cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Valley-selective Klein tunneling through superlattice barrier in graphene
Creators: name: An, Xing-Tao
name: Yao, Wang
Publisher: name: arXiv
Year: 2019
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Graphene electrons feature a pair of massless Dirac cones of opposite pseudospin chirality at two valleys. Klein tunneling refers to the intriguing capability of these chiral electrons to penetrate through high and wide potential barrier. The two valleys have been treated independently in the literature, where time reversal symmetry dictates that neither the normal incidence transmission nor the angle-averaged one can have any valley polarization. Here we show that, when intervalley scattering by barrier is accounted, graphene electrons normally incident at a superlattice barrier can experience a fully valley-selective Klein tunneling, i.e. perfect transmission in one valley, and perfect reflection in the other. Intervalley backscattering creates staggered pseudospin gaps in the superlattice barrier, which, combined with the valley contrast in pseudospin chirality, determines the valley polarity of Klein tunneling. The angle averaged transmission can have a net valley polarization of 20% for a 5-period barrier, and exceed 75% for a 20-period barrier. Our finding points to an unexpected opportunity to realize valley functionalities in graphene electronics.
description: 15 pages, 4 figures
Oxidative stress enhances the expression of 2′,3′-cyclic phosphate-containing RNAs
Creators: name: Shigematsu, Megumi
name: Kirino, Yohei
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology
subject: 60506 Virology

description: Eukaryotic cells equip robust systems to respond to stress conditions. In stressed mammalian cells, angiogenin endoribonuclease cleaves anticodon-loops of tRNAs to generate tRNA halves termed tRNA-derived stress-induced RNAs (tiRNAs), which promote stress granule formation and regulate translation. The 5′-tiRNAs (5′-tRNA halves) contain a 2′,3′-cyclic phosphate (cP) and thus belong to cP-containing RNAs (cP-RNAs). The cP-RNAs form a hidden layer of the transcriptome because standard RNA-seq cannot amplify and sequence them. In this study, we performed genome-wide analyses of short cP-RNA transcriptome in oxidative stress-exposed human cells. Using cP-RNA-seq that can specifically sequence cP-RNAs, we identified tiRNAs and numerous other cP-RNAs that are mainly derived from rRNAs and mRNAs. Although tiRNAs were produced from a wide variety of tRNA species, abundant species of tiRNAs were derived from a focal specific subset of tRNAs. Regarding rRNA- and mRNA-derived cP-RNAs, determination of the processing sites of substrate RNAs revealed highly-specific RNA cleavage events between pyrimidines and adenosine in generation of those cP-RNAs. Those cP-RNAs were derived from specific loci of substrate RNAs rather than from the overall region, implying that cP-RNAs are produced by regulated biogenesis pathways and not by random degradation events. We experimentally confirmed the identified sequences to be expressed as cP-RNAs in the cells, and their expressions were upregulated upon induction of oxidative stress. These analyses of the cP-RNA transcriptome unravel an abundant class of short ncRNAs that accumulate in cells under oxidative stress.
Figure S4: Pol IV 21-22 nt siRNAs are enriched in AGO1 from Arabidopsis RNA polymerase IV generates 21–22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes
Creators: name: Panda, Kaushik
name: McCue, Andrea D.
name: R. Keith Slotkin
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: Plant Biology
subject: 60408 Genomics

description: sRNA accumulation from different loci is shown in total, AGO1-IP or negative control mock-IP samples in wt Col inflorescence tissue. A) High enrichment of all miRNAs in AGO1-IP vs mock-IP. B) and C) Positive controls miR166 and miR171 [45] show high enrichment of specific mature miRNA in AGO1. D) miRNA 390a is known to be incoporated specifically into AGO7 and not AGO1 [45,46] and is shown here as a negative control demonstrating no enrichment of mature miRNA in AGO1-IP vs mock. E) Only a subset of 24 nt sRNA from Pol IV 24 nt clusters are incorporated into AGO1-IP (AGO1-IP/total < 0.2) but the ones that do are enriched compared to mock (AGO1-IP- /mock IP > 2). and F) 21-22 nt sRNAs from Pol IV 21-22 nt clusters show genome-wide enrichment into AGO1 (AGO1-IP/total > 2) like all miRNAs in A. AGO1-IP/mock enrichment (>3) is not as high as miRNAs but higher than the negative control miR390a. Together these data demonstrate that Pol IV-dependent 21-22 nt sRNAs are incorporated into AGO1.
Synthesis and biological evaluation of thieno[3,2-c]pyrazol-3-amine derivatives as potent glycogen synthase kinase 3β inhibitors for Alzheimer’s disease
Creators: name: Yan, Ning
name: Shi, Xiao-Long
name: Tang, Long-Qian
name: Wang, De-Feng
name: Li, Xun
name: Liu, Chao
name: Liu, Zhao-Peng
Publisher: name: Taylor & Francis
Year: 2022
Subjects: Biochemistry
Cell Biology
Molecular Biology
Neuroscience
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Cancer
Hematology
Virology

description: Glycogen synthase kinase 3β (GSK-3β) catalyses the hyperphosphorylation of tau protein in the Alzheimer’s disease (AD) pathology. A series of novel thieno[3,2-c]pyrazol-3-amine derivatives were designed and synthesised and evaluated as potential GSK-3β inhibitors by structure-guided drug rational design approach. The thieno[3,2-c]pyrazol-3-amine derivative 16b was identified as a potent GSK-3β inhibitor with an IC50 of 3.1 nM in vitro and showed accepted kinase selectivity. In cell levels, 16b showed no toxicity on the viability of SH-SY5Y cells at the concentration up to 50 μM and targeted GSK-3β with the increased phosphorylated GSK-3β at Ser9. Western blot analysis indicated that 16b decreased the phosphorylated tau at Ser396 in a dose-dependent way. Moreover, 16b effectively increased expressions of β-catenin as well as the GAP43, N-myc, and MAP-2, and promoted the differentiated neuronal neurite outgrowth. Therefore, the thieno[3,2-c]pyrazol-3-amine derivative 16b could serve as a promising GSK-3β inhibitor for the treatment of AD.
The stress specific impact of ALKBH1 on tRNA cleavage and tiRNA generation
Creators: name: Rashad, Sherif
name: Xiaobo Han
name: Sato, Kanako
name: Eikan Mishima
name: Abe, Takaaki
name: Teiji Tominaga
name: Kuniyasu Niizuma
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 111714 Mental Health
subject: FOS: Health sciences

description: tiRNAs are small non-coding RNAs produced when tRNA is cleaved under stress. tRNA methylation modifications has emerged in recent years as important regulators for tRNA structural stability and sensitivity to cleavage and tiRNA generation during stress, however, the specificity and higher regulation of such a process is not fully understood. Alkbh1 is a m1A demethylase that leads to destabilization of tRNA and enhanced tRNA cleavage. We examined the impact of Alkbh1 targeting via gene knockdown or overexpression on B35 rat neuroblastoma cell line fate following stresses and on tRNA cleavage. We show that Alkbh1 impact on cell fate and tRNA cleavage is a stress specific process that is impacted by the demethylating capacity of the cellular stress in question. We also show that not all tRNAs are cleaved equally following Alkbh1 manipulation and stress, and that Alkbh1 KD fails to rescue tRNAs from cleavage following demethylating stresses. These findings shed a light on the specificity and higher regulation of tRNA cleavage and should act as a guide for future work exploring the utility of Alkbh1 as a therapeutic target for cancers or ischaemic insult.
A search for X-ray variability in the open cluster NGC 2516
Creators: name: Ramsay, Gavin
name: Harra, Louise
name: Kay, Hilary
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present the results of a search for X-ray variability in the galactic open cluster NGC 2516. This cluster has been observed on 8 occasions using XMM-Newton making it an excellent target for such a study. We find 4 sources which show significant variability, implying the detection of one significantly variable source every 25ksec. All sources exhibit spectra which can be fitted using an absorbed one or two temperature thermal plasma model. The brightest of these flares also show a prominent Iron line near ~7.0keV. All 4 sources lie near the observed main sequence of NGC 2516 suggesting they are cluster members. We propose that at least 3 of the 4 objects are RS CVn systems. We compare the properties of the brightest flare with those of solar flares.
description: Accepted for publication in MNRAS, 6 pages
Delivering Culturally Competent Care to the Lesbian, Gay, Bisexual, and Transgender (LGBT) Population
Creators: name: McEwing, Evan M
Publisher: name: University of Massachusetts Amherst
Year: 2017

Purpose: To this day, the lesbian, gay, bisexual, and transgender (LGBT) communities still experience negative health outcomes due to social stigma and discrimination. Additionally, nursing has lagged behind other health professions in the promotion of culturally competent care to members of this minority group. Several national authorities on LGBT health have proposed guidelines for providing such care to the LGBT population; however, many nursing schools are not integrating these recommendations into their curricula. Methods: Using these national guidelines, an educational program was developed for BSN students at a large south Florida university to improve competency in providing care for LGBT individuals. The goal was to improve nursing providers’ attitudes, knowledge and skills in the care of the LGBT community. 120 BSN students completed online modules regarding LGBT health disparities and a disaster simulation requiring the placement of a transgender individual in proper emergency housing. Participants were surveyed pre- and post- intervention as well as one month after to assess if any changes observed had persisted. Results: Overall cultural competence scores increased significantly from baseline to post-test and did not decline significantly at one month follow-up. Notable improvements in the instrument sub-scales (knowledge, skills, and awareness) were also noted. Finally, both the presenter and the program received positive ratings regarding the usefulness of the program and its applicability to nursing practice. Conclusion: Educational content focused on providing culturally competent care for LGBT individuals may lead to improvements in providers’ awareness, skills, and knowledge about the unique needs of the LGBT population.
title: Foxtail Millet :
title: Guidelines for the Conduct of Tests for Distinctness, Uniformity and Stability.
titleType: Subtitle
Creators: name: International Union For The Protection Of New Varieties Of Plants,
Publisher: name: International Union for the Protection of New Varieties of Plants,
Year: 0
Subjects: New Varieties of Plants
Foxtail Millet

description: The purpose of these guidelines (“Test Guidelines”) is to elaborate the principles contained in the General Introduction (document TG/1/3), and its associated TGP documents, into detailed practical guidance for the harmonized examination of distinctness, uniformity and stability (DUS) and, in particular, to identify appropriate characteristics for the examination of DUS and production of harmonized variety descriptions.
title: Impact of Simplified Stationary Cavity Beam Loading on the Longitudinal Feedback System for SIS100
Creators: name: Groß, Kerstin
name: Klingbeil, Harald
name: Lens, Dieter Etienne Mia
Publisher: name: Joint Accelerator Conferences Website
Year: 2022

description: The main synchrotron SIS100 of the Facility for Antiproton and Ion Research (FAIR) will be equipped with a bunch-by-bunch feedback system to damp longitudinal beam oscillations. In the basic layout, one three-tap finite impulse response (FIR) filter will be used for each single bunch and oscillation mode. The detected oscillations are used to generate a correction voltage in dedicated broadband radio frequency (RF) cavities. The digital filter is completely described by two parameters, the feedback gain and the passband center frequency, which have to be defined depending on the longitudinal beam dynamics. In earlier works, the performance of the closed loop control with such an FIR-filter was analyzed and compared to simulations and measurements with respect to the damping of coherent dipole and quadrupole modes, the first modes of oscillation. This contribution analyzes the influence of cavity beam loading on the closed loop performance and the choice of the feedback gain and passband center frequency to verify future high current operation at FAIR.
Non-Hermitian approach for quantum plasmonics
Creators: name: Cortes, Cristian L.
name: Otten, Matthew
name: Gray, Stephen K.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We examine the limits of applicability of a simple non-Hermitian model for exciton/plasmon interactions in the presence of dissipation and dephasing. The model can be used as an alternative to the more complete Lindblad density matrix approach and is computationally and conceptually simpler. We find that optical spectra in the linear regime can be adequately described by this approach. The model can fail, however, under continuous optical driving in some circumstances. In the case of two quantum dots or excitons interacting with a plasmon, the model can also describe coherences and entanglement qualitatively when both dissipation and dephasing are present, and quantitatively in the limit with no dephasing. The model can also be extended to the case of many quantum dots interacting with a plasmon and results, within the single-excitation manifold, are presented for the fifty quantum dot case.
The Temperature of the CMB at 10 GHz
Creators: name: Fixsen, D. J.
name: Kogut, A.
name: Levin, S.
name: Limon, M.
name: Lubin, P.
name: Mirel, P.
name: Seiffert, M.
name: Wollack, E.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We report the results of an effort to measure the low frequency portion of the spectrum of the Cosmic Microwave Background Radiation (CMB), using a balloon-borne instrument called ARCADE (Absolute Radiometer for Cosmology, Astrophysics, and Diffuse Emission). These measurements are to search for deviations from a thermal spectrum that are expected to exist in the CMB due to various processes in the early universe. The radiometric temperature was measured at 10 and 30 GHz using a cryogenic open-aperture instrument with no emissive windows. An external blackbody calibrator provides an in situ reference. A linear model is used to compare the radiometer output to a set of thermometers on the instrument. The unmodeled residuals are less than 50 mK peak-to-peak with a weighted RMS of 6 mK. Small corrections are made for the residual emission from the flight train, atmosphere, and foreground Galactic emission. The measured radiometric temperature of the CMB is 2.721 +/- 0.010 K at 10 GHz and 2.694 +/- 0.032 K at 30 GHz.
description: 8 pages including 5 figures. Submitted to The Astrophysical Journal
Educational Intervention for Identification of Metabolic Syndrome (ICD-10 E88.81): Presentation of a Toolkit for Providers and Staff in Two Primary Care Settings
Creators: name: Russell, Sadie
Publisher: name: University of Massachusetts Amherst
Year: 2016

Metabolic syndrome plays a vital role in present-day primary care. The ICD-10 diagnostic coding for this set of symptoms more comprehensively identifies patients with increased risk of cardiovascular events and comorbidities. Metabolic syndrome affects one-third of adults in the US and is defined as the presence of three of the following characteristics: abdominal obesity, hypertension, elevated triglycerides, low high-density lipoprotein, and elevated fasting plasma glucose. Proper screening for metabolic syndrome can identify complex patients before conditions like hypertension or type II diabetes develop. Management of metabolic syndrome emphasizes prevention and prioritizes lifestyle modifications as first-line treatment. Despite strong evidence supporting the use of metabolic syndrome as a key diagnostic code, it is not being routinely identified and documented in primary care.  Moreover, without proper screening, identification, and coding for metabolic syndrome in primary care, management and lifestyle modifications may not be initiated in a timely way or at all. This shows evidence of the large gap between what we know about metabolic syndrome and how to identify it and what is actually happening in primary care. Purpose: To address this gap, a DNP project was implemented at two primary care sites. Its purpose was to increase primary care provider knowledge, identification, and ICD-10 coding of metabolic syndrome, leading to better office visit follow-up and enhanced patient outcomes. Toolkit: A toolkit was developed based on the 2009 American College of Preventive Medicine Metabolic Syndrome Time Tool and accompanying verbal presentation with a PowerPoint. The intervention was provided live at two primary care sites to healthcare staff, including providers (NP, PA, MD) and nurses (RN, LPN). Outcomes: Valuable data were obtained regarding enhancement of provider knowledge and perceptions of metabolic syndrome, as well as their engagement with and use of the toolkit. Conclusion: Use of metabolic syndrome as a key ICD code is supported by strong evidence, primary care providers are amenable to its use, yet remain slow to adapt it into their medical records systems. Further investigation in this area is needed.
Nanoscale-SiC doping for enhancing Jc and Hc2 in the Superconducting MgB2
Creators: name: Dou, S. X.
name: Braccini, V.
name: Soltanian, S.
name: Klie, R.
name: Zhu, Y.
name: Li, S.
name: Wang, X. L.
name: Larbalestier, D.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: The effect of nanoscale-SiC doping of MgB2 was investigated using transport and magnetic measurements. It was found that there is a clear correlation between the critical temperature Tc, the resistivity r, the residual resistivity ratio, RRR = R(300K)/R(40K), the irreversibility field H* and the alloying state in the samples. SiC-doping introduced many nano-scale precipitates, provoking an increase of r(40K) from 1 mW-cm (RRR = 15) for the clean limit sample to 300 mW-cm (RRR = 1.75) for the SiC-doped sample, leading to significant enhancement of Hc2 and H* with only minor effect on Tc. EELS analysis revealed a number of nano-scale impurity phases: Mg2Si, MgO, MgB4, BOx, SixByOz, BC and unreacted SiC in the doped sample. TEM study showed an extensive domain structure of 2-4nm domains induced by SiC doping. The Jc for the 10% nano-SiC doped sample increased substantially at all fields and temperatures compared to the undoped samples, due to the strong increase in Hc2 and H* produced by SiC doping.
Improving the Detection and Management of Hypertension in Adults in the Primary Care Setting:  A Quality Improvement Project Based on the Chronic Care Model  using Blood Pressure Monitoring and Clinical Practice Guidelines
Creators: name: Cutler, Michelle A
Publisher: name: University of Massachusetts Amherst
Year: 2016

Background:  Hypertension (HTN) is a common, costly, and deadly disease that is often under recognized, under diagnosed, and undertreated in the primary care setting.  Despite the presence of effective treatment strategies, uncontrolled HTN remains a persistent problem.
Purpose:  The aim of this Doctor of Nursing Practice (DNP) project was to improve the quality of HTN care delivered to adults in a primary care practice. Goals were targeted to decrease providers’ clinical inertia by improving their ability to make better diagnosis and treatment decisions after reviewing more comprehensive objective data.
Methods:  Using the Chronic Care Model in an independent primary care setting in New Hampshire an ambulatory blood pressure monitoring (ABPM), home blood pressure monitoring (HBPM), clinical practice guidelines, and patient and provider education were used to improve the detection and management of hypertension.  Patients were followed over two to three visits including an initial visit for ABPM set-up and up to two subsequent HTN follow-up visits.  
Results/Interpretations: One hundred percent of patients who underwent successful ABPM had their HTN status assessed and those with uncontrolled HTN had changes made to their medications to improve control.  The percentage of patients with uncontrolled HTN decreased by more than half at visit two (44.7%) compared with visit three (20%), which was statistically significantly different, t (58) = 2.25, p = 0.028, 95% CI [0.027, 0.466].
Implications:  QI projects addressing provider, system, and patient barriers may be effective at overcoming the barrier of providers’ clinical inertia and improving some patients’ self-management of their disease resulting in improved HTN control.  
Keywords: ambulatory blood pressure monitoring, chronic care model, clinical inertia, home blood pressure monitoring, hypertension, practice guideline, primary care, self-efficacy
Fast longitudinal beam dynamics optimization in x-ray FEL linear accelerators
Creators: name: Qiang, Ji
Publisher: name: arXiv
Year: 2019
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: A high peak current, flat longitudinal phase space electron beam is desirable for efficient x-ray free electron laser (FEL) radiation in next generation light sources. To attain such a beam requires the extensive design of the linear accelerator (linac) including both linear and nonlinear effects. In this paper, we propose a lumped longitudinal beam dynamics model for fast optimization of the electron beam longitudinal phase space through the accelerator. This model is much faster than available tracking programs and also shows good agreement with the fully three-dimensional element-by-element multi-particle simulations. We applied this model in a parallel multi-objective differential evolution optimization program to an existing LCLS-II superconducting linac design and obtained an optimal solution with significantly higher core peak current than the original design.
Additional file 10 of Characterisation of the enzyme transport path between shipworms and their bacterial symbionts
Creators: name: Pesante, Giovanna
name: Sabbadin, Federico
name: Elias, Luisa
name: Steele-King, Clare
name: Shipway, J. Reuben
name: Dowle, Adam A.
name: Li, Yi
name: Busse-Wicher, Marta
name: Dupree, Paul
name: Besser, Katrin
name: Cragg, Simon M.
name: Bruce, Neil C.
name: McQueen-Mason, Simon J.
Publisher: name: figshare
Year: 2021
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 10: Table S4. Details of the proteins for which heterologous recombinant expression from symbionts cDNA was successful. The annotation was performed against the NCBI non-redundant database, the signal peptides were identified with the Signal P4.1 server and the CAZy domains were searched using dbCAN. Dis. bonds = disulfide bonds. File format .DOCX.
QCD Corrections to Electroweak Vector Boson Scattering at Small Scattering Angles
Creators: name: Peters, Krisztian
name: Vacca, Gian Paolo
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We investigate the role of a certain class of QCD corrections to electroweak vector boson scattering at small scattering angles and large energies. These are present since, from the perturbative analysis, the vector bosons may dissociate into quark-antiquark pairs giving rise to colour dipoles interacting through gluon exchanges. After the computation of the vector boson impact factors, we present expressions for the lowest order QCD scattering amplitude and for the leading logarithmic BFKL amplitude. Particularly we discuss numerical results for the process $γγ\to ZZ$. The QCD corrections to the cross section resulting from the interference with the electroweak ones are estimated and compared with the leading pure electroweak part. Corrections resulting from the leading log BFKL amplitude are of the order of few percent already at the $0.5 - 1$ TeV energy range.
description: 21 pages,9 figures, discussion on the helicity-flip impact factors added, typos corrected
Screening for Depression in the Primary Care Clinics in Saudi Arabia
Creators: name: Taleb, Hadi
Publisher: name: University of Massachusetts Amherst
Year: 2016

Background: Depression has a significant morbidity rate internationally and it is associated with poor health status and reduced quality of life in the community. A lack of identification of depression on primary care practices has been associated with lack of screening tools or specific protocols and lack of adherence to practice-level guidelines and depression screening implementation. Purpose: This project assessed whether primary care medical providers in Saudi Arabia were able to recognize the symptoms of depression in their patients and tested a new protocol and tools to address the issue. This study focused on the population that was visiting a large Healthcare Medical Facility in Dhahran, Saudi Arabia. Results: 150 patients were screened. The results indicated that up to 34.6 % of the patients turned out to be positive with majority being women of reproductive age. It also indicates that majority of the people in need of these services are women. Conclusion: This has confirmed the need for such a screening tool in primary health care facilities in Saudi Arabia. The results further indicate that early diagnosis of depression by such facilities will lead to improved management, increase quality of life, and potentially save resources for the patients who would have been referred, making this project very timely and relevant.
Figure S1: miRNA-normalized abundance of TE small RNAs from Arabidopsis RNA polymerase IV generates 21–22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes
Creators: name: Panda, Kaushik
name: McCue, Andrea D.
name: R. Keith Slotkin
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: Plant Biology
subject: 60408 Genomics

description: Reads per million (RPM) sequenced miRNAs of TE siRNAs in wt Col and pol IV mutant plants in three different tissue types - seedling, inflorescence and pollen. For each tissue type Pol IV-independent miRNAs were determined by comparing sRNA abundances between wt Col and pol IV mutant plants. The counts of Pol IV-independent miRNAs were then used to normalize tissue specific accumulation of TE siRNAs.
Arabidopsis tRNA-derived fragments as potential modulators of translation
Creators: name: Lalande, Stéphanie
name: Merret, Rémy
name: Salinas-Giegé, Thalia
name: Drouard, Laurence
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Developmental Biology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: Plant Biology
subject: 60506 Virology

description: Transfer RNA-derived fragments (tRFs) exist in all branches of life. They are involved in RNA degradation, regulation of gene expression, ribosome biogenesis. In archaebacteria, kinetoplastid, yeast, and human cells, they were also shown to regulate translation. In Arabidopsis, the tRFs population fluctuates under developmental or environmental conditions but their functions are yet poorly understood. Here, we show that populations of long (30–35 nt) or short (19–25 nt) tRFs produced from Arabidopsis tRNAs can inhibit in vitro translation of a reporter gene. Analysing a series of oligoribonucleotides mimicking natural tRFs, we demonstrate that only a limited set of tRFs possess the ability to affect protein synthesis. Out of a dozen of tRFs, only two deriving from tRNAAla(AGC) and tRNAAsn(GUU) strongly attenuate translation in vitro. Contrary to human tRF(Ala), the 4 Gs present at the 5ʹ extremity of Arabidopsis tRF(Ala) are not implicated in this inhibition while the G18 and G19 residues are essential. Protein synthesis inhibition by tRFs does not require complementarity with the translated mRNA but, having the capability to be associated with polyribosomes, tRFs likely act as general modulation factors of the translation process in plants.
Collision geometry scaling of Au+Au pseudorapidity density from sqrt(s_NN) = 19.6 to 200 GeV
Creators: name: Back, B. B.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: The centrality dependence of the midrapidity charged particle multiplicity in Au+Au collisions at sqrt(s_NN) = 19.6 and 200 GeV is presented. Within a simple model, the fraction of hard (scaling with number of binary collisions) to soft (scaling with number of participant pairs) interactions is consistent with a value of x = 0.13 +/- 0.01(stat) +/- 0.05(syst) at both energies. The experimental results at both energies, scaled by inelastic p(pbar)+p collision data, agree within systematic errors. The ratio of the data was found not to depend on centrality over the studied range and yields a simple linear scale factor of R_(200/19.6) = 2.03 +/- 0.02(stat) +/- 0.05(syst).
description: 5 pages, 4 figures, submitted to PRC-RC
Figure S3: Development expression pattern of factors involved in Pol IV-dependent sRNA production from Arabidopsis RNA polymerase IV generates 21–22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes
Creators: name: Panda, Kaushik
name: McCue, Andrea D.
name: R. Keith Slotkin
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: Plant Biology
subject: 60408 Genomics

description: RPKM expression values of various proteins involved in Pol IV-dependent sRNA production of Pol IV-dependent RNA-directed DNA methylation (RdDM). Data were accessed from eFP-Seq Browser (42). Klepikova et al's data (41) were used to show expression in differential developmental time points. Green box shows the inflorescence tissue used for almost all data reported in this study (unless specified otherwise). Red box highlights the pollen developmental time during which multiple factors are less expressed.
Facilitating your article searches with the Unpaywall plugin (15-minute presentation)
Creators: name: Muller, Floriane
name: Santos, Anouk
Publisher: name: Université de Genève
Year: 2023
Subjects: scientific articles
access to articles
paywall
open access

description: This is the slide deck of the rendez-vous de l'information scientifique organised by the University of Geneva Library on October 25, 2023 and devoted to unpaywall. 
Objective: To access scientific articles that are normally subject to a fee, free of charge and in one click, using the Unpaywall plugin
Description: Despite the numerous subscriptions offered by the Library, some articles remain inaccessible unless you pay to access them. Some tools such as unpaywall allow to quickly locate an accessible version of the article if it is present elsewhere on the web (for instance on an institutional publication repository), and to immediately access the pdf in one click.
Contents:

presentation of the tool
demonstration of how it works
details on the types of article (versions) obtained through this tool
mention of alternatives: other similar tools, library services
title: Dana :
title: Directrices para la ejecución del examen de la distinción, la homogeneidad y la estabilidad.
titleType: Subtitle
Creators: name: International Union For The Protection Of New Varieties Of Plants,
Publisher: name: International Union for the Protection of New Varieties of Plants,
Year: 0
Subjects: Plants
New Varieties of Plants
Foxtail Millet

description: La finalidad de estas directrices (“directrices de examen”) es elaborar los principios que figuran en la Introducción General (documento TG/1/3) y sus documentos TGP conexos, con objeto de que sirvan de orientación práctica y detallada para el examen armonizado de la distinción, homogeneidad y estabilidad (DHE) y en particular, para identificar los caracteres apropiados para el examen DHE y producir descripciones armonizadas de variedades.
Holographic quantum singularity
Creators: name: Tanaka, Izumi
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this study, we have analytically considered a dislocation in three-dimensional Weyl semimetal and its holographic model. A quantum singularity that originated in the dislocation creates a defect in momentum space. This defect causes topologically protected zero-energy mode bound to the quantum singularity. The defect has two aspects: First, it prevents the formation of a topological winding number. Second, it provides another topological number around itself. The gauge field adjusts these effects of the defect, and it is possible to control the phase transition. Further, from holographic duality, the quantum singularity is mapped onto a domain wall of classical gravity. We find that the domain wall causes a violation of gauge invariance of bulk spacetime. We also demonstrate that the quantum singularity is comparable to the anomaly from the gauge invariance breaking of the bulk spacetime, and holographic entanglement entropy reveals the information encoded in the defect of momentum space.
description: 16 pages, 4 figures
Design and Calibration of a Cryogenic Blackbody Calibrator at Centimeter Wavelengths
Creators: name: Kogut, A.
name: Wollack, E.
name: Fixsen, D. J.
name: Limon, M.
name: Mirel, P.
name: Levin, S.
name: Seiffert, M.
name: Lubin, P. M.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We describe the design and calibration of an external cryogenic blackbody calibrator used for the first two flights of the Absolute Radiometer for Cosmology, Astrophysics, and Diffuse Emission (ARCADE) instrument. The calibrator consists of a microwave absorber weakly coupled to a superfluid liquid helium bath. Half-wave corrugations viewed 30 deg off axis reduce the return loss below -35 dB. Ruthenium oxide resistive thermometers embedded within the absorber monitor the temperature across the face of the calibrator. The thermal calibration transfers the calibration of a reference thermometer to the flight thermometers using the flight thermometer readout system. Data taken near the superfluid transition in 8 independent calibrations 4 years apart agree within 0.3 mK, providing an independent verification of the thermometer calibration at temperatures near that of the cosmic microwave background.
description: 5 pages including 5 figures. Submitted to Review of Scientific Instruments
Facilitating your article searches with the Unpaywall plugin (15-minute presentation)
Creators: name: Muller, Floriane
name: Santos, Anouk
Publisher: name: Université de Genève
Year: 2024
Subjects: scientific articles
access to articles
paywall
open access

description: This is the slide deck of the rendez-vous de l'information scientifique organised by the University of Geneva Library on October 24, 2024 and devoted to unpaywall. 

Objective: To access scientific articles that are normally subject to a fee, free of charge and in one click, using the Unpaywall plugin

Description: Despite the numerous subscriptions offered by the Library, some articles remain inaccessible unless you pay to access them. Some tools such as unpaywall allow to quickly locate an accessible version of the article if it is present elsewhere on the web (for instance on an institutional publication repository), and to immediately access the pdf in one click.

Contents:

presentation of the tool

demonstration of how it works

details on the types of article (versions) obtained through this tool

mention of alternatives: other similar tools, library services
Microscopic calculation of inelastic proton scattering off $^{18}$O, $^{10}$Be, $^{12}$Be, and $^{16}$C for study of neutron excitation in neutron-rich nuclei
Creators: name: Kanada-En'yo, Yoshiko
name: Ogata, Kazuyuki
Publisher: name: arXiv
Year: 2019
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The microscopic coupled-channel calculation of inelastic proton scattering is performed for the study of neutron excitations in $2^+_1$ states of $^{18}$O, $^{10}$Be, $^{12}$Be, and $^{16}$C. Proton-nucleus potentials in the coupled-channel calculation are microscopically derived by folding the Melbourne $g$-matrix $NN$ interaction with matter and transition densities of target nuclei obtained by the structure model calculation of antisymmetrized molecular dynamics. The calculated result reasonably reproduces the elastic and inelastic proton scattering cross sections, and supports the dominant contribution of neutron in the $2^+_1$ excitation of $^{12}$Be and $^{16}$C as well as $^{18}$O. Sensitivity of the inelastic scattering cross sections to the neutron transition density is discussed. The exotic feature of the neutron transition density with the amplitude in the outer region in $^{12}$Be and $^{16}$C is focused.
description: 15 pages, 13 figures
Scholia and Glosses on the Heavenly Ladder of John Climacus and Associated Texts in Sinai gr. 417
Creators: name: Duffy, John M.
Publisher: name: Parekbolai. An Electronic Journal for Byzantine Literature
Year: 2025
Subjects: John Climacus, scholia, glosses, monastic scholarship, Elias of Crete, Matthew Rader

description: This study offers the first edition of the rich collection of scholia and glosses on the Heavenly Ladder of John Climacus preserved in the 10th cent. manuscript Sinaiticus gr. 417. The carefully prepared and beautifully written book contains two sets of scholarly comments in the margins copied by two distinct hands: those written by the main scribe in vermillion ink and the second group added, not much later, in black ink by a copyist using a cursive script. A fairly large number of the scholia from Sin. 417 later found their way into both the (unpublished) 12th cent. commentary on the Ladder by Elias of Crete and the scholia published from a 14th cent. manuscript by Matthew Rader in 1633
 
description: Parekbolai. An Electronic Journal for Byzantine Literature, Vol 15 (2025)
Improving HPV Vaccination Initiation and Completion Rates: A QI Project
Creators: name: Varughese, Princy M
Publisher: name: University of Massachusetts Amherst
Year: 2016

Human papillomavirus (HPV) is a common sexually transmitted infection in the United States and is the cause of most cervical cancers in women, as well as anogenital cancers, oropharyngeal cancer, and genital warts in both men and women (Centers for Disease Control [CDC], 2014b). The HPV vaccine is recommended for preteen girls and boys to protect against HPV infections (CDC, 2011). In line with the goal of Healthy People 2020, the purpose of this evidence-based quality improvement (QI) project was to implement a text message reminder system, and calculate the completion rate of the 3-dose HPV vaccination series among adolescents in a pediatric clinic in a small city in Texas. The results were compared to the vaccination rates from a previously used reminder system. The project was of a single-group. pre-test–post-test design. Participants were adolescents aged 9–18 years who had begun, or were set to begin, the 3-dose HPV vaccine series during the project implementation period (October 2015–April 2016). Data from a random review of 100 charts of adolescents reminded using the prior system (prior to implementation) for the same vaccine appointments were used for comparison with the new reminder system data. Enrollees received up to 3 text message reminders for each appointment. They were surveyed to evaluate their preference of a reminder system. Using data from the prior system (n = 100), 11% of adolescents completed the three-dose HPV vaccine series compared to 46.9% from the text messaging system group (n = 49). Both groups showed a better completion rate among females. Based on surveys, 24 (80%) were in favor of text message reminders. This project shows that text message reminders offer an effective method of sending appointment reminders to increase the initiation and completion rates of the HPV vaccine series.
tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal-immune-activation autism model
Creators: name: Zhangli Su
name: Frost, Elizabeth L.
name: Lammert, Catherine R.
name: Przanowska, Roza K.
name: Lukens, John R.
name: Anindya Dutta
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: tRNA-derived small fragments (tRFs) and tRNA halves have emerging functions in different biological pathways, such as regulating gene expression, protein translation, retrotransposon activity, transgenerational epigenetic changes and response to environmental stress. However, small RNAs like tRFs and microRNAs in the maternal-fetal interface during gestation have not been studied extensively. Here we investigated the small RNA composition of mouse placenta/decidua, which represents the interface where the mother communicates with the foetus, to determine whether there are specific differences in tRFs and microRNAs during fetal development and in response to maternal immune activation (MIA). Global tRF expression pattern, just like microRNAs, can distinguish tissue types among placenta/decidua, fetal brain and fetal liver. In particular, 5ʹ tRNA halves from tRNAGly, tRNAGlu, tRNAVal and tRNALys are abundantly expressed in the normal mouse placenta/decidua. Moreover, tRF and microRNA levels in the maternal-fetal interface change dynamically over the course of embryonic development. To see if stress alters non-coding RNA expression at the maternal-fetal interface, we treated pregnant mice with a viral infection mimetic, which has been shown to promote autism-related phenotypes in the offspring. Acute changes in the levels of specific tRFs and microRNAs were observed 3–6 h after MIA and are suppressed thereafter. A group of 5ʹ tRNA halves is down-regulated by MIA, whereas a group of 18-nucleotide tRF-3a is up-regulated. In conclusion, tRFs show tissue-specificity, developmental changes and acute response to environmental stress, opening the possibility of them having a role in the fetal response to MIA.
Additional file 3 of The obesity paradox and hypoglycemia in critically ill patients
Creators: name: Plečko, Drago
name: Bennett, Nicolas
name: Mårtensson, Johan
name: Bellomo, Rinaldo
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 3. Missingness of key physiological parameters across BMI groups in the first day of ICU admission (table). A tabular summary of missingness of creatinine, lactate, bilirubin, platelets, PaO2/FiO2 ratio, Mean Arterial Pressure, GCS and glucose.
Facilitating your article searches with the Unpaywall plugin (15-minute presentation)
Creators: name: Muller, Floriane
name: Santos, Anouk
Publisher: name: Zenodo
Year: 2023
Subjects: scientific articles
access to articles
paywall
open access

description: This is the slide deck of the rendez-vous de l'information scientifique organised by the University of Geneva Library on April 24, 2023 and devoted to unpaywall. Please note that this presentation has been offered before, in French and in English, but slides where then not uploaded to Zenodo. Objective: To access scientific articles that are normally subject to a fee, free of charge and in one click, using the Unpaywall plugin Description: Despite the numerous subscriptions offered by the Library, some articles remain inaccessible unless you pay to access them. Some tools such as unpaywall allow to quickly locate an accessible version of the article if it is present elsewhere on the web (for instance on an institutional publication repository), and to immediately access the pdf in one click. Contents: presentation of the tool demonstration of how it works details on the types of article (versions) obtained through this tool mention of alternatives: other similar tools, library services
A lattice theory for low energy fermions at finite chemical potential
Creators: name: Chen, Jiunn-Wei
name: Kaplan, David B.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Nuclear Theory (nucl-th)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We construct a lattice theory describing a system of interacting nonrelativistic spin s=1/2 fermions at nonzero chemical potential. The theory is applicable whenever the interparticle separation is large compared to the range of the two-body potential, and does not suffer from a sign problem. In particular, the theory could be useful in studying the thermodynamic limit of fermion systems for which the scattering length is much larger than the interparticle spacing, with applications to realistic atomic systems and dilute neutron gases.
description: Revised introduction, several typos fixed. Conforms to version accepted for publication in Phys. Rev. Lett