Miracle-dz/UniFAR-FTUs huggingface dataset:
Crowding Induces Entropically-Driven Changes to DNA Dynamics That Depend on Crowder Structure and Ionic Conditions

Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a topic of debate. To address this problem, we use single-molecule fluorescence microscopy and custom particle-tracking algorithms to investigate the impact of varying macromolecular crowding conditions on the transport and conformational dynamics of large DNA molecules. Specifically, we measure the mean-squared center-of-mass displacements, as well as the conformational size, shape, and fluctuations, of individual 115 kbp DNA molecules diffusing through various in vitro solutions of crowding polymers. We determine the role of crowder structure and concentration, as well as ionic conditions, on the diffusion and configurational dynamics of DNA. We find that branched, compact crowders (10 kDa PEG, 420 kDa Ficoll) drive DNA to compact, whereas linear, flexible crowders (10, 500 kDa dextran) cause DNA to elongate. Interestingly, the extent to which DNA mobility is reduced by increasing crowder concentrations appears largely insensitive to crowder structure (branched vs. linear), despite the highly different configurations DNA assumes in each case. We also characterize the role of ionic conditions on crowding-induced DNA dynamics. We show that both DNA diffusion and conformational size exhibit an emergent non-monotonic dependence on salt concentration that is not seen in the absence of crowders.
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In this paper we present a scalable way to learn and detect objects using a 3D representation based on HOG patches placed on a 3D cuboid. The model consists of a single 3D representation that is shared among views. Similarly to the work of Fidler et al. [5], at detection time this representation is projected on the image plane over the desired viewpoints. However, whereas in [5] the projection is done at image-level and therefore the computational cost is linear in the number of views, in our model every view is approximated at feature level as a linear combination of the pre-computed fronto-parallel views. As a result, once the fronto-parallel views have been computed, the cost of computing new views is almost negligible. This allows the model to be evaluated on many more viewpoints. In the experimental results we show that the proposed model has a comparable detection and pose estimation performance to standard multiview HOG detectors, but it is faster, it scales very well with the number of views and can better generalize to unseen views. Finally, we also show that with a procedure similar to label propagation it is possible to train the model even without using pose annotations at training time.
Decreased vasopressin-mediated renal water reabsorption in rats with compensated liver cirrhosis.

Experiments were performed to investigate vasopressin type 2 receptor (V2)-mediated renal water reabsorption and the renal expression of the vasopressin-regulated water channel aquaporin-2 (AQP-2) in cirrhotic rats with sodium retention but without ascites. In addition, the expression of the furosemide-sensitive type 1 Na-K-2Cl cotransporter (BSC-1) and the natriuretic response to an intravenous test dose furosemide (7.5 mg/kg) during acute V2-receptor blockade was measured. Acute V2-receptor blockade with the selective nonpeptide antagonist OPC-31260 (800 μg ⋅ kg-1 ⋅ h-1) was performed during conditions in which volume depletion was prevented by computer-driven, servo-controlled intravenous volume replacement with 150 mM glucose. OPC-31260 produced a significantly smaller increase in urine flow rate (-26%) and free water clearance (-18%) in cirrhotic rats than in control rats. The natriuretic response to an intravenous test dose furosemide (7.5 mg/kg) was significantly increased in cirrhotic rats (+52%), but pretreatment with OPC-31260 did not affect the natriuretic response to furosemide in neither cirrhotic nor in control rats. Semiquantitative immunoblotting showed a significant downregulation of AQP-2 in the renal cortex (-72%) and in the outer medulla (-44%). The relative expression of BSC-1 in the outer medulla was unchanged in cirrhotic rats. The corticopapillary gradient of Na was significantly increased in cirrhotic rats. Since daily urine flow rate was similar in cirrhotic and sham-operated rats, we suggest that non-vasopressin-mediated water reabsorption is increased in cirrhotic rats probably as a result of an increased corticomedullary gradient due to exaggerated NaCl reabsorption in the thick ascending limb of Henle's loop.
Quality of Coated Particles: Physical - Mechanical Characterization of Polymeric Film Coatings

All coated particle producers, when applying the coating layer(s) would like to know precisely what is the best coating system to use in order to answer customer’s requests. It is, therefore, of very high relevance for many industries, to have a clear understanding of what are the parameters I need to trigger in order to generate the requested quality. Such understanding was the target of this work. The specific equipments designed at Delft University of Technology enabled us to measure the resistance to attrition and the resistance to abrasion of both reference coating agents and commercially pre-mixed coating systems. The resistance to attrition was directly related to the intrinsic properties of the coating material, to the process parameters used to apply the coating layer (fluid bed coating in this case) and to the conditions in which the particles are stored. The viscoelastic properties of the coating layers were measured by using nano indentation. Very good correlation between the viscoelasticity term, tan ? , and the resistance to attrition was found. Cast and sprayed films were produced as representation of the coating film. The morphology and the structure of coating layers were mimicked much better by sprayed films which could be obtained by novel equipment designed during this work. To assess the quality of the coating layer and determine how efficient the coating process was, X-Ray micro tomography in combination with image analysis was used. This gave us a very robust set of data which could be used to correlate the quality of the coating layer to the parameters chosen during coating process and those two with the final performance of the coated particles in respect of resistance to attrition/abrasion. Finally commercially available pre-mixed coating systems were used as case study. By comparing them with the reference coating agents we could proof and quantify how important are the additives, plasticisers in primis, in increasing the coating quality and, therefore, the resistance to mechanical stresses.
Development and Validation of the Consumer Health Activation Index

Background. Although there has been increasing interest in patient engagement, few measures are publicly available and suitable for patients with limited health literacy. Objective. We sought to develop a Consumer Health Activation Index (CHAI) for use among diverse patients. Methods. Expert opinion, a systematic literature review, focus groups, and cognitive interviews with patients were used to create and revise a potential set of items. Psychometric testing guided by item response theory was then conducted among 301 English-speaking, community-dwelling adults. This included differential item functioning analyses to evaluate item performance across participant health literacy levels. To determine construct validity, CHAI scores were compared to scales measuring similar personality constructs. Associations between the CHAI and physical and mental health established predictive validity. A second study among 9,478 adults was used to confirm CHAI associations with health outcomes. Results. Exploratory factor analyses revealed a single-factor solution with a 10-item scale. The CHAI showed good internal consistency (alpha = 0.81) and moderate test–retest reliability (ICC = 0.53). Reading grade level was found to be at the 6th grade. Moderate to strong correlations were found with similar constructs (Multidimensional Health Locus of Control, r = 0.38, P < 0.001; Conscientiousness, r = 0.41, P < 0.001). Predictive validity was demonstrated through associations with functional health status measures (depression, r = −0.28, P < 0.001; anxiety, r = −0.22, P < 0.001; and physical functioning, r = 0.22, P < 0.001). In the validation sample, the CHAI was significantly associated with self-reported physical and mental health (r = 0.31 and 0.32 respectively; both P < 0.001). Conclusions. The CHAI appears to be a valid, reliable, and easily administered tool that can be used to assess health activation among adults, including those with limited health literacy. Future studies should test the tool in actual use and explore further applications.
Blood glucose patterns and appetite in time-blinded humans: carbohydrate versus fat.

We assessed the extent to which a possible synchronization between transient blood glucose declines and spontaneous meal initiation would lend support to the interpretation of a preload study with isoenergetic (1 MJ) isovolumetric high-fat or simple carbohydrate (CHO) preload drinks. Ten men (18-30 yr) fasted overnight and then were time blinded and made aware that they could request meals anytime. At first meal requests, volunteers consumed a preload; ad libitum meals were offered at subsequent requests. Postabsorptively, transient declines in blood glucose were associated with meal requests (χ2 = 8.29). Subsequent meal requests occurred during "dynamic declines" in blood glucose after the peak induced by drink consumption (100%). These meal requests took twice as long to occur after high-fat than after CHO preloads (fat = 126 ± 21, CHO = 65 ± 15 min), consistent with differences in interpolated 65-min satiety scores (fat = 38 ± 8.2, CHO = 16 ± 4). Postprandially, transient blood glucose declines were associated with meal requests (χ2 = 4.30). Spontaneous meal initiations were synchronized with transient and dynamic blood glucose declines. Synchronization of intermeal interval and dynamic declines related to higher satiating efficiency from high-fat preloads than from simple CHO preloads.
Handwritten word spotting in Indic scripts using foreground and background information

In this paper we present a line based word spotting system based on Hidden Markov Model for offline Indic scripts such as Bangla (Bengali) and Devanagari. We propose a novel approach of combining foreground and background information of text line images for keyword-spotting by character filler models. The candidate keywords are searched from a line without segmenting character or words. A significant improvement in performance is noted by using both foreground and background information than anyone alone. Pyramid Histogram of Oriented Gradient (PHOG) feature has been used in our word spotting framework and it outperforms other existing features of word spotting. The framework of combining foreground and background information has been evaluated in IAM dataset (English script) to show the robustness of the proposed approach.
Sparse and deep generalizations of the FRAME model

In the pattern theoretical framework developed by Grenander and advocated by Mumford for computer vision and pattern recognition, different patterns are represented by statistical generative models. The FRAME (Filters, Random fields, And Maximum Entropy) model is such a generative model for texture patterns. It is a Markov random field model (or a Gibbs distribution, or an energy-based model) of stationary spatial processes. The log probability density function of the model (or the energy function of the Gibbs distribution) is the sum of translation-invariant potential functions that are one-dimensional non-linear transformations of linear filter responses. In this paper, we review two generalizations of this model. One is a sparse FRAME model for non-stationary patterns such as objects, where the potential functions are location specific, and they are non-zero only at a selected collection of locations. The other generalization is a deep FRAME model where the filters are defined by a convolutional neural network (CNN or ConvNet). This leads to a deep convolutional energy-based model. The local modes of the energy function satisfies an auto-encoder which we call the Hopfield auto-encoder. The model can be learned by an “analysis by synthesis” algorithm that iterates a sampling step for synthesis and a learning step for analysis. The algorithm admits an adversarial interpretation where the learning step and sampling step play a minimax game based on a value function. We can recruit a generator model as a direct and approximate sampler of the deep energy-based model to speed up the sampling step, and the two models can be learned simultaneously by a cooperative learning algorithm.
Alveolar macrophage apoptosis and TNF-a, but not p53, expression correlate with murine response to bleomycin

LUIS A. ORTIZ,1 KRYZTOF MOROZ,2 JING-YAO LIU,2 GARY W. HOYLE,1 TIMOTHY HAMMOND,3 RAYMOND F. HAMILTON,4 ANDRIJ HOLIAN,4 WILLIAM BANKS,5 ARNOLD R. BRODY,2 AND MITCHELL FRIEDMAN1 Sections of 1Pulmonary Diseases, Critical Care and Environmental Medicine and 3Nephrology, Department of Medicine, and 2Lung Biology Program, Department of Pathology, Tulane University Medical Center, New Orleans, Louisiana 70112; 4Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Texas Medical School, Houston, Texas 77030; and 5Division of Geriatrics, St. Louis University, St. Louis, Missouri 63104
Adult human colonic subepithelial myofibroblasts express extracellular matrix proteins and cyclooxygenase-1 and -2.

Interactions between epithelial cells and subepithelial myofibroblasts are increasingly recognized as important in the regulation of epithelial cell function. We have established primary cultures of subepithelial myofibroblasts from adult human colonic mucosal samples denuded of epithelial cells and maintained in culture. During culture of mucosal tissue, subepithelial myofibroblasts migrated out via basement membrane pores before establishment in culture. Despite prolonged culture and passage, the myofibroblasts maintained their phenotype, as demonstrated by expression of α-smooth muscle actin and vimentin. The cells expressed transcripts and protein for cyclooxygenase (COX)-1 and -2 enzymes, and their release of prostaglandin E2(PGE2) was inhibited by selective COX-1 and -2 inhibitors. The myofibroblasts also expressed the extracellular matrix (ECM) proteins collagen type IV, laminin-β1 and -γ1, and fibronectin. Adult human colonic subepithelial myofibroblasts may influence epithelial cell function via products of COX-1 and -2 enzymes, such as PGE2 and secreted ECM proteins.
Perceived opportunities in the workplace : A new explanation for the gender wage gap

The present research offers a new explanation for the gender wage gap by showing that differences in payments may already emerge at the perception level and lead women to forgo participation in high paying, but challenging tasks. Specifically, we show that women shy away from challenges but at the same time engage in such challenges when opportunities are slightly re-framed and appear less extreme. Our experimental results are based on an artefactual field experiment with workers from a Swiss cleaning and facility management firm, who work in a low-skill entry-level job. In this environment the willingness to embrace new challenges is one of the main drivers for professional advancement. While men are more than 10 times more likely to accept a high paying challenge in our control treatment, this gap is strongly reduced in a slightly re-framed decision environment making the challenge appear less extreme. These findings are in line with women overestimating the difficulty of unknown tasks and we show that minimally more information overcomes this perceptual difference. Our results contribute to the present debate on affirmative action and suggest that a focus on the perception of challenges may be a fruitful alternative to promote the success of women in the workplace.
Angle Domain Hybrid Precoding and Channel Tracking for Millimeter Wave Massive MIMO Systems

The millimeter-wave (mm-wave) massive multiple-input multiple-output (MIMO) system has gained much attention for its considerable improvement in system throughput. However, the cost of complex hardware, e.g., radio frequency (RF) chains, hinders it from practical deployment. In this paper, we propose an angle domain hybrid precoding and channel tracking method by exploring the spatial features of the mm-wave massive MIMO channel. The number of the effective spatial beams, or equivalently the RF chains, is enormously decreased via the operation of spatial rotation. The users are then scheduled by the angle division multiple access scheme, which groups users according to their direction of arrivals (DOAs). Meanwhile, a channel tracking method is designed for the subsequent data transmission through a small number of pilot symbols. Specifically, the channel information is divided into the DOA information and the gain information, where the DOA information is tracked by a modified unscented Kalman filter and the gain information is estimated from beam training. Numerical results are provided to corroborate our studies.
Stem Cell Transplantation Enhances Endogenous Brain Repair after Experimental Stroke

Stem cell transplantation for stroke treatment has been a promising therapy in small and large animal models, and many clinical trials are ongoing to establish this strategy in a clinical setting. However, the mechanism underlying functional recovery after stem cell transplantation has not been fully established and there is still a need to determine the ideal subset of stem cells for such therapy. We herein reviewed the recent evidences showing the underlying mechanism of functional recovery after cell transplantation, focusing on endogenous brain repair. First, angiogenesis/neovascularization is promoted by trophic factors including vascular endothelial growth factor secreted from stem cells, and stem cells migrated to the lesion along with the vessels. Second, axonal sprouting, dendritic branching, and synaptogenesis were enhanced altogether in the both ipsilateral and contralateral hemisphere remapping the pyramidal tract across the board. Finally, endogenous neurogenesis was also enhanced although little is known how much these neurogenesis contribute to the functional recovery. Taken together, it is clear that stem cell transplantation provides functional recovery via endogenous repair enhancement from multiple ways. This is important to maximize the effect of stem cell therapy after stroke, although it is still undetermined which repair mechanism is mostly contributed.
Studies on nonisothermal crystallization of ultra–high molecular weight polyethylene in liquid paraffin

The nonisothermal crystallization kinetics for ultra–high molecular weight polyethylene (UHMWPE) in liquid paraffin (LP) systems was investigated through differential scanning calorimetry (DSC) measurement. The influence of UHMWPE concentration and cooling rate on crystallization mechanism and spherulitc structure as implied by the modified Avrami equation and Mo's analysis was determined, whereas the Ozawa's approach fails to describe the crystallization behaviors of these UHMWPE-diluent systems. As a result, in the modified Avrami analysis, it was found that the Avrami exponent is constant around five at various concentrations of UHMWPE and cooling rates. Further, the value of F(T) in the Mo's approach increases with the increasing of relative crystallinity and UHMWPE content in the blends. The nonisothermal crystallization kinetics presented here are the first for UHMWPE-diluent systems. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci, 2006
Effect of Melatonin Supplementation on Antioxidant Status and DNA Damage in High Intensity Trained Athletes

Abstract The aim of the study was to evaluate the effect of melatonin supplementation on antioxidant capacity and DNA damage in high intensity interval training (HIIT) athletes. A 2-week randomised, double-blinded, placebo-controlled trial with two groups was conducted. Placebo (PG) and melatonin (MG) (20 mg/d) athletes were monitored over a two-week period of HIIT and strength training. The total antioxidant capacity (TAC) and the glutathione peroxidase (GPx) and superoxide dismutase (SOD) activities were analysed in blood samples. DNA damage was measured in isolated lymphocytes by comet assay prior to and immediately after exercise. The supplementation increased plasma melatonin levels in the melatonin-treated group (p<0.05) after two weeks of intervention. Analysis of antioxidant status indicated higher (p<0.05) TAC and GPx in MG than PG post-intervention. No differences were found in SOD enzyme activity. DNA damage was diminished in MG (p<0.05) compared to PG in post-training conditions. Antioxidant status was associated with DNA damage (r=-0.679; p=0.047) in the melatonin-treated athletes. The present study suggest that melatonin supplementation improves antioxidant status and may prove to have beneficial effects preventing DNA damage induced by high intensity training.
Computational aspects of localized deformations in amorphous glassy polymers

Amorphous glassy polymers are prone to strain localization due to the particular constitutive behaviour of these materials where yield is followed immediately by intrinsic strain softening and where increasing strain hardening occurs at continued deformation. With a view on the reliable analysis of localization phenomena, this paper presents a so-called rate tangent formulation of a recently proposed constitutive model for the rate-dependent, large strain behaviour of glassy polymers. As part of the derivation, rate forms are presented for non-Gaussian three-chain. eight-chain and full network models for rubber elasticity. The implementation in viscoplastic-type finite element formulations is discussed, and is used, as an example, to study shear localization in glassy polymers under plane strain or axisymmetric compression. Computations with different material parameters confirm existing experimental observations that localization can take place in relatively diffuse (widening) shear bands or in families of relatively fine (multiplying) shear bands.