Miracle-dz/UniFAR-FTUs huggingface dataset:
The Domain I-Domain III Linker Plays an Important Role in the Fusogenic Conformational Change of the Alphavirus Membrane Fusion Protein

ABSTRACT The alphavirus Semliki Forest virus (SFV) infects cells through a low-pH-dependent membrane fusion reaction mediated by the virus fusion protein E1. Acidic pH initiates a series of E1 conformational changes that culminate in membrane fusion and include dissociation of the E1/E2 heterodimer, insertion of the E1 fusion loop into the target membrane, and refolding of E1 to a stable trimeric hairpin conformation. A highly conserved histidine (H3) on the E1 protein was previously shown to promote low-pH-dependent E1 refolding. An SFV mutant with an alanine substitution at this position (H3A) has a lower pH threshold and reduced efficiency of virus fusion and E1 trimer formation than wild-type SFV. Here we addressed the mechanism by which H3 promotes E1 refolding and membrane fusion. We identified E1 mutations that rescue the H3A defect. These revertants implicated a network of interactions that connect the domain I-domain III (DI-DIII) linker region with the E1 core trimer, including H3. In support of the importance of these interactions, mutation of residues in the network resulted in more acidic pH thresholds and reduced efficiencies of membrane fusion. In vitro studies of truncated E1 proteins demonstrated that the DI-DIII linker was required for production of a stable E1 core trimer on target membranes. Together, our results suggest a critical and previously unidentified role for the DI-DIII linker region during the low-pH-dependent refolding of E1 that drives membrane fusion.
Xylanolytic complex from Aspergillus giganteus: production and characterization

An Aspergillus giganteus strain was isolated as an excellent producer of xylanase associated with low levels of cellulase. Optimal xylanase production was obtained in liquid Vogel medium containing xylan as carbon source, pH 6.5 to 7.0, at 25 °C and under shaking at 120 rpm during 84h. Among the several carbon sources tested, higher xylanase production was verified in xylan, xylose, sugar‐cane bagasse, wheat bran and corn cob cultures, respectively. Optimal conditions for activity determination were 50 °C and pH 6.0. The xylanolytic complex of A. giganteus showed low thermal stability with T50 of 2 h, 13 min and 1 min when it was incubated at 40, 50 and 60 °C, respectively, and high stability from pH 4.5 to 10.5, with the best interval between 7.0 to 7.5. This broad range of stability in alkali pH indicates a potential applicability in some industrial processes, which require such condition. Xylanolytic activity of A. giganteus was totally inhibited by Hg+2, Cu+2 and SDS at 10 mM. The analysis of the products from the oat spelts xylan hydrolysis through thin‐layer chromatography indicated endoxylanase activity, lack of debranching enzymes and β‐xylosidase activity in assay conditions.
A deep neural network approach to fusing vision and heteroscedastic motion estimates for low-SWaP robotic applications

Due both to the speed and quality of their sensors and restrictive on-board computational capabilities, current state-of-the-art (SOA) size, weight, and power (SWaP) constrained autonomous robotic systems are limited in their abilities to sample, fuse, and analyze sensory data for state estimation. Aimed at improving SWaP-constrained robotic state estimation, we present Multi-Hypothesis DeepEfference (MHDE) — an unsupervised, deep convolutional-deconvolutional sensor fusion network that learns to intelligently combine noisy heterogeneous sensor data to predict several probable hypotheses for the dense, pixel-level correspondence between a source image and an unseen target image. This new multi-hypothesis formulation of our previous architecture, DeepEfference [1], has been augmented to handle dynamic heteroscedastic sensor and motion noise and computes hypothesis image mappings and predictions at 150–400 Hz depending on the number of hypotheses being generated. MHDE fuses noisy, heterogeneous sensory inputs using two parallel architectural pathways and n (1, 2, 4, or 8 in this work) multi-hypothesis generation subpathways to generate n pixel-level predictions and correspondences between source and target images. We evaluated MHDE on the KITTI Odometry dataset [2] and benchmarked it against DeepEfference [1] and DeepMatching [3] by mean pixel error and runtime. MHDE with 8 hypotheses outperformed DeepEfference in root mean squared (RMSE) pixel error by 103% in the maximum heteroscedastic noise condition and by 18% in the noise-free condition. MHDE with 8 hypotheses was over 5, 000% faster than DeepMatching with only a 3% increase in RMSE.
On the Core of Directed Acyclic Graph Games

There lies a network structure between fixed tree and minimum cost spanning tree networks that has not been previously analyzed from a cooperative game theoretic perspective, namely, directed acyclic graph (DAG) networks. In this paper we consider the cost allocation game defined on DAG-networks. We briefly discuss the relation of DAG-games with other network-based cost games. We demonstrate that in general a DAG-game is not concave, even its core might be empty, but we provide an efficiently verifiable condition satisfied by a large class of directed acyclic graphs that is sufficient for balancedness of the associated DAG-game. We introduce a network canonization process and prove various structural results for the core of canonized DAG-games. In particular, we characterize classes of coalitions that have a constant payoff in the core. In addition, we identify a subset of the coalitions that is sufficient to determine the core.
Cell heterogeneity in human ovarian carcinoma

There is a growing awareness that the cellular organization of human carcinomas is based on tissue-specific differentiation similar to their normal tissue equivalents. Furthermore, tumor growth appears to depend on cell renewal processes; i.e., expansion of tumor cell number derives from the effects of cell renewal, proliferation, differentiation, and loss (Steel, 1977; Mackillop et al., 1983a). Tumor tissue has therefore been described as a caricature of a normal renewal tissue (Pierce et al., 1977). The cell subpopulation most responsible for the behavior of a renewal hierarchy is the stem cell population. A schematic representation of a stem cell hierarchy is shown in Figure 1. The ultimate growth potential of an individual tumor cell is conventionally considered to be inversely related to the cell's acquisition of tissuespecific differentiation features. Stem cells can be defined as those cells with the capacity to undergo a renewal division; i.e., to replace themselves with identical stem cells rather than more differentiated daughter cells (Mackillop et al., 1983a).
Causes of Infertility as Predictors of Subsequent Cancer Risk

Background: Although studies have found elevated risks of certain cancers linked to infertility, the underlying reasons remain unclear. Methods: In a retrospective cohort study of 12,193 U.S. women evaluated for infertility between 1965 and 1988, 581 cases of cancer were identified through 1999. We used standardized incidence ratios (SIRs) to compare cancer risk with the general population. Analyses within the cohort estimated rate ratios (RRs) associated with infertility after adjusting for other risk predictors. Results: Infertility patients demonstrated a higher cancer risk than the general population (SIR = 1.23; 95% confidence interval [CI] = 1.1–1.3), with nulligravid (primary infertility) patients at even higher risk (1.43; 1.3–1.6). Particularly elevated risks among primary infertility patients were observed for cancers of the uterus (1.93) and ovaries (2.73). Analyses within the cohort revealed increased RRs of colon, ovarian, and thyroid cancers, and of melanomas associated with endometriosis. Melanomas were linked with anovulatory problems, whereas uterine cancers predominated among patients with tubal disorders. When primary infertility patients with specific causes of infertility were compared with unaffected patients who had secondary infertility, endometriosis was linked with distinctive excesses of cancers of the colon (RR = 2.40; 95% CI = 0.7–8.4), ovaries (2.88; 1.2–7.1), and thyroid (4.65; 0.8–25.6) cancers, as well as melanomas (2.32; 0.8–6.7). Primary infertility due to anovulation particularly predisposed to uterine cancer (2.42; 1.0–5.8), and tubal disorders to ovarian cancer (1.61; 0.7–3.8). Primary infertility associated with male-factor problems was associated with unexpected increases in colon (2.85; 0.9–9.5) and uterine (3.15; 1.0–9.5) cancers. Conclusions: The effects of infertility may extend beyond gynecologic cancers. Thyroid cancers and melanomas deserve specific attention, particularly with respect to endometriosis.
Ill‐health reported by schoolchildren during questionnaire surveys in Ghana, Mozambique and Tanzania

Background Insufficient attention has been paid to the health problems of school‐age children in sub‐Saharan Africa. A questionnaire administered to schoolchildren about their ill‐health has been developed to identify schools in which urinary schistosomiasis occurs. The data collected during the interviews can also be used to assess other common health problems.
Reverse power flow control possibilities of galvanically isolated impedance-source DC-DC converters

Galvanically isolated impedance-source (IS) dc-dc converters are a high performance solution proven for emerging power electronics applications. However, studies of their bidirectional operation have been scarce. Focus in this paper is on the reverse power transfer possibilities of the high performance quasi-Z-source (qZS) series resonant dc-dc converter. This enables extension of functionality and application range of the converter to the energy storage and buffering systems. Two novel methods of reverse power flow control were introduced: one that requires no qZS network reconfiguration and is based on the resonant properties of the given topology, while the other is based on the qZS network reconfiguration into LC filter and does not depend on whether an IS converter is resonant or not. Experimental study was conducted for the power level of 250 W within the output voltage range of 20 V to 30 V. Experimental results corroborate the theoretical predictions and show that one of the methods is superior to the other by efficiency values and curve flatness.
Diarrhoea-predominant irritable bowel syndrome: an organic disorder with structural abnormalities in the jejunal epithelial barrier

Objective Recently, the authors demonstrated altered gene expression in the jejunal mucosa of diarrhoea-predominant irritable bowel syndrome patients (IBS-D); specifically, the authors showed that genes related to mast cells and the intercellular apical junction complex (AJC) were expressed differently than in healthy subjects. The aim of the authors here was to determine whether these alterations are associated with structural abnormalities in AJC and their relationship with mast cell activation and IBS-D clinical manifestations. Design A clinical assessment and a jejunal biopsy were obtained in IBS-D patients (n=45) and healthy subjects (n=30). Mucosal mast cell number and activation were determined by quantifying CD117+ cells/hpf and tryptase expression, respectively. Expression and distribution of AJC specific proteins were evaluated by western blot and confocal microscopy. AJC ultrastructure was assessed by transmission electron microscopy. Results Compared with healthy subjects, IBS-D patients exhibited: (a) increased mast cell counts and activation; (b) increased protein expression of claudin-2, reduced occludin phosphorylation and enhanced redistribution from the membrane to the cytoplasm; and (c) increased myosin kinase expression, reduced myosin phosphatase and, consequently, enhanced phosphorylation of myosin. These molecular alterations were associated with ultrastructural abnormalities at the AJC, specifically, perijunctional cytoskeleton condensation and enlarged apical intercellular distance. Moreover, AJC structural alterations positively correlated both with mast cell activation and clinical symptoms. Conclusion The jejunal mucosa of IBS-D patients displays disrupted apical junctional complex integrity associated with mast cell activation and clinical manifestations. These results provide evidence for the organic nature of IBS-D, a heretofore model disease of functional gastrointestinal disorders.
The People's Tycoon: Henry Ford and the American Century

In 1897, Ford finished his second prototype automobile and in 1898 he went to search for investors for his first real venture; in 1899 the Detroit Automobile Company was a fact. Unfortunately, this soon turned out to become a failure (the prototype wasn’t a very good car, car parts were mainly fabricated elsewhere and often needed adjustments, Ford kept altering the – mechanical – design of the car and in general, Ford seemed to have a difficulty with authority). In 1901, the Detroit Automobile Company was dissolved.
Nature of Steady Flow in Entangled Fluids Revealed by Superimposed Small Amplitude Oscillatory Shear

We carry out a systematic investigation into steady-state shear behavior of six entangled solutions based on a superposition of continuous shear and small amplitude oscillatory shear (SAOS). During steady shear in the shear thinning regime, the superimposed SAOS frequency sweep measurements reveal characteristics of viscous liquids, e.g., terminal dynamics, on the experimental time scale of the reciprocal shear rate. The residual entanglement network retains the same level of elastic stiffness as the equilibrium system does. Consistent with the convective constraint release idea, chains in the network are forced to pass around each other as they must do so to undergo steady flow. When such a sample is examined at significantly short time scales, chains are unable to pass around and the signature of this residual entanglement is that the storage modulus is greater than the loss modulus at higher frequencies than the applied shear rate. The particle-tracking velocimetric observations confirm that whether sh.
Uncoupling of ganglioside biosynthesis by Brefeldin A.

We have studied the effect of Brefeldin A (BFA), an antiviral antibiotic, on glycosphingolipid metabolism in primary cultured cerebellar cells. Cells were labeled metabolically with [14C]galactose, or pulse-labeled with precursors of glycosphingolipid biosynthesis; i.e., [14]serine, [3H]palmitic acid or [3H]sphingosine. In all cases BFA (1 microgram/ml) strongly inhibited (75-95%) ganglioside biosynthesis beyond the stage of GM3 and GD3, that is the formation of GM1, GD1a, GT1b and GQ1b. Simultaneously an accumulation of GlcCer, LacCer, GM3 and GD3 was observed (up to 2000%). These effects could be reversed fully by removal of the BFA from the culture medium. These results indicate that the LacCer-, GM3- and GD3-synthases of murine cerebellar cells are localized together on the proximal site of the Golgi apparatus, probably in the cis-Golgi compartment. It is probable that sphingomyelin synthase and some of the other glycosyltransferases involved in ganglioside biosynthesis are localized in distinct compartments beyond the cis Golgi.
CycleGAN, a Master of Steganography

CycleGAN (Zhu et al. 2017) is one recent successful approach to learn a transformation between two image distributions. In a series of experiments, we demonstrate an intriguing property of the model: CycleGAN learns to "hide" information about a source image into the images it generates in a nearly imperceptible, high-frequency signal. This trick ensures that the generator can recover the original sample and thus satisfy the cyclic consistency requirement, while the generated image remains realistic. We connect this phenomenon with adversarial attacks by viewing CycleGAN's training procedure as training a generator of adversarial examples and demonstrate that the cyclic consistency loss causes CycleGAN to be especially vulnerable to adversarial attacks.
Transplantation of allograft chondrocytes embedded in agarose gel into cartilage defects of rabbits.

OBJECTIVE Durable healing of full-thickness articular cartilage defects has been considered for a long time as a highly desirable, but unlikely event to occur. In recent years, conflicting reports on the outcome of in vitro and in vivo studies on chondrocyte and cartilage grafting into animal and human joints have raised new arguments for and against controlled repair of articular cartilage following injury. Some of the problems result from insufficient characterization of implant and repair tissue, and from too short follow up phases. Here we describe a new approach to repair articular cartilage defects in rabbit knees by allografting chondrocytes cultured in agarose gels. DESIGN The implants were monitored over 6-18 months and graded histologically, immunohistochemically, and electron microscopically, using a grading scale based on seven evaluation criteria. Control implants of pure agarose produced poor fibrous substitute tissue, insufficient healing and incomplete filling of the cartilage defects. After transplantation of allogenic chondrocytes embedded in agarose, the quality of the newly formed repair cartilage was superior with respect to type II collagen and proteoglycan content and cellular architecture when compared with untreated defects. Superficial fibrillation and degradation were significantly diminished or prevented. RESULTS New subchondral bone formed at the level of the previous subchondral bone. In most cases the repair tissue merged with the host articular cartilage; normal calcified cartilage was the only tissue zone that did not participate in the integration of the transplant. By gross evaluation 24% of grafts showed an extent of recovery never observed in controls. The best results were obtained after 18 months when 47% of the grafts (N = 15) developed a morphologically stable hyaline cartilage. CONCLUSION These studies demonstrate that agarose-embedded chondrocyte may prove a valuable tool for controlled repair of articular cartilage defects.
Dynamic Rearrangements Determine Genome Organization and Useful Traits in Soybean1[C][W]

Soybean (Glycine max) is a paleopolyploid whose genome has gone through at least two rounds of polyploidy and subsequent diploidization events. Several studies have investigated the changes in genome structure produced by the relatively recent polyploidy event, but little is known about the ancient polyploidy due to the high frequency of gene loss after duplication. Our previous study, regarding a region responsible for bacterial leaf pustule, reported two homeologous Rxp regions produced by the recent whole-genome duplication event. In this study, we identified the full set of four homeologous Rxp regions (ranging from 1.96 to 4.60 Mb) derived from both the recent and ancient polyploidy events, and this supports the quadruplicated structure of the soybean genome. Among the predicted genes on chromosome 17 (linkage group D2), 71% of them were conserved in a recently duplicated region, while 21% and 24% of duplicated genes were retained in two homeologous regions formed by the ancient polyploidy. Furthermore, comparative analysis showed a 2:1 relationship between soybean and Medicago truncatula, since M. truncatula did not undergo the recent polyploidy event that soybean did. Unlike soybean, M. truncatula homeologous regions were highly fractionated and their synteny did not exist, revealing different rates of diploidization process between the two species. Our data show that extensive synteny remained in the four homeologous regions in soybean, even though the soybean genome experienced dynamic genome rearrangements following paleopolyploidy events. Moreover, multiple Rxp quantitative trait loci on different soybean chromosomes actually comprise homeologous regions produced by two rounds of polyploidy events.
Explosives detection by using 8-microcantilever chips with self-heating elements modified with exchanged BEA type zeolites

Si microcantilevers with internal heating elements and modified with selective zeolite coatings have been developed and used for the selective detection of 2-nitrotoluene (o-MNT) in vapor phase as probe molecule of nitroderivates explosives family (TNT, picric acid). In particular, transition metal exchanged BEA zeolites have been deployed as a sensitive layer over microfabricated chips containing 8 Si-cantilevers by microdropping technique. Limit of detection (LOD) values below 1 ppm have been attained at room temperature conditions for Co-BEA coatings. Integrated heater provides an easy and fast regeneration of the zeolite adsorption capability, enhancing sensor reproducibility and sensitivity. The explosives recognition capability of the sensing platform could be notably enhanced by tuning the sensing temperature. The calculated apparent isosteric sorption values for single compounds have been revealed as valuable tool for O-MNT identification in multicomponent mixtures.
PRDM1/Blimp-1 Controls Effector Cytokine Production in Human NK Cells

NK cells are major effectors of the innate immune response through cytolysis and bridge to the adaptive immune response through cytokine release. The mediators of activation are well studied; however, little is known about the mechanisms that restrain activation. In this report, we demonstrate that the transcriptional repressor PRDM1 (also known as Blimp-1 or PRDI-BF1) is a critical negative regulator of NK function. Three distinct PRDM1 isoforms are selectively induced in the CD56dim NK population in response to activation. PRDM1 coordinately suppresses the release of IFN-γ, TNF-α, and TNF-β through direct binding to multiple conserved regulatory regions. Ablation of PRDM1 expression leads to enhanced production of IFN-γ and TNF-α but does not alter cytotoxicity, whereas overexpression blocks cytokine production. PRDM1 response elements are defined at the IFNG and TNF loci. Collectively, these data demonstrate a key role for PRDM1 in the negative regulation of NK activation and position PRDM1 as a common regulator of the adaptive and innate immune response.
The keratin-related Ouroboros proteins function as immune antigens mediating tail regression in Xenopus metamorphosis

Tail resorption during amphibian metamorphosis has been thought to be controlled mainly by a cell-autonomous mechanism of programmed cell death triggered by thyroid hormone. However, we have proposed a role for the immune response in metamorphosis, based on the finding that syngeneic grafts of tadpole tail skin into adult Xenopus animals are rejected by T cells. To test this, we identified two tail antigen genes called ouro1 and ouro2 that encode keratin-related proteins. Recombinant Ouro1 and Ouro2 proteins generated proliferative responses in vitro in T cells isolated from naive adult Xenopus animals. These genes were expressed specifically in the tail skin at the climax of metamorphosis. Overexpression of ouro1 and ouro2 induced T-cell accumulation and precocious tail degeneration after full differentiation of adult-type T cells when overexpressed in the tail region. When the expression of ouro1 and ouro2 were knocked down, tail skin tissue remained even after metamorphosis was complete. Our findings indicate that Ouro proteins participate in the process of tail regression as immune antigens and highlight the possibility that the acquired immune system contributes not only to self-defense but also to remodeling processes in vertebrate morphogenesis.