Miracle-dz/UniFAR-FTUs huggingface dataset:
Are hue and saturation carried in different neural channels?

Chromatic discrimination data show that a smaller physical stimulus change is required to detect a change in hue than to detect a change in saturation [Palette30, 21 (1968); Proc. R. Soc. London Ser. B283, 20160164 (2016)PRLBA40080-464910.1098/rspb.2016. 0164], and, on this basis, it has been suggested that hue and saturation are carried in different neural channels [Color Space and Its Divisions: Color Order from Antiquity to the Present (Wiley, 2003), p. 311]. We used an adaptation paradigm to test explicitly for separate mechanisms, measuring hue and saturation detection thresholds before and after adaptation to hue and saturation stimuli. Within-condition adaptation did not elevate detection thresholds significantly more than between-condition adaptation. We therefore did not find psychophysical evidence for a neural channel that extracts hue thresholds more effectively than the neural channel or channels that determine saturation thresholds.
Geochemistry of the Seamounts at the Southeast Chatham Rise, New Zealand

The submarine Chatham Rise, east Zealandia, is a key location of the early continental breakup of the eastern Gondwana (< 100 Ma; [1]). It has been suggested that a mantle plume beneath Zealandia and West Antarctica existed and that a slab window formed as a consequence of the collision of the Hikurangi oceanic plateau with the Chatham Rise, allowing deeper mantle material to upwell and hence cause the rifting. However, the exact processes that have led to this rifting and the sequence of reorganization in the upper mantle in course of and after the breakup of Zealandia from West Antarctica are still unclear. We present new major and trace element and Sr–Nd and high-precision Pb isotope data from submarine samples recovered during the R/V Sonne research expedition SO246 at the southeast Chatham Rise, covering the Chatham Rise Terrace and adjacent areas of the margin and the abyssal plain. The samples include alkali and tholeiitic basalts and minor basanite and trachybasalt, all of which have a composition between ocean island basalt (OIB) and mid-ocean-ridge basalt (MORB). Trace element ratios (e.g., Th/Yb, Nb/Yb) indicate that all but one seamount were derived from enriched sources at a low degree of melting, while one of the seamounts close to the abyssal plain was derived from a depleted mantle source at a high degree of melting. Sr-Nd-Pb isotope variations further support contribution of at least three distinct mantle source components, including a HIMU (high time-integrated U/Pb)-type sources, an enriched mantle (EM)-type sources, and a depleted mantle (N-MORB)-type source. These observations appear to be consistent with previous published data and models proposed by [2] and [3]. These sources will be placed in a chronological framework by incorporating further geochemical data and ArAr ages, providing us better insights into the sequence of events and magmatic processes that occurred at this region.
A Policy-Based Architecture for Protecting 802.11 WLANS Against DDOS Attacks

The security mechanisms available in 802.11WLANs are considered to be extremely vulnerable to malicious attacks. This paper proposes a policy-based architecture to protect 802.11 WLANs against Distributed Denial of Service (DDoS) attacks. The architecture proposed is based on the 802.1X standard, which forms the basis of the Robust Security Network (RSN) framework. The main focus of our work is to develop a policy-based server that can control certain actions taken by WLAN access points so that proper countermeasures will be taken whenever a DDoS attack occurs. The policies are both rule and case based and are contained in a Policy Based Security Server (PBSS). The approach taken is to simulate the behaviour of this architecture when faced with a range of DDoS attack strategies, and to use this to characterise the type of security policies required by the PBSS.
Phosphorylation of IRE1 at S729 regulates RIDD in B cells and antibody production after immunization

To relieve endoplasmic reticulum (ER) stress, IRE1 splices XBP1 messenger RNA (mRNA) or engages regulated IRE1-dependent decay (RIDD) of other mRNAs. Upon XBP1 deficiency, IRE1 switches to perform RIDD. We examined IRE1 in XBP1-deficient B cells and discovered that IRE1 undergoes phosphorylation at S729. We generated an anti–phospho-S729 antibody to investigate such phosphorylation. Compared with pharmacological ER stress inducers or Toll-like receptor ligands, the bacterial subtilase cytotoxin has an unusual capability in causing rapid and strong phosphorylation at S729 and triggering B cells to express spliced XBP1. To assess the function of S729 in IRE1, we generated S729A knock-in mice and found S729 is critically important for lipopolysaccharide-stimulated plasmablasts to respond to additional ER stress and for antibody production in response to immunization. We further crossed mice carrying an S729A mutation or &Dgr;IRE1 (missing the kinase domain) with B cell–specific XBP1-deficient mice to trigger RIDD and discovered a critical role for S729 in regulating RIDD in B cells.
Cooling interventions for athletes: An overview of effectiveness, physiological mechanisms, and practical considerations

ABSTRACT Exercise-induced increases in core body temperature could negative impact performance and may lead to development of heat-related illnesses. The use of cooling techniques prior (pre-cooling), during (per-cooling) or directly after (post-cooling) exercise may limit the increase in core body temperature and therefore improve exercise performance. The aim of the present review is to provide a comprehensive overview of current scientific knowledge in the field of pre-cooling, per-cooling and post-cooling. Based on existing studies, we will discuss 1) the effectiveness of cooling interventions, 2) the underlying physiological mechanisms and 3) practical considerations regarding the use of different cooling techniques. Furthermore, we tried to identify the optimal cooling technique and compared whether cooling-induced performance benefits are different between cool, moderate and hot ambient conditions. This article provides researchers, physicians, athletes and coaches with important information regarding the implementation of cooling techniques to maintain exercise performance and to successfully compete in thermally stressful conditions.
Fast Synchrotron X‐Ray Tomography of Dynamic Processes in Liquid Aluminium Alloy Foam  

Series of fast synchrotron X‐ray tomographies are taken continuously at a rate of up to 5 Hz, while aluminium alloy precursors are foamed in an X‐ray transparent setup for several minutes using infra‐red (IR) lasers for heating. The entire foaming process from the solid precursor to the expanded liquid foam is captured. The analysis of the sequence of tomographies is done with an emphasis on nucleation and bubble growth. In early stages of foaming, bubble and crack formation and evolution are observed. We analyze the nucleation stage and obtain quantitative results for the number of nucleation centers and their distribution and derive the nucleation rate as a function of time.
Nonalcoholic fatty liver disease The author's work is supported by a Merit Award from the Department of Veterans Affairs and by DK-072187 from the National Institutes of Health. Published, JLR Papers in Press, December 12, 2008.

Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease in the United States and, indeed, worldwide. It has become a global public health issue. In the United States, the prevalence in the general population is estimated at ∼20%, while that in the morbidly obese population at ∼75-92% and in the pediatric population at ∼13–14%. The progressive form of NAFLD, nonalcoholic steatohepatitis, is estimated at ∼3–5%, with ∼3–5% of these having progressed to cirrhosis. Thus, the numbers of individuals at risk for end-stage liver disease and development of primary liver cancer is large. NAFLD is an independent risk factor for cardiovascular disease, leads to increased all-cause mortality, and to increased liver-related mortality. This review focuses on recent advances in our understanding of the NAFLD disease spectrum, including etiology, diagnosis, treatment, and genetic and environmental risk factors and suggests future directions for research in this important area.
The Use of Endometrial Cancer Patient–Derived Organoid Culture for Drug Sensitivity Testing Is Feasible

Objective Patient-derived organoids (PDOs), used in multiple tumor types, have allowed evaluation of tumor characteristics from individual patients. This study aimed to assess the feasibility of applying PDO in vitro culture for endocrine-based and drug sensitivity testing in endometrial cancer. Methods Endometrial cancer cells were enzymatically dissociated from tumors retrieved from fresh hysterectomy specimens and cultured within basement membrane extract in serum-free medium. An organoid growth assay was developed to assess the inhibitory effects of a variety of drugs including endocrine treatments. Organoid cultures were also prepared for histological and immunohistochemical comparison to the tumors of origin. Results Fifteen endometrial cancer specimens were successfully cultured as PDOs. Small spherical structures formed within 24 hours, and many continued to grow to larger, denser organoids, providing the basis for an organoid growth assay. The STAT3 transcription factor inhibitor, BBI608 (Napabucasin), strongly inhibited growth in almost all PDO cultures, suggesting that stemness programing is involved in organoid formation and/or growth. Inhibition by different growth factor receptor tyrosine kinase inhibitors was observed in several PDO specimens. Four cultures were inhibited by fulvestrant, implying the importance of estrogen-receptor signaling in some PDO cultures. Organoids closely resembled their tumors of origin in both histomorphology and immunohistochemical expression. Conclusions The use of endometrial cancer PDO cultures for development of drug sensitivity testing for individual patient tumors is feasible. The potential value of the PDO model for clinical decision making will require clinical trial evaluation.
PAX6 molecular analysis and genotype–phenotype correlations in families with aniridia from Australasia and Southeast Asia

Purpose Aniridia is a congenital disorder caused by variants in the PAX6 gene. In this study, we assessed the involvement of PAX6 in patients with aniridia from Australasia and Southeast Asia. Methods Twenty-nine individuals with aniridia from 18 families originating from Australia, New Caledonia, Cambodia, Sri Lanka, and Bhutan were included. The PAX6 gene was investigated for sequence variants and analyzed for deletions with multiplex ligation-dependent probe amplification. Results We identified 11 sequence variants and six chromosomal deletions, including one in mosaic. Four deleterious sequence variants were novel: p.(Pro81HisfsTer12), p.(Gln274Ter), p.(Ile29Thr), and p.(Met1? ). Ocular complications were associated with a progressive loss of visual function as shown by a visual acuity ≤ 1.00 logMAR reported in 65% of eyes. The prevalence of keratopathy was statistically significantly higher in the Australasian cohort (78.6%) compared with the Southeast Asian cohort (9.1%, p=0.002). Variants resulting in protein truncating codons displayed limited genotype–phenotype correlations compared with other variants. Conclusions PAX6 variants and deletions were identified in 94% of patients with aniridia from Australasia and Southeast Asia. This study is the first report of aniridia and variations in PAX6 in individuals from Cambodia, Sri Lanka, Bhutan, and New Caledonia, and the largest cohort from Australia.
Skeletal muscle and mortality results from the InCHIANTI Study.

BACKGROUND Sarcopenia, the age-related loss of muscle mass, may not be an isolated process but is associated with an increase in fat mass. The aim of this study was to estimate the mortality risk of sarcopenia in the presence or absence of obesity. METHODS Data are from 934 participants aged 65 years or older, enrolled in the "Invecchiare in Chianti" study, and followed for 6 years. At baseline, a peripheral quantitative computerized tomography (pQCT) scan was performed on all participants to evaluate the muscle density, and the muscular and fat cross-sectional areas of the calf. Walking speed was measured on a 7-m track. Cox proportional hazard models were performed to estimate the association of pQCT measures (per 1 standard deviation increase) with mortality. RESULTS Unadjusted analyses showed significant associations of muscle density (hazard ratio [HR] 0.78, 95% confidence interval [CI] 0.69-0.88), muscle area (HR 0.75, 95% CI 0.66-0.86), and fat area (HR 0.82, 95% CI 0.73-0.92) with mortality. After adjustment for potential confounders, no body composition parameter was significantly associated with mortality. Walking speed (used as a reference measure to verify whether the negative results were due to peculiarities of the study sample) confirmed its well-established association with mortality risk (HR 0.73, 95% CI 0.60-0.88). These results did not change after the analyses were stratified according to sarcopenia and body mass index groups, and restricted to participants with frailty or a high inflammatory profile. CONCLUSIONS Calf skeletal muscle and fat mass are not significant risk factors for mortality in community-dwelling older adults. Walking speed confirmed to be a powerful predictor of health-related events.
Production, characterization, and assessment of a stable analog of the response regulator CheY‐phosphate from Thermotoga maritima

Phosphorylation of CheY promotes association with the flagellar motor and ultimately controls the directional bias of the motor. However, biochemical studies of activated CheY‐phosphate have been challenging due to the rapid hydrolysis of the aspartyl‐phosphate in vitro. An inert analog of Tm CheY‐phosphate, phosphono‐CheY, was synthesized by chemical modification and purified by cation‐exchange chromatography. Changes in HPLC retention times, chemical assays for phosphate and free thiol, and mass spectrometry experiments demonstrate modification of Cys54 with a phosphonomethyl group. Additionally, a crystal structure showed electron density for the phosphonomethyl group at Cys54, consistent with a modification at that position. Subsequent biochemical experiments confirmed that protein crystals were phosphono‐CheY. Isothermal titration calorimetry and fluorescence polarization binding assays demonstrated that phosphono‐CheY bound a peptide derived from FliM, a native partner of CheY‐phosphate, with a dissociation constant of ∼29 µM, at least sixfold more tightly than unmodified CheY. Taken together these results suggest that Tm phosphono‐CheY is a useful and unique analog of Tm CheY‐phosphate.
Experiences of stigma among family members of persons living with schizophrenia: a systematic review protocol.

REVIEW QUESTION/OBJECTIVE The aim of this qualitative systematic review is to explicate the experiences of stigma among family members of persons living with schizophrenia in any setting where they receive care. More specifically, the review will: (i) describe the experiences of stigma among family members of persons living with schizophrenia, (ii) describe the factors that influence the experiences of stigma, and (iii) describe the strategies and approaches used to cope with the stigma.
Bright-Pixel Defects in Irradiated CCD Image Sensors

We have examined environmental radiation sources for digital cameras to find the origins of bright-pixel defects known to accumulate with time. We show that beta and gamma emissions from camera parts and lenses cause image transients, but permanent damage can occur with alpha particles from the CCD cover glass. Our experiments with 14-MeV- and thermal-neutron beams confirm that cosmic rays are the primary cause of new imager bright points.
popFBA: tackling intratumour heterogeneity with Flux Balance Analysis

Motivation: Intratumour heterogeneity poses many challenges to the treatment of cancer. Unfortunately, the transcriptional and metabolic information retrieved by currently available computational and experimental techniques portrays the average behaviour of intermixed and heterogeneous cell subpopulations within a given tumour. Emerging single‐cell genomic analyses are nonetheless unable to characterize the interactions among cancer subpopulations. In this study, we propose popFBA, an extension to classic Flux Balance Analysis, to explore how metabolic heterogeneity and cooperation phenomena affect the overall growth of cancer cell populations. Results: We show how clones of a metabolic network of human central carbon metabolism, sharing the same stoichiometry and capacity constraints, may follow several different metabolic paths and cooperate to maximize the growth of the total population. We also introduce a method to explore the space of possible interactions, given some constraints on plasma supply of nutrients. We illustrate how alternative nutrients in plasma supply and/or a dishomogeneous distribution of oxygen provision may affect the landscape of heterogeneous phenotypes. We finally provide a technique to identify the most proliferative cells within the heterogeneous population. Availability and implementation: the popFBA MATLAB function and the SBML model are available at https://github.com/BIMIB‐DISCo/popFBA. Contact: chiara.damiani@unimib.it
Time Trends of Dietary and Lifestyle Factors and Their Potential Impact on Diabetes Burden in China

OBJECTIVE To examine the secular trends in risk factors, estimate their impact on type 2 diabetes burden from 1991 to 2011, and project trends in the next 20 years. RESEARCH DESIGN AND METHODS Risk factor distributions were based on data from the China Health and Nutrition Survey 1991–2011. Diabetes cases attributable to all nonoptimal levels of each risk factor were estimated by applying the comparative risk assessment method. RESULTS In 2011, high BMI was the leading individual attributable factor for diabetes cases in China responsible for 43.8 million diabetes cases with a population-attributable fraction of 46.8%. Low whole-grain intake and high refined grain intake were the leading dietary risk factors in China responsible for 37.8 million and 21.8 million diabetes-attributable cases, respectively. The number of attributable diabetes cases associated with low physical activity, high blood pressure, and current smoking was 29.5, 21.6, and 9.8 million, respectively. Although intakes of low-fat dairy products, nuts, fruit, vegetables, and fish and seafood increased moderately over time, the average intake was below optimal levels in 2011 and were responsible for 15.8, 11.3, 9.9, 6.0, 3.6, and 2.6 million diabetes cases, respectively. Meanwhile, intakes of processed meat, red meat, and sugar-sweetened beverage showed increasing trends over time and were responsible for 2.8, 1.8, and 0.5 million diabetes cases, respectively, in 2011. CONCLUSIONS A high BMI and low intake of whole grains but high intake of refined grains are the most important individual risk factors related to Chinese diabetes burden; low physical activity and high blood pressure also significantly contributed.
INVESTIGATION OF THE FEASIBILITY OF AN OPTICAL IMAGING SYSTEM FOR THE APPLICATION OF IN VIVO FLOW CYTOMETRY

This thesis investigates the feasibility of employing an optical imaging system for the application of in vivo flow cytometry for detecting rare circulating tumor cells (CTCs) in vasculature. This investigation presented used three optical imaging configurations: a Nikon Eclipse E600 fluorescence microscope with a PIXIS 2048B CCD camera; a Nikon Eclipse E600 fluorescence microscope with a ThorLabs DCC 3240N CMOS camera; and a custom built confocal microendoscope with a ThorLabs DCC 3240N CMOS camera. These systems were employed to gain insight as to what signal to noise ratios and sensitivities are required to sufficiently detect fluorescently labeled cancer cells. This work presents general concepts of fluorescence and confocal microscopy, the experimental setups employed, and experimental measurements and results obtained. The experimental measurements involved the following: the simulation of flow cytometry by imaging green fluorescent microspheres, with a fluorescence excitation range of 505-515 nm and a diameter of 15μm, in a square crit tube moving on a translational stage, and imaging a selection of cells that included MCF10A breast cells (non-cancerous), OVCAR3 ovarian cancer cells, and patient derived xenogram (PDX) breast cancer cells, which express folatereceptor proteins on their surface. We fluorescently labeled these cells with the introduction of a new folate-receptor targeted fluorescent contrast agent OTL38, made by On Target Laboratories. The results established that we were able to image and detect fluorescence microspheres with a minimum signal to noise ratio (SNR) of 2.3 using the ThorLabs DCC 3240N camera on the Nikon Fluorescence microscope. We were able to image and detect the cells used on all three system configurations. Analyzing the different cell uptake efficacies of the contrast agent OTL38, we established that the SNR levels were variable when imaging PDX breast cancer cells. We propose future work to investigate possible effects on the variability of SNR results, as well as, and future steps in designing a real-time optical fluorescence imaging system for in vivo flow cytometry.
Keeping it tight: The relationship between bacterial dysbiosis, septate junctions, and the intestinal barrier in Drosophila

ABSTRACT Maladaptive changes in the intestinal flora, typically referred to as bacterial dysbiosis, have been linked to intestinal aging phenotypes, including an increase in intestinal stem cell (ISC) proliferation, activation of inflammatory pathways, and increased intestinal permeability1,2. However, the causal relationships between these phenotypes are only beginning to be unravelled. We recently characterized the age-related changes that occur to septate junctions (SJ) between adjacent, absorptive enterocytes (EC) in the fly intestine. Changes could be observed in the overall level of SJ proteins, as well as the localization of a subset of SJ proteins. Such age-related changes were particularly noticeable at tricellular junctions (TCJ)3. Acute loss of the Drosophila TCJ protein Gliotactin (Gli) in ECs led to rapid activation of stress signalling in stem cells and an increase in ISC proliferation, even under axenic conditions; a gradual disruption of the intestinal barrier was also observed. The uncoupling of changes in bacteria from alterations in ISC behaviour and loss of barrier integrity has allowed us to begin to explore the interrelationship of these intestinal aging phenotypes in more detail and has shed light on the importance of the proteins that contribute to maintenance of the intestinal barrier.