cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of Function and mechanism of MCM8 in the development and progression of colorectal cancer
Creators: name: Yu, Shaojun
name: Dai, Weixing
name: Zhao, Senlin
name: Yang, Yongzhi
name: Xu, Ye
name: Wang, Jianwei
name: Deng, Qun
name: He, Jinghu
name: Shi, Debing
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 1: Figure S1. (A) The transfection efficiencies of shMCM8 andshCtrl in HCT116 and RKO cells were evaluated through observing thefluorescence of GFP on lentivirus vector. (B) The ability of 3 shRNAs tosilence MCM8 was evaluated by qPCR. Data were shown as mean ± standarddeviation (SD). *P<0.05, **P<0.01, ***P<0.001. Figure S2. (A) The scatter plot of gene expressionprofiling in RKO cells with or without MCM8 knockdown. (B) The volcano plot ofgene expression profiling in RKO cells with or without MCM8 knockdown. Red dotsrepresent the DEGs. (C) The enrichment of the DEGs in canonical signalingpathways was analyzed by IPA. (D) The enrichment of the DEGs in IPA disease andfunction was analyzed by IPA. Figure S3. The histogram of Role of BRCA1 in DNA damage response pathway. Figure S4. (A) The transfectionefficiencies of shCtrl, shCHSY1, shMCM8+shCHSY1 in RKO cells were evaluatedthrough observing the fluorescence of GFP on lentivirus vector. (B) Theknockdown efficiencies of 3 shRNAs designed for CHSY1 knockdown were evaluatedby qPCR. Data was shown as mean ± SD. **P< 0.01. Figure S5. Knockdown ofCHSY1 deepens the impacts of MCM8 depletion on CRC. (A) The mRNA expression ofCHSY1 and MCM8 in different groups of cells was detected by qPCR. (B) Theprotein levels of CHSY1 and MCM8 in different groups of cells were detected bywestern blotting. (C) MTT assay was performed to investigate the effects ofCHSY1 knockdown or simultaneous CHSY1 and MCM8 knockdown on cell proliferation.(D) Flow cytometry was utilized to show the effects of CHSY1 knockdown orsimultaneous CHSY1 and MCM8 knockdown on cell apoptosis. (E, F) The effects ofCHSY1 knockdown or simultaneous CHSY1 and MCM8 knockdown on cell migration wereevaluated by wound-healing assay (E) and Transwell assay (F). Representativeimages were randomly selected from 3 independent experiments. Data were shownas mean ± standard deviation (SD). *P<0.05,**P<0.01, ***P<0.001. Table S1. Antibodies used in western blotting and IHC. Table S2. The target sequences andshRNA sequences. Table S3. Primersused in qPCR. Table S4. Relationshipbetween MCM8 expression and tumor characteristics in patients with colorectalcancer analyzed by Spearman rank correlation analysis.
A complete sample of bright Swift Long Gamma Ray Bursts: testing the spectral-energy correlations
Creators: name: Nava, L.
name: Salvaterra, R.
name: Ghirlanda, G.
name: Ghisellini, G.
name: Campana, S.
name: Covino, S.
name: Cusumano, G.
name: D'Avanzo, P.
name: D'Elia, V.
name: Fugazza, D.
name: Melandri, A.
name: Sbarufatti, B.
name: Vergani, S. D.
name: Tagliaferri, G.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We use a nearly complete sample of Gamma Ray Bursts (GRBs) detected by the Swift satellite to study the correlations between the spectral peak energy Ep of the prompt emission, the isotropic energetics Eiso and the isotropic luminosity Liso. This GRB sample is characterized by a high level of completeness in redshift (90%). This allows us to probe in an unbiased way the issue related to the physical origin of these correlations against selection effects. We find that one burst, GRB 061021, is an outlier to the Ep-Eiso correlation. Despite this case, we find strong Ep-Eiso and Ep-Liso correlations for the bursts of the complete sample. Their slopes, normalisations and dispersions are consistent with those found with the whole sample of bursts with measured redshift and Ep. This means that the biases present in the total sample commonly used to study these correlations do not affect their properties. Finally, we also find no evolution with redshift of the Ep-Eiso and Ep-Liso correlations.
description: MNRAS in press, 9 pages, 4 figures, 2 tables. This version matches the published version in MNRAS
Oreochromis mossambicus
Creators: name: Zainal Abidin, Danial Hariz
name: Lavoué, Sébastien
name: Mohd Abu Hassan Alshari, Norli Fauzani
name: Mohd. Nor, Siti Azizah
name: A. Rahim, Masazurah
name: Mohammed Akib, Noor Adelyna
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Perciformes
Cichlidae
Oreochromis
Oreochromis mossambicus

description: Oreochromis mossambicus (Peters, 1852) Figure 3P Material examined. MALAYSIA • 1, 103 mm TL; Kedah State, Kampung Batu Lintang, Pompang Batu Lintang; 05.624°N, 100.395°E; 19 Apr. 2019; Danial H. Zainal Abidin, Norli F.M.A.H. Alshari leg.; USMFC (47) 00005.
description: Published as part of Zainal Abidin, Danial Hariz, Lavoué, Sébastien, Mohd Abu Hassan Alshari, Norli Fauzani, Mohd. Nor, Siti Azizah, A. Rahim, Masazurah & Mohammed Akib, Noor Adelyna, 2021, Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters, pp. 601-631 in Check List 17 (2) on page 626, DOI: 10.15560/17.2.601
Rapid re-identification of human samples using portable DNA sequencing
Creators: name: Zaaijer, Sophie
name: Gordon, Assaf
name: Speyer, Daniel
name: Piccone, Robert
name: Groen, Simon Cornelis
name: Erlich, Yaniv
Publisher: name: Columbia University
Year: 2017
Subjects: subject: Cytology
subject: Genetics
subject: FOS: Biological sciences
subject: Genomics
subject: DNA fingerprinting
subject: Cell lines
subject: Computer science

description: DNA re-identification is used for a broad suite of applications, ranging from cell line authentication to forensics. However, current re-identification schemes suffer from high latency and limited access. Here, we describe a rapid, inexpensive, and portable strategy to robustly re-identify human DNA called 'MinION sketching'. MinION sketching requires as few as 3 min of sequencing and 60-300 random SNPs to re-identify a sample enabling near real-time applications of DNA re-identification. Our method capitalizes on the rapidly growing availability of genomic reference data for cell lines, tissues in biobanks, and individuals. This empowers the application of MinION sketching in research and clinical settings for periodic cell line and tissue authentication. Importantly, our method enables considerably faster and more robust cell line authentication relative to current practices and could help to minimize the amount of irreproducible research caused by mix-ups and contamination in human cell and tissue cultures.
title: Thermophoresis in Aqueous Systems
Creators: name: Pu, Di
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: Interfacial transport phenomena
subject: Thermophoresis
subject: Noncovalent interactions
subject: Electrical double layer
subject: Hydrogen bond
subject: The Fokker-Planck equation
subject: Engineering--Chemical
subject: Physics--Molecular
subject: Chemistry--Analytical

description: Thermophoretic transport of colloidal particles in aqueous media, driven by temperature gradients, plays a crucial role in applications such as separation, enrichment, and biochemical sensing. The interplay between colloid size, surface chemistry, electrolyte composition, and background temperature govern thermophoretic behavior, though inconsistencies remain in both theoretical and experimental studies. This work addresses unresolved aspects of colloid thermophoresis, focusing on the size, temperature, and surface chemistry dependencies of the Soret coefficient in aqueous solutions. A mode-coupling model within the Fokker-Planck framework was developed to describe colloid thermophoresis, capturing the contributions of both bulk and interfacial effects. The analysis indicates that, while bulk effects are independent of colloid size, interfacial effects such as electrostatic, hydration entropy, and depletion interactions exhibit distinct size dependencies. For silica microspheres, the ionic shielding effect negatively impacts the Soret coefficient because of the dissociation of terminal silanol groups at the silica-water interfaces, whereas the hydration entropy effect provides a positive contribution. In contrast, polystyrene nanoparticles show positive ionic shielding contributions driven by temperature-dependent variations in Bjerrum length, with hydration entropy interactions exerting a negative influence on the overall Soret coefficient. For protein suspensions of T4 lysozymes, it was shown that the interplay between bulk viscosity effect and interfacial interactions determined the overall Soret coefficient. Surface chemistry effects were further explored in surfactant solutions below the critical micelle concentration (CMC). Silica microspheres in non-ionic surfactants, such as Tween 20 and Triton X-100, exhibited enhanced hydration entropy interactions due to surfactant-assisted silanol dissociation. In anionic surfactant solutions, the adsorption of DS- at the solid-liquid interface governed thermophoretic behavior. For soft surfactant-laden micro-droplets, increasing droplet size with temperature amplified ionic shielding contributions but led to negative hydration entropy effects, driven by charge regulation at the liquid-liquid interface. The findings provide insight into the fundamental mechanisms driving thermophoresis in aqueous colloidal systems, offering pathways for improved separation, enrichment, and biochemical sensing in microfluidic environments.
Singular Vectors of Sums of Rectangular Random Matrices and Optimal Estimators of High-Rank Signals: The Extensive Spike Model
Creators: name: Landau, Itamar D.
name: Mel, Gabriel C.
name: Ganguli, Surya
Publisher: name: arXiv
Year: 2023
Subjects: subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Across many disciplines from neuroscience and genomics to machine learning, atmospheric science and finance, the problems of denoising large data matrices to recover signals obscured by noise, and of estimating the structure of these signals, are of fundamental importance. A key to solving these problems lies in understanding how the singular value structure of a signal is deformed by noise. This question has been thoroughly studied in the well-known spiked matrix model, in which data matrices originate from low-rank signals perturbed by additive noise, in an asymptotic limit where the size of these matrices tends to infinity but the signal rank remains finite. We first show, strikingly, that the singular value structure of large finite matrices (of size $\sim 1000$) with even moderate-rank signals, as low as $10$, is not accurately predicted by the finite-rank theory, thereby limiting the application of this theory to real data. To address these deficiencies, we analytically compute how the singular values and vectors of an arbitrary high-rank signal matrix are deformed by additive noise. We next study an asymptotic limit corresponding to an $\textit{extensive}$ spike model, in which the rank of the hidden signal is proportional to the size of the data matrix, while both tend to infinity. We map out the phase diagram of the singular value structure of the extensive spike model as a joint function of signal strength and rank. We further exploit these analytics to derive optimal rotationally invariant denoisers to recover hidden $\textit{high}$-rank signals from data, as well as optimal invariant estimators of the signal covariance structure. Overall, our results provide fundamental theory governing how high-dimensional signals are deformed by additive noise, together with practical formulas for optimal denoising and covariance estimation.
description: 25 pages, 10 figures
title: The Influence of Substrate Surface Roughness Parameters on the Frictional and Adhesive Properties of Graphene Monolayers
Creators: name: Macdonald, Malcolm Geoffrey
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: Tribology
subject: Adhesion
subject: Graphene
subject: Friction
subject: Roughness
subject: Skewness
subject: Contact Mode AFM
subject: Tapping Mode AFM
subject: Materials Science
subject: Engineering--Mechanical

description: 2D lubricating materials, such as graphene, are becoming more prevalent in micro and nanoscale technology. As this technology continues to advance and become smaller, it is likewise becoming important to understand the material properties of graphene at the micro and nano scale. As a solid lubricant, graphene is deposited onto surfaces to reduce friction between parts that rub together. Therefore, it is important to understand how substrate surface parameters, such as roughness, influence the frictional and adhesive properties of graphene. This thesis investigates load-dependent friction analysis and phase change analysis experiments using AFM on graphene, which was deposited onto silicon oxide wafers. There were four different combinations of scratched and heated silicon oxide wafers with graphene monolayers mechanically exfoliated onto them. Load-dependent friction analysis revealed that samples that had negative skewness were shown to reverse the effect that heat had on the graphene silicon substrate. A model to explain this behaviour is proposed wherein graphene on a heated substrate will conform to the shape of a valley caused by scratching the silicon substrate. As an AFM tip slides into the valley, more contact between the tip and graphene occurs, which potentially allows for more puckering between the graphene and the tip as the tip emerges from the valley. This potential puckering decreases the conformity between the graphene and the silicon. Additionally, scratched samples were shown to increase the chances that graphene monolayers would fold. Tapping mode experiments investigating substrate surface adhesion found that increased substrate surface roughness was correlated with an increase in phase change. This is thought to be caused by graphene poorly conforming to unheated samples—which will result in higher phase changes—and conforming well to heated samples—which will result in lower phase changes. Heating the samples was shown to decrease the phase change and the variance of the phase change. At higher roughness', the phase change of heated samples would also increase. This is thought to be because there may be many regions of suspended graphene between the peaks of highly rough surfaces, which result in a greater phase change measurement.
Characterization of maize producing households in Masvingo and Bikita districts in Zimbabwe
Creators: name: Shamiso Chikobvu
name: Chiputwa, Brian
name: Langyintuo, Augustine
name: Rovere, Roberto La
name: Milfred Mwangi
Publisher: name: Gates Open Research
Year: 2019

description: Characterization of maize producing households in Masvingo and Bikita districts in Zimbabwe
Revisiting Coupling Selection Rules in Heterotic Orbifold Models
Creators: name: Kobayashi, Tatsuo
name: Parameswaran, Susha L.
name: Ramos-Sanchez, Saul
name: Zavala, Ivonne
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study L-point couplings between twisted sector fields in heterotic orbifold compactifications, using conformal field theory. Selection rules provide an easy way to identify which couplings are non-vanishing. Those used in the current literature are gauge invariance, R-charge conservation and the space group selection rule, but they are not the whole story. We revive and refine a fourth selection rule, due to symmetries in the underlying torus lattice, and introduce a fifth one, due to the existence or not of classical worldsheet instanton solutions to mediate the couplings. We consider briefly the phenomenological consequences of the additional rules, in particular for recent orbifold constructions whose field content correspond to that of the MSSM. The structure of the exotic mass matrices is unaltered and many dimension-5 proton-decay operators vanish.
description: 27 pages, v2: several clarifications, matches JHEP version. v3: supercedes journal version, erratum to appear in JHEP; correction to "rule 5" equations, main ideas unchanged
Sculpting ion channel functional expression with engineered ubiquitin ligases
Creators: name: Kanner, Scott A.
name: Morgenstern, Travis James
name: Colecraft, Henry M.
Publisher: name: Columbia University
Year: 2017
Subjects: Ion channels
Ubiquitin
Calcium-dependent potassium channels
Molecular biology
Cytology

description: The functional repertoire of surface ion channels is sustained by dynamic processes of trafficking, sorting, and degradation. Dysregulation of these processes underlies diverse ion channelopathies including cardiac arrhythmias and cystic fibrosis. Ubiquitination powerfully regulates multiple steps in the channel lifecycle, yet basic mechanistic understanding is confounded by promiscuity among E3 ligase/substrate interactions and ubiquitin code complexity. Here we targeted the catalytic domain of E3 ligase, CHIP, to YFP-tagged KCNQ1 ± KCNE1 subunits with a GFP-nanobody to selectively manipulate this channel complex in heterologous cells and adult rat cardiomyocytes. Engineered CHIP enhanced KCNQ1 ubiquitination, eliminated KCNQ1 surface-density, and abolished reconstituted K+ currents without affecting protein expression. A chemo-genetic variation enabling chemical control of ubiquitination revealed KCNQ1 surface-density declined with a ~ 3.5 hr t1/2 by impaired forward trafficking. The results illustrate utility of engineered E3 ligases to elucidate mechanisms underlying ubiquitin regulation of membrane proteins, and to achieve effective post-translational functional knockdown of ion channels.
title: Avoidable Acute Care Use by Persons with Rheumatoid Arthritis: A Population-Based Study
Creators: name: Contreras, Danielle Ysabelle
Publisher: name: Arts
Year: 2025
Subjects: subject: Rheumatoid Arthritis
subject: Acute Care Use
subject: Hospitalizations
subject: Emergency Department Visits
subject: Ambulatory Care Sensitive Conditions
subject: Health Services Research
subject: Epidemiology

description: Rheumatoid Arthritis (RA) is Canada’s most common chronic inflammatory joint disease, affecting 1.2% of Canadians 16 years and older, and is more prevalent among females. People with RA have an increased risk of mortality compared to the general population due to comorbidities such as cardiovascular disease, depression, and osteoporosis. The presence of these comorbidities can lead to increased healthcare utilization, including hospitalizations. Most healthcare interactions for treating and monitoring RA occur in the outpatient setting, usually with a family physician or a rheumatologist. Ambulatory Care Sensitive Conditions (ACSCs) were thus derived as a list of conditions where appropriate ambulatory care would prevent or reduce the need for hospital admission. The objective of this thesis is to estimate incidence rates of avoidable acute care use by persons with RA relative to the general population. The RA cohort was established by identifying individuals meeting a validated case definition for RA based on ICD-9-CM and ICD-10-CA codes in years 2002-2023. Four general population controls were matched to each RA case by age, sex, and date of diagnosis. Acute care use for ACSCs including grand mal seizures, chronic lower respiratory diseases, asthma, diabetes, heart failure and pulmonary edema, hypertension, and angina from 2007-2023 were identified by established diagnostic codes. Incidence rate ratios were calculated using a multivariable regression model adjusting for age, sex, and location of residence. A Cox proportional hazards model was used to identify predictors of avoidable hospitalizations among RA patients. RA cases had a 14% higher risk of hospitalization and a 6% higher rate of ED visits for any ACSC compared those without RA. Significant predictors of ACSC hospitalizations for RA cases were increasing age, prolonged exposure to corticosteroids, being from a rural location, and having comorbid conditions, especially if the comorbid condition is an ACSC. Persons with RA are at a higher risk of potentially avoidable acute care use compared to those without RA. Improved ambulatory care access and quality, inclusive of primary care and contributing role of subspecialty care, is proposed to prevent unnecessary hospitalizations and reduce burden on the acute care system.
title: Manipulating DNA repair through the delivery of engineered DNA repair variants
Creators: name: Iyer, Shriya Vaidyanathan
Publisher: name: Cumming School of Medicine
Year: 2025
Subjects: subject: DNA
subject: Repair
subject: Virus like particles
subject: Double strand breaks
subject: PARP inhibitors
subject: DNA repair variants
subject: Biochemistry
subject: Biology
subject: Biology--Molecular

description: DNA repair pathways are essential for maintaining genomic stability and preventing diseases like cancer. Targeting these pathways has emerged as a key therapeutic strategy with agents like Doxorubicin that induces double-strand breaks (DSBs), and PARP inhibitors (PARPi) that exploit synthetic lethality, manipulating DNA repair to sensitize cancer cells to treatment. Building on this principle, engineered virus-like particles (eVLPs), originally developed for genome editing, offer a novel platform to deliver engineered DNA repair proteins into cells. My thesis explores the potential of eVLPs to manipulate DNA repair pathways through the delivery of BRCA1 protein variants. BRCA1 variants were engineered by introducing mutations, C61G and S1655F, known to impair homologous recombination (HR) repair. eVLPs were produced carrying BRCA1(WT), BRCA1(C61G), or BRCA1(S1655F) as protein cargo, and their effects on DNA repair were measured in human breast cancer cells (MCF7) treated with Doxorubicin and Olaparib. The study aimed to evaluate whether eVLP- delivered BRCA1 variants could sensitize cells to DNA damaging agents, offering a novel way to modulate DNA repair pathways. By combining protein engineering with eVLP based delivery, this work explores the potential for repurposing eVLPs to manipulate DNA repair and potentially enhance sensitivities towards DNA damaging agents for improved therapeutic outcomes.
New cases of super-flares on slowly rotating solar-type stars and large amplitude super-flares in G- and M-type main-sequence stars
Creators: name: Althukair, A. k.
name: Tsiklauri, D.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: In our previous work, we searched for super-flares on different types of stars while focusing on G-type dwarfs using entire Kepler data to study statistical properties of the occurrence rate of super-flares. Using these new data, as a by-product, we found fourteen cases of super-flare detection on thirteen slowly rotating Sun-like stars with rotation periods of 24.5 to 44 days. This result supports earlier conclusion by others that the Sun may possibly have a surprise super-flare. Moreover, we found twelve and seven new cases of detection of exceptionally large amplitude super-flares on six and four main-sequence stars of G- and M-type, respectively. No large-amplitude flares were detected in A, F, or K main-sequence stars. Here we present preliminary analysis of these cases. The super-flare detection, i.e. an estimation of flare energy, is based on a more accurate method compared to previous studies. We fit an exponential decay function to flare light curves and study the relation between e-folding decay time, $τ$, vs. flare amplitude and flare energy. We find that for slowly rotating Sun-like stars, large values of $τ$ correspond to small flare energies and small values of $τ$ correspond to high flare energies considered. Similarly, $τ$ is large for small flare amplitudes and $τ$ is small for large amplitudes considered. However, there is no clear relation between these parameters for large amplitude super-flares in the main sequence G- and M-type stars, as we could not establish clear functional dependence between the parameters via standard fitting algorithms.
description: The final version is accepted for publication in Research in Astronomy and Astrophysics (2023)
Drepane longimana
Creators: name: Zainal Abidin, Danial Hariz
name: Lavoué, Sébastien
name: Mohd Abu Hassan Alshari, Norli Fauzani
name: Mohd. Nor, Siti Azizah
name: A. Rahim, Masazurah
name: Mohammed Akib, Noor Adelyna
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Perciformes
Drepaneidae
Drepane
Drepane longimana

description: Drepane longimana (Bloch & Schneider, 1801) Material examined. MALAYSIA • 1, 99 mm TL; Kedah State, Merbok, Pompang Sungai Merbok; 05.664°N, 100.381°E; 6 Dec. 2018; Danial H. Zainal Abidin, Norli F.M.A.H. Alshari leg.; USMFC (60) 00002.
description: Published as part of Zainal Abidin, Danial Hariz, Lavoué, Sébastien, Mohd Abu Hassan Alshari, Norli Fauzani, Mohd. Nor, Siti Azizah, A. Rahim, Masazurah & Mohammed Akib, Noor Adelyna, 2021, Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters, pp. 601-631 in Check List 17 (2) on page 626, DOI: 10.15560/17.2.601
title: Investigating the Reconstitution and Function of Peritoneal Cavity Macrophages after LPS-induced Peritonitis
Creators: name: Tejada, Oscar Ernesto
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: Peritoneal macrophages
subject: LPS peritonitis
subject: GATA6 cavity macrophage
subject: Fate-mapping
subject: Omentum
subject: Bone-marrow derived macrophage
subject: Immunology
subject: FOS: Clinical medicine

description: The tissue-resident macrophages of the peritoneum are sentinel immune cells, in constant motion within the serous fluid of the abdomen. Like most tissue macrophages, the GATA6+ large peritoneal macrophages (LPMs) are responsible for the clearance and removal of pathogens that may break through the defensive barriers of the abdomen. However, upon inflammation incurred by the response of the immune system to foreign matter, the LPM population seemingly disappears and down-regulates its signature cell markers. The aim of this thesis project was to elucidate the fate of the large peritoneal macrophages after stimulation with an inflammatory agent as well as the eventual return of the macrophage resident cell population. This work used genetically engineered, LPM and monocyte-derived fate mapping mice to track the location and re-constitution of the large peritoneal cavity macrophage population after lipopolysaccharide (LPS)-induced peritonitis. A double recombinase, GATA6 and Lyz-M genetically driven fate mapping mouse was engineered to report on the large peritoneal population in response to a biologically relevant dose of lipopolysaccharide. Spectral flow cytometry and confocal whole mount imaging was used to investigate the ‘disappearance’ of LPM from the peritoneal cavity upon stimulation of the noxious agent. After 10 days of LPS administration, the LPM fate mapping mouse and the Ms4a3-monocyte derived reporter mouse were used to illustrate the repopulation of endogenous LPMs and newly recruited monocytes that contribute to the macrophage pool upon resolution of inflammation. My findings suggest that LPMs concentrate and localize at ‘milky spots’ of the omentum. Upon resolution of inflammation, the resident macrophage pool was made up both endogenous GATA6 and bone marrow-derived macrophages.
Differential requirements of androgen receptor in luminal progenitors during prostate regeneration and tumor initiation
Creators: name: Chua, Chee Wai
name: Epsi, Nusrat J.
name: Leung, Eva Yung
name: Xuan, Shouhong
name: Lei, Ming
name: Li, Bo
name: Bergren, Sarah
name: Hibshoosh, Hanina
name: Mitrofanova, Antonina
name: Shen, Michael M.
Publisher: name: Columbia University
Year: 2018
Subjects: Biology
Prostate--Cancer
Regenerative medicine
Androgens--Receptors
Stem cells

description: Master regulatory genes of tissue specification play key roles in stem/progenitor cells and are often important in cancer. In the prostate, androgen receptor (AR) is a master regulator essential for development and tumorigenesis, but its specific functions in prostate stem/progenitor cells have not been elucidated. We have investigated AR function in CARNs (CAstration-Resistant Nkx3.1-expressing cells), a luminal stem/progenitor cell that functions in prostate regeneration. Using genetically--engineered mouse models and novel prostate epithelial cell lines, we find that progenitor properties of CARNs are largely unaffected by AR deletion, apart from decreased proliferation in vivo. Furthermore, AR loss suppresses tumor formation after deletion of the Pten tumor suppressor in CARNs; however, combined Pten deletion and activation of oncogenic Kras in AR-deleted CARNs result in tumors with focal neuroendocrine differentiation. Our findings show that AR modulates specific progenitor properties of CARNs, including their ability to serve as a cell of origin for prostate cancer.
Synthesis and self-assembly properties of thiacrown-cyclized tetrathiafulvalene organogelators
Creators: name: Hou, Ruibin
name: Xu, Chao
name: Yan, Jiajia
name: Xia, Yan
name: Li, Dongfeng
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Microbiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: A novel low-molecular-weight organogelator (1) based on thiacrown-cyclized tetrathiafulvalene has been synthesized through cross-coupling reaction of crown-fused 1,3-dithiole-2-one 3 and the thione 4 in the presence of triethyl phosphite. The molecular structure of 1 was fully characterized by nuclear magnetic resonance spectroscopy, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and infrared spectroscopy. Gel-forming-ability experiments showed that the gelator could only form an opaque gel in dimethyl sulfoxide by sonication. The xerogel morphology observed by scanning electron microscopy showed an amorphous wrinkled structure. The gel exhibited varied responses to various external stimuli, including temperature, chemical oxidation, anions, and Na+ ions.
Waldschutzinfo Nr. 2023-03 der NW-FVA
Creators: name: Plašil, Pavel
name: Bothe, Elke
name: Rohde, Martin
Publisher: name: Zenodo
Year: 2023
Subjects: Winterbodensuche, Kiefernschadinsekten

description: Waldschutzinfo Nr. 2023-03 der Nordwestdeutschen Forstlichen Versuchsanstalt (NW-FVA) Göttingen zum Thema Ergebnisse der Winterbodensuche 2022/23 in Sachsen-Anhalt
Bond percolation on a class of correlated and clustered random graphs
Creators: name: Allard, Antoine
name: Hébert-Dufresne, Laurent
name: Noël, Pierre-André
name: Marceau, Vincent
name: Dubé, Louis J.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Social and Information Networks (cs.SI)
subject: Physics and Society (physics.soc-ph)
subject: Populations and Evolution (q-bio.PE)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: We introduce a formalism for computing bond percolation properties of a class of correlated and clustered random graphs. This class of graphs is a generalization of the Configuration Model where nodes of different types are connected via different types of hyperedges, edges that can link more than 2 nodes. We argue that the multitype approach coupled with the use of clustered hyperedges can reproduce a wide spectrum of complex patterns, and thus enhances our capability to model real complex networks. As an illustration of this claim, we use our formalism to highlight unusual behaviors of the size and composition of the components (small and giant) in a synthetic, albeit realistic, social network.
description: 16 pages and 4 figures
Development of an ultrasensitive spectrophotometric method for carmine determination based on fluorescent carbon dots
Creators: name: Hu, Qin
name: Sun, Huijuan
name: Liu, Lingfei
name: Xiao, Lixia
name: Yang, Zhen-Quan
name: Rao, Shengqi
name: Gong, Xiaojuan
name: Han, Jie
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology

description: A high-efficiency spectrophotometric method based on nitrogen-doped fluorescent carbon dots (N-FCDs) was developed for the ultrasensitive determination of carmine (CRM) in foodstuffs. The N-FCDs were fabricated via a one-pot hydrothermal method with m-phenylenediamine as the starting material. The detection principle was based on the fluorescence quenching effect of N-FCDs by CRM, where their interaction was due to the inner filter effect (IFE) and static quenching. A good linear relationship was established for CRM detection in a concentration range of 0.1–10.0 μM with a detection limit as low as 11.2 nM. The proposed method achieved satisfactory results for CRM determination in commercial food products with recoveries better than 98.6% and relative standard deviations (RSDs) less than 4.07%. The method established in this study was simple, ultrasensitive and reliable for rapid detecting CRM in a food matrix, which could be potentially used as a useful sensing agent for the analysis of additive food colourants.
Generic bounds on dipolar gravitational radiation from inspiralling compact binaries
Creators: name: Arun, K. G.
Publisher: name: arXiv
Year: 2012
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Various alternative theories of gravity predict dipolar gravitational radiation in addition to quadrupolar radiation. We show that gravitational wave (GW) observations of inspiralling compact binaries can put interesting constraints on the strengths of the dipole modes of GW polarizations. We put forward a physically motivated gravitational waveform for dipole modes, in the Fourier domain, in terms of two parameters: one which captures the relative amplitude of the dipole mode with respect to the quadrupole mode ($α$) and the other a dipole term in the phase ($β$). We then use this two parameter representation to discuss typical bounds on their values using GW measurements. We obtain the expected bounds on the amplitude parameter $α$ and the phase parameter $β$ for Advanced LIGO (AdvLIGO) and Einstein Telescope (ET) noise power spectral densities using Fisher information matrix. AdvLIGO and ET may at best bound $α$ to an accuracy of $\sim10^{-2}$ and $\sim10^{-3}$ and $β$ to an accuracy of $\sim10^{-5}$ and $\sim10^{-6}$ respectively.
description: Matches with the published version
Automated analysis of long-term grooming behavior in Drosophila using a k-nearest neighbors classifier
Creators: name: Qiao, Bing
name: Li, Chiyuan
name: Allen, Victoria Wing
name: Shirasu-Hiza, Mimi M.
name: Syed, Sheyum
Publisher: name: Columbia University
Year: 2018
Subjects: subject: Drosophila
subject: Neurosciences
subject: FOS: Clinical medicine
subject: Systems biology
subject: Circadian rhythms
subject: Grooming behavior in animals

description: Despite being pervasive, the control of programmed grooming is poorly understood. We addressed this gap by developing a high-throughput platform that allows long-term detection of grooming in Drosophila melanogaster. In our method, a k-nearest neighbors algorithm automatically classifies fly behavior and finds grooming events with over 90% accuracy in diverse genotypes. Our data show that flies spend ~13% of their waking time grooming, driven largely by two major internal programs. One of these programs regulates the timing of grooming and involves the core circadian clock components cycle, clock, and period. The second program regulates the duration of grooming and, while dependent on cycle and clock, appears to be independent of period. This emerging dual control model in which one program controls timing and another controls duration, resembles the two-process regulatory model of sleep. Together, our quantitative approach presents the opportunity for further dissection of mechanisms controlling long-term grooming in Drosophila.
The QCD Phase Transition Region with Domain Wall Quarks
Creators: name: Lin, Zhongjie
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Results will be presented from a study of the QCD transition region using 2+1 flavors of fermions and a dislocation suppressing gauge action on a lattice with temporal extent of 8 and spatial extent 16 (1.9 - 2.7 fm). A series of temperatures from 140 through 200 MeV, separated by 10 MeV have been studied. All the simulations lie on a line of constant physics with 200 MeV pions, realized using domain wall fermion, a chirally symmetric fermion formulation. The chiral condensates, susceptibility, anomalous symmetry breaking and a detailed study of the Dirac spectrum will be described and compared with earlier staggered results.
description: 3 pages, 2 figures, talk given at the 19th Particles and Nuclei International Conference (PANIC11), Massachusetts Institute of Technology, USA, from July 24-30, 2011
title: Exploring Perceptions of the BIPOC Acronym in Canadian Social Discourse
Creators: name: Natynczyk, Evangelina Vanesa
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: BIPOC
subject: fast-terminology
subject: racial equity
subject: inclusive language
subject: qualitative research
subject: social media
subject: Sociology
subject: FOS: Sociology

description: This thesis examines perceptions of the BIPOC (Black, Indigenous, People of Colour) acronym within Canadian social discourse through a qualitative lens grounded in critical race theory. It offers insights into how professionals engaged in anti-racism efforts and diversity initiatives, along with the broader online community, navigate this terminology using semi-structured interviews and social media analysis. The study employs a multi-method approach, including content analysis of interviews and publicly available social media data, with a focus on X (formerly Twitter) to investigate the discourse surrounding the BIPOC acronym. This research highlights nuances influencing understandings of racial equity and inclusion under such umbrella terms and ‘fast-terminology’, considering emerging power dynamics associated with their use. Through this exploration, the findings contribute significantly to informed dialogue regarding equitable representation amidst evolving sociocultural landscapes, where language plays a pivotal role in shaping identity politics. It enhances the critical understanding of the societal implications of the BIPOC acronym, informing discussions around inclusive language, representation, and racial equity. The findings underscore the complexity of using racial and ethnic umbrella terms and emphasize the importance of contextualizing their usage within specific communities, contexts, and localities.
Anomaly detection search for new resonances decaying into a Higgs boson and a generic new particle $X$ in hadronic final states using $\sqrt{s} = 13$ TeV $pp$ collisions with the ATLAS detector
Creators: name: ATLAS Collaboration
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: A search is presented for a heavy resonance $Y$ decaying into a Standard Model Higgs boson $H$ and a new particle $X$ in a fully hadronic final state. The full Large Hadron Collider Run 2 dataset of proton-proton collisions at $\sqrt{s}= 13$ TeV collected by the ATLAS detector from 2015 to 2018 is used, and corresponds to an integrated luminosity of 139 fb$^{-1}$. The search targets the high $Y$-mass region, where the $H$ and $X$ have a significant Lorentz boost in the laboratory frame. A novel signal region is implemented using anomaly detection, where events are selected solely because of their incompatibility with a learned background-only model. It is defined using a jet-level tagger for signal-model-independent selection of the boosted $X$ particle, representing the first application of fully unsupervised machine learning to an ATLAS analysis. Two additional signal regions are implemented to target a benchmark $X$ decay into two quarks, covering topologies where the $X$ is reconstructed as either a single large-radius jet or two small-radius jets. The analysis selects Higgs boson decays into $b\bar{b}$, and a dedicated neural-network-based tagger provides sensitivity to the boosted heavy-flavor topology. No significant excess of data over the expected background is observed, and the results are presented as upper limits on the production cross section $σ(pp \rightarrow Y \rightarrow XH \rightarrow q\bar{q}b\bar{b}$) for signals with $m_Y$ between 1.5 and 6 TeV and $m_X$ between 65 and 3000 GeV.
description: 47 pages in total, author list starting page 30, 13 figures, 1 table. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HDBS-2019-23/
Nociceptive interneurons control modular motor pathways to promote escape behavior in Drosophila
Creators: name: Burgos, Anita
name: Honjo, Ken
name: Ohyama, Tomoko
name: Qian, Cheng Sam
name: Shin, Grace Ji-Eun
name: Gohl, Daryl M.
name: Silies, Marion
name: Tracey, W. Daniel
name: Zlatic, Marta
name: Cardona, Albert
name: Grueber, Wesley B.
Publisher: name: Columbia University
Year: 2018
Subjects: subject: Drosophila
subject: Neurosciences
subject: FOS: Clinical medicine
subject: Nociceptors
subject: Interneurons

description: Rapid and efficient escape behaviors in response to noxious sensory stimuli are essential for protection and survival. Yet, how noxious stimuli are transformed to coordinated escape behaviors remains poorly understood. In Drosophila larvae, noxious stimuli trigger sequential body bending and corkscrew-like rolling behavior. We identified a population of interneurons in the nerve cord of Drosophila, termed Down-and-Back (DnB) neurons, that are activated by noxious heat, promote nociceptive behavior, and are required for robust escape responses to noxious stimuli. Electron microscopic circuit reconstruction shows that DnBs are targets of nociceptive and mechanosensory neurons, are directly presynaptic to pre-motor circuits, and link indirectly to Goro rolling command-like neurons. DnB activation promotes activity in Goro neurons, and coincident inactivation of Goro neurons prevents the rolling sequence but leaves intact body bending motor responses. Thus, activity from nociceptors to DnB interneurons coordinates modular elements of nociceptive escape behavior.
Drepane punctata
Creators: name: Zainal Abidin, Danial Hariz
name: Lavoué, Sébastien
name: Mohd Abu Hassan Alshari, Norli Fauzani
name: Mohd. Nor, Siti Azizah
name: A. Rahim, Masazurah
name: Mohammed Akib, Noor Adelyna
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Perciformes
Drepaneidae
Drepane
Drepane punctata

description: Drepane punctata (Linnaeus, 1758) Figure 3Q Material examined. MALAYSIA • 3, 234– 278 mm TL; Kedah State, Kuala Kedah, Kuala Muda Whispering Market; 05.578°N, 100.341°E; 19 Mar. 2019; Danial H. Zainal Abidin, Norli F.M.A.H. Alshari leg.; USMFC (60) 00003.
description: Published as part of Zainal Abidin, Danial Hariz, Lavoué, Sébastien, Mohd Abu Hassan Alshari, Norli Fauzani, Mohd. Nor, Siti Azizah, A. Rahim, Masazurah & Mohammed Akib, Noor Adelyna, 2021, Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters, pp. 601-631 in Check List 17 (2) on page 626, DOI: 10.15560/17.2.601
Data of degradation and chromatogram of chlorothalonil degradation from Biotransformation of chlorothalonil by strain Stenotrophomonas acidaminiphila BJ1 isolated from farmland soil
Creators: name: Zhang, Qingming
name: Liu, Hongyu
name: Saleem, Muhammad
name: Wang, Caixia
Publisher: name: The Royal Society
Year: 2019

description: HPLC elution curves of chlorothalonil and metabolites.
title: Performance Enhancement of Cement Paste Using Biosilica Nanoparticles Derived from Agricultural Crop Residues
Creators: name: Alhalsa, Sohaib
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: cement
subject: strength
subject: hydration
subject: flow
subject: microstructure
subject: acid
subject: nano
subject: biosilica
subject: Engineering--Civil

description: Common disposal practices of agricultural crop residues can pose significant environmental challenges, including greenhouse gas (GHG) emissions and hazardous leachate generation. Incorporating these residues into concrete can reduce the landfill volume of residues and enhance the performance of concrete. Most of the existing studies to incorporate crop residues into concrete employed biosilica extracted at high temperatures, leading to substantial energy consumption and GHG emissions. This study, to the best of our knowledge, utilized biosilica nanoparticles obtained from wheat and rice husks using an advanced extraction technique at temperatures below 200 °C for the first time. The extracted biosilica was fully characterized and used in as-extracted and acid-treated forms in cement paste at 1, 3, and 5% by weight of cement. The pastes were tested for compressive strength, heat evolution, microstructure, and rheological behavior. The results showed that all cement pastes incorporating biosilica nanoparticles exhibited higher compressive strength than that of the reference paste at all the testing ages ranging from 3 to 91 days. The highest improvement in the compressive strength (48% compared to the reference sample) was observed for cement paste incorporating 3 wt% acid-treated biosilica from rice husk. This paste exhibited the highest hydration peak intensity and cumulative heat over the 7-day testing period. Moreover, all pastes containing biosilica nanoparticles had less alite and belite and more amorphous content the reference paste beyond 3 days. These pastes also contained low portlandite and high bound water contents at all ages. These findings highlight the cement hydration acceleration and pozzolanic reactivity of the biosilica nanoparticles in cement paste, which contributed to the enhanced compressive strength of the paste. Adding biosilica nanoparticles also increased the viscosity and yield stress of the cement paste although these effects varied based on the characteristics and content of the biosilica nanoparticles.