Miracle-dz/UniFAR-FTUs huggingface dataset:
Cool C4 Photosynthesis: Pyruvate Pi Dikinase Expression and Activity Corresponds to the Exceptional Cold Tolerance of Carbon Assimilation in Miscanthus × giganteus12[W][OA]

The bioenergy feedstock grass Miscanthus × giganteus is exceptional among C4 species for its high productivity in cold climates. It can maintain photosynthetically active leaves at temperatures 6°C below the minimum for maize (Zea mays), which allows it a longer growing season in cool climates. Understanding the basis for this difference between these two closely related plants may be critical in adapting maize to colder weather. When M. × giganteus and maize grown at 25°C were transferred to 14°C, light-saturated CO2 assimilation and quantum yield of photosystem II declined by 30% and 40%, respectively, in the first 48 h in these two species. The decline continued in maize but arrested and then recovered partially in M. × giganteus. Within 24 h of the temperature transition, the pyruvate phosphate dikinase (PPDK) protein content per leaf area transiently declined in M. × giganteus but then steadily increased, such that after 7 d the enzyme content was significantly higher than in leaves growing in 25°C. By contrast it declined throughout the chilling period in maize leaves. Rubisco levels remained constant in M. × giganteus but declined in maize. Consistent with increased PPDK protein content, the extractable PPDK activity per unit leaf area (Vmax,ppdk) in cold-grown M. × giganteus leaves was higher than in warm-grown leaves, while Vmax,ppdk was lower in cold-grown than in warm-grown maize. The rate of light activation of PPDK was also slower in cold-grown maize than M. × giganteus. The energy of activation (Ea) of extracted PPDK was lower in cold-grown than warm-grown M. × giganteus but not in maize. The specific activities and Ea of purified recombinant PPDK from M. × giganteus and maize cloned into Escherichia coli were similar. The increase in PPDK protein in the M. × giganteus leaves corresponded to an increase in PPDK mRNA level. These results indicate that of the two enzymes known to limit C4 photosynthesis, increase of PPDK, not Rubisco content, corresponds to the recovery and maintenance of photosynthetic capacity. Functionally, increased enzyme concentration is shown to increase stability of M. × giganteus PPDK at low temperature. The results suggest that increases in either PPDK RNA transcription and/or the stability of this RNA are important for the increase in PPDK protein content and activity in M. × giganteus under chilling conditions relative to maize.
The role of the antileukoprotease SLPI in smoking‐induced human papillomavirus‐independent head and neck squamous cell carcinomas

Recently, we showed that increased SLPI levels prevent human papillomavirus (HPV) infections and metastasis in smoking‐induced, non‐HPV‐driven head and neck squamous cell carcinoma (HNSCC). Here, we focus on the role of SLPI in non‐HPV‐driven HNSCC, investigating tumor tissue and non‐neoplastic mucosa from the same patients and from non‐HNSCC patients. Gene and protein expression of SLPI and gene expression of annexin 2 (a SLPI receptor), nicotine receptor (α7AChR) and arylhydrocarbon receptor (AhR) were analyzed in HNSCC patients (20 smokers; 16 nonsmokers). SLPI‐results were correlated with the patients' HPV status. Non‐neoplastic mucosa of HNSCC patients and normal mucosa from non‐HNSCC individuals (18 smokers; 20 nonsmokers) was analyzed for the same parameters. Tissue of the inferior turbinate (n = 10) was incubated with nicotine for analysis of the same genes. SLPI gene expression in tumor tissue was 109.26 ± 23.08 times higher in smokers versus nonsmokers. Non‐neoplastic mucosa of smokers showed also higher SLPI gene expression (10.49 ± 1.89‐fold non‐HNSCC; 18.02 ± 3.93‐fold HNSCC patients). Annexin 2 gene expression was also increased in smokers. SLPI data were corroborated by immunohistochemistry. A nicotine dependent correlation between SLPI and annexin 2 gene expression (r2 = 0.15, p < 0.001) was shown ex vivo. Nicotine and smoking increased α7AChR and AhR gene expression. Five patients, showing no/low SLPI expression, were HPV16‐positive. A significant correlation between smoking and SLPI expression in tumors and to our knowledge for the first time in mucosa of HNSCC and non‐HNSCC patients was established. Together with the finding that all patients with HPV infection showed no/low SLPI expression, these data support our intriguing hypothesis that smoking induced upregulated SLPI prevents HPV infections.
Nanoceria Attenuated High Glucose-Induced Oxidative Damage in HepG2 Cells

Objective Hyperglycemia, a common metabolic disorder in diabetes, can lead to oxidative damage. The use of antioxidants can benefit the control and prevention of diabetes side effects. This study aims to evaluate the effect of nanoceria particles, as an antioxidant, on glucose induced cytotoxicity, reactive oxygen species (ROS), lipid peroxidation (LPO) and glutathione (GSH) content in a human hepatocellular liver carcinoma cell line (HepG2) cell line. Materials and Methods In this experimental study, we divided HepG2 cells into these groups: i. Cells treated with 5 mM D-glucose (control), ii. Cells treated with 45 mM D- mannitol+5 mM D-glucose (osmotic control), iii. Cells treated with 50 mM D-glucose (high glucose), and iv. Cells treated with 50 mM D-glucose+nanoceria. Cell viability, ROS formation, LPO and GSH were measured and analyzed statistically. Results High glucose (50 mM) treatment caused significant cell death and increased oxidative stress markers in HepG2 cells. Interestingly, nanoceria at a concentration of 50 mM significantly decreased the high glucose-induced cytotoxicity, ROS formation and LPO. This concentration of nanoceria increased the GSH content in HepG2 cells (P<0.05). Conclusion The antioxidant feature of nanoceria particles makes it an attractive candidate for attenuation of hyperglycemia oxidative damage in different organs.
Active Model Selection

Classical learning assumes the learner is given a labeled data sample, from which it learns a model. The field of Active Learning deals with the situation where the learner begins not with a training sample, but instead with resources that it can use to obtain information to help identify the optimal model. To better understand this task, this paper presents and analyses the simplified "(budgeted) active model selection" version, which captures the pure exploration aspect of many active learning problems in a clean and simple problem formulation. Here the learner can use a fixed budget of "model probes" (where each probe evaluates the specified model on a random indistinguishable instance) to identify which of a given set of possible models has the highest expected accuracy. Our goal is a policy that sequentially determines which model to probe next, based on the information observed so far. We present a formal description of this task, and show that it is NP-hard in general. We then investigate a number of algorithms for this task, including several existing ones (eg, "Round-Robin", "Interval Estimation", "Gittins") as well as some novel ones (e.g., "Biased-Robin"), describing first their approximation properties and then their empirical performance on various problem instances. We observe empirically that the simple biased-robin algorithm significantly outperforms the other algorithms in the case of identical costs and priors.
ReCon: Revealing and Controlling Privacy Leaks in Mobile Network Traffic

Mobile systems have become increasingly popular for providing ubiquitous Internet access; however, recent studies demonstrate that software running on these systems extensively tracks and leaks users’ personally identiﬁable information (PII). We argue that these privacy leaks persist in large part because mobile users have little visibility into PII leaked through the network trafﬁc generated by their devices, and have poor control over how, when and where that trafﬁc is sent and handled by third parties. In this paper, we describe ReCon , a cross-platform system that reveals PII leaks and gives users control over them without requiring any special privileges or custom OSes. Specif-ically, our key observation is that PII leaks must occur over the network , so we implement our system in the network using a software middlebox built atop the Meddle platform. While this simpliﬁes access to users’ network ﬂows, the key challenges for detecting PII from the network perspective are 1) how to efﬁciently and accurately detect users’ PII without knowing a priori what their PII is and 2) whether to block, obfuscate, or ignore the PII leak. To address this, we use a machine learning approach to detect trafﬁc that contains PII, display these behaviors via a visualization tool and let the user decide how the system should act on transmitted PII. We discuss the design and implementation of the system and evaluate its methodology with measurements from controlled experiments and ﬂows from 16 users (19 devices) as part of an IRB-approved user study.
Sulfate determines the glucosinolate concentration of horseradish in vitro plants (Armoracia rusticana Gaertn., Mey. & Scherb.).

BACKGROUND Horseradish plants (Armoracia rusticana) contain high concentrations of glucosinolates. Former studies have revealed that Armoracia plants cultivated in vitro have markedly lower glucosinolate concentrations than those grown in soils. Yet, these studies neglected that the sulfate concentration in the growth medium may have had a strong impact on glucosinolate metabolism. Accordingly, in this study horseradish in vitro plants were cultivated with differing sulfate concentrations and the glucosinolate concentrations were quantified by ion pair HPLC. RESULTS Cultivation in 1.7 mmol L(-1) sulfate (as used in the prior studies) resulted in the accumulation of 16.2 µmol g(-1) DW glucosinolates, while the glucosinolate concentration increased to more than 23 µmol g(-1) DW when 23.5 mmol L(-1) sulfate was used in the medium. Correspondingly, the glucosinolate concentration decreased to 1.6 µmol g(-1) DW when sulfate concentration was lowered to 0.2 mmol L(-1). CONCLUSION Since the glucosinolate accumulation in relation to the sulfate concentration follows a typical saturation curve, we deduce that the availability of sulfate determines the glucosinolate concentration in horseradish in vitro plants.
Flows over time with load-dependent transit times

About forty years ago, Ford and Fulkerson studied maximum 'dynamic' s-t-flows in networks with fixed transit times on the edges and a fixed time horizon. They showed that there always exists an optimal solution which sends flow on certain s-t-paths at a constant rate as long as there is enough time left for the flow along a path to arrive at the sink.Although this result does not hold for the more general setting of flows over time with load-dependent transit times on the edges, we prove that there always exists a provably good solution of this structure. Moreover, such a solution can be determined very efficiently by only one minimum convex cost flow computation on the underlying 'static' network. Finally, we show that the time-dependent flow problem under consideration is NP-hard and even cannot be approximated with arbitrary precision in polynomial time, unless P=NP.
Cost-Based Placement of Virtualized Deep Packet Inspection Functions in SDN

In today's IT systems, cyber security requires fine-grained, flexible, adaptable and cost optimized monitoring mechanisms. The emergence of new networking technologies, like Network Function Virtualization (NFV) and Software Defined Networking (SDN), opens up new venues for large scale adoption of these cyber security tools. In particular, Deep Packet Inspection (DPI) engines can be virtualized and dynamically deployed as pieces of software on commodity hardware. Deploying such software DPI engines is costly in terms of license fees and power consumption. Designing cost effective DPI engine deployment strategies that meet the cybersecurity operational constraints is thus mandatory for the adoption of this approach. For this purpose, we propose a method, based on genetic algorithms, that optimizes the cost of DPI engine deployment, minimizing their number, the global network load and the number of unanalyzed flows. We conduct several experiments with different types of traffic and different cost structures. The results show that the method is able to reach a trade-off between the number of DPI engines and network load. Furthermore, the global cost can be reduced up to 58% when relaxing the constraint on the used link capacity, that is the provisioning rate.
Ideación y comportamiento suicida en embarazadas

SUMMARY The aim is to explore the occurrence of suicide ideation and behavior in pregnant women receiving prenatal care and to analyze the motives behind these behaviors. Although there are very few studies evaluating the prevalence of the suicide phenomenon (suicide, intentional injuries with or without the aim of taking one’s own life, ideas of harming oneself or death) during the prenatal period, it has been reported that pregnancy complications due to suicide attempts occur in 0.4 out of every 1 000 patients discharged from hospitals in the state of California in the United States and in one out of every 283 pregnant women in specialized mental health services. Suicide ideation occurs in 1.4% of English expectant mothers, 0.5% of Finnish ones and 27.8% of US pregnant women with psychiatric disorders. In Latin America, it is estimated to occur in 16.7% of pregnant teenagers. Although suicide ideation and suicide attempts during pregnancy are less frequent than at other times in life, they have major consequences, increasing the risk of death and affecting fetal development and pregnancy itself.
Evaluating Volunteers' Contributions in a Citizen Science Project

Today, with freely available data coming from different satellites and instruments, efficient algorithms for image classification, and increased connectivity and computing power, together with international policy initiatives, such as the United Nations Framework Convention of Climate Change Reducing Emissions from Deforestation and Forest Degradation (REDD) program, more and more countries are starting to invest in their own national forest monitoring schemes. Still, tropical forests remain under threat worldwide. Recently a citizen science project that enables citizens around the globe to be involved in forest monitoring tasks has been proposed. Called Forest Watchers (www.forestwatchers.net), its main goal is to allow volunteers (many of them with no scientific training) around the globe, with their own smartphones, tablets and notebooks, to review satellite images of forested regions, and confirm whether automatic assignments of forested and deforested regions are correct. Inspected images are then sent to a central database where results are integrated to generate up-to-date deforestation maps. This approach offers a low-cost way to both strengthen the scientific infrastructure and engage members of the public in science. Here we describe the procedures developed within the scope of the Forest Watchers project to assess the tasks performed by the volunteers. These procedures have been evaluated with data of one of the project's preliminary applications. Called BestTile, it asks volunteers to select among several images of the same area, which one has the least cloud cover. Results from more than 500 volunteers show that with simple statistical tests it is possible to attain a triple goal: to increase the overall efficiency of the data collecting tasks, by reducing the required number of volunteers per task, to identify malicious behavior and outliers, and to motivate volunteers, to continue their contributions.
The Relationship Between the Response of Clinical Symptoms and Plasma Olanzapine Concentration, Based on Pharmacogenetics: Juntendo University Schizophrenia Projects (JUSP)

The monitoring of plasma olanzapine concentrations has been found to be an important and useful tool for optimizing psychiatric treatment. The present study investigated the effect that clinical factors, such as smoking and age, and functional polymorphisms of UGT1A4, CYP1A2, and CYP2D6 genes have on plasma olanzapine concentration, as well as the effects of plasma olanzapine concentrations on Japanese schizophrenic patients' clinical symptoms. The subjects included 51 chronic schizophrenic patients whose symptoms were not controlled with chronic conventional antipsychotics and therefore were switched to olanzapine. Male smokers had a significantly lower olanzapine concentration-dose ratio and olanzapine/4′-N-desmethyl olanzapine ratio (which reflects CYP1A2 activity) than male nonsmokers and female nonsmokers. The results of a 2-way analysis of covariance showed that smoking had the main effect, rather than gender or age. The functional gene polymorphisms that were studied had no effect on the plasma olanzapine and metabolite concentrations. An improved total Brief Psychiatric Rating Scale (BPRS) score was not correlated with the plasma olanzapine concentration, but individual BPRS scores related to improvement of suspiciousness, hallucinations, and blunted affect were significantly correlated with plasma olanzapine concentration. Clinical factors, especially smoking, were more important modulators of olanzapine metabolism than the functional genotypes. Long-term olanzapine treatment with adequate plasma olanzapine concentrations could be more effective in improving some symptoms than treatment with conventional antipsychotics.
Accelerating Adobe Photoshop with reconfigurable logic

This paper presents the results of a project designed to produce a commercial application for reconfigurable logic. We describe how we took the popular image processing application Adobe Photoshop and used its plug-in technology to devise a set of FPGA-based filters to accelerate colour space conversion and image convolution operations. Some of the barriers that make it difficult to produce portable FPGA-based filters are explored.
Living well with dementia—development of the national dementia strategy for England

Dementia is one of the greatest societal challenges that we face. The profound negative impacts of dementia on people with dementia themselves, their families, and in terms of health and social service use are not in doubt. Powerful misconceptions exist concerning dementia including it being a normal part of aging; that there is nothing that can be done to help; and that it is better not to know. These have resulted in a situation where dementia has not been a priority for health policy makers and commissions. The direct result of this is that the large majority of people with dementia and their family carers do not benefit from the positive intervention and support that can promote wellbeing and prevent crises for all involved. At times it can seem that services have been designed to result in the avoidance of diagnosis and the consequent denial of care. In the UK only about a third of people with dementia receive a diagnosis of dementia.When they do it is usually late in the disorder, often at a time of crisis when it is too late to prevent the harm that has been caused to the person with dementia and their family (National Audit Office [NAO], 2007). In this paper we will focus on the development and the content of the English National Dementia Strategy which attempts to address this.
Reverse-safe authentication protocol for secure USB memories

USB memory devices are both portable and easily accessible, and have thus become one of the most popular forms of external storage device. However, if a USB device is lost, stolen, or hacked, it may lead to leakage of critical information. It is a logical outcome that malicious individuals will try to steal their colleagues' USB memories. Consequently, various USB products with built-in security functions have been developed. To our knowledge, there has been little or no security analysis and comparison of these devices. This paper explores technological and architectural approaches to secure USB memories while analyzing their vulnerabilities, especially for resistance to reverse engineering attacks on the authentication protocols and data decryption. In this analysis, we classify vulnerabilities of these devices into 12 categories to summarize the current security situations on USB memories. Additionally, we derive a more secure authentication protocol based on our analysis. It is expected for secure USB products, including USB memory devices, to be revised with enhanced authentication protocols as a result of this effort. Copyright © 2012 John Wiley & Sons, Ltd.
An Overview and Update of ATP7A Mutations Leading to Menkes Disease and Occipital Horn Syndrome

Menkes disease (MD) is a lethal multisystemic disorder of copper metabolism. Progressive neurodegeneration and connective tissue disturbances, together with the peculiar “kinky” hair, are the main manifestations. MD is inherited as an X‐linked recessive trait, and as expected the vast majority of patients are males. MD occurs because of mutations in the ATP7A gene and the vast majority of ATP7A mutations are intragenic mutations or partial gene deletions. ATP7A is an energy‐dependent transmembrane protein, which is involved in the delivery of copper to the secreted copper enzymes and in the export of surplus copper from cells. Severely affected MD patients die usually before the third year of life. A cure for the disease does not exist, but very early copper–histidine treatment may correct some of the neurological symptoms. This study reviews 274 published and 18 novel disease causing mutations identified in 370 unrelated MD patients, nonpathogenic variants of ATP7A, functional studies of the ATP7A mutations, and animal models of MD.
Different anesthesia regimes modulate the functional connectivity outcome in mice

The use of resting‐state functional MRI (rsfMRI) in preclinical research is expanding progressively, with the majority of resting‐state imaging performed in anesthetized animals. Since anesthesia may change the physiology and, in particular, the neuronal activity of an animal considerably, it may also affect rsfMRI findings. Therefore, this study compared rsfMRI data from awake mice with rsfMRI results obtained from mice anesthetized with α‐chloralose (120 mg/kg), urethane (2.5 g/kg), or isoflurane (1%).
Division site selection in Escherichia coli involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles

The MinCDE proteins of Escherichia coli are required for proper placement of the division septum at midcell. The site selection process requires the rapid oscillatory redistribution of the proteins from pole to pole. We report that the three Min proteins are organized into extended membrane-associated coiled structures that wind around the cell between the two poles. The pole-to-pole oscillation of the proteins reflects oscillatory changes in their distribution within the coiled structure. We also report that the E. coli MreB protein, which is required for maintaining the rod shape of the cell, also forms extended coiled structures, which are similar to the MreB structures that have previously been reported in Bacillus subtilis. The MreB and MinCDE coiled arrays do not appear identical. The results suggest that at least two functionally distinct cytoskeletal-like elements are present in E. coli and that structures of this type can undergo dynamic changes that play important roles in division site placement and possibly other aspects of the life of the cell.
Using Collocations for Topic Segmentation and Link Detection

We present in this paper a method for achieving in an integrated way two tasks of topic analysis: segmentation and link detection. This method combines word repetition and the lexical cohesion stated by a collocation network to compensate for the respective weaknesses of the two approaches. We report an evaluation of our method for segmentation on two corpora, one in French and one in English, and we propose an evaluation measure that specifically suits that kind of systems.