bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controls on Stream Water Age in a Saturation Overland Flow‐Dominated Catchment
Authors: Lapides Dana A. , Hahm W. Jesse , Rempe Daniella M. , Dietrich William E. , Dralle David N. 
Published: April 2022

AbstractWater age and flow pathways should be related; however, it is still generally unclear how integrated catchment runoff generation mechanisms result in streamflow age distributions at the outlet. Here, we combine field observations of runoff generation at the Dry Creek catchment with StorAge Selection (SAS) age models to explore the relationship between stream water age and runoff pathways. Dry Creek is a 3.5 km2catchment in the Northern California Coast Ranges with a Mediterranean climate, and, despite an average rainfall of ≈1,800 mm/yr, is an oak savannah due to the limited hillslope water storage capacity. Runoff lag to peak—after initial seasonal wet‐up—is rapid (∼1–2 hr), and total annual streamflow consists predominantly of saturation overland flow, based on field mapping of saturated extents and an inferred runoff threshold for the expansion of saturation extent beyond the geomorphic channel. SAS modeling based on daily isotope sampling reveals that streamflow is typically older than 1 day. Since streamflow primarily consists of overland flow, a significant portion of overland flow must not be event‐rain but instead derive from older, nonevent groundwater returning to the surface, consistent with field observations of exfiltrating head gradients, return flow through macropores, and extensive saturation days after storm events. We conclude that even in a watershed fed primarily by overland flow, runoff is primarily not composed of event water. Our findings have implications for the interpretation of stream chemistry and the assumptions built into widely used hydrograph separation inferences, namely, the assumption that overland flow consists of new (event) water.
An Overview of Aerosol Properties in Clear and Cloudy Sky Based on CALIPSO Observations
Authors: Hong Yulan , Di Girolamo Larry 
Published: March 2022

AbstractA full understanding of the climatological properties of aerosols is an important step towards characterizing their effects on climate. Utilizing the observations from Cloud‐Aerosol Lidar and Infrared Pathfinder Satellite Observations, we study cloud‐free and cloudy aerosol properties with attention on aerosol and cloud layer relative vertical positions. On a global scale, the cloud‐free aerosols account for about 56% of all detected aerosols with a mean optical depth () and mean uncertainty of 0.135 ± 0.047. The cloudy aerosols, accounting for 44%, have a larger and larger mean uncertainty of 0.143 ± 0.074 compared to the cloud‐free aerosols. The above‐cloud aerosols (∼4%), primarily composed of elevated smoke, dust/volcanic ash and polluted dust, have a much smaller of (0.056 ± 0.038). The below‐cloud aerosols (∼21%) have ∼ 0.165 0.087. The below‐cloud and cloud‐free aerosols show close probability density distributions and similar aerosol types, indicating that cloud‐free aerosol climatologies from passive sensors are likely representative of all‐sky conditions. In addition, about 27% of the detected aerosol profiles are found to have cloud layers vertically connected to the detected aerosol layers. The lidar backscatter profiles of these aerosols have larger median values than the cloud‐free, above‐cloud and below‐cloud aerosols. The seasonal variations of the cloud‐free and the cloudy aerosols significantly vary with regions. Our results imply that quantifying the impact of clouds, particularly cirrus due to the wide coverage of cirrus‐aerosol overlap, on aerosol direct radiative effect is crucial to assess aerosols' roles in the Earth‐climate system.
Modulation of the Intraseasonal Chlorophyll‐a Concentration in the Tropical Indian Ocean by the Central Indian Ocean Mode
Authors: Qin Jianhuang , Meng Ze , Xu Wenlong , Li Baosheng , Cheng Xuhua , Murtugudde Raghu 
Published: April 2022

AbstractThis study diagnoses the drivers of intraseasonal variability of mixed layer chlorophyll‐a (Chl) concentration in the tropical Indian Ocean during boreal summer (June–September) using a well‐tested coupled ocean‐ecosystem model. Results show that wind forcing is the primary source for energetic intraseasonal Chl concentration variability in the eastern Arabian Sea and western Bay of Bengal (BoB) modulated by the Central Indian Ocean (CIO) mode. The atmospheric anomalous anticyclone associated with the positive phase of CIO mode drives southeastward currents in the Arabian Sea, which transport nutrient and Chl towards the east. Simultaneously, the wind‐induced offshore currents strengthen upwelling in the western boundary of BoB, resulting in enhanced Chl in the upper ocean. Conversely, because of the formation of a barrier layer, the nutrient supply is suppressed along the equator, which causes a negative correlation between the CIO mode and Chl. This study complements the Madden‐Julian Oscillation forcing on the intraseasonal Chl concentration anomaly in the tropical Indian Ocean.
Expert consensus on dental caries management
Authors: Cheng Lei , Zhang Lu , Yue Lin , Ling Junqi , Fan Mingwen , Yang Deqin , Huang Zhengwei , Niu Yumei , Liu Jianguo , Zhao Jin , Li Yanhong , Guo Bin , Chen Zhi , Zhou Xuedong 
Published: March 2022

AbstractDental Caries is a kind of chronic oral disease that greatly threaten human being’s health. Though dentists and researchers struggled for decades to combat this oral disease, the incidence and prevalence of dental caries remain quite high. Therefore, improving the disease management is a key issue for the whole population and life cycle management of dental caries. So clinical difficulty assessment system of caries prevention and management is established based on dental caries diagnosis and classification. Dentists should perform oral examination and establish dental records at each visit. When treatment plan is made on the base of caries risk assessment and carious lesion activity, we need to work out patient‑centered and personalized treatment planning to regain oral microecological balance, to control caries progression and to restore the structure and function of the carious teeth. And the follow-up visits are made based on personalized caries management. This expert consensus mainly discusses caries risk assessment, caries treatment difficulty assessment and dental caries treatment plan, which are the most important parts of caries management in the whole life cycle.
Low probability of disease cure in advanced ovarian carcinomas before the PARP inhibitor era
Authors: You Benoit , Van Wagensveld Lilian , Tod Michel , Sonke Gabe S. , Horlings Hugo M. , Kruitwagen R. F. P. M. , Du Bois Andreas , Selle Frédéric , Perren Timothy , Pfisterer Jacobus , Joly Florence , Cook Adrian , Kaminsky Marie Christine , Wollschlaeger Kerstin , Lortholary Alain , Tome Oliver , Leary Alexandra , Freyer Gilles , Van Der Aa Maaike , Colomban Olivier 
Published: March 2022

Abstract
Background
In ovarian carcinomas, the likelihood of disease cure following first-line medical-surgical treatment has been poorly addressed. The objective was to: (a) assess the likelihood of long-term disease-free (LDF) > 5 years; and (b) evaluate the impact of the tumour primary chemosensitivity (assessed with the modelled CA-125 KELIM) with respect to disease stage, and completeness of debulking surgery.

Methods
Three Phase III trial datasets (AGO-OVAR 9; AGO-OVAR 7; ICON-7) were retrospectively investigated in an “adjuvant dataset”, whilst the Netherlands Cancer Registry was used in a “neoadjuvant dataset”. The prognostic values of KELIM, disease stage and surgery outcomes regarding the likelihood of LDF were assessed using univariate/multivariate analyses.

Results
Of 2029 patients in the “adjuvant dataset”, 82 (4.0%) experienced LDF (Stage I–II: 25.9%; III: 2.1%; IV: 0.5%). Multivariate analyses identified disease stage and KELIM (OR = 4.24) as independent prognostic factors. Among the 1452 patients from the “neoadjuvant dataset”, 36 (2.4%) had LDF (Stage II–III: 3.3%; IV: 1.3%). Using multivariate tests, high-risk diseases (OR = 0.18) and KELIM (OR = 2.96) were significant.

Conclusion
The probability of LDF > 5 years after first-line treatment in 3486 patients (<4%) was lower than thought. These data could represent a reference for future studies meant to assess progress related to PARP inhibitors.
Assembly mechanism of the pleomorphic immature poxvirus scaffold
Authors: Hyun Jaekyung , Matsunami Hideyuki , Kim Tae Gyun , Wolf Matthias 
Published: March 2022

AbstractIn Vaccinia virus (VACV), the prototype poxvirus, scaffold protein D13 forms a honeycomb-like lattice on the viral membrane that results in formation of the pleomorphic immature virion (IV). The structure of D13 is similar to those of major capsid proteins that readily form icosahedral capsids in nucleocytoplasmic large DNA viruses (NCLDVs). However, the detailed assembly mechanism of the nonicosahedral poxvirus scaffold has never been understood. Here we show the cryo-EM structures of the D13 trimer and scaffold intermediates produced in vitro. The structures reveal that the displacement of the short N-terminal α-helix is critical for initiation of D13 self-assembly. The continuous curvature of the IV is mediated by electrostatic interactions that induce torsion between trimers. The assembly mechanism explains the semiordered capsid-like arrangement of D13 that is distinct from icosahedral NCLDVs. Our structures explain how a single protein can self-assemble into different capsid morphologies and represent a local exception to the universal Caspar-Klug theory of quasi-equivalence.
Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles
Authors: Jones Ross D. , Qian Yili , Ilia Katherine , Wang Benjamin , Laub Michael T. , Del Vecchio Domitilla , Weiss Ron 
Published: March 2022

AbstractEngineered signaling networks can impart cells with new functionalities useful for directing differentiation and actuating cellular therapies. For such applications, the engineered networks must be tunable, precisely regulate target gene expression, and be robust to perturbations within the complex context of mammalian cells. Here, we use bacterial two-component signaling proteins to develop synthetic phosphoregulation devices that exhibit these properties in mammalian cells. First, we engineer a synthetic covalent modification cycle based on kinase and phosphatase proteins derived from the bifunctional histidine kinase EnvZ, enabling analog tuning of gene expression via its response regulator OmpR. By regulating phosphatase expression with endogenous miRNAs, we demonstrate cell-type specific signaling responses and a new strategy for accurate cell type classification. Finally, we implement a tunable negative feedback controller via a small molecule-stabilized phosphatase, reducing output expression variance and mitigating the context-dependent effects of off-target regulation and resource competition. Our work lays the foundation for establishing tunable, precise, and robust control over cell behavior with synthetic signaling networks.
Meta-programmable analog differentiator
Authors: Sol Jérôme , Smith David R. , del Hougne Philipp 
Published: March 2022

AbstractWe present wave-based signal differentiation with unprecedented fidelity and flexibility by purposefully perturbing overmoded random scattering systems such that zeros of their scattering matrices lie exactly at the desired locations on the real frequency axis. Our technique overcomes limitations of hitherto existing approaches based on few-mode systems, both regarding their extreme vulnerability to fabrication inaccuracies or environmental perturbations and their inability to maintain high fidelity under in-situ adaptability. We demonstrate our technique experimentally by placing a programmable metasurface with hundreds of degrees of freedom inside a 3D disordered metallic box. Regarding the integrability of wave processors, such repurposing of existing enclosures is an enticing alternative to fabricating miniaturized devices. Our over-the-air differentiator can process in parallel multiple signals on distinct carriers and maintains high fidelity when reprogrammed to different carriers. We also perform programmable higher-order differentiation. Conceivable applications include segmentation or compression of communication or radar signals and machine vision.
A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response
Authors: Gambardella G. , Viscido G. , Tumaini B. , Isacchi A. , Bosotti R. , di Bernardo D. 
Published: March 2022

AbstractCancer cells within a tumour have heterogeneous phenotypes and exhibit dynamic plasticity. How to evaluate such heterogeneity and its impact on outcome and drug response is still unclear. Here, we transcriptionally profile 35,276 individual cells from 32 breast cancer cell lines to yield a single cell atlas. We find high degree of heterogeneity in the expression of biomarkers. We then train a deconvolution algorithm on the atlas to determine cell line composition from bulk gene expression profiles of tumour biopsies, thus enabling cell line-based patient stratification. Finally, we link results from large-scale in vitro drug screening in cell lines to the single cell data to computationally predict drug responses starting from single-cell profiles. We find that transcriptional heterogeneity enables cells with differential drug sensitivity to co-exist in the same population. Our work provides a framework to determine tumour heterogeneity in terms of cell line composition and drug response.
A probabilistic map of emotional experiences during competitive social interactions
Authors: Heffner Joseph , FeldmanHall Oriel 
Published: March 2022

AbstractTheories of emotion and decision-making argue that negative, high arousing emotions—such as anger—motivate competitive social choice (e.g., punishing and defecting). However, given the long-standing challenge of quantifying emotion and the narrow framework in which emotion is traditionally examined, it remains unclear which emotions are actually associated with motivating these types of choices. To address this gap, we combine machine learning algorithms with a measure of affect that is agnostic to any specific emotion label. The result is a probabilistic map of emotion that is used to classify the specific emotions experienced by participants in a variety of social interactions (Ultimatum Game, Prisoner’s Dilemma, and Public Goods Game). Our results reveal that punitive and uncooperative choices are linked to a diverse array of negative, neutrally arousing emotions, such as sadness and disappointment, while only weakly linked to anger. These findings stand in contrast to the commonly held assumption that anger drives decisions to punish, defect, and freeride—thus, offering new insight into the role of emotion in motiving social choice.
cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies
Authors: Pedersen Christina Bligaard , Dam Søren Helweg , Barnkob Mike Bogetofte , Leipold Michael D. , Purroy Noelia , Rassenti Laura Z. , Kipps Thomas J. , Nguyen Jennifer , Lederer James Arthur , Gohil Satyen Harish , Wu Catherine J. , Olsen Lars Rønn 
Published: March 2022

AbstractCombining single-cell cytometry datasets increases the analytical flexibility and the statistical power of data analyses. However, in many cases the full potential of co-analyses is not reached due to technical variance between data from different experimental batches. Here, we present cyCombine, a method to robustly integrate cytometry data from different batches, experiments, or even different experimental techniques, such as CITE-seq, flow cytometry, and mass cytometry. We demonstrate that cyCombine maintains the biological variance and the structure of the data, while minimizing the technical variance between datasets. cyCombine does not require technical replicates across datasets, and computation time scales linearly with the number of cells, allowing for integration of massive datasets. Robust, accurate, and scalable integration of cytometry data enables integration of multiple datasets for primary data analyses and the validation of results using public datasets.
Observation of optical gyromagnetic properties in a magneto-plasmonic metamaterial
Authors: Yang Weihao , Liu Qing , Wang Hanbin , Chen Yiqin , Yang Run , Xia Shuang , Luo Yi , Deng Longjiang , Qin Jun , Duan Huigao , Bi Lei 
Published: March 2022

AbstractMetamaterials with artificial optical properties have attracted significant research interest. In particular, artificial magnetic resonances with non-unity permeability tensor at optical frequencies in metamaterials have been reported. However, only non-unity diagonal elements of the permeability tensor have been demonstrated to date. A gyromagnetic permeability tensor with non-zero off-diagonal elements has not been observed at the optical frequencies. Here we report the observation of gyromagnetic properties in the near-infrared wavelength range in a magneto-plasmonic metamaterial. The non-zero off-diagonal permeability tensor element causes the transverse magneto-optical Kerr effect under s-polarized incidence that otherwise vanishes if the permeability tensor is not gyromagnetic. By retrieving the permeability tensor elements from reflection, transmission, and transverse magneto-optical Kerr effect spectra, we show that the effective off-diagonal permeability tensor elements reach 10−3level at the resonance wavelength (~900 nm) of the split-ring resonators, which is at least two orders of magnitude higher than magneto-optical materials at the same wavelength. The artificial gyromagnetic permeability is attributed to the change in the local electric field direction modulated by the split-ring resonators. Our study demonstrates the possibility of engineering the permeability and permittivity tensors in metamaterials at arbitrary frequencies, thereby promising a variety of applications of next-generation nonreciprocal photonic devices, magneto-plasmonic sensors, and active metamaterials.
Dietary fat promotes antibiotic-induced Clostridioides difficile mortality in mice
Authors: Hazleton Keith Z. , Martin Casey G. , Orlicky David J. , Arnolds Kathleen L. , Nusbacher Nichole M. , Moreno-Huizar Nancy , Armstrong Michael , Reisdorph Nichole , Lozupone Catherine A. 
Published: April 2022

AbstractClostridioides difficile infection (CDI) is the leading cause of hospital-acquired diarrhea, and emerging evidence has linked dietary components with CDI pathogenesis, suggesting that dietary modulation may be an effective strategy for prevention. Here, we show that mice fed a high-fat/low-fiber “Western-type” diet (WD) had dramatically increased mortality in a murine model of antibiotic-induced CDI compared to a low-fat/low-fiber (LF/LF) diet and standard mouse chow controls. We found that the WD had a pro- C. difficile bile acid composition that was driven in part by higher levels of primary bile acids that are produced to digest fat, and a lower level of secondary bile acids that are produced by the gut microbiome. This lack of secondary bile acids was associated with a greater disturbance to the gut microbiome with antibiotics in both the WD and LF/LF diet compared to mouse chow. Mice fed the WD also had the highest level of toxin TcdA just prior to the onset of mortality, but not of TcdB or increased inflammation. These findings indicate that dietary intervention to decrease fat may complement previously proposed dietary intervention strategies to prevent CDI in high-risk individuals.
Cichlids and stingrays can add and subtract ‘one’ in the number space from one to five
Authors: Schluessel V. , Kreuter N. , Gosemann I. M. , Schmidt E. 
Published: March 2022

AbstractThe numerical understanding of cichlids and stingrays was examined regarding addition and subtraction abilities within the number space of one to five. Experiments were conducted as two-alternative forced-choice experiments, using a delayed matching to sample technique. On each trial, fish had to perform either an addition or subtraction, based on the presentation of two-dimensional objects in two distinct colors, with the color signaling a particular arithmetic process. Six cichlids and four stingrays successfully completed training and recognized specific colors as symbols for addition and subtraction. Cichlids needed more sessions than stingrays to reach the learning criterion. Transfer tests showed that learning was independent of straightforward symbol memorization. Individuals did not just learn to pick the highest or lowest number presented based on the respective color; instead, learning was specific to adding or subtracting ‘one’. Although group results were significant for both species in all tests, individual results varied. Addition was learned more easily than subtraction by both species. While cichlids learned faster than stingrays, and more cichlids than stingrays learned the task, individual performance of stingrays exceeded that of cichlids. Previous studies have provided ample evidence that fish have numerical abilities on par with those of other vertebrate and invertebrate species tested, a result that is further supported by the findings of the current study.
Rapid surface uplift and crustal flow in the Central Andes (southern Peru) controlled by lithospheric drip dynamics
Authors: Göğüş Oğuz H. , Sundell Kurt , Uluocak Ebru Şengül , Saylor Joel , Çetiner Uğurcan 
Published: April 2022

AbstractThe high flux magmatism, crustal shortening/extension and plateau formation in Cordilleran orogenic systems have been explained by removal of lithosphere (lower crust and the sub-arc mantle lithosphere) that develops beneath the magmatic arc and hinterland regions. However, the primary role of this process driving surface uplift, and crustal deformation is not well understood. Here, reconciling geodynamic model predictions with lithospheric structure and paleoelevation estimates, we suggest that viscous drip-type lithospheric removal from beneath the Central (Peruvian) Andes can explain several tectonic features: (1) “double humped” shaped/axisymmetric topographic profile and rapid surface rise (up to 1.2 km in ~ 4.31 Myrs); (2) thicker crust associated with the lower surface elevation of the Altiplano plateau (Lake Titicaca region) (negative residual topography) and higher topography and thinner crust of Western and Eastern Cordilleras (positive residual topography); and (3) faster wave speed (colder)/sub-Moho anomaly underlying the Altiplano, surrounded by slower speed anomalies on both western arc-forearc areas and parts of the eastern Cordillera and Sub-Andes. Our results emphasize the important role of lithospheric drip and associated mantle dynamics in the transient evolution of Andean orogeny controlling surface uplift and crustal flow and thickening.
Increased generosity under COVID-19 threat
Authors: Fridman Ariel , Gershon Rachel , Gneezy Ayelet 
Published: March 2022

AbstractIn the face of crises—wars, pandemics, and natural disasters—both increased selfishness and increased generosity may emerge. In this paper, we study the relationship between the presence of COVID-19 threat and generosity using a four-year longitudinal dataset (N = 696,942) capturing real donations made before and during the pandemic, as well as allocations from a 6-month dictator game study (N = 1003 participants) during the early months of the pandemic. Consistent with the notion of “catastrophe compassion” and contrary to some prior research showing a tendency toward self-interested behavior under threat, individuals across both datasets exhibited greater financial generosity when their county experienced COVID-19 threat. While we find that the presence of threat impacted individual giving, behavior was not sensitive to threat level. Our findings have significant societal implications and advance our understanding of economic and psychological theories of social preferences under threat.