Miracle-dz/UniFAR-FTUs huggingface dataset:
A Type System for Self-Recursion ( Extended Version )

A fundamental aspect of object-oriented languages is how recursive functions are defined. One semantic approach is to use simple record types and explicit recursion (i.e. fix) to define mutually recursive units of functionality. Another approach is to use records and recursive types to describe recursion through a “self” parameter. Many systems rely on both semantic approaches as well as combinations of universally quantified types, existentially quantified types, and mixin operators to encode patterns of method reuse, data encapsulation, and “open recursion” through self. These more complex mechanisms are needed to support many important use cases, but they often lack desirable theoretical properties, such as decidability, and can be difficult to implement, because of the equirecursive interpretation that identifies mu-types with their unfoldings. Furthermore, these systems do not apply to languages without explicit recursion (such as JavaScript, Python, and Ruby). In this paper, we present a statically typed calculus of functional objects called ISOLATE that can reason about a pattern of mixin composition without relying on an explicit fixpoint operation. To accomplish this, ISOLATE extends a standard isorecursive type system with a mechanism for checking the “mutual consistency” of a collection of functions, that is, that all of the assumptions about self are implied by the collection itself. We prove the soundness of ISOLATE via a type-preserving translation to a calculus with F-bounded polymorphism. Therefore, ISOLATE can be regarded as a stylized subset of the more expressive calculus that admits an interesting class of programs yet is easy to implement. In the future, we plan to investigate how other, more complicated forms of mixin composition (again, without explicit recursion) may be supported by lightweight type systems.
Flat ORAM: A Simplified Write-Only Oblivious RAM Construction for Secure Processor Architectures

Oblivious RAM (ORAM) is a cryptographic primitive which obfuscates the access patterns to a storage thereby preventing privacy leakage via access patterns. So far in the current literature only ‘fully functional’ ORAMs are widely studied which can protect, at a cost of considerable performance penalty, against the strong adversaries who have access to the memory address bus and can monitor all read and write operations. However, for weaker and more common adversaries who can learn the pattern of write accesses only (not reads), a fully functional ORAM turns out to be an overkill, since only write accesses need to be obfuscated. A simple ‘write-only’ ORAM is sufficient for such adversaries, and, more interestingly, is preferred as it can offer far more performance and energy efficiency than the fully functional ORAM. In this work, we present Flat ORAM: a simplified and efficient write-only ORAM scheme for secure processors. To the best of our knowledge, this is the first ever proposal of a write-only ORAM tailored for secure processor architectures. The proposed Flat ORAM avoids almost all the redundancy incurred by a Path ORAM, while seamlessly adopting its basic structures (e.g. Position Map, Stash) as well as crucial optimizations proposed over the past decade. Specific to writeonly ORAMs, we introduce a new ORAM structure called Occupancy Map (OccMap) which contains memory occupancy information vital for correctness and efficiency of our scheme. Our simulation results show that, on average, Flat ORAM only incurs a moderate slowdown of 2.9× over the insecure DRAM for memory intensive benchmarks among Splash2 and 1.5× for SPEC06. Compared to the closest existing writeonly ORAM scheme called HIVE, Flat ORAM offers ≈ 50% performance gain and 45-65% energy savings on average.
Free Bits and Non-Approximability ( Extended

This paper investigates the possibility that tight hardnes s of approximation results may be derived for several combinatorial optimization problems via the “pcp-connect ion” (a.k.a., the FGLSS-reduction [FGLSS]). We study the amortized free bit-complexity of probabilistic verifie rs and “invert the FGLSS-reduction” by showing that an NP-hardness result for the approximation of MaxClique to wi thin a factor ofN1=(g+1) would imply a probabilistic verifier for NP with logarithmic randomness and amortized fr ee-bit complexityg. In addition, we present a new proof system for NP in which the amortized free-bit complexi ty is 2 which yields (via the FGLSS-reduction) that approximating the clique to within a factor of N1=3 (in anN -vertex graph) is NP-hard. The new proof system is based on a new code and means for checking codewords. This machiner y is used to obtain improved non-approximability results for Max-SNP problems such as Max-2SAT, Max-3SAT, Ma x-CUT and Min-VC. This extended abstract provides less technical detail than customary. The interested reader is referred to our (124-pages) technical report [BGS]. Advanced Networking Laboratory, IBM T.J. Watson Research C enter, P.O. Box 704, Yorktown Heights, NY 10598, USA. e-mail : mihir@watson.ibm.com. y Department of Computer Science and Applied Mathematics, We izmann Institute of Sciences, Rehovot, Israel. e-mail: oded@wisdom. weizmann.ac. il. Partially supported by grant No. 92-00226 from the US–Isra el Binational Science Foundation (BSF), Jerusalem, Israel . z Research Division, IBM T.J. Watson Research Center, P.O. Bo x 218, Yorktown Heights, NY 10598, USA. e-mail: madhu@watson. ibm.com.
Robust Anomaly Detection Using Support Vector Machines

—Using the 1998 DARPA BSM data set collected at MIT’s Lincoln Labs to study intrusion detection systems, the performance of robust support vector machines (RSVMs) was compared with that of conventional support vector machines and nearest neighbor classiﬁers in separating normal usage proﬁles from intrusive proﬁles of computer programs. The results indicate the superiority of RSVMs not only in terms of high intrusion detection accuracy and low false positives but also in terms of their generalization ability in the presence of noise and running time.
Egocentric depth judgments in optical, see-through augmented reality

A fundamental problem in optical, see-through augmented reality (AR) is characterizing how it affects the perception of spatial layout and depth. This problem is important because AR system developers need to both place graphics in arbitrary spatial relationships with real-world objects, and to know that users will perceive them in the same relationships. Furthermore, AR makes possible enhanced perceptual techniques that have no real-world equivalent, such as x-ray vision, where AR users are supposed to perceive graphics as being located behind opaque surfaces. This paper reviews and discusses protocols for measuring egocentric depth judgments in both virtual and augmented environments, and discusses the well-known problem of depth underestimation in virtual environments. It then describes two experiments that measured egocentric depth judgments in AR. Experiment I used a perceptual matching protocol to measure AR depth judgments at medium and far-field distances of 5 to 45 meters. The experiment studied the effects of upper versus lower visual field location, the x-ray vision condition, and practice on the task. The experimental findings include evidence for a switch in bias, from underestimating to overestimating the distance of AR-presented graphics, at ~ 23 meters, as well as a quantification of how much more difficult the x-ray vision condition makes the task. Experiment II used blind walking and verbal report protocols to measure AR depth judgments at distances of 3 to 7 meters. The experiment examined real-world objects, real-world objects seen through the AR display, virtual objects, and combined real and virtual objects. The results give evidence that the egocentric depth of AR objects is underestimated at these distances, but to a lesser degree than has previously been found for most virtual reality environments. The results are consistent with previous studies that have implicated a restricted field-of-view, combined with an inability for observers to scan the ground plane in a near-to-far direction, as explanations for the observed depth underestimation.
Acinetobacter baumannii Virulence Is Mediated by the Concerted Action of Three Phospholipases D

Acinetobacter baumannii causes a broad range of opportunistic infections in humans. Its success as an emerging pathogen is due to a combination of increasing antibiotic resistance, environmental persistence and adaptation to the human host. To date very little is known about the molecular basis of the latter. Here we demonstrate that A. baumannii can use phosphatidylcholine, an integral part of human cell membranes, as sole carbon and energy source. We report on the identification of three phospholipases belonging to the PLD superfamily. PLD1 and PLD2 appear restricted to the bacteria and display the general features of bacterial phospholipases D. They possess two PLDc_2 PFAM domains each encompassing the HxKx4Dx6GS/GGxN (HKD) motif necessary for forming the catalytic core. The third candidate, PLD3, is found in bacteria as well as in eukaryotes and harbours only one PLDc_2 PFAM domain and one conserved HKD motif, which however do not overlap. Employing a markerless mutagenesis system for A. baumannii ATCC 19606T, we generated a full set of PLD knock-out mutants. Galleria mellonella infection studies as well as invasion experiments using A549 human lung epithelial cells revealed that the three PLDs act in a concerted manner as virulence factors and are playing an important role in host cell invasion.
Motion representations for the Lafferriere-Sussmann algorithm for nilpotent control systems

Motion representations for the Lafferriere-Sussmann algorithm for nilpotent control systems In this paper, an extension of the Lafferriere-Sussmann algorithm of motion planning for driftless nilpotent control systems is analyzed. It is aimed at making more numerous admissible representations of motion in the algorithm. The representations allow designing a shape of trajectories joining the initial and final configuration of the motion planning task. This feature is especially important in motion planning in a cluttered environment. Some natural functions are introduced to measure the shape of a trajectory in the configuration space and to evaluate trajectories corresponding to different representations of motion.
Sungear: interactive visualization and functional analysis of genomic datasets

UNLABELLED Sungear is a software system that supports a rapid, visually interactive and biologist-driven comparison of large datasets. The datasets can come from microarray experiments (e.g. genes induced in each experiment), from comparative genomics (e.g. genes present in each genome) or even from non-biological applications (e.g. demographics or baseball statistics). Sungear represents multiple datasets as vertices in a polygon. Each possible intersection among the sets is represented as a circle inside the polygon. The position of the circle is determined by the position of the vertices represented in the intersection and the area of the circle is determined by the number of elements in the intersection. Sungear shows which Gene Ontology terms are over-represented in a subset of circles or anchors. The intuitive Sungear interface has enabled biologists to determine quickly which dataset or groups of datasets play a role in a biological function of interest. AVAILABILITY A live online version of Sungear can be found at http://virtualplant-prod.bio. nyu.edu/cgi-bin/sungear/index.cgi
Sustainable energy consumption monitoring in residential settings

The continuous growth of energy needs and the fact that unpredictable energy demand is mostly served by unsustainable (i.e. fossil-fuel) power generators have given rise to the development of Demand Response (DR) mechanisms for flattening energy demand. Building effective DR mechanisms and user awareness on power consumption can significantly benefit from fine-grained monitoring of user consumption at the appliance level. However, installing and maintaining such a monitoring infrastructure in residential settings can be quite expensive. In this paper, we study the problem of fine-grained appliance power-consumption monitoring based on one house-level meter and few plug-level meters. We explore the trade-off between monitoring accuracy and cost, and exhaustively find the minimum subset of plug-level meters that maximize accuracy. As exhaustive search is time- and resource-consuming, we define a heuristic approach that finds the optimal set of plug-level meters without utilizing any other sets of plug-level meters. Based on experiments with real data, we found that few plug-level meters - when appropriately placed - can very accurately disaggregate the total real power consumption of a residential setting and verified the effectiveness of our heuristic approach.
Plasticity aspects of nano scale contact

1 Introduction11.1 Motivation. 11.2 Objectives. 31.3 Challenges. 32 State of the Art52.1 Finite Element Method. 52.2 Discrete Dislocations Dynamics. 62.3 Molecular Dynamics. 82.4 Coupled Atomistics and Discrete Dislocations. 103 Preliminary Results133.1 Pure MD Nanoscratching. 133.1. 1 Motivation. 133.1. 2 Simulation Setup. 133.1. 3 Molecular Dynamics / Molecular Statics Approach. 153.1. 4 Discussion of Results. 163.2 Coupled Indentation. 173.2. 1 Motivation and Setup. 183.2. 2 Discussion of Results. 194 Conclusions and Outlook214.1 Conclusions. 214.2 Outlook. 224.2. 1 CADD parallelisation and extension to 3D. 224.2. 2 Computation of W
The Barbados Eye Study. Prevalence of open angle glaucoma.

OBJECTIVE To describe the design of the Barbados Eye Study and report on the prevalence of open angle glaucoma (OAG) in a predominantly black study population. DESIGN Population-based prevalence study. SETTING AND PARTICIPANTS Residents of Barbados, West Indies, identified from a simple random sample of Barbadian-born citizens 40 through 84 years old. DATA COLLECTION Participants had a comprehensive study visit that included automated perimetry, applanation tonometry, and fundus photography; persons with specific examination findings, as well as a 10% sample of participants, were referred for an ophthalmologic examination and additional tests. OUTCOME A diagnosis of OAG required both visual field and optic disc criteria for glaucoma damage after excluding other causes. RESULTS The 4709 participants (83.5% of those eligible) had demographic characteristics that were similar to the census population. Of the 4631 participants who were tested at the study site, 95% completed Humphrey automated perimetry and 97% had photographic or clinical disc gradings; 93% of those referred completed the ophthalmologic examination. In this adult population, the prevalence of OAG by self-reported race was 7.0% (302/4314) in black, 3.3% (6/184) in mixed-race, and 0.8% (1/133) in white or other participants. In black and mixed-race participants, the prevalence reached 12% at age 60 years and older and was higher in men (8.3%) than in women (5.7%), with an age-adjusted male-female ratio of 1.4. In addition, over 3% of the participants were classified as having suspect OAG. CONCLUSIONS To our knowledge, the Barbados Eye Study is the largest glaucoma study ever conducted in a black population and identified more people with OAG than did any previous population study. The prevalence of OAG was high, especially at older ages and in men. Among participants 50 years old or older, one in 11 had OAG, and prevalence increased to one in six at age 70 years or older. The results highlight the public health importance of OAG in the Afro-Caribbean region and have implications for other populations.
Analysis of the Phospholipid Profile of Metaphase II Mouse Oocytes Undergoing Vitrification

Oocyte freezing confers thermal and chemical stress upon the oolemma and various other intracellular structures due to the formation of ice crystals. The lipid profiles of oocytes and embryos are closely associated with both, the degrees of their membrane fluidity, as well as the degree of chilling and freezing injuries that may occur during cryopreservation. In spite of the importance of lipids in the process of cryopreservation, the phospholipid status in oocytes and embryos before and after freezing has not been investigated. In this study, we employed mass spectrometric analysis to examine if vitrification has an effect on the phospholipid profiles of mouse oocytes. Freshly prepared metaphase II mouse oocytes were vitrified using copper grids and stored in liquid nitrogen for 2 weeks. Fresh and vitrified-warmed oocytes were subjected to phospholipid extraction procedure. Mass spectrometric analyses revealed that multiple species of phospholipids are reduced in vitrified-warmed oocytes. LIFT analyses identified 31 underexpressed and 5 overexpressed phospholipids in vitrified mouse oocytes. The intensities of phosphatidylinositol (PI) {18∶2/16∶0} [M−H]− and phosphatidylglycerol (PG) {14∶0/18∶2} [M−H]− were decreased the most with fold changes of 30.5 and 19.1 in negative ion mode, respectively. Several sphingomyelins (SM) including SM {d38∶3} [M+H]+ and SM {d34∶0} [M+K]+ were decreased significantly in positive ion mode. Overall, the declining trend of multiple phospholipids demonstrates that vitrification has a marked effect on phospholipid profiles of oocytes. These results show that the identified phospholipids can be used as potential biomarkers of oocyte undergoing vitrification and will allow for the development of strategies to preserve phospholipids during oocyte cryopreservation.
Linear prediction approach to direction estimation of cyclostationary signals in multipath environment

We investigate the estimation of the directions-of-arrival (DOA) of closely spaced narrowband cyclostationary signals in the presence of multipath propagation. By exploiting the spatial and temporal properties of most communication signals, we propose a new cyclic forward-backward linear prediction (FBLP) approach for coherent signals impinging on a uniform linear array (ULA). In the proposed algorithm, the evaluation of the cyclic array covariance matrix is avoided, and the difficulty of choosing the optimal time lag parameter is alleviated. As a result, the proposed approach has two advantages: (1) the computational load is relatively reduced, and (2) the robustness of estimation is significantly improved. The performance of the proposed approach is confirmed through numerical examples, and it is shown that this approach is superior in resolving the closely spaced coherent signals with a small length of array data and at relatively low signal-to-noise ratio (SNR).
Role of high-sensitivity C-reactive protein measurements in HIV patients

As we herald into the 21st century, the quality of life and the repertoire of highly active antiretroviral therapy (HAART) have considerably improved. However, considerable work is still needed to educate the population about primary and secondary prevention modalities. Moreover, regular monitoring of immune response with patients on HAART with conventional biomarkers is still a problem in low resource settings which needs to be addressed. We aim to review high-sensitivity C-reactive protein as a potential biomarker in this regard.
Development and Validation of a Real-Time Taqman® Polymerase Chain Reaction Assay for the Detection of Mycoplasma gallisepticum in Naturally Infected Birds

Abstract In this study, we report the development and validation of a real-time polymerase chain reaction (PCR) assay using a Taqman®-labeled probe for the detection of Mycoplasma gallisepticum (MGLP assay). The MGLP assay was highly specific with a detection limit of 25 template copies per reaction and a quantification limit of 100 template copies per reaction. Validation of the assay was completed with 1247 samples (palatine cleft and tracheal swabs) from M. gallisepticum-positive and -negative chicken flocks. The MGLP assay was compared to an enzyme-linked immunosorbent assay (ELISA), a conventional polymerase chain reaction assay (mgc2 PCR), and isolation of M. gallisepticum from naturally infected flocks. A total of 805 samples collected from negative flocks, as verified by ELISA and/or mgc2 PCR, were negative by the MGLP assay. A total of 442 samples were collected from positive flocks, of which a total of 228 samples were positive by the MGLP assay. These results agreed for 98.87% of the samples when tested by mgc2 PCR. When comparing the MGLP assay with M. gallisepticum isolation, the MGLP assay was more sensitive than isolation for detecting positive birds from a positive flock, 172/265 and 50/265, respectively. Overall, the MGLP assay and M. gallisepticum isolation agreed for 52.8% of the samples tested. In conclusion, the MGLP assay was highly specific, sensitive, and reproducible, and allowed the quantification of template copies directly from clinical samples.
Storing Text Using Integer Codes

Traditionally, text is stored on computers as a stream of characters. The goal of this research is to store text in a form that facilitates word manipulation whilst reducing storage space. A word list with syntactic linear ordering is stored and words in a text are given two-byte integar codes that point to their respective positions in this list. The implementation of the encoding scheme is described and the performance statistics of this encoding scheme is presented.
An Estimated Monetary DSGE Model with Unemployment and Staggered Nominal Wage Bargaining

We develop and estimate a medium scale macroeconomic model that allows for unemployment and staggered nominal wage contracting. In contrast to most existing quantitative models, employment adjustment is on the extensive margin and the employment of existing workers is efficient. Wage rigidity, however, affects the hiring of new workers. The former is introduced via the staggered Nash bargaining setup of Gertler and Trigari (2006). A robust finding is that the model with wage rigidity provides a better description of the data than does a flexible wage version. Overall, the model fits the data roughly as well as existing quantitative macroeconomic models, such as Smets and Wouters (2007) or Christiano, Eichenbaum, and Evans (2005). More work is necessary, however, to ensure a robust identification of the key labor market parameters. Copyright (c) 2008 The Ohio State University.
Analysis and Modeling of Manual Summarization of Japanese Broadcast News

We describe our analysis and modeling of the summarization process of Japanese broadcast news. We have studied the entire manual summarization process of the Japan Broadcasting Corporation (NHK). The staff of NHK has been making manual summarizations of news text on a daily basis since December 2000. We interviewed these professional abstractors and obtained a considerable amount of news summaries. We matched the summary with the original text, investigated the news text structure, and thereby analyzed the manual summarization process. We then developed a summarization model on which we intend to build a summarization system.
Magnetoresistance and ion bombardment induced magnetic patterning

In this thesis the combination of the magnetic patterning of the unidirectional anisotropy and the tunnel magnetoresistance effect is investigated. In my diploma thesis, it has been shown that it is in principle possible to use the magnetic patterning by ion bombardment to magnetically structure the pinned layer in magnetic tunnel junctions (MTJs) with alumina barrier. Furthermore, it has been shown that the side effects which have been observed after this treatment can be at least reduced by an additional heating step. Starting from this point, the applicability of ion bombardment induced magnetic patterning (IBMP) in general and the combination of IBMP and MTJs in particular is investigated and new applications are developed.