Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning Static Object Segmentation from Motion Segmentation

This thesis describes the SANE (Segmentation According to Natural Examples) algorithm for learning to segment objects in static images from video data. SANE uses background subtraction to find the segmentation of moving objects in videos. This provides object segmentation information for each video frame. The collection of frames and segmentations forms a training set that SANE uses to learn the image and shape properties that correspond to the observed motion boundaries. Then, when presented with new static images, the model infers segmentations similar to the observed motion segmentations. SANE is a general method for learning environment-specific segmentation models. Because it is self-supervised, it can adapt to a new environment and new objects with relative ease. Comparisons of its output to a leading image segmentation algorithm demonstrate that motion-defined object segmentation is a distinct problem from traditional image segmentation. The model outperforms a trained local boundary detector because it leverages the shape information it learned from the training data. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
An uncommon pattern of cardiac invasion in hepatocellular carcinomaHCC, hepatocellular carcinoma

Hepatocellular carcinoma (HCC), the most common primary malignant tumour of the liver, is a highly vascular neoplasm usually arising in a cirrhotic liver. In addition to the diagnosis of primary lesion, an assessment for extrahepatic metastasis is needed. Herein, an extremely uncommon pattern of heart invasion in a patient with advanced HCC is described. A 75-year-old man was admitted to the Hospital of Zumarraga, Zumarraga, Spain, for moderate abdominal pain, asthenia and weight loss. He denied having dyspnoea, orthopnoea, cough, palpitation or peripheral oedemas. Three years earlier, HCC had been diagnosed in the eighth segment, and the patient had received several courses of transcatheter …
Endothelial Notch1 Is Required for Proper Development of the Semilunar Valves and Cardiac Outflow Tract

Background Congenital heart disease is the most common type of birth defect, affecting ≈2% of the population. Malformations involving the cardiac outflow tract and semilunar valves account for >50% of these cases predominantly because of a bicuspid aortic valve, which has an estimated prevalence of 1% in the population. We previously reported that mutations in NOTCH1 were a cause of bicuspid aortic valve in nonsyndromic autosomal‐dominant human pedigrees. Subsequently, we described a highly penetrant mouse model of aortic valve disease, consisting of a bicuspid aortic valve with thickened cusps and associated stenosis and regurgitation, in Notch1‐haploinsufficient adult mice backcrossed into a Nos3‐null background. Methods and Results Here, we described the congenital cardiac abnormalities in Notch1 +/− ;Nos3 −/− embryos that led to ≈65% lethality by postnatal day 10. Although expected Mendelian ratios of Notch1 +/− ;Nos3 −/− embryos were found at embryonic day 18.5, histological examination revealed thickened, malformed semilunar valve leaflets accompanied by additional anomalies of the cardiac outflow tract including ventricular septal defects and overriding aorta. The aortic valve leaflets of Notch1 +/− ;Nos3 −/− embryos at embryonic day 15.5 were significantly thicker than controls, consistent with a defect in remodeling of the semilunar valve cushions. In addition, we generated mice haploinsufficient for Notch1 specifically in endothelial and endothelial‐derived cells in a Nos3‐null background and found that Notch1 fl/+;Tie2‐Cre +/− ;Nos3 −/− mice recapitulate the congenital cardiac phenotype of Notch1 +/− ;Nos3 −/− embryos. Conclusions Our data demonstrate the role of endothelial Notch1 in the proper development of the semilunar valves and cardiac outflow tract.
Light-activated shape memory polymers and associated applications

Continuous product development and technology integration efforts using shape memory polymers (SMPs) have uncovered a need for faster response times. As with most smart materials, SMP responds to a specific stimulus. Traditionally SMP is triggered by thermal stimulus; increasing the temperature of the SMP above a Tg will transition the polymer from a glassy state to a rubbery state. The transition is reversible upon cooling below the Tg. It has been determined that many SMP applications can be significantly enhanced with non-thermal triggering. Non-thermal triggering eliminates the need for heating mechanisms and reduces cycle time. Furthermore, it has been found that with a faster response time many new applications become viable. Previous successful attempts have been made to improve response time of SMP by increasing its thermal conductivity with various thermally conductive additives1. However, thermal heating and cooling of polymers and composites of substantial thickness, thermally conductive or not, takes time. In an effort to facilitate system integration and increase the response time of SMP, researchers at Cornerstone Research Group, Inc. (CRG) have sought to eliminate the thermal dependency of SMP by developing light-activated shape memory polymer (LASMP). In this work, monomers which contain photo-crosslinkable groups in addition to the primary polymerizable groups were developed. These monomers were formulated and cured with other monomers to form LASMP. The mechanical properties of these materials, the kinetics, and the reversibility of the light-activated shape memory effect were studied. The near-, mid-, and far-term potential of this new material technology for system level applications is discussed.
Distance Between a Point and a Convex Cone in $n$ -Dimensional Space: Computation and Applications

This paper presents an algorithm to compute the minimum distance from a point to a convex cone in n-dimensional space. The convex cone is represented as the set of all nonnegative combinations of a given set. The algorithm generates a sequence of simplicial cones in the convex cone, such that their distances to the single point converge to the desired distance. In many cases, the generated sequence is finite, and therefore, the algorithm has finite-convergence property. Recursive formulas are derived to speed up the computation of distances between the single point and the simplicial cones. The superior efficiency and effectiveness of this algorithm are demonstrated by applications to force-closure test, system equilibrium test, and contact force distribution, which are fundamental problems in the research of multicontact robotic systems. Theoretical and numerical comparisons with previous work are provided.
Upregulation of vascular angiotensin II receptor gene expression by low-density lipoprotein in vascular smooth muscle cells.

BACKGROUND Because LDL and the angiotensin II type 1 (AT1) receptor are thought to be involved in the pathogenesis of chronic vascular disease, we studied possible interactions between these two biological systems in cultured rat vascular smooth muscle cells. METHODS AND RESULTS Incubation of vascular smooth muscle cells with 100 micrograms/mL LDL profoundly increased AT1 receptor mRNA to approximately 250% of control levels as assessed by Northern hybridization analysis. This effect is maximal 12 hours after addition of LDL to the culture medium and is sustained for up to 24 hours. The LDL-induced upregulation is dose dependent, with a maximal effect obtained with 100 micrograms/mL LDL. There is a correlative increase of cell surface-associated AT1 receptors as assessed by saturation radioligand binding assays. The half-life of AT1 receptor mRNA is increased substantially by LDL compared with that of cells treated only with 5,6-dichlorobenzimidazole to block transcription. Angiotensin II-induced elevation of cytosolic calcium concentration is significantly increased in vascular smooth muscle cells pretreated with LDL to 368 +/- 41 nmol/L compared with control cells pretreated with vehicle (248 +/- 33 nmol/L). Moreover, angiotensin II-induced DNA synthesis is markedly enhanced when cells are coincubated with 100 micrograms/mL LDL. CONCLUSIONS These data reveal a significant upregulation of AT1 receptor gene expression by LDL in vascular smooth muscle cells through mechanisms that involve posttranscriptional mRNA stabilization. Ultimately, this AT1 receptor upregulation leads to an elevated functional response of vascular smooth muscle cells on angiotensin II stimulation.
On the dislocation mechanism of amorphization of Si by indentation

The formation of an amorphous phase underneath a Vickers indentation produced on a Si(001) surface at room temperature has been observed by cross-sectional transmission electron microscopy. Two types of location are observed for the amorphous phase. One is formed just underneath the image of the indentation and the other is parallel to the slip planes of Si. It is concluded that the latter type, at least, is formed as a result of activation of dislocations which is induced by an external shear stress combined with a hydrostatic pressure.
Characterization of the anterior cingulate cortex in adult tree shrew

The anterior cingulate cortex (ACC) is a key brain region for the perception of pain and emotion. Cellular and molecular mechanisms of the ACC are usually investigated in rodents such as mice and rats. Studies of synaptic mechanisms in primates are limited. To facilitate the translation of basic results from rodents to humans, it is critical to use a primate-like animal model for the investigation of the ACC. The tree shrew presents a great opportunity for this as they have similar genome sequences to primates and are considered to have many similarities to primates. In the present study, by combining anatomy, immunostaining and micro-optical sectioning tomography methods, we examined the morphological properties of the ACC in the tree shrew and compared them with the mouse and rat. We found that the ACC in the tree shrew is significantly larger than those found in the mouse and rat. The sizes of cell bodies of ACC pyramidal cells in tree shrew are also larger than that found in the mouse or rat. Furthermore, there are significantly more apical/basal dendritic branches and apical dendritic spines of ACC pyramidal neurons in tree shrew. These results demonstrate that pyramidal cells of the ACC in tree shrews are more advanced than those found in rodents (mice and rats), indicating that the tree shrew can be used as a useful animal model for studying the cellular mechanism for ACC-related physiological and pathological changes in humans.
A New Clustering Algorithm Partition K-Means

K-means is a classic algorithm of partition clustering, its speed is very fast, well, the clustering result is very sensitive to the initial cores. As a result, algorithm K-means does not always get the Global Optimization. To solve this problem, this paper proposes a new algorithm partition K-means, which selects the initial cores with a partition method and then cluster the data set with K-means. The experiment shows that the new algorithm gets better effect and better efficiency than the original algorithm K-means.
Susceptibility of glomerular filtration rate estimations to variations in creatinine methodology: a study in older patients

Background: It is recommended that measurement of serum creatinine should be supplemented with a creatinine-based estimation of glomerular filtration rate (GFR). The influence of creatinine methodology on these estimates is not always appreciated. We have studied differences in creatinine methods and their influence on GFR estimation specifically in older people. Methods: In all, 46 older patients (mean age 80 y, range 69-92 y) with predominantly mild or moderate kidney disease were studied. Serum creatinine was measured using a rate Jaffe method and two different enzymatic methods. Isotope dilution mass spectrometry served as the reference creatinine method. GFR was estimated using both the Modification of Diet in Renal Disease (MDRD) and Cockcroft and Gault formulae: a 51Cr-EDTA GFR estimation served as the reference GFR method. Results: Both enzymatic methods produced creatinine results that were significantly different (P < 0.001) from the reference method. The Jaffe method over- and underestimated creatinine at low and high concentrations, respectively. The most likely explanation for these differences relates to standardization of the assays. Irrespective of creatinine method, the Cockroft and Gault formula tended to underestimate GFR, and the MDRD formula to overestimate GFR. Use of the differing creatinine methods to estimate GFR produced predictable biases of the estimate, with mean GFR estimates varying by 14% across the creatinine methods. Conclusion: Estimates of GFR depend critically upon the accuracy and precision of the creatinine measurement used in their calculation.
On the Spectra of General Random Graphs

We consider random graphs such that each edge is determined by an independent random variable, where the probability of each edge is not assumed to be equal. We use a Chernoff inequality for matrices to show that the eigenvalues of the adjacency matrix and the normalized Laplacian of such a random graph can be approximated by those of the weighted expectation graph, with error bounds dependent upon the minimum and maximum expected degrees. In particular, we use these results to bound the spectra of random graphs with given expected degree sequences, including random power law graphs. Moreover, we prove a similar result giving concentration of the spectrum of a matrix martingale on its expectation.
Learning a Generative Model for Validity in Complex Discrete Structures

Deep generative models have been successfully used to learn representations for high-dimensional discrete spaces by representing discrete objects as sequences, for which powerful sequence-based deep models can be employed. Unfortunately, these techniques are significantly hindered by the fact that these generative models often produce invalid sequences: sequences which do not represent any underlying discrete structure. As a step towards solving this problem, we propose to learn a deep recurrent validator model, which can estimate whether a partial sequence can function as the beginning of a full, valid sequence. This model not only discriminates between valid and invalid sequences, but also provides insight as to how individual sequence elements influence the validity of the overall sequence, and the existence of a corresponding discrete object. To learn this model we propose a reinforcement learning approach, where an oracle which can evaluate validity of complete sequences provides a sparse reward signal. We believe this is a key step toward learning generative models that faithfully produce valid sequences which represent discrete objects. We demonstrate its effectiveness in evaluating the validity of Python 3 source code for mathematical expressions, and improving the ability of a variational autoencoder trained on SMILES strings to decode valid molecular structures.
Background determination‐based detection of scattered peaks

In many instances of signal and image processing, it is indispensable to precisely distinguish scattered peaks from a background, e.g., camera signals in microscopy. Here we addressed the detection of Gaussian signals in simulated line profiles (LP) comparable with e.g., fluorescence microscopy data. In a first step, we measured the applicability of histogram‐based global background estimation. We find that the method is valid for typical scattered Gaussian signals if they are averagely separated by interpeak distances of 5.5 standard deviations. This enabled us to design global background determination‐based peak detection (GBPD). GBPD was compared with two local background determination‐based signal detection methods that had been designed for analysis of electrophysiological data andmicroscopy images, respectively. We were able to prove via receiver–operator characteristic (ROC) comparisons of signal‐to‐noise ratio (SNR), interpeak distance, and filtering behavior that, when applicable, GBPD brings advantages in knowledge needed a priori, performance at any SNR, controllability and spatial resolution. Microsc. Res. Tech. 73:1115–1122, 2010. © 2010 Wiley‐Liss, Inc.
Resources for the comprehensive discovery of functional RNA elements

Transcriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck to the application of these methods in diverse cell-lines, tissues and developmental stages, is the availability of validated IP-quality antibodies. Using IP followed by immunoblot assays, we have developed a validated repository of 438 commercially available antibodies that interrogate 365 unique RBPs. In parallel, 362 short-hairpin RNA (shRNA) constructs against 276 unique RBPs were also used to confirm specificity of these antibodies. These antibodies can characterize subcellular RBP localization. With the burgeoning interest in the roles of RBPs in cancer, neurobiology and development, these resources are invaluable to the broad scientific community. Detailed information about these resources is publicly available at the ENCODE portal (https://www.encodeproject.org/). Highlights Antibodies against 365 unique RBPs successfully immunoprecipitate the RBPs Short-hairpin RNAs against 276 unique RBPs confirm the specificity of RBP antibodies Antibodies characterize subcellular localization of RBPs Antibody and hairpin RNA information are provided at https://www.encodeproject. org/
A finite-element model for piezoelectric composite laminates

A finite-element model based on the classical laminated plate theory is developed for the active vibration control of a composite plate containing distributed piezoelectric sensors and actuators. The formulation is derived from the variational principle. The piezoelectrics' mass and stiffness are taken into account in the present model. A simple negative velocity feedback control algorithm coupling the direct and converse piezoelectric effects is used to actively control the dynamic response of an integrated structure through a closed control loop. The static analysis and active vibration suppression of a cantilever composite plate are performed as a numerical example to verify the proposed model. The modal superposition technique and the Newmark- method are used in the numerical simulation to calculate the dynamic response of the laminated composite plate.
Physical activity and exercise recommendations for stroke survivors: an American Heart Association scientific statement from the Council on Clinical Cardiology, Subcommittee on Exercise, Cardiac Rehabilitation, and Prevention; the Council on Cardiovascular Nursing; the Council on Nutrition, Physical

Annually, 700 000 people in the United States suffer a stroke, or ≈1 person every 45 seconds, and nearly one third of these strokes are recurrent.1 More than half of men and women under the age of 65 years who have a stroke die within 8 years.1 Although the stroke death rate fell 12% from 1990 to 2000, the actual number of stroke deaths increased by 9.9%. This represents a leveling off of prior declines.2 Moreover, the incidence of stroke is likely to continue to escalate because of an expanding population of elderly Americans; a growing epidemic of diabetes, obesity, and physical inactivity among the general population; and a greater prevalence of heart failure patients.3 When considered independently from other cardiovascular diseases, stroke continues to be the third leading cause of death in the United States. Improved short-term survival after a stroke has resulted in a population of an estimated 4 700 000 stroke survivors in the United States.1 The majority of recurrent events in stroke survivors are recurrent strokes, at least for the first several years.4 Moreover, individuals presenting with stroke frequently have significant atherosclerotic lesions throughout their vascular system and are at heightened risk for, or have, associated comorbid cardiovascular disease.5,6 Accordingly, recurrent stroke and cardiac disease are the leading causes of mortality in stroke survivors. Both coronary artery disease (CAD) and ischemic stroke share links to many of the same predisposing, potentially modifiable risk factors (hypertension, abnormal blood lipids and lipoproteins, cigarette smoking, physical inactivity, obesity, and diabetes mellitus), which highlights the prominent role lifestyle plays in the origin of stroke and cardiovascular disease.5,7,8 Modification of multiple risk factors through a combination of comprehensive lifestyle interventions and appropriate pharmacological therapy is now recognized as the cornerstone of initiatives aimed …
The C/H3 Domain of p300 Is Required to Protect VRK1 and VRK2 from their Downregulation Induced by p53

Background The vaccinia-related kinase 1 (VRK1) protein, an activator of p53, can be proteolytically downregulated by an indirect mechanism, which requires p53-dependent transcription. Principal Findings In this work we have biochemically characterized the contribution of several p53 transcriptional cofactors with acetyl transferase activity to the induction of VRK1 downregulation that was used as a functional assay. Downregulation of VRK1 induced by p53 is prevented in a dose dependent manner by either p300 or CBP, but not by PCAF, used as transcriptional co-activators, suggesting that p53 has a different specificity depending on the relative level of these transcriptional cofactors. This inhibition does not require p53 acetylation, since a p53 acetylation mutant also induces VRK1 downregulation. PCAF can not revert the VRK1 protection effect of p300, indicating that these two proteins do not compete for a common factor needed to induce VRK1 downregulation. The protective effect is also induced by the C/H3 domain of p300, a region implicated in binding to several transcription factors and SV40 large T antigen; but the protective effect is lost when a mutant C/H3Del33 is used. The protective effect is a consequence of direct binding of the C/H3 domain to the transactivation domain of p53. A similar downregulatory effect can also be detected with VRK2 protein. Conclusions/Significance Specific p53-dependent effects are determined by the availability and ratios of its transcriptional cofactors. Specifically, the downregulation of VRK1/VRK2 protein levels, as a consequence of p53 accumulation, is thus dependent on the levels of the p300/CBP protein available for transcriptional complexes, since in this context this cofactor functions as a repressor of the effect. These observations point to the relevance of knowing the cofactor levels in order to determine one effect or another.