Miracle-dz/UniFAR-FTUs huggingface dataset:
The Di-Symbiotic Systems in the Aphids Sipha maydis and Periphyllus lyropictus Provide a Contrasting Picture of Recent Co-Obligate Nutritional Endosymbiosis in Aphids

Dependence on multiple nutritional bacterial symbionts forming a metabolic unit has repeatedly evolved in many insect species that feed on nutritionally unbalanced diets such as plant sap. This is the case for aphids of the subfamilies Lachninae and Chaitophorinae, which have evolved di-symbiotic systems in which the ancient obligate nutritional symbiont Buchnera aphidicola is metabolically complemented by an additional nutritional symbiont acquired more recently. Deciphering how different symbionts integrate both metabolically and anatomically in such systems is crucial to understanding how complex nutritional symbiotic systems function and evolve. In this study, we sequenced and analyzed the genomes of the symbionts B. aphidicola and Serratia symbiotica associated with the Chaitophorinae aphids Sipha maydis and Periphyllus lyropictus. Our results show that, in these two species, B. aphidicola and S. symbiotica complement each other metabolically (and their hosts) for the biosynthesis of essential amino acids and vitamins but with distinct metabolic reactions supported by each symbiont depending on the host species. Furthermore, the S. symbiotica symbiont associated with S. maydis appears to be strictly compartmentalized into the specialized host cells housing symbionts in aphids, the bacteriocytes, whereas the S. symbiotica symbiont associated with P. lyropictus exhibits a highly invasive phenotype, presumably because it is capable of expressing a larger set of virulence factors, including a complete flagellum for bacterial motility. Such contrasting levels of metabolic and anatomical integration for two S. symbiotica symbionts that were recently acquired as nutritional co-obligate partners reflect distinct coevolutionary processes specific to each association.
The columnar structure of human telomeric chromatin suggests mechanisms for telomere maintenance

Telomeres, the ends of eukaryotic chromosomes, play pivotal roles in ageing and cancer and are targets of DNA damage and response. However, little is known about the structure and organization of telomeric chromatin at the molecular level. We used electron microscopy and single-molecule magnetic tweezers to characterize well-defined telomeric chromatin fibers of kilobasepair length. The cryo-EM structure of the compact telomeric tetranucleosome revealed a novel columnar folding, unusually short nucleosome repeat length of ∼132bp and the role of the histone N-terminal tails in stabilizing this structure. This is the first near-high resolution structure of chromatin with a native DNA sequence. The columnar structure exposes the DNA, making them susceptible to DNA damage. The telomeric tetranucleosome also exists in an alternative well-defined state, with one nucleosome open, accessible to protein factors. This suggests that protein factors, which plays a role in maintaining telomeres, can bind to telomeric chromatin in its compact heterochromatic form. The features of the telomeric chromatin structure reveals important insights of significant relevance for telomere function in vivo that provides information on mechanisms of nucleosome recognition by chromatin factors
HCP5 prevents ubiquitination-mediated UTP3 degradation to inhibit apoptosis by activating c-Myc transcriptional activity

Inducing cancer cell apoptosis through cytotoxic reagents is the main therapeutic strategy for diverse cancer types. However, several antiapoptotic factors impede curative cancer therapy by driving cancer cells to resist cytotoxic agent-induced apoptosis, thus leading to refractoriness and relapse. To define critical antiapoptotic factors that contribute to chemoresistance in esophageal squamous cell carcinoma (ESCC), we generated two pairs of parental and apoptosis-resistant cell models through cisplatin (DDP) induction and then performed whole-transcriptome sequencing. We identified the long noncoding RNA (lncRNA) histocompatibility leukocyte antigen complex P5 (HCP5) as the chief culprit for chemoresistance. Mechanistically, HCP5 interacts with UTP3 small subunit processome component (UTP3) and prevents UTP3 degradation from E3 ligase tripartite motif containing 29 (TRIM29)-mediated ubiquitination. UTP3 then recruits c-Myc to activate vesicle-associated membrane protein 3 (VAMP3) expression. Activated VAMP3 suppresses caspase-dependent apoptosis and eventually leads to chemoresistance. Accordingly, the expression level of the HCP5/UTP3/c-Myc/VAMP3 axis in chemoresistant patients is significantly higher than that in chemosensitive patients. Thus, our study demonstrated that the HCP5/UTP3/c-Myc/VAMP3 axis plays an important role in the inhibition of cancer cell apoptosis and that HCP5 can be a promising chemosensitive target for cancer treatment.
Resolving the fate of trace metals during microbial remineralization of phytoplankton biomass in precursor banded iron formation sediments

Banded Iron Formations (BIFs) have long been considered a sedimentary record of seawater trace metal composition during the Precambrian. However, recent work has suggested that the trace metal composition of BIFs was derived from phytoplankton biomass, not seawater. In this model, phytoplankton biomass settles from the photic zone to the seafloor sediments, where it is then oxidized by heterotrophic microbes, such as dissimilatory Fe(III) reducing (DIR) bacteria, for energy generation. Remineralization of this biomass released the trace metals associated with organic molecules from phytoplankton (i.e., in metalloproteins), allowing these metals to be captured by Fe (oxyhydr)oxides and preserved in BIFs. While there is compelling evidence that the phytoplankton biomass served as a trace metal shuttle to precursor BIF sediments, it is unclear whether the degradation of biomass by DIR bacteria would liberate the biogenic trace metals as the model proposes. This work tests this hypothesis by using anoxic incubations of a model DIR bacterium (Shewanella oneidensis MR-1) with phytoplankton biomass as energy and carbon sources and ferrihydrite, a poorly crystalline Fe(III) oxyhydroxide (Fe(OH)3), as electron acceptor. Our results show that while S. oneidensis MR-1 can consume some of the carbon substrates found in phytoplankton biomass, there is no evidence that S. oneidensis MR-1 degraded metalloproteins which would have liberated trace metals. In the context of the Precambrian, these data imply that other heterotrophic bacteria, such as fermenters, may have had a larger role in the liberation of trace metals from dead biomass during early BIF development. Highlights Phytoplankton are the proposed source of trace metals to banded iron formations Iron reducers are hypothesized to release metals from phytoplankton biomass Experiments show that iron reducers do not liberate metals when degrading biomass Other microbial heterotrophs must have liberated the biogenic trace metals
Fuzzy Clustered Inverse Regression

Sliced inverse regression (SIR), introduced by K.C. Li in 1991, is a very general and fast procedure for dimension reduction in regression. For small samples, however, results of SIR are influenced by the choice of slices. In this paper, we propose a fuzzified version of SIR in which slices are replaced by fuzzy clusters. We compare the small sample behavior of the original SIR and the proposed one on simulated data.
Mimetic finite difference methods for diffusion equations on non-orthogonal AMR meshes

A begonia plant named Kanon characterized by its rose pink double sterile flowers up to 6 cm. in diameter, medium size dark green crisp foliage vigorous, upright, self-branching and mounded growth habit, flowering year around, and by its ability to maintain good flower quality for long periods of time.
Endothelial glycocalyx degradation predisposes for transfusion‐associated acute lung injury

Transfusion‐associated acute lung injury (TRALI), a major cause of transfusion morbidity, arises from two events: an initial alteration in host susceptibility, followed by exposure to mediators in transfused blood products. We hypothesized that pulmonary endothelial glycocalyx degradation was a predisposing event in TRALI. We created a mouse model of TRALI, administering IV lipopolysaccharide (LPS) 2h prior to the administration of bioactive lipids (arachidonic acid, lysophosphatidylcholine) identified in stored human RBC units. Enzymatic cleavage of glycocalyx heparan sulfates similarly predisposed for TRALI, suggesting a role for glycocalyx degradation in host susceptibility to injury. Glycocalyx degradation could be detected in human blood via identification of heparan degradation products, defined by a heparinase effect of >; 15% on thromboelastography r‐time. Presence of circulating heparinoids was associated with a 50% risk (2/4) of plasma transfusion‐induced lung injury in bleeding patients with liver disease; patients with no circulating heparinoids had 0% risk (0/3). Endothelial glycocalyx degradation predisposes for TRALI and can serve as a biomarker for transfusion risk. NHLBI K08HL105538.
Stochastic Homogenization of a Two-Dimensional Granular Medium

In order to describe the macroscopic behavior of granular media, a statistical micro to macro level transition model is first developed, based on Jaynes’ principle of maximum entropy. The model formulation translates into a strictly convex, nonlinear optimization problem. It is tested by solving model examples of two dimensional granular structures. Next, a Lagrangian dual formulation of the maximum entropy problem is derived and analyzed. The dual formulation, which is confirmed to be computationally more efficient than the primal one, is applied in solving an evolution problem for a regular granular structure subjected to a biaxial compression loading with a prescribed lateral stress. Results show that the model is capable of predicting the response, in terms of stress and strain, throughout the evolution of the structure, and a satisfactory agreement is observed with the physical solution that is known a priori.
The Role of the K2P Channels TASK‐1, TREK‐1 and TREK‐2 in the Use of Treprostinil Therapy in Pulmonary Arterial Hypertension

Pulmonary arterial hypertension (PAH) is a progressive and ultimately fatal disease affecting ~6 people per million, per year (1). Recent studies have reported mutations in the two‐pore domain potassium (K2P) channel TASK‐1 (KCNK3) giving rise to PAH (2). Treprostinil is a stable prostacyclin analogue often administered as a therapy in PAH, to keep blood vessels open. Its mode of action is thought to occur through an interaction with prostanoid receptors, DP2, EP2 and IP (3). Patients undergoing continuous subcutaneous treprostinil infusion can often exhibit severe pain at the site of delivery (4). In this study we investigate the action of treprostinil on TASK‐1 and on two other K2P channels, TREK‐1 (KCNK2) and TREK‐2 (KCNK10), which regulate the excitability of sensory neurons and are implicated in pain (5).
Chronic Hypoxia increases Orai1 and Orai2 Expression in Pulmonary Arterial Smooth Muscle

Chronic hypoxia (CH) causes pulmonary arterial smooth muscle cell (PASMC) contraction and proliferation. We have shown that resting intracellular calcium concentration ([Ca2+]i) was elevated in PASMCs from chronically hypoxic rats (10%O2; 21 days) due to enhanced Ca2+ influx through store‐operated Ca2+ channels, which are likely composed of TRPC and Orai proteins and interact with Stim proteins. In this study, we investigated the effects of hypoxia on the expression of Orai1, 2, 3 and Stim1 and 2. We found that CH increased Orai1 and Orai2 and decreased Stim2 mRNA and protein levels in distal pulmonary arteries from rats; however, the mRNA and protein expression of Orai3 and Stim1 were not altered. Ex vivo exposure to prolonged hypoxia (4% O2, 60 h) increased mRNA and protein expression of Orai1 and Orai2 in rat PASMCs; however, it did not alter either mRNA or protein expression of Orai3, Stim1 or Stim2. Overexpressing hypoxia inducible factor‐1 (HIF‐1) increased Orai2 mRNA and protein expression, without changing Orail expression in PASMCs, and the hypoxia‐induced increase in Orai2 mRNA and protein expression were diminished in pulmonary arteries from HIF‐1α herozygous null mice. Thus, we conclude that CH increases Orai1 and Orai2 expression in PASMCs, and that the latter is HIF‐1α‐dependent. The change in Orai1 and Orai2 expression may contribute to the enhanced resting [Ca2+]i in chronically hypoxic PASMCs.
Biologically Equivalent Dose in Construction of Tumor Control Probability Curve for Hepatocellular Carcinoma Treated by Radiotherapy

Background : The incorporation of biologically effective dose (BED) or equivalent total dose in 2 gy fraction (EQD₂) in tumor control probability (TCP) equation allows the fitting of clinical data to yield a mathematical function useful for predicting outcome of dose-fractionation. Purpose : To establish a logistic function describing the dependence of TCP on BED or EQD₂for hepatocellular carcinoma (HCC) treated by radiation and to ecaluate the validity BED- and EQD₂- derived functions in predicting effects of dose-fractionations particularly those relevant to stereotactic body radiotherapy (SBRT). Methods and Materials : Eight clinical papers published during 2000 and 2008 were selected to fitting.Dose and dose per fraction were converted to BED and EQD₂with an α/β of 10 Gy for HCC. These biologically equivalent dose and their associated survival rate at 2 years were fitted to a logit-transformed equation.The difference between slopes of logit-regression lines was analyzed by t-test. The parameters of fit were used for defining the logistic functions which were used to calculate TCPs for dose-fractionation schemes typically used in SBRT. Results : Two significant logit-transformed regression lines were established (P = 0.0119) and enabled the construction of two TCP curves described by following logistic functions:The r2 for the curve fitting was 0.83. The established functions were used to calculate TCP for series of fractionation schemes relevant to SBRT and this allowed paperbased study of dose escalation and pre-clinical evaluation of the chosen scheme for treatment of HCC with SBRT. Neither slopes of two curves nor TCPs calculated by BED and EQD2 were statistically different (P > 0.5). Validity of TCP prediction was supported by published data on treatment of HCC with SBRT. Conclusion : BED- or EQD2-derived logistic function is equally reliable in predicting effects of dose-fractionations for HCC particularly those typically used in SBRT.
Perancangan Racking System Dan Tata Letak Gudang Barang Jadi (Finished Goods Warehouse Di PT.PTS (Prakasa Trada Solusi).

Warehouse is one of the most important part in a manufacturing company (product maker) because it can overcome the frequent between cycle production and consumption. All goods stored at the warehouse is temporary before it continues to the next process.One of the activities often done in a warehouse is material handling. It has not a value added to the product so it necessary to be minimized. All goods found at the warehouse needs to be maintained properly because it is the company's assets that are stored for a certain time. PT. PTS (Prakasa Trada Solusi) is a company which concern in supply-chain management. PT. PTS makes a product, storing, and sending to the customers in accordance with demand from it partner. One of the partners of PT. PTS is PT. BRODO Ganesha Indonesia with one of the product it ordered is male’s adult shoes. The problems that occurred in PT. PTS’s warehouse are limited storage area, products storage still use a block stacking system that causes damage to the packaging, the FIFO concept is not running so there are some products stored longer than usual, product storage is not neatly arranged so it makes material handling tools is difficult to move, and storage of products is still random so material handling cost becomes high. With these condition, to increase the capacity of the warehouse without expansion is used method of racking system that can increase the warehouse capaicty from 11.742 box to 14.688 box or about 11,15% with some benefits, there are FIFO concept can be run, products are neatly arranged so material handling tools can run without a hitch, and the carrying capacity of material handling tools can be improved until 70 box/one time transport because the proposed aisle for Trolley is 1,5 meter. In addition to minimize material handling cost used storage method using class-based storage based on popularity can reduce material handling cost from Rp 787.878,81/month to Rp 282.732,32/month or about 47,18%. Key Words : Finished Goods Warehousing Layout Design, Racking System, ClassBases Storage berdasarkan Popularity, FIFO (First-In First-Out).
Massive thin accretion discs. III, Comparison with the observations

Une comparaison detaillee de modeles theoriques de disques d'accretion minces avec les spectres de 101 noyaux galactiques actifs brillants est presentee. Les modeles ont ete decrits dans les articles I et II de la serie (I : Laor A. et Netzer H., 1989, Mon. Not. R. astr. Soc., 238 ; II : Laor A., Netzer H., et Piram T., 1990, Mon. Not. R. astr. Soc., 242), ces modeles tiennent compte de tous les effets relativistes et utilisent une approximation amelioree pour le spectre local.
Severe hemorrhage attenuates cardiopulmonary chemoreflex (CCR) control of renal and adrenal sympathetic nerves via adenosine operating in the nucleus of the solitary tract (NTS)

During severe hemorrhage adrenal sympathoactivation is accompanied by paradoxical renal sympathoinhibition and bradycardia. Adenosine operating in the NTS via A1 and A2a receptors contributes to the paradoxical effects and it inhibits CCR mediated sympathoinhibition (Am J Physiol 291: H2453‐H2461, 2006; 303: R539‐R550, 2012; FASEB J 25: 844.3, 2011). Therefore, we hypothesized that adenosine released into the NTS during severe hemorrhage will attenuate the CCR and that blockade of NTS adenosine receptors will reverse this attenuation. We compared renal and adrenal sympathetic responses evoked by right atrial injections of 5HT3 receptor agonist, phenylbiguanide (PBG, 1–8 μg/kg), under control conditions, during hemorrhage and during hemorrhage after blockade of NTS adenosine receptors with bilateral microinjections of 8‐(p‐sulfophenyl) theophylline (1 nmol/100 nl) in urethane/chloralose anesthetized rats. Hemorrhage significantly attenuated the CCR responses and blockade of NTS adenosine receptors reversed this attenuation. We conclude that adenosine released into the NTS contributes to the paradoxical posthemorrhagic effects but it also serves as a negative feedback regulator of the CCR. HL‐67814
Neutron Scattering Studies of Cuprates and Iron Pnictides

Presented within are neutron scattering studies of several different high temperature superconducting materials: BaFe1.9Ni0. 1As2[Barium Iron Nickel Arsenic], BaFe1.85Ni0. 15As2[Barium Iron Nickel Arsenic], Ba0.67K0. 33Fe2As2[Barium Potassium Iron Arsenic], and Pr0.88LaCe0. 12CuO4−δ[Praseodymium Lanthanum Cerium Copper Oxide]. The main focus is on the magnetic excitations within the systems. For BaFe1.9Ni0. 1As2 [Barium Iron Nickel Arsenic], we measured the intensity of its magnetic excitations and compared the results with excitations in antiferromagnetic non-superconducting BaFe2As2[Barium Iron Arsenic]. We find electron-doping only affects spin excitations below 100 meV while the total size of the magnetic moment and the energy distribution do not change much. It shows that the magnetic moments in both materials are similar to insulating copper oxides, an indicator of the importance of strong electron correlations in high temperature superconductivity. For both BaFe1.85Ni0. 15As2[Barium Iron Nickel Arsenic] and Ba0.67K0. 33Fe2As2[Barium Potassium Iron Arsenic], we use polarized inelastic neutron scattering to study
The complexity of derivations of matrix identities

In this thesis we are concerned with building logical foundations for Linear Algebra, from the perspective of proof complexity. As the cornerstone of our logical theories, we use Berkowitz's parallel algorithm for computing the coefficients of the characteristic polynomial of a matrix. Standard Linear Algebra textbooks use Gaussian Elimination as the main algorithm, but they invariably use the (very infeasible) Lagrange expansion to prove properties of this algorithm. The main contribution of this thesis is a (first) feasible proof of the Cayley-Hamilton Theorem, and related principles of Linear Algebra (namely, the axiomatic definition of the determinant, the cofactor expansion formula, and multiplicativity of the determinant). Furthermore, we show that these principles are equivalent, and the equivalence can be proven feasibly. We also show that a large class of matrix identities, such as: AB=I→BA=I proposed by S. A. Cook as a candidate for separating Frege and Extended Frege propositional proof systems, all have feasible proofs, and hence polynomially-bounded Extended Frege proofs. We introduce the notion of completeness for these matrix identities. As the main tool to prove our results, we design three logical theories: LA⊂ LAP⊂ ∀LAP LA is a three-sorted quantifier-free theory of Linear Algebra. The three sorts are indices, field elements and matrices. This is a simple theory that allows us to formalize and prove all the basic properties of matrices (roughly the properties that state that the set of matrices is a ring). The theorems of LA have polynomially-bounded Frege proofs. We extend LA to LAP by adding a new function, P, which is intended to denote matrix powering, i.e., P( n, A) means An. LAP is well suited for formalizing Berkowitz's algorithm, and it is strong enough to prove the equivalence of some fundamental principles of Linear Algebra. The theorems of LAP translate into quasi-polynomially-bounded Frege proofs. We finally extend LAP to ∀LAP by allowing induction on formulas with ∀ matrix quantifiers. This new theory is strong enough to prove the Cayley-Hamilton Theorem, and hence (by our equivalence) all the major principles of Linear Algebra. The theorems of ∀LAP translate into polynomially-bounded Extended Frege proofs.
Multisections of Lefschetz fibrations and mapping class group factorizations

The purpose of this article is to initiate a study of positive multisections of Lefschetz fibrations via positive factorizations in mapping class groups of surfaces. We show that, using our methods, one can effectively capture various interesting surfaces in symplectic 4-manifolds as multisections, such as Seiberg-Witten basic classes or the curious 2-section of a genus two Lefschetz fibration which leads to a counter-example to Stipsicz's conjecture on fiber sum indecomposable Lefschetz fibrations.