cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Relaxed exponential molecular clock phylogeny with node numbers;Maximum likelihood phylogeny;Changing ice coverage across the North Atlantic over the last 30 000 years ;Samples used in this study;Genetic differentiation from Holocene deglaciation drove rapid genetic diversification of Atlantic walrus
Creators: name: Ruiz-Puerta, Emily J.
name: Keighley, Xénia
name: Desjardins, Sean P. A.
name: Gotfredsen, Anne Birgitte
name: Pan, Shyong En
name: Star, Bastiaan
name: Boessenkool, Sanne
name: Barrett, James H.
name: McCarthy, Morgan L.
name: Andersen, Liselotte W.
name: Born, Erik W.
name: Howse, Lesley R.
name: Szpak, Paul
name: Pálsson, Snæbjörn
name: Malmquist, Hilmar J.
name: Rufolo, Scott
name: Jordan, Peter D.
name: Olsen, Morten Tange
Publisher: name: The Royal Society
Year: 2023
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Genomics

description: 1. Figure S1. Relaxed exponential clock Bayesian phylogeny identical to Figure 1 in the main text, but providing node numbers for easier interpretation of each nodes’ posterior, age and 95% HPD, as provided in Supplementary Table S3. ;Phylogeny obtained from IQtree ;Sea-ice changes across the North Atlantic in delineation with the Atlantic walrus current population structure ;Table with the all the information for each sample used in this study;Genetic differentiation among North Atlantic walrus populations.
Searching for coherent pulsations in ultraluminous X-ray sources
Creators: name: Doroshenko, V.
name: Santangelo, A.
name: Ducci, L.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Luminosities of ultraluminous X-ray sources (ULXs) are uncomfortably large if compared to the Eddington limit for isotropic accretion onto stellar-mass object. Most often either supercritical accretion onto stellar mass black hole or accretion onto intermediate mass black holes is invoked the high luminosities of ULXs. However, the recent discovery of coherent pulsations from M82 ULX with NuSTAR showed that another scenario implying accretion onto a magnetized neutron star is possible for ULXs. Motivated by this discovery, we re-visited the available XMM-Newton archival observations of several bright ULXs with a targeted search for pulsations to check whether accreting neutron stars might power other ULXs as well. We have found no evidence for significant coherent pulsations in any of the sources including the M82 ULX. We provide upper limits for the amplitude of possibly undetected pulsed signal for the sources in the sample.
description: 2 pages, 1 figure, submitted to A&A
Analysis of the microbunching instability in a mid-energy electron linac
Creators: name: Huang, Dazhang
name: Gu, Qiang
name: Wang, Zhen
name: Zhang, Meng
name: Ng, King Yuen
Publisher: name: arXiv
Year: 2014
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: Microbunching instability usually exists in the linear accelerator (linac) of a free electron laser (FEL) facility. If it is not controlled effectively, the beam quality will be damaged seriously and the machine will not operate properly. In the electron linac of a soft X-Ray FEL device, because the electron energy is not very high, the problem can become even more serious. As a typical example, the microbunching instability in the linac of the proposed Shanghai Soft X-ray Free Electron Laser facility (SXFEL) is investigated in detail by means of both analytical formulae and simulation tools. In the study, a new mechanism of introducing random noise into the beam current profile as the beam passes through a chicane-type bunch compressor is proposed. The higher-order modes that appear in the simulations suggest that further improvement of the current theoretical model of the instability is needed.
description: 7 pages, 15 figures. arXiv admin note: substantial text overlap with arXiv:1304.7437
MIGNEX Case Study Brief SOM1 – Migration and development dynamics in Erigavo, Somalia (Somaliland)
Creators: name: Ahmed, Fatuma
name: Hagen-Zanker, Jessica
name: Hannah, Murray
Publisher: name: Peace Research Institute Oslo
Year: 2022

description: Young adults are hopeful for the future of Erigavo amid sustained improvement in security and expansion in infrastructure. Migration aspirations are low, though internal migration is common.

Key Takeaways

Relative to other locations in Somalia and Somaliland, Erigavo is considered safe by residents. Some 67% consider it safe to walk the streets at night.

Among those young adults who would prefer to stay in Somalia and Somaliland over the next five years (69%), the majority (77%) would rather stay in Erigavo than migrate internally.

Two-thirds (66%) of young adults expect to stay in Erigavo in the next five years, though 34% expect to leave, often for better livelihoods, health services or education opportunities elsewhere in the country.
An Unsupervised Ensemble-based Markov Random Field Approach to Microscope Cell Image Segmentation
Creators: name: Antal, Balint
name: Remenyik, Bence
name: Hajdu, Andras
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: In this paper, we propose an approach to the unsupervised segmentation of images using Markov Random Field. The proposed approach is based on the idea of Bit Plane Slicing. We use the planes as initial labellings for an ensemble of segmentations. With pixelwise voting, a robust segmentation approach can be achieved, which we demonstrate on microscope cell images. We tested our approach on a publicly available database, where it proven to be competitive with other methods and manual segmentation.
miR-24 Regulates Intrinsic Apoptosis Pathway in Mouse Cardiomyocytes
Creators: name: Qian, Li
name: Wang, Li
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Numerous cardiac diseases, including myocardial infarction (MI) and chronic heart failure, have been associated with cardiomyocyte apoptosis. Promoting cell survival by inhibiting apoptosis is one of the effective strategies to attenuate cardiac dysfunction caused by cardiomyocyte loss. miR-24 has been shown as an anti-apoptotic microRNA in various animal models. In vivo delivery of miR-24 into a mouse MI model suppressed cardiac cell death, attenuated infarct size, and rescued cardiac dysfunction. However, the molecular pathway by which miR-24 inhibits cardiomyocyte apoptosis is not known. Here we found that miR-24 negatively regulates mouse primary cadiomyocyte cell death through functioning in the intrinsic apoptotic pathways. In ER-mediated intrinsic pathway, miR-24 genetically interacts with the CEBP homologous gene CHOP as knocking down of CHOP partially attenuated the induced apoptosis by miR-24 inhibition. In mitochondria–involved intrinsic pathway, miR-24 inhibits the initiation of apoptosis through suppression of Cytochrome C release and Bax translocation from cytosol to mitochondria. These results provide mechanistic insights into the miR-24 mediated anti-apoptotic effects in murine cardiomyocytes.
Optimizing and automating QIIME2 Microbiome data analysis using the Snakemake pipeline (Snaq)
Creators: name: Attayeb Mohsen
name: Yi-An Chen
name: Osorio, Rodolfo S. Allendes
name: Higuchi, Chihiro
name: Mizuguchi, Kenji
Publisher: name: F1000 Research Limited
Year: 2022

description: Introduction
 Optimizing a protocol for 16S microbiome data analysis with QIIME2 is challenging for biologists with no programming experience. It involves a multi-step process and multiple parameters and options that must be tested and determined. Usually, researchers need to investigate various options, which requires running the analysis several times and comparing the results to decide the best set of tools and parameters for the data under investigation. Such an optimization process requires a substantial effort. In addition, it leads to several copies of the results with different sets of parameters, making the process relatively inefficient and difficult to reproduce.
 Results
 By combining the analysis strengths of QIIME2 with the flexibility in the definition of pipelines provided by Snakemake, here we introduce "Snaq," a snakemake pipeline that helps automate and optimize 16S data analysis using QIIME2. Snaq incorporates the definition of analysis rules with the intention of following a descriptive file name scheme, providing the functionality required to achieve faster protocol optimization, full pipeline automation, and handling data accumulation.
 Discussion
 Snaq offers a descriptive file naming system and automatically analyzes a data set by downloading and installing the required databases and classifiers, all through a single command-line instruction. It works natively on Linux, Mac. It works on Windows through containers and is potentially extendable by adding new rules.
 To make the pipeline versatile and easily adjustable, we adopted a convention of including all the critical parameter values inside a target file name and called this scheme descriptive target file naming. At the same time, other parameters are left as default. This means that Snakemake will parse the target file name and infer the sequence of steps and the parameter values needed. Then the target file will be created accordingly.
 Conclusion
 This pipeline will substantially reduce the efforts in sending commands and prevent the confusion caused by the accumulation of analysis results due to testing multiple parameters. Moreover, adding new rules can extend Snaq according to the users' needs.

 Github repository
 https://github.com/attayeb/snaq
Fiber quality of cotton hybrids obtained on the base of introgressive form
Creators: name: Egamberdieva, Saida
name: Tillakhоn Seytnazarova
Publisher: name: International   Agricultural   Journal
Year: 2018
Subjects: introgressive form
cotton fiber quality
spinning consistency index

description: Some results of using introgressive form of cotton have fiber quality type II and III with geographically distant forms of high G.T.O. We studied the inheritance of fiber quality components in a hybrids F1-F3. Involvement in the selection introgressive form obtained with the wild diploid species G.trilobum Skovsted and ruderal subspecies G.hirsutum L. ssp. yucatanense and G.hirsutum ssp. punctatum var. purpurascens (Poir.) Mauer allowed us to bring new hybrids of medium staple cotton to the rich genetic basis.
Modeling Neutralization Kinetics of HIV by Broadly Neutralizing Monoclonal Antibodies in Genital Secretions Coating the Cervicovaginal Mucosa
Creators: name: Forest, M. Gregory
name: McKinley, Scott A.
name: Shi, Feng
name: Wang, Simi
name: Chen, Alex
name: Lai, Samuel K.
name: Mucha, Peter J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Eliciting broadly neutralizing antibodies (bnAb) in cervicovaginal mucus (CVM) represents a promising “first line of defense” strategy to reduce vaginal HIV transmission. However, it remains unclear what levels of bnAb must be present in CVM to effectively reduce infection. We approached this complex question by modeling the dynamic tally of bnAb coverage on HIV. This analysis introduces a critical, timescale-dependent competition: to protect, bnAb must accumulate at sufficient stoichiometry to neutralize HIV faster than virions penetrate CVM and reach target cells. We developed a model that incorporates concentrations and diffusivities of HIV and bnAb in semen and CVM, kinetic rates for binding (kon) and unbinding (koff) of select bnAb, and physiologically relevant thicknesses of CVM and semen layers. Comprehensive model simulations lead to robust conclusions about neutralization kinetics in CVM. First, due to the limited time virions in semen need to penetrate CVM, substantially greater bnAb concentrations than in vitro estimates must be present in CVM to neutralize HIV. Second, the model predicts that bnAb with more rapid kon, almost independent of koff, should offer greater neutralization potency in vivo. These findings suggest the fastest arriving virions at target cells present the greatest likelihood of infection. It also implies the marked improvements in in vitro neutralization potency of many recently discovered bnAb may not translate to comparable reduction in the bnAb dose needed to confer protection against initial vaginal infections. Our modeling framework offers a valuable tool to gaining quantitative insights into the dynamics of mucosal immunity against HIV and other infectious diseases.
Development of elements of technology of cultivation of amaranth in cover crops on irrigated lands sredneshirotnykh plains of Dagestan
Creators: name: Shapovalov Dmitry Anatolyevich
name: Savinova Svetlana Viktorovna
name: Musayev Habib Magomedovich
Publisher: name: International   Agricultural   Journal
Year: 2018
Subjects: amaranth
mellow
Kizlyarets
medium saline irrigated lands
methods of sowing
phenology
productivity

description: The data of a three-year experiment to establish the optimal irrigation regime of amaranth varieties Kizlyarets in the sowing on medium saline soils of plain Dagestan. Analysis of the data on leaf area showed that the maximum results were recorded on crops in wide way of planting with a spacing of 45 cm and a minimum on crops with a row spacing of 70 cm. When comparing the options for irrigation regime, it was revealed that the best results were recorded when pre-irrigation moisture threshold 80-85% of the smallest moisture capacity, and the mode of irrigation at 60-65% is much lower. The higher yield of amaranth was also at the irrigation regime pre-irrigation threshold of 80-85% of the lowest moisture capacity, with a wide – row method of sowing with row spacing of 45 cm-up to 35 tons per hectare.
Mst1 Directs Myosin IIa Partitioning of Low and Higher Affinity Integrins during T Cell Migration
Creators: name: Huang, Yina H.
name: Wang, Xinxin
name: Sauer, Karsten
name: Cooke, Michael P.
name: Wiltshire, Tim
name: Jaeger, Emily R.
name: Walker, John R.
name: Mathis, Nancy L.
name: Xu, Xiaolu
name: Lagler-Ferrez, Erica
name: Batalov, Serge
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Chemokines promote T cell migration by transmitting signals that induce T cell polarization and integrin activation and adhesion. Mst1 kinase is a key signal mediator required for both of these processes; however, its molecular mechanism remains unclear. Here, we present a mouse model in which Mst1 function is disrupted by a hypomorphic mutation. Microscopic analysis of Mst1-deficient CD4 T cells revealed a necessary role for Mst1 in controlling the localization and activity of Myosin IIa, a molecular motor that moves along actin filaments. Using affinity specific LFA-1 antibodies, we identified a requirement for Myosin IIa-dependent contraction in the precise spatial distribution of low and higher affinity LFA-1 on the membrane of migrating T cells. Mst1 deficiency or Myosin inhibition resulted in multipolar cells, difficulties in uropod detachment and mis-localization of low affinity LFA-1. Thus, Mst1 regulates Myosin IIa dynamics to organize high and low affinity LFA-1 to the anterior and posterior membrane during T cell migration.
MIGNEX Case Study Brief PAK3 - Migration and development dynamics in Keti Bandar, Pakistan
Creators: name: Erdal, Marta Bivand
name: Khan, Furrukh
name: Memon, Rashid
name: Nisar, Sehr
name: Raj, Prithvi
name: Ramchand, Neha
name: Hannah, Murray
Publisher: name: Peace Research Institute Oslo
Year: 2022

description: The Indus River Delta has shaped lives and livelihoods in Keti Bandar, a once-prosperous fishing port where the impacts of climate change and debt in a global, fishery-based economy are pervasive.

Key Takeaways

Many young adults reported feeling a strong connection with Keti Bandar, and a sense of peace and safety there.

Migration – both internal and international – is not a widespread occurrence, nor an aspiration. The majority of young adults (95%) expected to stay in Keti Bandar in the next five years.

Keti Bandar had been experiencing internal in-migration, increasingly from nearby islands that became uninhabitable due to rising sea levels.
Graphene as a tunable THz reservoir for shaping the Mollow triplet of an artificial atom via plasmonic effects
Creators: name: Forati, Ebrahim
name: Hanson, George W.
name: Hughes, Stephen
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Using a realistic quantum master equation we show that the resonance fluorescence spectra of a two-level artificial atom (quantum dot) can be tuned by adjusting its photonic local density of states via biasing of one or more graphene monolayers. The structured photon reservoir is included using a photon Green function theory which fully accounts for the loss and dispersion. The field-driven Mollow triplet spectrum can be actively controlled by the graphene bias in the THz frequency regime. We also consider the effect of a dielectric support environment, and multiple graphene layers, on the emitted fluorescence. Finally, thermal bath effects are considered and shown to be important for low THz frequencies.
mTOR Inhibition Induces Compensatory, Therapeutically Targetable MEK Activation in Renal Cell Carcinoma
Creators: name: Krishnan, Bhavani
name: Wilson, Harper L.
name: Damrauer, Jeffrey S.
name: Smith, Aleisha M.
name: Yeh, Jen Jen
name: Kim, William Y.
name: Bailey, Sean T.
name: Li, Mingqing
name: Zhou, Bing
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Rapamycin derivatives allosterically targeting mTOR are currently FDA approved to treat advanced renal cell carcinoma (RCC), and catalytic inhibitors of mTOR/PI3K are now in clinical trials for treating various solid tumors. We sought to investigate the relative efficacy of allosteric versus catalytic mTOR inhibition, evaluate the crosstalk between the mTOR and MEK/ERK pathways, as well as the therapeutic potential of dual mTOR and MEK inhibition in RCC. Pharmacologic (rapamycin and BEZ235) and genetic manipulation of the mTOR pathway were evaluated by in vitro assays as monotherapy as well as in combination with MEK inhibition (GSK1120212). Catalytic mTOR inhibition with BEZ235 decreased proliferation and increased apoptosis better than allosteric mTOR inhibition with rapamycin. While mTOR inhibition upregulated MEK/ERK signaling, concurrent inhibition of both pathways had enhanced therapeutic efficacy. Finally, primary RCC tumors could be classified into subgroups [(I) MEK activated, (II) Dual MEK and mTOR activated, (III) Not activated, and (IV) mTOR activated] based on their relative activation of the PI3K/mTOR and MEK pathways. Patients with mTOR only activated tumors had the worst prognosis. In summary, dual targeting of the mTOR and MEK pathways in RCC can enhance therapeutic efficacy and primary RCC can be subclassified based on their relative levels of mTOR and MEK activation with potential therapeutic implications.
MUC5AC Upstream Complex Repetitive Region Length Polymorphisms Are Associated with Susceptibility and Clinical Stage of Gastric Cancer
Creators: name: Wang, Jinshen
name: Wang, Chenghua
name: Liu, Yiqing
name: Guo, Xueliang
name: Zhang, Chunqing
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: MUC5AC was deemed to be involved in gastric carcinogenesis since aberrant MUC5AC expression has been repeatedly detected in patients with gastric cancer (GC). In this study, length polymorphisms in a complicated repetitive region adjacent to MUC5AC promoter were assessed in 230 patients with GC and 328 cancer-free controls. Alleles of 1.4 and 1.8 kb were significantly more prevalent in GC group than in controls. In contrast, 2.3 and 2.8 kb alleles occurred at significantly lower frequencies in patients than in controls. Alleles were then classified into susceptible (S; 1.4 and 1.8 kb), protective (P; 2.3 and 2.8 kb) and null (N; all other alleles) categories with respect to their linkage with the susceptibility to GC. Individuals with genotype SS had a 2.7-fold increased risk of GC occurrence, but PN genotype was associated with a significantly reduced risk of this cancer. Moreover, homozygous or heterozygous individuals with one or two copies of 1.4 kb allele showed an earlier age of onset and more advanced metastasis stage compared with patients without this allele (Bonferroni corrected p = 1.35×10−4 and 6.60×10−4 accordingly), whereas homozygous patients with two copies of 1.8 kb allele were linked to less advanced GC TNM stage. Our results suggest that certain genetic variations in MUC5AC upstream repetitive region are associated with the susceptibility and progression of GC.
Efficacy of growth regulators in cover crops of amaranth sredneshirotnykh on irrigated lands of flat Dagestan
Creators: name: Shapovalov Dmitry Anatolyevich
name: Savinova Svetlana Viktorovna
name: Musayev Habib Magomedovich
Publisher: name: International   Agricultural   Journal
Year: 2018
Subjects: irrigated saline lands
irrigated crops
amaranth varieties
growth regulators
leaf surface
yield

description: In 2015-2017, in the context of the Tersk-Sulak subprovince of the Republic of Dagestan on irrigated saline lands, studies aimed at the study of adaptive potential of amaranth varieties (Kizlyar (standard), Valentine, Iriston) with the use of growth regulators were conducted. As a result, it is revealed that the applied growth regulators contribute to the reduction of the vegetation period of the studied varieties. In addition, the regulators have increased the area of the leaf surface and net productivity of crops. In the analysis of the harvest data found that the higher the data provided a variety of Iriston and lows of Valentine's day. Applied growth regulators increased the yield on average by 13.4-15.3% for varieties.
Effects of Geometry on Near Quantum Ground State Behaviour of Phonon-Trapping Acoustic Cavities
Creators: name: Goryachev, Maxim
name: Tobar, Michael E.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: This work presents some peculiarities of the near quantum ground state behaviour of curved (phonon trapping) Bulk Acoustic Wave (BAW) cavities when compared to a conventional mechanical resonator. The curved cavity system resolves the quandary of the conventional mechanical system where the Bose-Einstein distribution requires higher frequencies for lower quantum occupation factors contrary to the constraint of an inverse frequency dependence of the quantum fluctuations of displacement. We demonstrate how the non-trivial cavity geometry can lead to better phonon trapping, enhancing the variance of zero-point-fluctuations of displacement. This variance becomes independent of overtone number (or BAW resonance frequency) overcoming the constraint and allowing better observation of quantum effects in a mechanical system. The piezoelectric electro-mechanical coupling approach is qualitatively compared to the parametric optomechanical technique for the curved BAW cavities. In both cases the detectible quantity grows proportional to the square root of the overtone number, and thus the resonance frequency. Also, the phonon trapping improves with higher overtone numbers, which allows the electrode size to be reduced such that in the optimal case the parasitic capacitive impedance becomes independent of the overtone number, allowing effective coupling to very high frequency overtones.
description: New J. Phys., 2014
Workplace factors affecting the workplace wellbeing of women and marginalised groups in the European Union: protocol for a scoping review.
Creators: name: Kraljević, Katja
Publisher: name: Open Science Framework
Year: 2023
Subjects: subject: Medicine and Health Sciences
subject: Occupational Health and Industrial Hygiene
subject: Women's Health
subject: Public Health
subject: job quality
subject: workplace wellbeing
subject: work life balance
subject: marginalised workers
subject: health inequalities
subject: women workers
subject: job satisfaction

description: This scoping review protocol outlines the methodology that will be used to review literature concerning workplace factors and their relationship to the workplace wellbeing -- as defined by job quality, work-life balance and job satisfaction -- of women and marginalised groups in the European Union.
MIGNEX Case Study Brief PAK2 - Migration and development dynamics in Youhanabad, Pakistan
Creators: name: Erdal, Marta Bivand
name: Khan, Furrukh
name: Noor, Wardah
name: Batool, Jovairiah
name: Aneeb UI Hassan Qureshi, Muhammad
name: Karimi, Behroz
name: Ahmad, Arslan
name: Hannah, Murray
Publisher: name: Peace Research Institute Oslo
Year: 2022

description: Youhanabad – the largest Christian-majority area in Pakistan – is an urban neighbourhood of Lahore undergoing major educational and infrastructural expansion.

Key Takeaways

Youhanabad has been, and continues to be, shaped by internal in-migration of Christians of different denominations.

International mobility and development interventions are often tied to different church-based networks in the area.

Overall, out-migration is low: most young adults (78%) expect to stay in Youhanabad in the next five years. Migration aspirations are also low, with most (88%) preferring to stay.
Photoionization microscopy in terms of local frame transformation theory
Creators: name: Giannakeas, P.
name: Robicheaux, F.
name: Greene, Chris H.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Two-photon ionization of an alkali-metal atom in the presence of a uniform electric field is investigated using a standardized form of local frame transformation and generalized quantum defect theory. The relevant long-range quantum defect parameters in the combined Coulombic plus Stark potential is calculated with eigenchannel R-matrix theory applied in the downstream parabolic coordinate $η$. The present formulation permits us to express the corresponding microscopy observables in terms of the local frame transformation, and it gives a critical test of the accuracy of the Harmin-Fano theory permitting a scholastic investigation of the claims presented in Zhao {\it et al.} [Phys. Rev. A 86, 053413 (2012)].
description: corrected typos, added references
Assessment of optimum soil features and plant food compound deficiency using the methods based on feedback principles
Creators: name: Savich, Vitaliy Igorevich
name: Borisov, Boris Anoryevich
name: Gukalov, Victor Vladimirovich
Publisher: name: International   Agricultural   Journal
Year: 2018
Subjects: soil fertility
need for food compounds
photosynthesis
complex compounds
sorption properties of roots

description: The expediency of assessment of plant biophile element supply using the feedback principles is shown in this paper. The experimental data on assessment of plant needs for food compounds by chloroplastid activity, the content of positively and negatively charged cation complex compounds, by the photosynthesis parame-ters of plants developing in soil suspension after bringing the ions under study into the suspension are presented. The methods are based on principle addition into the soil or plants and on the plant feedback analysis and the extremum assessment. The expediency of their use for the assessment of plant needs for food compounds (plant species and cultivars depending on their stage of development) has been shown by their absorption out of the analysed soil suspension, and then out of the culture solution. The assess-ment of sorption properties of plant root systems is provided.
Multi-Scale Imaging and Informatics Pipeline for In Situ Pluripotent Stem Cell Analysis
Creators: name: Lerou, Paul H.
name: Baccei, Anna
name: Lu, Junjie
name: Gorman, Bryan R.
name: Lowry, Nathan C.
name: Purvis, Jeremy E.
name: Mangoubi, Rami S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Human pluripotent stem (hPS) cells are a potential source of cells for medical therapy and an ideal system to study fate decisions in early development. However, hPS cells cultured in vitro exhibit a high degree of heterogeneity, presenting an obstacle to clinical translation. hPS cells grow in spatially patterned colony structures, necessitating quantitative single-cell image analysis. We offer a tool for analyzing the spatial population context of hPS cells that integrates automated fluorescent microscopy with an analysis pipeline. It enables high-throughput detection of colonies at low resolution, with single-cellular and sub-cellular analysis at high resolutions, generating seamless in situ maps of single-cellular data organized by colony. We demonstrate the tool's utility by analyzing inter- and intra-colony heterogeneity of hPS cell cycle regulation and pluripotency marker expression. We measured the heterogeneity within individual colonies by analyzing cell cycle as a function of distance. Cells loosely associated with the outside of the colony are more likely to be in G1, reflecting a less pluripotent state, while cells within the first pluripotent layer are more likely to be in G2, possibly reflecting a G2/M block. Our multi-scale analysis tool groups colony regions into density classes, and cells belonging to those classes have distinct distributions of pluripotency markers and respond differently to DNA damage induction. Lastly, we demonstrate that our pipeline can robustly handle high-content, high-resolution single molecular mRNA FISH data by using novel image processing techniques. Overall, the imaging informatics pipeline presented offers a novel approach to the analysis of hPS cells that includes not only single cell features but also colony wide, and more generally, multi-scale spatial configuration.
The factors in the development of renewable energy sources in the Republic of Kazakhstan
Creators: name: Yeleukulova, Aina N.
Publisher: name: International   Agricultural   Journal
Year: 2018
Subjects: environmental factor
renewable energy sources
energy deficit
energy sector
fuel and energy resource
energy

description: The article is devoted to the factors contributing to the development of renewable energy sources in the Republic of Kazakhstan. The international practice of development of alternative energy sources in ecology, increase in prices for the electric power and deficiency of energy consumption was analyzed. The negative consequences on the environment and the human body from the functioning of energy enterprises were indicated. The dynamics of growth in the tariff for electricity was analyzed.
Example Authentication of Key Biological and/or Chemical Resources
Creators: name: Bandrowski, Anita
Publisher: name: UC San Diego Library
Year: 2016
Subjects: National Institutes of Health
Reproducibility
Scientific rigor
Transparency
Validation
Antibodies
Cell lines

description: Effective on or after January 25, 2016, most NIH and AHRQ research grant applications are required to comply with the NIH Policy on Rigor and Reproducibility. This resource is an example document for meeting the requirement for an Authentication of Key Biological and/or Chemical Resources.
Exclusion of Cosmic Rays in Protoplanetary Disks. II. Chemical Gradients and Observational Signatures
Creators: name: Cleeves, L. I.
name: Bergin, Edwin A.
name: Adams, Fred C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The chemical properties of protoplanetary disks are especially sensitive to their ionization environment. Sources of molecular gas ionization include cosmic rays, stellar X-rays and short-lived radionuclides, each of which varies with location in the disk. This behavior leads to a significant amount of chemical structure, especially in molecular ion abundances, which is imprinted in their submillimeter rotational line emission. Using an observationally motivated disk model, we make predictions for the dependence of chemical abundances on the assumed properties of the ionizing field. We calculate the emergent line intensity for abundant molecular ions and simulate sensitive observations with the Atacama Large Millimeter/Sub-millimeter Array (ALMA) for a disk at D=100 pc. The models readily distinguish between high ionization rates ($ζ\gtrsim10^{-17}$ s$^{-1}$ per H$_2$) and below, but it becomes difficult to distinguish between low ionization models when $ζ\lesssim10^{-19}$ s$^{-1}$. We find that \htdp\ emission is not detectable for sub-interstellar CR rates with ALMA (6h integration), and that \ntdp\ emission may be a more sensitive tracer of midplane ionization. HCO$^+$ traces X-rays and high CR rates ($ζ_{\rm{CR}}\gtrsim10^{-17}$ s$^{-1}$), and provides a handle on the warm molecular ionization properties where CO is present in the gas. Furthermore, species like HCO$^+$, which emits from a wide radial region and samples a large gradient in temperature, can exhibit ring-like emission as a consequence of low-lying rotational level de-excitation near the star. This finding highlights a scenario where rings are not necessarily structural or chemical in nature, but simply a result of the underlying line excitation properties.
description: 25 pages, 14 figures; accepted to ApJ
title: In the Betweens
title: An Exploration of the Interstices
titleType: Subtitle
Creators: name: Opalinski, Yvonne
Publisher: name: Lancaster University
Year: 2022
Subjects: Interstices
Spacetime
subject-object collapse
Duchamp's gap
Dyad
Renga
quantum mechanics
generative dispersion
third substance

description: This thesis and its accompanying project are part of a critical exploration of space, identified as the interstices. Space is considered a void, a measure of separation or a counterfoil that accentuates material mass in art. In spite of these traditional associations, my aim is to alter how we think of space not only in art, but as a creative, cross-disciplinary medium. This research project investigates the minutia of space where sound, drawing, animation and poetry form a scholarly framework in conjunction with physiology, physics and philosophy to open interstitial encounters. As a structural tool and a macroscopic example of the organic interstices, the Japanese art of renga runs through this thesis to guide us inside those spaces. Through this interdisciplinary approach, the project shapes an awareness of space as a material of substantive metamorphosis outside of time. By integrating media, this project establishes a new method of bringing things together inside a reworked renga continuum between virtual and physical. Accordingly, a new way of understanding from the inside out has been developed to shatter conventional separations, beginning with those divisions between artist, artwork and audience. As such, the subject-object gap is challenged as a method for knowledge acquisition, creative thinking and doing. This study affirms that in the dissolution of separations antiquated grooves of thinking no longer function and knowledge cannot be limited to a set information point in a moment of time. Rather, their disintegration is a mandatory condition for physical-intellectual knowing within quantum reconfigurations. Understanding then occurs inside the infinite renga circle. The expanded spatial poems developed in this project demonstrate this new way of thinking and being. As a result, a fundamentally different method of looking at things is presented inside the spaces of the interstices and from this materiality an ultimately transferrable research tool has been developed for interdisciplinary knowledge generation.
Multi-Task Linear Programming Discriminant Analysis for the Identification of Progressive MCI Individuals
Creators: name: Yu, Guan
name: Shen, Dinggang
name: Thung, Kim-Han
name: Liu, Yufeng
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Accurately identifying mild cognitive impairment (MCI) individuals who will progress to Alzheimer's disease (AD) is very important for making early interventions. Many classification methods focus on integrating multiple imaging modalities such as magnetic resonance imaging (MRI) and fluorodeoxyglucose positron emission tomography (FDG-PET). However, the main challenge for MCI classification using multiple imaging modalities is the existence of a lot of missing data in many subjects. For example, in the Alzheimer's Disease Neuroimaging Initiative (ADNI) study, almost half of the subjects do not have PET images. In this paper, we propose a new and flexible binary classification method, namely Multi-task Linear Programming Discriminant (MLPD) analysis, for the incomplete multi-source feature learning. Specifically, we decompose the classification problem into different classification tasks, i.e., one for each combination of available data sources. To solve all different classification tasks jointly, our proposed MLPD method links them together by constraining them to achieve the similar estimated mean difference between the two classes (under classification) for those shared features. Compared with the state-of-the-art incomplete Multi-Source Feature (iMSF) learning method, instead of constraining different classification tasks to choose a common feature subset for those shared features, MLPD can flexibly and adaptively choose different feature subsets for different classification tasks. Furthermore, our proposed MLPD method can be efficiently implemented by linear programming. To validate our MLPD method, we perform experiments on the ADNI baseline dataset with the incomplete MRI and PET images from 167 progressive MCI (pMCI) subjects and 226 stable MCI (sMCI) subjects. We further compared our method with the iMSF method (using incomplete MRI and PET images) and also the single-task classification method (using only MRI or only subjects with both MRI and PET images). Experimental results show very promising performance of our proposed MLPD method.
Import substitution industrialization in agro-industrial sector and poultry product subcomplex under sanctions
Creators: name: Kondratenko Ilya, S.
Publisher: name: International   Agricultural   Journal
Year: 2018
Subjects: sanctions
import substitution industrialization
poultry product subcomplex

description: In article the impact of sanctions and counter-sanctions on food products and also possible ways to address the issue of self-sufficiency are considered. The imposition of an embargo, in fact, provided benchmark of development of the Russian economy, and, in particular, agro-industrial sector. This benchmark is import substitution industrialization (ISI). The government of the Russian Federation has taken a plan of action which included amendment of legal acts governing agro-industrial sector. However, existing expertise of food embargoes shows that condition is important but insufficient for rational ISI. Using data from Russia and Sverdlovsk oblast, this article argues that, in general, national situation gives cause for concern for a number of reasons, and basically due to a feature of agricultural sector, leading to its rigidities and impossibility of rapid production increase. However, the author asserts that task of ISI of some agricultural products, in particular, poultry products is progressing positively in selected areas, for example, in Sverdlovsk oblast. In this climate commitment to ISI became a natural reaction to action of the U.S. and some other countries. And it was well received by enterprises of poultry product subcomplex of Sverdlovsk oblast (the producers of agriculture and food just enhanced their status). It is necessary to adjust program of the State's regulation of agro-industrial sector to successfully implement the ISI policy under economic sanctions.
Supplemental Figure 1 from Linguistic law-like compression strategies emerge to maximize coding efficiency in marmoset vocal communication
Creators: name: Risueno-Segovia, Cristina
name: Dohmen, Deniz
name: Gultekin, Yasemin B.
name: Pomberger, Thomas
name: Hage, Steffen R.
Publisher: name: The Royal Society
Year: 2023
Subjects: Neuroscience
Cognitive Science not elsewhere classified
Animal Behaviour

description: Human language follows statistical regularities or linguistic laws. For instance, Zipf's law of brevity states that the more frequently a word is used, the shorter it tends to be. All human languages adhere to this word structure. However, it is unclear whether Zipf's law emerged de novo in humans or whether it also exists in the non-linguistic vocal systems of our primate ancestors. Using a vocal conditioning paradigm, we examined the capacity of marmoset monkeys to efficiently encode vocalizations. We observed that marmosets adopted vocal compression strategies at three levels: (i) increasing call rate, (ii) decreasing call duration and (iii) increasing the proportion of short calls. Our results demonstrate that marmosets, when able to freely choose what to vocalize, exhibit vocal statistical regularities consistent with Zipf's law of brevity that go beyond their context-specific natural vocal behaviour. This suggests that linguistic laws emerged in non-linguistic vocal systems in the primate lineage.
Superconductivity in the vicinity of antiferromagnetic order in CrAs
Creators: name: Wu, Wei
name: Cheng, Jinguang
name: Matsubayashi, Kazuyuki
name: Kong, Panpan
name: Lin, Fukun
name: Jin, Changqing
name: Wang, Nanlin
name: Uwatoko, Yoshiya
name: Luo, Jianlin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: One of the common features of unconventional, magnetically mediated superconductivity as found in the heavy-fermions, high-transition-temperature (high-Tc) cuprates, and iron pnictides superconductors is that the superconductivity emerges in the vicinity of long-range antiferromagnetically ordered state.[1] In addition to doping charge carriers, the application of external physical pressure has been taken as an effective and clean approach to induce the unconventional superconductivity near a magnetic quantum critical point (QCP).[2,3] Superconductivity has been observed in a majority of 3d transition-metal compounds,[4-9] except for the Cr- and Mn-based compounds in the sense that the low-lying states near Fermi level are dominated by their 3d electrons. Herein, we report on the discovery of superconductivity on the verge of antiferromagnetic order in CrAs via the application of external high pressure. Bulk superconductivity with Tc ~ 2 K emerges at the critical pressure Pc ~ 8 kbar, where the first-order antiferromagnetic transition at TN = 265 K under ambient pressure is completely suppressed. Abnormal normal-state properties associated with a magnetic QCP have been observed nearby Pc. The close proximity of superconductivity to an antiferromagnetic order suggests an unconventional pairing mechanism for the superconducting state of CrAs. The present finding opens a new avenue for searching novel superconductors in the Cr and other transitional-metal based systems.
Philippe Baveye and Biochar
Creators: name: Telly, Phil
Publisher: name: figshare
Year: 2023
Subjects: Biological adaptation
Evolutionary impacts of climate change

description: There has been a lot of literature promoting the benefits of using biochar or agrichar in agriculture and environmental conservation. However, despite the enthusiasm, experimental evidence supporting these claims remains weak and inconclusive. To address this, a tale of two researchers Philip and Johannes is a cautionary tale about the dangers of arrogance and envy. While confidence and self-assurance are important qualities, they must be balanced with humility and respect for others. Ultimately, it is hard work, dedication, and a commitment to excellence that lead to success, not boasting and self-promotion.
Mylognathus priscus
Creators: name: Leidy, J.
Publisher: name: Zenodo
Year: 1860
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Holocephali
Chimaeriformes
Chimaeridae
Mylognathus
Mylognathus priscus

description: Mylognathus priscus. The very singular-looking fish, Chimaera, of the European seas, was represented during the Miocene period in Nebraska, by a genus for which the above name has been proposed. Its former existence is indicated by specimens of dental plates, like those of Chimaera, adapted to the crushing of mollusca and Crustacea, used as food. The specimens, consisting of an upper maxillary and a premaxillary plate, were obtained by Dr. Hayden from the Great Lignite Basin near Long Lake, Nebraska. The upper maxillary plate, (figs. 24, 25, 26, plate 11,) consists of a narrow triangular bone, containing two teeth. The specimen is broken at its two extremities, and when perfect appears to have been a little over an inch in length. Its posterior part is 3 4 3/lines wide, and about 4 1/2 lines thick. The free convex surfaces of the peculiar porous teeth, occupy nearly the entire length and breadth of the bone, (fig. 25, plate 11,) and are separated from each other by an oblique, linear tract. The anterior tooth is lozenge-shaped in outline, and when perfect appears to have been about 1/2 an inch in length, and 1 4 3/lines in breadth. The posterior tooth, somewhat ellipsoidal in outline, appears, when perfect, to have been about 8 lines long, and is three lines wide. The premaxillary dental plate, (figs. 27—30, plate 11,) is irregularly lozenge-shaped in its vertical outline antero-posteriorly, is a little over an inch in its long diameter, 5 lines in its depth, and 3 lines in its greatest thickness. Its anterior border is convex, the inner and outer surfaces are vertical, slightly depressed planes, and the crushing surface is concave. Explanation of Figures, Plate 11. Figures 24—30. Upper maxillary plates of Mylognathus priscus, of the natural size. Figure 24. Inner view of the maxillary plate, exhibiting the surfaces of the two teeth projecting below. Figure 25. Oral or inferior surface of the same. Figure 26. Posterior extremity of the same, exhibiting the columnar structure of the teeth. Figures 27, 28. Outer and inner view of a pre-maxillary plate. Figures 29, 30. Triturating surface and upper view of the same.
description: Published as part of Leidy, J., 1860, Extinct vertebrata from the Judith River and Great Lignite formations of Nebraska., pp. 139-154 in Transactions of the American Philosophical Society 11 on pages 153-154, DOI: 10.5281/zenodo.1064078