julilili42/papers huggingface dataset:
Compute Trends Across Three Eras of Machine Learning
2022-02-15

Compute, data, and algorithmic advances are the three fundamental factors that guide the progress of modern Machine Learning (ML). In this paper we study trends in the most readily quantified factor - compute. We show that before 2010 training compute grew in line with Moore's law, doubling roughly every 20 months. Since the advent of Deep Learning in the early 2010s, the scaling of training compute has accelerated, doubling approximately every 6 months. In late 2015, a new trend emerged as firms developed large-scale ML models with 10 to 100-fold larger requirements in training compute. Based on these observations we split the history of compute in ML into three eras: the Pre Deep Learning Era, the Deep Learning Era and the Large-Scale Era. Overall, our work highlights the fast-growing compute requirements for training advanced ML systems.
A Chromosome Scale Assembly of an Australian Puccinia striiformis f. sp. tritici Isolate of the PstS1 Lineage
2022-02-15

Support was provided to S.Periyannan by the Australian Research Council (ARC) with funding through the Discovery Early Career Researcher Award (DE17010015) and to B. Schwessinger by the ARC Future Fellowship (FT180100024)
Comparison of soil production, chemical weathering, and physical erosion rates along a climate and ecological gradient (Chile) to global observations
2022-02-15

Abstract. Weathering of bedrock to produce regolith is essential for sustaining life on Earth and global biogeochemical cycles. The rate of this process is influenced not only by tectonics, but also by climate and biota. We present new data on soil production, chemical weathering, and physical erosion rates from the large climate and ecological gradient of the Chilean Coastal Cordillera (26 to 38∘ S). Four Chilean study areas are investigated and span (from north to south) arid (Pan de Azúcar), semi-arid (Santa Gracia), Mediterranean (La Campana), and temperate humid (Nahuelbuta) climate zones. Observed soil production rates in granitoid soil-mantled hillslopes range from ∼7 to 290 t km−2 yr−1 and are lowest in the sparsely vegetated and arid north and highest in the Mediterranean setting. Calculated chemical weathering rates range from zero in the arid north to a high of 211 t km−2 yr−1 in the Mediterranean zone. Chemical weathering rates are moderate in the semi-arid and temperate humid zones (∼20 to 50 t km−2 yr−1). Similarly, physical erosion rates are lowest in the arid zone (∼11 t km−2 yr−1) and highest in the Mediterranean climate zone (∼91 t km−2 yr−1). The contribution of chemical weathering to total denudation rates is lower in the arid north than further south. However, due to heterogeneities in lithologies and Zr concentrations, reported chemical weathering rates and chemical depletion fractions are affected by large uncertainties. Comparison of Chilean results to published global data collected from hillslope settings underlain by granitoid lithologies documents similar patterns in soil production, chemical weathering, and total denudation rates for varying mean annual precipitation and vegetation cover amounts. We discuss the Chilean and global data in the light of contending model frameworks in the literature and find that observed variations in soil production rates bear the closest resemblance to models explicitly accounting for variations in soil thickness and biomass.
Development of the First Covalent Monopolar Spindle Kinase 1 (MPS1/TTK) Inhibitor
2022-02-15

Monopolar spindle kinase 1 (MPS1/TTK) is a key element of the mitotic checkpoint and clinically evaluated as a target in the treatment of aggressive tumors such as triple-negative breast cancer. While long drug-target residence times have been suggested to be beneficial in the context of therapeutic MPS1 inhibition, no irreversible inhibitors have been reported. Here we present the design and characterization of the first irreversible covalent MPS1 inhibitor, <b>RMS-07</b>, targeting a poorly conserved cysteine in the kinase's hinge region. <b>RMS-07</b> shows potent MPS1 inhibitory activity and selectivity against all protein kinases with an equivalent cysteine but also in a broader kinase panel. We demonstrate potent cellular target engagement and pronounced activity against various cancer cell lines. The covalent binding mode was validated by mass spectrometry and an X-ray crystal structure. This proof of MPS1 covalent ligandability may open new avenues for the design of MPS1-specific chemical probes or drugs.
Molecular Basis of Rhodomyrtone Resistance in Staphylococcus aureus
2022-02-15

Antibiotic resistance is a growing public health problem, and alternative antibiotics are urgently needed. Rhodomyrtone (Rom), an antimicrobial compound originally isolated from Rhodomyrtus tomentosa , is active against multiple resistant Gram-positive pathogens.
No difference between slow oscillation up‐ and down‐state cueing for memory consolidation during sleep
2022-02-15

Summary The beneficial effects of sleep for memory consolidation are assumed to rely on the reactivation of memories in conjunction with the coordinated interplay of sleep rhythms like slow oscillations and spindles. Specifically, slow oscillations are assumed to provide the temporal frame for spindles to occur in the slow oscillations up‐states, enabling a redistribution of reactivated information within hippocampal–neocortical networks for long‐term storage. Memory reactivation can also be triggered externally by presenting learning‐associated cues (like odours or sounds) during sleep, but it is presently unclear whether there is an optimal time‐window for the presentation of such cues in relation to the phase of the slow oscillations. In the present within‐subject comparison, participants ( n = 16) learnt word‐pairs visually presented with auditory cues of the first syllable. These syllables were subsequently used for real‐time cueing either in the up‐ or down‐state of endogenous slow oscillations. Contrary to our hypothesis, we found differences in memory performance neither between up‐ and down‐state cueing, nor between word‐pairs that were cued versus uncued. In the up‐state cueing condition, higher amounts of rapid eye movement sleep were associated with better memory for cued contents, whereas higher amounts of slow‐wave sleep were associated with better memory for uncued contents. Evoked response analyses revealed signs of cue processing in both conditions. Interestingly, both up‐ and down‐state cueing evoked a similar spindle response with the induced slow oscillations up‐state at ~1000 ms post‐cue. We speculate that our cueing procedure triggered generalised reactivation processes that facilitated the consolidation of both cued and uncued memories irrespective of the slow oscillation phase.
Hard X-ray luminosity functions of cataclysmic variables: joint Swift/BAT and Gaia data
2022-02-15

ABSTRACT Cataclysmic variables (CVs) are the most numerous population among the Galactic objects emitting in hard X-rays. Most probably, they are responsible for the extended hard X-ray emission of the Galactic ridge and the central Galactic regions. Here, we consider the sample of CVs detected in the all-sky hard X-ray Swift/BAT survey, which were also detected by Gaia and thus have reliable distance estimates. Using these data, we derive accurate estimates for local number density per solar mass ( ) and luminosity density per solar mass ( erg s−1 M ) for objects in the sample. These values appear to be in good agreement with the integrated Galactic ridge X-ray emission and nuclear stellar cluster luminosities. Analysis of the differential luminosity functions dρM/d(log10Lx) and dρL/d(log10Lx) confirms that there are two populations of hard X-ray-emitting CVs. Intermediate polars dominate at luminosities L &amp;gt; 1033 erg s−1, whereas non-magnetic CVs and polars are much more numerous but have lower luminosities on average. As a consequence, the contribution of these populations to the observed hard X-ray luminosity is almost equivalent.
Regulation of canonical Wnt signalling by the ciliopathy protein MKS1 and the E2 ubiquitin-conjugating enzyme UBE2E1
2022-02-15

Primary ciliary defects cause a group of developmental conditions known as ciliopathies. Here, we provide mechanistic insight into ciliary ubiquitin processing in cells and for mouse model lacking the ciliary protein Mks1. In vivo loss of Mks1 sensitises cells to proteasomal disruption, leading to abnormal accumulation of ubiquitinated proteins. We identified UBE2E1, an E2 ubiquitin-conjugating enzyme that polyubiquitinates β-catenin, and RNF34, an E3 ligase, as novel interactants of MKS1. UBE2E1 and MKS1 colocalised, and loss of UBE2E1 recapitulates the ciliary and Wnt signalling phenotypes observed during loss of MKS1. Levels of UBE2E1 and MKS1 are co-dependent and UBE2E1 mediates both regulatory and degradative ubiquitination of MKS1. We demonstrate that processing of phosphorylated β-catenin occurs at the ciliary base through the functional interaction between UBE2E1 and MKS1. These observations suggest that correct β-catenin levels are tightly regulated at the primary cilium by a ciliary-specific E2 (UBE2E1) and a regulatory substrate-adaptor (MKS1).
Everybody is able to reflect, or aren't they? Evaluating the development of medical professionalism via a longitudinal portfolio mentoring program from a student perspective
2022-02-15

Introduction: Reflective competence is fundamental for responsible medical practice and must be systematically incorporated in medical training. To promote this, a longitudinal portfolio-based mentoring program was made mandatory at the Medical Faculty of the University of Tübingen in 2013. This study examines medical students' attitudes toward professional reflection and toward the program in general to draw conclusions about conditions as well as the needs-based design of the program. Method: In winter semester 2017/18, a retrospective questionnaire survey with free text fields was conducted (total sample: N=1.405; students S 1-9; response 37%; S 1-4 “Pre-clinic”: n=231; S 5-9 “Clinic”: n=241). Opinion trends of semester groups were identified through seven semi-structured interviews with semester speaker and peer tutors. Results: Differences in understanding and attitudes resulted in three positions: 1=approval, 2=ambivalence, 3=rejection. All three groups included individuals from pre-clinical and clinical settings with varying levels of experience. Prior experience and hidden curriculum influenced the position. Opinion trends confirmed the feedback. Conclusion: Although reflection appears in the National Competence-based Learning Objectives Catalogue for Medicine (NKLM), reflective competence is not regarded as equivalent to other study content. Motivation, commitment on the part of the mentors, and a trusting mentor-mentee relationship are effective. The flexibility of the portfolio in terms of content and methodology, as well as the curricular integration of the program are also beneficial.
Mitigating the effects of particle background on the Athena Wide Field Imager
2022-02-15

The Wide Field Imager (WFI) flying on Athena will usher in the next era of studying the hot and energetic Universe. Among Athena's ambitious science programs are observations of faint, diffuse sources limited by statistical and systematic uncertainty in the background produced by high-energy cosmic ray particles. These particles produce easily identified "cosmic-ray tracks" along with less easily identified signals produced by secondary photons or x-rays generated by particle interactions with the instrument. Such secondaries produce identical signals to the x-rays focused by the optics and cannot be filtered without also eliminating these precious photons. As part of a larger effort to estimate the level of unrejected background and mitigate its effects, we here present results from a study of background-reduction techniques that exploit the spatial correlation between cosmic-ray particle tracks and secondary events. We use Geant4 simulations to generate a realistic particle background signal, sort this into simulated WFI frames, and process those frames in a similar way to the expected flight and ground software to produce a realistic WFI observation containing only particle background. The technique under study, self-anti-coincidence (SAC), then selectively filters regions of the detector around particle tracks, turning the WFI into its own anti-coincidence detector. We show that SAC is effective at improving the systematic uncertainty for observations of faint, diffuse sources, but at the cost of statistical uncertainty due to a reduction in signal. If sufficient pixel pulse-height information is telemetered to the ground for each frame, then this technique can be applied selectively based on the science goals, providing flexibility without affecting the data quality for other science. The results presented here are relevant for any future silicon-based pixelated x-ray imaging detector and could allow the WFI and similar instruments to probe to truly faint x-ray surface brightness.
Non‐tuberculous mycobacteria isolation from presumptive tuberculosis patients in Lambaréné, Gabon
2022-02-15

Abstract Objective The prevalence of clinical cases of pulmonary non‐tuberculous mycobacteria (NTM) is increasing worldwide. The aim of this study was to determine the proportion and the NTM species isolated from presumptive tuberculosis patients in Lambaréné, Gabon. Method From January 2018 to December 2020, sputum samples from presumptive TB patients were analysed at the tuberculosis reference laboratory of the Centre de Recherches Médicales de Lambaréné. Two sputum samples were collected per patient, and culture was performed using Bactec MGIT 960. The GenoType Mycobacterium CM/AS was used for NTM isolates confirmation and species differentiation. Results Among 1363 sputum samples analysed, 285 (20.9%) were Auramin acid fast bacilli (AFB) smear‐positive. NTM were isolated in 137/1363 (10%) of the samples. The most prevalent NTM species was Mycobacterium intracellulare ( n = 74; 54%). Conclusion These results show the presence of NTM among presumptive TB patients in Gabon, which could potentially complicate TB diagnosis. This presents a new public health challenge, and emphasises the need to consider NTM in planning the prevention and management of tuberculosis control.
Upgrading anaerobic digestion within the energy economy – the methane platform
2022-02-15

Throughout history, the first and foremost role of urban water management has been the protection of human health and the local aquatic environment. To this end, the practice of (waste-)water treatment has maintained a central focus on the removal of pollutants through dissipative pathways. Approaches like – in the case of wastewater treatment – the activated sludge process, which makes 'hazardous things' disappear, have benefitted our society tremendously by safeguarding human and environmental health. While conventional (waste-)water treatment is regarded as one of the greatest engineering achievements of the 20th century, these dissipative approaches will not suffice in the 21st century as we enter the era of the circular economy. A key challenge for the future of urban water management is the need to re-envision the role of water infrastructure, still holding paramount the safeguard of human and environmental health while also becoming a more proactive force for sustainable development through the recovery of resources embedded in urban water.This book aims (i) to explain the basic principles governing resource recovery from water (how much is there, really); (ii) to provide a comprehensive overview and critical assessment of the established and emerging technologies for resource recovery from water; and (iii) to put resource recovery from water in a legal, economic (including the economy of scale of recovered products), social (consumer's point of view), and environmental sustainability framework.This book serves as a powerful teaching tool at the graduate entry master level with an aim to help develop the next generation of engineers and experts and is also highly relevant for seasoned water professionals and practicing engineers.ISBN: 9781789060317 (Paperback)ISBN: 9781780409566 (eBook)
Silica incorporated chitosan-sodium alginate nanocomposite scaffolds for tissue engineering applications
2022-02-15

Here, we report on hydrothermally synthesized silica nanoparticles at three different weight percentages (0.5, 1, and 1.5%) and incorporated into chitosan-sodium alginate composite (4:4). The above biomimetic nanocomposites were prepared using solvent casting technique. Physico-chemical, in-vitro biocompatibility, antibacterial properties and cytotoxicity of silica nanoparticles and their biomimetic nanocomposites were analyzed. The studies on biomimetic nanocomposites showed rich in-vitro biocompatibility with improved physico-chemical parameters when compared to silica nanoparticles. Biomimetically made chitosan-sodium alginate scaffold (1 wt %) contained silica nanoparticles and yielded better biocompatibility under in vitro conditions. This material is considered as suitable for tissue engineering and biomedical uses.
Nitrogen Gain and Loss Along an Ecosystem Sequence: From Semi-desert to Rainforest
2022-02-15

Plants and microorganisms, besides the climate, drive nitrogen (N) cycling in ecosystems. Our objective was to investigate N losses and N acquisition strategies along a unique ecosystem-sequence (ecosequence) ranging from arid shrubland through Mediterranean woodland to temperate rainforest. These ecosystems differ in mean annual precipitation, mean annual temperate, and vegetation cover, but developed on similar granitoid soil parent material, were addressed using a combination of molecular biology and soil biogeochemical tools. Soil N and carbon (C) contents, δ 15 N signatures, activities of N acquiring extracellular enzymes as well as the abundance of soil bacteria and fungi, and diazotrophs in bulk topsoil and rhizosphere were determined. Relative fungal abundance in the rhizosphere was higher under woodland and forest than under shrubland. This indicates toward plants' higher C investment into fungi in the Mediterranean and temperate rainforest sites than in the arid site. Fungi are likely to decompose lignified forest litter for efficient recycling of litter-derived N and further nutrients. Rhizosphere—a hotspot for the N fixation—was enriched in diazotrophs (factor 8 to 16 in comparison to bulk topsoil) emphasizing the general importance of root/microbe association in N cycle. These results show that the temperate rainforest is an N acquiring ecosystem, whereas N in the arid shrubland is strongly recycled. Simultaneously, the strongest 15 N enrichment with decreasing N content with depth was detected in the Mediterranean woodland, indicating that N mineralization and loss is highest (and likely the fastest) in the woodland across the continental transect. Higher relative aminopeptidase activities in the woodland than in the forest enabled a fast N mineralization. Relative aminopeptidase activities were highest in the arid shrubland. The highest absolute chitinase activities were observed in the forest. This likely demonstrates that (a) plants and microorganisms in the arid shrubland invest largely into mobilization and reutilization of organically bound N by exoenzymes, and (b) that the ecosystem N nutrition shifts from a peptide-based N in the arid shrubland to a peptide- and chitin-based N nutrition in the temperate rainforest, where the high N demand is complemented by intensive N fixation in the rhizosphere.
Using Blood-Test Parameters to Define Biological Age among Older Adults: Association with Morbidity and Mortality Independent of Chronological Age Validated in Two Separate Birth Cohorts
2022-02-15

Abstract Biomarkers defining biological age are typically laborious or expensive to assess. Instead, in the current study, we identified parameters based on standard laboratory blood tests across metabolic, cardiovascular, inflammatory, and kidney functioning that had been assessed in the Berlin Aging Study (BASE; n = 384) and Berlin Aging Study II (BASE-II, n = 1,517). We calculated biological age using those 12 parameters that individually predicted mortality hazards over 26 years in BASE. In BASE, older biological age was associated with more physician-observed morbidity and higher mortality hazards, over and above the effects of chronological age, sex, and education. Similarly, in BASE-II, biological age was associated with physician-observed morbidity and subjective health, over and above the effects of chronological age, sex, and education as well as alternative biomarkers including telomere length, DNA methylation age, skin age, and subjective age. We discuss the importance of biological age as one indicator of aging.
Constraining Neutron-Star Matter with Microscopic and Macroscopic Collisions
2022-02-15

Data release associated with the preprint "Constraining Neutron-Star Matter with Microscopic and Macroscopic Collisions'' (2021; arxiv:2107.06229[nucl-th])\\n\\nData includes:\\n\\nEOS files:\\n\\n\\n\\tchiral effective field theory (CEFT) up to 1nsat and extended with speed-of-sound extension (cse)\\n\\tCEFT up to 1.5 nsat and cse\\n\\tCEFT up to 1.5 nsat and extended with piecewise-polytrope\\n\\tCEFT up to 1.0 nsat, cse and enforced a uniform distribution on a radius for 1.4 solar mass neutron star (R14)\\n\\tCEFT up to 1.5 nsat, cse and enforced a uniform distribution on R14\\n\\n\\nPosterior probability files: details to be found in README.txt\\n\\nData used in Fig.1 and Fig.2 are included
Constraining Neutron-Star Matter with Microscopic and Macroscopic Collisions
2022-02-15

Data release associated with the preprint "Constraining Neutron-Star Matter with Microscopic and Macroscopic Collisions'' (2021; arxiv:2107.06229[nucl-th])\\n\\nData includes:\\n\\nEOS files:\\n\\n\\n\\tchiral effective field theory (CEFT) up to 1nsat and extended with speed-of-sound extension (cse)\\n\\tCEFT up to 1.5 nsat and cse\\n\\tCEFT up to 1.5 nsat and extended with piecewise-polytrope\\n\\tCEFT up to 1.0 nsat, cse and enforced a uniform distribution on a radius for 1.4 solar mass neutron star (R14)\\n\\tCEFT up to 1.5 nsat, cse and enforced a uniform distribution on R14\\n\\n\\nPosterior probability files: details to be found in README.txt