cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Identification of a developmentally regulated septin and involvement of the septins in spore formation in Saccharomyces cerevisiae
Creators: name: Fares, H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1996

description: The Saccharomyces cerevisiae CDC3, CDC10, CDC11, and CDC12 genes encode a family of related proteins, the septins, which are involved in cell division and the organization of the cell surface during vegetative growth. A search for additional S. cerevisiae septin genes using the polymerase chain reaction identified SPR3, a gene that had been identified previously on the basis of its sporulation-specific expression. The predicted SPR3 product shows 25-40% identity in amino acid sequence to the previously known septins from S. cerevisiae and other organisms. Immunoblots confirmed the sporulation-specific expression of Spr3p and showed that other septins are also present at substantial levels in sporulating cells. Consistent with the expression data, deletion of SPR3 in either of two genetic backgrounds had no detectable effect on exponentially growing cells. In one genetic background, deletion of SPR3 produced a threefold reduction in sporulation efficiency, although meiosis appeared to be completed normally. In this background, deletion of CDC10 had no detectable effect on sporulation. In the other genetic background tested, the consequences of the two deletions were reversed. Immunofluorescence observations suggest that Spr3p, Cdc3p, and Cdc11p are localized to the leading edges of the membrane sacs that form near the spindle-pole bodies and gradually extend to engulf the nuclear lobes that contain the haploid chromosome sets, thus forming the spores. Deletion of SPR3 does not prevent the localization of Cdc3p and Cdc11p, but these proteins appear to be less well organized, and the intensity of their staining is reduced. Taken together, the results suggest that the septins play important but partially redundant roles during the process of spore formation.
PROTEIN-PROTEIN INTERACTIONS AND NOVEL BIOMARKERS IN POLYCYSTIC OVARIAN SYNDROME
Creators: name: Zafar, Madeeha
name: Silverman, Rosalind
name: Silverman, Lorelei
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 429999
subject: Other health sciences not elsewhere classified

description: Polycystic ovary syndrome (PCOS) is a complex metabolic, endocrine and reproductive disorder that affects 5-10% women of reproductive age. It is characterized by hyperandrogenism, insulin resistance, and chronic inflammation. However, exact etiology of polycystic ovarian syndrome is unknown but genetic and environmental factors may play a role. There is no cure for PCOS, but treatments can help manage the symptoms and prevent complications. Our research integrates a systematic examination of proteomics related to PCOS, employing tools like STRING, PANTHER, and the Human Protein Atlas to discover new proteins associated with PCOS, explicitly focusing on HSP90AA1. Notably, these findings have led to identifying new potential biomarkers that could transform polycystic ovarian syndrome management. These newly discovered biomarkers are expected to play a crucial role in early-stage diagnosis, prognosis, and personalized treatment, thereby advancing the understanding of PCOS. The article concludes with a focus on future research to support these findings, aiming to expedite the development of innovative diagnostic tools and therapeutic strategies for this challenging disease.
Probing superfast quarks in nuclei through dijet production at the LHC
Creators: name: Freese, Adam J.
name: Sargsian, Misak M.
name: Strikman, Mark I.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Experiment (nucl-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We investigate dijet production from proton-nucleus collisions at the Large Hadron Collider (LHC) as a means for observing superfast quarks in nuclei with Bjorken $x>1$. Kinematically, superfast quarks can be identified through directly measurable jet kinematics. Dynamically, their description requires understanding several elusive properties of nuclear QCD, such as nuclear forces at very short distances, as well as medium modification of parton distributions in nuclei. In the present work, we develop a model for nuclear parton distributions at large $x$ in which the nuclear dynamics at short distance scales are described by two- and three-nucleon short range correlations (SRCs). Nuclear modifications are accounted for using the color screening model, and an improved description of the EMC effect is reached by using a structure function parametrization that includes higher-twist contributions. We apply QCD evolution at the leading order to obtain nuclear parton distributions in the kinematic regime of the LHC, and based on the obtained distributions calculate the cross section for dijet production. We find not only that superfast quarks can be observed at the LHC, but also that they provide sensitivity to the practically unexplored three-nucleon SRCs in nuclei. Additionally, the LHC can extend our knowledge of the EMC effect to large $Q^2$ where higher-twist effects are negligible.
description: 44 pages, 17 figures, final version to be published in EJPC
ปัจจัยที่ส่งผลต่อความเข้มแข็งของวิสาหกิจชุมชน ตำบลหวายเหนียว อำเภอท่ามะกา จังหวัดกาญจนบุรี
Creators: name: ศราวุฒิ ครุฑศิริ
Publisher: name: College of Politics and Governance (COPAG), Mahasarakham University
Year: 2022
Subjects: Strength of Community Enterprise
Participation
Leadership
Local Wisdom

description: Journal of Politics and Governance, 12, 1, 149-167
A Systematic Literature Review of Nutrition Interventions Implemented to Address Food Insecurity as a Social Determinant of Health
Creators: name: Reis H.
name: Norris K.
name: Haynes-Maslow L.
name: Jilcott Pitts S.
Publisher: name: Multidisciplinary Digital Publishing Institute (MDPI)
Year: 2023

description: Background: Policy initiatives have provided funding for non-acute nutrition interventions to address food insecurity as a social determinant of health, but more research is needed to understand the outcomes of these initiatives in order to determine the areas of highest impact. Therefore, the purpose of this systematic review was to evaluate the outcomes that were assessed in three nutrition interventions (produce prescription programs, medically tailored meals, and community supported agriculture) that aim to address food insecurity as a social determinant of health, and this was undertaken in order to identify future areas of study that can heighten impact. Methods: This systematic review was performed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) criteria. A list of search terms and keywords were compiled by the research team. A Boolean search was conducted from 1 January 2000 to 1 January 2023 in the PubMed advanced search database. Results: A total of 1015 articles were initially pulled from the PubMed database, and, after a screening process, 21 articles were included in our review. Nineteen of the articles focused on adult populations or families and two focused on children. The main outcomes assessed were changes in self-reported dietary intake, while a few of the articles addressed feasibility and cost-related outcomes. Conclusions: More research is needed to assess whether nutritional interventions to address food insecurity as a social determinant of health are feasible and more cost effective in the long term. Additionally, more work should be conducted in pediatric populations, which could have a robust return on investment in terms of both healthcare utilization and healthcare expenditure.
Rho-stimulated contractility drives the formation of stress fibers and focal adhesions
Creators: name: Chrzanowska-Wodnicka, M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1996

description: Activated rhoA, a ras-related GTP-binding protein, stimulates the appearance of stress fibers, focal adhesions, and tyrosine phosphorylation in quiescent cells (Ridley, A.J., and A. Hall, 1992. Cell. 70:389-399). The pathway by which rho triggers these events has not been elucidated. Many of the agents that activate rho (e.g., vasopressin, endothelin, lysophosphatidic acid) stimulate the contractility of smooth muscle and other cells. We have investigated whether rho's induction of stress fibers, focal adhesions, and tyrosine phosphorylation is the result of its stimulation of contractility. We demonstrate that stimulation of fibroblasts with lysophosphatidic acid, which activates rho, induces myosin light chain phosphorylation. This precedes the formation of stress fibers and focal adhesions and is accompanied by increased contractility. Inhibition of contractility by several different mechanisms leads to inhibition of rho-induced stress fibers, focal adhesions, and tyrosine phosphorylation. In addition, when contractility is inhibited, integrins disperse from focal adhesions as stress fibers and focal adhesions disassemble. Conversely, upon stimulation of contractility, diffusely distributed integrins are aggregated into focal adhesions. These results suggest that activated rho stimulates contractility, driving the formation of stress fibers and focal adhesions and elevating tyrosine phosphorylation. A model is proposed to account for how contractility could promote these events.
IPBES Invasive Alien Species Assessment, data management report of Chapter 3. Figure 3.5
Creators: name: Hulme, Philip E.
name: Renard Truong, Tanara
Publisher: name: Zenodo
Year: 2023
Subjects: Data management report

description: This data management report explains the development procedure of Figure 3.5 which is a network diagram illustrates the extent of knowledge on indirect (blue circles), direct (green circles) drivers of biodiversity change and natural drivers (grey circle), and their interactions. The thickness of the lines between drivers is indicative of the number of papers that jointly addressed the two linked drivers. The size of the stroke of each circle reflects the number of papers on a particular driver in relation to invasive alien species. Figure 3.5 is in chapter 3 of IPBES invasive alien species assessment report (https://doi.org/10.5281/zenodo.7430727)
Classicalization of Quantum Variables and Quantum-Classical Hybrids
Creators: name: Koide, T.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The extraction of classical degrees of freedom in quantum mechanics is studied in the stochastic variational method. By using this classicalization, a hybrid model constructed from quantum and classical variables (quantum-classical hybrids) is derived. In this procedure, conservation laws such as energy are maintained, and Ehrenfest's theorem is still satisfied with modification. The criterion for the applicability of quantum-classical hybrids is also discussed.
description: 6 pages, 5 figures, section 4.4 and two figures were added, typos were corrected
A Septin-based Hierarchy of Proteins Required for Localized Deposition of Chitin in the Saccharomyces cerevisiae Cell Wall
Creators: name: Pringle, John R.
name: Valle, Giorgio
name: Fares, Hanna
name: Adams, Alison E.M.
name: DeMarini, Douglas J.
name: Chuang, John S.
name: Virgilio, Claudio De
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1997

description: Just before bud emergence, a Saccharomyces cerevisiae cell forms a ring of chitin in its cell wall; this ring remains at the base of the bud as the bud grows and ultimately forms part of the bud scar marking the division site on the mother cell. The chitin ring seems to be formed largely or entirely by chitin synthase III, one of the three known chitin synthases in S. cerevisiae. The chitin ring does not form normally in temperature-sensitive mutants defective in any of four septins, a family of proteins that are constituents of the “neck filaments” that lie immediately subjacent to the plasma membrane in the mother-bud neck. In addition, a synthetic-lethal interaction was found between cdc12-5, a temperature-sensitive septin mutation, and a mutant allele of CHS4, which encodes an activator of chitin synthase III. Two-hybrid analysis revealed no direct interaction between the septins and Chs4p but identified a novel gene, BNI4, whose product interacts both with Chs4p and Cdc10p and with one of the septins, Cdc10p; this analysis also revealed an interaction between Chs4p and Chs3p, the catalytic subunit of chitin synthase III. Bni4p has no known homologues; it contains a predicted coiled-coil domain, but no other recognizable motifs. Deletion of BNI4 is not lethal, but causes delocalization of chitin deposition and aberrant cellular morphology. Overexpression of Bni4p also causes delocalization of chitin deposition and produces a cellular morphology similar to that of septin mutants. Immunolocalization experiments show that Bni4p localizes to a ring at the mother-bud neck that lies predominantly on the mother-cell side (corresponding to the predominant site of chitin deposition). This localization depends on the septins but not on Chs4p or Chs3p. A GFP-Chs4p fusion protein also localizes to a ring at the mother-bud neck on the mother-cell side. This localization is dependent on the septins, Bni4p, and Chs3p. Chs3p, whose normal localization is similar to that of Chs4p, does not localize properly in bni4, chs4, or septin mutant strains or in strains that accumulate excess Bni4p. In contrast, localization of the septins is essentially normal in bni4, chs4, and chs3 mutant strains and in strains that accumulate excess Bni4p. Taken together, these results suggest that the normal localization of chitin synthase III activity is achieved by assembly of a complex in which Chs3p is linked to the septins via Chs4p and Bni4p.
Allele-specific quantification of human leukocyte antigen transcript isoforms by nanopore sequencing
Creators: name: Weimer, Eric T.
name: Hughes, Andrew E. O.
name: Montgomery, Maureen C.
name: Liu, Chang
Publisher: name: Frontiers Media SA
Year: 2023

description: Introduction While tens of thousands of HLA alleles have been identified by DNA sequencing, the contribution of alternative splicing to HLA diversity is not well characterized. In this study, we sought to determine if long-read sequencing could be used to accurately quantify allele-specific HLA transcripts in primary human lymphocytes. Methods cDNA libraries were prepared from peripheral blood lymphocytes from 12 donors and sequenced by nanopore long-read sequencing. HLA reads were aligned to donor-specific reference sequences based on the known type of each donor. Allele-specific exon utilization was calculated as the proportion of reads aligning to each allele containing known exons, and transcript isoforms were quantified based on patterns of exon utilization within individual reads. Results Splice variants were rare among class I HLA genes (median exon retention rate 99%–100%), except for several HLA-C alleles with exon 5 spliced out of up to 15% of reads. Splice variants were also rare among class II HLA genes (median exon retention rate 98%–100%), except for HLA-DQB1. Consistent with previous work, exon 5 of HLA-DQB1 was spliced out in alleles with a mutated splice acceptor site at rs28688207. Surprisingly, a 28% loss of exon 5 was also observed in HLA-DQB1 alleles with an intact splice acceptor site at rs28688207. Discussion We describe a simple bioinformatic workflow to quantify allele-specific expression of HLA transcript isoforms. Further studies are warranted to characterize the repertoire of HLA transcripts expressed in different cell types and tissues across diverse populations.
Early-melting snowpatch plant communities are transitioning into novel states
Creators: name: Morgan, John
name: Walker, Zachary
Publisher: name: La Trobe
Year: 2023
Subjects: classificationCode: 310406
subject: Evolutionary impacts of climate change

description: Snowpatch plant community distribution and composition are strongly tied to the duration of long-lasting snow cover in alpine areas; they are vulnerable to global climatic changes that result in warmer temperatures and longer growing seasons. We used a revisitation study to quantify early-melting snowpatch floristic and functional diversity change in southern Australia, and document shrub size-class distributions over time to detect evidence for their encroachment into snowpatches, a key prediction with climatic change. Early-melting snowpatch vegetation has declined in areal extent, changed in species composition, and shrub and tussock grass cover has increased, but changes in functional trait diversity were less clear. Species gains, particularly by non-clonal species, accounted for most of the floristic change observed. Shrub recruitment was ongoing by most shrub species. Biotic differentiation is occurring; many early-melting snowpatches are transitioning to a novel state with changed composition and taller vegetation structure, but there is little evidence for species loss having occurred. Given enough time, however, the long-term loss of species is likely (i.e. biotic homogenisation) if taller shrubs outcompete short-statured snowpatch species. Our results provide evidence that this alpine ecosystem is forming a novel community with an uncertain future.
Astral Microtubule Dynamics in Yeast: A Microtubule-based Searching Mechanism for Spindle Orientation and Nuclear Migration into the Bud
Creators: name: Shaw, Sidney L.
name: Bloom, Kerry
name: Yeh, Elaine
name: Salmon, E.D.
name: Maddox, Paul
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1997

description: Localization of dynein–green fluorescent protein (GFP) to cytoplasmic microtubules allowed us to obtain one of the first views of the dynamic properties of astral microtubules in live budding yeast. Several novel aspects of microtubule function were revealed by time-lapse, three-dimensional fluorescence microscopy. Astral microtubules, about four to six in number for each pole, exhibited asynchronous dynamic instability throughout the cell cycle, growing at ≅0.3–1.5 μm/min toward the cell surface then switching to shortening at similar velocities back to the spindle pole body (SPB). During interphase, a conical array of microtubules trailed the SPB as the nucleus traversed the cytoplasm. Microtubule disassembly by nocodozole inhibited these movements, indicating that the nucleus was pushed around the interior of the cell via dynamic astral microtubules. These forays were evident in unbudded G1 cells, as well as in late telophase cells after spindle disassembly. Nuclear movement and orientation to the bud neck in S/G2 or G2/M was dependent on dynamic astral microtubules growing into the bud. The SPB and nucleus were then pulled toward the bud neck, and further microtubule growth from that SPB was mainly oriented toward the bud. After SPB separation and central spindle formation, a temporal delay in the acquisition of cytoplasmic dynein at one of the spindle poles was evident. Stable microtubule interactions with the cell cortex were rarely observed during anaphase, and did not appear to contribute significantly to spindle alignment or elongation into the bud. Alterations of microtubule dynamics, as observed in cells overexpressing dynein-GFP, resulted in eventual spindle misalignment. These studies provide the first mechanistic basis for understanding how spindle orientation and nuclear positioning are established and are indicative of a microtubule-based searching mechanism that requires dynamic microtubules for nuclear migration into the bud.
Additional file 1 of Individualized lifestyle intervention in PCOS women (IPOS): a study protocol for a multicentric randomized controlled trial for evaluating the effectiveness of an individualized lifestyle intervention in PCOS women who wish to conceive
Creators: name: Malhotra, Neena
name: Arora, Taruna Katyal
name: Suri, Vanita
name: Jena, Saubhagya Kumar
name: Verma, Asha
name: Gowri, Mahasampath
name: Kapoor, Nitin
name: Chalga, Manjeet Singh
name: Kulkarni, Bharati
name: Kamath, Mohan S.
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Mathematical Sciences not elsewhere classified
subject: Cancer

description: Additional file 1.
Quench Dynamics in Confined 1+1-Dimensional Systems
Creators: name: Engelhardt, Dalit
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We present a framework for investigating the response of conformally-invariant confined 1+1-dimensional systems to a quantum quench. While conformal invariance is generally destroyed in a global quantum quench, systems that can be described as or mapped to integrable deformations of a CFT may present special instances where a conformal field theory-based analysis could provide useful insight into the non-equilibrium dynamics. We investigate this possibility by considering a quench analogous to that of the Quantum Newton's Cradle experiment [Nature 440, 900 (2006)] and demonstrating qualitative agreement between observables derived in the CFT framework and those of the experimental system. We propose that this agreement may be a feature of the proximity of the experimental system to an integrable deformation of a c=1 CFT.
description: 6 pages, to appear in J. Phys. A
Association of anxiety and depressive symptoms with C-reactive protein in diverse Latinos: Results from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)
Creators: name: Camacho Á.
name: Guerrero L.R.
name: González H.M.
name: Kohn J.N.
name: Allison M.A.
name: Jimenez D.E.
name: Wassertheil-Smoller S.
name: Tarraf W.
name: Talavera G.A.
name: Hong S.
name: Gallo L.
name: Perreira K.
Publisher: name: Public Library of Science
Year: 2023

description: BACKGROUND: High sensitivity C-reactive protein (hsCRP) is a marker of systemic inflammation that has been associated with persistent depressive symptoms. Depression and anxiety are frequently associated with a chronic inflammatory state, yet the nature of this relationship has not been rigorously examined in diverse Hispanic/Latino populations. We aimed to study the association of anxiety and depressive symptoms as well as comorbid presentations, with circulating high sensitivity C-reactive protein (hsCRP) levels in a large Latino cohort of diverse heritages. We hypothesized a significant positive associations of both anxiety and depressive symptoms and hsCRP levels and potential variations among the heritage groups. METHODS: Depressive symptoms and anxiety were measured by the Center for Epidemiological Studies Depression Scale (CES-D) and State-Trait Anxiety Inventory (STAI), respectively. Serum hsCRP (hsCRP) levels of 15,448 participants (age 18 to 75 years; 52.3% women) from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) were measured and categorized based on the established cardiovascular disease (CVD) risk reference values (< 1mg/L, low; 1-<3 mg/L, intermediate; ≥ 3mg/L, high). RESULTS: Mean CES-D, STAI scores, and hsCRP levels were 7.0 (SD = 5.9), 17.0 (SD = 5.7), and 3.84 (SD = 7.85), respectively. Generalized linear modeling, adjusted for sociodemographic characteristics revealed significant associations between depression (exp(β) = 1.12; p<0.01) and anxiety symptoms (exp(β) = 1.10; p<0.05) with continuous hsCRP levels. For categorical values of hsCRP, one SD increase in CES-D and STAI scores was associated with a 10% and 8% increase in the RRRs of high vs. low hsCRP, respectively. However, these relationships between CES-D or STAI and hsCRP were no longer statistically significant after adjustment for CVD risk factors and medications. CONCLUSION: We found modest associations between anxiety and depressive symptoms and systemic inflammation measured by hsCRP among diverse Hispanics/Latinos that did not appreciably differ between heritage groups.
CENP-E Function at Kinetochores Is Essential for Chromosome Alignment
Creators: name: Maddox, P.
name: Chan, G.K.T.
name: Schaar, B.T.
name: Salmon, E.D.
name: Yen, T.J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1997

description: CENP-E is a kinesin-like protein that binds to kinetochores and may provide functions that are critical for normal chromosome motility during mitosis. To directly test the in vivo function of CENP-E, we microinjected affinity-purified antibodies to block the assembly of CENP-E onto kinetochores and then examined the behavior of these chromosomes. Chromosomes lacking CENP-E at their kinetochores consistently exhibited two types of defects that blocked their alignment at the spindle equator. Chromosomes positioned near a pole remained mono-oriented as they were unable to establish bipolar microtubule connections with the opposite pole. Chromosomes within the spindle established bipolar connections that supported oscillations and normal velocities of kinetochore movement between the poles, but these bipolar connections were defective because they failed to align the chromosomes into a metaphase plate.Overexpression of a mutant that lacked the amino-terminal 803 amino acids of CENP-E was found to saturate limiting binding sites on kinetochores and competitively blocked endogenous CENP-E from assembling onto kinetochores. Chromosomes saturated with the truncated CENP-E mutant were never found to be aligned but accumulated at the poles or were strewn within the spindle as was the case when cells were microinjected with CENP-E antibodies. As the motor domain was contained within the portion of CENP-E that was deleted, the chromosomal defect is likely attributed to the loss of motor function.The combined data show that CENP-E provides kinetochore functions that are essential for monopolar chromosomes to establish bipolar connections and for chromosomes with connections to both spindle poles to align at the spindle equator. Both of these events rely on activities that are provided by CENP-E's motor domain.
Advances in the Management of Early-Stage Triple-Negative Breast Cancer
Creators: name: Brunk E.
name: Abdou Y.G.
name: Bhardwaj P.V.
name: Spanheimer P.M.
name: Wang Y.
Publisher: name: Multidisciplinary Digital Publishing Institute (MDPI)
Year: 2023

description: Triple-negative breast cancer (TNBC) is a subtype of breast cancer with both inter- and intratumor heterogeneity, thought to result in a more aggressive course and worse outcomes. Neoadjuvant therapy (NAT) has become the preferred treatment modality of early-stage TNBC as it allows for the downstaging of tumors in the breast and axilla, monitoring early treatment response, and most importantly, provides important prognostic information that is essential to determining post-surgical therapies to improve outcomes. It focuses on combinations of systemic drugs to optimize pathologic complete response (pCR). Excellent response to NAT has allowed surgical de-escalation in ideal candidates. Further, treatment algorithms guide the systemic management of patients based on their pCR status following surgery. The expanding knowledge of molecular pathways, genomic sequencing, and the immunological profile of TNBC has led to the use of immune checkpoint inhibitors and targeted agents, including PARP inhibitors, further revolutionizing the therapeutic landscape of this clinical entity. However, subgroups most likely to benefit from these novel approaches in TNBC remain elusive and are being extensively studied. In this review, we describe current practices and promising therapeutic options on the horizon for TNBC, surgical advances, and future trends in molecular determinants of response to therapy in early-stage TNBC.
A unified streamflow drought index for both perennial and intermittent rivers at global scale
Creators: name: Cammalleri, Carmelo
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Mathematical Sciences not elsewhere classified
subject: Computational Biology

description: The modelling of streamflow drought is usually performed with different approaches for perennial and intermittent rivers, as no-flow periods require a dedicated statistical treatment. Here, a unified drought index is proposed by extending the threshold method to all flow regimes. The method generalizes the approach commonly adopted for low-flow droughts by accounting for the probability of occurrence in a yearly reference period. Application to a global dataset for 1991–2020, derived from ERA5-forced LISFLOOD model simulations, demonstrates how consistent outcomes can be obtained in all major perennial and intermittent streams. A simplified version of the method is also discussed, detailing how reliable drought detection can be achieved in many parts of the world (e.g. central Europe, the eastern US for low-flow, and northern Russia and the Middle East for no-flow) even when the frequency distribution of the spells in time is replaced by the simpler average number of events.
Realizing the Willis equations with pre-stresses
Creators: name: Xiang, Zhihai
name: Yao, Ruiwen
Publisher: name: arXiv
Year: 2014
Subjects: subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences
subject: 74A99 (Primary), 74J05 (Secondary)

description: This paper proves that the linear elastic behavior of the material with inhomogeneous pre-stresses can be described by the Willis equations. In this case, the additional terms in the Willis equations, compared with the classical linear elastic equations for homogeneous media, are related to the gradient of pre-stresses. In this way, the material length scale is naturally incorporated in the framework of continuum mechanics. All these findings also coincide with the results of transformation elastodynamics, so that they can meet the requirement of the principle of material objectivity and the principle of general invariance.
description: 13 pages, 2 figures
Accurate chromosome segregation by probabilistic self-organization
Creators: name: Saka, Yasushi
name: Giuraniuc, Claudiu V.
name: Ohkura, Hiroyuki
Publisher: name: arXiv
Year: 2014
Subjects: subject: Subcellular Processes (q-bio.SC)
subject: FOS: Biological sciences

description: Background: For faithful chromosome segregation during cell division, correct attachments must be established between sister chromosomes and microtubules from opposite spindle poles through kinetochores (chromosome bi-orientation). Incorrect attachments of kinetochore microtubules (kMTs) lead to chromosome mis-segregation and aneuploidy, which is often associated with developmental abnormalities such as Down syndrome and diseases including cancer. The interaction between kinetochores and microtubules is highly dynamic with frequent attachments and detachments. However, it remains unclear how chromosome bi-orientation is achieved with such accuracy in such a dynamic process. Results: To gain new insight into this essential process, we have developed a simple mathematical model of kinetochore-microtubule interactions during cell division in general, i.e. both mitosis and meiosis. Firstly, the model reveals that the balance between attachment and detachment probabilities of kMTs is crucial for correct chromosome bi-orientation. With the right balance, incorrect attachments are resolved spontaneously into correct bi-oriented conformations while an imbalance leads to persistent errors. In addition, the model explains why errors are more commonly found in the first meiotic division (meiosis I) than in mitosis and how a faulty conformation can evade the spindle assembly checkpoint, which may lead to a chromosome loss. Conclusions: The proposed model, despite its simplicity, helps us understand one of the primary causes of chromosomal instability - aberrant kinetochore-microtubule interactions. The model reveals that chromosome bi-orientation is a probabilistic self-organization, rather than a sophisticated process of error detection and correction.
Characterizing host-pathogen interactions between Zostera marina and Labyrinthula zosterae
Creators: name: Burge, Colleen A.
name: Crandall, Grace
name: Loeher, Malina M.
name: Van Alstyne, Kathryn L.
name: Alidoost Salimi, Mahsa
name: Swanger, Megan
name: Eisenlord, Morgan E.
name: Lee, James Sanghyun
name: Groner, Maya L.
name: Dayal, Sukanya
name: Stoops, Mark
name: Shore, Amanda
name: Venkataraman, Yaamini R.
name: Fast, Mark D.
Publisher: name: Frontiers Media SA
Year: 2023

description: Introduction Seagrass meadows serve as an integral component of coastal ecosystems but are declining rapidly due to numerous anthropogenic stressors including climate change. Eelgrass wasting disease, caused by opportunistic Labyrinthula spp., is an increasing concern with rising seawater temperature. To better understand the host-pathogen interaction, we paired whole organism physiological assays with dual transcriptomic analysis of the infected host and parasite. Methods Eelgrass (Zostera marina) shoots were placed in one of two temperature treatments, 11° C or 18° C, acclimated for 10 days, and exposed to a waterborne inoculation containing infectious Labyrinthula zosterae (Lz) or sterile seawater. At two- and five-days post-exposure, pathogen load, visible disease signs, whole leaf phenolic content, and both host- and pathogen- transcriptomes were characterized. Results Two days after exposure, more than 90% of plants had visible lesions and Lz DNA was detectable in 100% percent of sampled plants in the Lz exposed treatment. Concentrations of total phenolic compounds were lower after 5 days of combined exposure to warmer temperatures and Lz, but were unaffected in other treatments. Concentrations of condensed tannins were not affected by Lz or temperature, and did not change over time. Analysis of the eelgrass transcriptome revealed 540 differentially expressed genes in response to Lz exposure, but not temperature. Lz-exposed plants had gene expression patterns consistent with increased defense responses through altered regulation of phytohormone biosynthesis, stress response, and immune function pathways. Analysis of the pathogen transcriptome revealed up-regulation of genes potentially involved in breakdown of host defense, chemotaxis, phagocytosis, and metabolism. Discussion The lack of a significant temperature signal was unexpected but suggests a more pronounced physiological response to Lz infection as compared to temperature. Pre-acclimation of eelgrass plants to the temperature treatments may have contributed to the limited physiological responses to temperature. Collectively, these data characterize a widespread physiological response to pathogen attack and demonstrate the value of paired transcriptomics to understand infections in a host-pathogen system.
IPBES Invasive Alien Species Assessment, data management report for Chapter 3. Section 3.5.4: Urbanisation and pollution
Creators: name: Camacho-Cervantes, Morelia
Publisher: name: Zenodo
Year: 2023
Subjects: Data management report

description: Section 3.5.4 assesses the interaction between urbanisation and pollution as a driver for the introduction of invasive alien species in Chapter 3 of IPBES thematic assessment of invasive alien species and their control. The experts conducted a systematic review to report on the existing knowledge on these drivers and possible reports of their interaction. This systematic review consists in the main source of evidence for the section.
Clinic presentation delay and tuberculosis treatment outcomes in the Lake Victoria region of East Africa: A multi-site prospective cohort study
Creators: name: Seeley, Janet
name: Bahemuka, Ubaldo M.
name: Emch, Michael
name: Weir, Sharon S.
name: Mulholland, Grace E.
name: Nanyonjo, Gertrude
name: Okech, Brenda A.
name: Kwena, Zachary A.
name: Pettifor, Audrey
name: Edwards, Jessie K.
name: Jeremiah, Kidola
name: Herce, Michael E.
Publisher: name: Public Library of Science
Year: 2023

description: In the Lake Victoria region of East Africa, little is known about delays between tuberculosis (TB) symptom onset and presentation at a clinic. Associations between clinic presentation delay and TB treatment outcomes are also poorly understood. In 2019, we abstracted data from routine TB treatment records for all adults (n = 776) initiating TB treatment in a 6-month period across 12 health facilities near Lake Victoria. We interviewed 301 cohort members and assessed whether they experienced a clinic presentation delay longer than 6 weeks. We investigated potential clinical and demographic correlates of clinic presentation delay and examined the association between clinic presentation delay and an unfavorable TB treatment outcome (death, loss to follow-up, or treatment failure). Clinic presentation delay was common, occurring among an estimated 54.7% (95% CI: 48.9%, 61.2%) of cohort members, though no specific correlates were identified. Clinic presentation delay was slightly associated with unfavorable TB treatment outcomes. The 180-day risk of an unfavorable outcome was 14.2% (95% CI: 8.0%, 20.4%) among those with clinic presentation delay, compared to 12.7% (95% CI: 5.1%, 20.3%) among those presenting earlier. Multi-level community-based interventions may be necessary to reduce clinic presentation delays in communities near Lake Victoria.
Embedding calculus knot invariants are of finite type
Creators: name: Budney, Ryan
name: Conant, James
name: Koytcheff, Robin
name: Sinha, Dev
Publisher: name: arXiv
Year: 2014
Subjects: subject: Algebraic Topology (math.AT)
subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 57M27, 55R80, 55P99, 57R40, 55T99

description: We show that the map on components from the space of classical long knots to the n-th stage of its Goodwillie-Weiss embedding calculus tower is a map of monoids whose target is an abelian group and which is invariant under clasper surgery. We deduce that this map on components is a finite type-(n-1) knot invariant. We also compute the second page in total degree zero for the spectral sequence converging to the components of this tower as Z-modules of primitive chord diagrams, providing evidence for the conjecture that the tower is a universal finite-type invariant over the integers. Key to these results is the development of a group structure on the tower compatible with connect-sum of knots, which in contrast with the corresponding results for the (weaker) homology tower requires novel techniques involving operad actions, evaluation maps, and cosimplicial and subcubical diagrams.
description: Revised maps to the infinitesimal mapping space model in Sections 3 and 4 and analysis of cubical diagrams in Section 5. Minor expository and organizational changes throughout. Now 28 pages, 4 figures
A Role of Tyrosine Phosphatase in Acetylcholine Receptor Cluster Dispersal and Formation
Creators: name: Dai, Zhengshan
name: Benjamin Peng, H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: Innervation of the skeletal muscle involves local signaling, leading to acetylcholine receptor (AChR) clustering, and global signaling, manifested by the dispersal of preexisting AChR clusters (hot spots). Receptor tyrosine kinase (RTK) activation has been shown to mediate AChR clustering. In this study, the role of tyrosine phosphatase (PTPase) in the dispersal of hot spots was examined. Hot spot dispersal in cultured Xenopus muscle cells was initiated immediately upon the presentation of growth factor–coated beads that induce both AChR cluster formation and dispersal. Whereas the density of AChRs decreased with time, the fine structure of the hot spot remained relatively constant. Although AChR, rapsyn, and phosphotyrosine disappeared, a large part of the original hot spot–associated cytoskeleton remained. This suggests that the dispersal involves the removal of a key linkage between the receptor and its cytoskeletal infrastructure. The rate of hot spot dispersal is inversely related to its distance from the site of synaptic stimulation, implicating the diffusible nature of the signal. PTPase inhibitors, such as pervanadate or phenylarsine oxide, inhibited hot spot dispersal. In addition, they also affected the formation of new clusters in such a way that AChR microclusters extended beyond the boundary set by the clustering stimuli. Furthermore, by introducing a constitutively active PTPase into cultured muscle cells, hot spots were dispersed in a stimulus- independent fashion. This effect of exogenous PTPase was also blocked by pervanadate. These results implicate a role of PTPase in AChR cluster dispersal and formation. In addition to RTK activation, synaptic stimulation may also activate PTPase which acts globally to destabilize preexisting AChR hot spots and locally to facilitate AChR clustering in a spatially discrete manner by countering the action of RTKs.
Anaphase A Chromosome Movement and Poleward Spindle Microtubule Flux Occur At Similar Rates in Xenopus Extract Spindles
Creators: name: Maddox, Paul S.
name: Desai, Arshad
name: Salmon, E.D.
name: Mitchison, Timothy J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: We have used local fluorescence photoactivation to mark the lattice of spindle microtubules during anaphase A in Xenopus extract spindles. We find that both poleward spindle microtubule flux and anaphase A chromosome movement occur at similar rates (∼2 μm/min). This result suggests that poleward microtubule flux, coupled to microtubule depolymerization near the spindle poles, is the predominant mechanism for anaphase A in Xenopus egg extracts. In contrast, in vertebrate somatic cells a “Pacman” kinetochore mechanism, coupled to microtubule depolymerization near the kinetochore, predominates during anaphase A. Consistent with the conclusion from fluorescence photoactivation analysis, both anaphase A chromosome movement and poleward spindle microtubule flux respond similarly to pharmacological perturbations in Xenopus extracts. Furthermore, the pharmacological profile of anaphase A in Xenopus extracts differs from the previously established profile for anaphase A in vertebrate somatic cells. The difference between these profiles is consistent with poleward microtubule flux playing the predominant role in anaphase chromosome movement in Xenopus extracts, but not in vertebrate somatic cells. We discuss the possible biological implications of the existence of two distinct anaphase A mechanisms and their differential contributions to poleward chromosome movement in different cell types.
Cognitive phenotypes in late-onset epilepsy: results from the atherosclerosis risk in communities study
Creators: name: Schneider, Andrea L. C.
name: Reyes, Anny
name: McDonald, Carrie R.
name: Johnson, Emily L.
name: Gottesman, Rebecca F.
name: Kucharska-Newton, Anna M.
Publisher: name: Frontiers Media SA
Year: 2023

description: Introduction Cognitive phenotyping is a widely used approach to characterize the heterogeneity of deficits in patients with a range of neurological disorders but has only recently been applied to patients with epilepsy. In this study, we identify cognitive phenotypes in older adults with late-onset epilepsy (LOE) and examine their demographic, clinical, and vascular profiles. Further, we examine whether specific phenotypes pose an increased risk for progressive cognitive decline. Methods Participants were part of the Atherosclerosis Risk in Communities Study (ARIC), a prospective longitudinal community-based cohort study of 15,792 individuals initially enrolled in 1987–1989. LOE was identified from linked Centers for Medicare and Medicaid Services claims data. Ninety-one participants with LOE completed comprehensive testing either prior to or after seizure onset as part of a larger cohort in the ARIC Neurocognitive Study in either 2011–2013 or 2016–2017 (follow-up mean = 4.9 years). Cognitive phenotypes in individuals with LOE were derived by calculating test-level impairments for each participant (i.e., ≤1 SD below cognitively normal participants on measures of language, memory, and executive function/processing speed); and then assigning participants to phenotypes if they were impaired on at least two tests within a domain. The total number of impaired domains was used to determine the cognitive phenotypes (i.e., Minimal/No Impairment, Single Domain, or Multidomain). Results At our baseline (Visit 5), 36.3% met criteria for Minimal/No Impairment, 35% for Single Domain Impairment (with executive functioning/ processing speed impaired in 53.6%), and 28.7% for Multidomain Impairment. The Minimal/No Impairment group had higher education and occupational complexity. There were no differences in clinical or vascular risk factors across phenotypes. Of those participants with longitudinal data (Visit 6; n = 24), 62.5% declined (i.e., progressed to a more impaired phenotype) and 37.5% remained stable. Those who remained stable were more highly educated compared to those that declined. Discussion Our results demonstrate the presence of identifiable cognitive phenotypes in older adults with LOE. These results also highlight the high prevalence of cognitive impairments across domains, with deficits in executive function/processing speed the most common isolated impairment. We also demonstrate that higher education was associated with a Minimal/No Impairment phenotype and lower risk for cognitive decline over time.
Decoding the Complexity of Immune–Cancer Cell Interactions: Empowering the Future of Cancer Immunotherapy
Creators: name: Cao, Yanguang
name: Maffuid, Kaitlyn
Publisher: name: MDPI
Year: 2023

description: The tumor and tumor microenvironment (TME) consist of a complex network of cells, including malignant, immune, fibroblast, and vascular cells, which communicate with each other. Disruptions in cell–cell communication within the TME, caused by a multitude of extrinsic and intrinsic factors, can contribute to tumorigenesis, hinder the host immune system, and enable tumor evasion. Understanding and addressing intercellular miscommunications in the TME are vital for combating these processes. The effectiveness of immunotherapy and the heterogeneous response observed among patients can be attributed to the intricate cellular communication between immune cells and cancer cells. To unravel these interactions, various experimental, statistical, and computational techniques have been developed. These include ligand–receptor analysis, intercellular proximity labeling approaches, and imaging-based methods, which provide insights into the distorted cell–cell interactions within the TME. By characterizing these interactions, we can enhance the design of cancer immunotherapy strategies. In this review, we present recent advancements in the field of mapping intercellular communication, with a particular focus on immune–tumor cellular interactions. By modeling these interactions, we can identify critical factors and develop strategies to improve immunotherapy response and overcome treatment resistance.