host individuals examined. Analyses were done using the phylogenetically independent contrast method. Host population density and parasite species richness were strongly positively correlated when the effects of host body weight had been controlled for. Controlling for other variables did not change this, and the relationship was found regardless of method used to correct for uneven sampling effort among host species. A positive relationship between parasite species richness and host body weight was also found, but the effect of host densities had to be controlled for to see this. These relationships between host traits and species richness of directly transmitted parasites are stronger than patterns found using data on indirectly transmitted mammalian parasites, and suggests that links between host traits and parasite species richness are stronger than previously suggested. The results are consistent with parasite species richness being positively linked to pathogen transmission rates and reductions in transmission rates possibly increasing extinction probabilities in parasite populations. The results also suggest that parasites may exert a cost of increases in rate of population energy usage, and thus show that pathogens may be important in generating independence between body mass and rate of population energy usage among host species.
Avian Haematozoa: mortality and pathogenicity

A review of 5640 articles on avian blood parasites showed that 236 reported mortality or gross pathogenicity in birds, and 89% of them were concerned with mortality in domesticated birds and how to control the blood parasites involved. Only 6% of records concerned birds in zoological gardens; the remainder referred to mortality in wild birds.
Anuran Locomotion: Structure and Function. I. Preliminary Observations on Relation between Jumping and Osteometrics of Appendicular and Postaxial Skeleton

The jumping abilities of Bufo marinus, Bufo terrestris, Hyla crucifer and Rana clamitans were determined by averaging the distances jumped in two trials, each of five successive jumps. The smallest absolute and relative jumping abilities were possessed by Bufo, the greatest absolute jumping ability by Rana, and the greatest relative jumping ability by Hyla. Each frog jumped was skeletonized in order to test the correlation of jumping ability and osteological characteristics. Approximately 30 measurements taken of the postaxial and appendicular skeleton were converted into a series of proportions to reflect functional complexes. The proportions, in the main, possess low variability and, thus, high stability within each genus. By associating jumping abilities with proportions, several morphological and functional trends are disclosed. Notably, strong jumpers share a rectangular presacral platform, short forelimbs, large forefeet, short scapulae, long hindlimbs, and tibiofibula longer than femur.
An analysis of environmental and economic implications of nil and restricted grazing systems designed to reduce nitrate leaching from New Zealand dairy farms. II. Pasture production and cost/benefit analysis

Abstract Nitrate leaching from animal urine is perceived to be a serious consequence of dairy farming. Previous results suggested that nil and restricted grazing systems could reduce nitrate leaching by up to 50%. It is likely that such systems may also increase pasture production. However, potential disadvantages include reduction in the clover content of pastures and increase in capital and/or operating costs. This paper examines the economic implications of nil and restricted grazing systems based on data from an average New Zealand dairy farm and from a long‐term farmlet study. The analyses suggested that pasture production increased by about 20% and 2–8%, respectively, compared with a conventional grazing system. Based on the average New Zealand dairy farm, the costs/benefit analysis of the nil grazing system suggested a negative return on capital of about ‐10%. For the restricted grazing system, the average return on capital was about 9% (range: ‐4 to 25%) and depended largely on the efficiency of animal excreta use. On farms where an effluent application system is already in place, the average return on capital was 17% (range: 2 to 50%). Based on the farmlet study, the cost/benefit analysis of both grazing systems suggested a small negative return on capital, except when the costs of an effluent application system were excluded. It is concluded that a restricted grazing system for the average New Zealand dairy farm is likely to be economically viable, on farms where an effluent application system or a feed pad is already in place.
Meningioma 1 is indispensable for mixed lineage leukemia-rearranged acute myeloid leukemia

Mixed lineage leukemia (MLL/KMT2A) rearrangements (MLL-r) are one of the most frequent chromosomal aberrations in acute myeloid leukemia. We evaluated the function of Meningioma 1 (MN1), a co-factor of HOXA9 and MEIS1, in human and murine MLL-rearranged leukemia by CRISPR-Cas9 mediated deletion of MN1. MN1 was required for in vivo leukemogenicity of MLL positive murine and human leukemia cells. Loss of MN1 inhibited cell cycle and proliferation, promoted apoptosis and induced differentiation of MLL-rearranged cells. Expression analysis and chromatin immunoprecipitation with sequencing from previously reported data sets demonstrated that MN1 primarily maintains active transcription of HOXA9 and HOXA10, which are critical downstream genes of MLL, and their target genes like BCL2, MCL1 and Survivin. Treatment of MLL-rearranged primary leukemia cells with anti-MN1 siRNA significantly reduced their clonogenic potential in contrast to normal CD34+ hematopoietic progenitor cells, suggesting a therapeutic window for MN1 targeting. In summary, our findings demonstrate that MN1 plays an essential role in MLL fusion leukemias and serve as a therapeutic target in MLL-rearranged acute myeloid leukemia.
Antibiotic Resistance and Molecular Epidemiological Characteristics of Streptococcus agalactiae Isolated from Pregnant Women in Guangzhou, South China

Streptococcus agalactiae colonization in pregnant women can cause postpartum intrauterine infections and life-threatening neonatal infections. To formulate strategies for the prevention and treatment of S. agalactiae infections, we performed a comprehensive analysis of antibiotic resistance and a molecular-based epidemiological investigation of S. agalactiae in this study. Seventy-two S. agalactiae strains, collected from pregnant women, were subjected to antibiotic susceptibility tests; then, the screened erythromycin and clindamycin nonsusceptible isolates were used for macrolides and clindamycin resistance genes detection, respectively. Detection of resistance genes, serotyping, and determination of virulence genes were performed by polymerase chain reaction. The clonal relationships among the colonized strains were evaluated by multilocus sequence typing. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) mass peak analysis was performed to discriminate the specific sequence types (STs). In our study, 69.4% and 47.2% of the strains were nonsusceptible to erythromycin and clindamycin, respectively; the multidrug resistance rate was 66.7%. All erythromycin nonsusceptible strains harbored resistance genes, whereas only 52.9% of the clindamycin nonsusceptible strains possessed the linB gene. Erythromycin resistance was mainly mediated by the ermB or mefA/E genes. Four serotypes were identified, and the most common serotype was serotype III (52.8%), followed by Ib (22.2%), Ia (18.0%), and II (4.2%). All the strains were divided into 18 STs that were assigned to nine clonal complexes. Most of the major STs were distributed into specific serotypes, including ST19/serotype III, ST17/serotype III, ST485/serotype Ia, ST862/serotype III, and ST651/serotype III. Analysis of virulence genes yielded seven clusters, of which bca-cfb-scpB-lmb (61.6%) was the predominant virulence gene cluster. Among all ST strains distributed in this region, only the ST17 strains had a mass peak at 7620 Da. The outcomes of this study are beneficial for the epidemiological comparison of colonized S. agalactiae in different regions and may be helpful for developing the strategies for the prevention of S. agalactiae infection in Guangzhou. Furthermore, our results show that MALDI-TOF MS can be used for the rapid identification of the ST17 strains.
Differential screening of a human pancreatic adenocarcinoma λgt11 expression library has identified increased transcription of elongation factor ef‐1α in tumour cells

A human pancreatic adenocarcinoma λgt11 expression library was differentially screened with mRNA derived from normal and cancerous pancreatic tissues. Five clones preferentially hybridized with pancreatic adenocarcinoma mRNA. cDNA inserts from 4 of these clones were amplified by PCR, labelled with α32P and used in Northern blot analysis against mRNA prepared from a variety of tumour and normal tissues. λGER‐4 identified a pancreas‐associated mRNA (> 10 kb) with no homology with known sequences at either the nucleic or amino‐acid level. λGER‐2 identified a 1.7‐kb mRNA transcript that was over‐expressed in mRNA prepared from pancreas, colon, breast, lung and gastric tumours relative to normal tissues. Sequence analysis and restriction‐enzyme mapping showed that this clone was completely homologous with the active form of human elongation factor EF‐1α. This high level of EF‐1α‐mRNA expression in tumour tissues lends support to the increasing evidence that EF‐1α is an important regulator of the cell cycle.