Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact on high‐grade serous ovarian cancer of obesity and lipid metabolism‐related gene expression patterns: the underestimated driving force affecting prognosis

To investigate whether specific obesity/metabolism‐related gene expression patterns affect the survival of patients with ovarian cancer. Clinical and genomic data of 590 samples from the high‐grade ovarian serous carcinoma (HGOSC) study of The Cancer Genome Atlas (TCGA) and 91 samples from the Australian Ovarian Cancer Study were downloaded from the International Cancer Genome Consortium (ICGC) portal. Clustering of mRNA microarray and reverse‐phase protein array (RPPA) data was performed with 83 consensus driver genes and 144 obesity and lipid metabolism‐related genes. Association between different clusters and survival was analyzed with the Kaplan–Meier method and a Cox regression. Mutually exclusive, co‐occurrence and network analyses were also carried out. Using RNA and RPPA data, it was possible to identify two subsets of HGOSCs with similar clinical characteristics and cancer driver mutation profiles (e.g. TP53), but with different outcome. These differences depend more on up‐regulation of specific obesity and lipid metabolism‐related genes than on the number of gene mutations or copy number alterations. It was also found that CD36 and TGF‐ß are highly up‐regulated at the protein levels in the cluster with the poorer outcome. In contrast, BSCL2 is highly up‐regulated in the cluster with better progression‐free and overall survival. Different obesity/metabolism‐related gene expression patterns constitute a risk factor for prognosis independent of the therapy results in the Cox regression. Prognoses were conditioned by the differential expression of obesity and lipid metabolism‐related genes in HGOSCs with similar cancer driver mutation profiles, independent of the initial therapeutic response.
Exposure of Brown Recluse and Brown Widow Spiders (Araneae: Sicariidae, Theridiidae) to a Commercial Sulfuryl Fluoride Fumigation

ABSTRACT The body of pesticide research on spiders is sparse with most studies using topical or residual applications to assess efficacy. Data on the effects of fumigation on spider survivorship are scarce in the scientific literature. In this study, we exposed adult male and female brown recluse spiders, Loxosceles reclusa Gertsch & Mulaik, and female brown widow spiders, Latrodectus geometricus C. L. Koch, to a commercial fumigation event using sulfuryl fluoride directed at termite control. General consensus from the pest control industry is that fumigation is not always effective for control of spiders for a variety of reasons, including insufficient fumigant dosage, particularly, for contents of egg sacs that require a higher fumigant dosage for control. We demonstrated that a sulfuryl fluoride fumigation with an accumulated dosage of 162 oz-h per 1,000 ft3 at 21°C over 25 h (≈1.7× the drywood termite dosage) directed at termites was sufficient to kill adult brown recluse and brown widow spiders. The effectiveness of commercial fumigation practices to control spiders, and particularly their egg sacs, warrants further study.
Learning to Segment Human by Watching YouTube

An intuition on human segmentation is that when a human is moving in a video, the video-context (e.g., appearance and motion clues) may potentially infer reasonable mask information for the whole human body. Inspired by this, based on popular deep convolutional neural networks (CNN), we explore a very-weakly supervised learning framework for human segmentation task, where only an imperfect human detector is available along with massive weakly-labeled YouTube videos. In our solution, the video-context guided human mask inference and CNN based segmentation network learning iterate to mutually enhance each other until no further improvement gains. In the first step, each video is decomposed into supervoxels by the unsupervised video segmentation. The superpixels within the supervoxels are then classified as human or non-human by graph optimization with unary energies from the imperfect human detection results and the predicted confidence maps by the CNN trained in the previous iteration. In the second step, the video-context derived human masks are used as direct labels to train CNN. Extensive experiments on the challenging PASCAL VOC 2012 semantic segmentation benchmark demonstrate that the proposed framework has already achieved superior results than all previous weakly-supervised methods with object class or bounding box annotations. In addition, by augmenting with the annotated masks from PASCAL VOC 2012, our method reaches a new state-of-the-art performance on the human segmentation task.
Polybenzoxazine foams: Modeling mechanical properties

Flame-retardant polybenzoxazine foams containing 1% phosphorus were prepared from diphenolic acid-based benzoxazine and 9,10-dihydro-9-oxa-10-(1-hydroxy-1-methylethyl)phosphaphenanthrene-10-oxide. Statistical predictive models were developed to determine the influence of the foaming time (tf) and foaming temperature (Tf) on the density, compressive modulus, and compressive strength of the foams. Results showed that the density of the foams exhibited great dependence on tf, whereas both compressive properties were more dependent on Tf and tf. Additionally, the flammability of the foams was also characterized by the limiting oxygen index. The presence of 9,10-dihydro-9-oxa-10-(1-hydroxy-1-methylethyl)phosphaphenanthrene-10-oxide greatly improved the flame retardancy of the resulting foams.
Practical cryptography

From the Publisher: In today's world, security is a top concern for businesses worldwide. Without a secure computer system, you don't make money, you don't expand, and -- bottom line -- you don't survive. Cryptography holds great promise as the technology to provide security in cyberspace. Amazingly enough, no literature exists about how to implement cryptography and how to incorporate it into real-world systems. With Practical Cryptography, an author team of international renown provides you with the first hands-on cryptographic product implementation guide, bridging the gap between cryptographic theory and real-world cryptographic applications.
Generation of Kcnma1fl-tdTomato, a conditional deletion of the BK channel α subunit in mouse

BK large conductance calcium‐activated K+ channels (KCa1.1) are expressed widely across many tissues, contributing to systemic regulation of cardiovascular, neurological, and other specialized physiological functions. The pore‐forming α subunit is encoded by the Kcnma1 gene, originally named mSlo1 in mouse and slowpoke in Drosophila. Global deletion in mouse (Kcnma1−/−) produces a plethora of defects in neuron and muscle excitability, as well as other phenotypes related to channel function in nonexcitable cells. While homozygous null mice are viable, the ubiquitous loss of BK function has complicated the interpretation of phenotypes involving the interaction of multiple cell types which independently express BK channels. Here, we report the generation of a targeted allele for conditional inactivation of Kcnma1 using the Cre‐loxP system (Kcnma1fl‐tdTomato). Cre‐mediated recombination generates a null allele, and BK currents were not detectable in neurons and muscle cells from Nestin‐Cre; Kcnma1fl/fl and SM22α‐Cre; Kcnma1fl/fl mice, respectively. tdTomato expression was detected in Cre‐expressing tissues, but not in Cre‐negative controls. These data demonstrate the utility of Kcnma1fl‐tdTomato for conditional deletion of the BK channel, facilitating the understanding of tissue‐specific contributions to physiological function in vivo.
Pooled sample testing for Bonamia ostreae: A tale of two SYBR Green real-time PCR assays

Pooled testing of samples is a common laboratory practice to increase efficiency and reduce expenses. We investigated the efficacy of 2 published SYBR Green real-time PCR assays when used to detect the haplosporidian parasite Bonamia ostreae in pooled samples of infected oyster tissue. Each PCR targets a different gene within the B. ostreae genome: the actin 1 gene or the 18S rRNA gene. Tissue homogenates (150 mg) of the New Zealand flat oyster Ostrea chilensis were spiked with ~1.5 × 103 purified B. ostreae cells to create experimental pools of 3, 5, and 10. Ten positive replicates of each pool size were assayed twice with each PCR and at 2 different amounts of DNA template. The PCR targeting the actin 1 gene was unable to reproducibly detect B. ostreae in any pool size. Conversely, the 18S rRNA gene PCR could reproducibly detect B. ostreae in pools of up to 5. Using a general linear model, there was a significant difference in the number of pools that correctly detected B. ostreae between each PCR (p < 0.01) and each pool size (p < 0.01). It is likely that the single copy actin 1 gene is more likely to be diluted and not detected by pooling than the multi-copy 18S rRNA gene. Our study highlights that validation data are necessary for pooled sample testing because detection efficacy may not be comparable to individual sample testing.
Multiparameter Sensor Interface Circuit With Integrative Baseline/Offset Compensation by Switched-Capacitor Level Shifting/Balancing

The proposed sensor interface circuit provides an integrative baseline/offset compensation to give higher adaptability and effectiveness for multiparameter sensing microsystems. Capacitive/resistive and voltage type sensors are dealt with and switched-capacitor-based circuits are mostly employed to facilitate integrative baseline/offset cancellation and interface various types of sensors. For integrative signal conditioning, sensor signals are first converted to voltage signals and then given rail-to-rail baseline compensation and fine offset cancellation of 0.7 mV/bit. At the same time, each interface circuit demonstrates a large total conversion gain (C: 194 mV/fF, R: 6260 mV/k $\Omega$ , V: 230 V/V) and a coefficient of determination (R2) over 0.998, which indicates a high conversion linearity.
Relative Wealth Concerns and Complementarities in Information Acquisition

This article studies how relative wealth concerns, in which a person's satisfaction with their own consumption depends on how much others are consuming, affect investors' incentives to acquire information. We find that such externalities can generate complementarities in information acquisition within the standard rational expectations paradigm. When agents are sensitive to the wealth of others, they herd on the same information, trying to mimic each other's trading strategies. We show that there can be multiple herding equilibria in which different communities pursue different information acquisition strategies. This multiplicity of equilibria generates price discontinuities: An infinitesimal shift in fundamentals can lead to a discrete price movement. The Author 2010. Published by Oxford University Press on behalf of The Society for Financial Studies. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org. , Oxford University Press.
A computational framework for mapping the timing of vegetative phase change.

Phase change plays a prominent role in determining the form of growth and development. Although considerable attention has been focused on identifying the regulatory control mechanisms of phase change, a detailed understanding of the genetic architecture of this phenomenon is still lacking. We address this issue by deriving a computational model. The model is founded on the framework of functional mapping aimed at characterizing the interplay between quantitative trait loci (QTLs) and development through biologically meaningful mathematical equations. A multiphasic growth equation was implemented into functional mapping, which, via a series of hypothesis tests, allows the quantification of how QTLs regulate the timing and pattern of vegetative phase transition between independently regulated, temporally coordinated processes. The model was applied to analyze stem radial growth data of an interspecific hybrid family derived from two Populus species during the first 24 yr of ontogeny. Several key QTLs related to phase change have been characterized, most of which were observed to be in the adjacent regions of candidate genes. The identification of phase transition QTLs, whose expression is regulated by endogenous and environmental signals, may enhance our understanding of the evolution of development in changing environments.
Ultrafast exciton dynamics of J-aggregates in room temperature solution studied by third-order nonlinear optical spectroscopy and numerical simulation based on exciton theory

We report a study of the exciton dynamics in 1,1′-diethyl-3,3′-bis(sulforpropyl)-5,5′,6,6′ -tetrachlorobenzimidacarbocyanine (BIC) J-aggregates in water solution at room temperature by third-order nonlinear optical spectroscopy and numerical simulations based on exciton theory. The temporal profiles of the transient grating signals depend strongly on the excitation intensity as a result of exciton–exciton annihilation. On the other hand, the peak shift measurement gives information on the fluctuations of the transition frequency of the system. The peak shift decays with time constants of 26 and 128 fs. There is no finite peak shift on a longer time scale. The electronic state of J-aggregates is described by a Frenkel exciton Hamiltonian, and the exciton population relaxation processes is described by Redfield equations. Based on the numerical simulations, the peak shift data can only be explained even qualitatively when both exchange narrowing and exciton relaxation process are included in the model. The .
Breathing control center neurons that promote arousal in mice

A tiny group of neurons in the brainstem matches breathing rate to the level of calmness versus arousal. The calming effect of breathing The rhythmic activity of a cluster of neurons in the brainstem initiates breathing. This cluster is composed of distinct, though intermingled, subgroups of neurons. Yackle et al. found a small, molecularly defined neuronal subpopulation in this breathing rhythm generator that directly projects to a brain center that plays a key role in generalized alertness, attention, and stress (see the Perspective by Sheikbahaei and Smith). Removal of these cells did not affect normal breathing but left the animals unusually calm. The breathing center thus has a direct and dramatic influence on higher-order brain function. Science, this issue p. 1411; see also p. 1370 Slow, controlled breathing has been used for centuries to promote mental calming, and it is used clinically to suppress excessive arousal such as panic attacks. However, the physiological and neural basis of the relationship between breathing and higher-order brain activity is unknown. We found a neuronal subpopulation in the mouse preBötzinger complex (preBötC), the primary breathing rhythm generator, which regulates the balance between calm and arousal behaviors. Conditional, bilateral genetic ablation of the ~175 Cdh9/Dbx1 double-positive preBötC neurons in adult mice left breathing intact but increased calm behaviors and decreased time in aroused states. These neurons project to, synapse on, and positively regulate noradrenergic neurons in the locus coeruleus, a brain center implicated in attention, arousal, and panic that projects throughout the brain.
On the Optimization of Distributed Compression in Multirelay Cooperative Networks

In this paper, we consider multirelay cooperative networks for the Rayleigh fading channel, where each relay, upon receiving its own channel observation, independently compresses it and forwards the compressed information to the destination. Although the compression at each relay is distributed using Wyner-Ziv coding, there exists an opportunity for jointly optimizing compression at multiple relays to maximize the achievable rate. Considering Gaussian signaling, a primal optimization problem is formulated accordingly. We prove that the primal problem can be solved by resorting to its Lagrangian dual problem, and an iterative optimization algorithm is proposed. The analysis is further extended to a hybrid scheme, where the employed forwarding scheme depends on the decoding status of each relay. The relays that are capable of successful decoding perform a decode-and-forward (DF) scheme, and the rest conduct distributed compression. The hybrid scheme allows the cooperative network to adapt to the changes of the channel conditions and benefit from an enhanced level of flexibility. Numerical results from both spectrum and energy efficiency perspectives show that the joint optimization improves efficiency of compression and identify the scenarios where the proposed schemes outperform the conventional forwarding schemes. The findings provide important insights into the optimal deployment of relays in a realistic cellular network.
Assessment of breast cancer disability: agreement between expert assessment and patient reports

Abstract Objective: To estimate the extent of agreement between health professionals’ (ClinRO) and patients’ (PRO) ratings on disabilities associated with breast cancer (impairments, activity limitations and participation restrictions). Design: Cross-sectional. Methods: Health care professionals measured arm impairments, activity limitations and participation restrictions with the international classification of functioning (ICF) breast cancer core set. Participants filled five outcomes measures targeting health aspects of QOL that were previously mapped to the ICF. Agreement between ClinRO and PRO was estimated with quadratic Kappa. Results: About 245 paired clinician and participant completed the outcomes measures. A total of 60 items mapped to 24 different ICF breast cancer core set codes, which provide 68 analyses for agreement. Impairment was better addressed with PROs (mostly poor and fair level of agreement); Activity limitations, both PROs and self-reported outcomes (SRO) (fair); participation restrictions, PROs (fair). Conclusion: Clinicians usually underestimate the symptoms and impairments of the patients, leading to a greater proportion of poor agreement. PRO’s provide valuable information on impairments at the mental function level and pain. ClinRO’s provide more valuable information on physically assessed impairments (oedema). Activity limitations and participation restrictions, excluding reporting the difficulty aspect of various life situations, can be either SRO or ObsRO. Implications for rehabilitation Impairments, activity limitation and participation restrictions are common sequelae of breast cancer treatment, which ultimately may affect the person’s quality of life and should be investigated early on in the continuum of care. Clinicians should rely on the symptoms’ reported by the patient regarding lymphedema and should identify the presence and severity of it. Patients inform best on the severity of pain, fatigue and mental distress experienced during and post-breast cancer treatment as clinicians tend to underestimate them. Clinicians and patients concur on presence and severity of activity limitations but not on difficulty, which can only be assessed from the patient’s perspective.
A Bioeconomic Model of Marine Reserve Creation

Abstract This paper employs a dynamic and spatial model of renewable resource exploitation to investigate the effects of marine reserve creation. The model combines a metapopulation model incorporating resource patch heterogeneity and dispersal with a behaviorally based spatially explicit harvesting model that assumes that fishermen choose location in a manner that eliminates spatial arbitrage opportunities. The combined spatial bioeconomic model is used to simulate the effects of reserve creation under various ecological structures. We identify parameter configurations and ecological dispersal processes that give rise to a double-payoff in which both aggregate biomass and harvest increase after an area of the fishery is set aside and protected from exploitation.
Controlling Pre-leukemic Thymocyte Self-Renewal

T cell acute lymphoblastic leukemia (T-ALL) develops in a multistep process whereby thymic progenitor cells gradually accumulate genetic and epigenetic changes, eventually leading to fully transformed immature lymphoblasts. Aberrant activation of transcription factor oncogenes is considered a core component of the oncogenic program that drives malignant T cell transformation. For example, the TAL1 (SCL) and LYL1 basic Helix-Loop-Helix (bHLH) transcription factors, as well as the LIM domain–only proteins LMO1 or LMO2, are activated by chromosomal translocations or interstitial deletions in a large fraction of primary T-ALLs. Notably, these leukemias often present with activating NOTCH1 mutations, suggesting that enhanced NOTCH signaling and aberrant TAL1, LYL1, LMO1, and/or LMO2 expression are collaborative events in the multistep pathogenesis of T-ALL [1], [2]. Recent experimental evidence uncovered the existence of long-lived pre-leukemic stem cells (pre-LSCs) with self-renewal properties, allowing clonal expansion and subsequent acquisition of oncogenic mutations leading to cancer [3], [4]. For example, DNMT3A mutant pre-LSCs were shown to survive chemotherapy and represent a reservoir for leukemic progression and hematological relapse in acute myeloid leukemia (AML) [5], [6]. Although the concept of pre-leukemic stem cells has been previously proposed in the context of T-ALL [7], the actual molecular mechanisms by which T cell-specific oncogenes regulate pre-LSC activity of thymic precursors remains largely unexplored. Notably, these mechanistic insights could provide valuable input for the development of novel therapeutic strategies that can effectively eradicate quiescent and therapy-resistant clones [4], [6], [7].
Compassionate use of bedaquiline for the treatment of multidrug-resistant and extensively drug-resistant tuberculosis: interim analysis of a French cohort.

BACKGROUND Bedaquiline is a new antibiotic that was approved for the treatment of multidrug-resistant (MDR) tuberculosis. We aimed to evaluate the short-term microbiological efficacy and the tolerability profile of bedaquiline. METHODS We performed a retrospective cohort study among patients with MDR tuberculosis receiving bedaquiline for compassionate use between January 2010 and July 2013 and evaluated at 6 months of bedaquiline treatment. RESULTS A total of 35 patients with MDR tuberculosis were included in the study. Nineteen (54%) had extensively drug-resistant (XDR) tuberculosis, and 14 (40%) had isolates resistant to fluoroquinolones (Fqs) or second-line injectables. Bedaquiline was associated with a median of 4 (range, 2-5) other drugs, including linezolid in 33 (94%) cases. At 6 months of bedaquiline treatment, culture conversion was achieved in 28 of 29 (97%) cases with culture-positive pulmonary tuberculosis at bedaquiline initiation. Median time to culture conversion was 85 days (range, 8-235 days). Variables independently associated with culture conversion were treatment with a Fq (P = .01), absence of lung cavities (P < .001), and absence of hepatitis C virus infection (P = .001). A total of 7 patients (20%) experienced a ≥60-ms increase in QT interval, leading to bedaquiline discontinuation in 2 (6%) cases. Severe liver enzyme elevation occurred in 2 patients (6%). During the study period, 1 death (3%) occurred and was reported as unrelated to tuberculosis or antituberculosis treatment. CONCLUSIONS The use of bedaquiline combined with other active drugs has the potential to achieve high culture conversion rates in complicated MDR and XDR tuberculosis cases, with a reassuring safety profile at 6 months of treatment.