cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Astrocyte morphology
Creators: name: Murai, Keith K
name: Khakh, Baljit S
name: Baldwin, Katherine T
Publisher: name: Elsevier
Year: 2023

description: Astrocytes are predominant glial cells that tile the central nervous system (CNS). A cardinal feature of astrocytes is their complex and visually enchanting morphology, referred to as bushy, spongy, and star-like. A central precept of this review is that such complex morphological shapes evolved to allow astrocytes to contact and signal with diverse cells at a range of distances in order to sample, regulate, and contribute to the extracellular milieu, and thus participate widely in cell-cell signaling during physiology and disease. The recent use of improved imaging methods and cell-specific molecular evaluations has revealed new information on the structural organization and molecular underpinnings of astrocyte morphology, the mechanisms of astrocyte morphogenesis, and the contributions to disease states of reduced morphology. These insights have reignited interest in astrocyte morphological complexity as a cornerstone of fundamental glial biology and as a critical substrate for multicellular spatial and physiological interactions in the CNS.
Cratomorphus Motschulsky 1853
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Cratomorphus

description: Genus Cratomorphus Motschulsky, 1853
MTZ: SO, TV, SS, CS; NTR: BB, VE, YU
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 299, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Additional file 4: of Implementation of integration strategies between primary care units and a regional general hospital in Brazil to update and connect health care professionals: a quasi-experimental study protocol
Creators: name: Bracco, Mario
name: Mafra, Ana
name: Abdo, Alexandre
name: Colugnati, Fernando
name: Dalla, Marcello
name: Demarzo, Marcelo
name: Ises Abrahamsohn
name: Rodrigues, Aline
name: Delgado, Ana
name: Glauber Dos Prazeres
name: Teixeira, José
name: Possa, Silvio
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Socio-demographic health professional questionnaire. (DOCX 38 kb)
Brain network connectivity during peer evaluation in adolescent females: Associations with age, pubertal hormones, timing, and status
Creators: name: Miller, Adam Bryant
name: Eisenlohr-Moul, Tory
name: Prinstein, Mitchell J.
name: Rudolph, Karen D.
name: Pelletier-Baldelli, Andrea
name: Rudolph, Marc D.
name: Slavich, George M.
name: Sheridan, Margaret A.
name: Martin, Sophia
name: Srabani, Ellora M.
name: Hastings, Paul D.
name: Nock, Matthew K.
name: Giletta, Matteo
Publisher: name: Elsevier
Year: 2024

description: Despite copious data linking brain function with changes to social behavior and mental health, little is known about how puberty relates to brain functioning. We investigated the specificity of brain network connectivity associations with pubertal indices and age to inform neurodevelopmental models of adolescence. We examined how brain network connectivity during a peer evaluation fMRI task related to pubertal hormones (dehydroepiandrosterone and testosterone), pubertal timing and status, and age. Participants were 99 adolescents assigned female at birth aged 9-15 (M = 12.38, SD = 1.81) enriched for the presence of internalizing symptoms. Multivariate analysis revealed that within Salience, between Frontoparietal - Reward and Cinguloopercular - Reward network connectivity were associated with all measures of pubertal development and age. Specifically, Salience connectivity linked with age, pubertal hormones, and status, but not timing. In contrast, Frontoparietal - Reward connectivity was only associated with hormones. Finally, Cinguloopercular - Reward connectivity related to age and pubertal status, but not hormones or timing. These results provide evidence that the salience processing underlying peer evaluation is jointly influenced by various indices of puberty and age, while coordination between cognitive control and reward circuitry is related to pubertal hormones, pubertal status, and age in unique ways.
Intermolecular C-H activation effected by CP*W(NO)-containing complexes
Creators: name: Tsang, Jenkins Yin Ki
Publisher: name: University of British Columbia
Year: 2008

description: Thermolysis of Cp*W(NO)(CH₂CMe₃)₂ (2.1) in halo, methoxy, or phenylethynyl-substituted benzenes leads to the formation of the alkylidene intermediateCp*W(NO)(=CHCMe₃) which selectively activates ortho C-H bonds of the organicsubstrates. The ortho-regioselectivity diminishes as the size of the substituent increasesfrom F (97 %) to C-=CPh (51 %). In the solid-state structure of all complexes the ortho-substituent is not coordinated to the metal centre; rather, the metal centre is engaged inagostic interactions with a neopentyl methylene C-H bond. Mechanistic studies on the chlorobenzene reaction reveal that the ortho-C-H-activation product is preferentially formed via thermal isomerization from the meta / para-C-H-activation isomers. Reactions between Cp*W(NO)(CH₂EMe₃)Cl (E = C or Si) and a variety of bis(allyl)magnesium reagents lead to the expected formation of Cp*W(NO)(alkyl)(allyl)complexes. Cp*W(N0)(CH₂CMe₃)(η³-CH₂CHCH₂) (3.5), Cp*W(N0)(CH₂CMe₃)(η³-CH₂CMeCH₂) (3.6), Cp*W(N0)(CH₂CMe₃)(η³-CH₂CHCHMe) (3.7),Cp*W(N0)(CH₂CMe₃)(η³-CH₂CHCHPh) (3.8) and Cp*W(N0)(CH₂SiMe₃)(η³-CH₂CHCHMe) (3.9) have thus been synthesized in moderate yields. The solid-state molecular structures of 3.5 and 3.7-3.9 feature a σ-π distorted ally! ligand in the endoconformation. Complex 3.5 reacts with pyrrolidine at RT to form Cp*W(NO)(NC₄H8)(CHMeCH₂NC₄H8) (3.10), a nucleophilic-attack product. Complexes 3.6-3.9 effect the concurrent N-H and α-C-H activation of pyrrolidine at RT and form alkyl-amido complexes analogous to the previously known Cp*W(N0)(CH₂EMe)(NC₄H₇-2-CMe₂CH=CH₂) (3.12). Thermolysis of Cp*W(N0)(CH₂CMe₃)(η³-CH₂CHCHMe) (3.7) at RT leads to the loss of neopentane and the formation of the η²-diene intermediate Cp*W(N0)(η²-CH₂=CHCH=CH₂) (A) which has been isolated as a PMe₃ adduct. In the presence of saturated organic substrates, C-H activation occurs exclusively at the methyl positions of the molecule. Reactions between intermediate A and unsaturated substrates lead to coupling between the coordinated η²-diene and the unsaturation on the organic molecule.Treatment of Cp*W(N0)(n-C₅H₁₁)(η³-CH₂CHCHMe) (4.1) with I₂ at -60 °C produces n-C₅H₁₁ I in moderate yields. Thermolysis of Cp*W(N0)(CH₂CMe₃)(η³-CH₂CHCHPh) (3.8) in benzene at 75 °C for one day leads to the exclusive formation of Cp*W(N0)(H)(η³-PhCHCHCHPh) (5.1).Trapping, labelling, and monitoring experiments suggest that 5.1 is formed via 1) the loss of neopentane and the generation of the allene intermediate Cp*W(N0)(η²-CH₂=C=CHPh), 2) the C-H activation of benzene resulting in a phenyl phenylallyl complex, and 3) the thermal isomerization of this latter species to 5.1.
Socioemotional Wealth Impact on Farmer's Readiness to Retire
Creators: name: Walls, William Isaac
Publisher: name: Purdue University Graduate School
Year: 2024
Subjects: classificationCode: 380101
subject: Agricultural economics

description: The practice of succession is utilized across many aspects of society, especially as it pertains to family farms. Historically, farm family businesses have been an integral part of the United States economy, and continuation of these family farms is not only a goal of theirs but needed for a thriving agricultural sector. This study seeks to discover how socioemotional wealth, having a successor interested in taking over the business, and perceived success in the farm family business impacts a farmer’s readiness to retire. The 2023 Farm Succession Survey was used to implement a logit regression and test hypothesized variables along with other business and owner demographic variables, in relation to incumbents feeling “rich and ready to go”. We find that the high amounts of socioemotional wealth experienced by respondents correlated with incumbents who were less ready to retire. Whereas, having a successor interested, perceiving the business as successful, and age increased the likelihood that respondents felt ready to retire. Socioemotional wealth brings a certain nuance to family farm business succession strategies, since it is a critical factor that influences both the positive and negative sides of succession planning decisions. Succession reflects the life cycles of farm households and businesses. Thus, understanding the emotions of the people involved in the succession practices of farm family businesses becomes more important as this may be a barrier to farmer retirement and subsequent land access for younger generations interested in farming as a career.
Additional file 8 of Markers associated with heading and aftermath heading in perennial ryegrass full-sib families
Creators: name: Arojju, Sai
name: Barth, Susanne
name: Milbourne, Dan
name: Conaghan, Patrick
name: Velmurugan, Janaki
name: Hodkinson, Trevor
name: Byrne, Stephen
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S8. Phylogenetic tree of candidate heading gene PRR37. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [67]. The tree is mid-point rooted, drawn to scale, with branch lengths proportional to the number of substitutions per site. All positions containing gaps and missing data were eliminated. Evolutionary analyses were conducted in MEGA 6.06 [66]. All the associated Lolium and rice proteins were highlighted. (PDF 38 kb)
Rheological Tuning of Entangled Polymer Networks by Transient Cross-links
Creators: name: Forest, M. Gregory
name: Cao, Xue-Zheng
Publisher: name: American Chemical Society (ACS)
Year: 2019

description: The remarkable functionalities of transiently cross-linked, biopolymer networks are increasingly becoming translated into synthetic materials for biomedical and materials science applications. Various computational and theoretical models, representing different transient cross-linking mechanisms, have been proposed to mimic biological and synthetic polymer networks, and to interpret experimental measurements of rheological, transport, and self-repair properties. Herein, we employ molecular dynamics simulations of a baseline entangled polymer melt coupled with parametrized affinities for binding and unbinding of transient cross-links (CLs). From these assumptions alone, we determine the emergent CL mean density and fluctuations, and the induced rheology, across the 2-parameter space of binding and unbinding affinities for a moderately long chain, entangled the polymer melt. For sufficiently weak (short-lived) CLs, nonmonotonicity emerges with respect to the affinity to form CLs: the stress relaxation, viscous, and elastic moduli all shift above the baseline if CLs form rapidly, reverse below the baseline as CLs form slowly, and reverse again, recovering the baseline as CLs form very slowly. For sufficiently strong (long-lived) CLs and sufficiently fast CL formation, a dramatic rise emerges in the viscous and elastic moduli at all frequencies, more prominently in the elastic moduli at medium to high frequencies, inducing a sol-gel transition. These results are placed in context with the experimental and theoretical literature on transient polymer networks.
Cratomorphus anitae Zaragoza-Caballero 1996
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Cratomorphus
Cratomorphus anitae

description: Cratomorphus anitae Zaragoza-Caballero, 1996
MEXICO: CS Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 299, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Additional file 2: of Implementation of integration strategies between primary care units and a regional general hospital in Brazil to update and connect health care professionals: a quasi-experimental study protocol
Creators: name: Bracco, Mario
name: Mafra, Ana
name: Abdo, Alexandre
name: Colugnati, Fernando
name: Dalla, Marcello
name: Demarzo, Marcelo
name: Ises Abrahamsohn
name: Rodrigues, Aline
name: Delgado, Ana
name: Glauber Dos Prazeres
name: Teixeira, José
name: Possa, Silvio
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Sociodemographic patient’s questionnaire. (DOCX 50 kb)
A sharp interface method for an immersed viscoelastic solid
Creators: name: Puelz, Charles
name: Griffith, Boyce E.
Publisher: name: Elsevier
Year: 2020

description: The immersed boundary-finite element method (IBFE) is an approach to describing the dynamics of an elastic structure immersed in an incompressible viscous fluid. In this formulation, there are generally discontinuities in the pressure and viscous stress at fluid-structure interfaces. The standard immersed boundary approach, which connects the Lagrangian and Eulerian variables via integral transforms with regularized Dirac delta function kernels, smooths out these discontinuities, which generally leads to low order accuracy. This paper describes an approach to accurately resolve pressure discontinuities for these types of formulations, in which the solid may undergo large deformations. Our strategy is to decompose the physical pressure field into a sum of two pressure-like fields, one defined on the entire computational domain, which includes both the fluid and solid subregions, and one defined only on the solid subregion. Each of these fields is continuous on its domain of definition, which enables high accuracy via standard discretization methods without sacrificing sharp resolution of the pressure discontinuity. Numerical tests demonstrate that this method improves rates of convergence for displacements, velocities, stresses, and pressures as compared to the conventional IBFE method. Further, it produces much smaller errors at reasonable numbers of degrees of freedom. The performance of this method is tested on several cases with analytic solutions, a nontrivial benchmark problem of incompressible solid mechanics, and an example involving a thick, actively contracting torus.
Additional file 4: of Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network
Creators: name: Richard, Arianne
name: Peters, James
name: Lee, James
name: Vahedi, Golnaz
name: SchĂ¤Ffer, Alejandro
name: Siegel, Richard
name: Lyons, Paul
name: Smith, Kenneth
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: This file includes Supplemental Methods and Figures S1â  S8 with legends. (PDF 954 kb)
Limited processivity of single motors improves overall transport flux of self-assembled motor-cargo complexes
Creators: name: Forest, M Gregory
name: Lai, Samuel K
name: Patel, Keshav B
name: Newby, Jay M
name: Mao, Shengtan
Publisher: name: American Physical Society (APS)
Year: 2019

description: Single kinesin molecular motors can processively move along a microtubule (MT) a few micrometers on average before dissociating. However, cellular length scales over which transport occurs are several hundred microns and more. Why seemingly unreliable motors are used to transport cellular cargo remains poorly understood. We propose a theory for how low processivity, the average length of a single bout of directed motion, can enhance cellular transport when motors and cargos must first diffusively self-assemble into complexes. We employ stochastic modeling to determine the effect of processivity on overall cargo transport flux. We show that, under a wide range of physiologically relevant conditions, possessing "infinite" processivity does not maximize flux along MTs. Rather, we find that lowering processivity, i.e., weaker binding of motors to MTs, can improve transport flux. These results shed light on the relationship between processivity and transport efficiency and offer a theory for the physiological benefits of low motor processivity.
Cratomorphus ayalai Zaragoza-Caballero 1996
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Cratomorphus
Cratomorphus ayalai

description: Cratomorphus ayalai Zaragoza-Caballero, 1996
MEXICO: CS Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 299, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Additional file 3: Figure S2. of Efficacy and safety of bevacizumab plus chemotherapy compared to chemotherapy alone in previously untreated advanced or metastatic colorectal cancer: a systematic review and meta-analysis
Creators: name: Botrel, Tobias
name: Clark, Luciana
name: Paladini, Luciano
name: Otรกvio Clark
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Hematology

description: Comparative effect in non-hematologic toxicities of chemotherapy with bevacizumab versus chemotherapy alone. (PDF 864 kb)
Cratomorphus concolor
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Cratomorphus
Cratomorphus concolor

description: Cratomorphus concolor (Perty, 1830)
MEXICO:CM, CS, HG, PU, QR, SL, TB, VE, YU; Panama
= Lampyris concolor Perty, 1830
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 299, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Additional file 9 of Markers associated with heading and aftermath heading in perennial ryegrass full-sib families
Creators: name: Arojju, Sai
name: Barth, Susanne
name: Milbourne, Dan
name: Conaghan, Patrick
name: Velmurugan, Janaki
name: Hodkinson, Trevor
name: Byrne, Stephen
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S9. Phylogenetic tree of candidate heading gene SOC1. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [67]. The tree is mid-point rooted, drawn to scale, with branch lengths proportional to the number of substitutions per site. All positions containing gaps and missing data were eliminated. Evolutionary analyses were conducted in MEGA 6.06 [66]. All the associated Lolium and Arabidopsis proteins were highlighted. (PDF 42 kb)
Additional file 3: of Implementation of integration strategies between primary care units and a regional general hospital in Brazil to update and connect health care professionals: a quasi-experimental study protocol
Creators: name: Bracco, Mario
name: Mafra, Ana
name: Abdo, Alexandre
name: Colugnati, Fernando
name: Dalla, Marcello
name: Demarzo, Marcelo
name: Ises Abrahamsohn
name: Rodrigues, Aline
name: Delgado, Ana
name: Glauber Dos Prazeres
name: Teixeira, José
name: Possa, Silvio
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Questionnaire on treatment adherence. (DOCX 72 kb)
LPS-binding IgG arrests actively motile Salmonella Typhimurium in gastrointestinal mucus
Creators: name: Miao, Ed
name: Lai, Samuel K.
name: Schroeder, Holly A.
name: Subramani, Babu
name: Newby, Jay
name: Schaefer, Alison
name: Tubbs, Alan
name: Forest, M. Gregory
Publisher: name: Elsevier
Year: 2020

description: The gastrointestinal (GI) mucosa is coated with a continuously secreted mucus layer that serves as the first line of defense against invading enteric bacteria. We have previously shown that antigen-specific immunoglobulin G (IgG) can immobilize viruses in both human airway and genital mucus secretions through multiple low-affinity bonds between the array of virion-bound IgG and mucins, thereby facilitating their rapid elimination from mucosal surfaces and preventing mucosal transmission. Nevertheless, it remains unclear whether weak IgG-mucin crosslinks could reinforce the mucus barrier against the permeation of bacteria driven by active flagella beating, or in predominantly MUC2 mucus gel. Here, we performed high-resolution multiple particle tracking to capture the real-time motion of hundreds of individual fluorescent Salmonella Typhimurium in fresh, undiluted GI mucus from Rag1âˆ’/âˆ’ mice, and analyzed the motion using a hidden Markov model framework. In contrast to control IgG, the addition of anti-lipopolysaccharide IgG to GI mucus markedly reduced the progressive motility of Salmonella by lowering the swim speed and retaining individual bacteria in an undirected motion state. Effective crosslinking of Salmonella to mucins was dependent on Fc N-glycans. Our findings implicate IgG-mucin crosslinking as a broadly conserved function that reduces mucous penetration of both bacterial and viral pathogens.
Method development for the comprehensive analysis of post translational modifications by mass spectometry
Creators: name: Hoffman, Michael David
Publisher: name: University of British Columbia
Year: 2008

description: Signal Transduction is mediated by protein complexes whose spatial- and temporal-distribution, composition and function within cells are often regulated by different post-translational modifications (PTM). As PTMs add or subtract a specific mass difference to a protein, mass spectrometry becomes very amenable for modification analysis. These modifications have conventionally been monitored by fragmenting the modified protein or peptide by collision induced dissociation (CID) within the mass spectrometer, and then screening for the characteristic neutral fragment or fragment ion (marker ion), which is particular to the modification in question. Unfortunately, there are two major issues with respect to the traditional mass spectrometric analysis of PTMs: (1) as there are over 300 known types of modifications, the characteristic fragmentation of only a fraction of these modifications has been studied and (2) the traditional mass spectrometric approaches can only monitor these modifications sequentially, and thus comprehensive modification analysis would be unfeasible considering the breadth of PTMs. The following work aims to address these issues by (1) analyzing PTMs that have never been characterized mass spectrometrically and (2) developing a multiplexed technique for comprehensive PTM monitoring by simultaneously screening for all known characteristic fragments. With respect to the first issue, the characteristic fragmentation of lipid modifications and HNO-induced modifications was investigated. The most prevalent indicator(s) of the modification within the mass spectra are as follows: fragmentation of N-terminal myristoylated peptides produced marker ions at 240 and 268 Th, fragmentation of cysteine farnesylated peptides produced a marker ion at 205 Th and a neutral fragment of 204 Da, and fragmentation of cysteine palmitoylated peptides produced a neutral fragment of 272 Th. For HNO-induced modifications, fragmentation of the sulfinamide- and sulfinic acid-modified peptides produced a neutral fragment of 65 Da and 66 Da, respectively. With respect to the second issue, a multiplexed technique for monitoring modifications that fragment as neutral losses, termed Multiple Neutral Loss Monitoring (MNM), has been developed, successfully validated, and then shown to be the most sensitive approach for PTM analysis. MNM, combined with a second multiplexed approach, targeted Multiple Precursor Ion Monitoring, has been used to provide a comprehensive PTM analysis.
Additional file 1: of Efficacy and safety of bevacizumab plus chemotherapy compared to chemotherapy alone in previously untreated advanced or metastatic colorectal cancer: a systematic review and meta-analysis
Creators: name: Botrel, Tobias
name: Clark, Luciana
name: Paladini, Luciano
name: Otรกvio Clark
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Biotechnology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Hematology

description: Quality assessment (risk of bias) of randomized studies evaluating bevacizumab plus chemotherapy in patients with mCRC in first line chemotherapy. (DOCX 46 kb)
An immersed interface-lattice Boltzmann method for fluid-structure interaction
Creators: name: Kolahdouz, Ebrahim M.
name: Griffith, Boyce E.
name: Qin, Jianhua
Publisher: name: Elsevier
Year: 2021

description: An immersed interface-lattice Boltzmann method (II-LBM) is developed for modeling fluid-structure systems. The key element of this approach is the determination of the jump conditions that are satisfied by the distribution functions within the framework of the lattice Boltzmann method where forces are imposed along a surface immersed in an incompressible fluid. In this initial II-LBM, the discontinuity related to the normal component of the interfacial force is sharply resolved by imposing the relevant jump conditions using an approach that is analogous to imposing the corresponding pressure discontinuity in the incompressible Navier-Stokes equations. We show that the jump conditions for the distribution functions are the same in both single-relaxation-time and multi-relaxation-time LBM formulations. Tangential forces are treated using the immersed boundary-lattice Boltzmann method (IB-LBM). In our implementation, a level set approach is used to impose jump conditions for rigid-body models. For flexible boundary models, we describe the moving interface by interpolating the positions of marker points that move with the fluid. The II-LBM introduced herein is compared to a direct forcing IB-LBM for rigid-body fluid-structure interaction, and a classical IB-LBM for cases involving elastic interfaces. Higher order accuracy is observed with the II-LBM as compared to the IB-LBM for selected benchmark problems. Although our II-LBM only imposes jump conditions corresponding to the pressure, the error in the velocity field is demonstrated to be much smaller for the II-LBM than the IB-LBM. The II-LBM is also demonstrated to provide superior volume conservation when simulating flexible boundaries.
Additional file 7 of Markers associated with heading and aftermath heading in perennial ryegrass full-sib families
Creators: name: Arojju, Sai
name: Barth, Susanne
name: Milbourne, Dan
name: Conaghan, Patrick
name: Velmurugan, Janaki
name: Hodkinson, Trevor
name: Byrne, Stephen
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S7. Phylogenetic tree of candidate heading gene CRY2. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [67]. The tree is mid-point rooted, drawn to scale, with branch lengths proportional to the number of substitutions per site. All positions containing gaps and missing data were eliminated. Evolutionary analyses were conducted in MEGA 6.06 [66]. All the associated Lolium and Arabidopsis proteins were highlighted. (PDF 40 kb)
Cratomorphus elevatus Olivier 1896
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Cratomorphus
Cratomorphus elevatus

description: Cratomorphus elevatus Olivier, 1896
MEXICO Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 299, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Efficiency enhancement of organic thin-film phototransistors due to photoassisted charge injection
Creators: name: Jagoo, Zafrullah
name: McNeil, L. E.
name: Jurchescu, Oana D.
name: Lamport, Zachary A.
Publisher: name: AIP Publishing
Year: 2021

description: Understanding the underlying physics of charge transport in organic semiconductors under illumination is important for the development of novel optoelectronic applications. We study the effects of monochromatic light in the visible spectrum on the channel of an organic thin-film transistor based on 2,8-difluoro-5,11-bis(triethylsilylethynyl) anthradithiophene. When the channel of the transistor was illuminated with red, green, or blue light, more charge carriers were measured than what exciton generation from photon absorption alone could provide, leading to a photon-to-charge-carrier conversion efficiency much larger than 100%. We explain this phenomenon using a model incorporating space-charge limited photocharges and enhanced hole injection from the source electrode due to lowering of the potential barrier by photogenerated electrons.
Cratomorphus halffteri Zaragoza-Caballero 2012
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Cratomorphus
Cratomorphus halffteri

description: Cratomorphus halffteri Zaragoza-Caballero, 2012a
MEXICO: CX Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 299, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
High-Photoresponsivity Transistors Based on Small-Molecule Organic Semiconductors
Creators: name: Jurchescu, Oana D.
name: McNeil, Laurie E.
name: Lamport, Zachary A.
name: Jagoo, Zafrullah
Publisher: name: American Chemical Society (ACS)
Year: 2022

description: We investigate the viability of 2,8-difluoro-5,11-bisÂ­(triethylsilylethynyl)Â­anthradithiophene (diF-TES ADT) as a photosensor and show that there is a direct correlation between the absorption spectrum of the material and the magnitude of the resulting drain current in a field-effect transistor device made from it. We show that the diF-TES ADT device exhibits very high photosensitivity and photoresponsivity for green and blue light. We also propose a hybrid device structure that leverages the high absorptivities of two organic semiconductors to make a sandwich device with high phototransistor metrics across all wavelengths of visible light.
Antibody-Mediated Immobilization of Virions in Mucus
Creators: name: Forest, M. Gregory
name: Wang, Ying-Ying
name: Lai, Samuel K.
name: Jensen, Melanie A.
name: McKinley, Scott A.
Publisher: name: Springer Nature
Year: 2019

description: Antibodies have been shown to hinder the movement of herpes simplex virus virions in cervicovaginal mucus, as well as other viruses in other mucus secretions. However, it has not been possible to directly observe the mechanisms underlying this phenomenon, so the nature of virion-antibody-mucin interactions remain poorly understood. In this work, we analyzed thousands of virion traces from single particle tracking experiments to explicate how antibodies must cooperate to immobilize virions for relatively long time periods. First, using a clustering analysis, we observed a clear separation between two classes of virion behavior: freely diffusing and immobilized. While the proportion of freely diffusing virions decreased with antibody concentration, the magnitude of their diffusivity did not, implying an all-or-nothing dichotomy in the pathwise effect of the antibodies. Proceeding under the assumption that all binding events are reversible, we used a novel switch-point detection method to conclude that there are very few, if any, state switches on the experimental timescale of 20Â s. To understand this slow state switching, we analyzed a recently proposed continuous-time Markov chain model for binding kinetics and virion movement. Model analysis implied that virion immobilization requires cooperation by multiple antibodies that are simultaneously bound to the virion and mucin matrix and that there is an entanglement phenomenon that accelerates antibody-mucin binding when a virion is immobilized. In addition to developing a widely applicable framework for analyzing multistate particle behavior, this work substantially enhances our mechanistic understanding of how antibodies can reinforce a mucus barrier against passive invasive species.
Cratomorphus hoffmannae Zaragoza-Caballero 1996
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Cratomorphus
Cratomorphus hoffmannae

description: Cratomorphus hoffmannae Zaragoza-Caballero, 1996
MEXICO: PU Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 299, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Experimental Data and PBPK Modeling Quantify Antibody Interference in PEGylated Drug Carrier Delivery
Creators: name: Wessler, Timothy
name: Lai, Samuel K.
name: Talkington, Anne M.
name: Cao, Yanguang
name: Forest, M. Gregory
Publisher: name: Springer Nature
Year: 2021

description: Physiologically-based pharmacokinetic (PBPK) modeling is a popular drug development tool that integrates physiology, drug physicochemical properties, preclinical data, and clinical information to predict drug systemic disposition. Since PBPK models seek to capture complex physiology, parameter uncertainty and variability is a prevailing challenge: there are often more compartments (e.g., organs, each with drug flux and retention mechanisms, and associated model parameters) than can be simultaneously measured. To improve the fidelity of PBPK modeling, one approach is to search and optimize within the high-dimensional model parameter space, based on experimental time-series measurements of drug distributions. Here, we employ Latin Hypercube Sampling (LHS) on a PBPK model of PEG-liposomes (PL) that tracks biodistribution in an 8-compartment mouse circulatory system, in the presence (APA+) or absence (naive) of anti-PEG antibodies (APA). Near-continuous experimental measurements of PL concentration during the first hour post-injection from the liver, spleen, kidney, muscle, lung, and blood plasma, based on PET/CT imaging in live mice, are used as truth sets with LHS to infer optimal parameter ranges for the full PBPK model. The data and model quantify that PL retention in the liver is the primary differentiator of biodistribution patterns in naive versus APA+ mice, and spleen the secondary differentiator. Retention of PEGylated nanomedicines is substantially amplified in APA+ mice, likely due to PL-bound APA engaging specific receptors in the liver and spleen that bind antibody Fc domains. Our work illustrates how applying LHS to PBPK models can further mechanistic understanding of the biodistribution and antibody-mediated clearance of specific drugs.
Compensatory remodeling of a septo-hippocampal GABAergic network in the triple transgenic Alzheimer's mouse model
Creators: name: Zhang, Wei-Ting
name: Chen, Ze-Ka
name: Cohen, Todd J
name: Wickersham, Ian R
name: Bao, Hechen
name: Li, Ya-Dong
name: Wander, Connor M
name: ChÃ©ry, Samantha L
name: Sullivan, Heather A
name: Shih, Yen-Yu Ian
name: Tart, Dalton S
name: Chao, Tzu-Hao Harry
name: Song, Juan
name: Luo, Yan-Jia
name: Asrican, Brent
Publisher: name: Springer Nature
Year: 2023

description: Background Alzheimer's disease (AD) is characterized by a progressive loss of memory that cannot be efficiently managed by currently available AD therapeutics. So far, most treatments for AD that have the potential to improve memory target neural circuits to protect their integrity. However, the vulnerable neural circuits and their dynamic remodeling during AD progression remain largely undefined. Methods Circuit-based approaches, including anterograde and retrograde tracing, slice electrophysiology, and fiber photometry, were used to investigate the dynamic structural and functional remodeling of a GABAergic circuit projected from the medial septum (MS) to the dentate gyrus (DG) in 3xTg-AD mice during AD progression. Results We identified a long-distance GABAergic circuit that couples highly connected MS and DG GABAergic neurons during spatial memory encoding. Furthermore, we found hyperactivity of DG interneurons during early AD, which persisted into late AD stages. Interestingly, MS GABAergic projections developed a series of adaptive strategies to combat DG interneuron hyperactivity. During early-stage AD, MS-DG GABAergic projections exhibit increased inhibitory synaptic strength onto DG interneurons to inhibit their activities. During late-stage AD, MS-DG GABAergic projections form higher anatomical connectivity with DG interneurons and exhibit aberrant outgrowth to increase the inhibition onto DG interneurons. Conclusion We report the structural and functional remodeling of the MS-DG GABAergic circuit during disease progression in 3xTg-AD mice. Dynamic MS-DG GABAergic circuit remodeling represents a compensatory mechanism to combat DG interneuron hyperactivity induced by reduced GABA transmission.
Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets
Creators: name: Plotkin, Alec
name: Stanley, Natalie
name: Yi, Haidong
Publisher: name: Springer Nature
Year: 2024

description: Background To analyze the large volume of data generated by single-cell technologies and to identify cellular correlates of particular clinical or experimental outcomes, differential abundance analyses are often applied. These algorithms identify subgroups of cells whose abundances change significantly in response to disease progression, or to an experimental perturbation. Despite the effectiveness of differential abundance analyses in identifying critical cell-states, there is currently no systematic benchmarking study to compare their applicability, usefulness, and accuracy in practice across single-cell modalities. Results Here, we perform a comprehensive benchmarking study to objectively evaluate and compare the benefits and potential downsides of current state-of-the-art differential abundance testing methods. We benchmarked six single-cell testing methods on several practical tasks, using both synthetic and real single-cell datasets. The tasks evaluated include effectiveness in identifying true differentially abundant subpopulations, accuracy in the adequate handling of batch effects, runtime efficiency, and hyperparameter usability and robustness. Based on various evaluation results, this paper gives dataset-specific suggestions for the practical use of differential abundance testing approaches. Conclusions Based on our benchmarking study, we provide a set of recommendations for the optimal usage of single-cell DA testing methods in practice, particularly with respect to factors such as the presence of technical noise (for example batch effects), dataset size, and hyperparameter sensitivity.
Measurement error correction in particle tracking microrheology
Creators: name: Newby, Jay
name: Cribb, Jeremy
name: Hill, David B.
name: Forest, M. Gregory
name: Ling, Yun
name: Lysy, Martin
name: Seim, Ian
Publisher: name: Institute of Mathematical Statistics
Year: 2022

description: In diverse biological applications, particle tracking of passive microscopic species has become the experimental measurement of choice – when either the materials are of limited volume, or so soft as to deform uncontrollably when manipulated by traditional instruments. In a wide range of particle tracking experiments, a ubiquitous finding is that the mean squared displacement (MSD) of particle positions exhibits a power-law signature, the parameters of which reveal valuable information about the viscous and elastic properties of various biomaterials. However, MSD measurements are typically contaminated by complex and interacting sources of instrumental noise. As these often affect the high-frequency bandwidth to which MSD estimates are particularly sensitive, inadequate error correction can lead to severe bias in power law estimation and thereby, the inferred viscoelastic properties. In this article, we propose a novel strategy to filter high-frequency noise from particle tracking measurements. Our filters are shown theoretically to cover a broad spectrum of high-frequency noises, and lead to a parametric estimator of MSD power-law coefficients for which an efficient computational implementation is presented. Based on numerous analyses of experimental and simulated data, results suggest our methods perform very well compared to other denoising procedures.
Rigidity Percolation in Disordered 3D Rod Systems
Creators: name: Mucha, Peter J.
name: Heroy, Samuel
name: Forest, M. Gregory
name: Shi, Feng
name: Taylor, Dane
Publisher: name: Society for Industrial & Applied Mathematics (SIAM)
Year: 2022

description: In composite materials composed of a soft polymer matrix and rigid, high aspect-ratio particles, the composite undergoes a transition in mechanical strength when the incorporated particle phase surpasses a critical density. This phenomenon, termed rheological percolation, is well known to occur in many polymer-rod and polymer-platelet composites at a critical density that exceeds the conductivity percolation threshold (which occurs when the conducting particles form a large connected component that spans the composite). Contact percolation in rod-like composites has been routinely exploited to engineer thermal or electrical conductivity in otherwise nonconducting polymers, and the characterization of contact percolation is well established. Mechanical or rheological percolation, however, has evaded a complete theoretical explanation and predictive description. A natural hypothesis is that rheological percolation is due to a rigidity phenomenon, whereby a large rigid component of inclusions spans the composite. Here we build an algorithm to detect the rigidity percolation threshold in rod-polymer composites. We model the composites as systems of randomly distributed, soft-core (intersecting at contact) rods and study the emergence of a giant (i.e., spanning) rigid component. Building on our previous results for two-dimensional composites, we develop an approximate algorithm that identifies spanning rigid components through hierarchically identifying and compressing provably rigid motifs—equivalently, decomposing a giant rigid component into rigid assemblies of a hierarchy of successively smaller rigid components. We apply this algorithm to random monodisperse systems that are generated in Monte Carlo simulations to estimate a rigidity percolation threshold (critical density) and explore its dependence on rod aspect ratio. We show that this transition point—like its contact percolation analogue—scales inversely with the excluded volume of a rod. Moreover, this implies that the critical contact number (i.e., the number of contacts per rod at the rigidity percolation threshold) is constant for aspect ratios above some relatively low value and is lower than the prediction from Maxwell’s isostatic condition.