Miracle-dz/UniFAR-FTUs huggingface dataset:
The comparison of CHCA solvent compositions for improving LC-MALDI performance and its application to study the impact of aflatoxin B1 on the liver proteome of diabetes mellitus type 1 mice

In nanoflow liquid chromatography-matrix-assisted laser desorption/ionization tandem time-of-flight (nanoLC-MALDI-TOF/TOF) approaches, it is critical to directly apply small amounts of the sample elutes on the sample target using a nanoLC system due to its low flow rate of 200 ~ 300 nl/min. It is recommended to apply a sheath liquid containing a matrix with a several μL/min flow rate at the end of the nanoLC column to ensure a larger co-eluted droplet for more reproducible sample spotting and avoid the laborious task of post-manual matrix spotting. In this study, to achieve a better nanoLC-MALDI performance on sample spotting, we first compared α-Cyano-4-hydroxycinnamic acid (CHCA) solvent composition for efficiently concentrating nanoLC elutes on an anchor chip. The solvent composition of isopropanol (IPA): acetonitrile (ACN):acetone:0.1% Trifluoroacetic acid (TFA) (2:7:7:2) provided strong and homogeneous signals with higher peptide ion yields than the other solvent compositions. Then, nanoLC-MALDI-TOF/TOF was applied to study the impact of aflatoxin B1 on the liver proteome from diabetes mellitus type 1 mice. Aflatoxin B1 (AFB1), produced by Aspergillus flavus and Aspergillus parasiticus is a carcinogen and a known causative agent of liver cancer. To evaluate the effects of long-term exposure to AFB1 on type 1 diabetes mellitus (TIDM), the livers of T1DM control mice and mice treated with AFB1 were analyzed using isotope-coded protein labeling (ICPL)-based quantitative proteomics. Our results showed that gluconeogenesis, lipid, and oxidative phosphorylation mechanisms, normally elevated in T1DM, were disordered following AFB1 treatment. In addition, major urinary protein 1 (MUP1), an indicator of increased insulin sensitivity, was significantly decreased in the T1DM/AFB1 group and may have resulted in higher blood glucose levels compared to the T1DM group. These results indicate that T1DM patients should avoid the AFB1 intake, as they could lead to increased blood glucose levels and disorders of energy-producing mechanisms.
On selecting a measure of retrieval effectiveness

It was argued in Part I (see JASIS, March‐April 1973 p. 87) that the best way to evaluate a retrieval system is, in principle at least, to elicit subjective estimates of the system's utility to its users, quantified in terms of the numbers of utiles (e.g. dollars) they would have been willing to give up in exchange for the privilege of using the system; and a naive methodology was outlined for evaluating retrieval systems on this basis. But the impracticality of the naive evaluation procedure as it stands raises the questions: How can one decide which practical measure is likely to yield results most closely resembling those of the naive methodology? And how can one tell whether the resemblance is close enough to make applying the measure worth while? In the present paper two kinds of solution to these problems are taken up. The first answers the questions in terms of the reasonableness of the simplifying assumptions needed to get from the naive measure to the proposed substitute. The second answers it by experimentation.
Assessment of Three-and-a-Half-Year-Old Children's Emerging Phonological Awareness in a Computer Animation Context

Four computer-animated tasks were created to analyze the underlying structure of emerging phonological awareness at 3.5 years of age and to explore the factors that influence children's (N = 91) performance on the tasks. Our findings indicated that already at this young age, children are able to master tasks demanding identification, blending, and continuation of phonological units when the tasks are presented in a motivating assessment context. In line with earlier research, children showed higher mastery in dealing with words and syllables than in dealing with phonemes. Targets in the initial position of a word were easier for children to identify than those in the final position. Our analysis provided support for two major dimensions of emerging phonological awareness based on the cognitive operations of the tasks: identification and blending of phonological units.
Fixing Races for Fun and Profit: How to Abuse atime

Dean and Hu proposed a probabilistic countermeasure to the classic access(2)/open(2) TOCTTOU race condition in privileged Unix programs [4]. In this paper, we describe an attack that succeeds with very high probability against their countermeasure. We then consider a stronger randomized variant of their defense and show that it, too, is broken. We conclude that access(2) must never be used in privileged Unix programs. The tools we develop can be used to attack other filesystem races, underscoring the importance of avoiding such races in secure software.
NOTIONS FOR RSA INTEGERS Full version

The key-generation algorithm for the RSA cryptosystem is sp ecified in several standards, such as PKCS#1, IEEE 1363-2000, FIPS 186 -3, ANSI X9.44, or ISO/IEC 18033-2. All of them substantially differ in their r equirements. This indicates that for computing a “secure” RSA modulus it does not ma t er how exactly one generates RSA integers. In this work we show that this is inde ed the case to a large extend: First, we give a theoretical framework that will ena ble us to easily compute the entropy of the output distribution of the considered sta ndards and show that it is comparatively high. To do so, we compute for each standard th e number of integers they define (up to an error of very small order) and discuss dif ferent methods of generating integers of a specific form. Second, we show that fact oring such integers is hard, provided factoring a product of two primes of similar s ize is hard.
Prime time news: The influence of primed positive and negative emotion on susceptibility to false memories

We examined the relation between emotion and susceptibility to misinformation using a novel paradigm, the ambiguous stimuli affective priming (ASAP) paradigm. Participants (N = 88) viewed ambiguous neutral images primed either at encoding or retrieval to be interpreted as either highly positive or negative (or neutral/not primed). After viewing the images, they either were asked misleading or non-leading questions. Following a delay, memory accuracy for the original images was assessed. Results indicated that any emotional priming at encoding led to a higher susceptibility to misinformation relative to priming at recall. In particular, inducing a negative interpretation of the image at encoding led to an increased susceptibility of false memories for major misinformation (an entire object not actually present in the scene). In contrast, this pattern was reversed when priming was used at recall; a negative reinterpretation of the image decreased memory distortion relative to unprimed images. These findings suggest that, with precise experimental control, the experience of emotion at event encoding, in particular, is implicated in false memory susceptibility.
A multi-view projection 3D video processing technology

At present the naked eye 3D display has only one appropriate viewpoint, and the slight movement of the viewer position will cause crosstalk and affect the viewing experience. To solve this problem, this paper presents an FPGA-based multi-view projection naked eye 3D video processing method. The video sources will be divided into nine equal parts, and each of them will be enlarged as the original resolution. The zoomed ones will be sent to nine projectors, then eight appropriate naked eye 3D display views will be achieved after the following optical processing. Taking into account the actual amplification effects, hardware limitations, the complexity of algorithm and other factors, the image magnification will adopt the bilinear interpolation algorithm.
R-tree-based data migration and self-tuning strategies in shared-nothing spatial databases

In order to provide fast and timely answers to queries in the context of spatial databases and GIS, we present our solution for effective data migration and tuning strategies in shared-nothing parallel spatial databases. Our purpose is to improve the performance of the indexes. Our approach has the following features. First, our scheme is self-tuning, dynamic as well as query-centric and it can adapt to dynamically changing user access patterns. Second, a global distributed R-tree-based indexing method is employed to facilitate effective data migration. Third, unlike traditional partitioning strategies where each processing element (PE) contains data from a single region of space, we allow each PE to store data from multiple and disjoint regions. This minimizes overlap in regions as well as coverage.We implemented the proposed scheme and conducted an extensive performance study on Fujitsu's AP3000 machine with 32 workstations using real datasets. Our experimental results show that our load-balancing strategy can distribute the load effectively across the PEs in the system, thereby reducing response times of incoming queries.
International Union of Pharmacology LVII: Recommendations for the Nomenclature of Receptors for Relaxin Family Peptides

Although the hormone relaxin was discovered 80 years ago, only in the past 5 years have the receptors for relaxin and three other receptors that respond to related peptides been identified with all four receptors being G-protein-coupled receptors. In this review it is suggested that the receptors for relaxin (LGR7) and those for the related peptides insulin-like peptide 3 (LGR8), relaxin-3 (GPCR135), and insulin-like peptide 5 (LGPCR142) be named the relaxin family peptide receptors 1 through 4 (RXFP1-4). RXFP1 and RXFP2 are leucine-rich repeat-containing G-protein-coupled receptors with complex binding characteristics involving both the large ectodomain and the transmembrane loops. RXFP1 activates adenylate cyclase, protein kinase A, protein kinase C, phosphatidylinositol 3-kinase, and extracellular signaling regulated kinase (Erk1/2) and also interacts with nitric oxide signaling. RXFP2 activates adenylate cyclase in recombinant systems, but physiological responses are sensitive to pertussis toxin. RXFP3 and RXFP4 resemble more conventional peptide liganded receptors and both inhibit adenylate cyclase, and in addition RXFP3 activates Erk1/2 signaling. Physiological studies and examination of the phenotypes of transgenic mice have established that relaxin has roles as a reproductive hormone involved in uterine relaxation (some species), reproductive tissue growth, and collagen remodeling but also in the cardiovascular and renal systems and in the brain. The connective tissue remodeling properties of relaxin acting at RXFP1 receptors have potential for the development of agents effective for the treatment of cardiac and renal fibrosis, asthma, and scleroderma and for orthodontic remodelling. Agents acting at RXFP2 receptors may be useful for the treatment of cryptorchidism and infertility, whereas antagonists may be used as contraceptives. The brain distribution of RXFP3 receptors suggests that actions at these receptors have the potential for the development of antianxiety and antiobesity drugs.
Effect of “Deqi” during the Study of Needling “Wang's Jiaji” Acupoints Treating Spasticity after Stroke

Background. Acupuncture has been shown to reduce spasticity and prevent the onset of spasticity after stroke. The purpose of this study is to assess the effect of “Deqi” during needling “Wang's Jiaji” acupoints treating spasticity in the early stage of stroke. Methods. This study is a multicenter, prospective, randomized, controlled trial. 238 patients with stroke (<21 days) participated and were randomly allocated to the verum-acupuncture (n = 121) group or sham-acupuncture group (n = 117). The verum-acupuncture group received verum acupuncture required to produce the sense of “Deqi” while the sham-acupuncture group received sham acupuncture without “Deqi. ” Patients in both groups followed the same 30 min acupuncture regimen 5 times per week for a period of 4 weeks. Scales of MAS, FMA, ADL, MBI, NIHSS, SS-QOL, and MRS were measured at baseline and at 2, 4, and 12 weeks after intervention. Results. Significant differences were observed between two groups. The MRS rating composition has the statistical difference after 4 weeks (P = 0.017). The score of MAS, FMA, Barthel, and SSQOL in verum-acupuncture group has increased significantly compared with the sham-acupuncture group after 12 weeks. There was 14% reduction of higher muscle tension in the verum-acupuncture group. Conclusion. Acupuncture “Wang's Jiaji” points with sensation of “Deqi” in the early stage may reduce the occurrence and decrease the severity of spasticity after stroke.
How good are agile methods?

The software industry seems to be embracing yet another change to the way it does business. Because of their emphasis on agility and time-to-market, many programming shops are moving to agile methods. Unlike more traditional approaches, these methods focus on generating early releases of working products using mostly collaborative techniques such as pair programming, refactoring, and having customers work on site as team members. Programmers use these releases-which are working products, not prototypes-to demonstrate features and functions to stakeholders involved in their use, marketing, and support. This article surveys the experience software engineers in a wide, range of industries have had in deploying agile methods.
CosTLO: Cost-Effective Redundancy for Lower Latency Variance on Cloud Storage Services

We present CosTLO, a system that reduces the high latency variance associated with cloud storage services by augmenting GET/PUT requests issued by end-hosts with redundant requests, so that the earliest response can be considered. To reduce the cost overhead imposed by redundancy, unlike prior efforts that have used this approach, CosTLO combines the use of multiple forms of redundancy. Since this results in a large number of configurations in which CosTLO can issue redundant requests, we conduct a comprehensive measurement study on S3 and Azure to identify the configurations that are viable in practice. Informed by this study, we design CosTLO to satisfy any application's goals for latency variance by 1) estimating the latency variance offered by any particular configuration, 2) efficiently searching through the configuration space to select a cost-effective configuration among the ones that can offer the desired latency variance, and 3) preserving data consistency despite CosTLO's use of redundant requests. We show that, for the median PlanetLab node, CosTLO can halve the latency variance associated with fetching content from Amazon S3, with only a 25% increase in cost.
Simple Computation-Universal Cellular Spaces

The special izat ion of the theory of cellular spaces (cellular au tomata ) to those spaces which compute par t ia l recursive funct ions is presented. Neighborhood reduct ion and state-set reduct ion are shown to be pa r t i cu la r ly simple in this special theory, and one dimension is proved to be sufficient for computa t ion universa l i ty . Several computa t ion-un iversa l cellular spaces (CUCS's) are exhibi ted which are simple in the sense t h a t each cell has only a small number q of s ta tes and a small number p of neighbors. For example, a 1-dimensional CUCS with pq = 36 is presented. Two quite different proofs of the existence of a I -dimensional CUCS with only two neighbors are given. Final ly , one of the theorems derived is used to settle three open decidabi l i ty questions.
Optimal Conservation Outcomes Require Both Restoration and Protection

Conservation outcomes are principally achieved through the protection of intact habitat or the restoration of degraded habitat. Restoration is generally considered a lower priority action than protection because protection is thought to provide superior outcomes, at lower costs, without the time delay required for restoration. Yet while it is broadly accepted that protected intact habitat safeguards more biodiversity and generates greater ecosystem services per unit area than restored habitat, conservation lacks a theory that can coherently compare the relative outcomes of the two actions. We use a dynamic landscape model to integrate these two actions into a unified conservation theory of protection and restoration. Using nonlinear benefit functions, we show that both actions are crucial components of a conservation strategy that seeks to optimise either biodiversity conservation or ecosystem services provision. In contrast to conservation orthodoxy, in some circumstances, restoration should be strongly preferred to protection. The relative priority of protection and restoration depends on their costs and also on the different time lags that are inherent to both protection and restoration. We derive a simple and easy-to-interpret heuristic that integrates these factors into a single equation that applies equally to biodiversity conservation and ecosystem service objectives. We use two examples to illustrate the theory: bird conservation in tropical rainforests and coastal defence provided by mangrove forests.
NetCents: A Lightweight Protocol for Secure Micropayments

NetCents is a lightweight, flexible and secure protocol for electronic commerce over the Internet that is designed to support purchases ranging in value from a fraction of a penny and up. NetCents differs from previous protocols in several respects: NetCents uses (vendor-independent) floating scrips as signed containers of electronic currency, passed from vendor to vendor. This allows NetCents to incorporate decentralized verification of electronic currency at a vendor's server with offline payment capture. Customer trust is not required within this protocol and a probabilistic verification scheme is used to effectively limit vendor fraud. An online arbiter is implemented that will ensure proper delivery of purchased goods and that can settle most customer/vendor disputes. NetCents can be extended to support fully anonymous payments. In this paper we describe the NetCents protocol and present experimental results of a prototype implementation.
Parametrizing multicore architectures for multiple sequence alignment

Sequence alignment is one of the fundamental tasks in bioinformatics. Due to the exponential growth of biological data and the computational complexity of the algorithms used, high performance computing systems are required. Although multicore architectures have the potential of exploiting the task-level parallelism found in these workloads, efficiently harnessing systems with hundreds of cores requires deep understanding of the applications and the architecture. When incorporating large numbers of cores, performance scalability will likely saturate shared hardware resources like buses and memories. In this paper we evaluate the performance impact of various configurations of an accelerator-based multicore architecture with the aim of revealing and quantifying the bottlenecks. Then, we compare against a multicore using general-purpose processors and discuss the performance gap. Our target application is ClustalW, one of the most popular programs for Multiple Sequence Alignment. Different input data sets are characterized and we show how they influence performance. Simulation results show that due to the high computation-to-communication ratio and the transfer of data in large chunks, memory latency is well tolerated. However, bandwidth is critical to achieving maximum performance. Using a 32KB cache configuration with 4 banks can capture most of the memory traffic and therefore avoid expensive off-chip transactions. On the other hand, using a hardware queue for the tasks synchronization allows us to handle a large number of cores. Finally, we show that using a simple load balancing strategy, we can increase performance of general-purpose cores by 28%.
A subject-specific frequency band selection for efficient BCI- an interval type-2 fuzzy inference system approach

The Common Spatial Pattern (CSP) is an effective algorithm used in EEG based Brain Computer Interface (BCI) to extract discriminative features, however, its effectiveness depends upon the subject-specific frequency bands. Also, the generated features using CSP are non-stationary in nature. In this paper, we propose a Meta-cognitive Interval type-2 Neuro-Fuzzy Inference System to handle non-stationarity in CSP features with recursive band elimination to find subject-specific frequency bands, together known as (McIT2NFIS-RBE). McIT2NFIS uses the non-stationary features generated by CSP as its input and models it as uncertainty using Interval type-2 fuzzy sets in the antecedent of fuzzy rules. The recursive band elimination (RBE) employs the McIT2NFIS training algorithm to recursively eliminate all the features of a band, one at a time. It aims to improve the performance by removing features of a band one at a time, whose elimination will not have any effect on the training performance. The performance of McIT2NFIS-RBE is evaluated using the publicly available dataset-IIa from BCI competition dataset IV [26]. The results highlight the performance of McIT2NFIS-RBE over other algorithms.
Indonesian Traditional Meatball

Indonesian traditional meat balls (bakso) can be classified as traditional restructured meat and it is produced by mixing fine ground meat, cooking salt, garlic and tapioca starch into a batter which is then formed into balls ranging in size from a marble to a ping-pong ball before they are cooked in boiling water. The consumer’s acceptances were influenced by the quality of bakso, location of sale, price and product accessibility. Whilst the “unique taste and promotional tools strategies” offered by cottage meatballs processors were positively related to their education level. Early and late post mortem meats as well as frozen meat are suitable as the main raw material in bakso production. Bakso made from late post mortem (LPM) had similar textural properties compared to the one prepared using early post mortem meat (EPM) although it had a higher elasticity especially when 15% tapioca starch added during preparation of those products. The micrograph of EPM and LPM bakso showed that myosin and actomyosin network appears as thin thread lines or protein strands that interconnect between one another, forming a web-like net matrix, while the tapioca granules appear as dense granules aggregated into one another. The non-meat ingredients especially tapioca starch and other starches which can be used as substitution material of tapioca starch were also discussed. The addition of 10–15% tapioca starch and boiling temperature of 90oC gave the best bakso quality.
Role of the Perigenual Anterior Cingulate and Orbitofrontal Cortex in Contingency Learning in the Marmoset

Two learning mechanisms contribute to decision-making: goal-directed actions and the “habit” system, by which action-outcome and stimulus-response associations are formed, respectively. Rodent lesion studies and human neuroimaging have implicated both the medial prefrontal cortex (mPFC) and the orbitofrontal cortex (OFC) in the neural basis of contingency learning, a critical component of goal-directed actions, though some published findings are conflicting. We sought to reconcile the existing literature by comparing the effects of excitotoxic lesions of the perigenual anterior cingulate cortex (pgACC), a region of the mPFC, and OFC on contingency learning in the marmoset monkey using a touchscreen-based paradigm, in which the contingent relationship between one of a pair of actions and its outcome was degraded selectively. Both the pgACC and OFC lesion groups were insensitive to the contingency degradation, whereas the control group demonstrated selectively higher performance of the nondegraded action when compared with the degraded action. These findings suggest the pgACC and OFC are both necessary for normal contingency learning and therefore goal-directed behavior.