Miracle-dz/UniFAR-FTUs huggingface dataset:
Explorations in Sentence Fusion

The invention provides methods and compositions for expressing a recombinant gene in eukaryotic cells, especially fungi, preferably yeast. The invention provides transcriptional regulating elements having a novel nucleotide sequence which are capable of trancriptionally regulating the expression of a cis joined gene, typically in response to the availability of certain nutrients to the host cell. Preferred regulatory elements are responsive to nutrient depletion, particulary glucose, ethanol, phosphate or a nitrogen source. Nucleic acid constructs comprising such regulatory elements operably linked to recombinant genes, cells comprising such regulatory elements, and methods of producing recombinant protein in such cells are also provided. The invention discloses regulatory elements which are induced through the ras gene product. Accordingly, the disclosed expression systems also provide a convenient marker for ras gene function. Finally, the invention also provides methods and compositions for the diagnosis and treatment of fungal infection. In particular, the invention provides gp37-derived peptides encoded by YGP1 and gp37- selective binding agents, such as antibodies.
Impact Assessment of Hypothesized Cyberattacks on Interconnected Bulk Power Systems

The first-ever Ukraine cyberattack on power grid has proven its devastation by hacking into their critical cyber assets. With administrative privileges accessing substation networks/local control centers, one intelligent way of coordinated cyberattacks is to execute a series of disruptive switching executions on multiple substations using compromised supervisory control and data acquisition systems. These actions can cause significant impacts to an interconnected power grid. Unlike the previous power blackouts, such high-impact initiating events can aggravate operating conditions, initiating instability that may lead to system-wide cascading failure. A systemic evaluation of “nightmare” scenarios is highly desirable for asset owners to manage and prioritize the maintenance and investment in protecting their cyberinfrastructure. This survey paper is a conceptual expansion of real-time monitoring, anomaly detection, impact analyses, and mitigation framework that emphasizes on the resulting impacts, both on steady-state and dynamic aspects of power system stability. Hypothetically, we associate the combinatorial analyses of steady state on substations/components outages and dynamics of the sequential switching orders as part of the permutation. The expanded framework includes: 1) critical/non-critical combination verification; 2) cascade confirmation; and 3) combination re-evaluation. This paper ends with a discussion of the open issues for metrics and future design pertaining the impact quantification of cyber-related contingencies.
Mechanisms of Quinidine‐Induced Depression of Maximum Upstroke Velocity in Ovine Cardiac Purkinje Fibers

A major advance in understanding how quinidine depresses maximum upstroke velocity (Vmax) is the Hondeghem-Katzung mathematical model which incorporates voltage-independent rate constants for binding to and unbinding from resting, open, and inactive Na channels, and a voltage shift of −40 mV for the Hodgkin-Huxley h-kinetics of quinidine-associated Na channels. Using a double microelectrode voltage clamp technique to control transmembrane voltage and apply conditioning pulses, we found that quinidine blockade increased as transmembrane voltage became more positive in the range −60 to +40 mV, and that the rate of quinidine dissociation increased as transmembrane voltage became more negative in the range −60 to −140 mV. The relationship of Vmax to transmembrane voltage obtained at drive cycles from 500 msec to 20 seconds conformed to the model modified to include voltage-dependent rate constants without the postulated −40-mV shift for quinidine-associated channels. Thus binding of quinidine to inactive Na channels and unbinding from resting channels are both voltage-dependent and can explain frequency and voltage dependent actions of quinidine on Vmax without any voltage shift for quinidine-associated channels.
UC Irvine UC Irvine Electronic Theses and Dissertations Title Generating Formal Verification Properties from Natural Language Hardware Specifications

OF THE DISSERTATION Generating Formal Verification Properties from Natural Language Hardware Specifications By Christopher Bryant Harris Doctor of Philosophy in Electrical and Computer Engineering University of California, Irvine, 2015 Professor Ian G. Harris, Chair Verification of modern digital systems can consume up to 70% of the design cycle. Verification engineers must create formal properties which reflect correct operation from design specifications or other documents. This process of creating formal correctness properties from textual descriptions is a laborious task which is difficult to automate. In this work I investigate the creation of formal verification properties from textual descriptions written in natural language. I present two approaches that utilize natural language processing (NLP) and machine learning techniques for the automatic generation of verification properties. In the first approach a set of correctness properties expressed in natural language, called natural language assertions (NLAs), is divided into subsets of structurally similar sentences. A generalized formal property template for each subset is used to provide a mapping from each sentence to a well specified verification property. Experimental results show that this methodology reduces the number of formal properties which must be manually created by up to an order of magnitude. In the second approach I create a custom attributed formal grammar which captures the English semantics of a temporal tree logic. A translation system is implemented which uses this attribute grammar to perform a semantic parsing of NLAs. Attributes for each grammatical production in the parse tree are then used to build a fully specified formal xii property for each NLA. Experimental results show that valid formal properties are generated from English NLAs in over 90% of test cases. In evaluating the translation system it was observed that translation rates for NLAs are strongly dependent on the quality of the formal grammar used. High translation rates require a finely tuned custom grammar. To facilitate the creation of such a grammar I propose a new learning algorithm which automatically generates custom attribute grammars from a small set of NLAs and formal properties. This machine generated grammar is used in the NLA translation system to create formal properties from NLAs taken from two design documents for designs in the same product family. Experimental results show that the learned attribute grammar is of sufficient quality to successfully translate up to 88% of NLAs.
Tinmith-Hand: unified user interface technology for mobile outdoor augmented reality and indoor virtual reality

This paper presents a unified user interface technology, using 3D interaction techniques, constructive solid geometry and a glove-based menuing system, known as Tinmith-Hand, to support mobile outdoor augmented reality (AR) applications and indoor virtual reality (VR) applications. Tinmith-Hand uses similar concepts for both domains, so that AR and VR applications are consistent and simple to use. The future goal of this user interface is to allow collaboration between outdoor AR and indoor VR systems.
Mechanical alloying of FeAl intermetallic powder for metal injection moulding process

The Fe–48 at. -%Al powder used for powder injection moulding (PIM) was prepared by mechanical alloying in a high energy planetary ball mill and subsequent vacuum annealing. The effects of stearic acid (SA) as the process control agent on powder characteristics were investigated using X-ray diffractometer, laser particle size analysis and scanning electron microscopy. The dependence of solvent debinding efficiency of PIM feedstock on the powder characteristics was also studied. The results indicate that a low SA content for ball milling helps to prepare near spherical, coarse powder particles that exhibit good solvent debinding efficiency. On the contrary, a high SA content leads to thin layered, small particles with poor PIM solvent debinding efficiency. An intermediate SA content such as 1 wt-% makes the ball milled powder combine the advantageous characteristics for PIM process.
Preserving privacy in collaborative filtering through distributed aggregation of offline profiles

In recommender systems, usually, a central server needs to have access to users' profiles in order to generate useful recommendations. Having this access, however, undermines the users' privacy. The more information is revealed to the server on the user-item relations, the lower the users' privacy is. Yet, hiding part of the profiles to increase the privacy comes at the cost of recommendation accuracy or difficulty of implementing the method. In this paper, we propose a distributed mechanism for users to augment their profiles in a way that obfuscates the user-item connection to an untrusted server, with minimum loss on the accuracy of the recommender system. We rely on the central server to generate the recommendations. However, each user stores his profile offline, modifies it by partly merging it with the profile of similar users through direct contact with them, and only then periodically uploads his profile to the server. We propose a metric to measure privacy at the system level, using graph matching concepts. Applying our method to the Netflix prize dataset, we show the effectiveness of the algorithm in solving the tradeoff between privacy and accuracy in recommender systems in an applicable way.
Causality, mediation and time: a dynamic viewpoint

Summary. Time dynamics are often ignored in causal modelling. Clearly, causality must operate in time and we show how this corresponds to a mechanistic, or system, understanding of causality. The established counterfactual definitions of direct and indirect effects depend on an ability to manipulate the mediator which may not hold in practice, and we argue that a mechanistic view may be better. Graphical representations based on local independence graphs and dynamic path analysis are used to facilitate communication as well as providing an overview of the dynamic relations ‘at a glance’. The relationship between causality as understood in a mechanistic and in an interventionist sense is discussed. An example using data from the Swiss HIV Cohort Study is presented.
A Light-weight Method for Trace Analysis to Support Fault Diagnosis in Concurrent Systems

This paper discusses a light-weight approach to the analysis of traces of partially ordered events collected during the execution of a concurrent or distributed system through the use of XML technology. Traces contain information about the creation and termination of threads or objects and the exchange of messages and other types of communication among them. Traces are transformed according to property patterns, visualised and analysed to support fault diagnosis of concurrent systems. We present an approach using XML technology and report the findings of an initial industrial project.
Matrices With Small Coherence Using $p$-Ary Block Codes

In contrast to the vast amount of literature in random matrices in the field of compressed sensing, the subject of deterministic matrix design is at its early stages. Since these deterministic matrices are usually constructed using the polynomials in finite Galois fields, the number of rows (number of samples) is restricted to some specific integers such as prime powers. In this paper, besides extending a previous matrix design based on the binary BCH codes to the p-ary codes, we introduce matrices with wide variety of options for the number of rows. Simulation results demonstrate that these matrices perform almost as well as random matrices.
The Branched-Chain Amino Acid Transaminase Gene Family in Arabidopsis Encodes Plastid and Mitochondrial Proteins 1

Branched-chain amino acid transaminases (BCATs) play a crucial role in the metabolism of leucine, isoleucine, and valine. They catalyze the last step of the synthesis and/or the initial step of the degradation of this class of amino acids. In Arabidopsis, seven putative BCAT genes are identified by their similarity to their counterparts from other organisms. We have now cloned the respective cDNA sequences of six of these genes. The deduced amino acid sequences show between 47.5% and 84.1% identity to each other and about 30% to the homologous enzymes from yeast (Saccharomyces cerevisiae) and mammals. In addition, many amino acids in crucial positions as determined by crystallographic analyses of BCATs from Escherichia coli and human (Homo sapiens) are conserved in the AtBCATs. Complementation of a yeast bat1/ bat2 double knockout strain revealed that five AtBCATs can function as BCATs in vivo. Transient expression of BCAT:green fluorescent protein fusion proteins in tobacco (Nicotiana tabacum) protoplasts shows that three isoenzymes are imported into chloroplasts (AtBCAT-2, -3, and -5), whereas a single enzyme is directed into mitochondria (AtBCAT-1).
Are TCP extensions middlebox-proof?

Besides the traditional routers and switches, middleboxes such as NATs, firewalls, IDS or proxies have a growing importance in many networks, notably in entreprise and wireless access networks. Many of these middleboxes modify the packets that they process. For this, they to implement (a subset of) protocols like TCP. Despite the deployment of these middleboxes, TCP continues to evolve on the endhosts and little is known about the interactions between TCP extensions and the middleboxes. In this paper, we experimentally evaluate the interference between middleboxes and the Linux TCP stack. For this, we first propose MBtest, a set of Click elements that model middlebox behavior. We use it to experimentally evaluate how three TCP extensions interact with middleboxes. We also analyzes measurements of the interference between Multipath TCP and middleboxes in fifty different networks.
Damage Tolerance Capability of an Al-Cu-Mg-Ag Alloy (2139)

The effects of dispersoid forming elements on the mechanical properties of Al-Cu- Mg-Ag alloys are examined. It is found that a small amount of Zr addition is detrimental to the damage tolerance of Al-Cu-Mg-Ag alloys in artificially aged temper, while Mn addition is beneficial. The superior damage tolerance capability of Alloy 2139 is demonstrated by comparing it to other high performance alloys used for DT critical applications
Model-Based Reinforcement Learning in Continuous Environments Using Real-Time Constrained Optimization

Reinforcement learning for robot control tasks in continuous environments is a challenging problem due to the dimensionality of the state and action spaces, time and resource costs for learning with a real robot as well as constraints imposed for its safe operation. In this paper we propose a model-based reinforcement learning approach for continuous environments with constraints. The approach combines model-based reinforcement learning with recent advances in approximate optimal control. This results in a bounded-rationality agent that makes decisions in real-time by efficiently solving a sequence of constrained optimization problems on learned sparse Gaussian process models. Such a combination has several advantages. No high-dimensional policy needs to be computed or stored while the learning problem often reduces to a set of lower-dimensional models of the dynamics. In addition, hard constraints can easily be included and objectives can also be changed in real-time to allow for multiple or dynamic tasks. The efficacy of the approach is demonstrated on both an extended cart pole domain and a challenging quadcopter navigation task using real data.
Enhanced expression of ephrins and thrombospondins in the dermis of patients with early diffuse systemic sclerosis: potential contribution to perturbed angiogenesis and fibrosis.

OBJECTIVE To determine the skin and fibroblast expression of ephrins (EphB4 and EphrinB2) and thrombospondins (TSPs: TSP1 and TSP2) in patients with SSc. METHODS All experiments were performed in skin sections and dermal fibroblasts issued from control and clinically involved/non-involved SSc skin biopsies. Dermal fibroblasts were stimulated with hypoxia or TGF-β, or treated with TGF-β-neutralizing antibodies. Ephrin and TSP mRNA levels were assessed in skin tissue and dermal fibroblasts by in situ hybridization and quantitative RT-PCR, respectively, and protein levels were assessed by immunohistochemistry and western blots, respectively. RESULTS Enhanced ephrin and TSP mRNA and protein levels were observed in clinically involved SSc skin. EphrinB2, TSP1 and TSP2 mRNA and protein levels were also up-regulated in non-involved SSc skin. Similar mRNA and protein levels of ephrinB2 and EphB4 were detected in unstimulated and stimulated control and SSc dermal fibroblasts. TSP1 and TSP2 mRNA and protein levels were significantly increased in fibroblasts issued from involved and non-involved SSc skin. This up-regulation was not modified by hypoxic exposure, but was markedly reduced by the addition of TGF-β-neutralizing antibodies. Stimulation of healthy fibroblasts with TGF-β significantly increased TSP1 and TSP2 mRNA and protein levels. CONCLUSION EphB4 and EphrinB2 are up-regulated in clinically involved skin of SSc patients, suggesting their participation in SSc-perturbed angiogenesis. TSP1 and TSP2 are up-regulated in both clinically involved and non-involved SSc skin and are constitutively overexpressed in a TGF-β-dependent and hypoxia-independent manner in SSc dermal fibroblasts, suggesting their potential early contribution in SSc pathogenesis.
-angelic Choice for Process Algebra

The-angelic choice is an operator that captures the behaviour of the external choice of CSP in a branching time setting. The idea of the-angelic choice is to delay any choice until an observable action happens. In this way, this new operator avoids preemption introduced by internal actions (actions). It is studied in theories with abstraction, more precisely, branching bisimulation and-bisimulation and failure semantics. In addition, an ilustrative example of application is given.
RRB1 and RRB2 encode maize retinoblastoma-related proteins that interact with a plant D-type cyclin and geminivirus replication protein

Unlike mammalian and yeast cells, little is known about how plants regulate G1 progression and entry into the S phase of the cell cycle. In mammalian cells, a key regulator of this process is the retinoblastoma tumor suppressor protein (RB). In contrast, G1 control in Saccharomyces cerevisiae does not utilize an RB-like protein. We report here the cloning of cDNAs from two Zea mays genes, RRB1 and RRB2, that encode RB-related proteins. Further, RRB2 transcripts are alternatively spliced to yield two proteins with different C termini. At least one RRB gene is expressed in all the tissues examined, with the highest levels seen in the shoot apex. RRB1 is a 96-kDa nuclear protein that can physically interact with two mammalian DNA tumor virus oncoproteins, simian virus 40 large-T antigen and adenovirus E1A, and with a plant D-type cyclin. These associations are abolished by mutation of a conserved cysteine residue in RRB1 that is also essential for RB function. RRB1 binding potential is also sensitive to deletions in the conserved A and B domains, although differences exist in these effects compared to those of human RB. RRB1 can also bind to the AL1 protein from tomato golden mosaic virus (TGMV), a protein which is essential for TGMV DNA replication. These results suggest that G1 regulation in plant cells is controlled by a mechanism which is much more similar to that found in mammalian cells than that in yeast.
Association between Dietary Patterns and Depressive Symptoms Over Time: A 10-Year Follow-Up Study of the GAZEL Cohort

Background Data on the association between dietary patterns and depression are scarce. The objective of this study was to examine the longitudinal association between dietary patterns and depressive symptoms assessed repeatedly over 10 years in the French occupational GAZEL cohort. Methods A total of 9,272 men and 3,132 women, aged 45–60 years in 1998, completed a 35-item Food Frequency Questionnaire (FFQ) at baseline. Dietary patterns were derived by Principal Component Analysis. Depressive symptoms were assessed by the Center for Epidemiologic Studies Depression scale (CES-D) in 1999, 2002, 2005 and 2008. The main outcome measure was the repeated measures of CES-D. Longitudinal analyses were performed with logistic regression based on generalized estimating equations. Principal Findings The highest quartile of low-fat, western, high snack and high fat-sweet diets in men and low-fat and high snack diets in women were associated with higher likelihood of depressive symptoms at the start of the follow-up compared to the lowest quartile (OR between 1.16 and 1.50). Conversely, the highest quartile of traditional diet (characterized by fish and fruit consumption) was associated with a lower likelihood of depressive symptoms in women compared to the lowest quartile, with OR = 0.63 [95%CI, 0.50 to 0.80], as the healthy pattern (characterized by vegetables consumption) with OR = 0.72 [95%CI, 0.63 to 0.83] and OR = 0.75 [95%CI, 0.61 to 0.93] in men and women, respectively. However, there was probably a reverse causality effect for the healthy pattern. Conclusion This longitudinal study shows that several dietary patterns are associated with depressive symptoms and these associations track over time.
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BACKGROUND & AIMS The diagnostic criteria for celiac disease require small-bowel mucosal villous atrophy with crypt hyperplasia (Marsh III). However, mucosal damage develops gradually and patients may evince clinical symptoms before histologic changes appear. Endomysial antibodies are specific in predicting forthcoming villous atrophy. We hypothesized that patients with mild enteropathy but positive endomysial antibodies benefit from a gluten-free diet (GFD) similarly to patients with more severe enteropathy. METHODS Small-bowel endoscopy together with clinical evaluations was performed in all together 70 consecutive adults with positive endomysial antibodies. Of these, 23 had only mild enteropathy (Marsh I-II) and they were randomized either to continue on a gluten-containing diet or start a GFD. After 1 year, clinical, serologic, and histologic evaluations were repeated. A total of 47 participants had small-bowel mucosal lesions compatible with celiac disease (Marsh III), and these served as disease controls. RESULTS In the gluten-containing diet group (Marsh I-II) the small-bowel mucosal villous architecture deteriorated in all participants, and the symptoms and abnormal antibody titers persisted. In contrast, in the GFD group (Marsh I-II) the symptoms were alleviated, antibody titers decreased, and mucosal inflammation diminished equally to celiac controls (Marsh III). When the trial was completed, all participants chose to continue on a life-long GFD. CONCLUSIONS Patients with endomysial antibodies benefit from a GFD regardless of the degree of enteropathy. The diagnostic criteria for celiac disease need re-evaluation: endomysial antibody positivity without atrophy belongs to the spectrum of genetic gluten intolerance, and warrants dietary treatment.