Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Application of Biparametric MRI Texture Analysis for Detection and Evaluation of High-Grade Prostate Cancer in Zone-Specific Regions.

OBJECTIVE The purpose of this study was to investigate the performance of biparametric MRI texture analysis (TA) in detecting and evaluating high-grade prostate cancer in zone-specific regions. MATERIALS AND METHODS A retrospective study included 184 consecutively registered biopsy-naive patients in whom prostate cancer was suspected who were undergoing multiparametric prostate MRI. MR images were scored and evaluated by two readers using the Prostate Imaging Reporting and Data System version 2 (PI-RADSv2) and biparametric MRI TA in separate sessions. Interobserver agreement on PI-RADSv2 score and textural parameters of biparametric MRI was evaluated. The logistic regression model based on TA was built for different zones of the prostate. ROC analysis was used to compare the TA-based model with other parameters alone. The correlation of each parameter with Gleason score of high-grade prostate cancer was also assessed. RESULTS Reader reliability ranged from moderate to good for PI-RADSv2 (Cohen κ = 0.525-0.616) and from good to excellent for textural metrics (intraclass correlation coefficient, 0.745-0.925). Diagnostic performance was significantly improved by use of the TA-based model (transition zone AUC, 0.87; peripheral zone AUC, 0.89) in comparison with PI-RADSv2 and other texture parameters alone. For the transition zone, entropy had moderate to good correlation with the Gleason score of high-grade prostate cancer (r = 0.562, p = 0.004). In the peripheral zone, entropy (r = 0.614, p = 0.003) and inertia (r = 0.663, p = 0.002) had moderate to good correlations with Gleason score. CONCLUSION The results of this clinical study indicate that a TA-based model that includes biparametric MRI can be used for identifying high-grade prostate cancer and that specific parameters extracted from TA may be additional tools for assessing tumor aggressiveness.
The BALAD-2 and GALAD biomarker models for hepatocellular carcinoma.

PJ The role of biomarkers in hepatocellular carcinoma (HCC) is controversial. [For example, the best-known biomarker in HCC? ] [OK]is α-fetoprotein (AFP), which has been around for more than 50 years. Many hepatologists use AFP as a diagnostic aid, but there are probably an equal number who do not think that the biomarker is any help because it is, reputablyreputably, relatively nonspecific. Thus, there are 2 schools of thought: one that believes that there is a role for biomarkers in HCC and one that does not.
Modulation of the pharmacokinetics, therapeutic and adverse effects of NSAIDs by Chinese herbal medicines

Introduction: Concomitant use of NSAIDs and Chinese herbal medicines (CHMs) is frequent, yet summarized information on their interactions is lacking. Areas covered: A systematic review of literature in four evidence-based English databases was performed. Articles which reported CHMs altering the pharmacokinetics, therapeutic and adverse effects of NSAIDs were identified and summarized. Such interactions may lead to beneficial, detrimental or no change in outcomes. The current review covers four therapeutic effects of NSAIDs, including: i) anti-inflammatory; ii) analgesic; iii) antiplatelet, cardiovascular and cerebrovascular; and iv) anticancer effects and four adverse effects of NSAIDs, including: i) gastrointestinal ulcer; ii) nephrotoxicity; iii) hepatotoxicity; and iv) antiplatelet effects and bleeding. Expert opinion: While majority of CHMs demonstrated effectiveness in alleviating NSAIDs-induced adverse effects and potentiating the therapeutic effects, this review provides insights for development of CHMs as add-on medications to NSAIDs therapies. However, since limited information was from well-designed clinical trials, the findings are not yet conclusive and more clinical studies are warranted to provide guidance for healthcare professionals. In future, researches on interactions between NSAIDs and CHMs are expected to grow and modern approaches such as pharmacogenomics might enhance the throughput and accuracy of identifying clinically relevant interactions.
Azacitidine in Lower-Risk Myelodysplastic Syndromes: A Meta-Analysis of Data from Prospective Studies.

BACKGROUND After erythropoiesis-stimulating agent (ESA) failure, lenalidomide and hypomethylating agents are the only remaining treatment options for most patients with lower-risk myelodysplastic syndromes (LR-MDS). Optimal choice of these agents as front-line therapy in non-del(5q) LR-MDS is unclear. Because azacitidine clinical data mainly describe experience in higher-risk MDS, we performed a meta-analysis of patient-level data to evaluate azacitidine in patients with red blood cell (RBC) transfusion-dependent LR-MDS. MATERIALS AND METHODS We searched English-language articles for prospective phase II and III azacitidine clinical trials and patient registries published between 2000 and 2015, and Embase abstracts from 2015 conferences. Patient-level data from identified relevant studies were provided by investigators. Meta-analyses followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Efficacy endpoints were RBC transfusion independence (TI) and Clinical Benefit (RBC-TI, erythroid response, and complete or partial remission, per International Working Group 2006 criteria for MDS). RESULTS Data for 233 patients from 6 clinical studies and 1 registry study met criteria for inclusion in analyses. Overall, 90.3% of patients had non-del(5q) LR-MDS. Pooled estimates from random-effects models of RBC-TI and Clinical Benefit were 38.9% and 81.1%, respectively; for the ESA-refractory subgroup, they were 40.5% and 77.3%; and for patients with isolated anemia, they were 41.9% and 82.5%. In multivariate analyses, planned use of ≥6 azacitidine treatment cycles was significantly predictive of response. CONCLUSION Azacitidine effects in these patients, most with non-del(5q) LR-MDS, were promising and generally similar to those reported for lenalidomide in similar patients. The choice of initial therapy is important because most patients eventually stop responding to front-line therapy and alternatives are limited. IMPLICATIONS FOR PRACTICE Lower-risk myelodysplastic syndromes (LR-MDS) are primarily characterized by anemia. After erythropoiesis-stimulating agent (ESA) failure, lenalidomide and hypomethylating agents are the only remaining treatment options for most patients. This meta-analysis of 233 azacitidine-treated red blood cell (RBC) transfusion-dependent patients with LR-MDS (92.3% non-del[5q]) from 7 studies showed 38.9% became RBC transfusion-independent. There is no clear guidance regarding the optimal choice of lenalidomide or hypomethylating agents for patients with non-del(5q) LR-MDS following ESA failure. Clinical presentation (e.g., number of cytopenias) and potential outcomes after hypomethylating agent failure are factors to consider when making initial treatment decisions for LR-MDS patients.
Category independent object proposals using quantum superposition

Object proposals improve the efficiency of object detection by providing probable locations of objects in an image. Most of the state-of-the-art object proposal methods employ a supervised approach and learn object features from ground truth annotations. We present a novel unsupervised approach for generating object proposals that is based on the human visual system and quantum mechanical principles. Despite of being devoid of any learnt priors pertaining to objects in images, the proposed method is shown to yield competitive results with supervised approaches.
The E ff ects of Informational Frictions on Credit Reallocation

This paper studies the role of an informational friction limiting the reallocation of credit after a shock. Lenders have private information about their borrowers, and borrowers left looking for a new lender are adversely selected. Exploiting the financial crisis as a shock to relationships in the U.S. corporate loan market, I provide evidence that lenders use their information to choose which relationships to end when reducing lending. To quantify the effects of this friction on aggregate lending, I model a credit market with three layers of information: (i) all lenders have some information about borrowers, but (ii) each lender has private information about its existing borrowers, and (iii) the econometrician observes neither. I introduce a novel empirical approach that identifies this private information separately from information common to all lenders. At the borrower level, the probability that a firm finds a new lender after a breakup would be 30% higher if there were no private information. At the aggregate level, $15 billion new loans were not made because of this friction. A naive model ignoring information common to all lenders overestimates the effects of the information gap threefold relative to my estimates. Moreover, interventions supporting weak lenders exacerbate adverse selection and reduce the share of borrowers that are able to reallocate toward new lenders.
Patient characteristics, prognostic factors and outcome of dogs with high‐grade primary mediastinal lymphoma

The goals of this retrospective study were to determine the patient characteristics of dogs with high-grade primary mediastinal lymphoma and to determine outcome and associated prognostic factors. A total of 42 dogs were identified, in which 36 received treatment and had follow-up information available. The most common clinical signs included lethargy, anorexia and polyuria/polydipsia. Hypercalcemia and pleural effusion were common findings at diagnosis. The phenotype was almost exclusively T-cell, most often in association with lymphoblastic cytomorphology as defined by the World Health Organization (WHO) lymphoma classification scheme. The overall progression-free survival (PFS) and overall survival (OS) were 133 and 183 days, respectively. Treatment with a CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone) protocol was associated with an improved PFS (144 days) and OS (194 days) when compared with dogs that received other medical therapies (P = .005 and P = .002, respectively); the absence of pleural effusion at diagnosis was associated with an increased OS but not PFS. These results suggest that while the prognosis for dogs with mediastinal lymphoma is poor, survival may be improved with treatment using a CHOP-based protocol.
The Secret Sharer: Measuring Unintended Neural Network Memorization & Extracting Secrets

Machine learning models based on neural networks and deep learning are being rapidly adopted for many purposes. What those models learn, and what they may share, is a significant concern when the training data may contain secrets and the models are public—e.g., when a model helps users compose text messages using models trained on all users’ messages. This paper presents exposure, a simple-to-compute metric that can be applied to any deep learning model for measuring the memorization of secrets. Using this metric, we show how to extract those secrets efficiently using black-box API access. Further, we show that unintended memorization occurs early, is not due to overfitting, and is a persistent issue across different types of models, hyperparameters, and training strategies. We experiment with both real-world models (e.g., a state-ofthe-art translation model) and datasets (e.g., the Enron email dataset, which contains users’ credit card numbers) to demonstrate both the utility of measuring exposure and the ability to extract secrets. Finally, we consider many defenses, finding some ineffective (like regularization), and others to lack guarantees. However, by instantiating our own differentiallyprivate recurrent model, we validate that by appropriately investing in the use of state-of-the-art techniques, the problem can be resolved, with high utility.
Genomic testing in cancer: Patient knowledge, attitudes, and expectations

Genomic testing in cancer (GTC) characterizes genes that play an important role in the development and growth of a patient's cancer. This form of DNA testing is currently being studied for its ability to guide cancer therapy. The objective of the current study was to describe patients' knowledge, attitudes, and expectations toward GTC.
Photonic-band-gap engineering for volume plasmon polaritons in multiscale multilayer hyperbolic metamaterials

We theoretically study the propagation of large-wavevector waves (volume plasmon polaritons) in multilayer hyperbolic metamaterials with two levels of structuring. We show that when the parameters of a subwavelength metal-dielectric multilayer ("substructure") are modulated ("superstructured") on a larger, wavelength scale, the propagation of volume plasmon polaritons in the resulting multiscale hyperbolic metamaterials is subject to photonic band gap phenomena. A great degree of control over such plasmons can be exerted by varying the superstructure geometry. When this geometry is periodic, stop bands due to Bragg reflection form within the volume plasmonic band. When a cavity layer is introduced in an otherwise periodic superstructure, resonance peaks of the Fabry-Perot nature are present within the stop bands. More complicated superstructure geometries are also considered. For example, fractal Cantor-like multiscale metamaterials are found to exhibit characteristic self-similar spectral signatures in the volume plasmonic band. Multiscale hyperbolic metamaterials are shown to be a promising platform for large-wavevector bulk plasmonic waves, whether they are considered for use as a new kind of information carrier or for far-field subwavelength imaging.
Does spatial attention modulate the earliest component of the visual evoked potential?

ABSTRACT Whether visual spatial attention can modulate feedforward input to human primary visual cortex (V1) is debated. A prominent and long-standing hypothesis is that visual spatial attention can influence processing in V1, but only at delayed latencies suggesting a feedback-mediated mechanism and a lack of modulation during the initial afferent volley. The most promising challenge to this hypothesis comes from an event-related potential (ERP) study that showed an amplitude enhancement of the earliest visual ERP component, called the ‘C1’, in response to spatially attended relative to spatially unattended stimuli. In the Kelly et al. study, several important experimental design modifications were introduced, including tailoring the stimulus locations and recording electrodes to each individual subject. In the current study, we employed the same methodological procedures and tested for attentional enhancements of the C1 component in each quadrant of the visual field. Using the same analysis strategies as Kelly et al., we found no evidence for an attention-based modulation of the C1 (measured from 50–80 ms). Attention-based amplitude enhancements were clear and robust for the subsequent P1 component (90–140 ms). Thus, despite using methods specifically designed to reveal C1 attention effects, the current study provided no confirmatory evidence for such effects.
Stent retriever thrombectomy combined with local thrombolytic therapy for cerebral venous sinus thrombosis: A case report

The present study reports the effect of successful treatment of cerebral venous sinus thrombosis (CVST) with stent retriever thrombectomy combined with local thrombolytic therapy. Medical records of 29 patients were retrospectively analyzed following a diagnosis of CVST with magnetic resonance venography (MRV) or digital subtraction angiography (DSA). Systemic anticoagulation was the initial treatment in all patients following admission. In group A, stent retriever thrombectomy combined with local thrombolytic therapy was performed on 14 patients who met the criteria of endovascular therapy. Stent-assisted angioplasty was also performed when patients presented with venous sinus stenosis. A total of 15 patients in group B received systemic anticoagulant treatment. Subsequently, warfarin was administered orally for 3 to 12 months as a continuous anticoagulant therapy. International normalized ratio was monitored when patients were receiving anticoagulant therapy. Additionally, clinical presentation, decision to escalate therapy, recanalization, Glasgow Coma Scale, modified Rankin Scale (mRS) and the clinical outcome was assessed. A total of 14 patients (9 female patients, 5 male patients), with ages ranging from 17 to 57 years, met the criteria of endovascular therapy. The clinical symptoms of 12 patients had improved after receiving endovascular therapy and only 2 patients suffered from intracranial hemorrhage following the procedure. Complete recanalization of venous sinus was exhibited in 10/14 (71.4%) patients in group A when compared with 1/15 (6.7%) patients in group B. mRS were improved in the 12-month follow-up in groups A and B when compared with that at admission. In the present study, patients with acute CVST treated with stent retriever thrombectomy combined with local thrombolytic therapy had a favorable outcome. To conclude, the present study provides a treatment option in treating CVST, particularly for patients that present with evident cortical venous outflow stasis or deteriorate neurology, despite appropriate anticoagulant therapy.
Ergodic Control of Switching Diffusions

We study the ergodic control problem of switching diffusions representing a typical hybrid system that arises in numerous applications such as fault-tolerant control systems, flexible manufacturing systems, etc. Under fairly general conditions, we establish the existence of a stable, nonrandomized Markov policy which almost surely minimizes the pathwise long-run average cost. We then study the corresponding Hamilton--Jacobi--Bellman (HJB) equation and establish the existence of a unique solution in a certain class. Using this, we characterize the optimal policy as a minimizing selector of the Hamiltonian associated with the HJB equations. As an example we apply the results to a failure-prone manufacturing system and obtain closed form solutions for the optimal policy.
Arabidopsis E3 ubiquitin ligase PLANT U-BOX13 (PUB13) regulates chitin receptor LYSIN MOTIF RECEPTOR KINASE5 (LYK5) protein abundance.

Long-chain chitooligosaccharides are fungal microbe-associated molecular patterns (MAMPs) that are recognized by LYSIN MOTIF RECEPTOR KINASE5 (LYK5), inducing the formation of a complex with CHITIN ELICITOR RECEPTOR KINASE1 (CERK1). Formation of this complex leads to activation of the CERK1 intracellular kinase domain and induction of plant innate immunity in Arabidopsis. We found that addition of chitooctaose induced LYK5 protein accumulation as a result of de novo gene expression and the inhibition of LYK5 protein degradation. Screening the putative E3 ligases for interaction with LYK5 identified PLANT U-BOX13 (PUB13), which complexed with LYK5, but this complex dissociated upon addition of chitooctaose. Consistent with these results, LYK5 protein abundance was higher in pub13 mutants compared with the wild type without chitooctaose treatment, while similar abundance was detected with the addition of chitooctaose. The pub13 mutants showed hypersensitivity to chitooctaose-induced rapid responses, such as the production of reactive oxygen species (ROS) and mitogen-activated protein (MAP) kinase phosphorylation, but exhibited normal responses to subsequent long-term chitooctaose treatment, such as gene expression and callose deposition. In addition, PUB13 could ubiquitinate the LYK5 kinase domain in vitro. Taken together, our results suggest an important regulatory function for the turnover of LYK5 mediated by the E3 ligase PUB13.
Assessing Social Risks Prior to Commencement of a Clinical Trial: Due Diligence or Ethical Inflation?

Assessing social risks has proven difficult for IRBs. We undertook a novel effort to empirically investigate social risks before an HIV prevention trial among drug users in Thailand and China. The assessment investigated whether law, policies and enforcement strategies would place research subjects at significantly elevated risk of arrest, incarceration, physical harm, breach of confidentiality, or loss of access to health care relative to drug users not participating in the research. The study validated the investigator's concern that drug users were subject to serious social risks in the site localities, but also suggested that participation in research posed little or no marginal increase in risk and might even have a protective effect. Our experience shows that it is feasible to inform IRB deliberations with actual data on social risks, but also raises the question of whether and when such research is an appropriate use of scare research resources.
The Effects of Attendance on Academic Performance: Panel Data Evidence for Introductory Microeconomics

Abstract: The author presents new evidence on the effects of attendance on academic performance. He used a large panel data set for introductory microeconomics students to explicitly take into account the effect of unobservable factors correlated with attendance, such as ability, effort, and motivation. He found that neither proxy variables nor instrumental variables provide a solution to the omitted variable bias. Panel estimators indicate that attendance has a smaller but significant impact on performance. Lecture and classes have a similar effect on performance individually, although their impact cannot be identified separately. Overall, the results indicate that, after controlling for unobservable student characteristics, attendance has a statistically significant and quantitatively relevant effect on student learning.
The evolution of fishes and corals on reefs: form, function and interdependence

Coral reefs are renowned for their spectacular biodiversity and the close links between fishes and corals. Despite extensive fossil records and common biogeographic histories, the evolution of these two key groups has rarely been considered together. We therefore examine recent advances in molecular phylogenetics and palaeoecology, and place the evolution of fishes and corals in a functional context. In critically reviewing the available fossil and phylogenetic evidence, we reveal a marked congruence in the evolution of the two groups. Despite one group consisting of swimming vertebrates and the other colonial symbiotic invertebrates, fishes and corals have remarkably similar evolutionary histories. In the Paleocene and Eocene [66–34 million years ago (Ma)] most modern fish and coral families were present, and both were represented by a wide range of functional morphotypes. However, there is little evidence of diversification at this time. By contrast, in the Oligocene and Miocene (34–5.3 Ma), both groups exhibited rapid lineage diversification. There is also evidence of increasing reef area, occupation of new habitats, increasing coral cover, and potentially, increasing fish abundance. Functionally, the Oligocene–Miocene is marked by the appearance of new fish and coral taxa associated with high‐turnover fast‐growth ecosystems and the colonization of reef flats. It is in this period that the functional characteristics of modern coral reefs were established. Most species, however, only arose in the last 5.3 million years (Myr; Plio–Pleistocene), with the average age of fish species being 5.3 Myr, and corals just 1.9 Myr. While these species are genetically distinct, phenotypic differences are often limited to variation in colour or minor morphological features. This suggests that the rapid increase in biodiversity during the last 5.3 Myr was not matched by changes in ecosystem function. For reef fishes, colour appears to be central to recent diversification. However, the presence of pigment patterns in the Eocene suggests that colour may not have driven recent diversification. Furthermore, the lack of functional changes in fishes or corals over the last 5 Myr raises questions over the role and importance of biodiversity in shaping the future of coral reefs.