Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonparametric Maximum Likelihood Methods for Binary Response Models With Random Coefficients

Abstract The venerable method of maximum likelihood has found numerous recent applications in nonparametric estimation of regression and shape constrained densities. For mixture models the nonparametric maximum likelihood estimator (NPMLE) of Kiefer and Wolfowitz plays a central role in recent developments of empirical Bayes methods. The NPMLE has also been proposed by Cosslett as an estimation method for single index linear models for binary response with random coefficients. However, computational difficulties have hindered its application. Combining recent developments in computational geometry and convex optimization, we develop a new approach to computation for such models that dramatically increases their computational tractability. Consistency of the method is established for an expanded profile likelihood formulation. The methods are evaluated in simulation experiments, compared to the deconvolution methods of Gautier and Kitamura and illustrated in an application to modal choice for journey-to-work data in the Washington DC area. Supplementary materials for this article are available online.
Negotiating screen time: A mother’s struggle over ‘no screen time’ with her infant son

The literature on infant and toddler screen time has been built on two traditions—cognitive models of learning and sociocultural models of learning. Cognitive studies have cautioned against the use of screen time for young children because clinical research has not shown children can learn as effectively from screens as they do from human interaction and might delay children’s cognitive development. Conversely, qualitative research has described the social ways children learn and use digital technology through social interactions with other people in their homes. This paper reports on an autoethnographic study of how digital tools were embedded in the everyday ways of life in my home during my son’s first 18 months of life. I present a first-hand account of the tensions I experienced as I grappled with the American Academy of Pediatrics’ recommendation of no, ‘digital media use (except video-chatting) in children younger than 18–24 months’ (p. 3). I juxtapose screen time recommendations with the everyday realities of my life as a first-time mother in the 21st century. Throughout the study, I was enmeshed in two roles—researcher and mother—and drew on phenomenology to describe my infant son and my lived experiences using digital technology in our home. My researcher persona was influenced by the traditions and perspectives of sociocultural theories and new literacy studies and the positive learning that can occur while using digital technology. I noted how digital tools were ingrained in daily moments and ways of life, particularly those which used the TV and smartphones, and could not be removed. Yet, my mother persona felt guilty about our use of digital technology and I struggled with the messages I received from news and social media that warned against screen time for infants and toddlers.
Eigenvalue and Generalized Eigenvalue Problems: Tutorial

This paper is a tutorial for eigenvalue and generalized eigenvalue problems. We first introduce eigenvalue problem, eigen-decomposition (spectral decomposition), and generalized eigenvalue problem. Then, we mention the optimization problems which yield to the eigenvalue and generalized eigenvalue problems. We also provide examples from machine learning, including principal component analysis, kernel supervised principal component analysis, and Fisher discriminant analysis, which result in eigenvalue and generalized eigenvalue problems. Finally, we introduce the solutions to both eigenvalue and generalized eigenvalue problems.
External Human-Machine Interfaces on Automated Vehicles: Effects on Pedestrian Crossing Decisions

Objective: In this article, we investigated the effects of external human-machine interfaces (eHMIs) on pedestrians’ crossing intentions. Background: Literature suggests that the safety (i.e., not crossing when unsafe) and efficiency (i.e., crossing when safe) of pedestrians’ interactions with automated vehicles could increase if automated vehicles display their intention via an eHMI. Methods: Twenty-eight participants experienced an urban road environment from a pedestrian’s perspective using a head-mounted display. The behavior of approaching vehicles (yielding, nonyielding), vehicle size (small, medium, large), eHMI type (1. baseline without eHMI, 2. front brake lights, 3. Knightrider animation, 4. smiley, 5. text [WALK]), and eHMI timing (early, intermediate, late) were varied. For yielding vehicles, the eHMI changed from a nonyielding to a yielding state, and for nonyielding vehicles, the eHMI remained in its nonyielding state. Participants continuously indicated whether they felt safe to cross using a handheld button, and “feel-safe” percentages were calculated. Results: For yielding vehicles, the feel-safe percentages were higher for the front brake lights, Knightrider, smiley, and text, as compared with baseline. For nonyielding vehicles, the feel-safe percentages were equivalent regardless of the presence or type of eHMI, but larger vehicles yielded lower feel-safe percentages. The Text eHMI appeared to require no learning, contrary to the three other eHMIs. Conclusion: An eHMI increases the efficiency of pedestrian-AV interactions, and a textual display is regarded as the least ambiguous. Application: This research supports the development of automated vehicles that communicate with other road users.
Speed Invariant Time Surface for Learning to Detect Corner Points With Event-Based Cameras

We propose a learning approach to corner detection for event-based cameras that is stable even under fast and abrupt motions. Event-based cameras offer high temporal resolution, power efficiency, and high dynamic range. However, the properties of event-based data are very different compared to standard intensity images, and simple extensions of corner detection methods designed for these images do not perform well on event-based data. We first introduce an efficient way to compute a time surface that is invariant to the speed of the objects. We then show that we can train a Random Forest to recognize events generated by a moving corner from our time surface. Random Forests are also extremely efficient, and therefore a good choice to deal with the high capture frequency of event-based cameras ---our implementation processes up to 1.6Mev/s on a single CPU. Thanks to our time surface formulation and this learning approach, our method is significantly more robust to abrupt changes of direction of the corners compared to previous ones. Our method also naturally assigns a confidence score for the corners, which can be useful for postprocessing. Moreover, we introduce a high-resolution dataset suitable for quantitative evaluation and comparison of corner detection methods for event-based cameras. We call our approach SILC, for Speed Invariant Learned Corners, and compare it to the state-of-the-art with extensive experiments, showing better performance.
Location dependence of the transcriptional response of a potential G-quadruplex in gene promoters under oxidative stress

Abstract Oxidation of the guanine (G) heterocycle to 8-oxo-7,8-dihydroguanine (OG) in mammalian gene promoters was demonstrated to induce transcription. Potential G-quadruplex forming sequences (PQSs) in promoters have a high density of G nucleotides rendering them highly susceptible to oxidation and possible gene activation. The VEGF PQS with OG or an abasic site were synthesized at key locations in the SV40 or HSV-TK model promoters to determine the location dependency in the gene expression profile in human cells. The PQS location with respect to the transcription start site (TSS) and strand of occupancy (coding versus non-coding strand) are key parameters that determine the magnitude and direction in which gene expression changes with the chemically modified VEGF PQS. The greatest impact observed for OG or F in the PQS context in these promoters was within ∼200 bp of the TSS. Established PQSs found to occur naturally in a similar location relative to the TSS for possible oxidation-induced gene activation include c-MYC, KRAS, c-KIT, HIF-1α, PDGF-A and hTERT. The studies provide experimental constraints that were used to probe bioinformatic data regarding PQSs in the human genome for those that have the possibility to be redox switches for gene regulation.
Dephosphorylation of protamine 2 at serine 56 is crucial for murine sperm maturation in vivo

Sperm maturation requires keeping protamine 2 dephosphorylated to enable tight DNA packaging. Protamine dephosphorylation for fertility During the final stage of spermatogenesis, protamines tightly package DNA in the mature sperm. Itoh et al. generated mice deficient in the heat shock protein and chaperone Hspa4l, which is implicated in spermatogenesis. The mice were infertile with malformed sperm heads, a phenotype similar to that of mice deficient in the phosphatase Ppp1cc2. The authors showed that Hspa4l was required to release Ppp1cc2 from a complex with other chaperones, enabling its translocation to chromatin. In vitro studies showed that Ppp1cc2 dephosphorylated protamine 2 at Ser56. Expression of the unphosphorylatable protamine 2 S56A mutant reversed the infertility of Hspa4l-deficient mice, suggesting that the dephosphorylation of protamine 2 at Ser56 is important for its role in sperm maturation. The posttranslational modification of histones is crucial in spermatogenesis, as in other tissues; however, during spermiogenesis, histones are replaced with protamines, which are critical for the tight packaging of the DNA in sperm cells. Protamines are also posttranslationally modified by phosphorylation and dephosphorylation, which prompted our investigation of the underlying mechanisms and biological consequences of their regulation. On the basis of a screen that implicated the heat shock protein Hspa4l in spermatogenesis, we generated mice deficient in Hspa4l (Hspa4l-null mice), which showed male infertility and the malformation of sperm heads. These phenotypes are similar to those of Ppp1cc-deficient mice, and we found that the amount of a testis- and sperm-specific isoform of the Ppp1cc phosphatase (Ppp1cc2) in the chromatin-binding fraction was substantially less in Hspa4l-null spermatozoa than that in those of wild-type mice. We further showed that Ppp1cc2 was a substrate of the chaperones Hsc70 and Hsp70 and that Hspa4l enhanced the release of Ppp1cc2 from these complexes, enabling the freed Ppp1cc2 to localize to chromatin. Pull-down and in vitro phosphatase assays suggested the dephosphorylation of protamine 2 at serine 56 (Prm2 Ser56) by Ppp1cc2. To confirm the biological importance of Prm2 Ser56 dephosphorylation, we mutated Ser56 to alanine in Prm2 (Prm2 S56A). Introduction of this mutation to Hspa4l-null mice (Hspa4l−/−; Prm2S56A/S56A) restored the malformation of sperm heads and the infertility of Hspa4l−/− mice. The dephosphorylation signal to eliminate phosphate was crucial, and these results unveiled the mechanism and biological relevance of the dephosphorylation of Prm2 for sperm maturation in vivo.
Probing the extragalactic fast transient sky at minute time-scales with DECam

Searches for optical transients are usually performed with a cadence of days to weeks, optimized for supernova discovery. The optical fast transient sky is still largely unexplored, with only a few surveys to date having placed meaningful constraints on the detection of extragalactic transients evolving at sub-hour time-scales. Here, we present the results of deep searches for dim, minute-time-scale extragalactic fast transients using the Dark Energy Camera, a core facility of our all-wavelength and all-messenger Deeper, Wider, Faster programme. We used continuous 20 s exposures to systematically probe time-scales down to 1.17 min at magnitude limits g > 23 (AB), detecting hundreds of transient and variable sources. Nine candidates passed our strict criteria on duration and non-stellarity, all of which could be classified as flare stars based on deep multiband imaging. Searches for fast radio burst and gamma-ray counterparts during simultaneous multifacility observations yielded no counterparts to the optical transients. Also, no long-term variability was detected with pre-imaging and follow-up observations using the SkyMapper optical telescope. We place upper limits for minute-time-scale fast optical transient rates for a range of depths and time-scales. Finally, we demonstrate that optical g-band light-curve behaviour alone cannot discriminate between confirmed extragalactic fast transients such as prompt GRB flashes and Galactic stellar flares.
Adaptive Optimistic Concurrency Control for Heterogeneous Workloads

Optimistic concurrency control (OCC) protocols validate whether a transaction has conflicts with other concurrent transactions after this transaction completes its execution. In this work, we demonstrate that the validation phase has a great influence on the performance of modern in-memory database systems, especially under heterogeneous workloads. The cost of validating operations in a transaction is determined by two main factors. The first factor is the operation type. An OCC protocol would take much less cost on validating a single-record read operation than validating a key-range scan operation. The second factor is the workload type. Existing schemes in OCC variants for validating key-range scan perform differently under various workloads. Although various validation schemes share the same goal of guaranteeing a transaction schedule to be serializable, there are remarkable differences between the costs they introduced. These observations motivate us to design an optimistic concurrency control which can choose a low-cost validation scheme at runtime, referred to as adaptive optimistic concurrency control (AOCC). First, at transaction-level granularity, AOCC can assign a validation method to a transaction according to the features of its operations. Furthermore, for each operation in a transaction, the validation method is selected according to not only the number of accessed records but also the instant characteristics of workloads. Experimental results show that AOCC has good performance and scalability under heterogeneous workloads mixed with point accesses and predicate queries.
Clinical Significance of Pleural Attachment and Indentation of Subsolid Nodule Lung Cancer

Purpose Lung cancers presenting as subsolid nodule commonly have peripheral location, making the cancer-pleura relationship noteworthy. We aimed to evaluate the effect of pleural attachment and/or indentation on visceral pleural invasion (VPI) and recurrence-free survival. Materials and Methods Patients who underwent curative resection of lung cancer as subsolid nodules from April 2007 to January 2016 were retrospectively evaluated. They were divided into four groups according to their relationship with the pleura. Clinical, radiographical, and pathological findings were analyzed. Results Among 404 patients with malignant subsolid nodule, 120 (29.7%) had neither pleural attachment nor indentation, 26 (6.4%) had attachment only, 117 (29.0%) had indentation only, and 141 (34.9%) had both. VPI was observed in nodules of 36 patients (8.9%), but absent in nonsolid nodules and in those without pleural attachment and/or indentation. Compared to subsolid nodules with concurrent pleural attachment and indentation, those with attachment only (odds ratio, 0.12; 95% confidence interval [CI], 0.02 to 0.98) and indentation only (odds ratio, 0.10; 95% CI, 0.03 to 0.31) revealed lower odds of VPI. On subgroup analysis, the size of the solid portion was associated with VPI among those with pleural attachment and indentation (p=0.021). Such high-risk features for VPI were associated with earlier lung cancer recurrence (adjusted hazard ratio, 3.31; 95% CI, 1.58 to 6.91). Conclusion Concurrent pleural attachment and indentation are risk factors for VPI, and the odds increase with larger solid portion in subsolid nodules. Considering the risk of recurrence, early surgical resection could be encouraged in these patients.
Velocity control for improving flow through a bottleneck

A bottleneck can largely deteriorate the flow, such as a traffic light or an on-ramp at a road. To alleviate bottleneck situations, one of the important strategies is to control input rate to suit the state of the road. In this study, we propose an effective velocity control of traveling particles, in which the particle velocity depends on the state of a bottleneck. To analyze our method, we modify the totally asymmetric simple exclusion process (TASEP) and introduce a slow-to-start rule, which we refer to as controlled TASEP in the present paper. Flow improvement is verified in numerical simulations and theoretical analyses by using controlled TASEP.
Sequence effects on size, shape, and structural heterogeneity in Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs), which are present in large numbers in eukaryotic proteomes, lack well-defined three-dimensional structures, thus challenging the archetypal notion of structure-function relationships. Determining the ensemble of conformations that IDPs explore under physiological conditions is the first step in understanding their diverse cellular functions. Here, we quantitatively characterize the structural features of IDPs as a function of sequence and length using molecular simulations of a coarse-grained model. For diverse IDP sequences, with the number of residues ***(Nt) ranging from 24 to 441, our simulations not only reproduce the radii of gyration (Rg) obtained from experiments, with the maximum deviation being no more than ≈ 18%, but also predict the full scattering intensity profiles in quantitative agreement with Small Angle X-ray Scattering experiments. The Rg values are well-described by the standard Flory scaling law, , with ν ≈ 0.588, making it tempting to assert that IDPs behave as polymers in a good solvent. However, clustering analysis reveals a menagerie of structures explored by IDPs is diverse, with the extent of heterogeneity being highly sequence-dependent, even though ensemble-averaged properties, such as the dependence of Rg on chain length, may suggest synthetic polymer-like behavior in a good solvent. For example, we show that for the highly charged Prothymosin-α a substantial fraction of conformations is highly compact. Even if the sequence compositions are similar, as is the case for α-Synuclein and a truncated construct from the Tau protein, there are substantial differences in the conformational heterogeneity. Taken together, these observations imply that metrics based on net charge or related quantities alone cannot be used to anticipate the phases of IDP, either in isolation or in complex with partner IDPs or RNA. Our work sets the stage for probing the interactions of IDPs with each other, with folded protein domains, or with partner RNAs, which are critical for describing the structures of stress granules and biomolecular condensates with important cellular functions.
Modelling Social Evolutionary Processes and Peer Effects in Agricultural Trade Networks: the Rubber Value Chain in Indonesia

Understanding market participants' channel choices is important to policy makers because it yields information on which channels are effective in transmitting information. These channel choices are the result of a recursive process of social interactions and determine the observable trading networks. They are characterized by feedback mechanisms due to peer interaction and therefore need to be understood as complex adaptive systems (CAS). When modelling CAS, conventional approaches like regression analyses face severe drawbacks since endogeneity is omnipresent. As an alternative, process-based analyses allow researchers to capture these endogenous processes and multiple feedback loops. This paper applies an agent-based modelling approach (ABM) to the empirical example of the Indonesian rubber trade. The feedback mechanisms are modelled via an innovative approach of a social matrix, which allows decisions made in a specific period to feed back into the decision processes in subsequent periods, and allows agents to systematically assign different weights to the decision parameters based on their individual characteristics. In the validation against the observed network, uncertainty in the found estimates, as well as under determination of the model, are dealt with via an approach of evolutionary calibration: a genetic algorithm finds the combination of parameters that maximizes the similarity between the simulated and the observed network. Results indicate that the sellers' channel choice decisions are mostly driven by physical distance and debt obligations, as well as peer-interaction. Within the social matrix, the most influential individuals are sellers that live close by to other traders, are active in social groups and belong to the ethnic majority in their village.
A lightweight BFT consensus protocol for blockchains

We present a general consensus framework that allows to easily introduce a customizable Byzantine fault tolerant consensus algorithm to an existing (delegated) proof-of-stake blockchain. We prove the safety of the protocol under the assumption that less than 1/3 of the block proposers are Byzantine. The framework further allows for consensus participants to choose subjective decision thresholds in order to obtain safety even in the case of a larger proportion of Byzantine block proposers. Moreover, the liveness of the protocol is shown if less than 1/3 of the block proposers crash. Based on the framework, we introduce Lisk-BFT, a Byzantine fault tolerant consensus algorithm for the Lisk blockchain. Lisk-BFT integrates with the existing block proposal, requires only two additional integers in block headers and no additional messages. The protocol is simple and provides safety in the case of static proposers if less than 1/3 of the block proposers are Byzantine. For the case of dynamically changing proposers, we proof the safety of the protocol assuming a bound on the number of Byzantine proposers and the number of honest proposers that can change at one time. We further show the liveness of the Lisk-BFT protocol for less than 1/3 crashing block proposers.
Numerical observation of a glassy phase in the three-dimensional Coulomb glass

The existence of an equilibrium glassy phase for charges in a disordered potential with long-range electrostatic interactions has remained controversial for many years. Here we conduct an extensive numerical study of the disorder-temperature phase diagram of the three-dimensional Coulomb glass model using population annealing Monte Carlo to thermalize the system down to extremely low temperatures. Our results strongly suggest that, in addition to a charge order phase, a transition to a glassy phase can be observed, consistent with previous analytical and experimental studies.