Miracle-dz/UniFAR-FTUs huggingface dataset:
The Cdc42 GEF, Gef1, promotes uniform protein distribution along the actomyosin ring to enable concentric furrowing

During cytokinesis, fission yeast coordinates actomyosin ring constriction with septum ingression, resulting in concentric furrow formation. Mechanisms coordinating septum ingression with the actomyosin ring remain unclear. We report that cells lacking the Cdc42 activator Gef1, combined with an activated allele of the formin, Cdc12, display non-concentric furrowing. Although cells that furrow non-concentrically display normal actomyosin rings, the scaffold Cdc15 is unevenly distributed along the ring. This suggests that after ring assembly, uniform Cdc15 distribution along the ring drives proper furrow formation. We find that Cdc15 levels at the ring are reduced in the activated cdc12 mutant, or upon disruption of Arp2/3 complex-dependent endocytic patches. Furthermore, Cdc15 levels in endocytic patches increase in gef1 mutants. We hypothesize that assembled rings recruit Cdc15 from endocytic patches. Patches with higher Cdc15 levels and slower ring-association rate lead to uneven Cdc15 distribution. Based on this hypothesis we developed a mathematical model that captures experimentally observed Cdc15 distributions along the ring. We propose that, at the ring, Gef1 and endocytic events promote uniform Cdc15 distribution to enable proper septum ingression and concentric furrow formation. Summary Statement Gef1 and endocytic events at the assembled actomyosin ring facilitate uniform Cdc15 distribution along the ring thus enabling concentric furrow formation.
Clustering of the structures of protein kinase activation loops: A new nomenclature for active and inactive kinase structures

Targeting protein kinases is an important strategy for intervention in cancer. Inhibitors are directed at the conserved active conformation or a variety of inactive conformations. While attempts have been made to classify these conformations, a structurally rigorous catalogue of states has not been achieved. The kinase activation loop is crucial for catalysis and begins with the conserved DFGmotif (Asp-Phe-Gly). This motif is observed in two major classes of conformations, DFGin - an ensemble of active and inactive conformations where the Phe residue is in contact with the C-helix of the N-terminal lobe, and DFGout - an inactive form where Phe occupies the ATP site exposing the C-helix pocket. We have developed a clustering of kinase conformations based on the backbone dihedral angles of the sequence X-D-F, where X is the residue before the DFGmotif, and the DFG-Phe side-chain rotamer, utilizing a density-based clustering algorithm. We have identified 8 distinct conformations and labeled them based on their Ramachandran regions (A=alpha, B=beta, L=left) and the Phe rotamer (minus, plus, trans). Our clustering divides the DFGin group into six clusters including ‘BLAminus,’ which contains active structures, and two common inactive forms, ‘BLBplus’ and ‘ABAminus. ’ DFGout structures we have are predominantly in the ‘BBAminus’ conformation, which is essentially required for binding Type II inhibitors. Structural features such as the C-helix position and the overall activation loop conformation are strongly associated with our clusters. Our structurally intuitive nomenclature will aid in understanding the conformational dynamics of these proteins and structure-based development of kinase drugs. Significance statement Protein kinases play important roles in different signaling pathways and are widely studied as drug targets. Their active site exhibits remarkable structural variation as observed in the large number of available crystal structures which are determined in apo-form and in complex with natural ligands and inhibitors. We have developed a clustering scheme and nomenclature to categorize and label all the observed conformations in human protein kinases. This has enabled us to clearly define the geometry of the active state and to distinguish closely related inactive states which were previously not characterized. We believe that our classification of kinase conformations will help in better understanding the conformational dynamics of these proteins and the development of inhibitors against them.
Nonbinary branching of myelinated dendrites at nodal networks on afferent terminal arbors in paddlefish electroreceptors

The branching of vertebrate neuronal processes, axons or dendrites, is predominantly binary, where a proximal neuronal process bifurcates into two distal progeny. Here, we illustrate counterexamples where neuronal processes branched into more than 2, up to 6, progeny branches, in one step. These were branch points of myelinated dendrites in the peripheral terminals of ALLn cranial nerve afferents innervating the Lorenziniantype ampullary electroreceptors on the rostrum of paddlefish, Polyodon spathula. We imaged afferent terminals fluorescently (in widefield stacks, with deconvolution) after immunolabling of afferent terminals for neuronal cytoplasmic neurofilament-H (NEFH), myelin markers (MBP, P0), or nodal ion channels (Nav1.x, Kv1.1), or after migration of DiI in dendrite membranes. Branched afferent terminals formed a laminar radial radiation beneath a receptive field, parallel to the skin surface, with two serial stages: (1) Starting at each afferent’s centric first branchpoint, each of a small group of 2–4 (most often 3) afferents branched radially into 2–4 (usually 3) generations of myelinated dendrites, whose internodes were covered by sheaths immunoreactive for antigenic markers of myelin (MBP+/P0+), ending distally at ~15 heminode presumed spike initiation zones. (2) From the latter, bundles of unmyelinated (MBP-/P0-) sensory neuron (NEFH+) processes projected distally to innervate electrosensory neuroepithelia of adjacent ampullary organs. The nonbinary branch points that we imaged were in stage-1, on myelinated dendrites. Branch points always coincided with composite systems of nodes, in which each progeny dendrite started at a narrowed nodal segment expressing voltage gated sodium ion channels at high density. These narrowed nodal segments of multiple progeny branched in parallel from a parent’s blunt distal end. Hence the branch point nodal complexes formed multisite excitable systems, likely strongly coupled due to proximity.
Wearable Technology and Analytics as a Complementary Toolkit to Optimize Workload and to Reduce Injury Burden

Wearable sensors enable the real-time and non-invasive monitoring of biomechanical, physiological, or biochemical parameters pertinent to the performance of athletes. Sports medicine researchers compile datasets involving a multitude of parameters that can often be time consuming to analyze in order to create value in an expeditious and accurate manner. Machine learning and artificial intelligence models may aid in the clinical decision-making process for sports scientists, team physicians, and athletic trainers in translating the data acquired from wearable sensors to accurately and efficiently make decisions regarding the health, safety, and performance of athletes. This narrative review discusses the application of commercial sensors utilized by sports teams today and the emergence of descriptive analytics to monitor the internal and external workload, hydration status, sleep, cardiovascular health, and return-to-sport status of athletes. This review is written for those who are interested in the application of wearable sensor data and data science to enhance performance and reduce injury burden in athletes of all ages.
Investigation Of ULTEM 9085 For Use In 3-D Printed Orbital Structures

Additive manufacturing is revolutionizing industries ranging from medicine to space. However, the structural characteristics of plastic parts created by these methods are not as well understood as their more established counterparts. This research explored two relevant areas: how the structural characteristics of ULTEM 9085 plastic behaved after exposure to orbital conditions and the design of the cross-sectional area of a beam to be 3-D printed in microgravity based on the expected loads from the printer. To study orbital effects, ULTEM 9085 was printed into 1/4th scale ASTM D63814 dogbones using a Stratasys 450mc printer. These dogbones were placed in a vacuum chamber and exposed to ultraviolet (UV) radiation and high temperatures. The dogbones were removed regularly from the testing environments after up to 980 hours in the chamber and subjected to axial loading tests using an MTS Microtester. Using the initial shape of the dogbones and the collected force values, the stressstrain curve for each sample in each exposure duration was found, and the Young’s modulus, Ultimate Tensile Strength (UTS), Yield Tensile Strength (YTS), Poisson’s ratio, and Fracture Strain calculated. The ULTEM 9085 became stronger as a result of the vacuum and more brittle as a result of the UV radiation. Simultaneously, data from previous studies into ULTEM 9085’s structural characteristics was imported into Hyperworks’ Optistruct software module. The data was used to optimize a beam’s internal structure based on several possible loading configurations expected during printing on orbit. A general design was selected and its maximum allowable end moment was found. The above information will be helpful in designing ULTEM 9085 structures for use on orbit.
scRMD: Imputation for single cell RNA-seq data via robust matrix decomposition

Motivation Single cell RNA-sequencing (scRNA-seq) technology enables whole transcriptome profiling at single cell resolution and holds great promises in many biological and medical applications. Nevertheless, scRNA-seq often fails to capture expressed genes, leading to the prominent dropout problem. These dropouts cause many problems in down-stream analysis, such as significant noise increase, power loss in differential expression analysis and obscuring of gene-to-gene or cell-to-cell relationship. Imputation of these dropout values thus becomes an essential step in scRNA-seq data analysis. Results In this paper, we model the dropout imputation problem as robust matrix decomposition. This model has minimal assumptions and allows us to develop a computational efficient imputation method scRMD. Extensive data analysis shows that scRMD can accurately recover the dropout values and help to improve downstream analysis such as differential expression analysis and clustering analysis. Contact ruibinxi@math.pku. edu.cn
Functions of Macrophages in the Maintenance of Intestinal Homeostasis

Intestinal macrophages constitute the largest pool of macrophages in the body and have emerged as crucial sentinels for pathogen recognition and elimination. The source and development of intestinal macrophages, as well as their distinct properties have been well documented. Intestinal macrophages exert their functions in the maintenance of intestinal homeostasis by shaping host-microbiota symbiosis, managing gut inflammation, crosstalking with T cells, and facilitating wound repair. Recently, nutritional regulation of intestinal macrophages has attracted substantial attention and is becoming a promising approach to disease prevention and control. Understanding the mechanisms employed by intestinal macrophages in mediating intestinal immune homeostasis and inflammation, as well as the mode of action of dietary nutrients in the modulating functions of intestinal macrophages, represents an opportunity to prevent and control inflammatory bowel diseases.
IMPLICAÇÕES DA SUSTENTABILIDADE NA CADEIA DE SUPRIMENTOS: UM ESTUDO DE CASO EM UMA EMPRESA ATACADISTA

A gestao de cadeias de suprimento sustentavel consiste na aplicacao de atividades sustentaveis, considerando o Triple Botton Line (ambiental, social e economico), na gestao de cadeia de suprimentos. As organizacoes tendem a expandir as praticas que levem a sustentabilidade por pressoes dos stakeholders , e por uma questao de sobrevivencia no mercado. Sendo assim, esta pesquisa tem como objetivo descrever e analisar as praticas sustentaveis de uma empresa focal, bem como sua relacao com a cadeia de fornecimento, de modo a identificar se as praticas sustentaveis dos fornecedores afetam sua sustentabilidade. Como metodologia, utilizou-se um estudo de caso em uma empresa atacadista referencia no pais, situada na cidade de Uberlândia. Os resultados mostraram que a sustentabilidade da empresa focal esta diretamente relacionada com a sustentabilidade dos membros de sua cadeia de suprimentos. Tambem se constatou que as cadeias de suprimentos sustentaveis, alem de minimizar os impactos negativos das atividades organizacionais no meio ambiente e na sociedade, permitem a reducao custos, melhoria da imagem da empresa, promovem inovacao e conduzem relacoes mais fortes e duradouras com os membros da cadeia de abastecimento. A pesquisa contribui com a literatura por apresentar de forma pratica a sustentabilidade em uma cadeia de suprimentos de uma empresa atacadista brasileira, sendo um tema ainda pouco explorado nesse setor, de forma que a expansao das praticas sustentaveis pode proporcionar beneficios estrategicos.
Circulating Myeloid-Derived Suppressor Cell Subsets in Patients with Colorectal Cancer - Exploratory Analysis of Their Biomarker Potential.

BACKGROUND Myeloid-derived suppressor cells (MDSCs) contribute to tumor escape from host immune surveillance and to tumor progression by producing tumor-promoting factors. We focused on clinical and analytical MDSCs-related issues as potential biomarkers and immune regulators involved in tumor progression. PATIENTS AND METHODS We analyzed 10 patients with advanced colorectal carcinoma (CRC) with (M1 subgroup) or without (M0 subgroup) distant metastases at diagnosis. Peripheral blood was collected at diagnosis prior to treatment and subsequently 12 months after therapy initiation. Using multicolor flow cytometry MDSC subsets were evaluated. Monocytic MDSCs (M-MDSCs) were detected as CD45+ CD11b+ CD33+ HLA-DRlow/ CD14+ CD15-, granulocytic MDSCs (CD33hi PMN-MDSC) were detected as CD45+ CD11b+ CD33hi HLA-DRlow/ CD14 CD15+. For analytical and preanalytical studies, random fresh blood specimens predominantly from cancer patients were analyzed. RESULTS Levels of circulating M-MDSCs were not associated with metastatic disease within advanced CRC patients. Levels of circulating CD33hi PMN-MDSCs were elevated in patients with distant metastases compared to T3 M0 subgroup. Circulating M-MDSCs increased upon treatment initiation in 9 out of 10 patients. CD33hi PMN-MDSCs substantially dropped upon treatment initiation in 5 out of 10 patients and substantially increased in 2 out of 10 patients. Analytical part showed that absolute and relative counts within each MDSC subset are correlated. Coefficient of variation (CV) for repeatability was 6-11% for M-MDSCs and 25-44% for CD33hi PMN-MDSCs. CV for reproducibility was higher with 8-22% for M-MDSCs and 35-79% for CD33hi PMN-MDSCs demonstrating that delay in measurement of MDSCs in whole blood specimen may distort quantification of circulating MDSC subsets. CONCLUSION The quantification of MDSC subsets is substantially dependent on the type of specimen examined and its preanalytical processing. Exploratory analysis of M-MDSCs and CD33hi PMN-MDSCs in CRC patients revealed different dynamics of M-MDSC and CD33hi PMN-MDSC subsets in the context anti-cancer treatment. Key words: myeloid-derived suppressor cells - preanalytics - colorectal cancer - flow cytometry - immune monitoring.
MOLECULAR CHARACTERIZATION OF Tomato yellow leaf curl virus AND Fusarium oxysporum formae speciales AND RACEs OF TOMATO AREAs IN NORTHERN CYPRUs

Fusarium oxysporum (FO) and viruses have caused wilt, root, crown rots, mosaic, yellowing and curling on tomato plants and have resulted economic yield losses on tomato production areas at Northern Cyprus (NC) in 2011–2015 years. Typical FO symptoms showing greenhouse and open field areas used for collecting 62 plants and suspected Tomato yellow leaf curl virus (TYLCV) of 76 tomato plants have been studied respectively. In the researches, four different primers [uni,sp13,sp23,sprl] were used to determine the formae specialis and races of 62 isolates of FO isolates from different locations. PCR analyse studies have revealed that 81% of collected samples were Fusarium oxysporum f.sp. lycopersici (FOL) and 19% of them were Fusarium oxysporum f.sp. radicis-lycopersici (FORL). Additionally, further PCR analyses have identified that 37% of FOL samples were race 1, 15% were race 2 and 29% were race 3 identified respectively. The different samples of 76 tomato plants were tested with specific primers in PCR amplifications. Their results determined that the strains TYLCV-Israel, TYLCV-Sicilia, TYLCV-Mild of TYLCV found. The molecular techniques have suggested that Israel, Sicilia and Mild strain of TYLCV were present in the tomato production areas at NC. The TYLCV races with single or mixed infections and Fusarium oxysporum formae specialis and races are able to identify in molecular techniques in not only accurately but also reliably.
Radiolysis of Salts and Long-Term Storage Issues for Both Pure and Impure PuO{sub 2} Materials in Plutonium Storage Containers

The Material Identification and Surveillance (MIS) project sponsored a literature search on the effects of radiation on salts, with focus on alkali chlorides. The goal of the survey was to provide a basis for estimating the magnitude of {alpha} radiation effects on alkali chlorides that can accompany plutonium oxide (PuO{sub 2}) into storage. Chloride radiolysis can yield potentially corrosive gases in plutonium storage containers that can adversely affect long-term stability. This literature search was primarily done to provide a tutorial on this topic, especially for personnel with nonradiation chemistry backgrounds.
The geometry and electronic structure of Aristolochic acid : possible implications for a frozen resonance

Molecular mutagens and carcinogens are structures which carry chemical and electronic properties that disturb and interact with the genomic machinery. Principally, a rule of thumb for carcinogens is that carcinogens are expected to introduce covalent irreversible bonding to one or several types of DNA bases, causing errors in the reading frame for the polymerases. 8-methoxy-6-nitrophenanthro[3,4-d][1,3]dioxole-5-carboxylic acid, better known as Aristolochic acid (AA1) is a recognized carcinogen which causes urotherial cancer and is found in certain plants. Its structure is particularly interesting given that it is closely related to phenanthrene in its polycyclic arrangement, and has four functional groups, a carboxyl-, a nitro-, a methoxy- and a dioxolane group. In this work, the structure of AA1 has been resolved at the MPWPW91 density functional theory method in combination with Aug-cc-pVDZ basis sets. A geometry analysis shows that in AA1 the carboxyl group's torsion is caused by steric strain from the nitro group, which elevates the molecular plane of the first phenanthrene ring with 0.1A. The wavefunction analysis of AA1 shows that the ring deformation enhances a double π-bond localization in the first ring, adjacent to the dioxalane group, and results in a decrease of ring aromaticity and induces a potentially frozen resonance. Intermolecular and intramolecular interactions were characterized by atoms in molecules and reduced density gradient analysis. This study brings novel information on the geometry and electronic structure of AA1, which are important for the further knowledge of its transformation in vivo and in situ. Copyright © 2013 John Wiley & Sons, Ltd.
Inorganic Chemicals Handbook

Aluminium and aluminum alloys, Robert H. Brown aluminum, secondary, Walter B. Kropf aluminum chloride, H.Z. Hurlburt aluminum fluoride, cryolite, S.N. Sharma, et al aluminum sulfate, H.Z. Hurlburt ammonia, Orlando J. Quartulli, et al antimony and antimony alloys, Werner Joseph antimony oxides, Daniel W. Hurley arsenic and its compounds, Leonard O. Moore and Philip J. Ehman barium compounds, D.J. Muyskens, et al beryllium, J.A. Hawk, Jr, et al beryllium-Copper alloys, J.A. Hawk, Jr and Keith G. Wikle beryllium-Nickel alloy, J.A. Hawk, Jr, et al bismuth alloys and compounds, S.C. Carapella, Jr boric acid, D.A. Coleman bromination and bromine compounds, David W. Bunch and kestutis A. Keblys cadmium alloys and compounds, S.C. Carapella, Jr. calcium carbide, material balance, and quality control, Bimal Kumar Jain calcium chloride, Allen B. Mavity calcium cyanide, Herwig Hoger calcium fluoride (fluorspar), edited by John J. McKetta calcium phosphates, food grade, Kenneth J. Shaver calcium silicate insulation, Vinayake Kahol carbon, activated, R.S. Joyce carbon black, furnace black, Paul H. Johnson and C.R. Eberline carbon, reactivation, Zenji Matsumoto and Kouichi Mumusahi carbon black, nonfurnace types, E.J. Claassen carbon disulfide, A.B. Campanaro carbon monoxide, catalysts for its hydrogenation, C.R. Lahri and S. Ray chloralkali (chlorine), John E. Currey and Gerard G. Pumplin chloralkali plant, materials of construction, S. Krishnamurthy, et al chloralkali plant, projected engineering, Ashok V. Parekh and V. Narasimhan chlorine recovery from hydrogen chloride, Christiaan P. van Dijk and W.C. Schreiner chlorine dioxide, E.S. Atkinson chromium compounds, A.J. Kubicek cobalt alloys, D.J. Maykuth copper and copper alloys, W. Stuart Lyman copper chlorides, W.A. Satterwhite copper sulfate, W.A. Satterwhite deuterium and tritium, W.L. Marter and D.W. Hayes fluorine, edited by John J. McKetta gallium, J. Wilder, et al helium, Philip C. Tully hydrazine, James G. Rigsby hydrochloric acid, Jack E. Buice, et al hydrogen, effects on metals of construction, William P. Webb and Subhash C. Gupta hydrogen embrittlement, S. Mark Wilhelm hydrogen cyanide, A.M. Dowell III, et al Part contents.
Влияние порядка присоединения фрагментов HA2 и M2e вирусов гриппа A к флагеллину на свойства рекомбинантных белков

The ectodomain of the M2 protein (M2e) and the conserved fragment of the second subunit of hemagglutinin (HA2) are promising candidates for broadly protective vaccines. In this paper, we report on the design of chimeric constructs with differing orders of linkage of four tandem copies of M2e and the conserved fragment of HA2 (76-130) from phylogenetic group II influenza A viruses to the C-terminus of flagellin. The 3D-structure of two chimeric proteins showed that interior location of the M2e tandem copies (Flg-4M2e-HA2) provides partial α-helix formation nontypical of native M2e on the virion surface. The C-terminal position of the M2e tandem copies (Flg-HA2-4M2e) largely retained its native M2e conformation. These conformational differences in the structure of the two chimeric proteins were shown to affect their immunogenic properties. Different antibody levels induced by the chimeric proteins were detected. The protein Flg-HA2-4M2e was more immunogenic as compared to Flg-4M2e-HA2, with the former offering full protection to mice against a lethal challenge. We obtained evidence suggesting that the order of linkage of target antigens in a fusion protein may influence the 3D conformation of the chimeric construct, which leads to changes in immunogenicity and protective potency.