Miracle-dz/UniFAR-FTUs huggingface dataset:
Follow-up using fluorescence bronchoscopy for the patients with photodynamic therapy treated early lung cancer.

PURPOSE To evaluate the accuracy of fluorescence bronchoscopy by precise histological analysis of the photodynamic therapy (PDT) treated lesions. METHODS A retrospective study was conducted on thirteen patients (16 lesions) with centrally located early lung cancer (CLELC) had been undergone photodynamic therapy and had been followed up by fluorescence bronchoscopy. Fluorescence bronchoscopy was performed between 1 and 60 months after photodynamic therapy. RESULTS Of the 16 early carcinomas treated, 14 (87.5%) had a CR, 2 (12.5%) had a NR after initial PDT. Among the 14 carcinomas achieving a CR, 4 (29%) recurred locally from 6 to 12 months after initial PDT. A total of 62 surveillance auto fluorescence bronchoscopies (average; 4.5/patient) and 47 biopsies (average; 4/patient) were performed after PDT. The addition of the SAFE-3000 examination to conventional bronchoscopy increased the sensitivity of screening from 69% to 100%, which yielded a relative sensitivity of 145% with a negative predictive value of 100%. Out of 14 CR lesions, 9 lesions finally reverted to normal fluorescence. CR cases that did not show normal fluorescence were relapsed cases or a patient with complete response whose treated lesion showed fibrosis in the sub mucosa. Histopathological finding of the complete response sites which demonstrated temporal fluorescent defect consisted of inflammatory lesions, goblet cell hyperplasia, basal cell hyperplasia, squamous metaplasia or dysplasia. CONCLUSION our results confirm that SAFE-3000 allows accurate assessment of the quality and efficacy of PDT.
Oxidation Stability of Pig Liver Pâté with Increasing Levels of Natural Antioxidants (Grape and Tea)

The present study investigated the effect of the addition of increasing levels of the natural antioxidants tea (TEA) and grape seed extracts (GRA) on the physiochemical and oxidative stability of refrigerated stored pig pâtés. In addition, a synthetic antioxidant and a control batch were used, thus a total of eight batches of liver pâté were prepared: CON, BHT, TEA (TEA50, TEA200 and TEA1000) and GRA (GRA50, GRA200 and GRA1000). Pâté samples were analyzed following 0, 4, 8 and 24 weeks of storage. Color parameters were affected by storage period and level of antioxidant extract. Samples with TEA200 and GRA1000 levels of extracts showed lower total color difference between 0 and 24 weeks. At the end of storage period, the lower TBARs values were obtained in samples with the highest concentration on natural extract. Overall, the evolution of volatile compounds showed an increase in those ones that arise from the lipid oxidation and samples with TEA1000 extract showed the lowest values.
Analysis of the Caenorhabditis elegans innate immune response to Coxiella burnetii

The nematode Caenorhabditis elegans is well established as a system for characterization and discovery of molecular mechanisms mediating microbe-specific inducible innate immune responses to human pathogens. Coxiella burnetii is an obligate intracellular bacterium that causes a flu-like syndrome in humans (Q fever), as well as abortions in domesticated livestock, worldwide. Initially, when wild type C. elegans (N2 strain) was exposed to mCherry-expressing C. burnetii (CCB) a number of overt pathological manifestations resulted, including intestinal distension, deformed anal region and a decreased lifespan. However, nematodes fed autoclave-killed CCB did not exhibit these symptoms. Although vertebrates detect C. burnetii via TLRs, pathologies in tol-1(–) mutant nematodes were indistinguishable from N2, and indicate nematodes do not employ this orthologue for detection of C. burnetii. sek-1(–) MAP kinase mutant nematodes succumbed to infection faster, suggesting that this signaling pathway plays a role in immune activation, as previously shown for orthologues in vertebrates during a C. burnetii infection. C. elegans daf-2(–) mutants are hyper-immune and exhibited significantly reduced pathological consequences during challenge. Collectively, these results demonstrate the utility of C. elegans for studying the innate immune response against C. burnetii and could lead to discovery of novel methods for prevention and treatment of disease in humans and livestock.
A Study on the Perceived Value of Software Quality Assurance at JPL

As software quality assurance (SQA) moves from being a compliance-driven activity to one driven by value, it is important that all stakeholders involved in a software development project have a clear understanding of how SQA contributes to their efforts. However, a recent study at JPL indicates that different groups of stakeholders have significantly different perceptions about the value of SQA activities and their expectations of what constitutes SQA success. This lack of a common understanding of value has fragmented SQA efforts. Activities are driven by the desires of whichever group of stakeholders happens to hold the greatest influence at the moment leading the project as a whole not realizing the full or needed value of SQA. We examine this and other results of the recent study and how these impact both the real and the perceived value of SQA.
Automated analysis of rule-based access control policies

In this paper we show how access control policies can be specified using a general metamodel whose operational semantics is based on term rewriting systems. The choice of the specification language aims at easing the verification task, since essential properties of access control (e.g. every request by an individual of accessing a resource always receives an answer, and this answer is unique) can be formalized and proved using rewriting techniques. We show that automated analysis of rewrite-based security policies can be done using the CiME rewriting tool which is able to produce mechanically checkable traces of security policy properties, for instance through the Coq proof assistant.
The size of the underground economy in Japan

This paper empirically analyzes the size of the underground economy in Japan. The results show that (i) the size of the underground GDP peaked in the early 1990s but has been declining since; (ii) the underground economy reached its peak in around 1992, approximating 25% of nominal GDP; and (iii) two laws (the Act for the Prevention of Wrongful Acts by Members of Organized Crime Groups and the Act Regulating the Adult Entertainment Business, etc.) successfully worked to reduce the size of the underground economy.
Delirium in mechanically ventilated patients: validity and reliability of the confusion assessment method for the intensive care unit (CAM-ICU).

CONTEXT Delirium is a common problem in the intensive care unit (ICU). Accurate diagnosis is limited by the difficulty of communicating with mechanically ventilated patients and by lack of a validated delirium instrument for use in the ICU. OBJECTIVES To validate a delirium assessment instrument that uses standardized nonverbal assessments for mechanically ventilated patients and to determine the occurrence rate of delirium in such patients. DESIGN AND SETTING Prospective cohort study testing the Confusion Assessment Method for ICU Patients (CAM-ICU) in the adult medical and coronary ICUs of a US university-based medical center. PARTICIPANTS A total of 111 consecutive patients who were mechanically ventilated were enrolled from February 1, 2000, to July 15, 2000, of whom 96 (86.5%) were evaluable for the development of delirium and 15 (13.5%) were excluded because they remained comatose throughout the investigation. MAIN OUTCOME MEASURES Occurrence rate of delirium and sensitivity, specificity, and interrater reliability of delirium assessments using the CAM-ICU, made daily by 2 critical care study nurses, compared with assessments by delirium experts using Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, criteria. RESULTS A total of 471 daily paired evaluations were completed. Compared with the reference standard for diagnosing delirium, 2 study nurses using the CAM-ICU had sensitivities of 100% and 93%, specificities of 98% and 100%, and high interrater reliability (kappa = 0.96; 95% confidence interval, 0.92-0.99). Interrater reliability measures across subgroup comparisons showed kappa values of 0.92 for those aged 65 years or older, 0.99 for those with suspected dementia, or 0.94 for those with Acute Physiology and Chronic Health Evaluation II scores at or above the median value of 23 (all P<.001). Comparing sensitivity and specificity between patient subgroups according to age, suspected dementia, or severity of illness showed no significant differences. The mean (SD) CAM-ICU administration time was 2 (1) minutes. Reference standard diagnoses of delirium, stupor, and coma occurred in 25.2%, 21.3%, and 28.5% of all observations, respectively. Delirium occurred in 80 (83.3%) patients during their ICU stay for a mean (SD) of 2.4 (1.6) days. Delirium was even present in 39.5% of alert or easily aroused patient observations by the reference standard and persisted in 10.4% of patients at hospital discharge. CONCLUSIONS Delirium, a complication not currently monitored in the ICU setting, is extremely common in mechanically ventilated patients. The CAM-ICU appears to be rapid, valid, and reliable for diagnosing delirium in the ICU setting and may be a useful instrument for both clinical and research purposes.
The Nature of the Progenitor of the Type II-P Supernova 1999em

The masses and the evolutionary states of the progenitors of core-collapse supernovae (SNe) are not well constrained by direct observations. Stellar evolution theory generally predicts that massive stars with initial masses less than about 30 M☉ should undergo core collapse when they are cool M-type supergiants. However, the only two detections of an SN progenitor before explosion are SN 1987A and SN 1993J, and neither of these was an M-type supergiant. Recently, we have set an upper mass limit to the progenitor of Type II-P SN 1999gi of 9 M☉ from preexplosion Hubble Space Telescope images. In this paper we present high-quality ground-based VRI images of the site of the Type II-P SN 1999em (in NGC 1637) taken before explosion, which were extracted from the Canada-France-Hawaii Telescope archive. We determine a precise position of the SN on these images to an accuracy of 0. ″17. The host galaxy is close enough (7.5 ± 0.5 Mpc) that the bright supergiants are resolved as individual objects; however, we show that there is no detection of an object at the SN position before explosion that could be interpreted as the progenitor star. By determining the sensitivity limits of the VRI data and assuming that the reddening toward the progenitor is similar to that toward the SN itself, we derive bolometric luminosity limits for the progenitor. Comparing these to standard stellar evolutionary tracks that trace evolution up to the point of core carbon ignition, we initially derive an upper mass limit of approximately 12 M☉. However, we present evolutionary calculations that follow 7-12 M☉ stars throughout their C-burning lifetime and show that we can restrict the mass of the progenitor even further. Our calculations indicate that progenitors initially of 8-10 M☉ undergoing expected mass loss can also be excluded because a second dredge-up sends them to somewhat higher luminosities than a star of initially 12 M☉. These results limit the progenitor's initial main-sequence mass to a very narrow range of 12 M☉. We discuss the similarities between the Type II-P SNe 1999em and 1999gi and their progenitor mass limits and also consider all the direct evidence currently available on progenitors of core-collapse SNe. We suggest that SNe Type II-P originate only in intermediate mass stars of 8-12 M☉, which are in the red supergiant region, and that higher mass stars produce the other Type II subtypes. Finally, we present a discussion on the future possibilities of determining masses or mass limits and the evolutionary status of core-collapse events on a statistically larger sample, using virtual observatory initiatives such as ASTROVIRTEL.
Effect of exercise intensity on abdominal fat loss during calorie restriction in overweight and obese postmenopausal women : a randomized , controlled trial 1 – 4

Background: Exercise intensity may affect the selective loss of abdominal adipose tissue. Objective: This study showed whether aerobic exercise intensity affects the loss of abdominal fat and improvement in cardiovascular disease risk factors under conditions of equal energy deficit in women with abdominal obesity. Design: This was a randomized trial in 112 overweight and obese [body mass index (in kg/m): 25–40; waist circumference . 88 cm], postmenopausal women assigned to one of three 20-wk interventions of equal energy deficit: calorie restriction (CR only), CR plus moderate-intensity aerobic exercise (CR 1 moderate-intensity), or CR plus vigorous-intensity exercise (CR 1 vigorous-intensity). The diet was a controlled program of underfeeding during which meals were provided at individual calorie levels (’400 kcal/d). Exercise (3 d/wk) involved treadmill walking at an intensity of 45–50% (moderate-intensity) or 70–75% (vigorous-intensity) of heart rate reserve. The primary outcome was abdominal visceral
Evaluation of therapeutic effect of tumor-targeted therapy

The response evaluation criteria in solid tumors, which are based on tumor size alone, are the most frequently used and effective criteria by which to evaluate the tumor response to chemotherapy. However, the mechanism of tumor-targeted drugs is different from traditional cytotoxic drugs. Tumor-targeted drugs are designed to interfere with specific aberrant biological pathways involved in tumorigenesis. For this reason, the response evaluation in solid tumors is not adequate for the evaluation of targeted therapy. Molecular and functional imaging techniques such as dynamic contrast-enhanced perfusion computed tomography, dynamic contrast-enhanced magnetic resonance imaging, dynamic contrast-enhanced ultrasound, and fluorodeoxyglucose-positron emission tomography can reflect tumor blood flow and cellular metabolic changes directly, and are being used more frequently for the evaluation of targeted therapies. This article gives an overview of some of the new computed tomography criteria and the commonly used methods of targeted therapy evaluation.
Gaussian Process Regression Networks Supplementary Material

In this supplementary material, we discuss some further details of our ESS and VB inference (Sections 1 and 2), the computational complexity of our inference procedures (Section 3), and the correlation structure induced by the GPRN model (Section 4). We also discuss multimodality in the GPRN posterior (Section 5), SVLMC, and some background information and notation for Gaussian process regression (Section 7). Figure 1 shows the network structure of GPRN learned on the JURA dataset.
River restoration

River restoration is at the forefront of applied hydrologic science. However, many river restoration projects are conducted with minimal scientific context. We propose two themes around which a research agenda to advance the scientific basis for river restoration can be built. First, because natural variability is an inherent feature of all river systems, we hypothesize that restoration of process is more likely to succeed than restoration aimed at a fixed end point. Second, because physical, chemical, and biological processes are interconnected in complex ways across watersheds and across timescales, we hypothesize that restoration projects are more likely to be successful in achieving goals if undertaken in the context of entire watersheds. To achieve restoration objectives, the science of river restoration must include (1) an explicit recognition of the known complexities and uncertainties, (2) continued development of a theoretical framework that enables us to identify generalities among river systems and to ask relevant questions, (3) enhancing the science and use of restoration monitoring by measuring the most effective set of variables at the correct scales of measurement, (4) linking science and implementation, and (5) developing methods of restoration that are effective within existing constraints. Key limitations to river restoration include a lack of scientific knowledge of watershed‐scale process dynamics, institutional structures that are poorly suited to large‐scale adaptive management, and a lack of political support to reestablish delivery of the ecosystem amenities lost through river degradation. This paper outlines an approach for addressing these shortcomings.
Prolonged and Intermittent Bilateral Common Carotid Artery Occlusion Induces Brain Lipidome Changes in a Rat Stroke Model

Background: Recent studies suggest that prolonged and intermittent bilateral common carotid artery occlusion (prolonged bilateral common carotid artery occlusion (PO) and intermittent bilateral common carotid artery occlusion, respectively) can lead to reduced ischemia brain injury in ischemic tolerance. Objectives: In this study, we aimed to investigate the changes in brain lipidomics following prolonged and intermittent ischemic preconditioning. Materials and Methods: Two groups underwent bilateral common carotid artery occlusion either intermittently (for 3 continuous periods within a timeframe of 20 minutes, releasing 3 consecutive times, yielding a total of 9 minutes (intermittent bilateral common carotid artery occlusion)) or for 9 minutes continuously (prolonged bilateral common carotid artery occlusion). The third and fourth groups were used as control and sham (without ischemia) groups, respectively. The first three groups were subdivided into middle cerebral artery occlusion-operated (middle cerebral artery occlusion MCAO), for 60 minutes of ischemia) and intact (without any surgery) subgroups. After 1 hour of ischemia and 24 hours of reper- fusion, the neurologic deficit score (neurological deficit score (NDS)) and the infarct volume (infarct volume) were assessed in the middle cerebral artery occlusion-operated subgroup. Brain lipidomics were measured in the intact subgroup and the sham group. Results: Preconditioning with prolonged bilateral common carotid artery occlusion and intermittent bilateral common carotid artery occlusion significantly decreased the neurological deficit scores and infarct volume and increased the levels of phosphatidylethanolamine, sphingomyelin, cholesterol ester, cholesterol, phosphatidylcholine, and cerebroside in the brain compared with the control and sham groups. Prolonged bilateral common carotid artery occlusion and intermittent bilateral common carotid artery occlusion significantly decreased the brain ceramide and lyso- phosphatidylcholine levels. The triglyceride levels in both groups (intermittent bilateral common carotid artery occlusion and prolonged bilateral common carotid artery occlusion) did not change in comparison with the control and sham groups. Conclusions: Although it seems that further studies are needed to clarify the real mechanisms of ischemic tolerance, ischemic preconditioning could decrease brain ischemia injury via changes in brain lipidomics.
Microbiology assessment as a route for understanding mixed culture processes

Outline Polyhydroxyalkanoates (PHAs) are biopolymers stored by numerous bacteria as a carbon and energy source, with similar properties to synthetic plastics. These polymers have been conquering an important position in the market as an ecological alternative to conventional oil-based plastics, since they are both biobased and biodegradable. However, the costs associated to PHA production are still too high to make them truly competitive. One option to cut down PHA production costs is the use of wastewater/waste/surplus feedstocks and mixed microbial cultures (MMC).
Title 3 D OCT imaging in clinical settings : toward quantitative measurements of retinal structures

The acquisition speed of current FD-OCT (Fourier Domain Optical Coherence Tomography) instruments allows rapid screening of three-dimensional (3D) volumes of human retinas in clinical settings. To take advantage of this ability requires software used by physicians to be capable of displaying and accessing volumetric data as well as supporting post processing in order to access important quantitative information such as thickness maps and segmented volumes. We describe our clinical FD-OCT system used to acquire 3D data from the human retina over the macula and optic nerve head. B-scans are registered to remove motion artifacts and post-processed with customized 3D visualization and analysis software. Our analysis software includes standard 3D visualization techniques along with a machine learning support vector machine (SVM) algorithm that allows a user to semi-automatically segment different retinal structures and layers. Our program makes possible measurements of the retinal layer thickness as well as volumes of structures of interest, despite the presence of noise and structural deformations associated with retinal pathology. Our software has been tested successfully in clinical settings for its efficacy in assessing 3D retinal structures in healthy as well as diseased cases. Our tool facilitates diagnosis and treatment monitoring of retinal diseases.