Miracle-dz/UniFAR-FTUs huggingface dataset:
Implementation Techniques for SPMD Kernels on CPUs

More and more frameworks and simulations are developed using heterogeneous programming models such as OpenCL, SYCL, CUDA, or HIP. A significant hurdle to mapping these models to CPUs in a performance-portable manner is that implementing work-group barriers for such kernels requires providing forward-progress guarantees so that all work-items can reach the barrier. This work provides guidance for implementations of single-program multiple-data (SPMD) programming models, such as OpenCL, SYCL, CUDA, or HIP, on non-SPMD devices, such as CPUs. We discuss the trade-offs of multiple approaches to handling work-group-level barriers. We present our experience with the integration of two known compiler-based approaches for low-overhead work-group synchronization on CPUs. Thereby we discuss a general design flaw in deep loop fission approaches, as used in the popular Portable Computing Language (PoCL) project, that makes them miscompile certain kernels. For our evaluation, we integrate PoCL’s “loopvec” kernel compiler into hipSYCL and implement continuation-based synchronization (CBS) in the same. We compare both against hipSYCL’s library-only fiber implementation using diverse hardware: we use recent AMD Rome and Intel Icelake server CPUs but also two Arm server CPUs, namely Fujitsu’s A64FX and Marvell’s ThunderX2. We show that compiler-based approaches outperform library-only implementations by up to multiple orders of magnitude. Further, we adapt our CBS implementation into PoCL and compare it against its loopvec approach in both, PoCL and hipSYCL. We find that our implementation of CBS, while being more general than PoCL’s approach, gives comparable performance in PoCL and even surpasses it in hipSYCL. Therefore we recommend its use in general.
Compositional Security Definitions for Higher-Order Where Declassification

To ensure programs do not leak private data, we often want to be able to provide formal guarantees ensuring such data is handled correctly. Often, we cannot keep such data secret entirely; instead programmers specify how private data may be declassified. While security definitions for declassification exist, they mostly do not handle higher-order programs. In fact, in the higher-order setting no compositional security definition exists for intensional information-flow properties such as where declassification, which allows declassification in specific parts of a program. We use logical relations to build a model (and thus security definition) of where declassification. The key insight required for our model is that we must stop enforcing indistinguishability once a relevant declassification has occurred. We show that the resulting security definition provides more security than the most related previous definition, which is for the lower-order setting.
Live Pattern Matching with Typed Holes

Several modern programming systems, including GHC Haskell, Agda, Idris, and Hazel, support typed holes. Assigning static and, to varying degree, dynamic meaning to programs with holes allows program editors and other tools to offer meaningful feedback and assistance throughout editing, i.e. in a live manner. Prior work, however, has considered only holes appearing in expressions and types. This paper considers, from type theoretic and logical first principles, the problem of typed pattern holes. We confront two main difficulties, (1) statically reasoning about exhaustiveness and irredundancy when patterns are not fully known, and (2) live evaluation of expressions containing both pattern and expression holes. In both cases, this requires reasoning conservatively about all possible hole fillings. We develop a typed lambda calculus, Peanut, where reasoning about exhaustiveness and redundancy is mapped to the problem of deriving first order entailments. We equip Peanut with an operational semantics in the style of Hazelnut Live that allows us to evaluate around holes in both expressions and patterns. We mechanize the metatheory of Peanut in Agda and formalize a procedure capable of deciding the necessary entailments. Finally, we scale up and implement these mechanisms within Hazel, a programming environment for a dialect of Elm that automatically inserts holes during editing to provide static and dynamic feedback to the programmer in a maximally live manner, i.e. for every possible editor state. Hazel is the first maximally live environment for a general-purpose functional language.
Ventricular surface activation time imaging from clinical data: a quantitative comparison of two inverse approaches

Ventricular activation time maps for both the endocardium and epicardium were estimated from MRI and body-surface ECG mapping data which had been acquired under clinical conditions. The associated nonlinear inverse ill-posed problem was solved by two different approaches. The first approach (method A) was based on a linearization technique while the second (method B) employed an optimization routine for nonlinear ill-posed problems. Both methods utilized a second-order Tikhonov regularization in order to stabilize the inverse solution. The linearization technique could be demonstrated to perform better, particularly with regard to clinical implementations and applications. In two patients suffering from Wolff-Parkinson-White syndrome, the activation time maps were estimated and quantitatively compared.
Let's make it clear: systematic exploration of mitochondrial DNA– and RNA–protein complexes by complexome profiling

Complexome profiling (CP) is a powerful tool for systematic investigation of protein interactors that has been primarily applied to study the composition and dynamics of mitochondrial protein complexes. Here, we further optimised this method to extend its application to survey mitochondrial DNA- and RNA-interacting protein complexes. We established that high-resolution clear native gel electrophoresis (hrCNE) is a better alternative to preserve DNA- and RNA-protein interactions that are otherwise disrupted when samples are separated by the widely used blue native gel electrophoresis (BNE). In combination with enzymatic digestion of DNA, our CP approach improved the identification of a wide range of protein interactors of the mitochondrial gene expression system without compromising the detection of other multi-protein complexes. The utility of this approach was particularly demonstrated by analysing the complexome changes in human mitochondria with impaired gene expression after transient, chemically-induced mtDNA depletion. Effects of RNase on mitochondrial protein complexes were also evaluated and discussed. Overall, our adaptations significantly improved the identification of mitochondrial DNA- and RNA-protein interactions by CP, thereby unlocking the comprehensive analysis of a near-complete mitochondrial complexome in a single experiment.
A minimally-invasive method for ancient DNA sampling of Prehistoric bone and antler tools and hunting weapons

Internal and external bony tissues from diverse mammalian taxa are one of the primary animal raw materials exploited for technical and symbolic purposes by Eurasian Upper Palaeolithic hunter-gatherers. Identifying the source species used for osseous raw material is critical to gain insights into these populations’ behaviour, technology, and subsistence. The study of osseous tools has advanced in the last few years by combining archaeological and biomolecular methods. Ancient genomics opens many new analytical opportunities. Ancient DNA (aDNA) can provide a wealth of information about the animal sources of these objects. Unfortunately, aDNA analyses often involve destructive sampling. Here, we develop and apply a minimally-invasive aDNA sampling method for an assemblage of 42 prehistoric hunting weapons and tools from various Eurasian archaeological sites. We evaluated the impact of our approach on the specimens visually, microscopically and through Micro-CT scans. The surface impacts are marginal, ranging from 0.3-0.4 mm. Using a custom-made DNA capture kit for 54 mammalian species, we obtained sufficient aDNA to identify the taxa of 33% of the objects. For one of the tools, we recovered enough endogenous aDNA to infer the genetic affinities of the individual. Our results also demonstrate that ancient antler, one of the primary raw materials used during a large part of prehistory, is a reliable source of aDNA. Our minimally-invasive aDNA sampling method is therefore effective while preserving osseous objects for potential further analyses: morphometric, technical, genetic, radiometric and more.
Noncanonical interactions and conformational dynamics in cargo-Pex5-Pex14 ternary complex for peroxisomal import

Peroxisomes are membrane bound organelles which compartmentalize diverse metabolic processes in eukaryotic cells. Having no protein synthetic abilities, peroxisomes import all required enzymes from the cytosol through a peroxin (Pex) import system. In the first step, the Peroxisome Targeting Sequence 1 (PTS1)-marked cargo is recognized by soluble receptor, Pex5. The cargo-Pex5 complex then docks at the peroxisomal membrane translocon containing Pex14 and Pex13 and translocates into peroxisomal lumen, but the structural understanding is elusive. Here, we report a cryo-EM structure of cargo-Pex5-Pex14 ternary complex from Trypanosoma cruzi, the causative agent of human Chagas disease. Malate dehydrogenase (cargo) – Pex5 interface is characterized by a swinging motion of Pex5 restricted by secondary, PTS1 independent interactions. The Pex5-Pex14 interface reveals a noncanonical contact surface adjacent to the previously identified Wxxx(F/Y) motif. Mutational analysis demonstrates that noncanonical interactions did not evolve to increase the affinity, but rather to restrict the dynamics at the cost of affinity. Consequences for the peroxisomal transport are discussed. HIGHLIGHTS 1. The structure of a ternary complex (MDH-Pex5-Pex14) enabling cargo translocation via peroxisomal membrane was determined using cryo-EM. 2. Pex5 interface with the cargo (MDH) is characterized by significant conformational dynamics restricted by PTS1 independent interactions 3. Wxxx(F/Y) motif mediated docking of Pex14 at Pex5 is complemented by interactions at the noncanonical site.
Machine Learning exploratory technic detected that men might be up to eight times more affected by the control effect and three times more affected by the placebo effect than women

Background The Placebo effect has been historically described since the beginning of Medicine. When the most skeptical researchers say they do not believe in Noetic Science but use a placebo in their research, they generate an apparent contradiction. The present study aimed to understand the noetic influence on high-level athletes, using a sportomics strategy, statistical exploratory techniques of machine learning and holistic analysis. Methods The study included 14 volunteer volleyball athletes. Each volunteer was submitted to four running tests of 3,000 meters, on a 400-meter track, with one test each subsequent day. On the first day, the athletes performed the first test of 3,000, aiming to adapt to the trial (ADAPT 1), and on the second day, the same adaptation (ADAPT 2). On the third and fourth days, the placebos were introduced, and on the third day, the athletes received the information that that would be just a placebo, which was called (CONTROL). On the fourth day, when the identical placebo was given, the athletes received the information that it would be a new cutting-edge nutritional supplement being studied (PLACEBO). Results Men might be up to eight times more affected by the control effect and three times more by the placebo effect than women. Regarding performance, there was an antagonistic behavior concerning gender for the control effect and an agonistic effect for the placebo effect, but with less impact on women. Men also showed a faster adaptation to the test. Conclusion Noetic science, always considered but never assumed by researchers, is confirmed when the present study reveals that men are more affected by the control effect and the placebo effect than women, with antagonistic behavior concerning gender for the control effect and an agonist effect for the placebo effect, but with less impact on women about performance.
Rapid Quantification of First and Second Phase Insulin Secretion Dynamics using In vitro Platform for Improving Insulin Therapy

High-throughput quantification of the first- and second-phase insulin secretion dynamics is intractable with current methods. The fact that independent secretion phases play distinct roles in metabolism necessitates partitioning them separately and performing high-throughput compound screening to target them individually. We developed an insulin-nanoluc luciferase reporter system to dissect the molecular and cellular pathways involved in the separate phases of insulin secretion. We validated this method through genetic studies, including knockdown and overexpression, as well as small-molecule screening and their effects on insulin secretion. Furthermore, we demonstrated that the results of this method are well correlated with those of single-vesicle exocytosis experiments conducted on live cells. Thus, we can quantitatively determine the number of vesicles that fuse when a stimulus is applied. We have developed a robust methodology for screening small molecules and cellular pathways that target specific phases of insulin secretion, resulting in a better understanding of insulin secretion, which in turn will result in a more effective insulin therapy through the stimulation of endogenous glucose-stimulated insulin secretion.
Supplementary motor area in speech initiation: a large-scale intracranial EEG evaluation of stereotyped word articulation

Speech production is known to engage a distributed network. The brain regions responsible for the initiation of articulation are unclear, and they would be expected to coordinate a distributed network. Using direct intracranial recordings in a large cohort, during stereotyped speech production to eliminate confounds of phonological and semantic complexity, we performed a comprehensive analysis of cortical sites engaged in speech initiation. We found that the supplementary motor area (SMA) was the earliest speech motor region to be active prior to speech onset and was active almost exclusively prior to articulation. Broadband gamma activity in the SMA was predictive of the response time of word production, predicting response time from 250 ms after stimulus onset. Neural activity in SMA began at a highly predictable time after stimulus onset and extended until speech onset. SMA activity offset coincided with ventral premotor cortex and primary motor activity onset. This suggests that the SMA may coordinate the concerted activation of motor execution cortex. Our results support the idea that SMA is a key node in the speech initiation network. Significance statement Producing speech requires coordination across multiple brain regions. One cortical region - the supplementary motor area (SMA) - has long been a candidate region to coordinate across other regions to initiate speech production. In this study, we used human intracranial recordings from patients with epilepsy to investigate the role of the SMA in initiating speech. In a picture-naming task, subjects repeated the word “scrambled” scores of times; using this condition to eliminate any linguistic confounds, we found that the SMA was consistently one of the earliest regions to activate during word production. We also uncovered the SMA’s temporally precise tuning to speech onset at the single-trial level.
Interplay between Nrf2 and αB-crystallin in the lens and heart of zebrafish under proteostatic stress

A coordinated oxidative stress response, partly triggered by the transcription factor Nrf2, protects cells from the continual production of reactive oxygen species. Left unbuffered, reactive oxygen species can lead to protein aggregation which has been implicated in a spectrum of diseases including cataract of the ocular lens and myopathy of the heart. While proteostasis is maintained by diverse families of heat shock proteins, the interplay between the oxidative and proteostatic stress responses in the lens and the heart have not been investigated. Capitalizing on multiple zebrafish lines that have compromised function of Nrf2 and/or the two zebrafish small heat-shock proteins αBa- and αBb-crystallin, we uncovered a transcriptional relationship that leads to a substantial increase in αBb-crystallin transcripts in the heart in response to compromised function of Nrf2. In the lens, the concomitant loss of function of Nrf2 and αBa-crystallin leads to upregulation of the cholesterol biosynthesis pathway thus mitigating the phenotypic consequences of the αBa-crystallin knockout. In contrast, abrogation of Nrf2 function accentuates the penetrance of a heart edema phenotype characteristic of embryos of αB-crystallin knockout lines. Multiple molecular pathways, such as genes involved in extracellular interactions and implicated in cardiomyopathy, are revealed from transcriptome profiling thus identifying novel targets for further investigation. Together our transcriptome/phenotypic analysis establishes an intersection between the oxidative stress and chaperone responses in the lens and the heart.
Results of approximation and measure on mutational spaces

This thesis extends the machinery of Mutational Analysis to accommodate numerical methods that are commonly used today, such as the Midpoint Method, Heun Method, and Runge-Kutta Methods. This is done by developing Taylor expansions in Mutational Spaces of Higher Order. Another extension of Mutational Analysis to Stochastic Mutational Analysis is considered. This extension is used to accommodate more realistic and robust models than the deterministic counterpart. A biologically relevant model is used as an illustration of this extension.
The Relationship Between Daily Living Activities and Cognitive Function in the Elderly: Cross-Sectional Study

Objective: This study aimed to describe the relationship between activities of daily living and cognitive function community-dwelling elderly in an urban area. Methods: 872 Participants were randomly selected who aged ≥65 years living in Kayseri, Turkey, patients were registered with Family Health Centers. We used the Standardized Mini-Mental State Examination (SMMSE) to assess participants’ cognitive function, the Katz Index of Independence in Activities of Daily Living (ADL) to assess activities of daily living, the Instrumental Activities of Daily Living (IADL) scale to assess instrumental activities of daily living, and a questionnaire to assess sociodemographic characteristics. Results: Participants’ mean age was 71.9±5.5 years. The overall prevalence of IADL dependency was 17.6%; dependency was significantly higher in women than in men (by 5.5%). The prevalence of ADL dependency was 0.6%, and there was no sex difference. SMMSE and IADL scores decreased as age increased, whereas the ADL score did not change. Conclusions: Increased age is a fundamental component of cognitive impairment and limitation in activities of daily living. Community-dwelling adults aged ≥65 years with cognitive impairment should receive early evaluation for IADL dependency. In addition, a daily living activity scale that takes into account social, cultural and gender characteristics may be useful in early detection of dependence.
The Presidents' Day Cyclone of 18–19 February 1979: Synoptic Overview and Analysis of the Subtropical Jet Streak Influencing the Pre-Cyclogenetic Period

Abstract The Presidents' Day cyclone of 18–19 February 1979 was an intense and rapidly developing storm which produced heavy snowfall along the East Coast of the United States. An analysis of the cyclone is presented which isolates three jet streaks that appear to have played important roles in the development of two separate areas of heavy snow. One area of heavy snow developed prior to cyclogenesis and is linked, in part, to an increasingly unbalanced subtropical jet streak (STJ) and a noticeably ageostrophic low-level jet. The second area of heavy snow developed in conjunction with the explosive cyclogenesis off the East Coast as a polar jet streak and midtropospheric trough propagated toward the coastal region from the north-central United States. This paper examines the STJ in detail. The maximum wind speeds associated with the STJ increased by 15 to 20 m s-1 between 1200 GMT 17 and 1200 GMT 18 February 1979 as the jet propagated from the south-central toward the eastern United States. During the 24 .
A Theoretical Study of the Land and Sea Breeze Circulation.

Abstract Estoque's model for the sea breeze is modified with respect to some essential and other, less essential, details. It is shown among other things that the accelerational terms in the equation for the vertical component of motion are important and should therefore be retained. In addition, the equation of continuity is retained in its original form in order to prevent violation of the mass conservation law. The new model is integrated numerically and the results presented. The results include horizontal and vertical winds, mass conservation, vertical components of vorticity, time hodographs, temperatures (including vertical profiles), vertical transfer of sensible heat, and wind stress at the surface. Particular attention is paid to the land breeze phase of the circulation which so far has received little attention in the published literature. Further, the sea breeze front is discussed in some detail. The integration is carried out for three daily cycles setting out from an atmosphere at rest. The .
Deep Convection on Day 261 of GATE

Abstract Aircraft, radar, satellite and ship data, gathered on 18 September 1974 during GATE, have been brought to bear an clouds of the middle and upper troposphere associated with a cloud cluster occurring near the ridge axis of a 700 mb wave. Clouds penetrating above 2.5 km into the middle troposphere were organized in bands about 9 km apart, aligned roughly along the direction of the wind shear in the cloud layer. Radar echoes corresponding to the cumulus congestus were of lifetime roughly 30 min, top height 6 km and peak rainfall rate 1.3 mm h−1. The number density of such echoes increased from one in 15 000 km2 to a value about three times greater, while convergence at ∼950 hPa (obtained from satellite cloud tracking) increased from about 1.5 to 3 × 10−5 s−1. Convergence into a square box of side 150 km, circumnavigated by three aircraft in the moist layer, reached about 3.5 × 10−5 s−1 near cloud base. The upward flux of water vapor at cloud base was about 0.25 g m−2 s−1, equivalent to rain of inten.
Numerical Integration of the Shallow-Water Equations on a Twisted Icosahedral Grid

Abstract The streamfunction-velocity potential form of shallow-water equations, implemented on a spherical geodesic grid, offers an attractive solution to many of the problems associated with fluid-flow simulations in a spherical geometry. Here construction of a new type of spherical geodesic grid is outlined, and discretization of the equations is explained. The model is subjected to the NCAR suite of seven test cases for shallow-water models.
Optimal Center Location in Simple Networks

The general problem is that of locating a central facility in a network so as to minimize the sum of its distances from the sources of flow to it, each distance being appropriately weighted to reflect the associated flow volume and/or cost. In this paper, simple one-pass solution algorithms are given for two classes of topologically simple networks, namely those which are either acyclic or contain exactly one cycle. The first algorithm is based on a reduction procedure that may also yield useful simplification of problems involving general networks.