Miracle-dz/UniFAR-FTUs huggingface dataset:
Glyphosate-Resistant Palmer Amaranth (Amaranthus palmeri) Morphology, Growth, and Seed Production in Georgia

Abstract Herbicide-resistant Palmer amaranth has become the most economically detrimental weed of cotton in the southeast United States. With the continual marginalization of potential herbicide tools, research has expanded to include alternative means of affecting future Palmer amaranth populations by altering safe sites and reducing inputs to the seedbank population. The influence of delayed Palmer amaranth establishment on seed production potential has not been investigated in the southeast United States. Studies were conducted to evaluate the influence of time of Palmer amaranth establishment on morphology, growth, and seed production. The experiment was a factorial, with five levels of Palmer amaranth transplanting (0 to 12 wk after cotton planting) and two levels of crop type (cotton and noncrop). In the absence of crop competition, the first cohort of Palmer amaranth produced 446,000 seeds per plant. This potential seed production was reduced 50% when Palmer amaranth plants were established nearly 6 wk later. In contrast, the first Palmer amaranth cohort growing in competition with cotton produced 312,000 seeds, 30% less than was produced in the absence of competition. Interference from cotton shifted time to 50% seed production to nearly 4 wk earlier in the growing season, relative to plants without crop competition. Delayed establishment of Palmer amaranth simulates premature loss of herbicide efficacy and alters the competitive balance between cotton and Palmer amaranth. Although the planting time that resulted in 50% reduction in Palmer amaranth plant height at the end of the season was not affected by the presence of cotton, 50% reduction in plant width and biomass occurred within the first 3.8 wk of the growing season when growing with cotton, more than 4 wk earlier than Palmer amaranth growing without a crop. This suggests that early season weed control programs will have a large effect on Palmer amaranth potential growth and seed production, as well as crop yield. To implement soil seedbank reduction strategies effectively, information on mechanisms that regulate Palmer amaranth persistence in the soil seedbank is needed. Nomenclature: Palmer amaranth, Amaranthus palmeri (S.) Wats. AMAPA; cotton, Gossypium hirsutum L. ‘DP1050’.
Mechanics and Growth Form of the Moss Hylocomium splendens

Abstract The moss Hylocomium splendens has two different growth forms. Sympodial growth occurs where the apical meristem ceases activity annually and growth is continued by a lateral bud. Sympodial plants are vertical and self-supporting. Monopodial growth occurs when the apex continues growth. Monopodial plants are prostrate. The aims of the study were to examine stem mechanics of the different growth forms and to compare mechanical properties along stems. Stems of annual segments were subjected to three point bending tests. In sympodial plants the stiffness of the stem material increased significantly with segment age. Flexural rigidity increased significantly with age in segments from 1 to 4 years old, and then declined. Segment diameter decreased significantly with age in sympodial plants. Monopodial plants showed no significant effects of segment age on the diameter, material stiffness or flexural rigidity of stems. Sympodial segments were significantly wider, stronger, more rigid and composed of stiffer material with a higher stress at yield than monopodial segments, but did not have a larger proportion of strengthening material. Sympodial stems had significantly more cellulose than monopodial stems. The moss Hylocomium splendens shows a range of mechanical adaptations, as a self-supporting or a prostrate plant, which suit it to life in very different environments.
Effect of conceptus growth on the contents of the maternal gastrointestinal tract in ewes fed at a constant rate throughout gestation

Summary Multiparous Corriedale ewes were maintained on a constant feed intake such that the body weight (i.e. live weight less gravid uterus) of single-bearing ewes at the end of gestation approximated their live weight at mating. The ewes were allocated to one of five groups, designated for slaughter at 0, 50, 90, 120 and 140 days of gestation. At slaughter, the gravid uterus was removed, weighed and its components dissected out and the contents of all sections of the gastro-intestinal tract were removed, weighed and sampled. Foetal growth was described by a Gompertz model. It was predicted that, at day 150, a twin foetus would have been 0·95 of the weight of a single foetus but this difference was not statistically significant. The foetal proportion of the gravid uterus followed a sigmoid curve during gestation to reach a predicted value of 0·60 at day 150. Predicted birth weights represented 10·4 and 18·6% of maternal body weight in single- and twin-bearing ewes. The digesta content of the rumen and of the whole gastro-intestinal tract was not significantly affected by gestation. However, there was a tendency for the values to decline to day 90, then increase during the last third of gestation. It was suggested that the decline was due to hormonal rather than direct physical effects. By contrast, the amounts of organic digesta constituents in the rumen descreased as gestation progressed (P < 0·01) indicating an effect of gestation on rumen propulsive activity.
Individual variations in habitat use and morphology in brook charr

The specific objectives of this study were to determine if there is individual specialization in habitat use by lacustrine brook charr Salvelinus fontinalis and if so, if specialization is related to fish morphology. Localizations of 28 brook charr equipped with thermosensitive radiotransmitters were recorded during three summers (1991, 1992, and 1993) in two lakes of the Mastigouche Reserve (Quebec, Canada). Fifty per cent of the fish were found mainly in the benthic zone (hereafter benthic individuals), 18% in the pelagic zone (pelagic individuals), and 32% travelled regularly between the two zones (generalist individuals). The observed interindividual differences in habitat preference were related to differences in body morphology and coloration: (i) the pectoral fins of benthic and generalist individuals were significantly longer than those of pelagic ones; and (ii) the coloration of the lower flank of benthic and generalist individuals was silver-grey while that of pelagic individuals was red. The results of this study suggest that brook charr inhabiting oligotrophic lakes of the Canadian Shield exhibit trophic polymorphisms, where some individuals are specialists better adapted to feeding in the littoral zone whereas others are specialists better adapted to feeding in the pelagic zone. The potential for reproductive isolation between the two morphs is discussed.
Dose and Dose-Rate Effects of Low-Dose Ionizing Radiation on Activation of Trp53 in Immortalized Murine Cells

Abstract Sugihara, T. , Magae, J., Wadhwa, R. , Kaul, S. C. , Kawakami, Y. , Matsumoto, T. and Tanaka, K. Dose and Dose-Rate Effects of Low-Dose Ionizing Radiation on Activation of Trp53 in Immortalized Murine Cells. Radiat. Res. 162, 296– 307 (2004). A derivative of immortalized murine NIH/PG13Luc cells stably transfected with a Trp53-dependent luciferase reporter plasmid was used to study the transcriptional activity of Trp53 in response to radiation. The cell line was sensitive enough to detect the response of Trp53 to 0.2 cGy of 60Co γ radiation. To examine the biological effects of low-dose-rate 60Co γ radiation (from 0.1–10 cGy/h), we have analyzed the cell cycle, Trp53 transcriptional activity, and gene expression profiles of control and treated cells. Microarray analysis revealed up-regulation of six Trp53-mediated genes (Cdkn1a/ p21, Mdm2, Sip27, Ccng1/cyclin G1, Ei24/Pig8 and Dinb/ Polk) after exposure of cells to low-dose-rate radiation for 72 h. Using real-time PCR, a significant elevation in the expression of Ccng1/cyclin G1, Mdm2 and Cdkn1A/p21 was observed with low-dose-rate irradiation at dose rates over 5 cGy/ h. A dose-rate dependence was also observed for these three Trp53-mediated genes. The expression of Ccng1/cyclin G1 at high dose rates of γ rays was higher than that for low dose rate. However, the expression of Mdm2 for low-dose-rate γ rays was higher than for the high dose rate. Cells irradiated at low dose rates of 0.1 cGy/h and 1 cGy/h underwent G1-phase arrest. Furthermore, G2-phase growth arrest was observed in cells irradiated at the low dose rates of 5 cGy/h and 10 cGy/h, which correlated with Trp53-mediated Ccng1/cyclin G1 up-regulation. These results show that cellular response to radiation depended on the dose rate used; i.e., the responses seen at dose rates from 0.1–1 cGy/h were different from those observed at dose rates over 5 cGy/h.
Sub-Surface Molecular Analysis and Imaging in Turbid Media Using Time-Gated Raman Spectral Multiplexing

Obtaining molecular information deeper within optically turbid samples is valuable in many applications. However, in many cases this is challenging, in particular when the sample elicits strong laser-induced fluorescence emission. Here, we investigated the use of time-gated and micro-spatially offset Raman spectroscopy (micro-SORS) based on spectral multiplexing detection to obtain sub-surface molecular analysis and imaging for both fluorescing and non-fluorescing samples. The multiplexed spectral detection achieved with a digital micromirror device (DMD) allowed fast acquisition of the time-gated signals to enable three-dimensional Raman mapping (raster scanning in the lateral x,y plane and using time-of-flight calibration for the axial z-direction). Sub-millimeter resolution molecular depth mapping was achieved with dwell times on the order of seconds per pixel. To suppress fluorescence backgrounds and enhance Raman bands, time-gated Raman spectroscopy was combined with micro-SORS to recover Raman signals of red pigments placed behind a layer of optically turbid material. Using a defocusing micro-SORS approach, both fluorescence and Raman signals from the surface layers were further suppressed, which enhanced the Raman signals from the deeper sublayers containing the pigment. These results demonstrate that time-gated Raman spectroscopy based on spectral multiplexed detection, and in combination with micro-SORS, is a powerful technique for sub-surface molecular analysis and imaging, which may find practical applications in medical imaging, cultural heritage, forensics, and industry.
Measurement of Root Hydraulic Conductance

Plant root systems provide water, nutrients, and growth regulators to the shoot. Growth and production of a plant are often limited by the ability of the root to extract water and nutrients from the soil and transport them to the shoot. The transport of most nutrients and growth regulators occurs via the transpiration stream. The velocity and quantity of water moving from the root to the shoot determines the quantity and concentration of substances that arrive at the shoot. Understanding the forces and resistances that control the movement of water through the soil-plant-air continuum and the flux of potential chemical signals is essential to understanding the impact of the soil environment on root function and on root integration with the shoot. The objectives of this paper are: a) to discuss the nature of the resistances that limit water flux through the root, b) evaluate methods of measuring root hydraulic conductance, c) describe the effect of temperature and oxygen on root function, and d) discuss the nature of the signals that may be sent from the root to the shoot.
Longitudinal associations between inhibitory control and externalizing and internalizing symptoms in school-aged children

Abstract Inhibitory control (IC) deficits have been associated with psychiatric symptoms in all ages. However, longitudinal studies testing the direction of the associations in childhood are scarce. We used a sample of 2,874 children (7 to 9 years old) to test the following three hypotheses: (a) IC deficits are an underlying risk factor with a potentially causal role for psychopathology, (b) IC deficits are a complication of psychopathology, and (c) IC deficits and psychopathology are associated at the trait level but not necessarily causally related. We used the go/no-go task to assess IC, the parent-rated Strengths and Difficulties Questionnaire to evaluate externalizing/internalizing symptoms, and the random intercepts cross-lagged panel model to test the hypotheses. The results showed no support for the underlying risk factor hypothesis, suggesting that IC unlikely has a causal role in this age group's psychopathology. The complication hypothesis received support for externalizing symptoms, suggesting that externalizing symptoms may hamper the normal development of IC. IC deficits and both externalizing and internalizing symptoms were correlated at the trait level, indicating a possible common origin. We suggest that it may be useful to support children with externalizing symptoms to promote and protect their IC development.
Effects of Motivational Interviewing and Wearable Fitness Trackers on Motivation and Physical Activity: A Systematic Review

Objective: To systematically review the impacts of Wearable Fitness Trackers (WFTs), Motivational Interviewing (MI), and Self Determination Theory (SDT)–based interventions on physical activity (PA) and motivation for PA. Data Source: Manuscripts published between 2008 and 2018 in PubMed, Web of Science, CABAbstracts, and SPORTDiscus database were reviewed. Study Inclusion and Exclusion Criteria: Inclusion criteria were original pilot studies, randomized controlled trials (RCT), cross-sectional studies, qualitative assessments, prospective cohort studies, longitudinal observational studies, and pretest posttest designs published in peer-reviewed journals. Data Extraction: Studies were evaluated by 2 independent researchers for inclusion. Data Synthesis: Extracted data were synthesized in a tabular format and narrative summary. Results: Twenty-six studies met final inclusion criteria, 10 addressed WFT use and PA behavior, 4 investigated WFT use and its association with motivation for PA, and 10 examined SDT and/or MI and their effect on motivation for PA and/or PA behavior. Finally, 2 studies addressed SDT-based MI, WFT use, and the combined effect on PA behavior. Conclusions: While SDT-based interventions and MI positively impact motivation for PA and PA behavior, WFTs revealed mixed results. Wearable Fitness Trackers prove effective among individuals not currently meeting PA guidelines but have little impact on other populations. Self Determination Theory, MI, and WFTs use provides a promising combination of interventions to increase PA among sedentary individuals, though research is limited.
Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools

Abstract Human leukocyte antigen (HLA) can encode the human major histocompatibility complex (MHC) proteins and play a key role in adaptive and innate immunity. Emerging clinical evidences suggest that the presentation of tumor neoantigens and neoantigen-specific T cell response associated with MHC class I molecules are of key importance to activate the adaptive immune systemin cancer immunotherapy. Therefore, accurate HLA typing is very essential for the clinical application of immunotherapy. In this study, we conducted performance evaluations of 4 widely used HLA typing tools (OptiType, Phlat, Polysolver and seq2hla) for predicting HLA class Ia genes from WES and RNA-seq data of 28 cancer patients. HLA genotyping data using PCR-SBT method was firstly obtained as the golden standard and was subsequently compared with HLA typing data by using NGS techniques. For both WES data and RNA-seq data, OptiType showed the highest accuracy for HLA-Ia typing than the other 3 programs at 2-digit and 4-digit resolution. Additionally, HLA typing accuracy from WES data was higher than from RNA-seq data (99.11% for WES data versus 96.42% for RNA-seq data). The accuracy of HLA-Ia typing by OptiType can reach 100% with the average depth of HLA gene regions >20x. Besides, the accuracy of 2-digit and 4-digit HLA-Ia typing based on control samples was higher than tumor tissues. In conclusion, OptiType by using WES data from control samples with the high average depth (>20x) of HLA gene regions can present a probably superior performance for HLA-Ia typing, enabling its application in cancer immunotherapy.
Cathelicidin-mediated lipopolysaccharide signaling via intracellular TLR4 in colonic epithelial cells evokes CXCL8 production

ABSTRACT We hypothesized that the antimicrobial peptide cathelicidin has a physiological role in regulating gut inflammatory homeostasis. We determined that cathelicidin synergizes with LPS to facilitate its internalization and signaling via endosomic TLR4 in colonic epithelium, evoking synthesis of the human neutrophil chemoattractant, CXCL8 (or murine homolog, CXCL1). Interaction of cathelicidin with LPS in the control of CXCL8/CXCL1 synthesis was assessed in human colon epithelial cells, murine colonoids and cathelicidin-null mice (Camp−/- ). Mechanistically, human cathelicidin (LL-37), as an extracellular complex with LPS, interacted with lipid raft-associated GM1 gangliosides to internalize and activate intracellular TLR4. Two signaling pathways converged on CXCL8/CXCL1 production: (1) a p38MAPK-dependent pathway regulated by Src-EGFR kinases; and, (2) a p38MAPK-independent, NF-κB-dependent pathway, regulated by MEK1/2-MAPK. Increased cathelicidin-dependent CXCL8 secretion in the colonic mucosa activated human blood-derived neutrophils. These cathelicidin effects occurred in vitro at concentrations well below those needed for microbicidal function. The important immunomodulatory role of cathelicidins was evident in cathelicidin-null/Camp−/- mice, which had diminished colonic CXCL1 secretion, decreased neutrophil recruitment-activation and reduced bacterial clearance when challenged with the colitis-inducing murine pathogen, Citrobacter rodentium. We conclude that in addition to its known microbicidal action, cathelicidin has a unique pathogen-sensing role, facilitating LPS-mediated intestinal responses, including the production of CXCL8/CXCL1 that would contribute to an integrated tissue response to recruit neutrophils during colitis.
Loss of pollinator specialization revealed by historical opportunistic data: Insights from network-based analysis

We are currently facing a large decline in bee populations worldwide. Who are the winners and losers? Generalist bee species, notably those able to shift their diet to new or alternative floral resources, are expected to be among the least vulnerable to environmental change. However, studies of interactions between bees and plants over large temporal and geographical scales are limited by a lack of historical records. Here, we used a unique opportunistic century-old countrywide database of bee specimens collected on plants to track changes in the plant-bee interaction network over time. In each historical period considered, and using a network-based modularity analysis, we identified some major groups of species interacting more with each other than with other species (i.e. modules). These modules were related to coherent functional groups thanks to an a posteriory trait-based analysis. We then compared over time the ecological specialization of bees in the network by computing their degree of interaction within and between modules. “True” specialist species (or peripheral species) are involved in few interactions both inside and between modules. We found a global loss of specialist species and specialist strategies. This means that bee species observed in each period tended to use more diverse floral resources from different ecological groups over time, highly specialist species tending to enter/leave the network. Considering the role and functional traits of species in the network, combined with a long-term time series, provides a new perspective for the study of species specialization.
Alignment of stroma fibers, microvessel density and immune cell populations determine overall survival in pancreatic cancer—An analysis of stromal morphology

Introduction The aim of this study was to define histo-morphological stroma characteristics by analyzing stromal components, and to evaluate their impact on local and systemic tumor spread and overall survival in pancreatic ductal adenocarcinoma (PDAC). Methods and materials Patients who underwent oncologic resections with curative intent for PDAC were identified from a prospectively maintained database. Histological specimens were re-evaluated for morphological stroma features as stromal fibers, fibroblast morphology, stroma matrix density, microvessel density and distribution of immune cell populations. Results A total of 108 patients were identified undergoing curative resection for PDAC in the period from 2011–2016. 33 (30.6%) patients showed parallel alignment of stroma fibers while 75 (69.4%) had randomly oriented stroma fibers. As compared to parallel alignment, random orientation of stroma fibers was associated with larger tumor size (median 3.62 cm vs. median 2.87cm, p = 0.037), nodal positive disease (76.0% vs. 54.5%, p = 0.040), higher margin positive resection rates (41.9% vs. 15.2%, p = 0.008) and a trend for higher rates of T3/4 tumors (33.3% vs. 15.2%, p = 0.064). In univariate analysis, patients with parallel alignment of stroma fibers had improved overall survival rates as compared to patients with random orientation of stroma fibers (42 months vs. 22 months, p = 0.046). The combination of random orientation of stroma fibers and low microvessel density was associated with impaired overall survival rates (16 months vs. 36 months, p = 0.019). A high CD4/CD3 ratio (16 months vs. 33 months, p = 0.040) and high stromal density of CD163 positive cells were associated with reduced overall survival (27 months vs. 34 months, p = 0.039). In multivariable analysis, the combination of random orientation of stroma fibers and low microvessel density (HR 1.592, 95%CI 1.098–2.733, p = 0.029), high CD4/CD3 ratio (HR 2.044, 95%CI 1.203–3.508, p = 0.028) and high density of CD163 positive cells (HR 1.596, 95%CI 1.367–1.968, p = 0.036) remained independent prognostic factors. Conclusion Alignment of stroma fibers and microvessel density are simple histomorphological features serving as surrogate markers of local tumor progression dissemination and surgical resectability and determine prognosis in PDAC patients. High CD4/CD3 ratio and CD163 positive cell counts determine poor prognosis.
Survey of Diversity and Abundance of Ground-dwelling Arthropods in a Black Walnut-forage Alley-cropped System in the Mid-western United States

Abstract Alley cropping is an integrated land management practice growing economic crops between rows of trees. This paper examines the effects of alley cropping on carabid beetles and other ground dwelling arthropod predators on species diversity and abundance by testing for differences among ground vegetation treatments in alleyways. Arthropods were collected with pitfall traps in two alley-cropped areas using the ground cover treatments of alfalfa, smooth bromegrass, and a vegetation-free control. Although not generally statistically significant, brome had the lowest means of any of the ground vegetation treatments, possibly due to the relative impenetrability of the thick grass. We found few significant differences among treatments. Carabidae numbers were negatively correlated with relative humidity and positively correlated to soil temperature and moisture. Sampling methods other than pitfall trapping are needed in future studies to clarify the role of ground cover in arthropod predator diversity and abundance in an alley cropping practice.