bluuebunny/crossref_metadata_2025_split huggingface dataset:
Germline AGO2 mutations impair RNA interference and human neurological development
Authors: Lessel Davor , Zeitler Daniela M. , Reijnders Margot R. F. , Kazantsev Andriy , Hassani Nia Fatemeh , Bartholomäus Alexander , Martens Victoria , Bruckmann Astrid , Graus Veronika , McConkie-Rosell Allyn , McDonald Marie , Lozic Bernarda , Tan Ee-Shien , Gerkes Erica , Johannsen Jessika , Denecke Jonas , Telegrafi Aida , Zonneveld-Huijssoon Evelien , Lemmink Henny H. , Cham Breana W. M. , Kovacevic Tanja , Ramsdell Linda , Foss Kimberly , Le Duc Diana , Mitter Diana , Syrbe Steffen , Merkenschlager Andreas , Sinnema Margje , Panis Bianca , Lazier Joanna , Osmond Matthew , Hartley Taila , Mortreux Jeremie , Busa Tiffany , Missirian Chantal , Prasun Pankaj , Lüttgen Sabine , Mannucci Ilaria , Lessel Ivana , Schob Claudia , Kindler Stefan , Pappas John , Rabin Rachel , Willemsen Marjolein , Gardeitchik Thatjana , Löhner Katharina , Rump Patrick , Dias Kerith-Rae , Evans Carey-Anne , Andrews Peter Ian , Roscioli Tony , Brunner Han G. , Chijiwa Chieko , Lewis M. E. Suzanne , Jamra Rami Abou , Dyment David A. , Boycott Kym M. , Stegmann Alexander P. A. , Kubisch Christian , Tan Ene-Choo , Mirzaa Ghayda M. , McWalter Kirsty , Kleefstra Tjitske , Pfundt Rolph , Ignatova Zoya , Meister Gunter , Kreienkamp Hans-Jürgen 
Published: November 2020

AbstractARGONAUTE-2 and associated miRNAs form the RNA-induced silencing complex (RISC), which targets mRNAs for translational silencing and degradation as part of the RNA interference pathway. Despite the essential nature of this process for cellular function, there is little information on the role of RISC components in human development and organ function. We identify 13 heterozygous mutations in AGO2 in 21 patients affected by disturbances in neurological development. Each of the identified single amino acid mutations result in impaired shRNA-mediated silencing. We observe either impaired RISC formation or increased binding of AGO2 to mRNA targets as mutation specific functional consequences. The latter is supported by decreased phosphorylation of a C-terminal serine cluster involved in mRNA target release, increased formation of dendritic P-bodies in neurons and global transcriptome alterations in patient-derived primary fibroblasts. Our data emphasize the importance of gene expression regulation through the dynamic AGO2-RNA association for human neuronal development.
Time reversed optical waves by arbitrary vector spatiotemporal field generation
Authors: Mounaix Mickael , Fontaine Nicolas K. , Neilson David T. , Ryf Roland , Chen Haoshuo , Alvarado-Zacarias Juan Carlos , Carpenter Joel 
Published: November 2020

AbstractLossless linear wave propagation is symmetric in time, a principle which can be used to create time reversed waves. Such waves are special “pre-scattered” spatiotemporal fields, which propagate through a complex medium as if observing a scattering process in reverse, entering the medium as a complicated spatiotemporal field and arriving after propagation as a desired target field, such as a spatiotemporal focus. Time reversed waves have previously been demonstrated for relatively low frequency phenomena such as acoustics, water waves and microwaves. Many attempts have been made to extend these techniques into optics. However, the much higher frequencies of optics make for very different requirements. A fully time reversed wave is a volumetric field with arbitrary amplitude, phase and polarisation at every point in space and time. The creation of such fields has not previously been possible in optics. We demonstrate time reversed optical waves with a device capable of independently controlling all of light’s classical degrees of freedom simultaneously. Such a class of ultrafast wavefront shaper is capable of generating a sequence of arbitrary 2D spatial/polarisation wavefronts at a bandwidth limited rate of 4.4 THz. This ability to manipulate the full field of an optical beam could be used to control both linear and nonlinear optical phenomena.
Superiority of albumin–globulin ratio over albumin to predict mortality in patients undergoing peritoneal dialysis
Authors: Tsai Chun-Chieh , Hsieh Yao-Peng , Tsai Shr-Mei , Kor Chew-Teng , Chiu Ping-Fang 
Published: November 2020

AbstractThere is increasing evidence showing that albumin–globulin ratio (AGR) can predict the survival of patients in many types of malignancies. However, no study was done to explore the value of AGR in peritoneal dialysis (PD) patients. A total of 554 incident patients undergoing PD from January 2001 through July 2016 were enrolled for this retrospective observational study. The outcomes of interest were all-cause mortality and cardiovascular disease (CVD) mortality. Baseline patient’s socio-demographic data, pharmacotherapy, comorbidities, laboratory and PD-related parameters were collected and used in the multivariate Cox models. The predictive value of AGR on mortality risk was compared with other markers using area under the receiver operating characteristic curve (AUC) analysis. Among the study participants, there were 265 (47.83%) men and the mean follow-up time was 3.87 ± 3.15 years. Univariate Cox analysis showed that low AGR was significantly associated with worse outcomes in terms of all-cause and CVD mortality and it remained an independent predictor in the multivariate models. The fully adjusted hazard ratios for the low AGR group versus high AGR group were 2.12 (95% CI 1.34–3.35, p = 0.001) and 2.58 (95% CI 1.42–4.7, p = 0.002) for all-cause and CVD mortality, respectively. The predictive ability of AGR for mortality risk was superior to that of other biomarkers based on AUC calculations. In conclusion, low AGR was independently associated with higher all-cause and CVD mortality risks in patients undergoing PD.
Study of spatial and temporal aging characteristic of catalyzed diesel particulate filter catalytic performance used for diesel vehicle
Authors: Zhang Yun-hua , Lou Di-ming , Tan Pi-qiang , Hu Zhi-yuan 
Published: November 2020

AbstractCatalyzed diesel particulate filters (CDPFs) have been widespread used as a technically and economically feasible mean for meeting increasingly stringent emissions limits. An important issue affecting the performance of a CDPF is its aging with using time. In this paper, the effects of noble metal loadings, regions and using mileage on the aging performance of a CDPF were investigated by methods of X-ray diffraction (XRD), X-ray photoelectron spectroscopy and catalytic activity evaluation. Results showed that aging of the CDPF shifted the XRD characteristic diffraction peaks towards larger angles and increased the crystallinity, showing a slowing downward trend with the increase of the noble metal loadings. In addition, the increase of the noble metal loading would slow down the decline of Pt and Pt4+ concentration caused by aging. The characteristic temperatures of CO, C3H8 conversion and NO2 production increased after aging, and the more the noble metal loadings, the higher the range of the increase. But noticeably, excessive amounts of noble metals would not present the corresponding anti-aging properties. Specifically, the degree of aging in the inlet region was the deepest, the following is the outlet region, and the middle region was the smallest, which were also reflected in the increase range of crystallinity, characteristic temperatures of CO, C3H8 conversion and NO2 production, as well as the decrease range of Pt and Pt4+ concentrations. The increase of aging mileage reduced the size of the aggregates of the soot and ash in CDPFs, however, improved the degree of tightness between particles. Meanwhile Carbon (C) concentration in the soot and ash increased with the aging mileage.
Differential parameters between activity flare and acute infection in pediatric patients with systemic lupus erythematosus
Authors: Luo Kai-Ling , Yang Yao-Hsu , Lin Yu-Tsan , Hu Ya-Chiao , Yu Hsin-Hui , Wang Li-Chieh , Chiang Bor-Luen , Lee Jyh-Hong 
Published: November 2020

AbstractSystemic lupus erythematosus (SLE) patients are vulnerable to infections. We aim to explore the approach to differentiate active infection from disease activity in pediatric SLE patients. Fifty pediatric SLE patients presenting with 185 clinical visits were collected. The associations between both clinical and laboratory parameters and the outcome groups were analyzed using generalized estimating equations (GEEs). These 185 visits were divided into 4 outcome groups: infected-active (n = 102), infected-inactive (n = 11), noninfected-active (n = 59), and noninfected-inactive (n = 13) visits. Multivariate GEE (generalized estimating equation) analysis showed that SDI, SLEDAI-2K, neutrophil‐to‐lymphocyte ratio (NLR), hemoglobin, platelet, RDW-to-platelet ratio (RPR), and C3 are predictive of flare (combined calculated AUC of 0.8964 and with sensitivity of 82.2% and specificity of 90.9%). Multivariate GEE analysis showed that SDI, fever temperature, CRP, procalcitonin (PCT), lymphocyte percentage, NLR, hemoglobin, and renal score in SLEDAI-2k are predictive of infection (combined calculated AUC of 0.7886 and with sensitivity of 63.5% and specificity of 89.2%). We can simultaneously predict 4 different outcome with accuracy of 70.13% for infected-active group, 10% for infected-inactive group, 59.57% for noninfected-active group, and 84.62% for noninfected-inactive group, respectively. Combination of parameters from four different domains simultaneously, including inflammation (CRP, ESR, PCT), hematology (Lymphocyte percentage, NLR, PLR), complement (C3, C4), and clinical status (SLEDAI, SDI) is objective and effective to differentiate flares from infections in pediatric SLE patients.
Understanding Hydrogen Bonds
Authors: Grabowski Sławomir J 
Published: November 2020

Hydrogen bonded systems play an important role in all aspects of science but particularly chemistry and biology. Notably, the helical structure of DNA is heavily reliant on the hydrogens bonds between the DNA base pairs. Although the area of hydrogen bonding is one that is well established, our understanding has continued to develop as the power of both computational and experimental techniques has improved.
Understanding Hydrogen Bonds presents an up-to-date overview of our theoretical and experimental understanding of the hydrogen bond. Well-established and novel approaches are discussed, including quantum theory of ‘atoms in molecules’ (QTAIM); the electron localization function (ELF) method and Car–Parinnello molecular dynamics; the natural bond orbital (NBO) approach; and X-ray and neutron diffraction and spectroscopy. The mechanism of hydrogen bond formation is described and comparisons are made between hydrogen bonds and other types of interaction. The author also takes a look at new types of interaction that may be classified as hydrogen bonds with a focus on those with multicentre proton acceptors or with multicentre proton donors.
Understanding Hydrogen Bonds is a valuable reference for experimentalists and theoreticians interested in updating their understanding of the types of hydrogen bonds, their role in chemistry and biology, and how they can be studied.
Variability of Stuttering: Behavior and Impact
Authors: Tichenor Seth E. , Yaruss J. Scott 
Published: November 2020

Purpose
It has long been known that stuttering behaviors vary across time and situation. Preliminary evidence suggests that this variability negatively affects people who stutter and that stuttering behaviors are more variable than adverse impact associated with stuttering. More information is needed to determine how variability affects people who stutter and what the clinical and research implications of variability may be.

Method
Two hundred and four adults who stutter participated in a mixed-methods study exploring (a) how variability of stuttering affects people who stutter in comparison to other aspects of the condition and (b) which aspects of the overall experience of stuttering are variable.

Results

Analyses indicated that variability is very commonly experienced by people who stutter and that it is among the most frustrating aspects of the condition. Qualitative analyses revealed that variability is experienced in all aspects of the stuttering condition, including the observable behavior other affective, behavioral, and cognitive reactions; and the adverse impact of stuttering. Notable individual differences were found in terms of which specific aspects of the condition were more variable for different respondents. Overall, analyses revealed that the variability of different aspects of stuttering can be viewed in a hierarchy from most variable to least variable:
more external
aspects (e.g., frequency, duration),
more internal
aspects (e.g., covert behaviors, physical tension), and
cognitive–affective
experiences (e.g., negative thoughts, feelings, and self-image).

Discussion
These findings suggest that variability is a common and burdensome aspect of the experience of stuttering and underscore the importance of considering variability in stuttering behavior, reactions, and impact in research, assessment, and treatment for adults who stutter.
Wave-particle energy transfer directly observed in an ion cyclotron wave
Authors: Vech D. , Martinović M. M. , Klein K. G. , Malaspina D. M. , Bowen T. A. , Verniero J. L. , Paulson K. , Dudok de Wit T. , Kasper J. C. , Huang J. , Stevens M. L. , Case A. W. , Korreck K. , Mozer F. S. , Goodrich K. A. , Bale S. D. , Whittlesey P. L. , Livi R. , Larson D. E. , Pulupa M. , Bonnell J. , Harvey P. , Goetz K. , MacDowall R. 
Published: November 2020

Context. The first studies with Parker Solar Probe (PSP) data have made significant progress toward understanding of the fundamental properties of ion cyclotron waves in the inner heliosphere. The survey mode particle measurements of PSP, however, did not make it possible to measure the coupling between electromagnetic fields and particles on the time scale of the wave periods.
Aims. We present a novel approach to study wave-particle energy exchange with PSP.
Methods. We used the Flux Angle operation mode of the Solar Probe Cup in conjunction with the electric field measurements and present a case study when the Flux Angle mode measured the direct interaction of the proton velocity distribution with an ion cyclotron wave.
Results. Our results suggest that the energy transfer from fields to particles on the timescale of a cyclotron period is equal to approximately 3–6% of the electromagnetic energy flux. This rate is consistent with the hypothesis that the ion cyclotron wave was locally generated in the solar wind.
System simulations for the ALICE ITS detector upgrade
Authors: Voigt Nesbo Simon , Alme Johan , Bonora Matthias , Giubilato Piero , Helstrup Håvard , Lupi Matteo , Aglieri Rinella Gianluca , Röhrich Dieter , Schambach Joachim , Shahoyan Ruben , Velure Arild 
Published: November 2020

The ALICE experiment at the CERN LHC will feature several upgrades for Run 3, one of which is a new Inner Tracking System (ITS). The ITS upgrade is currently under development and commissioning, and will be installed during the ongoing long shutdown 2.A number of factors will have an impact on the performance and readout efficiency of the ITS in run 3, and to that end, a simulation model of the readout logic in the ALPIDE pixel sensor chips for the ITS was developed, using the SystemC library for system level modeling in C++. This simulation model is three orders of magnitude faster than a normal HDL simulation of the chip and facilitates simulations of an increased number of events for a large portion of the detector.In this paper, we present simulation results, where we have been able to quantify detector performance under different running conditions. The results are used for system configuration as well as for the ongoing development of the readout electronics.
FullSimLight: ATLAS standalone Geant4 simulation
Authors: Bandieramonte Marilena , Bianchi Riccardo Maria , Boudreau Joseph 
Published: November 2020

HEP experiments simulate the detector response by accessing all needed data and services within their own software frameworks. However decoupling the simulation process from the experiment infrastructure can be useful for a number of tasks, amongst them the debugging of new features, or the validation of multi-threaded vs sequential simulation code and the optimization of algorithms for HPCs. The relevant features and data must be extracted from the framework to produce a standalone simulation application.
As an example, the simulation of the detector response of the ATLAS experiment at the LHC is based on the Geant4 toolkit and is fully integrated in the experiment’s framework “Athena”. Recent developments opened the possibility of accessing a full persistent copy of the ATLAS geometry outside of the Athena framework. This is a prerequisite for running ATLAS Geant4 simulation standalone. In this paper we present the status of development of FullSimLight, a lightweight simulation prototype that is being developed with the goal of running ATLAS standalone Geant4 simulation with the actual ATLAS geometry. The purpose of FullSimLight is to simplify studies of Geant4 tracking and physics processes, including tests on novel architectures. We will also address the challenges related to the complexity of ATLAS’s geometry implementation, which precludes make persistent a complete detector description in a way that can be automatically read by standalone Geant4. This lightweight prototype is meant to ease debugging operations on the Geant4 side and to allow early testing of new Geant4 releases. It will also ease optimization studies and R&D activities related to HPC development: i.e. the possibility to offload partially/totally the simulation to GPUs/Accelerators without having to port the whole experimental infrastructure.
ServiceX A Distributed, Caching, Columnar Data Delivery Service
Authors: Galewsky B. , Gardner R. , Gray L. , Neubauer M. , Pivarski J. , Proffitt M. , Vukotic I. , Watts G. , Weinberg M. 
Published: November 2020

We will describe a component of the Intelligent Data Delivery Service being developed in collaboration with IRIS-HEP and the LHC experiments. ServiceX is an experiment-agnostic service to enable on-demand data delivery specifically tailored for nearly-interactive vectorized analysis. This work is motivated by the data engineering challenges posed by HL-LHC data volumes and the increasing popularity of python and Spark-based analysis workflows.
ServiceX gives analyzers the ability to query events by dataset metadata. It uses containerized transformations to extract just the data required for the analysis. This operation is colocated with the data to avoid transferring unnecessary branches over the WAN. Simple filtering operations are supported to further reduce the amount of data transferred.
Transformed events are cached in a columnar datastore to accelerate delivery of subsequent similar requests. ServiceX will learn commonly related columns and automatically include them in the transformation to increase the potential for cache hits by other users.
Selected events are streamed to the analysis system using an efficient wire protocol that can be readily consumed by a variety of computational frameworks. This reduces time-to-insight for physics analysis by delegating to ServiceX the complexity of event selection, slimming, reformatting, and streaming.
dCache – Efficient Message Encoding For Inter-Service Communication in dCache: Evaluation of Existing Serialization Protocols as a Replacement for Java Object Serialization
Authors: Morschel Lea , Adeyemi Olufemi , Garonne Vincent , Litvintsev Dmitry , Millar Paul , Mkrtchyan Tigran , Rossi Albert , Sahakyan Marina , Starek Juergen , Yasar Sibel 
Published: November 2020

As a well established, large-scale distributed storage system, dCache is used to manage and serve huge amounts of data collected by high energy physics, astrophysics and photon science experiments. Based on a microservices-like architecture, dCache is built as a modular distributed system, where each component provides a different core functionality. These services communicate by passing serialized messages to each other, a core behavior whose performance properties can consequently affect the entire system.
This paper compares and evaluates different data serialization protocols in computer science with the objective of replacing and improving upon Java Object Serialization (JOS), which has increasingly presented itself as no longer being sufficiently performant for encoding messages. The criteria for choosing a new framework are collected, analyzed and formalized. The primary motivation for replacing Java serialization for encoding dCache messages is increasing the general speed of message-passing and thereby reducing the round-trip time for user requests. Emphasis is also placed on schema evolution capabilities and framework usability. Approaches for generalizing (de)serialization speed and size measurements based on data structure complexity are introduced, criteria for measuring documentation, learning curve, maintainability and introduction effort are defined. Finally, several selected serialization protocols are evaluated and compared accordingly, concluding with a recommendation for a suitable JOS replacement.
Beyond HEP: Photon and accelerator science computing infrastructure at DESY
Authors: Beyer Christoph , Bujack Stefan , Dietrich Stefan , Finnern Thomas , Flemming Martin , Fuhrmann Patrick , Gasthuber Martin , Gellrich Andreas , Guelzow Volker , Hartmann Thomas , Reppin Johannes , Kemp Yves , Lewendel Birgit , Schluenzen Frank , Schuh Michael , Sternberger Sven , Voss Christian , Wengert Markus 
Published: November 2020

DESY is one of the largest accelerator laboratories in Europe. It develops and operates state of the art accelerators for fundamental science in the areas of high energy physics, photon science and accelerator development. While for decades high energy physics (HEP) has been the most prominent user of the DESY compute, storage and network infrastructure, various scientific areas as science with photons and accelerator development have caught up and are now dominating the demands on the DESY infrastructure resources, with significant consequences for the IT resource provisioning. In this contribution, we will present an overview of the computational, storage and network resources covering the various physics communities on site.
Ranging from high-throughput computing (HTC) batch-like offline processing in the Grid and the interactive user analyses resources in the National Analysis Factory (NAF) for the HEP community, to the computing needs of accelerator development or of photon sciences such as PETRA III or the European XFEL. Since DESY is involved in these experiments and their data taking, their requirements include fast low-latency online processing for data taking and calibration as well as offline processing, thus high-performance computing (HPC) workloads, that are run on the dedicated Maxwell HPC cluster.
As all communities face significant challenges due to changing environments and increasing data rates in the following years, we will discuss how this will reflect in necessary changes to the computing and storage infrastructures.
We will present DESY compute cloud and container orchestration plans as a basis for infrastructure and platform services. We will show examples of Jupyter notebooks for small scale interactive analysis, as well as its integration into large scale resources such as batch systems or Spark clusters.
To overcome the fragmentation of the various resources for all scientific communities at DESY, we explore how to integrate them into a seamless user experience in an Interdisciplinary Data Analysis Facility.