bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using machine learning to model the training scalability of convolutional neural networks on clusters of GPUs
Authors: Barrachina Sergio , Castelló Adrián , Catalán Mar , Dolz Manuel F. , Mestre Jose I. 
Published: August 2021

AbstractIn this work, we build a general piece-wise model to analyze data-parallel (DP) training costs of convolutional neural networks (CNNs) on clusters of GPUs. This general model is based on i) multi-layer perceptrons (MLPs) in charge of modeling the NVIDIA cuDNN/cuBLAS library kernels involved in the training of some of the state-of-the-art CNNs; and ii) an analytical model in charge of modeling the NVIDIA NCCL Allreduce collective primitive using the Ring algorithm. The CNN training scalability study performed using this model in combination with the Roofline technique on varying batch sizes, node (floating-point) arithmetic performance, node memory bandwidth, network link bandwidth, and cluster dimension unveil some crucial bottlenecks at both GPU and cluster level. To provide evidence of this analysis, we validate the accuracy of the proposed model against a Python library for distributed deep learning training.
Depression, anxiety, and stress in oral lichen planus: a systematic review and meta-analysis
Authors: De Porras-Carrique Teresa , González-Moles Miguel Ángel , Warnakulasuriya Saman , Ramos-García Pablo 
Published: August 2021

Abstract
Objectives
We present this systematic review and meta-analyses to evaluate current evidence on the prevalence of depression, anxiety, and stress in patients with oral lichen planus and their magnitude of association.

Material and methods
We searched PubMed, Embase, Web of Science, Scopus, PsycInfo, and Google Scholar for studies published before January 2021. We evaluated the quality of studies using a specific method for systematic reviews addressing prevalence questions, designed by the Joanna Briggs Institute. We carried out meta-analyses and performed heterogeneity, subgroups, meta-regression, and small-study effects analyses.

Results
Fifty-one studies (which recruited 6,815 patients) met the inclusion criteria. Our results reveal a high prevalence of depression (31.19%), anxiety (54.76%), and stress (41.10%) in oral lichen planus. Furthermore, OLP patients presented a significantly higher relative frequency than control group without OLP for depression (OR = 6.15, 95% CI = 2.73–13.89, p < 0.001), anxiety (OR = 3.51, 95% CI = 2.10–5.85, p < 0.001), and stress (OR = 3.64, 95% CI = 1.48–8.94, p = 0.005), showing large effect sizes. Subgroups meta-analyses showed the relevance of the participation of psychologists and psychiatrists in the diagnosis of depression, anxiety, and stress in patients with OLP. Multivariable meta-regression analysis showed the importance of the comorbidity of depression-anxiety in patients with OLP.

Conclusions
Our systematic review and meta-analysis show that patients with OLP suffer a higher prevalence of depression, anxiety, and stress, being more frequent than in general population.
Clinical relevance
In the dental clinic, especially dentists should be aware of depression, anxiety, and stress in OLP patients to achieve a correct referral.
Phosphorus removal in denitrifying woodchip bioreactors varies by wood type and water chemistry
Authors: Sanchez Bustamante-Bailon Ana Paula , Margenot Andrew , Cooke Richard A. C. , Christianson Laura E. 
Published: August 2021

AbstractDenitrifying woodchip bioreactors are a practical nitrogen (N) mitigation technology but evaluating the potential for bioreactor phosphorus (P) removal is highly relevant given that (1) agricultural runoff often contains N and P, (2) very low P concentrations cause eutrophication, and (3) there are few options for removing dissolved P once it is in runoff. A series of batch tests evaluated P removal by woodchips that naturally contained a range of metals known to sorb P and then three design and environmental factors (water matrix, particle size, initial dissolved reactive phosphorus (DRP) concentration). Woodchips with the highest aluminum and iron content provided the most dissolved P removal (13±2.5 mg DRP removed/kg woodchip). However, poplar woodchips, which had low metals content, provided the second highest removal (12±0.4 mg/kg) when they were tested with P-dosed river water which had a relatively complex water matrix. Chemical P sorption due to woodchip elements may be possible, but it is likely one of a variety of P removal mechanisms in real-world bioreactor settings. Scaling the results indicated bioreactors could remove 0.40 to 13 g DRP/ha. Woodchip bioreactor dissolved P removal will likely be small in magnitude, but any such contribution is an added-value benefit of this denitrifying technology.
Mechanical programming of arterial smooth muscle cells in health and ageing
Authors: Johnson Robert T. , Solanki Reesha , Warren Derek T. 
Published: August 2021

AbstractArterial smooth muscle cells (ASMCs), the predominant cell type within the arterial wall, detect and respond to external mechanical forces. These forces can be derived from blood flow (i.e. pressure and stretch) or from the supporting extracellular matrix (i.e. stiffness and topography). The healthy arterial wall is elastic, allowing the artery to change shape in response to changes in blood pressure, a property known as arterial compliance. As we age, the mechanical forces applied to ASMCs change; blood pressure and arterial wall rigidity increase and result in a reduction in arterial compliance. These changes in mechanical environment enhance ASMC contractility and promote disease-associated changes in ASMC phenotype. For mechanical stimuli to programme ASMCs, forces must influence the cell’s load-bearing apparatus, the cytoskeleton. Comprised of an interconnected network of actin filaments, microtubules and intermediate filaments, each cytoskeletal component has distinct mechanical properties that enable ASMCs to respond to changes within the mechanical environment whilst maintaining cell integrity. In this review, we discuss how mechanically driven cytoskeletal reorganisation programmes ASMC function and phenotypic switching.
Focal adhesion kinase inhibitor BI 853520 inhibits cell proliferation, migration and EMT process through PI3K/AKT/mTOR signaling pathway in ovarian cancer
Authors: Li Hong , Gao Yizhi , Ren Chenchen 
Published: August 2021

AbstractFocal adhesion kinase (FAK) activation has been reported to be associated with cell progression and metastasis in a wide variety of cancer cells. Target treatment by inhibiting FAK has achieved remarkable effects in several cancers, but the effect in ovarian cancer has not been reported. In this study, we determined the role and the underlying molecular mechanism of BI853520, a novel small chemical FAK inhibitor against ovarian cancer. Results show that phosphorylated FAK tyrosine 397 (p-FAK Y397) is highly expressed in ovarian cancer tumor tissues and cell lines (SKOV3 and OVCAR3). BI853520 treatment greatly suppresses cell proliferation, viability, migration, invasion, decreases anchorage-independent growth and motility in vitro. Besides, treatment with BI853520 increases biologic effects following combination with chemotherapy in ovarian cancer cell lines. In addition, BI853520 suppresses EMT in ovarian cancer cell lines. Mechanically, BI853520 treatment downregulates the activation of PI3K/AKT/mTOR signal pathway. Finally, mice model experiments confirm BI853520 treatment dramatically reduces tumor growth in vivo and suppresses the activation of PI3K/AKT/mTOR signal pathway. Taken together, our findings demonstrate that focal adhesion kinase inhibitor BI853520 inhibits cell proliferation, migration, invasion and EMT process through PI3K/AKT/mTOR signaling pathway in ovarian cancer, and BI853520 can offer a preclinical rationale for targeting repression of FAK in ovarian cancer.
A box, a trough and marbles: How the Reed-Frost epidemic theory shaped epidemiological reasoning in the 20th century
Authors: Engelmann Lukas 
Published: August 2021

AbstractThe article takes the renewed popularity and interest in epidemiological modelling for Covid-19 as a point of departure to ask how modelling has historically shaped epidemiological reasoning. The focus lies on a particular model, developed in the late 1920s through a collaboration of the former field-epidemiologists and medical officer, Wade Hampton Frost, and the biostatistician and population ecologist Lowell Reed. Other than former approaches to epidemic theory in mathematical formula, the Reed-Frost epidemic theory was materialised in a simple mechanical analogue: a box with coloured marbles and a wooden trough. The article reconstructs how the introduction of this mechanical model has reshaped epidemiological reasoning by shifting the field from purely descriptive to analytical practices. It was not incidental that the history of this model coincided with the foundation of epidemiology as an academic discipline, as it valorised and institutionalised new theoretical contributions to the field. Through its versatility, the model shifted the field’s focus from mono-causal explanations informed by bacteriology, eugenics or sanitary perspectives towards the systematic consideration of epidemics as a set of interdependent and dynamic variables.
›Grazie‹, charis, Gabe
Authors: Mainberger Sabine 
Published: August 2021

ZusammenfassungDie barocke grâce bildet die sozio-politische und ökonomische Kontrastfolie für das ideale Griechenland, das Winckelmann als Gesellschaft im Zeichen der charis entwirft. Es entspricht avant la lettre der Gaben tauschenden Gesellschaft im Sinne von Marcel Mauss. Der Begriff der charis deckt sich, wie an Pindar, einer entscheidenden Referenz des Gelehrten, deutlich ist, in vielen Hinsichten mit dem der Gabe. Winckelmann entwickelt Aspekte der charis und der Gabenbeziehung an der griechischen Lebensweise, den antiken Kunstwerken und der Kunstbetrachtung und konzipiert ›Grazie‹ als Verhältnis der Anerkennung. Seine Statuenbeschreibungen fungieren selbst als Gaben, die eine neue Art der Sozialität ermöglichen. Denn ein zeitgenössisches Pendant zu einer Gesellschaft, in der Schönheit ein fait social total bildet, ist die amikale Gemeinschaft der ästhetisch Sensibilisierten: In ihr kultivieren Gleichrangige einen liebend-vertrauten Umgang mit den Kunstwerken.
Aufwärtskompatibel? Zur Bedeutung struktureller und doktrinärer Nationalismen für die digitale Konstellation
Authors: Schünemann Wolf J. 
Published: August 2021

ZusammenfassungDer Beitrag unternimmt den Versuch, theoretische Ansätze der Nationalismusforschung auf die digitale Konstellation zu übertragen. Lassen sich konstitutive Merkmale der digitalen Konstellation und aktuelle digitalpolitische Entwicklungen unter Rückgriff auf Nationalismustheorien erklären? Erweisen sich Nationalismen, denen eine Hauptfunktion bei der Integration prädigitaler Sozialräume und dem Aufbau einer politischen Weltordnung zugekommen ist, damit gleichsam als aufwärtskompatibel? Um die Beharrungskraft (nicht die Ursprünge) des Nationalen in der digitalen Konstellation zu erklären, stützt sich der Beitrag zunächst auf Ansätze konstruktivistischer Nationalismustheorie. Den Grundstein des Modells bilden strukturelle Nationalismen, verstanden als unideologische, unbewusste und vielfach unauffällige Denk- und Reproduktionsweisen des Nationalen. Diese bieten Anknüpfungspunkte für doktrinäre Nationalismen, die die Autonomie nationaler Gesellschaften thematisieren und ihre Bewahrung zur politischen Zielsetzung erheben. Aus der Kombination lassen sich aktuelle digitalpolitische Entwicklungen erklären. Zwecks empirischer Illustration der verschränkten Mechanismen (strukturell und doktrinär) fokussiert der Beitrag nacheinander auf drei digitalpolitische Handlungs- und Problemfelder: die Verwaltung kritischer Ressourcen am Beispiel des Domain-Name-Systems (DNS), die Cybersicherheitspolitik im Hinblick auf den Schutz kritischer Infrastrukturen sowie schließlich die Bekämpfung von Desinformationskampagnen durch die Regulierung von Kommunikationsströmen.
COVID-19: potential therapeutics for pediatric patients
Authors: Younis Nour K. , Zareef Rana O. , Fakhri Ghina , Bitar Fadi , Eid Ali H. , Arabi Mariam 
Published: August 2021

AbstractThe global spread of COVID-19 has imparted significant economic, medical, and social burdens. Like adults, children are affected by this pandemic. However, milder clinical symptoms are often experienced by them. Only a minimal proportion of the affected patients may develop severe and complicated COVID-19. Supportive treatment is recommended in all patients. Antiviral and immunomodulatory medications are spared for hospitalized children with respiratory distress or severe to critical disease. Up till now, remdesivir is the only USFDA-approved anti-COVID-19 medication indicated in the majority of symptomatic patients with moderate to severe disease. Dexamethasone is solely recommended in patients with respiratory distress maintained on oxygen or ventilatory support. The use of these medications in pediatric patients is founded on evidence deriving from adult studies. No randomized controlled trials (RCTs) involving pediatric COVID-19 patients have assessed these medications’ efficacy and safety, among others. Similarly, three novel monoclonal anti-SARS-CoV-2 spike protein antibodies, bamlanivimab, casirivimab and imdevimab, have been recently authorized by the USFDA. Nonetheless, their efficacy has not been demonstrated by multiple RCTs. In this review, we aim to dissect the various potential therapeutics used in children with COVID-19. We aspire to provide a comprehensive review of the available evidence and display the mechanisms of action and the pharmacokinetic properties of the studied therapeutics. Our review offers an efficient and practical guide for treating children with COVID-19.
Endogenous estrogens—breast cancer and chemoprevention
Authors: Starek-Świechowicz Beata , Budziszewska Bogusława , Starek Andrzej 
Published: August 2021

AbstractBreast cancer is the most common female malignancy and the second leading cause of cancer related deaths. It is estimated that about 40% of all cancer in women is hormonally mediated. Both estrogens and androgens play critical roles in the initiation and development of breast cancer. Estrogens influence normal physiological growth, proliferation, and differentiation of breast tissues, as well as the development and progression of breast malignancy. Breast cancer is caused by numerous endo- and exogenous risk factors. The paper presents estrogen metabolism, in particular 17β-estradiol and related hormones. The mechanisms of estrogen carcinogenesis include the participation of estrogen receptors, the genotoxic effect of the estrogen metabolites, and epigenetic processes that are also presented. The role of reactive oxygen species in breast cancer has been described. It called attention to a role of numerous signaling pathways in neoplastic transformation. Chemoprotective agents, besides other phytoestrogens, classical antioxidants, synthetic compounds, and their mechanisms of action have been shown.
The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV–vis absorption spectroscopy study
Authors: Rumfeldt Jessica , Kurttila Moona , Takala Heikki , Ihalainen Janne A. 
Published: August 2021

AbstractSolvent access to the protein interior plays an important role in the function of many proteins. Phytochromes contain a specific structural feature, a hairpin extension that appears to relay structural information from the chromophore to the rest of the protein. The extension interacts with amino acids near the chromophore, and hence shields the chromophore from the surrounding solvent. We envision that the detachment of the extension from the protein surface allows solvent exchange reactions in the vicinity of the chromophore. This can facilitate for example, proton transfer processes between solvent and the protein interior. To test this hypothesis, the kinetics of the protonation state of the biliverdin chromophore fromDeinococcus radioduransbacteriophytchrome, and thus, the pH of the surrounding solution, is determined. The observed absorbance changes are related to the solvent access of the chromophore binding pocket, gated by the hairpin extension. We therefore propose a model with an “open” (solvent-exposed, deprotonation-active on a (sub)second time-scale) state and a “closed” (solvent-gated, deprotonation inactive) state, where the hairpin fluctuates slowly between these conformations thereby controlling the deprotonation process of the chromophore on a minute time scale. When the connection between the hairpin and the biliverdin surroundings is destabilized by a point mutation, the amplitude of the deprotonation phase increases considerably. In the absence of the extension, the chromophore deprotonates essentially without any “gating”. Hence, we introduce a straightforward method to study the stability and fluctuation of the phytochrome hairpin in its photostationary state. This approach can be extended to other chromophore-protein systems where absorption changes reflect dynamic processes of the protein.
Global Spatial Distribution of Dipolarization Fronts in the Saturn's Magnetosphere: Cassini Observations
Authors: Xu S. B. , Huang S. Y. , Yuan Z. G. , Deng X. H. , Jiang K. , Wei Y. Y. , Zhang J. , Zhang Z. H. , Xiong Q. Y. , Yu L. , Lin R. T. , Waite J. H. 
Published: August 2021

AbstractDipolarization front (DF), characterized by a sharp increase of the south‐north component of the magnetic field, is suggested to play an important role in transferring plasmas, magnetic fluxes, and energy in the planetary magnetosphere. Using the measurements from the Cassini spacecraft between January 1, 2005 and June 15, 2011, we successfully selected 96 DF events, and obtained the global spatial distribution of DFs in the Saturn's magnetosphere. For the first time, we found that DFs are distributed not only in the nightside magnetotail but also in the dayside magnetosphere. The dayside DF events are mainly located from X = 10 RS to X = 30 RS (RS is the Saturn's radius) while the nightside events have a wide range, up to X∼−50 RS. Moreover, the DFs are observed to be asymmetric in the south‐northern hemisphere: ∼70% of events in the northern hemisphere and ∼30% of events in the southern hemisphere, which is likely to be due to the asymmetric orbit coverage of the Cassini in south‐northern hemisphere. The occurrence of dayside DFs provides a strong evidence that the magnetic reconnection could also occur in the dayside of Saturn's magnetosphere. Thus, our results concerning the location and distribution of DFs are helpful for the study of the site of magnetic reconnection and energy transport/dissipation in Saturn's magnetosphere.
Mercury's Crustal Thickness and Contractional Strain
Authors: Watters Thomas R. , James Peter B. , Selvans Michelle M. 
Published: August 2021

AbstractThe crust of Mercury has experienced contraction on a global scale. Contractional deformation is expressed by a broadly distributed network of lobate thrust fault scarps. The most likely principal source of stress is global contraction from cooling of Mercury's interior. Global contraction alone would be expected to result in a uniformly distributed population of thrust faults. Mercury's fault scarps, however, often occur in long, linear clusters or bands. An analysis of the contractional strain as a function of crustal thickness, estimated in two crustal thickness models (CT1 and CT2) derived from gravity and topography data obtained during the MESSENGER mission, indicates the greatest contractional strain occurs in crust 50–60 km thick. On Earth, mantle downwelling can thicken and compress overlying crust, regionally concentrating thrust faults. Clusters of lobate scarps collocated with regions of thick crust suggest downward mantle flow contributed to the localization of lithosphere‐penetrating thrust faults.
Interpreting the Dependence of Cloud‐Radiative Adjustment on Forcing Agent
Authors: Salvi Pietro , Ceppi Paulo , Gregory Jonathan M. 
Published: August 2021

AbstractEffective radiative forcing includes a contribution by rapid adjustments, that is, changes in temperature, water vapor, and clouds that modify the energy budget. Cloud adjustments in particular have been shown to depend strongly on forcing agent. We perform idealized atmospheric heating experiments to demonstrate a relationship between cloud adjustment and the vertical profile of imposed radiative heating: boundary‐layer heating causes a positive cloud adjustment (a net downward radiative anomaly), while free‐tropospheric heating yields a negative adjustment. This dependence is dominated by the shortwave effect of changes in low clouds. Much of the variation in cloud adjustment among common forcing agents such as , , solar forcing, and black carbon is explained by the “characteristic altitude” (i.e., the vertical center‐of‐mass) of their heating profiles, through its effect on tropospheric stability.
Multiple Metrics Informed Projections of Future Precipitation in China
Authors: Wang Lei , Qian Yun , Leung L. Ruby , Chen Xiaodong , Sarangi Chandan , Lu Jian , Song Fengfei , Gao Yang , Lin Guangxing , Zhang Yaocun 
Published: August 2021

AbstractPredicting how regional precipitation will respond to future warming is among the most challenging undertaking in climate change projection. Despite sustained efforts to improve modeling and understanding of precipitation, the overall uncertainty in projecting regional precipitation has not been reduced substantially. Here, the potential for more robust precipitation projections is demonstrated through the use of discriminating metrics to subsample a multimodel ensemble. Using a two‐dimensional metric of precipitation and its relationship with large‐scale circulation indices in East Asia, 31 models in the Coupled Model Intercomparison Project Phase 5 (CMIP5) are classified into three groups. Models in the top performing group projected statistically significant increasing trends in precipitation and the regional precipitation patterns are more similar to each other than to the patterns in the bottom performing group. In contrast, models in the bottom performing group projected diverse responses, with overall small drying or no significant trends in precipitation.
Phylogenetic Underpinning of Groundwater Use by Trees
Authors: Knighton James , Fricke Evan , Evaristo Jaivime , de Boer Hugo Jan , Wassen Martin Joseph 
Published: August 2021

AbstractRoot water uptake (RWU) strategies shape climate‐vegetation feedbacks and ecosystem productivity. A fundamental relationship between RWU strategies and evolutionary histories (phylogeny) of trees, however, remains poorly understood. Establishing a phylogenetic basis for tree RWU, particularly groundwater use, could improve their representation in terrestrial biosphere models (TBMs) that are crucial for understanding hydrologic and ecosystem responses to climate perturbations. We explored possible phylogenetic bases for tree RWU using two independent data sets: (a) observed root and local groundwater depths representing 502 tree species, and (b) groundwater, soil, and xylem water isotopic evidence for groundwater uptake representing 412 species. Maximum rooting depths (RDMAX), the ratio between RDMAX and mean water table depth (WT) (RDMAX/WT), and isotopic evidence of groundwater uptake showed significant phylogenetic signals, suggesting that tree RWU strategies are more similar among closely related species. Our findings may be used to parameterize species‐level RWU in TBMs, particularly for data‐poor regions.