Miracle-dz/UniFAR-FTUs huggingface dataset:
Accurate Modeling of The Siemens S7 SCADA Protocol For Intrusion Detection And Digital Forensic

The Siemens S7 protocol is commonly used in SCADA systems for communications between a Human Machine Interface (HMI) and the Programmable Logic Controllers (PLCs). This paper presents a model-based Intrusion Detection Systems (IDS) designed for S7 networks. The approach is based on the key observation that S7 trac to and from a specic PLC is highly periodic; as a result, each HMI-PLC channel can be modeled using its own unique Deterministic Finite Automaton (DFA). The resulting DFA-based IDS is very sensitive and is able to ag anomalies such as a message appearing out of its position in the normal sequence or a message referring to a single unexpected bit. The intrusion detection approach was evaluated on trac from two production systems. Despite its high sensitivity, the system had a very low false positive rate - over 99.82% of the trac was identied as normal.
Xhosa-English Machine Translation : Working with a Low-Resource Language

This report details the author’s experiences as a Distributed Research Experience for Undergraduates (DREU) summer research intern at Carnegie Mellon University’s Language Technologies Institute. Under the guidance of Prof. Carolyn Rosé, the author attempted to implement a phrase-based translation (i.e., statistical machine translation, or SMT) system for translating Xhosa text into English using the MOSES toolkit. Xhosa (isiXhosa) is a Bantu language widely used in South Africa; it is a low-resource language for which there is not a bevy of widely available language resources such as dictionaries, morphological analyzers, and so forth. Consequently, the author’s work focuses heavily on the process of putting together a parallel text, or bitext, on which a working translation model could be trained.
Effect of pesticides on the population of Azospirillum sp. and on ammonification rate in two soils planted to groundnut (Arachis hypogaea L.)

Pesticides are usually applied simultaneously or serially for groundnut (Arachis hypogaea L.) crop protection. This type of pesticide application often leads to a combined contamination of pesticides and their residues in the soil. Pesticides used in groundnut cultivation - monocrotophos and chlorpyrifos, singly and in combination with mancozeb and carbendazim, respectively - were tested for their effects on the population of Azospirillum sp. and ammonification in two soils planted to groundnut in the Anantapur District of Andhra Pradesh, India. The size of the Azospirillum sp. population was initially low in both soils. Application of pesticides, singly and in combination up to 5.0 kg ha-1 , significantly increased the population of Azospirillum sp. after 7 and 14 days of incubation in vertisol soil, whereas in laterite soil, the application of pesticides in the same combination up to 2.5 kg ha-1 increased the population of Azospirillum sp. in similar conditions. Mineralization of peptone-nitrogen was profoundly increased when soil was treated with pesticides, singly or in combination, at 2.5 kg ha-1 in both soils. Vertisol soil that received monocrotophos and chlorpyrifos singly at 5.0 kg ha-1 showed a considerable increase in ammonification rate after 14 days of incubation. Due to the synergistic and additive interactions between pesticides and microorganisms, the population of Azospirillum sp. and the rate of ammonification increased at particular concentrations of pesticides (i.e 2.5 to 5.0 kg ha-1), but at higher concentrations (7.5 and 10.0 kg ha-1) the
Categories of ΔF508 homozygous cystic fibrosis twin and sibling pairs with distinct phenotypic characteristics

Abstract Cystic fibrosis (CF), the most common severe autosomal recessive trait among Caucasians, is caused by molecular lesions in the cystic fibrosis transmembrane conductance regulator gene (CFTR). The course of the multi-organ disease CF is highly variable, suggesting the influence of environmental factors and/or modulating genes other than CFTR on the disease phenotype. To evaluate the cause of CF disease variability, the European CF Twin and Sibling Study collected data on two clinical parameters most sensitive for the course and prognosis of CF, ie weight predicted for height (wfh)% (representative for the nutritional status) and FEVPerc (representative for the pulmonary status) for a cohort of 277 sibling pairs, 12 pairs of dizygous twins and 29 pairs of monozygous twins. Of these 318 CF twin and sib pairs, 114 were reported to be homozygous for the most frequent CF disease-causing lesion, ΔF508. Intra-pair discordance was assessed by the intra-pair differences with wfh% and FEVPerc and by DELTA, a composite parameter defined by linear combination of wfh% and FEVPerc in order to describe discordance with respect to the overall disease severity. Monozygous twins had a significantly lower DELTA than dizygous twins (P = 0.05) indicating that CF disease severity is modulated by an inherited component in addition to the CFTR gene itself. Extreme phenotypes are considered to be more informative for the analysis of any quantitative trait. Thus, we aimed to quantify disease severity and intra-pair discordance in order to select pairs with the extreme phenotypes DIS (discordant patient pairs), CON+ (concordant and mildy affected patient pairs) and CON− (concordant and severely affected patient pairs). The algorithm reliably discriminated between pairs DIS, CON+ and CON− among the cohort of ΔF508 homozygotes. The selected pairs from these categories demonstrated non-overlapping properties for wfh%, FEVPerc and the intra-pair difference of both parameters. Twin Research (2000) 3, 277–293.
Cross-coupling on microstrip line for substrate integrated waveguide (SIW) quasi-elliptic bandpass filter

This paper proposed a quasi-elliptic bandpass filter on substrate integrated waveguide (SIW) cavity with cross-coupling structure using microstrip line. Etched slots on the SIW cavity are used to produce electric coupling between two adjacent SIW resonators, the cross-coupling is obtained by a microstrip-line with embedded stubs above the SIW cavity. By using cross-coupling and embedded stubs, a SIW filter is constituted with transmission zeros at both sides of the passband. Finally, a third-order SIW quasi-elliptic filter at 3.7GHz is designed and fabricated in a two-layer substrate. The measured results are found in good agreement with the simulated ones.
Hydrogen peroxide induces association between glyceraldehyde 3‐phosphate dehydrogenase and phospholipase D2 to facilitate phospholipase D2 activation in PC12 cells

Oxidative stress or signaling is widely implicated in apoptosis, ischemia and mitogenesis. Previously, our group reported that the hydrogen peroxide (H2O2)‐dependent activation of phospholipase D2 (PLD2) in PC12 cells is involved in anti‐apoptotic effect. However, the precise mechanism of PLD2 activation by H2O2 was not revealed. To find H2O2‐dependent PLD2‐regulating proteins, we immunoprecipitated PLD2 from PC12 cells and found that glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) coimmunoprecipitated with PLD2 upon H2O2 treatment. This interaction was found to be direct by in vitro reconstitution of purified GAPDH and PLD2. In vitro studies also indicated that PLD2‐associated GAPDH was modified on its reactive cysteine residues. Koningic acid, an alkylator of GAPDH on catalytic cysteine residue, also increased interaction between the two proteins in vitro and enhanced PLD2 activity in PC12 cells. Blocking H2O2‐dependent modification of GAPDH with 3‐aminobenzamide resulted in the inhibition of the GAPDH/PLD2 interaction and attenuated H2O2‐induced PLD2 activation in PC12 cells. From the results, we suggest that H2O2 modifies GAPDH on its catalytic cysteine residue not only to inactivate the dehydrogenase activity of GAPDH but also to endow GAPDH with the ability to bind PLD2 and the resulting association is involved in the regulation of PLD2 activity by H2O2.
A di‐leucine‐based motif in the cytoplasmic tail of LIMP‐II and tyrosinase mediates selective binding of AP‐3

Among the various coats involved in vesicular transport, the clathrin associated coats that contain the adaptor complexes AP‐1 and AP‐2 are the most extensively characterized. The function of the recently described adaptor complex AP‐3, which is similar to AP‐1 and AP‐2 in protein composition but does not associate with clathrin, is not known. By monitoring surface plasmon resonance we observed that AP‐3 is able to interact with the tail of the lysosomal integral membrane protein LIMP‐II and that this binding depends on a DEXXXLI sequence in the LIMP‐II tail. Furthermore, AP‐3 bound to the cytoplasmic tail of the melanosome‐associated protein tyrosinase which contains a related EEXXXLL sequence. The tails of LIMP‐II and tyrosinase either did not interact, or only interacted poorly, with AP‐1 or AP‐2. In contrast, the cytoplasmic tails of other membrane proteins containing di‐leucine and/or tyrosine‐based sorting signals did not bind AP‐3, but AP‐1 and/or AP‐2. This points to a function of AP‐3 in intracellular sorting to lysosomes and melanosomes of a subset of cargo proteins via di‐leucine‐based sorting motifs.
Compressive Sampling Recovery for Natural Images

Compressive sampling (CS) is a novel data collection and coding theory which allows us to recover sparse or compressible signals from a small set of measurements. This paper presents a new model for natural image recovery, in which the smooth l0 norm and the approximate total-variation (TV) norm are adopted simultaneously. By using one-order gradient decrease, the speed of algorithm for this new model can be guaranteed. Experimental results demonstrate that the principle of the model is correct and the performance is as good as that based on TV model. The computing speed of the proposed method is two orders of magnitude faster than that of interior point method and two times faster than that of the Nesta optimization based on TV model.
The Village in the Jungle

in the text as well as in tables. Punekar presents an abundance of data; one wishes for more analysis, interpretation, and ethnographic detail along with the statistics. Punekar's major conclusion is that language ethnicity provides the primarysource of identity for each group. Intimacy is basically restricted to those who speak one's mother tongue. Formality defines the relationship across linguistic boundaries. Dealing with this as dyadic and diglossic or multiglossic would provide greater depth to the analysis. In addition, one wishes for more data showing language use in a variety of intimate and formal situations. Although this data would be likely to support Punekar's conclusions, a differentiation of language use into more situations than merely work and home—the classic formal and intimate situations—would be welcome. The finding that, beyond primary linguistic ethnicity, ties such as North versus South India and speaking a language linguistically similar to one's mother tongue do not form a basis for intimacy shows just how limited the assimilation between these groups has been. Indeed, Punekar believes that assimilation is inversely proportional to linguistic ethnicity. This book contains a wealth of data presented in a form that is valuable for others doing parallel research. For those not so involved, the book is too disjointed to provide an overall understanding of the North Indian migrant in Bangalore. Since Punekar has the data, one hopes she will continue her work along the lines she has begun. A more extensive analysis of linguistic ethnicity, the migrant at home, and the migrant at work—with correlations among these various categories— would be a welcome contribution to scholarship. Although the research is well documented in footnotes, the absence of a bibliography is regrettable. An appendix containing the questionnaire^) used in the field research would also be useful.
Carcass components at first estrus of rats on high-fat and low-fat diets: body water, protein, and fat.

Carcass analysis data show that weanling rats fed high-fat (HF) and low-fat (LF) diets until the day of first estrus had similar body compositions at estrus, although the HF rats had estrus significantly earlier and at a lighter body weight (P less than 0.01) than the LF-diet rats. Total water as percent of wet weight, protein as percent of wet weight, and the water/protein ratios of the HF- and LF-diet rats did not differ significantly, whereas the absolute amounts of body water and protein of the two diet groups differed significantly (P less than 0.01), in accord with means (+/- SEM) of total body water as percent of wet weight were 66.2 +/- 0.3% for the HF rats and 66.4 +/- 0.3% for the LF-diet rats, whereas the mean absolute total body water for the two diet groups was 69.7 +/- 2.2 g and 81.1 +/- 2.4 g, respectively (P less than 0.01). Carcass fat of the HF rats, 15.6 +/- 1.0 g, was identical with that of the LF-diet rats, 15.6 +/- 0.9 g. The HF rats were therefore relatively fatter, 14.6 +/- 0.6 wet weight %, than the LF-diet rats, 12.6 +/- 0.4 wet weight % (0.05 greater than P greater than 0.01). The percentage of water in the fat-free wet weight of the HF rats, 77.5 +/- 0.3%, was significantly (P less than 0.01) greater than that of the LF-diet rats, 76.1 +/- 0.3%. These data and the high percentages of total water of body weight show that at first estrus the HF- and LF-diet rats had not as yet attained an adult body composition, similar to the human female at menarche. Within each diet group, the percentages of total water/body weight, protein/wet weight and fat/wet weight, or fat/dry weight, did not change significantly with increasing age of estrus, whereas each absolute carcass component--body water, protein, and fat--increased significantly with increasing age of estrus. The carcass data support G.C. Kennedy's hypothesis that a metabolic signal, related to fat stores, is a signal for puberty in the rat and are in accord with the hypothesis that a critical body composition of fatness is necessary for estrus in the rat, as in the human female. The greater relative fatness of the HF-diet rats may be associated with higher levels of estrogen in the HF rats than in the LF-diet rats.
Fabrication of nanowires on orthogonal surfaces of microchannels and their effect on pool boiling

A novel microfabrication technique was developed to create silicon nanowires (SiNWs) on orthogonal surfaces of microchannels machined on top of a silicon wafer. Using a two-step metal-assisted etching process, the SiNW for the first time could be selectively fabricated on two different crystalline directions—the channel top and bottom surfaces oriented in the (1 0 0) direction while the sidewall surfaces in the (1 1 0) direction. Different SiNW etching conditions were investigated to get the optimal height, density, morphology and orientation for the SiNWs on the microchannels. The resulting samples were tested as heat sinks with water for their pool boiling applications. The sidewall SiNWs affected bubble behaviors and played important roles during the boiling process. The critical heat flux and the heat transfer coefficient both were thus improved compared to a plain silicon surface and a silicon chip with only microchannels.
Organization and Functions of Interacting Domains for Signaling by Protein-Protein Interactions

Information transfer from activated heterotrimeric guanine nucleotide-binding proteins (G proteins) to downstream effectors occurs through noncovalent protein-protein interactions. Such interactions involve multiple regions of contact between the G protein and the effector. Some of these regions mediate information transfer, as defined by their ability to change the activity of their downstream binding partners, whereas other interactions appear to contribute solely to binding affinity. Such modular configurations occur in functionally diverse proteins such as myosin and a regulator of the double-stranded DNA stimulated protein kinase (PKR) called PACT. In most cases, it appears that both charge complementarity and the architecture of the interacting surfaces provide the appropriate balance between specificity of interactions and their reversibility. Information transfer regions appear to display conformational flexibility in interactions. Such flexible interactions may be essential for the local conformational changes necessary to induce change in activity by an induced fit-type mechanism. Thus, a general mechanism for information transfer by protein-protein interactions could use specific regions that induce conformation changes in the downstream partner. Other binding regions may be arranged within the protein to impart specificity of recognition and thereby maintain overall contact between the partners during the conformational dynamics that occur in the signal-transfer process. This STKE review with two figures and 23 references discusses the molecular mechanisms by which information is transferred between interacting proteins in signaling pathways. Communication between protein partners in signaling pathways requires that the interactions between the partners be highly selective and that interactions be reversible. The reversibility of interactions ensures that interactions (and consequently communication) occur only when the system has received a signal at the receptor. The organization of interaction regions on signaling proteins into distinct domains that have specific and complementary spatial geometry in both proteins ensures that the interactions, even when of low affinity, can be highly selective. The ability of some of the interaction domains to actually transfer signals while others contribute only to overall binding affinity allows for information propagation through local conformational changes. Because this type of organization is observed in diverse proteins, such arrangements could constitute a general mechanism for information flow by noncovalent protein-protein interactions.
A general class of lower bounds in parameter estimation

A general class of Bayesian lower bounds on moments of the error in parameter estimation is formulated, and it is shown that the Cramer-Rao, the Bhattacharyya, the Bobrovsky-Zakai, and the Weiss-Weinstein lower bounds are special cases in the class. The bounds can be applied to the estimation of vector parameters and any given function of the parameters. The extension of these bounds to multiple parameter is discussed. >
Human Progesterone Receptor Displays Cell Cycle-Dependent Changes in Transcriptional Activity

ABSTRACT The human progesterone receptor (PR) contains multiple Ser-Pro phosphorylation sites that are potential substrates for cyclin-dependent kinases, suggesting that PR activity might be regulated during the cell cycle. Using T47D breast cancer cells stably transfected with an mouse mammary tumor virus (MMTV) chloramphenicol acetyltransferase reporter (Cat0) synchronized in different phases of the cell cycle, we found that PR function and phosphorylation is remarkably cell cycle dependent, with the highest activity in S phase. Although PR expression was reduced in the G2/M phase, the activity per molecule of receptor was markedly reduced in both G1 and G2/M phases compared to the results seen with the S phase of the cell cycle. Although PR is recruited to the MMTV promoter equivalently in the G1 and S phases, recruitment of SRC-1, SRC-3, and, consequently, CBP is reduced in G1 phase despite comparable expression levels of SRC-1 and SRC-3. In G2/M phase, site-specific phosphorylation of PR at Ser162 and at Ser294, a site previously reported to be critical for transcriptional activity and receptor turnover, was abolished. Treatment with the histone deacetylase inhibitor trichostatin A elevated G1 and G2/M activity to that of the S phase, indicating that the failure to recruit sufficient levels of active histone acetyltransferase is the primary defect in PR-mediated transactivation.
Comparative Study on Energy Consumption in Dynamic Window Secured Implicit Geographic Forwarding Routing Protocol

An Ideal WSNs should operate with the least possible energy required in order to increase the lifetime of the sensor nodes and at the same time, ensure network connectivity. But the Inherent power limitation makes power-awareness a critical requirement for WSN, this calls for the need to manage energy in sensor nodes. Also In order to ensure successful transmission of data from sensor node source to destination, it becomes necessary to maintain network availability. The network must be resilient to individual node failure which can happen due to zero power posses by the node and due to security attacks posed on the node and the network. Dynamic Window Secured Implicit Geographic Forwarding (DWSIGF) routing protocol has proven to be robust, efficient and resistant to some security attack which causes failure in network availability. However the extent to which energy is consumed in sensor nodes which deploys DWSIGF as its routing protocol has never been mentioned. In this research, we performed a comparative study on energy consumption in DWSIGF routing protocol. Using the first order radio model, we determined the energy consumed in a network. The protocol (DWSIGF) is matched up against its counterpart SIGF as the traffic is increased. Observation shows that DWSIGF due to the variable timing assigned to the CTS collection window, CTS signal fails to reach destination as collection window time expires, thus the need for retransmission. This in turn consumes more energy than the counterpart SIGF which has a fixed CTS collection time. The simulation work was done using Matlab 7.0. Energy consumed in the random variant of both protocols (DWSIGF and SIGF) was also observed to be higher than the priority variant of the protocols.
Identification of Genes Involved in the Biosynthesis of the Third and Fourth Sugars of the Methanococcus maripaludis Archaellin N-Linked Tetrasaccharide

ABSTRACT N-glycosylation is a protein posttranslational modification found in all three domains of life. Many surface proteins in Archaea, including S-layer proteins, pilins, and archaellins (archaeal flagellins) are known to contain N-linked glycans. In Methanococcus maripaludis, the archaellins are modified at multiple sites with an N-linked tetrasaccharide with the structure Sug-1,4-β-ManNAc3NAmA6Thr-1,4-β-GlcNAc3NAcA-1,3-β-GalNAc, where Sug is the unique sugar (5S)-2-acetamido-2,4-dideoxy-5-O-methyl-α-l-erythro-hexos-5-ulo-1,5-pyranose. In this study, four genes—mmp1084, mmp1085, mmp1086, and mmp1087—were targeted to determine their potential involvement of the biosynthesis of the sugar components in the N-glycan, based on bioinformatics analysis and proximity to a number of genes which have been previously demonstrated to be involved in the N-glycosylation pathway. The genes mmp1084 to mmp1087 were shown to be cotranscribed, and in-frame deletions of each gene as well as a Δmmp1086Δmmp1087 double mutant were successfully generated. All mutants were archaellated and motile. Mass spectrometry examination of purified archaella revealed that in Δmmp1084 mutant cells, the threonine linked to the third sugar of the glycan was missing, indicating a putative threonine transferase function of MMP1084. Similar analysis of the archaella of the Δmmp1085 mutant cells demonstrated that the glycan lacked the methyl group at the C-5 position of the terminal sugar, indicating that MMP1085 is a methyltransferase involved in the biosynthesis of this unique sugar. Deletion of the remaining two genes, mmp1086 and mmp1087, either singularly or together, had no effect on the structure of the archaellin N-glycan. Because of their demonstrated involvement in the N-glycosylation pathway, we designated mmp1084 as aglU and mmp1085 as aglV.