bluuebunny/crossref_metadata_2025_split huggingface dataset:
Jet impingement on the underside of a superhydrophobic surface
Authors: de la Cruz Roberto M. , Mäkiharju Simo A. 
Published: March 2022

Water patch topology and momentum loss resulting from a jet impacting on the underside of a flat plate with varied hydrophobicity were studied. The jet's Reynolds and Froude numbers ranged from 3700 to 31 000, and from 1 to 23, respectively. Hence effects of gravity were expected to be non-negligible, and data suggest that this is the case for hydrophobic surfaces. The interplay of gravity, surface tension, inertia and viscosity resulted in two distinct behaviours. On hydrophilic surfaces, water spread uniformly. Friction reduced momentum, and led to accumulation at the edges of the patch until gravity overcame surface tension and produced droplets. On hydrophobic surfaces, two rims formed, enclosing a thin laminar film. The patch shape was mostly determined by the balance of kinetic and surface energy. Dewetting occurred in most cases when the two rims merged, but for a narrow parameter, range water detached soon after impact and formed a type of skewed water bell. The transition in detachment topology was predicted reasonably by a simple model considering whether an attached or detached rim minimizes energy. Due to promotion of dewetting by gravity, the water patch area decreased compared to that reported in previous studies, which considered jet impingement on vertical surfaces and tops of horizontal surfaces. Owing to the application that motivated this study, the streamwise force on the plate was also measured. On hydrophobic surfaces the reduction in force correlated with the reduction in water patch area. Water patch area and momentum loss were both found to scale best with the contact-angle-modified Weber number.
Quantitative effects of environmental variation on stomatal anatomy and gas exchange in a grass model
Authors: Nunes Tiago D. G. , Slawinska Magdalena W. , Lindner Heike , Raissig Michael T. 
Published: March 2022

Abstract
Stomata are cellular pores on the leaf epidermis that allow plants to regulate carbon assimilation and water loss. Stomata integrate environmental signals to regulate pore apertures and adapt gas exchange to fluctuating conditions. Here, we quantified intraspecific plasticity of stomatal gas exchange and anatomy in response to seasonal variation in Brachypodium distachyon. Over the course of 2 years, we (a) used infrared gas analysis to assess light response kinetics of 120 Bd21-3 wild-type individuals in an environmentally fluctuating greenhouse and (b) microscopically determined the seasonal variability of stomatal anatomy in a subset of these plants. We observed systemic environmental effects on gas exchange measurements and remarkable intraspecific plasticity of stomatal anatomical traits. To reliably link anatomical variation to gas exchange, we adjusted anatomical gsmax calculations for grass stomatal morphology. We propose that systemic effects and variability in stomatal anatomy should be accounted for in long-term gas exchange studies.
The processing of bilingual (switched) compound verbs: Competition of words from different categories for lexical selection
Authors: Purmohammad Mehdi , Vorwerg Constanze , Abutalebi Jubin 
Published: March 2022

AbstractThis paper investigates the production of Persian–English bilingual compound verbs (BCVs) of the type [VERB+VERB]. In this type of code-switched structure, a lexical verb from the donor language English is combined with a light verb from the native language Persian. We tested the hypothesis that in Persian–English BCVs English verbs occupy the nominal slots of monolingual Persian complex predicates of the type [NOMINAL+VERB]. Two methodologies were used. A conversational-corpus analysis confirmed our predictions that Persian–English BCVs have translation-equivalent Persian compound verbs, that the English verbs denote the same action as the nominal constituents of those monolingual constructions, and that the support verbs tend to correspond in both types of compound verbs. A bilingual picture-word interference experiment provided evidence suggesting that English verbs interfere with the production of the nominal constituents of complex Persian verbs in Persian-bilingual speakers. We conclude that words from different word categories can compete for lexical access.
Hydrological Intensification Will Increase the Complexity of Water Resource Management
Authors: Ficklin Darren L. , Null Sarah E. , Abatzoglou John T. , Novick Kimberly A. , Myers Daniel T. 
Published: March 2022

AbstractGlobal warming intensifies the hydrological cycle by altering the rate of water fluxes to and from the terrestrial surface, resulting in an increase in extreme precipitation events and longer dry spells. Prior hydrological intensification work has largely focused on precipitation without joint consideration of evaporative demand changes and how plants respond to these changes. Informed by state‐of‐the‐art climate models, we examine projected changes in hydrological intensification and its role in complicating water resources management using a framework that accounts for precipitation surplus and evaporative demand. Using a metric that combines the difference between daily precipitation and daily evaporative demand (surplus events) and consecutive days when evaporative demand exceeds precipitation (deficit time), we show that, globally, surplus events will become larger (+11.5% and +18.5% for moderate and high emission scenarios, respectively) and the duration between them longer (+5.1%; +9.6%) by the end of the century, with the largest changes in the northern latitudes. The intra‐annual occurrence of these extremes will stress existing water management infrastructure in major river basins, where over one third of years during 2070–2100 under a moderate emissions scenario will be hydrologically intense (large intra‐annual increases in surplus intensity and deficit time), tripling that of the historical baseline. Larger increases in hydrologically intense years are found in basins with large reservoir capacity (e.g., Amazon, Congo, and Danube River Basins), which have significant populations, irrigate considerable farmland, and support threatened and endangered aquatic species. Incorporating flexibility into water resource infrastructure and management will be paramount with continued hydrological intensification.
Boulder Dislodgement During Coastal Storms and Tsunamis: Insights From a New Ensemble Model
Authors: Weiss Robert , Irish Jennifer , Goodman Tchernov Beverly 
Published: March 2022

AbstractBoulders are excellent candidate deposits to study coastal inundation events by storms and tsunamis due to their significant preservation potential. However, it is difficult to infer how and what forcing dislodged the boulder. We present a new model that enables ensemble and Monte‐Carlo‐type simulations to study the sensitivity of boulder, the fluid flow, and environmental parameters. Our examples show that boulder transport is complex and nonlinear, and to acknowledge the uncertainties of the boulder's preexisting transport conditions, a range of velocities and environmental parameters should be used to quantify the flow that caused boulder dislodgement.
Topographic Stabilization of Ocean Rings
Authors: Gulliver L. T. , Radko T. 
Published: March 2022

AbstractCoherent large‐scale vortices in the open ocean can retain their structure and properties for periods as long as several years. However, the patterns of potential vorticity in such vortices suggest that they are baroclinically unstable and therefore should rapidly disintegrate. This study proposes a plausible explanation of the longevity of large‐scale ocean rings based on bottom roughness, which restricts flow in the lower layer and thereby stabilizes the eddy. We perform a series of simulations in which topography is represented by the observationally derived Goff‐Jordan spectrum. We demonstrate that topography stabilizes coherent vortices and dramatically prolongs their lifespan. In contrast, the same vortices in the flat‐bottom model exhibit strong instability and fragmentation on the timescale of weeks. A critical depth variance exists that allows vortices to remain stable and circularly symmetric indefinitely. Our investigation underscores the essential role played by topography in the dynamics of large‐ and meso‐scale flows.
Rapid Watershed Delineation Using an Automatic Outlet Relocation Algorithm
Authors: Xie Jiaxin , Liu Xiaomang , Bai Peng , Liu Changming 
Published: March 2022

AbstractDelineating the boundaries of numerous watersheds is essential for hydrological analysis in the big data era. Various techniques, such as ArcGIS, have been developed to delineate watershed boundaries. However, existing techniques suffer from two laborious manual processes: (a) Determine flow accumulation thresholds through trial and error to derive digital stream networks; (b) Manually relocate watershed outlets to the correct stream networks. Here, we proposed an automatic outlet relocation (AOR) algorithm for rapid watershed delineation without manual processing. The AOR algorithm relocates outlets to correct stream networks by analyzing flow accumulation gradients along the flow directions. An experiment using the AOR algorithm in 1,398 watersheds across the contiguous United States showed that 94.1% of the watersheds were correctly delineated, compared to 81.3% accuracy of the ArcGIS relocation algorithm (Snap Pour Point). In addition, the AOR algorithm took 58 min to delineate the 1,398 watersheds on a 90 m‐resolution flow direction, while the ArcGIS algorithm required 586 min to perform the same task. Thus, the AOR algorithm offers an opportunity to automatically delineate a large number of watersheds for hydrological simulations in the big data era. Software with a graphical user interface for the AOR algorithm is freely available on GitHub (https://github.com/xiejx5/watershed_delineation).
Untargeted metabolic analysis in dried blood spots reveals metabolic signature in 22q11.2 deletion syndrome
Authors: Korteling Dorinde , Boks Marco P. , Fiksinski Ania M. , van Hoek Ilja N. , Vorstman Jacob A. S. , Verhoeven-Duif Nanda M. , Jans Judith J. M. , Zinkstok Janneke R. 
Published: March 2022

AbstractThe 22q11.2 deletion syndrome (22q11.2DS) is characterized by a well-defined microdeletion and is associated with increased risk of neurodevelopmental phenotypes including autism spectrum disorders (ASD) and intellectual impairment. The typically deleted region in 22q11.2DS contains multiple genes with the potential of altering metabolism. Deficits in metabolic processes during early brain development may help explain the increased prevalence of neurodevelopmental phenotypes seen in 22q11.2DS. However, relatively little is known about the metabolic impact of the 22q11.2 deletion, while such insight may lead to increased understanding of the etiology. We performed untargeted metabolic analysis in a large sample of dried blood spots derived from 49 22q11.2DS patients and 87 controls, to identify a metabolic signature for 22q11.2DS. We also examined trait-specific metabolomic patterns within 22q11.2DS patients, focusing on intelligence (intelligence quotient, IQ) and ASD. We used the Boruta algorithm to select metabolites distinguishing patients from controls, patients with ASD from patients without, and patients with an IQ score in the lowest range from patients with an IQ score in the highest range. The relevance of the selected metabolites was visualized with principal component score plots, after which random forest analysis and logistic regression were used to measure predictive performance of the selected metabolites. Analysis yielded a distinct metabolic signature for 22q11.2DS as compared to controls, and trait-specific (IQ and ASD) metabolomic patterns within 22q11.2DS patients. The metabolic characteristics of 22q11.2DS provide insights in biological mechanisms underlying the neurodevelopmental phenotype and may ultimately aid in identifying novel therapeutic targets for patients with developmental disorders.
Identification of a novel MAGT1 mutation supports a diagnosis of XMEN disease
Authors: Watson Christopher M. , Nadat Fatima , Ahmed Sammiya , Crinnion Laura A. , O’Riordan Sean , Carter Clive , Savic Sinisa 
Published: March 2022

AbstractXMEN (X-linked immunodeficiency with magnesium defect) is caused by loss-of-function mutations in MAGT1 which is encoded on the X chromosome. The disorder is characterised by CD4 lymphopenia, severe chronic viral infections and defective T-lymphocyte activation. XMEN patients are susceptible to Epstein-Barr virus infections and persistently low levels of intracellular Mg2+. Here we describe a patient that presented with multiple recurrent infections and a subsequent diffuse B-cell lymphoma. Molecular genetic analysis by exome sequencing identified a novel hemizygous MAGT1 nonsense mutation c.1005T>A (NM_032121.5) p.(Cys335*), confirming a diagnosis of XMEN deficiency. Follow-up immunophenotyping was performed by antibody staining and flow cytometry; proliferation was determined by 3H-thymidine uptake after activation by PHA and anti-CD3. Cytotoxic natural killer cell activity was assessed with K562 target cells using the NKTESTTM assay. While lymphocyte populations were superficially intact, B cells were largely naive with a reduced memory cell compartment. Translated NKG2D was absent on both NK and T cells in the proband, and normally expressed in the carrier mother. In vitro NK cell activity was intact in both the proband and his mother. This report adds to the growing number of identified XMEN cases, raising awareness of a, still rare, X-linked immunodeficiency.
Rapid expansion and extinction of antibiotic resistance mutations during treatment of acute bacterial respiratory infections
Authors: Chung Hattie , Merakou Christina , Schaefers Matthew M. , Flett Kelly B. , Martini Sarah , Lu Roger , Blumenthal Jennifer A. , Webster Shanice S. , Cross Ashley R. , Al Ahmar Roy , Halpin Erin , Anderson Michelle , Moore Nicholas S. , Snesrud Eric C. , Yu Hongwei D. , Goldberg Joanna B. , O’Toole George A. , McGann Patrick , Stam Jason A. , Hinkle Mary , McAdam Alexander J. , Kishony Roy , Priebe Gregory P. 
Published: March 2022

AbstractAcute bacterial infections are often treated empirically, with the choice of antibiotic therapy updated during treatment. The effects of such rapid antibiotic switching on the evolution of antibiotic resistance in individual patients are poorly understood. Here we find that low-frequency antibiotic resistance mutations emerge, contract, and even go to extinction within days of changes in therapy. We analyzed Pseudomonas aeruginosa populations in sputum samples collected serially from 7 mechanically ventilated patients at the onset of respiratory infection. Combining short- and long-read sequencing and resistance phenotyping of 420 isolates revealed that while new infections are near-clonal, reflecting a recent colonization bottleneck, resistance mutations could emerge at low frequencies within days of therapy. We then measured the in vivo frequencies of select resistance mutations in intact sputum samples with resistance-targeted deep amplicon sequencing (RETRA-Seq), which revealed that rare resistance mutations not detected by clinically used culture-based methods can increase by nearly 40-fold over 5–12 days in response to antibiotic changes. Conversely, mutations conferring resistance to antibiotics not administered diminish and even go to extinction. Our results underscore how therapy choice shapes the dynamics of low-frequency resistance mutations at short time scales, and the findings provide a possibility for driving resistance mutations to extinction during early stages of infection by designing patient-specific antibiotic cycling strategies informed by deep genomic surveillance.
Co-translational assembly orchestrates competing biogenesis pathways
Authors: Seidel Maximilian , Becker Anja , Pereira Filipa , Landry Jonathan J. M. , de Azevedo Nayara Trevisan Doimo , Fusco Claudia M. , Kaindl Eva , Romanov Natalie , Baumbach Janina , Langer Julian D. , Schuman Erin M. , Patil Kiran Raosaheb , Hummer Gerhard , Benes Vladimir , Beck Martin 
Published: March 2022

AbstractDuring the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examine structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally test candidate structural motifs and identify several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs may act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assemble co-translationally in only some but not all of the relevant biogenesis pathways. Our results highlight the regulatory complexity of assembly pathways.
Restoring and attributing ancient texts using deep neural networks
Authors: Assael Yannis , Sommerschield Thea , Shillingford Brendan , Bordbar Mahyar , Pavlopoulos John , Chatzipanagiotou Marita , Androutsopoulos Ion , Prag Jonathan , de Freitas Nando 
Published: March 2022

AbstractAncient history relies on disciplines such as epigraphy—the study of inscribed texts known as inscriptions—for evidence of the thought, language, society and history of past civilizations1. However, over the centuries, many inscriptions have been damaged to the point of illegibility, transported far from their original location and their date of writing is steeped in uncertainty. Here we present Ithaca, a deep neural network for the textual restoration, geographical attribution and chronological attribution of ancient Greek inscriptions. Ithaca is designed to assist and expand the historian’s workflow. The architecture of Ithaca focuses on collaboration, decision support and interpretability. While Ithaca alone achieves 62% accuracy when restoring damaged texts, the use of Ithaca by historians improved their accuracy from 25% to 72%, confirming the synergistic effect of this research tool. Ithaca can attribute inscriptions to their original location with an accuracy of 71% and can date them to less than 30 years of their ground-truth ranges, redating key texts of Classical Athens and contributing to topical debates in ancient history. This research shows how models such as Ithaca can unlock the cooperative potential between artificial intelligence and historians, transformationally impacting the way that we study and write about one of the most important periods in human history.
Integrated electronic skin (e-skin) for harvesting of TENG energy through push–pull ionic electrets and ion-ion hopping mechanism
Authors: Cheedarala Ravi Kumar , Song Jung Il 
Published: March 2022

AbstractThe development of highly durable, stretchable, and steady triboelectric nanogenerators (TENGs) is highly desirable to satisfy the tight requirement of energy demand. Here, we presented a novel integrated polymeric membrane that is designed by PEDOT: PSSa-naphthalene sulfonated polyimide (PPNSP)-EMI.BF4 Electronic skin (e-skin) for potential TENG applications. The proposed TENG e-skin is fabricated by an interconnected architecture with push–pull ionic electrets that can threshold the transfer of charges through an ion-hopping mechanism for the generation of a higher output voltage (Voc) and currents (Jsc) against an electronegative PTFE film. PPNSP was synthesized from the condensation of naphthalene-tetracarboxylic dianhydride, 2,2′-benzidine sulfonic acid, and 4,4′diaminodiphenyl ether through an addition copolymerization protocol, and PEDOT: PSSa was subsequently deposited using the dip-coating method. Porous networked PPNSP e-skin with continuous ion transport nano-channels is synthesized by introducing simple and strong molecular push–pull interactions via intrinsic ions. In addition, EMI.BF4 ionic liquid (IL) is doped inside the PPNSP skin to interexchange ions to enhance the potential window for higher output Voc and Iscs. In this article, we investigated the push–pull dynamic interactions between PPNSP-EMI.BF4 e-skin and PTFE and tolerable output performance. The novel PPNSP- EMI.BF4 e-skin TENG produced upto 49.1 V and 1.03 µA at 1 Hz, 74 V and 1.45 µA at 2 Hz, 122.3 V and 2.21 µA at 3 Hz and 171 V and 3.6 µA at 4 Hz, and 195 V and 4.43 µA at 5 Hz, respectively. The proposed novel TENG device was shown to be highly flexible, highly durable, commercially viable, and a prospective candidate to produce higher electrical charge outputs at various applied frequencies.
Normalization of clonal diversity in gene therapy studies using shape constrained splines
Authors: Del Core L. , Cesana D. , Gallina P. , Secanechia Y. N. Serina , Rudilosso L. , Montini E. , Wit E. C. , Calabria A. , Grzegorczyk M. A. 
Published: March 2022

AbstractViral vectors are used to insert genetic material into semirandom genomic positions of hematopoietic stem cells which, after reinfusion into patients, regenerate the entire hematopoietic system. Hematopoietic cells originating from genetically modified stem cells will harbor insertions in specific genomic positions called integration sites, which represent unique genetic marks of clonal identity. Therefore, the analysis of vector integration sites present in the genomic DNA of circulating cells allows to determine the number of clones in the blood ecosystem. Shannon diversity index is adopted to evaluate the heterogeneity of the transduced population of gene corrected cells. However, this measure can be affected by several technical variables such as the DNA amount used and the sequencing depth of the library analyzed and therefore the comparison across samples may be affected by these confounding factors. We developed an advanced spline-regression approach that leverages on confounding effects to provide a normalized entropy index. Our proposed method was first validated and compared with two state of the art approaches in a specifically designed in vitro assay. Subsequently our approach allowed to observe the expected impact of vector genotoxicity on entropy level decay in an in vivo model of hematopoietic stem cell gene therapy based on tumor prone mice.