Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial cytochrome c release in apoptosis occurs upstream of DEVD‐specific caspase activation and independently of mitochondrial transmembrane depolarization

Mitochondrial cytochrome c, which functions as an electron carrier in the respiratory chain, translocates to the cytosol in cells undergoing apoptosis, where it participates in the activation of DEVD‐specific caspases. The apoptosis inhibitors Bcl‐2 or Bcl‐xL prevent the efflux of cytochrome c from mitochondria. The mechanism responsible for the release of cytochrome c from mitochondria during apoptosis is unknown. Here, we report that cytochrome c release from mitochondria is an early event in the apoptotic process induced by UVB irradiation or staurosporine treatment in CEM or HeLa cells, preceding or at the time of DEVD‐specific caspase activation and substrate cleavage. A reduction in mitochondrial transmembrane potential (Δψm) occurred considerably later than cytochrome c translocation and caspase activation, and was not necessary for DNA fragmentation. Although zVAD‐fmk substantially blocked caspase activity, a reduction in Δψm and cell death, it failed to prevent the passage of cytochrome c from mitochondria to the cytosol. Thus the translocation of cytochrome c from mitochondria to cytosol does not require a mitochondrial transmembrane depolarization.
Social Media Marketing for Community Foundations: Analyzing Engagement and Determining Best Practices

Social media use has exploded in the past decade, and now all types of businesses and organizations are using social media platforms to reach consumers and stakeholders. In the philanthropic sector, foundations are using social media to spread messages about the work they fund, and to interact with potential donors and the general public. Community foundations, which most rely on public trust and support, are the type of philanthropic foundations that can particularly benefit from using social media to interact with donors and members of the community. However, simply having a presence on social media is no longer enough, and in order to build their brand, foundations must make an effort to effectively engage with their followers. This research looks at 29 of the top community foundations in terms of giving and assets, and analyzes their presence on Facebook. Data were recorded during the three-­‐month period from April to June 2013. High-­‐performing posts were also qualitatively analyzed to determine what type of posts were the most popular.
Dose Response of Almonds on Coronary Heart Disease Risk Factors: Blood Lipids, Oxidized Low-Density Lipoproteins, Lipoprotein(a), Homocysteine, and Pulmonary Nitric Oxide: A Randomized, Controlled, Crossover Trial

Background—Although recent studies have indicated that nut consumption may improve levels of blood lipids, nuts are not generally recommended as snacks for hyperlipidemic subjects because of their high fat content. Furthermore, the effective dose is still unknown. Methods and Results—The dose-response effects of whole almonds, taken as snacks, were compared with low-saturated fat (<5% energy) whole-wheat muffins (control) in the therapeutic diets of hyperlipidemic subjects. In a randomized crossover study, 27 hyperlipidemic men and women consumed 3 isoenergetic (mean 423 kcal/d) supplements each for 1 month. Supplements provided 22.2% of energy and consisted of full-dose almonds (73±3 g/d), half-dose almonds plus half-dose muffins, and full-dose muffins. Fasting blood, expired air, blood pressure, and body weight measurements were obtained at weeks 0, 2, and 4. Mean body weights differed <300 g between treatments. The full-dose almonds produced the greatest reduction in levels of blood lipids. Significant reductions from baseline were seen on both half- and full-dose almonds for LDL cholesterol (4.4±1.7%, P =0.018, and 9.4±1.9%, P <0.001, respectively) and LDL:HDL cholesterol (7.8±2.2%, P =0.001, and 12.0±2.1%, P <0.001, respectively) and on full-dose almonds alone for lipoprotein(a) (7.8±3.5%, P =0.034) and oxidized LDL concentrations (14.0±3.8%, P <0.001), with no significant reductions on the control diet. No difference was seen in pulmonary nitric oxide between treatments. Conclusions—Almonds used as snacks in the diets of hyperlipidemic subjects significantly reduce coronary heart disease risk factors, probably in part because of the nonfat (protein and fiber) and monounsaturated fatty acid components of the nut.
Shape from Photometric Ratio and Stereo

Abstract Based on the traditional problem formulation, it is difficult to integrate the two important vision cues, i.e., shading and stereo, for shape reconstruction due to conflicting albedo and image projection assumptions. In this research, we propose a novel scheme to integrate shading and stereo. First, by using the photometric ratio, we derive a new SFS (shape from shading) formulation where no albedo is needed for shape reconstruction. Then, we establish a unified framework for the integration of photometric ratio and stereo by employing perspective projection on a parametric surface via minimizing a cost functional which consists of a weighted sum of shading and stereo errors. Simulation results are given to show the performance of our new robust algorithm.
Vascular permeability factor: a tumor-derived polypeptide that induces endothelial cell and monocyte procoagulant activity, and promotes monocyte migration

Systemic infusion of low concentrations of tumor necrosis factor/cachectin (TNF) into mice that bear TNF-sensitive tumors leads to activation of coagulation, fibrin formation, and occlusive thrombosis exclusively within the tumor vascular bed. To identify mechanisms underlying the localization of this vascular procoagulant response, a tumor-derived polypeptide has been purified to homogeneity from supernatants of murine methylcholanthrene A-induced fibrosarcomas that induces endothelial tissue factor synthesis and expression (half- maximal response at approximately 300 pM), and augments the procoagulant response to TNF in a synergistic fashion. This tumor- derived polypeptide was identified as the murine homologue of vascular permeability factor (VPF) based on similar mobility on SDS-PAGE, an homologous NH2-terminal amino acid sequence, and recognition by a monospecific antibody to guinea pig VPF. In addition, VPF was shown to induce monocyte activation, as evidenced by expression of tissue factor. Finally, VPF was shown to induce monocyte chemotaxis across collagen membranes and endothelial cell monolayers. Taken together, these results indicate that VPF can modulate the coagulant properties of endothelium and monocytes, and can promote monocyte migration into the tumor bed. This suggests one mechanism through which tumor-derived mediators can alter properties of the vessel wall.
Sialoglycosylation of RBC in Visceral Leishmaniasis Leads to Enhanced Oxidative Stress, Calpain-Induced Fragmentation of Spectrin and Hemolysis

Visceral leishmaniasis (VL) caused by the intracellular parasite Leishmania donovani accounts for an estimated 12 million cases of human infection. It is almost always associated with anemia, which severely complicates the disease course. However, the pathological processes leading to anemia in VL have thus far not been adequately characterized to date. In studying the glycosylation patterns of peripheral blood cells we found that the red blood cells (RBC) of VL patients (RBC(VL)) express eight 9-O-acetylated sialoglycoproteins (9-O-AcSGPs) that are not detected in the RBC of healthy individuals (RBC(N)). At the same time, the patients had high titers of anti-9-O-AcSGP IgG antibodies in their sera. These two conditions appear to be linked and related to the anemic state of the patients, as exposure of RBC(VL) but not RBC(N) to anti-9-O-AcSGPs antibodies purified from patient sera triggered a series of responses. These included calcium influx via the P/Q-type but not L-type channels, activation of calpain I, proteolysis of spectrin, enhanced oxidative stress, lipid peroxidation, externalization of phosphatidyl serine with enhanced erythrophagocytosis, enhanced membrane fragility and, finally, hemolysis. Taken together, this study suggests that the enhanced hemolysis is linked to an impairment of membrane integrity in RBC(VL) which is mediated by ligand-specific interaction of surface 9-O-AcSGPs. This affords a potential explanation for the structural and functional features of RBC(VL) which are involved in the hemolysis related to the anemia which develops in VL patients.
Design of Miniaturized, Self-Out-Readable Cantilever Resonator for Highly Sensitive Airborne Nanoparticle Detection

In this paper, a self-out-readable, miniaturized cantilever resonator for highly sensitiveairborne nanoparticle (NP) detection is presented. The cantilever, which is operated in thefundamental in-plane resonance mode, is used as a microbalance with femtogram resolution. Toachieve a maximum measurement signal of the piezo resistive Wheatstone half-bridge, thegeometric parameters of the sensor design were optimized by finite element modelling (FEM). Struts at the sides of the cantilever resonator act as piezo resistors and enable an electrical read-outof the phase information of the cantilever movement whereby they do not contribute to theresonators rest mass. For the optimized design, a resonator mass of 0.93 ng, a resonance frequencyof ~440 kHz, and thus a theoretical sensitivity of 4.23 fg/Hz can be achieved. A μ-channel guiding aparticle-laden air flow towards the cantilever is integrated into the sensor chip. Electrically chargedNPs will be collected by an electrostatic field between the cantilever and a counter-electrode at theedges of the μ-channel. Such μ-channels will also be used to accomplish particle separation for sizeselectiveNP detection. Throughout, the presented airborne NP sensor is expected to demonstratesignificant improvements in the field of handheld, MEMS-based NP monitoring devices.
A Caspase Cascade Regulating Developmental Axon Degeneration

Axon degeneration initiated by trophic factor withdrawal shares many features with programmed cell death, but many prior studies discounted a role for caspases in this process, particularly Caspase-3. Recently, Caspase-6 was implicated based on pharmacological and knockdown evidence, and we report here that genetic deletion of Caspase-6 indeed provides partial protection from degeneration. However, we find at a biochemical level that Caspase-6 is activated effectively only by Caspase-3 but not other “upstream” caspases, prompting us to revisit the role of Caspase-3. In vitro, we show that genetic deletion of Caspase-3 is fully protective against sensory axon degeneration initiated by trophic factor withdrawal, but not injury-induced Wallerian degeneration, and we define a biochemical cascade from prosurvival Bcl2 family regulators to Caspase-9, then Caspase-3, and then Caspase-6. Only low levels of active Caspase-3 appear to be required, helping explain why its critical role has been obscured in prior studies. In vivo, Caspase-3 and Caspase-6-knockout mice show a delay in developmental pruning of retinocollicular axons, thereby implicating both Caspase-3 and Caspase-6 in axon degeneration that occurs as a part of normal development.
CANCER RESEARCH 1964: THOUGHTS ON THE CONTRIBUTIONS OF RADIATION BIOLOGY.

I am deeply grateful for the honor of addressing you as the President of your Association. At the same time, I feel more humble at this moment than ever before in the awareness of my own ignorance of cancer and of the gaps in knowledge that must be filled before the members of our profession will know adequately how to prevent and con trol the many diverse forms of neoplasia. Lest we become discouraged, however, it is heartening to reflect on the advances which have been made in but one of the many fields of cancer researchâ€”namely, radia tion biology. If we review our progress in this field alone, we cannot help but be gratified by the insight already gained and by the promise of the explorations now in progress. There is, furthermore, scarcely a more fitting place in which to review this subject than here in Chicago, for an association between ionizing radiation and cancer was first recorded in this city. The explanation for this association lies in the following letter (38):
Beneficial Effects of a Q-ter® Based Nutritional Mixture on Functional Performance, Mitochondrial Function, and Oxidative Stress in Rats

Background Mitochondrial dysfunction and oxidative stress are central mechanisms underlying the aging process and the pathogenesis of many age-related diseases. Selected antioxidants and specific combinations of nutritional compounds could target many biochemical pathways that affect both oxidative stress and mitochondrial function and, thereby, preserve or enhance physical performance. Methodology/Principal Findings In this study, we evaluated the potential anti-aging benefits of a Q-ter® based nutritional mixture (commercially known as Eufortyn®) mainly containing the following compounds: terclatrated coenzyme Q10 (Q-ter®), creatine and a standardized ginseng extract. We found that Eufortyn® supplementation significantly ameliorated the age-associated decreases in grip strength and gastrocnemius subsarcolemmal mitochondria Ca2+ retention capacity when initiated in male Fischer344 x Brown Norway rats at 21 months, but not 29 months, of age. Moreover, the increases in muscle RNA oxidation and subsarcolemmal mitochondrial protein carbonyl levels, as well as the decline of total urine antioxidant power, which develop late in life, were mitigated by Eufortyn® supplementation in rats at 29 months of age. Conclusions/Significance These data imply that Eufortyn® is efficacious in reducing oxidative damage, improving the age-related mitochondrial functional decline, and preserving physical performance when initiated in animals at early midlife (21 months). The efficacy varied, however, according to the age at which the supplementation was provided, as initiation in late middle age (29 months) was incapable of restoring grip strength and mitochondrial function. Therefore, the Eufortyn® supplementation may be particularly beneficial when initiated prior to major biological and functional declines that appear to occur with advancing age.
Molecular Systems Biology Peer Review Process File Rna Sequencing Reveals Two Major Classes of Gene Expression Levels in Metazoan Cells Transaction Report

(Note: With the exception of the correction of typographical or spelling errors that could be a source of ambiguity, letters and reports are not edited. The original formatting of letters and referee reports may not be reflected in this compilation.) Thank you again for submitting your work to Molecular Systems Biology. We have now heard back from the three referees whom we asked to evaluate your manuscript. As you will see from the reports below, the referees raise substantial concerns on your work, which, I am afraid to say, preclude its publication. The reviewers had substantial concerns that the observed bimodality of gene expression could be an artifact of the computational analysis, and felt that the generality of these observations across different cell types remained largely unclear. The editor notes three particularly important concerns: 1. The first reviewer was concerned that the choice of bowtie read mapping settings use in this work could lead to potential cross-mapping issues, which could potentially explain the bimodal distribution. 2. The second reviewer was concerned that the existence of the bimodal distribution rests heavily on the kernel density estimation based graph and the subsequent BIC-based model likelihood, and was concerned that different tests or parameter choices could lead to different conclusions.
Frankenhorse: Automatic Completion of Articulating Objects from Image-based Reconstruction

Reconstruction of scene geometry and semantics are important problems in vision, and increasingly brought together. The state of the art in Structure from Motion and Multi View Stereo (SfM+MVS) can already create accurate, dense reconstructions of scenes. Systems such as CMPMVS [2] are freely available and produce impressive results automatically. However, when assumptions break down or there is insufficient data, noise, extraneous geometry and holes appear in the reconstruction. We propose to solve these problems by introducing prior knowledge. We focus on the difficult class of articulating objects, such as people and animals. Prior modelling of these classes is difficult due to the articulation and large intra-class variation. We propose an automatic method for completion which does not rely on a prior model of the deformation or training data captured under controlled conditions. Instead, given far from perfect reconstructions, we simultaneously complete each using the well-reconstructed parts of the others. This is enabled by the data-driven piecewise-rigid 3D model alignment method of Chang and Zwicker [1]. This method estimates local coordinate frames on the meshes and proposes correspondences by matching local descriptors. Each correspondence determines a rigid alignment, which is used as a label in a graph labelling problem to determine a piecewise-rigid alignment which brings the meshes into correspondence while penalising stretching edges. Our main contributions are as follows. We present a novel, fully automatic method for the completion of noisy real SfM+MVS reconstructions which (1) exploits a set of noisy reconstructions of objects of the class, rather than relying on a large clean training set which is expensive to collect, (2) handles the articulation structure in the class of objects, allowing larger holes to be filled and with greater accuracy than a generic smoothness prior and (3) is exemplar-based, allowing details to be maintained that may be smoothed out in related learning-based approaches. Our method takes as its input sets of images of scenes each containing an object of a specific class. For each input image set, initially yielding an incomplete and cluttered reconstruction of the whole scene, the output is a completed model of the object, created using the other reconstructions. Our method consists of a pipeline of several stages, visualised in Figure 1. In the first stage, each scene is reconstructed using a SfM+MVS pipeline [2]. We then segment the objects from the scene by combining object detections in the images. In the third stage, we align each of
Effectiveness of RGB imagery from diverse sources for real-time urban flood water mapping

Timeliness is a critical requirement for the provision of information during disasters such as floods in urban areas. Images from RGB remote sensors (such as those carried on satellites, aircraft, UAVs and on the International Space Station) are potentially cost-effective data sources for real-time applications. This paper describes work undertaken to evaluate two high resolution RGB image datasets for rapid response mapping and monitoring of urban visible flood water extent. Our overall goal is to develop a robust methodology for universally applicable extraction of the flooded area information. The methods and results are demonstrated as a case study of the characterization and delineation of visible flood extent and its changes that occurred during the June 2013 city of Calgary flood event. The input imagery included very high resolution aerial photography and imagery acquired with the International Space Station’s (ISS) SERVIR Environmental Research and Visualization System (ISERV). The methodology development involved analysis and comparison of the spectral responses of urban land surface types, shadows and turbid flood water. Based on an understanding of these spectral properties, a universally applicable method was developed and assessed to extract visible flood water from RGB imagery.
The ecology of infectious disease: Effects of host diversity and community composition on Lyme disease risk

The extent to which the biodiversity and community composition of ecosystems affect their functions is an issue that grows ever more compelling as human impacts on ecosystems increase. We present evidence that supports a novel function of vertebrate biodiversity, the buffering of human risk of exposure to Lyme-disease-bearing ticks. We tested the Dilution Effect model, which predicts that high species diversity in the community of tick hosts reduces vector infection prevalence by diluting the effects of the most competent disease reservoir, the ubiquitous white-footed mouse (Peromyscus leucopus). As habitats are degraded by fragmentation or other anthropogenic forces, some members of the host community disappear. Thus, species-poor communities tend to have mice, but few other hosts, whereas species-rich communities have mice, plus many other potential hosts. We demonstrate that the most common nonmouse hosts are relatively poor reservoirs for the Lyme spirochete and should reduce the prevalence of the disease by feeding, but rarely infecting, ticks. By accounting for nearly every host species' contribution to the number of larval ticks fed and infected, we show that as new host species are added to a depauperate community, the nymphal infection prevalence, a key risk factor, declines. We identify important “dilution hosts” (e.g., squirrels), characterized by high tick burdens, low reservoir competence, and high population density, as well as “rescue hosts” (e.g., shrews), which are capable of maintaining high disease risk when mouse density is low. Our study suggests that the preservation of vertebrate biodiversity and community composition can reduce the incidence of Lyme disease.
A Study in CVaR Optimization and Joint Density Modeling

One promising risk metric is Conditional Value at Risk, or CVaR. This measure has many appealing properties, one of which seems paramount: it leaves the task of defining the joint density to the practitioner. We study CVaR as an objective function in a set of optimization problems. Rockafellar and Uryasev [1] suggested a linear programming formulation to solve such a problem. However, we note a curse of dimensionality issue with their proposal. We consider a smooth approximation to the objective function. We also, out of necessity, model a joint density for the assets we will concern ourselves with and test our methodology ex-post on real market data.
Fuel Cell Buses in U.S. Transit Fleets: Current Status 2012

This report is the sixth in an annual series of reports that summarize the progress of fuel cell electric bus (FCEB) development in the United States and discuss the achievements and challenges of introducing fuel cell propulsion in transit. The report also provides a snapshot of current FCEB performance results over the last year. There are 25 active FCEBs in demonstrations this year at eight locations.
Bis[1-methoxy-2,2,2-tris(pyrazol-1-yl-κN 2)ethane]nickel(II) bis(trifluoromethanesulfonate) methanol disolvate

In the title salt, [Ni(C12H14N6O)2](CF3SO3)2·2CH3OH, the NiII ion is coordinated by six N atoms from two tridentate 1-methoxy-2,2,2-tris(pyrazol-1-yl)ethane ligands in a distorted octahedral geometry. The NiII ion is situated on an inversion centre. The Ni—N distances range from 2.0589 (19) to 2.0757 (19) Å, intra-ligand N—Ni—N angles range from 84.50 (8) to 85.15 (8)°, and adjacent inter-ligand N—Ni—N angles range between 94.85 (8) and 95.50 (8)°. In the crystal, O—H⋯O hydrogen bonds between methanol solvent molecules and trifluoromethanesulfonate anions are observed.