Miracle-dz/UniFAR-FTUs huggingface dataset:
Static Performance Evaluation for Memory-Bound Computing: The MBRAM Model

We present the MBRAM model for static evaluation of the performance of memory-bound programs. The MBRAM model predicts the actual running time of a memory-bound program directly from pseudo-code. This means that the final running time can be predicted even before the program has been developed and benchmarked. In contrast to the “Big Oh” complexity model, which measures the time solely by counting the number of instructions executed, the MBRAM model predicts running times based on memory accesses, cache parameters, RAM bandwidth, and other important architectural parameters. As a result, the MBRAM model correctly ranks orders the actual running times for implementations of seven different O(n log n) sorting algorithms. In our suite of benchmarks, the MBRAM model consistently underestimates the actual running times, with errors ranging from 10% to 44%.
Inducing History Representations for Broad Coverage Statistical Parsing

We present a neural network method for inducing representations of parse histories and using these history representations to estimate the probabilities needed by a statistical left-corner parser. The resulting statistical parser achieves performance (89.1% F-measure) on the Penn Treebank which is only 0.6% below the best current parser for this task, despite using a smaller vocabulary size and less prior linguistic knowledge. Crucial to this success is the use of structurally determined soft biases in inducing the representation of the parse history, and no use of hard independence assumptions.
A teaching rotation and a student teaching qualification for senior medical students

Background: Physicians have a scholarly role, including educating others, be it patients, colleagues or students. This led UMC Utrecht to organize a one-week obligatory teacher training course for senior medical students and a six-week elective teaching rotation. Students who complete both may receive a student teaching qualification. They must show didactic skill, have experience with teaching and learn about medical education topics. Method: Between October 2004 and December 2006 60 students (about 10% of all final-year students) took the six-week rotation. Rotating students are attached to a 4–6 week undergraduate curriculum unit. The rotation includes 30 hours of independent teaching of junior medical students, studying the BMJ 's ABC of Learning and Teaching series and sitting a written exam on it, constructing 14 test questions, completing an advisory project for the unit coordinator and writing an essay on a medical education topic of choice. Conclusions: The senior students appear to attain the objectives of the rotation and evaluate it positively. The coordinating teacher-supervisors and the younger students are all generally satisfied to very satisfied with the student teachers. The curriculum benefits from the advisory projects and most essays are so well written that a selection is published as a booklet presented for teachers. These graduates start their career with a teaching qualification.
Error bounds for maximum likelihood matrix completion under sparse factor models

This paper examines a general class of matrix completion tasks where entry wise observations of the matrix are subject to random noise or corruption. Our particular focus here is on settings where the matrix to be estimated follows a sparse factor model, in the sense that it may be expressed as the product of two matrices, one of which is sparse. We analyze the performance of a sparsity-penalized maximum likelihood approach to such problems to provide a general-purpose estimation result applicable to any of a number of noise/corruption models, and describe its implications in two stylized scenarios - one characterized by additive Gaussian noise, and the other by highly-quantized one-bit observations. We also provide some supporting empirical evidence to validate our theoretical claims in the Gaussian setting.
PASSAGE Syntactic Representation: a Minimal Common Ground for Evaluation

The current PASSAGE syntactic representation is the result of 9 years of constant evolution with the aim of providing a common ground for evaluating parsers of French whatever their type and supporting theory. In this paper we present the latest developments concerning the formalism and show first through a review of basic linguistic phenomena that it is a plausible minimal common ground for representing French syntax in the context of generic black box quantitative objective evaluation. For the phenomena reviewed, which include: the notion of syntactic head, apposition, control and coordination, we explain how PASSAGE representation relates to other syntactic representation schemes for French and English, slightly extending the annotation to address English when needed. Second, we describe the XML format chosen for PASSAGE and show that it is compliant with the latest propositions in terms of linguistic annotation standard. We conclude discussing the influence that corpus-based evaluation has on the characteristics of syntactic representation when willing to assess the performance of any kind of parser.
Land Application of Manure for Beneficial Reuse

The concentration of animal production systems has increased efficiency and improved overall economic return for animal producers. This concentration, along with the advent of commercial fertilizers, has led to a change in the way animal producers view manure. Manure, once valued as a resource by farmers, is now treated as a waste. Air and water quality concerns that arise primarily from the under-utilization or inefficient use of manure contribute to these changing views. However, when properly used, manure is a resource and should be regulated as such. In the United States, the USDA/EPA Unified National Strategy for Animal Feeding Operations outlines how animal feeding operations should be regulated and acknowledges that land application at proper agronomic rates is the preferred use for manures. However, many limitations such as water quality concerns, uncertainty in manure nutrient availability, high transportation costs, and odor concerns cause some to question land application. This paper documents the benefits of land application of manure, discusses limitations that hinder greater manure utilization, and outlines research and extension needs for improving manure utilization.
Mechanical properties of intermetallic compounds in the Au–Sn system

The mechanical properties of intermetallic compounds in the Au–Sn system were investigated by nanoindentation. Measurements of hardness and elastic modulus were obtained for all of the confirmed room-temperature intermetallics in this system as well as the β phase (8 at.% Sn) and AuSn_4. Overall, it was found that the Au–Sn compounds have lower hardness and stiffness than common Cu–Sn compounds found in solder joints. This finding is in contrast to common knowledge of “Au embrittlement” due to the formation of either AuSn_4 or (Au,Ni)Sn4 intermetallic compounds. This difference in understanding of mechanical properties of these phases and the resulting joint strength is discussed in terms of reliability and possible failure mechanisms related to interface strength or microstructural effects. Indentation creep measurements performed on Au_5Sn, Au–Sn eutectic (29 at.% Sn) and AuSn indicate that these alloys are significantly more creep resistant than common soft solders, in keeping with typical observations of actual joint performance.
Nε-Fatty acylation of Rho GTPases by a MARTX toxin effector

Bacterial toxin fatty-acylates lysine residues A toxin produced by the bacterium that causes cholera has a catalytic activity that contributes to its effects on the cytoskeleton of host cells. Zhou et al. determined the protein structure of the Rho guanosine triphosphatase (GTPase)–inactivation domain of the toxin from Vibrio cholerae and found it to be similar to that of a human fatty acyltransferase. Indeed, the toxin peptide could catalyze fatty acylation of lysine residues of Rho-family GTPases, which regulate the actin cytoskeleton. Such covalent modification of lysine residues in mammalian proteins had been noted before, but the enzymes responsible were not known. Science, this issue p. 528 The mechanism of action of a toxin from the bacteria that causes cholera is elucidated. The multifunctional autoprocessing repeats-in-toxin (MARTX) toxins are a family of large toxins that are extensively distributed in bacterial pathogens. MARTX toxins are autocatalytically cleaved to multiple effector domains, which are released into host cells to modulate the host signaling pathways. The Rho guanosine triphosphatase (GTPase) inactivation domain (RID), a conserved effector domain of MARTX toxins, is implicated in cell rounding by disrupting the host actin cytoskeleton. We found that the RID is an Nε-fatty acyltransferase that covalently modifies the lysine residues in the C-terminal polybasic region of Rho GTPases. The resulting fatty acylation inhibited Rho GTPases and disrupted Rho GTPase–mediated signaling in the host. Thus, RID can mediate the lysine Nε-fatty acylation of mammalian proteins and represents a family of toxins that harbor N-fatty acyltransferase activities in bacterial pathogens.
A convergence analysis of stochastic collocation method for Navier-Stokes equations with random input data

Stochastic collocation method has proved to be an efficient method and been widely applied to solve various partial differential equations with random input data, including NavierStokes equations. However, up to now, rigorous convergence analyses are limited to linear elliptic and parabolic equations; its performance for Navier-Stokes equations was demonstrated mostly by numerical experiments. In this paper, we provide an error analysis of stochastic collocation method for a semi-implicit Backward Euler discretization for NSE and prove the exponential decay of the interpolation error in the probability space. Our analysis indicates that due to the nonlinearity, as final time T increases and NSE solvers pile up, the accuracy may be reduced significantly. Subsequently, the theoretical results are illustrated by the numerical test of time dependent fluid flow around a bluff body.
Tropomyosin and Myosin-II Cellular Levels Promote Actomyosin Ring Assembly in Fission Yeast

A combination of in vivo and in vitro approaches were used to show how tropomyosin and myosin-II contribute to contractile ring assembly in fission yeast. Ring assembly is sensitive to changes in the cellular levels of myosin-II, and tropomyosin works to maximize myosin-II motor function during this process by stabilizing actomyosin interactions.
Pregnancy Incidence and Correlates in a Clinical Trial Preparedness Study, North West Province South Africa

Introduction Women in HIV prevention trials often must typically agree to avoid pregnancy. Regardless, some become pregnant. Screening tools predicting pregnancy risk could maximize trial safety and efficiency. Objectives We assessed incidence and correlates of pregnancy among women at high HIV risk. Methods We enrolled sexually-active, HIV-negative women into an observational cohort (2008–2011). At enrolment demographic, contraceptive, reproductive, pregnancy intention and behavioural data were collected. Women reported if one or both partners wanted or intended for the couple to become pregnant. We measured gender role beliefs using a locally validated eight-point index. We tested HIV and pregnancy, and inquired about sexually transmitted infection symptoms (STIs) at enrollment and monthly. HIV testing included behavioural counselling and condom provision, but did not specifically counsel women to avoid pregnancy. Cox proportional hazard modelling evaluated the associations with pregnancy. The multivariate model included the following variables “Recent pregnancy attempts”, “Gender Roles Beliefs”, ”Self-reported STIs” and “Age”. Results We screened 1068 women and excluded (24.6%, 263/1068) who did not report risk behaviour. Non-pregnant, non-sterilized women aged 18–35 (median = 21 years) enrolled (n = 438). Most women reported one partner (74.7%) and a prior live birth (84.6%). Median follow-up time was 6 months (range 0.7–15.5). Pregnancy incidence was 25.1 per 100 women-years (n = 57 pregnancies). Conservative beliefs on gender roles (Adjusted Hazard Ratio (aHR) 1.8; 95% confidence interval [CI] 1.1–2.9), recent pregnancy attempts (aHR 1.9; 95% CI 1.1–3.4) and baseline self-reported STI (aHR 2.5; 95% CI 1.4–4.4) were associated with increased incident pregnancy. Report of no pregnancy intention was associated with lowered pregnancy risk (aHR 0.3; 95% CI 0.1–0.7). Conclusions We identified new and confirmed existing factors that can facilitate screening for pregnancy risk.
Design and Management of 3D Chip Multiprocessors Using Network-in-Memory

Long interconnects are becoming an increasingly important problem from both power and performance perspectives. This motivates designers to adopt on-chip network-based communication infrastructures and three-dimensional (3D) designs where multiple device layers are stacked together. Considering the trends towards increasing use of chip multiprocessing, it is timely to consider 3D chip multiprocessor design and memory networking issues, especially in the context of data management in large L2 caches. The overall goal of this paper is to study the challenges for L2 design and management in 3D chip multiprocessors. Our first contribution is to propose a router architecture and a topology design that makes use of a network architecture embedded into the L2 cache memory. Our second contribution is to demonstrate, through extensive experiments, that a 3D L2 memory architecture generates much better results than the conventional two-dimensional (2D) designs under different number of layers and vertical (inter-wafer) connections. In particular, our experiments show that a 3D architecture with no dynamic data migration generates better performance than a 2D architecture that employs data migration. This also helps reduce power consumption in L2 due to a reduced number of data movements
Gamma knife stereotactic radiosurgery for unilateral acoustic neuromas

Objective:To evaluate the clinical results achievable using current techniques of gamma knife stereotactic radiosurgery to treat sporadic unilateral acoustic neuromas. Methods:A retrospective review of 234 consecutive patients treated for unilateral acoustic neuromas between 1996 and 1999, with a mean (SD) follow up of 35 (16) months. Tumour control was assessed with serial radiological imaging and by the need for surgical intervention. Hearing preservation was assessed using Gardner-Robertson grades. Details of complications including cranial neuropathies and non-specific vestibulo-cochlear symptoms are included. Results:A tumour control rate in excess of 92% was achieved, with only 3% of patients undergoing surgery after radiosurgery. Results were less good for larger tumours, but control rates of 75% were achieved for 35–45 mm diameter lesions. Of patients with discernible hearing, Gardner-Robertson grades were unchanged in 75%. Facial nerve function was adversely affected in 4.5%, but fewer than 1% of patients had persistent weakness. Trigeminal symptoms improved in 3%, but developed in 5% of patients, being persistent in less than 1.5%. Transient non-specific vestibulo-cochlear symptoms were reported by 13% of patients. Conclusions:Tumour control rates, while difficult to define, are comparable after radiosurgery with those experienced after surgery. The complications and morbidity after radiosurgery are far less frequent than those encountered after surgery. This, combined with its minimally invasive nature, may make radiosurgery increasingly the treatment of choice for small and medium sized acoustic neuromas.
Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli

One of the paramount goals of synthetic biology is to have the ability to tune transcriptional networks to targeted levels of expression at will. As a step in that direction, we have constructed a set of unique binding sites for E. coli RNA Polymerase (RNAP) holoenzyme, designed using a model of sequence-dependent binding energy combined with a thermodynamic model of transcription to produce a targeted level of gene expression. This promoter set allows us to determine the correspondence between the absolute numbers of mRNA molecules or protein products and the predicted promoter binding energies measured in energy units. These binding sites adhere on average to the predicted level of gene expression over orders of magnitude in constitutive gene expression, to within a factor of in both protein and mRNA copy number. With these promoters in hand, we then place them under the regulatory control of a bacterial repressor and show that again there is a strict correspondence between the measured and predicted levels of expression, demonstrating the transferability of the promoters to an alternate regulatory context. In particular, our thermodynamic model predicts the expression from our promoters under a range of repressor concentrations between several per cell up to over per cell. After correcting the predicted polymerase binding strength using the data from the unregulated promoter, the thermodynamic model accurately predicts the expression for the simple repression strains to within . Demonstration of modular promoter design, where parts of the circuit (such as RNAP/TF binding strength and transcription factor copy number) can be independently chosen from a stock list and combined to give a predictable result, has important implications as an engineering tool for use in synthetic biology.
Fast recovery of evolutionary trees with thousands of nodes

We present a novel distance-based algorithm for evolutionary tree reconstruction. Our algorithm reconstructs the topology of a tree with n leaves in O(n2) time using O(n) working space. In the general Markov model of evolution the algorithm recovers the topology successfully with (1 — &Ogr;(1)) probability from sequences with polynomial length in n. Moreover, for almost all trees, our algorithm achieves the same success probability on polylogarithmic sample sizes. The theoretical results are supported by simulation experiments involving trees with 500, 1895, and 3135 leaves. The topologies of the trees are recovered with high success from 2000 bp DNA sequences.
Placing the poor while keeping the rich in their place

A central objective of modern US housing policy is deconcentrating poverty through "housing mobility programs" that move poor families into middle class neighborhoods. Pursuing these policies too aggressively risks inducing middle class flight, but being too cautious squanders the opportunity to help more poor families. This paper presents a stylized dynamicoptimization model that captures this tension. With base-caseparameter values, cost considerations limit mobility programs before flight becomes excessive. However, for modest departures reflecting stronger flight tendencies and/or weaker destination neighborhoods, other outcomes emerge. In particular, we find state-dependence and multiple equilibria, including both de-populated and oversized outcomes. For certain sets of parameters there exists a Skiba point that separates initial conditions for which the optimal strategy leads to substantial flight and depopulation from those for which the optimal strategy retains or even expands the middle class population. These results suggest the value of estimating middle-class neighborhoods' "carrying capacity" for absorbing mobility program placements and further modeling of dynamic response.
Comparing Mobile Privacy Protection through Cross-Platform Applications

With the rapid growth of the mobile market, security of mobile platforms is receiving increasing attention from both research community as well as the public. In this paper, we make the first attempt to establish a baseline for security comparison between the two most popular mobile platforms. We investigate applications that run on both Android and iOS and examine the difference in the usage of their security sensitive APIs (SS-APIs). Our analysis over 2,600 applications shows that iOS applications consistently access more SS-APIs than their counterparts on Android. The additional privileges gained on iOS are often associated with accessing private resources such as device ID, camera, and users’ contacts. A possible explanation for this difference in SS-API usage is that privileges obtained by an application on the current iOS platform are invisible to end users. Our analysis shows that: 1) third-party libraries (specifically advertising and analytic libraries) on iOS invoke more SS-APIs than those on Android; 2) Android application developers avoid requesting unnecessary privileges which will be shown in the permission list during application installation. Considering the fact that an Android application may gain additional privileges with privilege-escalation attacks and iOS provides a more restricted privilege set accessible by third-party applications, our results do not necessarily imply that Android provides better privacy protection than iOS. However, our evidence suggests that Apple’s application vetting process may not be as effective as Android’s privilege notification mechanism, particularly in protecting sensitive resources from third-party applications.
An improved computational constitutive model for glass

In 2011, Holmquist and Johnson presented a model for glass subjected to large strains, high strain rates and high pressures. It was later shown that this model produced solutions that were severely mesh dependent, converging to a solution that was much too strong. This article presents an improved model for glass that uses a new approach to represent the interior and surface strength that is significantly less mesh dependent. This new formulation allows for the laboratory data to be accurately represented (including the high tensile strength observed in plate-impact spall experiments) and produces converged solutions that are in good agreement with ballistic data. The model also includes two new features: one that decouples the damage model from the strength model, providing more flexibility in defining the onset of permanent deformation; the other provides for a variable shear modulus that is dependent on the pressure. This article presents a review of the original model, a description of the improved model and a comparison of computed and experimental results for several sets of ballistic data. Of special interest are computed and experimental results for two impacts onto a single target, and the ability to compute the damage velocity in agreement with experiment data. This article is part of the themed issue ‘Experimental testing and modelling of brittle materials at high strain rates’.