Miracle-dz/UniFAR-FTUs huggingface dataset:
Vegetation change in an ombrotrophic mire in northern England after excluding sheep

Abstract The role of sheep grazing on vegetation change in upland mires removed from livestock farming and surrounded by conifer plantation was investigated with a grazing trial at Butterburn Flow in northern England. Paired grazed and ungrazed plots from central and peripheral locations were compared over 14 yr. Vegetation data from 34 mires in Kielder Forest provided an ordination framework within which vegetation trends were investigated. A gradient from dry moorland/hummock to wet mire/hollow vegetation dominated this framework and may reflect hydrological variability and structural vegetation differences between the mires. Some species were significantly affected by change in grazing intensity and there were differences between the edge and the centre of the mire. Overall vegetation change depended upon the grazing management and the position of the plots such that the removal of sheep grazing decreased the cover of species typical of wet ombrotrophic conditions, but only at the periphery of the mire. The vegetation in one plot became very similar to that of mires elsewhere in Kielder Forest where sheep were removed several decades ago. Cessation of grazing on upland mires is likely to lead to slow structural and species change in vegetation at the mire edge with a long-term loss of ombrotrophic species. The nature conservation significance of these changes will depend upon whether or not management objectives target natural conditions or wish to maximize ombrotrophic vegetation. The context of external factors such as climate and pollution may, however, be more important in determining site condition on the wettest mires.
Interactions between coral restoration and fish assemblages: implications for reef management.

Corals create complex reef structures that provide both habitat and food for many fish species. Due to numerous natural and anthropogenic threats, many coral reefs are currently being degraded, endangering the fish assemblages they support. Coral reef restoration, an active ecological management tool, may help reverse some of the current trends in reef degradation through the transplantation of stony corals. While restoration techniques have been extensively reviewed in relation to coral survival, our understanding of the effects of adding live coral cover and complexity on fishes is in its infancy with a lack of scientifically-validated research. Here, we review the limited data on reef restoration and fish assemblages, and complement this with the more extensive understanding of complex interactions between natural reefs and fishes and how this might inform restoration efforts. We discuss which key fish species or functional groups may promote, facilitate or inhibit restoration efforts and, in turn, how restoration efforts can be optimised to enhance coral fish assemblages. By highlighting critical knowledge gaps in relation to fishes and restoration interactions, we aim to stimulate research into the role of reef fishes in restoration projects. A greater understanding of the functional roles of reef fishes would also help inform whether restoration projects can return fish assemblages to their natural compositions or whether alternative species compositions develop, and over what timeframe. While alleviation of local and global reef stressors remains a priority, reef restoration is an important tool; an increased understanding of the interactions between replanted corals and the fishes they support is critical for ensuring its success for people and nature. This article is protected by copyright. All rights reserved.
Implicit associative memory remains intact with age and extends to target-distractor pairs

ABSTRACT In this study, we use a novel, implicit memory paradigm to test forhyper-binding, or older adults’ tendency to form non-target associations. Participants viewed pictures of objects superimposed with text and made speeded categorization judgments about the objects across three blocks varying in binding demand. During the no- and some-binding blocks, participants decided if the pictured object alone could fit inside a drawer while ignoring superimposed non-words and words, respectively. During the full-binding block, participants decided if both items could fit inside a drawer together. At test, participants viewed intact and rearranged pairs from encoding and decided if both items could fit in a drawer together. Across two experiments, older adults responded faster to intact than rearranged pairs from both the some- and full-binding blocks, while young adults showed no difference in RTs. These findings suggest that implicit associative memory is preserved with age and extends to non-target information.
Fingerprint Profiles of Cuticular Fatty Acids in Three Adult Rhipicephalus Tick species: A New Tool for Identification

Ticks are obligatory blood parasites responsible for transmitting a variety of diseases to humans and animals. Since ticks share similar morphological features, accurate identification of tick species is important for control and management of disease-associated risks. Here, we report the application of gas chromatography mass spectrometry for analyses of cuticular fatty acid profiles for specific identification of female Rhipicephalus annulatus, Rhipicephalus bursa and Rhipicephalus sanguineus and establish the reliance of this assay on their nutritional status. Our findings demonstrated a unique pattern for each species under fed and unfed conditions. The cuticular fatty acid fractions were composed of a mixture of saturated and unsaturated straight-chain, terminally methylated and hydroxylated fatty acids. Our results show significant differences between the species tested under identical nutritional status, whereas the cuticular fatty acid profile pattern under fed versus unfed conditions in each species were similar. R. annulatus was distinguished by the high abundance of C10 to C14 fatty acids and the presence of 2-OH-C16, in contrast to R. sanguineus and R. bursa forming a higher percentage of C16 to C18. In addition, R. bursa was clearly distinguished from R. sanguineus by its high intensity of C14 and C20 as well as the presence of C12. Based on these results, we have established the ratio of the relative average abundance values of C16 to C14 as a Species Differentiation Index, enabling us to identify each of these species independent of its nutritional status. We suggest that fatty acid profiling may be useful as a relatively simple and reliable method to determine the species-specific identity of ticks.
A multi-nutrient model for the description of stoichiometric modulation of predation in micro- and mesozooplankton

Changes in predator behaviour when confronted with prey of disadvantageous composition have been termed stoichiometric modulation of predation (SMP; Mitra and Flynn, 2005; J. Plankton Res. 27, 393–399). Through SMP, a predator may compensate for (positive SMP) or compound (negative SMP) dietary deficiencies. While these responses are documented in experiments, albeit typically with poor parameterization, previous zooplankton models contain no explicit description of these events. A new multi-nutrient biomass-based generic zooplankton model is described, capable of handling SMP at the levels of ingestion and assimilation, for the exploration of zooplankton growth dynamics in situations where prey quality and quantity changes over time. SMP is enabled by configuring ingestion rate and assimilation efficiency descriptors as functions of food quality (indexed here to prey N:C). Sensitivity analysis of the new model shows the structure to be robust against variation in parameter (constant) values. The form of the model enables its use in population dynamic studies of different zooplankton groups; here, the model has been configured to represent micro- and mesozooplankton. It is shown that in the absence of inclusion of SMP, fits of the model to experimental data can be poor with potential for significant misrepresentation of trophic dynamics.
Mesenchymal stem cell in mice uterine and its therapeutic effect on osteoporosis.

Osteoporosis is a silent disease caused by low bone mineral density and is complicated by fractures. This study was designed to examine the differentiation of uterine stem cell-derived osteoprogenitor cells (UOPCs) both in vitro and in vivo, assessing their effectiveness in treating osteoporosis. CD271+/CD45- UOPCs were isolated from the endometrial tissue of inbred Balb/c mice through magnetic activated cell sorting. Stem cell differentiation assays were used for CD271+/CD45- UOPCs in vitro. In vivo, the UOPCs were implanted into mouse osteoporosis models through tail-vein injection for 8 weeks. Osteogenic differentiation was examined by X-rays and CT-scans. EGFP-labeled UOPCs, obtained from C57BL/6-Tg (ACTb-EGFP)1Osb/J mice, were used to assess cell survival in the osteoporosis model. The levels of osteogenic markers were assessed by enzyme-linked immunosorbent assay. In vitro, UOPCs were able to form into typical spheres and various differentiation. In vivo, implantation of UOPCs into osteoporosis model significantly increased bone mineral densities and bone microstructure parameters. The levels of a biochemical marker of bone metabolism, Semaphorin-3A, increased significantly. However, levels of RANKL decreased. Immunofluorescence staining of osteoporosis mice injected with GPF+ UOPCs showed their survival for up to seven days. In conclusion, stem cells with osteogenic differentiation potential can be isolated from uterine or endometrial tissue. These UOPCs can stably proliferate and differentiate in vitro or in vivo, which can inhibit bone resorption and osteoclast marker expression. In vivo, UOPCs significantly improved reduction in bone density caused by reduced estrogen levels. Such cell transplantation approach is potentially useful in the treatment of osteoporosis.
Do parent and self-report rating scales of executive function measure the same constructs with adolescents?

Abstract Objective There are numerous measures of executive function (EF), yet the multiple definitions and constructions of EF suggest that these measures may not be measuring the same construct or domains within EF. The purpose of this study was to examine the concurrent validity of the BRIEF and the CEFI parent and self-report forms with adolescents. Method Adolescent participants, ages 12–17 years, were recruited using a snowball method with recruitment targeting individuals from under-represented groups, as well as the general population. The resulting sample consisted of 52 cases with parent report. The adolescents were predominantly female (55.77%) and white (40.38%) with a mean age of 14.56 (1.72). Results For parent and adolescent self-report on both the BRIEF and CEFI, mean global scores were within the average range. To examine whether the two rating scales were measuring the same underlying constructs of EF, a multi-trait-multi-method (MTMM) model was conducted using correlated traits correlated methods (CTCM) and correlated traits uncorrelated methods (CTUM). Conclusion While the global scores obtained for the instruments measure EF similarly, there is less consistency in how the subdomains parse out and are labeled for each of the two scales. Implications for practice are discussed.
Regulatory variation and human disease

Regulatory variation and human disease Matthew T. Maurano Chair of the Supervisory Committee: Associate Professor John A. Stamatoyannopoulos Departments of Genome Sciences and Medicine Non-coding regulatory regions are strongly implicated in human disease via genetic studies. However, it is currently not possible to interpret reliably and systematically the functional consequences of genetic variation within any given transcription factor recognition sequence. To lay the groundwork for the assessment of regulatory variation in human disease, I comprehensively analyzed heritable genome-wide binding patterns of a major sequence-specific regulator (CTCF) in relation to genetic variability in binding site sequences across a three-generation pedigree as well as 19 diverse human cell types. We identified hundreds of genetic variants with reproducible quantitative effects on CTCF occupancy (both positive and negative). While these effects paralleled protein-DNA recognition energetics when averaged, they were extensively buffered by striking local context dependencies. Examining variation across multiple cell types, we observed highly reproducible yet surprisingly plastic genomic binding landscapes, indicative of strong cell-selective regulation of CTCF occupancy. Comparison with massively parallel bisulfite sequencing data indicates that 41% of variable CTCF binding is linked to differential DNA methylation, concentrated at two critical positions within the CTCF recognition sequence. These results establish the feasibility of studying the regulatory architecture of human disease. I then apply the framework developed in the CTCF model system to the interpretation of genomewide association studies (GWAS), which have identified many non-coding variants associated with common diseases and traits. We show that these variants are concentrated in regulatory DNA marked by DNase I hypersensitive sites (DHSs). 88% of such DHSs are active during fetal development, and are enriched for gestational exposure-related phenotypes. We identify distant gene targets for hundreds of DHSs that may explain phenotype associations. Disease-associated variants systematically perturb transcription factor recognition sequences, frequently alter allelic chromatin states, and form regulatory networks. We also demonstrate tissue-selective enrichment of more weakly disease-associated variants within DHSs, and the de novo identification of pathogenic cell types for Crohn’s disease, multiple sclerosis, and an electrocardiogram trait, without prior knowledge of physiological mechanisms. This dissertation establishes a framework for the study of regulatory variation, suggests pervasive involvement of regulatory DNA variation in common human disease, and provides pathogenic insights into diverse disorders.
A 2‐Phase Merge Filter Approach to Computer‐Aided Detection of Breast Tumors on 3‐Dimensional Ultrasound Imaging

The role of image analysis in 3‐dimensional (3D) automated breast ultrasound (ABUS) images is increasingly important because of its widespread use as a screening tool in whole‐breast examinations. However, reviewing a large number of images acquired from ABUS is time‐consuming and sometimes error prone. The aim of this study, therefore, was to develop an efficient computer‐aided detection (CADe) algorithm to assist the review process.
Testing glutathione-S-transferase for an association with facial eczema resistance in cattle

Resistance to facial eczema (FE) in cattle is known to be a heritable trait. The commonly used indicators of susceptibility in affected groups of animals are gamma glutamyl-transferase (GGT) and glutamate dehydrogenase (GDH), which indicate the severity of the liver injury associated with FE. Published research using mouse models suggests that glutathione-S-transferase (GST) may be a downstream indicator of variation in FE susceptibility, and a study was carried out in calves to test this. Friesian-sired and Jerseysired bull calves were purchased from dairy herds in spring 2004, artificially reared from about four days of age, weaned at 75-80 kg, monitored for base-line GGT activity in blood, and then dosed orally with sporidesmin. At 14 and 21 days after dosing, blood samples were taken to measure the activities of both GDH and GGT. A sample of 45 Friesian calves and 45 Jersey calves from the high and low outliers (using GDH activity within breed, 14 days after dosing) were blood-sampled 15 or 16 days after dosing and measured for GST activity, with 20-25 animals sampled each day, in balanced groups. There were significant differences in GST activity between high and low GDH groups (P < 0.01), and the pooled within-analysisday regression of GST activity on logGGT activity (day 21) was negative (P < 0.05). Results confirmed that low erythrocytic GST activity is an indicator of FE susceptibility, although the differences seen between resistant and susceptible animals are insufficient for use as a predictive tool.
Uncovering the biofumigant capacity of allyl isothiocyanate from several Brassicaceae crops against Fusarium pathogens in maize.

BACKGROUND Driven by environmental concerns, chemical fumigants are no longer allowed in many countries. Therefore, other strategies for reducing fungal inoculum in soils and on crop debris are being explored. In this study, several Brassicaceae crops were screened for their potential to control Fusarium gramineaum and Fusarium poae mycelial growth in an in vitro inverted Petri dish experiment. Volatile production was measured using a GC-MS headspace analysis. A selection of cultivars from each crop species was further investigated using a pot experiment with maize. RESULTS Ethiopian mustard (Brassica carinata) and brown mustard (Brassica juncea) released volatile allyl isothiocyanate (AITC), and a higher concentration of AITC was correlated with a better fungal growth reduction in the in vitro screening. Brown mustard cultivar Etamine completely inhibited growth of both Fusarium spp. Pure AITC in a solution with methanol resulted in a sigmoid dose-response curve for both Fusarium spp. tested. Fusarium poae seemed to be more tolerant to AITC than F. graminearum. A pot experiment revealed that the incorporation of brown mustard plant material could alleviate the clear negative effect of F. graminearum infection on maize growth. CONCLUSION This study showed the correlation between the fungistatic effect of biofumigation crops on Fusarium spp. , and their production of volatile AITC in vitro, without the addition of exogenous enzymes, and confirmed the biofumigation potential of brown mustard in a pot experiment with maize. These results may help farmers in selecting a green manure crop suitable for biofumigation. This article is protected by copyright. All rights reserved.
Article Commentary: Controversies Regarding the Diagnosis and Management of Ductal Carcinoma in Situ

Ductal carcinoma in situ (DCIS) is a premalignant condition, whose incidence is increasing in the current era of widespread screening mammography. While eminently treatable, there are innumerable controversies that surround this disease in terms of its diagnosis and treatment. We discuss these issues and review the data to date regarding this condition which affects roughly 20 per cent of all patients presenting with breast cancer.
Interceptive treatment effects of EF preformed appliance in pre-pubertal and pubertal skeletal Class II growing patients: A retrospective controlled study.

AIM Interceptive treatment has been devised to improve the outcomes on growth stage and mandibular repositioning in Class II patients. The aim of this study is to test the effectiveness of Functional education (EF) (OrthoPlus, Igny, France) preformed appliance in skeletal Class II growing patients at CVM2 and CMV3 stages. MATERIALS AND METHODS Study design: retrospective controlled study. Eighty skeletal Class II growing subjects were recruited for the study. Lateral X-rays and cephalograms were required at the beginning (T0) and at the end (T1) of the EF treatment to evaluate dento-skeletal changes. The same sub-division and sample size were adopted for respective untreated control groups. RESULTS At prepubertal stage, the EF device showed a significant reduction of upper incisors proclination. When comparing dentoskeletal variables in the pubertal groups, significant differences were shown. In the treated group the SN^B angle increased, with the B Downs landmark moving forward. Wits index improved by 2.16 mm in the study group with an increase of all mandibular linear measurements. Fewer but significant dental changes were shown for 11^41 angle, with a mean increase of 8.90°. STATISTICS For multiple comparisons, the Tukey test at 95% family-wise confidence level was used. The level of significance was set at p < 0.05. Statistical analyses were conducted using the R statistical package (version 3.0.3, R Core Team, Foundation for Statistical Computing, Vienna, Austria). CONCLUSIONS EF appliance seems to be effective in the treatment of Class II growing patients. Significant improvements in upper incisors proclination and mandibular elongation are shown.
Deletion of 2‐aminoadipic semialdehyde synthase limits metabolite accumulation in cell and mouse models for glutaric aciduria type 1

Glutaric aciduria type 1 (GA1) is an inborn error of lysine degradation characterized by acute encephalopathy that is caused by toxic accumulation of lysine degradation intermediates. We investigated the efficacy of substrate reduction through inhibition of 2‐aminoadipic semialdehyde synthase (AASS), an enzyme upstream of the defective glutaryl‐CoA dehydrogenase (GCDH), in a cell line and mouse model of GA1. We show that loss of AASS function in GCDH‐deficient HEK‐293 cells leads to an approximately fivefold reduction in the established GA1 clinical biomarker glutarylcarnitine. In the GA1 mouse model, deletion of Aass leads to a 4.3‐, 3.8‐, and 3.2‐fold decrease in the glutaric acid levels in urine, brain, and liver, respectively. Parallel decreases were observed in urine and brain 3‐hydroxyglutaric acid levels, and plasma, urine, and brain glutarylcarnitine levels. These in vivo data demonstrate that the saccharopine pathway is the main source of glutaric acid production in the brain and periphery of a mouse model for GA1, and support the notion that pharmacological inhibition of AASS may represent an attractive strategy to treat GA1.
DISTOMUM LASIUM LEIDY, 1891 (SYN. CERCARIAEUM LINTONI MILLER AND NORTHUP, 1926), THE LARVAL STAGE OF ZOÖGONUS RUBELLUS (OLSSON, 1868) (SYN. Z. MIRUS LOOSS, 1901)

In one of his last publications, Joseph Leidy (1891) described a larval trematode, Distomum lasium, from the digestive gland and gonad of Ilyanassa obsoleta at Beach Haven, New Jersey. The account, although brief, was sufficiently complete and definitive to permit positive identification of the species. Leidy reported that I. obsoleta was very abundant on the mud flats near Beach Haven and that on dissecting a number he â€œ? foundthat one in five or six was infested with the larval distomas enclosed in sponocysts, often in large numbers, embedded intheliverand associated genitalgland. The larvaealways appeared in the distoma-form and never as a cercaria. â€• He noted the shape and size of the sporocysts and of the tailless larvae, and for the latter he recorded the size of suckers, form of the excretory bladder, presence of spines on cuticula, and stylet in the dorsal wall of the oral sucker. This Species was reported by Linton (1915) from the same host at Woods Hole, Massachusetts. During the summers of 1909 and 1910 he had examined over one thousand specimens of I. obsolela and a record of his dissections is presented. Apparently unaware of Leidy's earlier paper, Linton gave a description of the sporocyst and the cercariaeum, but did not name the species. A comparison of the descriptions of Leidy and Linton shows substantial agreement and leaves no doubt concerning the identity of the parasites collected in New Jersey and Massachusetts. The account of Linton was confirmed and augmented by Miller and Northup (1926). These authors had likewise overlooked the reportofLeidy and they named the larvaCercariaeumlintoni.In a study of the seasonal infestation of Nassa obsolela with larval trema todes,theyexamined 8,875individuals collected from a limitedareain QuamquissetHarbornearWoods Hole, and found Cercariaeumlintoni