Miracle-dz/UniFAR-FTUs huggingface dataset:
Legacies of the Dust. A multiwavelength study of protoplanetary disks and young exoplanetary systems

The process of planet formation is intimately related with the birth of the host star. The new born star is surrounded by a disk of dust and gas, inevitable result of the conservation of angular momentum in these initial steps of mass collapse. This disk, in turn, will evolve with its host star, feeding it matter over time by accretion streams, and dissipating as the star matures. During this dissipation, dust grains will coalesce into larger bodies, and in some cases gain enough mass as to congregate into proto-planets, which eventually will establish a new planetary system. This process of star and planet formation, though, is still not completely understood. More data and observations are needed to set constraints to the models and theories. There is where this thesis comes into play. This work is an observational enterprise, which main goal is the identification of certain objects thought to be indications of key moments on the process of star and planet formation. One such kind of objects are transitional disks. These objects are considered to be one of the evolutionary steps in the process of disk evolution. They present infrared excesses at long wavelengths but little to none in the near-infrared. This is interpreted as a lack of dust in the inner regions of the disk, assuming that wavelength traces dust temperature, which is roughly proportional to the distance from the host star. This could have been caused by photoevaporation or dust clearance by a companion, possibly of planetary origin. In this work several transitional disks candidates were identified in the Lupus and Ophiucus star forming regions, using data from the Herschel Space Observatory. The identification of the transitional disks in these regions opens the door to future analysis. The objects identified in this work are perfect candidates for further follow-up. The interactions between the star and the disk are also crucial to understand the process of the formation of planets. The young star accretes gas from its protoplanetary disk, a process that contributes to the emission of highly energetic photons, in the form of X-rays or UV. These emissions, in turn, interact with the disk, modifying its evolution. This creates a circular relation, between disk-star-X-ray-disk, which effects are crucial for the evolution of an early exoplanetary system: these Xray photons play an essential role in the evolution of early planetary atmospheres. Analyzing these interactions and the processes that rule them, then, is of the utmost importance on the study of early exoplanet atmospheres. This work analyzes the relation between the accretion rates and the X-ray emission from a sample of sources in the Orion Nebula Cluster. An anti-correlation is found between both features, similar to that present in the Taurus Molecular Clouds. This could play
Loss of chromosome 11q21–23.1 and 17p and gain of chromosome 6p are independent prognostic indicators in B-cell non-Hodgkin's lymphoma

Comparative genomic hybridization (CGH) was employed to study chromosomal aberrations in relation to cell proliferation, apoptosis, and patient survival in 94 cases of B-cell non-Hodgkin’s lymphoma diagnosed between 1983 and 1993. Eighty cases had aberrations by CGH. Chromosomal regions 1p21–31.1 (10%), 6cen-q24 (12%), 8p (11%), 9p21-ter (14%), 11q21–23.1 (11%), 13q13–21.1 (12%), and 17p (15%) were frequently lost. Gains were found at 3q21-ter (22%), 6p (11%), 7p (12%), 8q23-ter (13%), 12cen-q15 (17%), 17q24-ter (13%), and 18q13.3–21 (20%). A high number of aberrations (≥ 4, 33 cases) was associated (P ≤ 0.001) with the mantle cell and diffuse large B-cell lymphoma subtypes, a high fraction of tumour cells in S phase, and short survival (RR (relative risk) = 3.7). Loss of 1p21–31.1, 8p, 9p21-ter, 11q21–23.1, and 13q13–21.1 were associated with mantle cell lymphoma (P ≤ 0.03), while gain of 6p and 12cen-q15 were more frequent in diffuse large B-cell and small lymphocytic lymphoma, respectively (P = 0.04). Loss of 8p and 17p, and gain of 3q21-ter, 6p, 7p, and 8q23-ter were associated with a high S phase fraction (P ≤ 0.03), but none of the aberrations were associated with tumour apoptotic fraction (P ≥ 0.13). The most important prognostic CGH parameters (P < 0.001) were losses of 11q21–23.1 (RR = 3.8) and 17p (RR = 4.4), and gain of 6p (RR = 4.2). The latter parameters and IPI were the only ones with independent prognostic value (RR = 10, 5.0, 6.7, and 3.7, respectively; P < 0.001) when assessed together with lymphoma sub-type, primary versus relapse cases, treatment, B symptoms, S phase fraction, and presence of BCL1 and BCL2 translocations. A combined CGH/IPI binary parameter had high prognostic value for patients receiving different treatments, with various lymphoma sub-types, and for primary as well as relapse cases. © 2001 Cancer Research Campaign http://www.bjcancer. com
Effects of gestational diabetes mellitus on proteins implicated in insulin signaling in human placenta

Objective. Placenta plays a central role in fetal nutrition. During gestational diabetes mellitus (GDM), it suffers structural and functional alterations which affect the health of both mother and fetus. In the present study we aimed to clarify if GDM modifies the amounts of leptin receptor (Ob-R) and of the main proteins implicated in insulin signal transmission (insulin receptor, insulin receptor substrate-1 and phosphatidylinositol-3-kinase subunit p85α) in human placenta; we also attempted to confirm the presence of estrogen receptor-α to determine the effect of GDM on its amount. Methods. Placentas were recovered from 30 women with uncomplicated pregnancies and 20 women who developed GDM. Western blotting and immunocytochemistry experiments were performed to investigate the above-mentioned proteins. Results. We observed that all proteins studied were increased in GDM. However, it is unknown if this is a consequence of GDM or the result of medical treatments used to mitigate the injurious effects of GDM. Conclusions. Probably, the changes we found are indicative of the protective role of the placenta prior to the injurious effects of GDM and/or an important indicator of placental aging. Some aspects related to the link between non-genomic estrogen action, the mitogenic action of insulin and the role of Ob-R in placenta from normal and GDM women need to be investigated in greater depth.
Yarbus, eye movements, and vision

The impact of Yarbus's research on eye movements was enormous following the translation of his book Eye Movements and Vision into English in 1967. In stark contrast, the published material in English concerning his life is scant. We provide a brief biography of Yarbus and assess his impact on contemporary approaches to research on eye movements. While early interest in his work focused on his study of stabilised retinal images, more recently this has been replaced with interest in his work on the cognitive influences on scanning patterns. We extended his experiment on the effect of instructions on viewing a picture using a portrait of Yarbus rather than a painting. The results obtained broadly supported those found by Yarbus.
Imaging the Urokinase Plasminongen Activator Receptor in Preclinical Breast Cancer Models of Acquired Drug Resistance

Subtype-targeted therapies can have a dramatic impact on improving the quality and quantity of life for women suffering from breast cancer. Despite an initial therapeutic response, cancer recurrence and acquired drug-resistance are commonplace. Non-invasive imaging probes that identify drug-resistant lesions are urgently needed to aid in the development of novel drugs and the effective utilization of established therapies for breast cancer. The protease receptor urokinase plasminogen activator receptor (uPAR) is a target that can be exploited for non-invasive imaging. The expression of uPAR has been associated with phenotypically aggressive breast cancer and acquired drug-resistance. Acquired drug-resistance was modeled in cell lines from two different breast cancer subtypes, the uPAR negative luminal A subtype and the uPAR positive triple negative subtype cell line MDA-MB-231. MCF-7 cells, cultured to be resistant to tamoxifen (MCF-7 TamR), were found to significantly over-express uPAR compared to the parental cell line. uPAR expression was maintained when resistance was modeled in triple-negative breast cancer by generating doxorubicin and paclitaxel resistant MDA-MB-231 cells (MDA-MB-231 DoxR and MDA-MB-231 TaxR). Using the antagonistic uPAR antibody 2G10, uPAR was imaged in vivo by near-infrared (NIR) optical imaging and 111In-single photon emission computed tomography (SPECT). Tumor uptake of the 111In-SPECT probe was high in the three drug-resistant xenografts (> 46 %ID/g) and minimal in uPAR negative xenografts at 72 hours post-injection. This preclinical study demonstrates that uPAR can be targeted for imaging breast cancer models of acquired resistance leading to potential clinical applications.
Requisite Role of Kv1.5 Channels in Coronary Metabolic Dilation.

RATIONALE In the working heart, coronary blood flow is linked to the production of metabolites, which modulate tone of smooth muscle in a redox-dependent manner. Voltage-gated potassium channels (Kv), which play a role in controlling membrane potential in vascular smooth muscle, have certain members that are redox-sensitive. OBJECTIVE To determine the role of redox-sensitive Kv1.5 channels in coronary metabolic flow regulation. METHODS AND RESULTS In mice (wild-type [WT], Kv1.5 null [Kv1.5(-/-)], and Kv1.5(-/-) and WT with inducible, smooth muscle-specific expression of Kv1.5 channels), we measured mean arterial pressure, myocardial blood flow, myocardial tissue oxygen tension, and ejection fraction before and after inducing cardiac stress with norepinephrine. Cardiac work was estimated as the product of mean arterial pressure and heart rate. Isolated arteries were studied to establish whether genetic alterations modified vascular reactivity. Despite higher levels of cardiac work in the Kv1.5(-/-) mice (versus WT mice at baseline and all doses of norepinephrine), myocardial blood flow was lower in Kv1.5(-/-) mice than in WT mice. At high levels of cardiac work, tissue oxygen tension dropped significantly along with ejection fraction. Expression of Kv1.5 channels in smooth muscle in the null background rescued this phenotype of impaired metabolic dilation. In isolated vessels from Kv1.5(-/-) mice, relaxation to H2O2 was impaired, but responses to adenosine and acetylcholine were normal compared with those from WT mice. CONCLUSIONS Kv1.5 channels in vascular smooth muscle play a critical role in coupling myocardial blood flow to cardiac metabolism. Absence of these channels disassociates metabolism from flow, resulting in cardiac pump dysfunction and tissue hypoxia.
Retrograde amnesia for semantic information in Alzheimer's disease

Patients with mild to moderate Alzheimer's disease and normal controls were tested on a retrograde amnesia test with semantic content (Neologism and Vocabulary Test, or NVT), consisting of neologisms to be defined. Patients showed a decrement as compared to normal controls, pointing to retrograde amnesia within semantic memory. No evidence for a gradient within this amnesia was found, although one was present on an autobiographic test of retrograde amnesia that had a wider time scale. Several explanations for these results are presented, including one that suggests that extended retrograde amnesia and semantic memory deficits are in fact one and the same deficit. (JINS, 2005, 11, 40–48.)
Involvement of transcriptional repressor ATF3 in acceleration of caspase protease activation during DNA damaging agent‐induced apoptosis

DNA topoisomerase inhibitors are effective chemotherapeutic agents on several solid tumor cells. They induce a specific signaling cascade that executes an active cell death process (apoptosis), including caspase activation, and the blockage of the signaling is associated with drug‐resistance of tumor cells. However, little is known about the initial signal transduction induced by the agents. In the present study, we screened genes that are initially upregulated in caspase‐independent manner. We found that the activating transcription factor 3 (ATF3) protein, a repressor of cyclic‐AMP responsive element (CRE)‐dependent transcription, was strongly induced among CRE‐BP/ATF members and subsequently accumulated in nuclei following camptothecin or etoposide treatment. During induction of apoptosis, the accumulation and the nuclear translocation of ATF3 coincided with the activation of caspase protease and were not inhibited by the broad caspase inhibitor Z‐VAD‐fmk, indicating that ATF3 induction is not a downstream event of caspase activation. When stably or transiently overexpressed, ATF3 markedly accelerated the drug‐induced apoptosis and enhanced caspase protease activation. ATF3 strongly downregulated CRE‐dependent transcription, while ATF3 did not affect the expression levels of Bcl‐2, Bcl‐x, or Bax. Our present results indicate that ATF3 plays a critical role in accelerating caspase protease activation and apoptosis. Since CRE‐dependent transcription functions as cell survival signaling, ATF3 could control the upstream signaling of apoptosis by repressing CRE‐dependent gene expression of cell survival factors. © 2001 Wiley‐Liss, Inc.
Molecular characterization of forest soil based Paenibacillus elgii and optimization of various culture conditions for its improved antimicrobial activity

Microorganisms have provided a bounty of bioactive secondary metabolites with very exciting biological activities such as antibacterial, antifungal antiviral, and anticancer, etc. The present study aims at the optimization of culture conditions for improved antimicrobial production of Paenibacillus elgii obtained from Wayanad forest of Western Ghats region of Kerala, India. A bacterial strain isolated from the Western Ghats forest soil of Wayanad, Kerala, India was identified as P. elgii by 16S rRNA gene sequencing. P. elgii recorded significant board spectrum activity against all human and plant pathogenic microorganism tested except Candida albicans. It has been well known that even minor variations in the fermentation medium may impact not only the quantity of desired bioactive metabolites but also the general metabolic profile of the producing microorganisms. Thus, further studies were carried out to assess the impact of medium components on the antimicrobial production of P. elgii and to optimize an ideal fermentation medium to maximize its antimicrobial production. Out of three media [nutrient broth (NA), Luria broth (LB) and Trypticase soy broth (TSB)] used for fermentation, TSB medium recorded significant activity. Glucose and meat peptone were identified as the best carbon and nitrogen sources, which significantly affected the antibiotic production when supplemented with TSB medium. Next the effect of various fermentation conditions such as temperature, pH, and incubation time on the production of antimicrobial compounds was studied on TSB + glucose + meat peptone and an initial pH of 7 and a temperature of 30°C for 3 days were found to be optimum for maximum antimicrobial production. The results indicate that medium composition in the fermentation media along with cultural parameters plays a vital role in the enhanced production of antimicrobial substances.
Depth synthesis and local warps for plausible image-based navigation

Modern camera calibration and multiview stereo techniques enable users to smoothly navigate between different views of a scene captured using standard cameras. The underlying automatic 3D reconstruction methods work well for buildings and regular structures but often fail on vegetation, vehicles, and other complex geometry present in everyday urban scenes. Consequently, missing depth information makes Image-Based Rendering (IBR) for such scenes very challenging. Our goal is to provide plausible free-viewpoint navigation for such datasets. To do this, we introduce a new IBR algorithm that is robust to missing or unreliable geometry, providing plausible novel views even in regions quite far from the input camera positions. We first oversegment the input images, creating superpixels of homogeneous color content which often tends to preserve depth discontinuities. We then introduce a depth synthesis approach for poorly reconstructed regions based on a graph structure on the oversegmentation and appropriate traversal of the graph. The superpixels augmented with synthesized depth allow us to define a local shape-preserving warp which compensates for inaccurate depth. Our rendering algorithm blends the warped images, and generates plausible image-based novel views for our challenging target scenes. Our results demonstrate novel view synthesis in real time for multiple challenging scenes with significant depth complexity, providing a convincing immersive navigation experience.
Medical malpractice concerns and defensive medicine: a nationwide survey of breast pathologists.

OBJECTIVES "Assurance behaviors" in medical practice involve providing additional services of marginal or no medical value to avoid adverse outcomes, deter patients from filing malpractice claims, or ensure that legal standards of care were met. The extent to which concerns about medical malpractice influence assurance behaviors of pathologists interpreting breast specimens is unknown. METHODS Breast pathologists (n = 252) enrolled in a nationwide study completed an online survey of attitudes regarding malpractice and perceived alterations in interpretive behavior due to concerns of malpractice. Associations between pathologist characteristics and the impact of malpractice concerns on personal and colleagues' assurance behaviors were determined by χ(2) and logistic regression analysis. RESULTS Most participants reported using one or more assurance behaviors due to concerns about medical malpractice for both their personal (88%) and colleagues' (88%) practices, including ordering additional stains, recommending additional surgical sampling, obtaining second reviews, or choosing the more severe diagnosis for borderline cases. Nervousness over breast pathology was positively associated with assurance behavior and remained statistically significant in a multivariable logistic regression model (odds ratio, 2.5; 95% confidence interval, 1.0-6.1; P = .043). CONCLUSIONS Practicing US breast pathologists report exercising defensive medicine by using assurance behaviors due to malpractice concerns.
Dissecting the role of the ϕ29 terminal protein DNA binding residues in viral DNA replication

Phage ϕ29 DNA replication takes place by a protein-priming mechanism in which the viral DNA polymerase catalyses the covalent linkage of the initiating nucleotide to a specific serine residue of the terminal protein (TP). The N-terminal domain of the ϕ29 TP has been shown to bind to the host DNA in a sequence-independent manner and this binding is essential for the TP nucleoid localisation and for an efficient viral DNA replication in vivo. In the present work we have studied the involvement of the TP N-terminal domain residues responsible for DNA binding in the different stages of viral DNA replication by assaying the in vitro activity of purified TP N-terminal mutant proteins. The results show that mutation of TP residues involved in DNA binding affects the catalytic activity of the DNA polymerase in initiation, as the Km for the initiating nucleotide is increased when these mutant proteins are used as primers. Importantly, this initiation defect was relieved by using the ϕ29 double-stranded DNA binding protein p6 in the reaction, which decreased the Km of the DNA polymerase for dATP about 130–190 fold. Furthermore, the TP N-terminal domain was shown to be required both for a proper interaction with the DNA polymerase and for an efficient viral DNA amplification.
Nyquist Stability Criterion of Sampled-Data Systems with the 2-Regularized Determinant and Its Applications to Robust Stability Analysis

Using the 2-regularized determinant associated with Hilbert-Schmidt operators, this paper derives a Nyquist stability criterion of sampled-data systems that covers the general setting of sampled-data systems, which gives a necessary and sufficient condition for internal stability of closed-loop sampled-data systems. This criterion is applied to the derivation of robust stability theorems such as the small-gain and passivity theorems with respect to the internal stability of sampled-data systems, by which the usefulness of the derived Nyquist stability criterion is demonstrated.
Epstein-Barr Virus DNA Load in Nasopharyngeal Brushings and Whole Blood in Nasopharyngeal Carcinoma Patients before and after Treatment

Purpose: Nasopharyngeal carcinoma (NPC) is consistently associated with Epstein-Barr virus (EBV) and highly prevalent in Indonesia. EBV-DNA load can be used for early diagnosis and may have prognostic value. In this study, EBV-DNA load was evaluated in minimal invasive nasopharyngeal (NP) brushings and whole blood for initial diagnosis and therapy assessment against the standard-of-care diagnosis by biopsy with EBV-RISH and standard EBV-IgA serology. Experimental Design: NP brushings and blood samples were collected from 289 consecutive ENT patients suspected of NPCs and 53 local healthy controls. EBV-DNA load was quantified by real-time PCR and serology by peptide-based EBV-IgA ELISA. Tissue biopsies were examined by routine histochemistry and by EBER RNA in situ hybridization. Results: Repeated NP brushing was well tolerated by patients and revealed high viral load in the 228 NPC cases at diagnosis than 61 non-NPC cancer cases and healthy controls (P < 0.001). The diagnostic value of EBV-DNA load in blood and EBV-IgA serology was inferior to the NP brush results. The level of EBV-DNA load in brushes of patients with NPC was not related to T, N, or M stage, whereas elevated EBV-DNA load in blood correlated with N and M stage. EBV-DNA levels in brushings and whole blood showed a significant reduction at 2 months after treatment (P = 0.001 and P = 0.005, respectively), which was not reflected in EBV-IgA serology. Conclusions: NP brush sampling combined with EBV-DNA load analysis is a minimal invasive and well-tolerated diagnostic procedure, suited for initial diagnosis and follow-up monitoring of NPCs. Clin Cancer Res; 19(8); 2175–86. ©2013 AACR.
Spatial patterns of stream solute concentrations in a steep mountainous catchment with a homogeneous landscape

The spatial patterns of stream solute concentrations in a catchment reflect its hydrology and biogeochemistry. The spatial relationship between drainage areas and solute concentrations may be asymptotic or convergent (large variation in small streams that becomes dampened as they merge into larger streams), probably depending on landscape features and/or solute type. Thus, we investigated the concentration spatial patterns of dissolved silica and major ions (Na+, K+, Mg2+, Ca2+, NO3−, SO42−, and Cl−) in steep, humid headwaters of a 4.27 km2 catchment on Tanakami Mountain, central Japan. Because the catchment had a nearly homogenous landscape of incised valley and granitic bedrock covered in forest, we could eliminate any potential effects of variable landscape features. We found convergent relationships between drainage area and solute concentrations for all solutes. The concentrations of all solutes were similar among sampling locations with an area of more than 0.1–1.5 km2 independent of variable biogeochemical property of measured solutes. When considering only the longitudinal profile, solute concentrations showed a mostly asymptotic pattern. Taken together, these results indicate that longitudinal profiles with asymptotic patterns form convergent solute spatial patterns and suggest that variation in zero‐order hollow discharges and the mixing of water from a variety of hillslopes control downstream chemistry.