cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
IntroUNET: Identifying introgressed alleles via semantic segmentation
Creators: name: Flagel, Lex
name: Ray, Dylan D.
name: Schrider, Daniel R.
Publisher: name: Public Library of Science
Year: 2024

description: A growing body of evidence suggests that gene flow between closely related species is a widespread phenomenon. Alleles that introgress from one species into a close relative are typically neutral or deleterious, but sometimes confer a significant fitness advantage. Given the potential relevance to speciation and adaptation, numerous methods have therefore been devised to identify regions of the genome that have experienced introgression. Recently, supervised machine learning approaches have been shown to be highly effective for detecting introgression. One especially promising approach is to treat population genetic inference as an image classification problem, and feed an image representation of a population genetic alignment as input to a deep neural network that distinguishes among evolutionary models (i.e. introgression or no introgression). However, if we wish to investigate the full extent and fitness effects of introgression, merely identifying genomic regions in a population genetic alignment that harbor introgressed loci is insufficient—ideally we would be able to infer precisely which individuals have introgressed material and at which positions in the genome. Here we adapt a deep learning algorithm for semantic segmentation, the task of correctly identifying the type of object to which each individual pixel in an image belongs, to the task of identifying introgressed alleles. Our trained neural network is thus able to infer, for each individual in a two-population alignment, which of those individual’s alleles were introgressed from the other population. We use simulated data to show that this approach is highly accurate, and that it can be readily extended to identify alleles that are introgressed from an unsampled “ghost” population, performing comparably to a supervised learning method tailored specifically to that task. Finally, we apply this method to data from Drosophila, showing that it is able to accurately recover introgressed haplotypes from real data. This analysis reveals that introgressed alleles are typically confined to lower frequencies within genic regions, suggestive of purifying selection, but are found at much higher frequencies in a region previously shown to be affected by adaptive introgression. Our method’s success in recovering introgressed haplotypes in challenging real-world scenarios underscores the utility of deep learning approaches for making richer evolutionary inferences from genomic data.
Australian Journal of Humanities and Islamic Studies Researh (Vol1, Issue 1)
Creators: name: Musharraf, Muhammad Nabeel
Publisher: name: figshare
Year: 2016
Subjects: Religious Studies
History
Ethnic Studies

description: Australian Journal of Humanities and Islamic Studies Research (AJHISR)
Published by: Australian Islamic LibraryVolume information: Vol1, Issue 1 (Jul-Dec-2015)
Language access differentially alters functional connectivity during emotion perception across cultures
Creators: name: Leshin, Joseph
name: Carter, Maleah J.
name: Doyle, Cameron M.
name: Lindquist, Kristen A.
Publisher: name: Frontiers
Year: 2024

description: Introduction It is often assumed that the ability to recognize the emotions of others is reflexive and automatic, driven only by observable facial muscle configurations. However, research suggests that accumulated emotion concept knowledge shapes the way people perceive the emotional meaning of others’ facial muscle movements. Cultural upbringing can shape an individual’s concept knowledge, such as expectations about which facial muscle configurations convey anger, disgust, or sadness. Additionally, growing evidence suggests that access to emotion category words, such as “anger,” facilitates access to such emotion concept knowledge and in turn facilitates emotion perception. Methods To investigate the impact of cultural influence and emotion concept accessibility on emotion perception, participants from two cultural groups (Chinese and White Americans) completed a functional magnetic resonance imaging scanning session to assess functional connectivity between brain regions during emotion perception. Across four blocks, participants were primed with either English emotion category words (“anger,” “disgust”) or control text (XXXXXX) before viewing images of White American actors posing facial muscle configurations that are stereotypical of anger and disgust in the United States. Results We found that when primed with “disgust” versus control text prior to seeing disgusted facial expressions, Chinese participants showed a significant decrease in functional connectivity between a region associated with semantic retrieval (the inferior frontal gyrus) and regions associated with semantic processing, visual perception, and social cognition. Priming the word “anger” did not impact functional connectivity for Chinese participants relative to control text, and priming neither “disgust” nor “anger” impacted functional connectivity for White American participants. Discussion These findings provide preliminary evidence that emotion concept accessibility differentially impacts perception based on participants’ cultural background.
Low-cost, compact, multi-purpose SLR system, Omni-SLR
Creators: name: Otsubo, Toshimichi
name: Araki, Hiroshi
name: Yokota, Yusuke
name: Kobayashi, Mihoko
name: Kouno, Kenji
name: Matsumoto, Takehiro
name: Nakajima, Junichi
name: Kensuke, Kokado
name: Aoyama, Yuichi
Publisher: name: Zenodo
Year: 2024
Subjects: Satellite Laser Ranging
Space Geodesy

description: We have designed and integrated a very minimum system for SLR, called Omni-SLR, aiming at a better and denser laser tracking network.  It is significantly small-size and low-cost in contrast to the existing SLR stations.  We have finished testing its core components such as a laser, a timer and a telescope mount, and we are currently assembling these components and developing software.  It is going to be installed and tested at the Ishioka Geodetic Station in 2024.  This project is linked with airbourne/satellite optical communications and optical time transfer where high precision tracking is essential.  The deployment to the Syowa Station, Antarctica, is also under consideration.
Liquid application dosing alters the physiology of air-liquid interface (ALI) primary human bronchial epithelial cell/lung fibroblast co-cultures and in vitro testing relevant endpoints
Creators: name: Martin, Elizabeth M.
name: Mallek, Nicholas M.
name: Dailey, Lisa A.
name: McCullough, Shaun D.
Publisher: name: Frontiers
Year: 2024

description: Differentiated primary human bronchial epithelial cell (dpHBEC) cultures grown under air-liquid interface (ALI) conditions exhibit key features of the human respiratory tract and are thus critical for respiratory research as well as efficacy and toxicity testing of inhaled substances (e.g., consumer products, industrial chemicals, and pharmaceuticals). Many inhalable substances (e.g., particles, aerosols, hydrophobic substances, reactive substances) have physiochemical properties that challenge their evaluation under ALI conditions in vitro. Evaluation of the effects of these methodologically challenging chemicals (MCCs) in vitro is typically conducted by “liquid application,” involving the direct application of a solution containing the test substance to the apical, air-exposed surface of dpHBEC-ALI cultures. We report that the application of liquid to the apical surface of a dpHBEC-ALI co-culture model results in significant reprogramming of the dpHBEC transcriptome and biological pathway activity, alternative regulation of cellular signaling pathways, increased secretion of pro-inflammatory cytokines and growth factors, and decreased epithelial barrier integrity. Given the prevalence of liquid application in the delivery of test substances to ALI systems, understanding its effects provides critical infrastructure for the use of in vitro systems in respiratory research as well as in the safety and efficacy testing of inhalable substances.
Davidson_Curtis_FinalProjectSubmission.pdf
Creators: name: Davidson, Andrew
Publisher: name: figshare
Year: 2018
Subjects: subject: 90302 Biomechanical Engineering
subject: FOS: Medical engineering

description: Essential Tremor (ET) is one of the most common movement disorders with millions affected in the US. Currently there are two main treatment options which are pharmaceuticals and deep brain stimulation (DBS). Pharmaceuticals are limited in their efficacy and DBS is highly invasive. Surprisingly, there has been very little work in developing assistive and rehabilitative devices for ET despite success in other movement related neurological disorders. A main obstacle to developing such devices is that characteristics such as where ET originates and how it propagates throughout the arm are unknown. The Neuromechanics Research Group at BYU is working to characterize ET by developing a 7 degree of freedom (DOF) linearized dynamic model of the arm, and by collecting ET patient muscle activity and joint displacement data to validate that model. To effectively model the arm, the inertia $I$, damping $D$, and stiffness $K$ of the arm for all 7 DOF must be accurate. There are currently collections of data for these parameters, but the inertia, damping, and stiffness matrices vary significantly between patients based on their physical parameters. The purpose of this work is to use optimization to improve the inertia, damping, and stiffness model impedance parameters. This is accomplished by inputting simulated ET patient joint torques and joint displacement data into a convex optimization model that returns the optimal inertia, damping, and stiffness matrices needed to complete the movement. These impedance parameters are used to calculate the corresponding optimal joint torques that occur during tremorous movement in each DOF. These torques allow for the development of a customized tremor suppression strategy for each patient, which targets the muscles that are inducing tremor.
Nucleosome conformation dictates the histone code
Creators: name: Sun Z.-W.
name: Venters B.J.
name: Musselman C.A.
name: Krajewski K.
name: Popova I.K.
name: Marunde M.R.
name: Weinzapfel E.N.
name: Taylor H.F.
name: Mukhsinova L.
name: Hall N.W.
name: Cheek M.A.
name: Keogh M.-C.
name: Novitzky K.
name: McAnarney E.T.
name: Meiners M.J.
name: Watson R.
name: Cowles M.W.
name: Fuchs H.A.
name: Burg J.M.
name: Howard S.A.
name: Onuoha U.C.
name: Gillespie Z.B.
name: Vaidya A.
Publisher: name: eLife
Year: 2024

description: Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized 'codes' that are read by specialized regions (reader domains) in chromatin-associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP: histone PTM] specificities, and thus decipher the histone code and guide epigenetic therapies. However, this has largely been done using the reductive approach of isolated reader domains and histone peptides, which cannot account for any higher-order factors. Here, we show that the [BPTF PHD finger and bromodomain: histone PTM] interaction is dependent on nucleosome context. The tandem reader selectively associates with nucleosomal H3K4me3 and H3K14ac or H3K18ac, a combinatorial engagement that despite being in cis is not predicted by peptides. This in vitro specificity of the BPTF tandem reader for PTM-defined nucleosomes is recapitulated in a cellular context. We propose that regulatable histone tail accessibility and its impact on the binding potential of reader domains necessitates we refine the 'histone code' concept and interrogate it at the nucleosome level.
Sword or Feather? The use and utility of suspended sentences in Tasmania
Creators: name: Bartels, Lorana
Publisher: name: University of Tasmania
Year: 2024

description: This thesis explores the use and utility of suspended sentences in Tasmania. Suspended sentences are currently available as a sentencing disposition in all Australian jurisdictions, but there is conflict between public and legal perceptions about the severity of the sanction, which may contribute to a lack of public confidence in the criminal justice system as a whole. The following issues are explored: How are suspended sentences used by judges and magistrates? What is the process for imposing a suspended sentence? How effective are suspended sentence as a specific deterrent or rehabilitative measure? How are breaches dealt with? The study examines the history of suspended sentences and the arguments for and against their use, as well as considering the principles and practice governing their use in Australia and overseas. In-depth interviews with Tasmanian judges and magistrates provide an invaluable source of information on judicial views on a range of issues pertaining to the use of suspended sentences. A quantitative analysis presents empirical information on the use of suspended sentences in the Supreme and Magistrates' Courts, while a qualitative analysis of sentencing remarks in the Supreme Court examines the relevance of a range of sentencing factors to the decision to suspend. The findings of a reconviction analysis are presented, indicating that suspended sentences may be an effective deterrent. Finally, a breach analysis examines offending conduct in breach of a suspended sentence, explores prosecution practices in respect of breaches and analyses judicial sentencing remarks in breach cases. The conclusion reviews the key findings and discusses how they support the main arguments for and against suspended sentences. The practical and policy implications of my findings are also considered. My research is not only of significance for Tasmania, but also has relevance and resonance for the Australian and international use of suspended sentences and will inform broader discussions about the utility of this sentencing option.
The first bismuth(II)–rhodium(II) oxypyridinate paddlewheel complexes: synthesis and structural characterization
Creators: name: Sunderland, Travis L.
name: Berry, John F.
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Marine Biology

description: The first examples of heterobimetallic Bi–Rh bonded complexes supported by heteroatom ligands have been synthesized and structurally characterized. BiRh(hp)4 (1) and BiRh(chp)4 (2) each adopt a [4,0]O polar geometry with Bi–Rh bond distances of 2.5409(4) and 2.5848(1) Å, respectively (hp = 2-hydroxypyridine, chp = 6-chloro-2-hydroxypyridine). The relative oxophilicity of bismuth compared to rhodium clearly influences the selective formation of the [4,0]O arrangement, even for the sterically crowded 2.
Prefusion-stabilized SARS-CoV-2 S2-only antigen provides protection against SARS-CoV-2 challenge
Creators: name: Hsieh C.-L.
name: Leist S.R.
name: Jangra R.K.
name: Zhou L.
name: Miller E.H.
name: West A.
name: Chandran K.
name: Baric R.S.
name: Schisler J.C.
name: Wang A.
name: McLellan J.S.
name: Powers J.M.
name: Zweigart M.R.
name: Tse A.L.
Publisher: name: Nature Research
Year: 2024

description: Ever-evolving SARS-CoV-2 variants of concern (VOCs) have diminished the effectiveness of therapeutic antibodies and vaccines. Developing a coronavirus vaccine that offers a greater breadth of protection against current and future VOCs would eliminate the need to reformulate COVID-19 vaccines. Here, we rationally engineer the sequence-conserved S2 subunit of the SARS-CoV-2 spike protein and characterize the resulting S2-only antigens. Structural studies demonstrate that the introduction of interprotomer disulfide bonds can lock S2 in prefusion trimers, although the apex samples a continuum of conformations between open and closed states. Immunization with prefusion-stabilized S2 constructs elicits broadly neutralizing responses against several sarbecoviruses and protects female BALB/c mice from mouse-adapted SARS-CoV-2 lethal challenge and partially protects female BALB/c mice from mouse-adapted SARS-CoV lethal challenge. These engineering and immunogenicity results should inform the development of next-generation pan-coronavirus therapeutics and vaccines.
Racial and ethnic differences in the degree of participation and retention in a decentralized cohort study of COVID-19 immunization in patients with inflammatory bowel diseases
Creators: name: Firestine A.M.
name: Craig R.
name: Boccieri M.
name: Kappelman M.D.
name: Long M.D.
name: Zhang X.
Publisher: name: Cambridge University Press
Year: 2024

description: Introduction: Disparities in the recruitment of minority populations in research are well-documented. However, the degree of participation and retention of minorities following enrollment is less known, particularly in decentralized studies. Although decentralized clinical research methods may allow researchers to engage broader study populations with less participation burden, they may present different retention challenges. To evaluate racial and ethnic differences in the degree of participation after enrollment in a decentralized study, we analyzed data from a cohort of patients with inflammatory bowel diseases following COVID-19 immunization. Methods: We compared by race and ethnicity the following post-enrollment participation metrics: response to > 50% of follow-up surveys, donation of a blood sample for antibody testing, consent to use of bio samples for future research, and withdrawal prior to study completion. Results: Overall, we observed higher levels of post-enrollment study participation among non-Hispanic White (NHW) participants as compared to Black or Hispanic participants: 95% of NHW participants completed follow-up versus 87% of Black participants and 91% of Hispanic participants, 73% of NHW participants provided bio samples versus 64% Black participants and 67% Hispanic participants, and 65% of NHW participants provided consent for future research versus 62% of Black participants and 52% of Hispanic participants. Conclusions: Our findings demonstrate that the degree of study participation after enrollment in this decentralized study differed by race and ethnicity, indicating that attention to diversity, equity, and inclusion is needed not only in clinical research recruitment but also throughout study administration.
Critical Success Factors of Innovative Lithuanian Life Sciences Startups
Creators: name: Dumbrovas, Karolis
Publisher: name: figshare
Year: 2016
Subjects: subject: 150399 Business and Management not elsewhere classified
subject: FOS: Economics and business

description: The purpose of this thesis is to identify the critical success factors of innovative Lithuanian life sciences start-ups that drives them to commercial success. Literature review identified factors that are critical to the success of technology (or knowledge) intensive start-ups in various ecosystems throughout the World, although there was no specific research made on start-ups’ critical success factors in the field of life sciences. Qualitative research was used to collect empirical data about innovative Lithuanian life sciences start-ups, which are developing new technologies, products or services, generating revenue, have more than one employee and are not experiencing any major financial difficulties. The findings of the research revealed that Lithuanian life sciences start-ups correspond to the global tendencies and same factors affect their operations as any other technology (or knowledge) intensive start-up, however start-ups are heavily dependent on the national and European Union funding opportunities.
gasoline_multirotor.pdf
Creators: name: Briggs, Dallin
name: Ellingson, Gary
Publisher: name: figshare
Year: 2016
Subjects: subject: 90602 Control Systems, Robotics and Automation
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Currently, there are numerous multirotor unmanned aerial vehicles (UAVs) that are available to commercial operators and to consumers that are capable of lifting small payloads for an endurance of approximately 30 minutes or less. While these current multirotors are good for short endurance missions, there are few options for larger, higher payload capacity multirotors that are able to maintain flight for longer than an hour. This paper describes the optimization process used to develop a multirotor platform that maximizes the flight time of a gasoline-fueled multirotor UAV by varying several design variables related to the power required and the aerodynamics of the model.
Simultaneous detection and quantification of multiple pathogen targets in wastewater
Creators: name: Rao, Gouthami
name: Lai, Amanda
name: Huang, Ching-Hua
name: Capone, Drew
name: Zhu, Kevin
name: Linden, Yarrow
name: Knoble, Abigail
name: Kim, Juhee
name: Brown, Joe
name: Bivins, Aaron
name: Clark, Ryan
Publisher: name: Public Library of Science
Year: 2024

description: Wastewater-based epidemiology has emerged as a critical tool for public health surveillance, building on decades of environmental surveillance work for pathogens such as poliovirus. Work to date has been limited to monitoring a single pathogen or small numbers of pathogens in targeted studies; however, few studies consider simultaneous quantitative analysis of a wide variety of pathogens, which could greatly increase the utility of wastewater surveillance. We developed a novel quantitative multi-pathogen surveillance approach (35 pathogen targets including bacteria, viruses, protozoa, and helminths) using TaqMan Array Cards (TAC) and applied the method on concentrated wastewater samples collected at four wastewater treatment plants in Atlanta, GA from February to October of 2020. From sewersheds serving approximately 2 million people, we detected a wide range of targets including many we expected to find in wastewater (e.g., enterotoxigenic E. coli and Giardia in 97% of 29 samples at stable concentrations) as well as unexpected targets including Strongyloides stercoralis (a human threadworm rarely observed in the USA). Other notable detections included SARS-CoV-2, but also several pathogen targets that are not commonly included in wastewater surveillance like Acanthamoeba spp., Balantidium coli, Entamoeba histolytica, astrovirus, norovirus, and sapovirus. Our data suggest broad utility in expanding the scope of enteric pathogen surveillance in wastewaters, with potential for application in a variety of settings where pathogen quantification in fecal waste streams can inform public health surveillance and selection of control measures to limit infections.
inertial-measurement-unit.pdf
Creators: name: Searle Vincent
Publisher: name: figshare
Year: 2016
Subjects: subject: Mechanical Engineering
subject: FOS: Mechanical engineering

description: Inertial Measurement Units (IMUs) are common sensors which output linear acceleration, angular velocity, and strength of the magnetic field. Unless calibrated, low-end IMUs lack the accuracy of a motion capture (MC) system. This paper presents a method for calibrating IMUs using a MC system to increase the accuracy of low-end IMUs. This was accomplished through gradient-free optimization in correlation with the Madgwick Filter. It will be shown that this method can produce a root mean square error of 3.63◦when compared to MC Euler angle estimations.
Synthesis of 5-Benzylamino and 5-Alkylamino-Substituted Pyrimido[4,5-c]quinoline Derivatives as CSNK2A Inhibitors with Antiviral Activity
Creators: name: Asressu, Kesatebrhan Haile
name: Moorman, Nathaniel J.
name: Wellnitz, James
name: Smith, Jeffery L.
name: Dickmander, Rebekah J.
name: Axtman, Alison D.
name: Popov, Konstantin I.
name: Willson, Timothy M.
Publisher: name: MDPI
Year: 2024

description: A series of 5-benzylamine-substituted pyrimido[4,5-c]quinoline derivatives of the CSNK2A chemical probe SGC-CK2-2 were synthesized with the goal of improving kinase inhibitor cellular potency and antiviral phenotypic activity while maintaining aqueous solubility. Among the range of analogs, those bearing electron-withdrawing (4c and 4g) or donating (4f) substituents on the benzyl ring as well as introduction of non-aromatic groups such as the cyclohexylmethyl (4t) were shown to maintain CSNK2A activity. The CSNK2A activity was also retained with N-methylation of SGC-CK2-2, but α-methyl substitution of the benzyl substituent led to a 10-fold reduction in potency. CSNK2A inhibition potency was restored with indene-based compound 4af, with activity residing in the S-enantiomer (4ag). Analogs with the highest CSNK2A potency showed good activity for inhibition of Mouse Hepatitis Virus (MHV) replication. Conformational analysis indicated that analogs with the best CSNK2A inhibition (4t, 4ac, and 4af) exhibited smaller differences between their ground state conformation and their predicted binding pose. Analogs with reduced activity (4ad, 4ae, and 4ai) required more substantial conformational changes from their ground state within the CSNK2A protein pocket.
РОЛЬ МОНАСТЫРЕЙ В РАЗВИТИИ СЛАВЯНСКОЙ ПИСЬМЕННОСТИ
Creators: name: Мухаммаджонова, Шахризода
name: Исаева, Зера
Publisher: name: Zenodo
Year: 2025

description: Статья посвящена всестороннему анализу роли и значения русских православных монастырей и монашества в историко-культурном контексте. Актуальность темы обусловлена необходимостью глубокого осмысления вклада православных монастырей в формирование и развитие национальной культуры, а также недостаточной степенью их научной проработанности в последние десятилетия.
The longitudinal association of stressful life events with depression remission among SHARP trial participants with depression and hypertension or diabetes in Malawi
Creators: name: Masiye, Jones
name: Akello, Harriet
name: Udedi, Michael
name: Hosseinipour, Mina C.
name: Dussault, Josée M.
name: Zimba, Chifundo C.
name: Pence, Brian W.
name: Gaynes, Bradley N.
name: Malava, Jullita Kenala
name: Landrum, Kelsey R.
Publisher: name: Public Library of Science
Year: 2024

description: Depressive disorders are leading contributors to morbidity in low- and middle-income countries and are particularly prevalent among people with non-communicable diseases (NCD). Stressful life events (SLEs) are risk factors for, and can help identify those at risk of, severe depressive illness requiring more aggressive treatment. Yet, research on the impact of SLEs on the trajectory of depressive symptoms among NCD patients indicated for depression treatment is lacking, especially in low resource settings. This study aims to estimate the longitudinal association of SLEs at baseline with depression remission achievement at three, six, and 12 months among adults with either hypertension or diabetes and comorbid depression identified as being eligible for depression treatment. Participants were recruited from 10 NCD clinics in Malawi from May 2019-December 2021. SLEs were measured by the Life Events Survey and depression remission was defined as achieving a Patient Health Questionaire-9 (PHQ-9) score <5 at follow-up. The study population (n = 737) consisted predominately of females aged 50 or higher with primary education and current employment. At baseline, participants reported a mean of 3.5 SLEs in the prior three months with 90% reporting ≥1 SLE. After adjustment, each additional SLE was associated with a lower probability of achieving depression remission at three months (cumulative incidence ratio (CIR) 0.94; 95% confidence interval: 0.90, 0.98, p = 0.002), six months (0.95; 0.92, 0.98, p = 0.002) and 12 months (0.96; 0.94, 0.99, p = 0.011). Re-expressed per 3-unit change, the probability of achieving depression remission at three, six, and 12 months was 0.82, 0.86, and 0.89 times lower per 3 SLEs (the median number of SLEs). Among NCD patients identified as eligible for depression treatment, recent SLEs at baseline were associated with lower probability of achieving depression remission at three, six, and 12 months. Findings suggest that interventions addressing SLEs during integrated NCD and depression care interventions (e.g., teaching and practicing SLE coping strategies) may improve success of depression treatment among adult patient populations in low-resource settings and may help identify those at risk of severe and treatment resistant depression.
Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells
Creators: name: Sarabipour S.
name: Bautch V.L.
name: Quigley K.M.
name: Kinghorn K.
name: Kovacs-Kasa A.
name: Gabhann F.M.
name: Annex B.H.
Publisher: name: Public Library of Science
Year: 2024

description: The vascular endothelial growth factor (VEGF) family of cytokines are key drivers of blood vessel growth and remodeling. These ligands act via multiple VEGF receptors (VEGFR) and co-receptors such as Neuropilin (NRP) expressed on endothelial cells. These membrane- associated receptors are not solely expressed on the cell surface, they move between the surface and intracellular locations, where they can function differently. The location of the receptor alters its ability to 'see' (access and bind to) its ligands, which regulates receptor activation; location also alters receptor exposure to subcellularly localized phosphatases, which regulates its deactivation. Thus, receptors in different subcellular locations initiate different signaling, both in terms of quantity and quality. Similarly, the local levels of co-expression of other receptors alters competition for ligands. Subcellular localization is controlled by intracellular trafficking processes, which thus control VEGFR activity; therefore, to understand VEGFR activity, we must understand receptor trafficking. Here, for the first time, we simultaneously quantify the trafficking of VEGFR1, VEGFR2, and NRP1 on the same cells-specifically human umbilical vein endothelial cells (HUVECs). We build a computational model describing the expression, interaction, and trafficking of these receptors, and use it to simulate cell culture experiments. We use new quantitative experimental data to parameterize the model, which then provides mechanistic insight into the trafficking and localization of this receptor network. We show that VEGFR2 and NRP1 trafficking is not the same on HUVECs as on non-human ECs; and we show that VEGFR1 trafficking is not the same as VEGFR2 trafficking, but rather is faster in both internalization and recycling. As a consequence, the VEGF receptors are not evenly distributed between the cell surface and intracellular locations, with a very low percentage of VEGFR1 being on the cell surface, and high levels of NRP1 on the cell surface. Our findings have implications both for the sensing of extracellular ligands and for the composition of signaling complexes at the cell surface versus inside the cell.
The first bismuth(II)–rhodium(II) oxypyridinate paddlewheel complexes: Synthesis and structural characterization
Creators: name: Sunderland, Travis Lee
name: Berry, John F.
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Marine Biology

description: The first examples of heterobimetallic Bi–Rh bonded complexes supported by heteroatom ligands have been synthesized and structurally characterized. BiRh(hp)4 (1) and BiRh(chp)4 (2) each adopt a [4,0]O polar geometry with Bi–Rh bond distances of 2.5409(4) and 2.5848(1) Å, respectively (hp = 2-hydroxypyridine, chp = 6-chloro-2-hydroxypyridine). The relative oxophilicity of bismuth compared to rhodium clearly influences the selective formation of the [4,0]O arrangement, especially for the sterically crowded 2.
starcraft-army-composition.pdf
Creators: name: Nakamoto, Teagan
name: Mathis, Tyler
Publisher: name: figshare
Year: 2016
Subjects: subject: 80201 Analysis of Algorithms and Complexity
subject: FOS: Computer and information sciences
subject: Uncategorized

description: Application of optimization techniques, including sequential quadratic programming and genetic algorithm, to StarCraft army composition and build order optimization
Using implementation mapping to refine strategies to improve implementation of an evidence-based mobile market intervention: a study protocol
Creators: name: Ammerman, Alice S.
name: Tirabassi, Jill N.
name: Canizares, Andy
name: Kasprzak, Christina M.
name: Leone, Lucia A.
name: Vermont, Leah N.
name: Lev, Samuel
name: Lally, Anne
Publisher: name: Frontiers
Year: 2024

description: Objectives The Veggie Van model is a mobile market model that is efficacious in increasing fruit and vegetable consumption for lower-income participants. The model is currently being evaluated for its effectiveness in a multi-state trial. Preliminary implementation data, collected through process measures surveys and implementation interviews, indicate that there are several barriers to implementation among partner organizations and implementation fidelity to the Veggie Van model was low. Consideration and planning for implementation ought to occur early and often throughout the research process order to ensure Veggie Van model effectiveness. This paper describes the step-by-step process for creating strategies to enhance implementation of Veggie Van model components. Methods Implementation mapping is a systematic process to develop implementation strategies through engagement with key stakeholders. We conducted a series of interviews (n = 31 representatives) with partner organizations (n = 8) to identify facilitators and barriers to Veggie Van model implementation. We then applied interview findings to an Implementation Mapping process to develop theory and practice-driven strategies to be integrated into existing implementation tools and technical assistance. Results We identified implementation outcomes (e.g., staff implement the Veggie Van model component of nutrition education with fidelity) and performance objectives (e.g., offer nutrition education, in the form of food lessons and/or food demonstrations, at least bi-weekly) to achieve them. We conducted a secondary qualitative analysis of the findings from implementation interviews with partner organizations to identify behavioral determinants (e.g., attitudinal beliefs, social support) which were combined with the performance objectives to generate change objectives (e.g., view the Veggie Van model as advantageous to an organization and communities served). To achieve the change objectives, we developed implementation strategies that would be integrated into existing Veggie Van training resources including an online toolkit, webinars and trainings, an annual mobile market conference, and technical assistance. Conclusion The development of theory and practice-driven implementation strategies will enable us to improve our implementation tools, thereby improving fidelity to the Veggie Van model among organizations and increasing the likelihood of its effectiveness. Detailing the design of a multifaceted implementation strategy using Implementation Mapping also provides a model to design similar strategies for other community-based interventions.
Viral afterlife: SARS-CoV-2 as a reservoir of immunomimetic peptides that reassemble into proinflammatory supramolecular complexes
Creators: name: Wong G.C.L.
name: Wolfgang M.C.
name: Schisler J.C.
name: Adkins J.N.
name: Yeaman M.R.
name: Weiss T.M.
name: Schepmoes A.A.
name: Nakamura Y.
name: Zhao R.
name: Mackman N.
name: Anda J.D.
name: Thurlow L.R.
name: Coady A.
name: Luo E.W.C.
name: Dokoshi T.
name: Nizet V.
name: Matsui T.
name: Gallo R.L.
name: Kulkarni N.N.
name: Lipton M.S.
name: Zhang Y.
name: Zurich R.
name: Lee H.
name: Lee M.W.
name: Chan L.C.
name: Hagan R.S.
name: Antoniak S.
name: Chen J.
name: Wang L.
name: Chen X.
name: Bharathi V.
name: Clair G.C.
name: Xu H.
name: Ursery L.T.
name: Li M.M.H.
Publisher: name: National Academy of Sciences
Year: 2024

description: It is unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to the strong but ineffective inflammatory response that characterizes severe Coronavirus disease 2019 (COVID-19), with amplified immune activation in diverse cell types, including cells without angiotensin-converting enzyme 2 receptors necessary for infection. Proteolytic degradation of SARS-CoV-2 virions is a milestone in host viral clearance, but the impact of remnant viral peptide fragments from high viral loads is not known. Here, we examine the inflammatory capacity of fragmented viral components from the perspective of supramolecular self-organization in the infected host environment. Interestingly, a machine learning analysis to SARS-CoV-2 proteome reveals sequence motifs that mimic host antimicrobial peptides (xenoAMPs), especially highly cationic human cathelicidin LL-37 capable of augmenting inflammation. Such xenoAMPs are strongly enriched in SARS-CoV-2 relative to low-pathogenicity coronaviruses. Moreover, xenoAMPs from SARS-CoV-2 but not low-pathogenicity homologs assemble double-stranded RNA (dsRNA) into nanocrystalline complexes with lattice constants commensurate with the steric size of Toll-like receptor (TLR)-3 and therefore capable of multivalent binding. Such complexes amplify cytokine secretion in diverse uninfected cell types in culture (epithelial cells, endothelial cells, keratinocytes, monocytes, and macrophages), similar to cathelicidin’s role in rheumatoid arthritis and lupus. The induced transcriptome matches well with the global gene expression pattern in COVID-19, despite using <0.3% of the viral proteome. Delivery of these complexes to uninfected mice boosts plasma interleukin-6 and CXCL1 levels as observed in COVID-19 patients.
title: “Free Like Other Freeborn People” or Just Another Form of Dependency?
title: Questioning the Situation of Manumitted Slaves in Early Modern Istanbul
titleType: AlternativeTitle
Creators: name: Wagner, Veruschka
Publisher: name: Bonn Center for Dependency and Slavery Studies
Year: 2022
Subjects: subject: Dependency and Slavery Studies
subject: Early Modern Period
subject: Ottoman Empire
subject: Istanbul
subject: Manumission
subject: Slave Agency
subject: ddc:940
subject: ddc:950

description: This paper aims to present some thoughts and research findings related to my ongoing project on Ottoman slavery and dependency. The project, entitled “Spatial and Social Mobility of Slaves from the Black Sea Region in Seventeenth-Century Istanbul,” is part of the Transottomanica project funded by the German Research Foundation (DFG). The project focuses on the mobility and agency of slaves and aims to give information about their legal and social status, their trajectories during and after enslavement, and their role in society. Based on the concept of asymmetrical dependency used by the Bonn Center for Dependency and Slavery Studies (BCDSS), my focus in this paper is on the legal and social status of slaves after their time of enslavement in terms of dependency. Drawing on entries in Istanbul-area court records of the sixteenth and the seventeenth centuries, I address the question of freedom, and present some preliminary results concerning forms of asymmetrical dependency that shaped slaves’ lives after emancipation.
Which types of social support matter for Black sexual minority men coping with internalized homophobia? Findings from a mediation analysis
Creators: name: Srivastava, Ankur
name: Hall, William J.
name: Eden, Tiffany M.
name: Dawes, Hayden C.
name: Williams, Denise Yookong
name: Matthews, Derrick D.
Publisher: name: Frontiers
Year: 2024

description: Background Minority stress theory views social support as a protective factor against the effects of minority-specific stressors like internalized homophobia (IH) on mental health in sexual minority populations. However, much of the empirical validation of this theory has been conducted within predominantly White samples, resulting in a limited understanding of how the theory applies to Black sexual minority individuals. Current examinations of social support fail to capture the nuances of how Black sexual minority men may access support systems differently, resulting in a need to investigate how social support, IH, and mental health operate for Black sexual minority men. This study examined relationships between IH, depression, and different types of social support (i.e., family, friends, Black community, gay community) using a mediation model. Methods We used data from the POWER (Promoting Our Worth Equity and Resilience) Study, which recruited Black sexual minority men at Black Pride events across six cities in the United States from 2014 to 2017, to test four mediation pathways concurrently in Stata 17. Participants (N = 4,430) completed a questionnaire assessing a variety of health and life domains, including depression symptoms, internalized homophobia, and social support. Results IH was positively associated with depression. Lower levels of family, friend, and Black community support were all positively associated with depression symptoms. Additionally, IH was positively associated with all types of support. Finally, family, friend, and Black community support partially mediated the relationship between IH and depression. Conclusions and implications Results suggest that the relationship between social support and depression is complex for Black sexual minority men. Findings suggest family support is an important factor for clinical intervention efforts targeting depression, and that gay community support systems should assess how their environments can better support Black sexual minority men. Overall, findings demonstrate the necessity of future examination of how social support functions differently within Black sexual minority communities.
balanced-steady-state-2.pdf
Creators: name: Taylor, Meredith
Publisher: name: figshare
Year: 2016
Subjects: subject: 90399 Biomedical Engineering not elsewhere classified
subject: FOS: Medical engineering
subject: 90699 Electrical and Electronic Engineering not elsewhere classified
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Balanced steady-state free precession (bSSFP) is a magnetic resonance imaging (MRI) technique where magnetic spins in the body are repeatedly excited over a short period of time to create a steady-state MRI signal. This technique provides high signal to noise ratio (SNR) in short scan times. However, the resulting signal profile is not uniform if there are inhomogeneties in the main magnetic field resulting in dark bands across the image. We can capitalize on this non-ideality and move these dark bands in subsequent images and fit a signal model to estimate tissue parameters. These parameters can help us better understand disease progression.
Overview of the PERFECOAT project and its approach and technologies
Creators: name: Wentzel, Alexander
Publisher: name: Zenodo
Year: 2024
Subjects: BioEconomy
BioBased
Paint
Coatings
Fillers
Binders
Pigments
WaterBourn

description: Presentation on paint and coating fundamentals held on 4 March 2024 in the first PERFECOAT webinar episode for yound researchers in the field of surface engineering.
Effects of Realistic Driving Profiles on the Degradation of Lithium-Ion Batteries
Creators: name: Kalk, Alexis
name: Clemens Holocher, Marc
name: Ohneseit, Sebastian
name: Kupper, Christian
name: Hiller, Marc
Publisher: name: Institute of Electrical and Electronics Engineers (IEEE)
Year: 2024
Subjects: State of Health
Realistic Driving Profile
SOH
Aging
Electrochemical impedance spectroscopy
Lithium-Ion Battery

description: Diese Studie untersucht die Alterungseigenschaften von Lithium-Ionen-Batterien unter konventionellen Zyklustests und realistischen Fahrprofiltests. Wir verwenden regelmäßige Kapazitätstests und elektrochemische Impedanzspektroskopie für eine umfassende Analyse des Gesundheitszustandes. Für diese Untersuchung haben wir handelsübliche, runde LiFePO$_4$-Zellen im Format 21700 verwendet. Die Ergebnisse zeigen einen stärkeren Kapazitätsverlust bei realistischen Fahrprofilen im Vergleich zu konventionellen Zyklen. Diese Diskrepanz deutet darauf hin, dass die Rekuperationsphasen ein Schlüsselfaktor für die beschleunigte Alterung von Lithium-Ionen-Batterien bei Elektrofahrzeugen sind. Diese Forschung unterstreicht die Bedeutung realistischer Belastungsszenarien für die Bewertung der Batterielebensdauer und kann zur Entwicklung fortschrittlicherer Batteriemanagementsysteme in Elektrofahrzeugen beitragen.
Die Entwicklung von Ämtern und Abhängigkeitsstrukturen im Frühchristentum
Creators: name: Hornung, Christian
Publisher: name: Bonn Center for Dependency and Slavery Studies
Year: 2022
Subjects: subject: Dependency and Slavery Studies
subject: Frühchristentum
subject: Ecclesiastical Dependency
subject: Syrische Didaskalie
subject: Cyprian von Karthago
subject: ddc:200
subject: ddc:230
subject: ddc:255
subject: ddc:930

description: This Working Paper provides a window on Christian Hornung’s current research as part of the Cluster of Excellence “Dependency and Slavery Studies.” His research focuses on the history of early Christian offices and institutions in the third century AD in terms of structures of asymmetrical dependency. Representative texts and authors to be analysed are the so-called Syriac Didascalia and Cyprian of Carthage. This selection of texts offers insights into the origins and theological rationales of the ecclesiastical dependency structures that developed with the emergence of different offices and lifestyles. Central to the analysis are not so much the practical aspects of how ecclesiastical offices developed, but rather processes of legitimation and derivation. The Working Paper concludes by pointing to further fields of research and current research gaps.
Pondscape: Schöneiche. (English version)
Creators: name: Mehner, Thomas
name: Mehner, Paula
name: Lemmens, Pieter
name: von Plüskow, Maria Louise
Publisher: name: Zenodo
Year: 2024
Subjects: Pondscape
Wetland
Ponds
Biodiversity
Nature-based solutions
Ecosystem services
Nature Contribution to people
Best practices

description: This Leaflet concerns the German pondscape "Schöneiche".

In the framework of the project PONDERFUL, a synthetic “leaflet” has been developed for each of thepondscapes making part of DEMO-sites implemented across Europe, Turkey and Uruguay. The main objective of the leaflets is to present a selection of science-based success stories in the implementation of pondscapes as Nature-based Solutions (NbS) for addressing societal challenges (such as climate change and biodiversity loss), and to promote the transferability of these practices elsewhere. The success stories are evidenced in this leaflet by the measurement of indicators of the NatureContribution to People, and by a cost-benefit analysis.

The leaflets were written and designed to interest and inspire professionals in land use planning andmanagement of natural areas, people active in NGOs, and also for a wider and more varied public.The information provided in the leaflet is intentionally simplified to avoid excessive jargon andscientific complexity and to remain accessible and understandable to a broad audience.