Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth, Reproductive Condition, and Digestive Tubule Atrophy of Pacific Oyster Crassostrea gigas in Gamakman Bay off the Southern Coast of Korea

ABSTRACT Spat of Pacific oysters (Crassostrea gigas) were collected from Gamakman Bay, Korea, and raised in a spat hardening facility located in the low intertidal zone of the bay for a “hardening/stunting” period of 10 mo. Seasonal changes in growth, reproductive condition, and digestive tubule atrophy (DTA) of these “hardened/stunted” oysters were monitored for more than a year after transplanting to a suspended longline system in a grow-out area in the bay. After transplantation, the hardened/stunted oysters showed a logarithmic increase in shell size for the first 4 mo, from June to October, and growth remained stable from late fall to early spring. During the 12 mo of the grow-out, the shell size of the hardened/stunted oysters increased from 15.4–74.2 mm, and tissue weight increased from 0.49–12.85 g. Histological analysis revealed that gametogenesis of hardened/stunted oysters commenced as early as February when water temperature remained at 10°C, and spawning occurred from July to September when water temperature reached 25–27°C. DTA assessed from histological analysis was higher from September to February, when the chlorophyll a level in the bay was lower. These data suggest that seasonal fluctuations in water temperature and food availability in the water column are the 2 main environmental parameters governing reproduction and growth of oyster in Gamakman Bay, and DTA could be a useful biomarker for monitoring the nutritional condition of oysters.
Phenotypic characterization of donkeys in Benishangul Gumuz National Regional State.

Fifteen morphometric measurements and eighteen qualitative traits were recorded on 323 randomly sampled adult donkeys (123 jacks and 200 jennets) to meet an objective of characterizing a heterogeneous donkey population of three phenotypic types (Sinnar, the locals and their crosses) found in Benishangul Gumuz region of Ethiopia. The General Linear Model and non-parametric test (chi-square) procedures of SAS software were used for the analysis of the morphometric data and qualitative traits, respectively. Means were separated using the Tukey-Kramer test. The studied morphometric measurements were significantly affected by the phenotypic type and partially affected by sex and sample location /district. Sinnar donkeys were significantly bigger and heavier than the local and the crosses. However, for some of the morphometric measurements no significance difference was observed between Sinnar and crosses implying the presence of heterosis. Heart girth measurements for Sinnar, local and crosses were 110.61±0.436, 106.18±0.448 and 108.87±1.251, respectively. Body weight estimates of 127.26±1.277, 113.40±1.312 and 121.13± 3.665 kg were obtained for Sinnar, the local and the crosses. There was sexual size dimorphism and depending on the type of morphometric trait either jacks or jennets show significantly (P<0.05) higher values as compared to the opposite sex. Jacks had wider chest (22.61 vs 22.09 cm.), thicker (24.40 vs 23.24 cm.), and longer cannon bone (31.00 vs 31.32 cm) than jennets, while the jennets possess wider hip (33.00 vs 31.69 cm.) and longer body (90.49 vs 88.52 cm.), back (67.37 vs 66.17), ear (24.42 vs 23.90 cm) and heavier estimated weight (122.47 vs 118.71 kg) than the jacks. Limited location effect was recorded showing donkeys from Guba district were comparatively the largest. Majority of the studied donkeys possess white abdominal color, unpigmented hoof and muzzle, short and medium hair size, plain body color pattern with long dorsal stripe without leg stripe, straight face and sloppy rump profile, medium tail length and thickness at the base of the tail. Qualitative differences (P<0.05) were also observed among the class categories. Further molecular level studies could supplement the current study and provide more refined classification of the various genotypes in the studied area. Similarly, characterization of the local donkeys found in other parts of the region and the Abyssinian donkeys in the adjoining areas is required.
Enzymatic antioxidant responses to biostimulants in maize and soybean subjected to drought

Water stress is one of the most important environmental factors inducing physiological changes in plants, such as decrease in the water potential of the cells, the stomatal closure; and the development of oxidative processes mediated by reactive oxygen species (ROS). Antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) are efficient scavengers of ROS. The aim of this research was to examine how the application of biostimulant based on humic substances and aminoacids may affect activity levels of SOD, CAT, and APX of maize and soybean plants under well-watered or drought stress conditions. Pots (4.5 L) were filled with a Typic Hapludult soil where the biostimulants doses were applied. It was taken leaf samples in order to analyze SOD, CAT, and APX activities in plants. SOD and APX activity levels were increased by application of biostimulant 1 in maize subjected to stress. Catalase activity was not enhanced in plants by using the biostimulants. The composition of the biostimulants was not able to enhance stress tolerance in maize and soybean plants subjected to water stress.
Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes

Abstract Transposable elements (TEs) are ubiquitous DNA segments capable of moving from one site to another within host genomes. The extant distributions of TEs in eukaryotic genomes have been shaped by both bona fide TE integration preferences in eukaryotic genomes and by selection following integration. Here, we compare TE target site distribution in host genomes using multiple de novo transposon insertion datasets in both plants and animals and compare them in the context of genome-wide transcriptional landscapes. We showcase two distinct types of transcription-associated TE targeting strategies that suggest a process of convergent evolution among eukaryotic TE families. The integration of two precision-targeting elements are specifically associated with initiation of RNA Polymerase II transcription of highly expressed genes, suggesting the existence of novel mechanisms of precision TE targeting in addition to passive targeting of open chromatin. We also highlight two features that can facilitate TE survival and rapid proliferation: tissue-specific transposition and minimization of negative impacts on nearby gene function due to precision targeting.
Hydrothermal Synthesis of Hematite Nanoparticles Decorated on Carbon Mesospheres and Their Synergetic Action on the Thermal Decomposition of Nitrocellulose

In this study, carbon mesospheres (CMS) and iron oxide nanoparticles decorated on carbon mesospheres (Fe2O3-CMS) were effectively synthesized by a direct and simple hydrothermal approach. α-Fe2O3 nanoparticles have been successfully dispersed in situ on a CMS surface. The nanoparticles obtained have been characterized by employing different analytical techniques encompassing Fourier transform infrared (FTIR) spectroscopy, Raman spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM). The produced carbon mesospheres, mostly spherical in shape, exhibited an average size of 334.5 nm, whereas that of Fe2O3 supported on CMS is at around 80 nm. The catalytic effect of the nanocatalyst on the thermal behavior of cellulose nitrate (NC) was investigated by utilizing differential scanning calorimetry (DSC). The determination of kinetic parameters has been carried out using four isoconversional kinetic methods based on DSC data obtained at various heating rates. It is demonstrated that Fe2O3-CMS have a minor influence on the decomposition temperature of NC, while a noticeable diminution of the activation energy is acquired. In contrast, pure CMS have a slight stabilizing effect with an increase of apparent activation energy. Furthermore, the decomposition reaction mechanism of NC is affected by the introduction of the nano-catalyst. Lastly, we can infer that Fe2O3-CMS may be securely employed as an effective catalyst for the thermal decomposition of NC.
Decline in Carbon Monoxide Transfer Coefficient in Chronic Obstructive Pulmonary Disease

Background: Although a reduced carbon monoxide transfer coefficient (Kco) is an important feature in chronic obstructive pulmonary disease (COPD), how it changes over time and its relationship with other clinical outcomes remain unclear. This study evaluated longitudinal changes in Kco and their relationship with other clinical outcomes. Methods: We evaluated patients with COPD from the Korean Obstructive Lung Disease cohort, followed up for up to ten years. Random coefficient models were used to assess the annual change in Kco over time. Participants were categorized into tertiles according to Kco decline rate. Baseline characteristics and outcomes, including changes in FEV1 and emphysema index, incidence of exacerbations, and mortality, were compared between categories. Results: A decline in Kco was observed in 92.9% of the 211 enrolled participants with COPD. Those with the most rapid decline (tertile 1) had a lower FEV1/FVC% (tertile 1: 43.8% ± 9.7%, tertile 2: 46.4% ± 10.5%, tertile 3: 49.2% ± 10.4%, p = 0.008) and a higher emphysema index at baseline (27.7 ± 14.8, 22.4 ± 16.1, 18.1 ± 14.5, respectively, p = 0.001). Tertile 3 showed a lower decline rate in FEV1 (16.3 vs. 27.1 mL/yr, p = 0.017) and a lower incidence of exacerbations (incidence rate ratio = 0.66, 95% CI = 0.44–0.99) than tertile 1. There were no differences in the change in emphysema index and mortality between categories. Conclusion: Most patients with COPD experienced Kco decline over time, which was greater in patients with more severe airflow limitation and emphysema. Decline in Kco was associated with an accelerated decline in FEV1 and more frequent exacerbations; hence, this should be considered as an important outcome measure in further studies.
Induced abortion and prematurity in a subsequent pregnancy: a study from Shanghai

To evaluate the impact of a first trimester induced abortion on the risks of low birth weight (LBW) and preterm birth in a subsequent pregnancy we conducted a pregnancy-based cohort study in Shanghai, China with recruitment from 15 general hospitals (or maternity and infant health institutes) from November 1993 to March 1998. Pregnant women with a history of induced abortion entered the abortion cohort and a reference cohort was established among women without such a history. All the subjects were enrolled before 64 days of gestation and interviewed five times until 42 days after delivery. Only singleton live births were analysed in this study. A total of 2953 pregnant women were enrolled and 2707 gave birth to live singletons. The overall incidence of LBW was 1·7%, 2·0% in the abortion cohort and 1·4% in the reference cohort. After controlling the potential confounders using logistic regression, the adjusted odds ratios were 1·7 (95% CI: 0·8-3·3) for LBW, 2·0 (95% CI: 0·9-4·7) for term LBW and 1·0 (95% CI: 0·6-1·5) for preterm birth, following an induced abortion pregnancy. Birth weight in the abortion cohort was 38·5 g higher than that of the reference cohort after adjustment for calender year at recruitment, couples' occupation, education, age, infant sex, maternal body mass index at recruitment, contraceptive use and gestation age. Previous first trimester induced abortion did not significantly increase the risk of LBW or preterm birth. The study was performed in a low-risk population and results may not be applicable to other settings.
Menstrual Cycle Length and Patterns in a Global Cohort of Women Using a Mobile Phone App: Retrospective Cohort Study

Background There is increasing information characterizing menstrual cycle length in women, but less information is available on the potential differences across lifestyle variables. Objective This study aimed to describe differences in menstrual cycle length, variability, and menstrual phase across women of different ages and BMI among a global cohort of Flo app users. We have also reported on demographic and lifestyle characteristics across median cycle lengths. Methods The analysis was run based on the aggregated anonymized dataset from a menstrual cycle tracker and ovulation calendar that covers all phases of the reproductive cycle. Self-reported information is documented, including demographics, menstrual flow and cycle length, ovulation information, and reproductive health and diseases. Data from women aged ≥18 years and who had logged at least three cycles (ie, 2 completed cycles and 1 current cycle) in the Flo app were included (1,579,819 women). Results Of the 1.5 million users, approximately half (638,683/1,579,819, 40.42%) were aged between 18 and 24 years. Just over half of those reporting BMIs were in the normal range (18.5-24.9 kg/m2; 202,420/356,598, 56.76%) and one-third were overweight or obese (>25 kg/m2; 120,983/356,598, 33.93%). A total of 16.32% (257,889/1,579,819) of women had a 28-day median cycle length. There was a higher percentage of women aged ≥40 years who had a 27-day median cycle length than those aged between 18 and 24 years (22,294/120,612, 18.48% vs 60,870/637,601, 9.55%), but a lower percentage with a 29-day median cycle length (10,572/120,612, 8.77% vs 79,626/637,601, 12.49%). There were a higher number of cycles with short luteal phases in younger women, whereas women aged ≥40 years had a higher number of cycles with longer luteal phases. Median menstrual cycle length and the length of the follicular and luteal phases were not remarkably different with increasing BMI, except for the heaviest women at a BMI of ≥50 kg/m2. Conclusions On a global scale, we have provided extensive evidence on the characteristics of women and their menstrual cycle length and patterns across different age and BMI groups. This information is necessary to support updates of current clinical guidelines around menstrual cycle length and patterns for clinical use in fertility programs.
Metformin: Sentinel of the Epigenetic Landscapes That Underlie Cell Fate and Identity

The biguanide metformin is the first drug to be tested as a gerotherapeutic in the clinical trial TAME (Targeting Aging with Metformin). The current consensus is that metformin exerts indirect pleiotropy on core metabolic hallmarks of aging, such as the insulin/insulin-like growth factor 1 and AMP-activated protein kinase/mammalian Target Of Rapamycin signaling pathways, downstream of its primary inhibitory effect on mitochondrial respiratory complex I. Alternatively, but not mutually exclusive, metformin can exert regulatory effects on components of the biologic machinery of aging itself such as chromatin-modifying enzymes. An integrative metabolo-epigenetic outlook supports a new model whereby metformin operates as a guardian of cell identity, capable of retarding cellular aging by preventing the loss of the information-theoretic nature of the epigenome. The ultimate anti-aging mechanism of metformin might involve the global preservation of the epigenome architecture, thereby ensuring cell fate commitment and phenotypic outcomes despite the challenging effects of aging noise. Metformin might therefore inspire the development of new gerotherapeutics capable of preserving the epigenome architecture for cell identity. Such gerotherapeutics should replicate the ability of metformin to halt the erosion of the epigenetic landscape, mitigate the loss of cell fate commitment, delay stochastic/environmental DNA methylation drifts, and alleviate cellular senescence. Yet, it remains a challenge to confirm if regulatory changes in higher-order genomic organizers can connect the capacity of metformin to dynamically regulate the three-dimensional nature of epigenetic landscapes with the 4th dimension, the aging time.
Phylogeny within the Chondracanthidae (Poecilostomatoida, Copepoda)

The existing systematics of the Chondracanthidae is based predominantly on female characters and divides them into two subfamilies: Chondracanthinae and Lernentominae. Phylogenetic analyses using maximum parsimony were performed using 186 male and female characters. Different trees were generated when male and female characters were analysed separately. Differential weighting showed that the female characters were dominant but not to a great extent and subsequent analyses were run with both partitions combined. Different trees were generated depending on the character setting (unordered, ordered and irreversible‐up). Interestingly, a basal backbone comprising the same nine ingroup taxa was present in all of the trees, although the sequence of those taxa could differ. Constraining the two subfamilies to be monophyletic caused the tree length to be increased and the Templeton and Kishino–Hasegawa tests showed the constrained tree to be significantly different from the unconstrained. The two subfamilies are considered invalid and Lernentominae Oakley, 1927 is formally synonymized with Chondracanthinae Milne Edwards, 1840. The validity of the Pharodidae was tested similarly. Pharodes tortugensis, representing the family Pharodidae, was always recovered nested deep within Chondracanthidae. The Pharodidae Illg, 1948 is therefore synonymized with the Chondracanthidae Milne Edwards, 1840.
SPR Biosensor Based on Polymer Multi-Mode Optical Waveguide and Nanoparticle Signal Enhancement

We present a surface plasmon resonance (SPR) biosensor that is based on a planar-optical multi-mode (MM) polymer waveguide structure applied for the detection of biomolecules in the lower nano-molar (nM) range. The basic sensor shows a sensitivity of 608.6 nm/RIU when exposed to refractive index changes with a measurement resolution of 4.3 × 10−3 RIU. By combining the SPR sensor with an aptamer-functionalized, gold-nanoparticle (AuNP)-enhanced sandwich assay, the detection of C-reactive protein (CRP) in a buffer solution was achieved with a response of 0.118 nm/nM. Due to the multi-mode polymer waveguide structure and the simple concept, the reported biosensor is well suited for low-cost disposable lab-on-a-chip applications and can be used with rather simple and economic devices. In particular, the sensor offers the potential for fast and multiplexed detection of several biomarkers on a single integrated platform.
Divergência genética entre progênies de maracujazeiro- amarelo com base em características das plântulas

O objetivo do presente trabalho foi avaliar a diversidade genetica entre 24 populacoes de maracujazeiro-amarelo, discriminando os caracteres mais importantes na avaliacao da divergencia genetica, com base em caracteristicas das plântulas. Foram coletadas sementes de frutos obtidos a partir de polinizacao natural de vinte e quatro populacoes segregantes de meios-irmaos de maracujazeiro-amarelo. Utilizou-se delineamento experimental inteiramente casualizado, em vinte e quatro tratamentos (populacoes segregantes), com quatro repeticoes, considerando-se como unidade experimental cada grupo de 50 sementes. Aos 28 dias, avaliaram-se a porcentagem de germinacao e o indice de velocidade de emergencia (IVE). Aos 45 dias, avaliaram-se porcentagem de sobrevivencia, altura das plântulas, comprimento de raiz, numero de folhas e massa da materia seca total das plântulas. Os dados obtidos foram submetidos a analise de variância, e as medias foram agrupadas pelo metodo de Scott & Knott. A diversidade genetica foi estudada de acordo com o metodo de agrupamento de Tocher, baseado na distância de Mahalanobis (D2) e variaveis canonicas. As caracteristicas que mais contribuiram para a divergencia genetica foram porcentagem de germinacao, numero de folhas e IVE. A populacao 20 pode ser recomendada para hibridacao com as outras populacoes devido a sua alta divergencia e tambem altas taxas de germinacao e vigor de sementes.
Hypomethylation of the cyclin D1 promoter in hepatitis B virus-associated hepatocellular carcinoma

Abstract The hypomethylation of the Cyclin D1 (CCND1) promoter induced by excess oxidative stress likely promotes the development of hepatitis B virus-associated hepatocellular carcinoma (HBV-HCC). We aimed to evaluate methylation status of the CCND1 promoter as a new plasma marker for the detection of HBV-HCC. We consecutively recruited 191 participants, including 105 patients with HBV-HCC, 54 patients with chronic hepatitis B (CHB), and 32 healthy controls (HCs). Using methylation-specific polymerase chain reaction, we identified the methylation status of the CCND1 promoter in plasma samples. We analyzed the expression levels of the CCND1 mRNA in peripheral blood mononuclear cells by using quantitative real-time PCR. We assessed the plasma levels of superoxide dismutase, 8-hydroxydeoxyguanosine and malondialdehyde by using enzyme-linked immunosorbent assays. Patients with HBV-HCC (23.81%) presented a reduced methylation frequency compared with patients with CHB (64.81%) or HCs (78.13%) (P < .001). When receiver operating characteristic curves were plotted for patients with HBV-HCC versus CHB, the methylation status of the CCND1 promoter yielded diagnostic parameter values for the area under the curve of 0.705, sensitivity of 76.19%, and specificity of 64.81%, thus outperforming serum alpha-fetoprotein (AFP), which had an area under the curve of 0.531, sensitivity of 36.19%, and specificity of 90.74%. Methylation of the CCND1 promoter represents a prospective diagnostic marker for patients with AFP-negative HBV-HCC and AFP-positive CHB. The expression levels of CCND1 mRNA was increased in patients with HBV-HCC compared with patients with CHB (Z = -4.946, P < .001) and HCs (Z = -6.819, P < .001). Both the extent of oxidative injury and antioxidant capacity indicated by the superoxide dismutase, 8-hydroxydeoxyguanosine and malondialdehyde levels were increased in patients with HBV-HCC. Clinical follow up of patients with HBV-HCC revealed a worse overall survival (P = .012, log-rank test) and a decreased progression-free survival (HR = 0.109, 95%CI: 0.031-0.384) for the unmethylated CCND1 group than methylated CCND1 group. Our study confirms that oxidative stress appears to correlate with plasma levels of CCND1 promoter methylation, and the methylation status of the CCND1 promoter represents a prospective biomarker with better diagnostic performance than serum AFP levels.
PAL Activity and Differential Ozone Sensitivity in Tobacco, Bean and Poplar

Two cultivars of tobacco and bean and two clones of poplar differing in their phenomenological response to ozone were exposed to a single ozone pulse. The first visible foliar injury appeared after 24-48 h in the sensitive material only. The constitutive levels of PAL activity of ozone resistant and sensitive cultivars/clones were similar. In sensitive material, ozone induced a marked, but transient, increase in PAL activity, which in tobacco cv. Bel-W3 and Pinto bean was associated with necrosis development. In the resistant material ozone stimulated PAL activity, but the levels remained lower than those observed in the sensitive material. Quantitative and qualitative determinations of phenolic compounds were carried out in the poplar clones. In the sensitive clone only the behaviour of caffeic acid was different, an increase being observed a week after the treatment. The resistant clone exhibited marked increase of all compounds assayed. The results are discussed in relation to the possible role of PAL and secondary metabolites to ozone toxicity mechanisms.