julilili42/papers huggingface dataset:
At the same time or one after the other? – Exploring reaction paths of nucleophilic substitution reactions using historic insights and experiments
2022-03-01

Das Titelbild zeigt im Hintergrund Christopher Ingold, Edward Hughes und Hilda Ingold (abgebildet mit Erlaubnis der Royal Society of Chemistry nach Chem. World 5(12), 2008, 50–53). Im Vordergrund ist der Mechanismus einer ein- sowie einer zweistufigen nukleophilen Substitutionsreaktion an Brombutan zu sehen. Pölloth, Häfner und Schwarzer erschließen in ihrem Beitrag die historische Erforschung von Reaktionsmechanismen durch einfache Experimente und einen history lift für den Schulunterricht.
Feasibility of Adjuvant Treatment with Abemaciclib—Real-World Data from a Large German Breast Center
2022-03-02

Abemaciclib significantly improves invasive disease-free survival when combined with endocrine therapy in clinical high-risk patients with HR+/Her2− early breast cancer (eBC). The objective of the following study was to model how many patients with eBC would be available for adjuvant treatment with abemaciclib in a real-world setting. Patients that underwent complete surgical treatment for eBC between January 2018 and December 2020 in a large single-center university hospital in Germany were eligible. Descriptive statistics were used to describe the patient population that could benefit from abemaciclib according to the inclusion criteria of monarchE. Of 1474 patients with eBC, 1121 (76.1%) had a HR+/Her2− subtype. Of these, 217 (19.4%) fulfilled the monarchE inclusion criteria. Within patients that fulfilled the monarchE inclusion criteria, 48.9% received no adjuvant or neoadjuvant chemotherapy. Thus, in a real-world situation, fewer patients will be pretreated with chemotherapy than was the case in monarchE. Breast care units are facing a significant patient burden, since the 2-year abemaciclib therapy requires regular monitoring of toxicities. Specific care concepts to strengthen therapy adherence as well as further studies to deescalate adjuvant systemic treatment and individualize CDK 4/6 inhibitor therapy are therefore needed.
Fragmentation and disk formation during high-mass star formation: The IRAM NOEMA (Northern Extended Millimeter Array) large program CORE
2022-03-02

Aims: We aim to understand the fragmentation as well as the disk formation, outflow generation and chemical processes during high-mass star formation on spatial scales of individual cores. Methods: Using the IRAM Northern Extended Millimeter Array (NOEMA) in combination with the 30m telescope, we have observed in the IRAM large program CORE the 1.37mm continuum and spectral line emission at high angular resolution (~0.4'') for a sample of 20 well-known high-mass star-forming regions with distances below 5.5kpc and luminosities larger than 10^4Lsun. Results: We present the overall survey scope, the selected sample, the observational setup and the main goals of CORE. Scientifically, we concentrate on the mm continuum emission on scales on the order of 1000AU. We detect strong mm continuum emission from all regions, mostly due to the emission from cold dust. The fragmentation properties of the sample are diverse. We see extremes where some regions are dominated by a single high-mass core whereas others fragment into as many as 20 cores. A minimum-spanning-tree analysis finds fragmentation at scales on the order of the thermal Jeans length or smaller suggesting that turbulent fragmentation is less important than thermal gravitational fragmentation. The diversity of highly fragmented versus singular regions can be explained by varying initial density structures and/or different initial magnetic field strengths. Conclusions: The smallest observed separations between cores are found around the angular resolution limit which indicates that further fragmentation likely takes place on even smaller spatial scales. The CORE project with its numerous spectral line detections will address a diverse set of important physical and chemical questions in the field of high-mass star formation.
Optimal ridge penalty for real-world high-dimensional data can be zero or negative due to the implicit ridge regularization
2022-03-02

A conventional wisdom in statistical learning is that large models require strong regularization to prevent overfitting. Here we show that this rule can be violated by linear regression in the underdetermined situation under realistic conditions. Using simulations and real-life high-dimensional data sets, we demonstrate that an explicit positive ridge penalty can fail to provide any improvement over the minimum-norm least squares estimator. Moreover, the optimal value of ridge penalty in this situation can be negative. This happens when the high-variance directions in the predictor space can predict the response variable, which is often the case in the real-world high-dimensional data. In this regime, low-variance directions provide an implicit ridge regularization and can make any further positive ridge penalty detrimental. We prove that augmenting any linear model with random covariates and using minimum-norm estimator is asymptotically equivalent to adding the ridge penalty. We use a spiked covariance model as an analytically tractable example and prove that the optimal ridge penalty in this case is negative when .
Prenatal dexamethasone treatment for classic 21-hydroxylase deficiency in Europe
2022-03-02

Objective To assess the current medical practice in Europe regarding prenatal dexamethasone (Pdex) treatment of congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency. Design and methods A questionnaire was designed and distributed, including 17 questions collecting quantitative and qualitative data. Thirty-six medical centres from 14 European countries responded and 30 out of 36 centres were reference centres of the European Reference Network on Rare Endocrine Conditions, EndoERN. Results Pdex treatment is currently provided by 36% of the surveyed centres. The treatment is initiated by different specialties, that is paediatricians, endocrinologists, gynaecologists or geneticists. Regarding the starting point of Pdex, 23% stated to initiate therapy at 4–5 weeks postconception (wpc), 31% at 6 wpc and 46 % as early as pregnancy is confirmed and before 7 wpc at the latest. A dose of 20 μg/kg/day is used. Dose distribution among the centres varies from once to thrice daily. Prenatal diagnostics for treated cases are conducted in 72% of the responding centres. Cases treated per country and year vary between 0.5 and 8.25. Registries for long-term follow-up are only available at 46% of the centres that are using Pdex treatment. National registries are only available in Sweden and France. Conclusions This study reveals a high international variability and discrepancy in the use of Pdex treatment across Europe. It highlights the importance of a European cooperation initiative for a joint international prospective trial to establish evidence-based guidelines on prenatal diagnostics, treatment and follow-up of pregnancies at risk for CAH.
Surgical Approach for Rapid and Minimally Traumatic Recovery of Human Inner Ear Tissues From Deceased Organ Donors
2022-03-02

Objective: To develop a surgical approach for rapid and minimally traumatic recovery of inner ear tissue from human organ and tissue donors to provide fresh tissue for use in inner ear research. Study Design: Exploration of novel surgical methodology and evaluation of the steps necessary for obtaining specimens from donors during the procurement of organs for transplantation. Setting: Donor procurement locations across multiple local hospitals and tissue processing at the microsurgical temporal bone laboratory. Patients Tissue Source: Human organ and tissue donors. Interventions: Dissection and procurement of the inner ear tissue. Main Outcome Measures: Development of rapid and minimally traumatic inner ear tissue recovery. Primarily, establishing an efficient process which includes collaboration with transplant network, implementing a consent protocol, developing and training an on-call recovery team, and designing a portable surgical kit suitable for use in a variety of settings. Results: The extraction procedure is described in three consecutive steps: the trans-canal exposure, the approach to the vestibule with extraction of the vestibular organs; and the approach to extract inner ear tissues from the cochlear duct. Conclusions: Organ and tissue donors are a promising and underutilized resource of inner ear organs for purposes of research and future translational studies. Using our modified technique through the trans-canal/trans-otic approach, we were able to extract tissues of the vestibular and auditory end organs in a timely manner.
Agricultural resources in the Bronze Age city of Tel Lachish
2022-03-02

Abstract In this paper, we present the results of the plant macrofossil analyses from the site of Tel Lachish, Israel with focus on the botanical assemblage of the Middle and Late Bronze Age layers collected in two different areas of the tell: Area S, a trench on the western edge of the site, whose samples belong to Late Bronze Age deposits, and Area P, the palace area on the top of the mound with samples ranging from the Middle to Late Bronze Age. Systematic sampling of these areas and analysis of the remains have extended our knowledge of the agricultural resources of one of the most influential Late Bronze Age cities in the southern Levant. Multivariate statistics have been applied to gain insight into regional patterns of crop growing. Fruit crops account for the majority of the identified remains from this site, which also included large quantities of Hordeum vulgare (barley) and Triticum dicoccum (emmer wheat) grains. The virtual lack of chaff remains is not solely a matter of preservation, since the Late Bronze Age assemblage preserved fragile small seeds. Rather, this finding suggests that cereal processing took place some distance from the area of deposition. Overall high diversity, ubiquity and proportions of fruit crops indicate that these played a fundamental role in their cultivation and probably also in cultural life at Lachish throughout the 15th–12th centuries bce .
Visual Motion Coherence Responses in Human Visual Cortex
2022-03-02

Random dot kinematograms (RDKs) have recently been used to train subjects with cortical scotomas to perform direction of motion discrimination, partially restoring visual motion perception. To study the recovery of visual perception, it is important to understand how visual areas in normal subjects and subjects with cortical scotomas respond to RDK stimuli. Studies in normal subjects have shown that blood oxygen level-dependent (BOLD) responses in human area hV5/MT+ increase monotonically with coherence, in general agreement with electrophysiology studies in primates. However, RDK responses in prior studies were obtained while the subject was performing fixation, not a motion discrimination condition. Furthermore, BOLD responses were gauged against a baseline condition of uniform illumination or static dots, potentially decreasing the specificity of responses for the spatial integration of local motion signals (motion coherence). Here, we revisit this question starting from a baseline RDK condition of no coherence, thereby isolating the component of BOLD response due specifically to the spatial integration of local motion signals. In agreement with prior studies, we found that responses in the area hV5/MT+ of healthy subjects were monotonically increasing when subjects fixated without performing a motion discrimination task. In contrast, when subjects were performing an RDK direction of motion discrimination task, responses in the area hV5/MT+ remained flat, changing minimally, if at all, as a function of motion coherence. A similar pattern of responses was seen in the area hV5/MT+ of subjects with dense cortical scotomas performing direction of motion discrimination for RDKs presented inside the scotoma. Passive RDK presentation within the scotoma elicited no significant hV5/MT+ responses. These observations shed further light on how visual cortex responses behave as a function of motion coherence, helping to prepare the ground for future studies using these methods to study visual system recovery after injury.
Project AutoVision: Localization and 3D Scene Perception for an Autonomous Vehicle with a Multi-Camera System
2022-03-02

Project AutoVision aims to develop localization and 3D scene perception capabilities for a self-driving vehicle. Such capabilities will enable autonomous navigation in urban and rural environments, in day and night, and with cameras as the only exteroceptive sensors. The sensor suite employs many cameras for both 360-degree coverage and accurate multi-view stereo; the use of low-cost cameras keeps the cost of this sensor suite to a minimum. In addition, the project seeks to extend the operating envelope to include GNSS-less conditions which are typical for environments with tall buildings, foliage, and tunnels. Emphasis is placed on leveraging multi-view geometry and deep learning to enable the vehicle to localize and perceive in 3D space. This paper presents an overview of the project, and describes the sensor suite and current progress in the areas of calibration, localization, and perception.
Generalisation in humans and deep neural networks
2022-03-02

We compare the robustness of humans and current convolutional deep neural networks (DNNs) on object recognition under twelve different types of image degradations. First, using three well known DNNs (ResNet-152, VGG-19, GoogLeNet) we find the human visual system to be more robust to nearly all of the tested image manipulations, and we observe progressively diverging classification error-patterns between humans and DNNs when the signal gets weaker. Secondly, we show that DNNs trained directly on distorted images consistently surpass human performance on the exact distortion types they were trained on, yet they display extremely poor generalisation abilities when tested on other distortion types. For example, training on salt-and-pepper noise does not imply robustness on uniform white noise and vice versa. Thus, changes in the noise distribution between training and testing constitutes a crucial challenge to deep learning vision systems that can be systematically addressed in a lifelong machine learning approach. Our new dataset consisting of 83K carefully measured human psychophysical trials provide a useful reference for lifelong robustness against image degradations set by the human visual system.
Diverse feature visualizations reveal invariances in early layers of deep neural networks
2022-03-02

Visualizing features in deep neural networks (DNNs) can help understanding their computations. Many previous studies aimed to visualize the selectivity of individual units by finding meaningful images that maximize their activation. However, comparably little attention has been paid to visualizing to what image transformations units in DNNs are invariant. Here we propose a method to discover invariances in the responses of hidden layer units of deep neural networks. Our approach is based on simultaneously searching for a batch of images that strongly activate a unit while at the same time being as distinct from each other as possible. We find that even early convolutional layers in VGG-19 exhibit various forms of response invariance: near-perfect phase invariance in some units and invariance to local diffeomorphic transformations in others. At the same time, we uncover representational differences with ResNet-50 in its corresponding layers. We conclude that invariance transformations are a major computational component learned by DNNs and we provide a systematic method to study them.
Real-Time Dense Mapping for Self-driving Vehicles using Fisheye Cameras
2022-03-02

We present a real-time dense geometric mapping algorithm for large-scale environments. Unlike existing methods which use pinhole cameras, our implementation is based on fisheye cameras which have larger field of view and benefit some other tasks including Visual-Inertial Odometry, localization and object detection around vehicles. Our algorithm runs on in-vehicle PCs at 15 Hz approximately, enabling vision-only 3D scene perception for self-driving vehicles. For each synchronized set of images captured by multiple cameras, we first compute a depth map for a reference camera using plane-sweeping stereo. To maintain both accuracy and efficiency, while accounting for the fact that fisheye images have a rather low resolution, we recover the depths using multiple image resolutions. We adopt the fast object detection framework YOLOv3 to remove potentially dynamic objects. At the end of the pipeline, we fuse the fisheye depth images into the truncated signed distance function (TSDF) volume to obtain a 3D map. We evaluate our method on large-scale urban datasets, and results show that our method works well even in complex environments.
You Say 'What', I Hear 'Where' and 'Why': (Mis-)Interpreting SQL to Derive Fine-Grained Provenance
2022-03-02

SQL declaratively specifies what the desired output of a query is. This work shows that a non-standard interpretation of the SQL semantics can, instead, disclose where a piece of the output originated in the input and why that piece found its way into the result. We derive such data provenance for very rich SQL dialects (including recursion, windowed aggregates, and user-defined functions) at the fine-grained level of individual table cells. The approach is non-invasive and implemented as a compositional source-level SQL rewrite: an input SQL query is transformed into its own interpreter that wields data dependencies instead of regular values. We deliberately design this transformation to preserve the shape of both data and query, which allows provenance derivation to scale to complex queries without overwhelming the underlying database system.
Turning Cliques into Paths to Achieve Planarity
2022-03-02

Motivated by hybrid graph representations, we introduce and study the following beyond-planarity problem, which we call -Clique2Path Planarity: Given a graph , whose vertices are partitioned into subsets of size at most , each inducing a clique, remove edges from each clique so that the subgraph induced by each subset is a path, in such a way that the resulting subgraph of is planar. We study this problem when is a simple topological graph, and establish its complexity in relation to -planarity. We prove that -Clique2Path Planarity is NP-complete even when and is a simple -plane graph, while it can be solved in linear time, for any , when is -plane.
Orthogonal and Smooth Orthogonal Layouts of 1-Planar Graphs with Low Edge Complexity
2022-03-02

While orthogonal drawings have a long history, smooth orthogonal drawings have been introduced only recently. So far, only planar drawings or drawings with an arbitrary number of crossings per edge have been studied. Recently, a lot of research effort in graph drawing has been directed towards the study of beyond-planar graphs such as 1-planar graphs, which admit a drawing where each edge is crossed at most once. In this paper, we consider graphs with a fixed embedding. For 1-planar graphs, we present algorithms that yield orthogonal drawings with optimal curve complexity and smooth orthogonal drawings with small curve complexity. For the subclass of outer-1-planar graphs, which can be drawn such that all vertices lie on the outer face, we achieve optimal curve complexity for both, orthogonal and smooth orthogonal drawings.
Arabidopsis PFA-DSP-type phosphohydrolases target specific inositol pyrophosphate messengers
2022-03-02

ABSTRACT Inositol pyrophosphates are signaling molecules containing at least one phosphoanhydride bond that regulate a wide range of cellular processes in eukaryotes. With a cyclic array of phosphate esters and diphosphate groups around myo -inositol, these molecular messengers possess the highest charge density found in nature. Recent work deciphering inositol pyrophosphate biosynthesis in Arabidopsis revealed important functions of these messengers in nutrient sensing, hormone signaling and plant immunity. However, despite the rapid hydrolysis of these molecules in plant extracts, very little is known about the molecular identity of the phosphohydrolases that convert these messengers back to their inositol polyphosphate precursors. Here, we investigate whether Arabidopsis Plant and Fungi Atypical Dual Specificity Phosphatases (PFA-DSP1-5) catalyze inositol pyrophosphate phosphohydrolase activity. We find that recombinant proteins of all five Arabidopsis PFA-DSP homologs display phosphohydrolase activity with a high specificity for the 5-β-phosphate of inositol pyrophosphates. We further show that heterologous expression of Arabidopsis PFA-DSP1-5 rescues wortmannin-sensitivity and deranged inositol pyrophosphate homeostasis caused by the deficiency of the PFA-DSP-type inositol pyrophosphate phosphohydrolase Siw14 in yeast. Heterologous expression in Nicotiana benthamiana leaves provided evidence that Arabidopsis PFA-DSP1 also displays 5-β-phosphate specific inositol pyrophosphate phosphohydrolase activity in planta . Our findings lay the biochemical basis and provide the genetic tools to uncover the roles of inositol pyrophosphates in plant physiology and plant development.
Functional Connectivity States of Alpha Rhythm Sources in the Human Cortex at Rest: Implications for Real-Time Brain State Dependent EEG-TMS
2022-03-03

Alpha is the predominant rhythm of the human electroencephalogram, but its function, multiple generators and functional coupling patterns are still relatively unknown. In this regard, alpha connectivity patterns can change between different cortical generators depending on the status of the brain. Therefore, in the light of the communication through coherence framework, an alpha functional network depends on the functional coupling patterns in a determined state. This notion has a relevance for brain-state dependent EEG-TMS because, beyond the local state, a network connectivity overview at rest could provide further and more comprehensive information for the definition of ‘instantaneous state’ at the stimulation moment, rather than just the local state around the stimulation site. For this reason, we studied functional coupling at rest in 203 healthy subjects with MEG data. Sensor signals were source localized and connectivity was studied at the Individual Alpha Frequency (IAF) between three different cortical areas (occipital, parietal and prefrontal). Two different and complementary phase-coherence metrices were used. Our results show a consistent connectivity between parietal and prefrontal regions whereas occipito-prefrontal connectivity is less marked and occipito-parietal connectivity is extremely low, despite physical closeness. We consider our results a relevant add-on for informed, individualized real-time brain state dependent stimulation, with possible contributions to novel, personalized non-invasive therapeutic approaches.