Miracle-dz/UniFAR-FTUs huggingface dataset:
Idle Port Scanning and Non-interference Analysis of Network Protocol Stacks Using Model Checking

Idle port scanning uses side-channel attacks to bounce scans off of a "zombie" host to stealthily scan a victim IP address or infer IP-based trust relationships between the zombie and victim. We present results from building a transition system model of a network protocol stack for an attacker, victim, and zombie, and testing this model for non-interference properties using model checking. Two new methods of idle scans resulted from our modeling effort, based on TCP RST rate limiting and SYN caches, respectively. Through experimental verification of these attacks, we show that it is possible to scan victims which the attacker is not able to route packets to, meaning that protected networks or ports closed by firewall rules can be scanned. This is not possible with the one currently known method of idle scan in the literature that is based on non-random IPIDs. For the future design of network protocols, a notion of trusted vs. untrusted networks and hosts (based on existing IP-based trust relationships) will enable shared, limited resources to be divided. For a model complex enough to capture the details of each attack and where a distinction between trusted and untrusted hosts can be made, we modeled RST rate limitations and a split SYN cache structure. Non-interference for these two resources was verified with symbolic model checking and bounded model checking to depth 1000, respectively. Because each transtion is roughly a packet, this demonstrates that the two respective idle scans are ameliorated by separating these resources.
Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice

Proteomic approaches require simple and efficient protein purification methodologies that are amenable to high throughput. Biotinylation is an attractive approach for protein complex purification due to the very high affinity of avidin/streptavidin for biotinylated templates. Here, we describe an approach for the single-step purification of transcription factor complex(es) based on specific in vivo biotinylation. We expressed the bacterial BirA biotin ligase in mammalian cells and demonstrated very efficient biotinylation of a hematopoietic transcription factor bearing a small (23-aa) artificial peptide tag. Biotinylation of the tagged transcription factor altered neither the factor's protein interactions or DNA binding properties in vivo nor its subnuclear distribution. Using this approach, we isolated the biotin-tagged transcription factor and at least one other known interacting protein from crude nuclear extracts by direct binding to streptavidin beads. Finally, this method works efficiently in transgenic mice, thus raising the prospect of using biotinylation tagging in protein complex purification directly from animal tissues. Therefore, BirA-mediated biotinylation of tagged proteins provides the basis for the single-step purification of proteins from mammalian cells.
Rationale for using apolipoprotein B and apolipoprotein A-I as indicators of cardiac risk and as targets for lipid-lowering therapy.

This editorial refers to ‘Prognostic value of apolipoprotein B and A-I in the prediction of myocardial infarction in middle-aged men and women: results from the MONICA/KORA Augsburg cohort study’† by C. Meisinger et al. , on page 271 Although low density lipoprotein (LDL) is recognized as the primary lipid-related risk factor, and therefore the primary target for lipid-lowering therapy,1–4 there are in fact several limitations of only using LDL cholesterol (LDL-C) as the primary risk variable.5,6 New data are accumulating which speak in favour of apolipoproteins (apo) as more informative risk indicators/factors. ApoB, which indicates the number of potentially atherogenic lipoprotein particles, and apoA-I, which reflects anti-atherogenic high density lipoprotein (HDL) particles, may be additional lipid-related variables that more accurately indicate cardiovascular (CV) risk than LDL-C. Thus, several studies have shown that apoB and apoA-I are strong predictors of myocardial infarction (MI). 7–9 The two largest of these studies are the AMORIS7 and the INTERHEART9 studies which both show a very strong direct relation between a high apoB/apoA-I ratio and an increased risk of fatal MI7 and acute MI (AMI). 9 Meisinger et al. 10 add another piece of important information along the same lines. ### Physiological and pathophysiological aspects of apoB and apoA-I metabolism ApoB is present in very low density lipoproteins (VLDL), intermediate density lipoproteins (IDL), large buoyant LDL, and small dense LDL (sd-LDL), with one molecule of apoB in each of these atherogenic particles. Thus, total apoB reflects the total number of atherogenic particles ( Figure 1 ). It is the apoB in the particles that leads to entrapment of these lipoproteins in the arterial wall. ApoB produced in the liver also stabilizes and allows the transport of cholesterol and triglycerides in plasma VLDL, IDL, large buoyant LDL, and sd-LDL ( Figure 1 ). In addition, apoB serves as the ligand … *Corresponding author. E-mail address : goran.walldius{at}astrazeneca.com
Protection against Anthrax Toxemia by Hexa-d-Arginine In Vitro and In Vivo

ABSTRACT The anthrax toxin protective antigen precursor is activated by proteolytic cleavage by furin or a furin-like protease. We present here data demonstrating that the small stable furin inhibitor hexa-d-arginine amide delays anthrax toxin-induced toxemia both in cells and in live animals, suggesting that furin inhibition may represent a reasonable avenue for therapeutic intervention in anthrax.
Implementation of Linear-Phase FIR Filters for a Rational Sampling-Rate Conversion Utilizing the Coefficient Symmetry

This paper proposes an efficient structure for implementing a linear-phase finite-impulse-response (FIR) filter of an arbitrary order N for the sampling-rate conversion by a rational factor of L/M , where L(M) is the integer upsampling (down-sampling) factor to be performed before (after) the actual filter. In this implementation, the coefficient symmetry of the linear-phase filter is exploited as much as possible and the number of delay elements is kept as low as possible while utilizing the following facts. When increasing (decreasing) the sampling rate by a factor of L(M), only every Lth input sample has a nonzero value (only every M th output sample has to be evaluated). In this way, the number of required multiplications per output sample is reduced approximately by a factor of two compared with the conventional polyphase implementation. The proposed implementation is first illustrated using two examples. Based on these examples, guidelines are then given on how to efficiently realize an Nth-order linear-phase FIR filter for a sampling-rate converter having an arbitrary rational conversion factor L/M. Finally, the implementation complexity of the proposed approach is evaluated and some examples are included, showing the efficiency of the proposed implementation compared with other existing ones.
Activity dynamics and behavioral correlates of CA3 and CA1 hippocampal pyramidal neurons

The CA3 and CA1 pyramidal neurons are the major principal cell types of the hippocampus proper. The strongly recurrent collateral system of CA3 cells and the largely parallel‐organized CA1 neurons suggest that these regions perform distinct computations. However, a comprehensive comparison between CA1 and CA3 pyramidal cells in terms of firing properties, network dynamics, and behavioral correlations is sparse in the intact animal. We performed large‐scale recordings in the dorsal hippocampus of rats to quantify the similarities and differences between CA1 (n > 3,600) and CA3 (n > 2,200) pyramidal cells during sleep and exploration in multiple environments. CA1 and CA3 neurons differed significantly in firing rates, spike burst propensity, spike entrainment by the theta rhythm, and other aspects of spiking dynamics in a brain state‐dependent manner. A smaller proportion of CA3 than CA1 cells displayed prominent place fields, but place fields of CA3 neurons were more compact, more stable, and carried more spatial information per spike than those of CA1 pyramidal cells. Several other features of the two cell types were specific to the testing environment. CA3 neurons showed less pronounced phase precession and a weaker position versus spike‐phase relationship than CA1 cells. Our findings suggest that these distinct activity dynamics of CA1 and CA3 pyramidal cells support their distinct computational roles. © 2012 Wiley Periodicals, Inc.
Safety Information Mining — What can NLP do in a disaster—

This paper describes efforts of NLP researchers to create a system to aid the relief efforts during the 2011 East Japan Earthquake. Speciﬁcally, we created a system to mine information regarding the safety of people in the disaster-stricken area from Twitter, a massive yet highly unorganized information source. We describe the large scale collaborative effort to rapidly create robust and effective systems for word segmentation, named entity recognition, and tweet classiﬁcation. As a result of our efforts, we were able to effectively deliver new information about the safety of over 100 people in the disaster-stricken area to a central repository for safety information.
VARIABLE SODIUM ABSORPTION IN A LOW-EXTINCTION TYPE Ia SUPERNOVA,

Recent observations have revealed that some Type Ia supernovae exhibit narrow, time-variable Na i D absorption features. The origin of the absorbing material is controversial, but it may suggest the presence of circumstellar gas in the progenitor system prior to the explosion, with significant implications for the nature of the supernova (SN) progenitors. We present the third detection of such variable absorption, based on six epochs of high-resolution spectroscopy of the Type Ia supernova SN 2007le from the Keck I Telescope and the Hobby–Eberly Telescope. The data span a time frame of approximately three months, from 5 days before maximum light to 90 days after maximum. We find that one component of the Na i D absorption lines strengthened significantly with time, indicating a total column density increase of ∼2.5 × 1012 cm−2. The data limit the typical timescale for the variability to be more than 2 days but less than 10 days. The changes appear to be most prominent after maximum light rather than at earlier times when the ultraviolet flux from the SN peaks. As with SN 2006X, we detect no change in the Ca ii H and K absorption lines over the same time period, rendering line-of-sight effects improbable and suggesting a circumstellar origin for the absorbing material. Unlike the previous two supernovae exhibiting variable absorption, SN 2007le is not highly reddened (EB − V = 0.27 mag), also pointing toward circumstellar rather than interstellar absorption. Photoionization calculations show that the data are consistent with a dense (107 cm−3) cloud or clouds of gas located ∼0.1 pc (3 × 1017 cm) from the explosion. These results broadly support the single-degenerate scenario previously proposed to explain the variable absorption, with mass loss from a nondegenerate companion star responsible for providing the circumstellar gas. We also present possible evidence for narrow Hα emission associated with the SN, which will require deep imaging and spectroscopy at late times to confirm.
The construction system of the brain

The ability to construct a hypothetical situation in one's imagination prior to it actually occurring may afford greater accuracy in predicting its eventual outcome. The recollection of past experiences is also considered to be a reconstructive process with memories recreated from their component parts. Construction, therefore, plays a critical role in allowing us to plan for the future and remember the past. Conceptually, construction can be broken down into a number of constituent processes although little is known about their neural correlates. Moreover, it has been suggested that some of these processes may be shared by a number of other cognitive functions including spatial navigation and imagination. Recently, novel paradigms have been developed that allow for the isolation and characterization of these underlying processes and their associated neuroanatomy. Here, we selectively review this fast-growing literature and consider some implications for remembering the past and predicting the future.
Generalizing Smoothness Constraints from Discrete Samples

We study how certain smoothness constraints, for example, piecewise continuity, can be generalized from a discrete set of analog-valued data, by modifying the error backpropagation, learning algorithm. Numerical simulations demonstrate that by imposing two heuristic objectives (1) reducing the number of hidden units, and (2) minimizing the magnitudes of the weights in the network during the learning process, one obtains a network with a response function that smoothly interpolates between the training data.
Frequency and risks of changes to clones

Code Clones - duplicated source fragments - are said to increase maintenance effort and to facilitate problems caused by inconsistent changes to identical parts. While this is certainly true for some clones and certainly not true for others, it is unclear how many clones are real threats to the system's quality and need to be taken care of. Our analysis of clone evolution in mature software projects shows that most clones are rarely changed and the number of unintentional inconsistent changes to clones is small. We thus have to carefully select the clones to be managed to avoid unnecessary effort managing clones with no risk potential.
Six degrees of freedom object pose estimation with fusion data from a time-of-flight camera and a color camera

Object six Degrees of Freedom (6DOF) pose estimation is a fundamental problem in many practical robotic applications, where the target or an obstacle with a simple or complex shape can move fast in cluttered environments. In this thesis, a 6DOF pose estimation algorithm is developed based on the fused data from a time-of-flight camera and a color camera. The algorithm is divided into two stages, an annealed particle filter based coarse pose estimation stage and a gradient decent based accurate pose optimization stage. In the first stage, each particle is evaluated with sparse representation. In this stage, the large inter-frame motion of the target can be well handled. In the second stage, the range data based conventional Iterative Closest Point is extended by incorporating the target appearance information and used for calculating the accurate pose by refining the coarse estimate from the first stage. For dealing with significant illumination variations during the tracking, spherical harmonic illumination modeling is investigated and integrated into both stages. The robustness and accuracy of the proposed algorithm are demonstrated through experiments on various objects in both indoor and outdoor environments. Moreover, real-time performance can be achieved with graphics processing unit acceleration.
Phosphor-based carrying capacity ofRiam Kanan river, South Kalimantan on caged fish farming

Caged fish farming at Riam Kanan Rivers, South Kalimantan has been done by the local farmers since 1986. The huge profit from this business triggers exploitation of the rivers without environmental consideration. As a consequence, it increased the fish mortality rate and the decrease of fish farmers’ income. In order to control the number of fish cages, a study in regard of its condition and/or carrying capacity is needed. The objective of this study was to estimate the amount of phosphorus (P) waste produced by the fish farming activity. The research was conducted from six cages with the size of 2.5 x 1.75 x 1 m: three cages with capacity of 220 fish per cage and the rest of 3 cages with capacity of 500 fish per cage. Cultivated fish is common carp (Cyprinus carpio L.) with the size of 57 cm long. Two times feeding per day with 5% body weight was applied. The cultivation was done for 16 weeks. The daily distribution of P of the caged fish farming was calculated based on the total amount of leftover food and the feces in 12 hours. The weight of leftover food and the feces, collected from the net surrounding the cages, were sampled every two weeks. The result indicated that the total P increased with the length cultivation. The total amount of P in every cage with capacity of 220 and 500 fish were approximately 0.035 g day and 0.207 g day, respectively. Hence, the optimum number of cages on Riam Kanan Rivers based on the existing P was as follow, cages with 220 and 500 fish were 60-64 and 10-12 units per 100 m, respectively.
Minimax estimators dominating the least-squares estimator

We present several analytical and numerical results demonstrating the superiority of minimax estimators over least-squares (LS) estimation. We show that, for any bounded parameter set, a linear minimax estimator achieves lower mean-squared error than the LS estimator, over the entire parameter set. When a parameter set is unknown, we propose to estimate the parameter set from the data, and show that in many cases, the obtained blind minimax estimator still dominates the LS estimator. The results are related to and compared with other LS-dominating estimators, such as the James-Stein estimator.
SCODE: A Secure Coordination-Based Data Dissemination to Mobile Sinks in Sensor Networks

For many sensor network applications such as military, homeland security, it is necessary for users (sinks) to access sensor networks while they are moving. However, sink mobility brings new challenges to secure routing in large-scale sensor networks. Mobile sinks have to constantly propagate their current location to all nodes, and these nodes need to exchange messages with each other so that the sensor network can establish and maintain a secure multi-hop path between a source node and a mobile sink. This causes significant computation and communication overhead for sensor nodes. Previous studies on sink mobility have mainly focused on efficiency and effectiveness of data dissemination without security consideration. In this paper, we propose a secure and energy-efficient data dissemination protocol — Secure COodination-based Data dissEmination (SCODE) — for mobile sinks in sensor networks. We take advantages of coordination networks (grid structure) based on Geographical Adaptive Fidelity (GAF) protocol to construct a secure and efficient routing path between sources and sinks. Our security analysis demonstrates that the proposed protocol can defend against common attacks in sensor network routing such as replay attacks, selective forwarding attacks, sinkhole and wormhole, Sybil attacks, HELLO flood attacks. Our performance evaluation both in mathematical analysis and simulation shows that the SCODE significantly reduces communication overhead and energy consumption while the latency is similar compared with the existing routing protocols, and it always delivers more than 90 percentage of packets successfully.
Decidability of context-explicit security protocols

An important problem in the analysis of security protocols is that of checking whether a protocol preserves secrecy, i.e., no secret owned by the honest agents is unintentionally revealed to the intruder. This problem has been proved to be undecidable in several settings. In particular, Durgin et al. prove the undecidability of the secrecy problem in the presence of an unbounded set of nonces, even when the message length is bounded. In this paper we prove that even in the presence of an unbounded set of nonces the secrecy problem is decidable for a reasonable subclass of protocols, which we call context-explicit protocols.
Pretransplant serum C-reactive protein and the risk of chronic allograft nephropathy in renal transplant recipients: a pilot case-control study.

Multiple factors contribute to the development of chronic allograft nephropathy (CAN) in renal transplant recipients, and atherogenesis is considered to be an important pathologic process contributing to the development of this disease. There is growing acknowledgment of the role of inflammation in the pathogenesis of atherosclerosis, and markers of inflammation, such as C-reactive protein (CRP), have been shown to predict atherosclerotic vascular disease in the general and end-stage renal disease populations. In this pilot study, we hypothesized that elevations in pretransplant concentrations of CRP predict an increased incidence of CAN after renal transplantation. This case-control study compared pretransplant CRP levels in patients with allograft dysfunction and biopsy-proven CAN (n = 15) with a control group of transplant recipients with normal allograft function (n = 43). The median concentration of serum CRP was significantly higher in the CAN versus the control patients (13.1 +/- 3.9 mg/L versus 3.5 +/- 2.5 mg/L; P = 0.01). This difference was sustained when restricting to patients who did not experience acute rejection. When dividing the patients into tertiles based on CRP concentration, the adjusted risk of CAN increased more than threefold with each increment in CRP by tertile (adjusted odds ratio, 3.16; P = 0.03). The findings of our pilot study show an association between pretransplant elevations of CRP and CAN in end-stage renal disease patients who go on to receive a renal transplant. Cohort studies in larger groups of transplant patients are needed to confirm a causal pathway between pretransplant inflammation, atherogenesis, and CAN.
Developing, evaluating, and refining an automatic generator of diagnostic multiple choice cloze questions to assess children's comprehension while reading*

Abstract We describe the development, pilot-testing, refinement, and four evaluations of Diagnostic Question Generator (DQGen), which automatically generates multiple choice cloze (fill-in-the-blank) questions to test children's comprehension while reading a given text. Unlike previous methods, DQGen tests comprehension not only of an individual sentence but of the context preceding it. To test different aspects of comprehension, DQGen generates three types of distractors: ungrammatical distractors test syntax; nonsensical distractors test semantics; and locally plausible distractors test inter-sentential processing. (1) A pilot study of DQGen 2012 evaluated its overall questions and individual distractors, guiding its refinement into DQGen 2014. (2) Twenty-four elementary students generated 200 responses to multiple choice cloze questions that DQGen 2014 generated from forty-eight stories. In 130 of the responses, the child chose the correct answer. We define the distractiveness of a distractor as the frequency with which students choose it over the correct answer. The incorrect responses were consistent with expected distractiveness: twenty-seven were plausible, twenty-two were nonsensical, fourteen were ungrammatical, and seven were null. (3) To compare DQGen 2014 against DQGen 2012, five human judges categorized candidate choices without knowing their intended type or whether they were the correct answer or a distractor generated by DQGen 2012 or DQGen 2014. The percentage of distractors categorized as their intended type was significantly higher for DQGen 2014. (4) We evaluated DQGen 2014 against human performance based on 1,486 similarly blind categorizations by twenty-seven judges of sixteen correct answers, forty-eight distractors generated by DQGen 2014, and 504 distractors authored by twenty-one humans. Surprisingly, DQGen 2014 did significantly better than humans at generating ungrammatical distractors and marginally better than humans at generating nonsensical distractors, albeit slightly worse at generating plausible distractors. Moreover, vetting DQGen 2014's output and writing distractors only when necessary would halve the time to write them all, and produce higher quality distractors.