bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single cell imaging-based chromatin biomarkers for tumor progression
Authors: Venkatachalapathy Saradha , Jokhun Doorgesh S. , Andhari Madhavi , Shivashankar G. V. 
Published: November 2021

AbstractTumour progression within the tissue microenvironment is accompanied by complex biomechanical alterations of the extracellular environment. While histopathology images provide robust biochemical markers for tumor progression in clinical settings, a quantitative single cell score using nuclear morphology and chromatin organization integrated with the long range mechanical coupling within the tumor microenvironment is missing. We propose that the spatial chromatin organization in individual nuclei characterises the cell state and their alterations during tumor progression. In this paper, we first built an image analysis pipeline and implemented it to classify nuclei from patient derived breast tissue biopsies of various cancer stages based on their nuclear and chromatin features. Replacing H&E with DNA binding dyes such as Hoescht stained tissue biopsies, we improved the classification accuracy. Using the nuclear morphology and chromatin organization features, we constructed a pseudo-time model to identify the chromatin state changes that occur during tumour progression. This enabled us to build a single-cell mechano-genomic score that characterises the cell state during tumor progression from a normal to a metastatic state. To gain further insights into the alterations in the local tissue microenvironments, we also used the nuclear orientations to identify spatial neighbourhoods that have been posited to drive tumor progression. Collectively, we demonstrate that image-based single cell chromatin and nuclear features are important single cell biomarkers for phenotypic mapping of tumor progression.
Hydroclimate change in the Garhwal Himalaya, India at 4200 yr BP coincident with the contraction of the Indus civilization
Authors: Niederman E. A. , Porinchu D. F. , Kotlia B. S. 
Published: November 2021

AbstractHigh-resolution analysis of a 3.80 m sediment core recovered from Deoria Tal, a mid-elevation lake located at 2393 m a.s.l. in the Garhwal Himalaya, documents long-term and abrupt hydroclimate fluctuations in northern India during the mid- to late Holocene. The sediment chronology, based on ten 14C dates, indicates the core spans 5200 years. Non-destructive, radiological imaging approaches (X-ray fluorescence (XRF), X-ray imaging, and CT scans) were used to assess the response of the lake system to changing hydroclimatic conditions. Variations in elemental concentrations and sediment density evidenced notable hydroclimate change episodes centered at 4850, 4200, and 3100 cal yr BP. Elevated detrital input, greater sediment density, decreased lake ventilation, and lower autochthonous productivity reflects lake deepening between 4350 and 4200 cal yr BP. An abrupt shift in elemental concentrations and sediment density indicated the onset of lake drawdown at 4200 cal yr BP and a negative hydroclimate anomaly between 4200 and 4050 cal yr BP. Lower detrital flux, decreased sediment density, increased oxygenation, and higher autochthonous productivity, reflects a reduction in lake volume between 3200 and 3100 cal yr BP. The potential link between abrupt climate change at 4200 cal yr BP and the contraction of the Indus civilization is explored.
Naturally occurring van der Waals heterostructure lengenbachite with strong in-plane structural and optical anisotropy
Authors: Dasgupta Arindam , Yang Xiaodong , Gao Jie 
Published: November 2021

AbstractLengenbachite is a naturally occurring layered mineral formed with alternating stacks of two constituent PbS-like and M2S3-like two-dimensional (2D) material layers due to the phase segregation process during the formation. Here, we demonstrate to achieve van der Waals (vdW) heterostructures of lengenbachite down to a few layer-pair thickness by mechanical exfoliation of bulk lengenbachite mineral. The incommensurability between the constituent isotropic 2D material layers makes the formed vdW heterostructure exhibit strong in-plane structural anisotropy, which leads to highly anisotropic optical responses in lengenbachite thin flakes, including anisotropic Raman scattering, linear dichroism, and anisotropic third-harmonic generation. Moreover, we exploit the nonlinear optical anisotropy for polarization-dependent intensity modulation of the converted third-harmonic optical vortices. Our study establishes lengenbachite as a new natural vdW heterostructure-based 2D material with unique optical properties for realizing anisotropic optical devices for photonic integrated circuits and optical information processing.
Amazon methane budget derived from multi-year airborne observations highlights regional variations in emissions
Authors: Basso Luana S. , Marani Luciano , Gatti Luciana V. , Miller John B. , Gloor Manuel , Melack John , Cassol Henrique L. G. , Tejada Graciela , Domingues Lucas G. , Arai Egidio , Sanchez Alber H. , Corrêa Sergio M. , Anderson Liana , Aragão Luiz E. O. C. , Correia Caio S. C. , Crispim Stephane P. , Neves Raiane A. L. 
Published: November 2021

AbstractAtmospheric methane concentrations were nearly constant between 1999 and 2006, but have been rising since by an average of ~8 ppb per year. Increases in wetland emissions, the largest natural global methane source, may be partly responsible for this rise. The scarcity of in situ atmospheric methane observations in tropical regions may be one source of large disparities between top-down and bottom-up estimates. Here we present 590 lower-troposphere vertical profiles of methane concentration from four sites across Amazonia between 2010 and 2018. We find that Amazonia emits 46.2 ± 10.3 Tg of methane per year (~8% of global emissions) with no temporal trend. Based on carbon monoxide, 17% of the sources are from biomass burning with the remainder (83%) attributable mainly to wetlands. Northwest-central Amazon emissions are nearly aseasonal, consistent with weak precipitation seasonality, while southern emissions are strongly seasonal linked to soil water seasonality. We also find a distinct east-west contrast with large fluxes in the northeast, the cause of which is currently unclear.
Ambulatory Voice Biofeedback: Acquisition and Retention of Modified Daily Voice Use in Patients With Phonotraumatic Vocal Hyperfunction
Authors: Van Stan Jarrad H. , Ortiz Andrew J. , Sternad Dagmar , Mehta Daryush D. , Huo Chuanbing , Hillman Robert E. 
Published: November 2021

Purpose:
Voice ambulatory biofeedback (VAB) has potential to improve carryover of therapeutic voice use into daily life. Previous work in vocally healthy participants demonstrated that motor learning inspired variations to VAB produced expected differences in acquisition and retention of modified daily voice use. This proof-of-concept study was designed to evaluate whether these VAB variations have the same desired effects on acquisition and retention in patients with phonotraumatic vocal hyperfunction (PVH).

Method:
Seventeen female patients with PVH wore an ambulatory voice monitor for 6 days: three baseline days, one biofeedback day, one short-term retention day, and one long-term retention day. Short- and long-term retention were 1- and 7-days postbiofeedback, respectively. Patients were block-randomized to receive one of three types of VAB: 100%, 25%, and Summary. Performance was measured in terms of adherence time below a subject-specific vocal intensity threshold.

Results:
All three types of VAB produced a biofeedback effect with 13 out of 17 patients displaying an increase in adherence time compared to baseline days. Additionally, multiple patients from each VAB group increased their adherence time during short- and/or long-term retention monitoring compared to baseline.

Conclusions:
These findings show that VAB can be associated with acquisition and retention of desired voice use in patients with PVH. Specifically, all three feedback types improved multiple patients' performance and retention for up to 1 week after biofeedback removal. Future work can investigate the impact of incorporating VAB into voice therapy.
Transition pathways connecting crystals and quasicrystals
Authors: Yin Jianyuan , Jiang Kai , Shi An-Chang , Zhang Pingwen , Zhang Lei 
Published: November 2021

SignificanceDespite the fact that tremendous efforts have been made on the study of quasicrystals since their discovery in 1984, nucleation of quasicrystals—the emergence of a quasicrystal from a crystalline phase—still presents an unsolved problem. The difficulties lie in that quasicrystals and crystals are incommensurate structures in general, so there are no obvious epitaxial relations between them. We solved this problem by applying an efficient numerical method to Landau theory of phase transitions and obtained the accurate critical nuclei and transition pathways connecting crystalline and quasicrystalline phases. The proposed computational methodology not only reveals the mechanism of nucleation of quasicrystals, but also paves the way to investigate a wide range of physical problems undergoing the first-order phase transitions.
Forecast-based attribution of a winter heatwave within the limit of predictability
Authors: Leach Nicholas J. , Weisheimer Antje , Allen Myles R. , Palmer Tim 
Published: November 2021

SignificanceThe question of how humans have influenced individual extreme weather events is both scientifically and socially important. However, deficiencies in climate models’ representations of key mechanisms within the process chains that drive weather reduce our confidence in estimates of the human influence on extreme events. We propose that using forecast models that successfully predicted the event in question could increase the robustness of such estimates. Using a successful forecast means we can be confident that the model is able to faithfully represent the characteristics of the specific extreme event. We use this forecast-based methodology to estimate the direct radiative impact of increased CO2concentrations (one component, but not the entirety, of human influence) on the European heatwave of February 2019.
Metagenomic discovery of CRISPR-associated transposons
Authors: Rybarski James R. , Hu Kuang , Hill Alexis M. , Wilke Claus O. , Finkelstein Ilya J. 
Published: November 2021

Significance
CRISPR-Cas systems confer bacteria and archaea with adaptive immunity against mobile genetic elements. These systems also participate in other cellular processes. For example, CRISPR-associated Tn7 transposons (CASTs) have co-opted nuclease-inactive CRISPR effector proteins to guide their transposition. We bioinformatically survey metagenomic databases to uncover CASTs, including systems with new architectures and ones that use distinct CRISPR subtypes. We also describe a putative non-Tn7 CAST that co-opts Cas12. Our findings propose mechanisms for vertical and horizontal CAST targeting and shed light on how CASTs have coevolved with CRISPR-Cas systems.
Kinematic self-replication in reconfigurable organisms
Authors: Kriegman Sam , Blackiston Douglas , Levin Michael , Bongard Josh 
Published: November 2021

SignificanceAlmost all organisms replicate by growing and then shedding offspring. Some molecules also replicate, but by moving rather than growing: They find and combine building blocks into self-copies. Here we show that clusters of cells, if freed from a developing organism, can similarly find and combine loose cells into clusters that look and move like they do, and that this ability does not have to be specifically evolved or introduced by genetic manipulation. Finally, we show that artificial intelligence can design clusters that replicate better, and perform useful work as they do so. This suggests that future technologies may, with little outside guidance, become more useful as they spread, and that life harbors surprising behaviors just below the surface, waiting to be uncovered.
Redox conditions correlated with vibronic coupling modulate quantum beats in photosynthetic pigment–protein complexes
Authors: Higgins Jacob S. , Allodi Marco A. , Lloyd Lawson T. , Otto John P. , Sohail Sara H. , Saer Rafael G. , Wood Ryan E. , Massey Sara C. , Ting Po-Chieh , Blankenship Robert E. , Engel Gregory S. 
Published: November 2021

Significance
Photosynthetic organisms evolved their light-harvesting antenna complexes to optimize energy transfer. It was recently shown that the redox environment can tune the mixing of electronic and vibrational states to steer energy through different pathways of a pigment–protein complex. Quantum beating signals in the spectra of pigment–protein complexes have been used to probe the excited-state dynamics within the complexes, but the microscopic dynamics that generate these signals and their role in promoting energy transfer are not fully understood. Here, we show that the redox environment that tunes energy transfer similarly tunes the quantum beating signals in the same complex. We find that the beats report on excited-state vibrations that maintain coherence through the vibronically enhanced energy transfer process.
Quinoa, potatoes, and llamas fueled emergent social complexity in the Lake Titicaca Basin of the Andes
Authors: Miller Melanie J. , Kendall Iain , Capriles José M. , Bruno Maria C. , Evershed Richard P. , Hastorf Christine A. 
Published: November 2021

Significance
Food production systems are critical components in the emergence of complex socioecological systems. In the Andes, societal complexity has often been related to the increasing production and consumption of maize by elites, but the importance of highland cultivated crops, such as potatoes, one of the most cultivated crops in the world, and quinoa, presently recognized as a “superfood,” remains largely underappreciated. Using stable isotopes including compound-specific amino acids, we reconstruct the diets of people living in southern Lake Titicaca, where the Tiwanaku state emerged. Over time, locally produced potatoes, quinoa, and llamas, by means of increasingly intensive practices, facilitated long-term food security, which sustained population growth, contributed to increasing sociopolitical complexity, and facilitated resiliency through episodes of significant climatic variation.
Individual and combined impact of physical fitness on health‐related quality of life during adolescence: DADOS Study
Authors: Solera‐Sanchez Alba , Adelantado‐Renau Mireia , Moliner‐Urdiales Diego , Beltran‐Valls Maria Reyes 
Published: November 2021

ABSTRACTThe purpose of the present study was to investigate the individual and combined impact of physical fitness components at baseline on health‐related quality of life (HRQoL) at 24‐month follow‐up in adolescents. This longitudinal research included 199 adolescents (13.9 ± 0.3 years at baseline) from the DADOS study. Cardiorespiratory fitness was assessed using the 20‐m shuttle run test. Muscular strength was assessed using the standing broad jump test. Motor competence was assessed using the 4 × 10‐m shuttle run test. A physical fitness z‐score was calculated as the mean of the z‐scores values of each fitness test. A fitness index ranging from 0 to 3 was created according to the number of physical fitness components in which participants achieved high levels according to normative values. HRQoL was evaluated by the KIDSCREEN‐10 questionnaire. Linear regression analyses showed that cardiorespiratory fitness, muscular strength, and the physical fitness z‐score at baseline were individually associated with HRQoL at follow‐up (β ranging from 0.123 to 0.183; all p < 0.05). Moreover, logistic regression analysis revealed that adolescents with a fitness index ≥1 at baseline were more likely to achieve high HRQoL at 24‐month follow‐up, compared with their peers with an index of 0 (OR ranging from 3.554 to 9.087; all p < 0.05). Our results revealed an individual and cumulative positive impact of physical fitness at baseline on HRQoL at 24‐month follow‐up. These findings underline the key role of promoting the enhancement of overall physical fitness components in order to improve adolescents’ health and well‐being.Highlights
Adolescents with high levels of cardiorespiratory fitness, muscular strength and motor competence will benefit from a greater physical and mental well‐being over the time.
The more physical fitness components with optimal levels, the greater likelihood of reaching better HRQoL over the time.
Public health authorities should focus on the promotion of multiple physical fitness components to increase adolescent's likelihood of achieving greater HRQoL over the time.
First-order perturbations of Gödel-type metrics in non-dynamical Chern–Simons modified gravity
Authors: Altschul B , Nascimento J R , Petrov A Yu , Porfírio P J 
Published: November 2021

Abstract
Gödel-type metrics that are homogeneous in both space and time remain, like the Schwarzschild metric, consistent within Chern–Simons modified gravity; this is true in both the non-dynamical and dynamical frameworks, each of which involves an additional pseudoscalar field coupled to the Pontryagin density. In this paper, we consider stationary first-order perturbations to these metrics in the non-dynamical framework. Under certain assumptions we find analytical solutions to the perturbed field equations. The solutions of the first-order field equations break the translational and cylindrical symmetries of the unperturbed metrics. The effective potential controlling planar geodesic orbits is also affected by the perturbation parameter, which changes the equilibrium radii for the orbits of both massive particles and massless photons.
Barnich–Troessaert bracket as a Dirac bracket on the covariant phase space
Authors: Wieland Wolfgang 
Published: November 2021

Abstract
The Barnich–Troessaert bracket is a proposal for a modified Poisson bracket on the covariant phase space for general relativity. The new bracket allows us to compute charges, which are otherwise not integrable. Yet there is a catch. There is a clear prescription for how to evaluate the new bracket for any such charge, but little is known how to extend the bracket to the entire phase space. This is a problem, because not every gravitational observable is also a charge. In this paper, we propose such an extension. The basic idea is to remove the radiative data from the covariant phase space. This requires second-class constraints. Given a few basic assumptions, we show that the resulting Dirac bracket on the constraint surface is nothing but the BT bracket. A heuristic argument is given to show that the resulting constraint surface can only contain gravitational edge modes.
Einstein gravity as a gauge theory for the conformal group
Authors: Herfray Yannick , Scarinci Carlos 
Published: November 2021

Abstract
General relativity in dimension n = p + q can be formulated as a gauge theory for the conformal group

S
O

p
+
1
,
q
+
1

, along with an additional field reducing the structure group down to the Poincaré group

I
S
O

p
,
q

. In this paper, we propose a new variational principle for Einstein geometry which realizes this fact. Importantly, as opposed to previous treatments in the literature, our action functional gives first order field equations and does not require supplementary constraints on gauge fields, such as torsion-freeness. Our approach is based on the ‘first order formulation’ of conformal tractor geometry. Accordingly, it provides a straightforward variational derivation of the tractor version of the Einstein equation. To achieve this, we review the standard theory of tractor geometry with a gauge theory perspective, defining the tractor bundle a priori in terms of an abstract principal bundle and providing an identification with the standard conformal tractor bundle via a dynamical soldering form. This can also be seen as a generalization of the so called Cartan–Palatini formulation of general relativity in which the ‘internal’ orthogonal group

S
O

p
,
q

is extended to an appropriate parabolic subgroup

P
⊂
S
O

p
+
1
,
q
+
1

of the conformal group.
Photothermal liquid release from arrayed Au nanorod/hydrogel composites for chemical stimulation
Authors: Seo Sang-Woo , Song Youngsik , Rostami Azmand Hojjat 
Published: November 2021

Abstract
Controlled photothermal actuation of liquid release is presented using periodically arrayed hydrogel columns in a macroporous silicon membrane. Thermo-responsive hydrogel is mixed with Gold (Au) nanorods, and surface plasmon-induced local heating by near-infrared (NIR) light is utilized as an actuation method. We adopted theoretical modeling, which treats the hydrogel as a poro-viscoelastic medium to understand the mechanical and liquid transport properties of the hydrogel. To demonstrate the feasibility of the liquid release control using NIR light, we first characterized the temperature response of Au nanorod embedded hydrogel in the silicon membrane using its optical transmission behavior to confirm the successful device fabrication. Next, the liquid release characteristics from the structure were studied using fluorescent imaging of fluorescein dye solution while pulsed NIR light was illuminated on the structure. We successfully demonstrate that the liquid release can be controlled using remote NIR illumination from the presented structure. Considering the periodically arrayed configuration with high spatial resolution, this will have a potential prospect for optically-addressable chemical release systems, which benefit retina prosthesis interfaces.
Mode coupling and locking of a Π-shaped cantilever resonator using laser-induced asymmetric modulation
Authors: Luo Wenyao , Gao Naikun , Li Yanyan , Zhao Zhixin , Liu Duo 
Published: November 2021

Abstract
Mechanical resonators, such as microcantilevers, demonstrate significant potential for use in information technology. Cantilevered beams of various geometries clamped at one end form the most ubiquitous structures in microelectromechanical systems that support multimode vibration for the detection, conversion, and processing of small signals. In this study, we demonstrate that the potential of these devices can be further extended by utilizing a strategy based on mode coupling and locking induced by asymmetric photothermal modulation. A cantilever was designed to have a Π-shape with a specific geometry such that the resonant frequencies of the two orthogonal modes are close to one another. Additionally, we show that mode coupling between the two modes, which are originally orthogonal to one another, can be achieved through laser-induced photothermal modulation. In particular, the two modes can be parametrically tuned to become degenerate through mode coupling with a significant increase in the quality factor from 112 to 839. This approach is universal and can be extended to improve the detection limits of microresonators in high-dissipation environments with enhanced signal-to-noise ratios.