bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnetotail Ion Structuring by Kinetic Ballooning‐Interchange Instability
Authors: Panov Evgeny V. , Lu San , Pritchett Philip L. 
Published: January 2022

AbstractBy combining three‐probe THEMIS observations and 3‐D Particle‐in‐Cell simulations, we identify key structures on the ion gyroradius scale that occur in connection with ballooning‐interchange instability heads in the Earth's magnetotail. The mesoscale structures occur at sites of strong ion velocity shear and vorticity where the thermal ion Larmor radius is about half of the width of the head. Finer structures occur at the smaller scales characterizing the wavelength of the electromagnetic ion cyclotron waves generated at the heads. These two processes act to erode and thin the current sheet, thereby forming a local magnetotail configuration that is favorable for reconnection.
Formation of the Evening Time F3 Layer Investigated Using Jicamarca Incoherent Scatter Radar Observations
Authors: Venkatesh K. , Patra A. K. 
Published: January 2022

AbstractThe formation of the evening time F3 layer remains elusive. One of the hypotheses for the formation of the evening time F3 layer relies on the height gradient in the vertical plasma drift. In this paper, we test the validity of the hypothesis using Jicamarca incoherent scatter radar observations of height profiles of electron density and vertical plasma drift. Results show that the evening F3 layer could occur when the plasma drift is moderate and the height gradient in the vertical plasma drift is small or insignificant. Given that the production in the evening hours is negligible, these results call for interpretation for understanding the formation of the evening F3 layer. We propose that in addition to the known role of vertical plasma drift, the height variation in the recombination loss of electrons plays an important role in the formation of evening F3 layer over the geomagnetic equator.
Fluid Simulations Accelerated With 16 Bits: Approaching 4x Speedup on A64FX by Squeezing ShallowWaters.jl Into Float16
Authors: Klöwer Milan , Hatfield Sam , Croci Matteo , Düben Peter D. , Palmer Tim N. 
Published: January 2022

AbstractMost Earth‐system simulations run on conventional central processing units in 64‐bit double precision floating‐point numbers Float64, although the need for high‐precision calculations in the presence of large uncertainties has been questioned. Fugaku, currently the world's fastest supercomputer, is based on A64FX microprocessors, which also support the 16‐bit low‐precision format Float16. We investigate the Float16 performance on A64FX with ShallowWaters.jl, the first fluid circulation model that runs entirely with 16‐bit arithmetic. The model implements techniques that address precision and dynamic range issues in 16 bits. The precision‐critical time integration is augmented to include compensated summation to minimize rounding errors. Such a compensated time integration is as precise but faster than mixed precision with 16 and 32‐bit floats. As subnormals are inefficiently supported on A64FX the very limited range available in Float16 is 6 × 10−5 to 65,504. We develop the analysis‐number format Sherlogs.jl to log the arithmetic results during the simulation. The equations in ShallowWaters.jl are then systematically rescaled to fit into Float16, using 97% of the available representable numbers. Consequently, we benchmark speedups of up to 3.8x on A64FX with Float16. Adding a compensated time integration, speedups reach up to 3.6x. Although ShallowWaters.jl is simplified compared to large Earth‐system models, it shares essential algorithms and therefore shows that 16‐bit calculations are indeed a competitive way to accelerate Earth‐system simulations on available hardware.
Diet-induced deficits in goal-directed control are rescued by agonism of group II metabotropic glutamate receptors in the dorsomedial striatum
Authors: Shipman Megan L. , Corbit Laura H. 
Published: January 2022

AbstractMany overweight or obese people struggle to sustain the behavioural changes necessary to achieve and maintain weight loss. In rodents, obesogenic diet can disrupt goal-directed control of responding for food reinforcers, which may indicate that diet can disrupt brain regions associated with behavioural control. We investigated a potential glutamatergic mechanism to return goal-directed control to rats who had been given an obesogenic diet prior to operant training. We found that an obesogenic diet reduced goal-directed control and that systemic injection of LY379268, a Group II metabotropic glutamate receptor (mGluR2/3) agonist, returned goal-directed responding in these rats. Further, we found that direct infusion of LY379268 into the dorsomedial striatum, a region associated with goal-directed control, also restored goal-directed responding in the obesogenic-diet group. This indicates that one mechanism through which obesogenic diet disrupts goal-directed control is glutamatergic, and infusion of a mGluR2/3 agonist into the DMS is sufficient to ameliorate deficits in goal-directed control.
Patient–clinician brain concordance underlies causal dynamics in nonverbal communication and negative affective expressivity
Authors: Ellingsen Dan-Mikael , Duggento Andrea , Isenburg Kylie , Jung Changjin , Lee Jeungchan , Gerber Jessica , Mawla Ishtiaq , Sclocco Roberta , Edwards Robert R. , Kelley John M. , Kirsch Irving , Kaptchuk Ted J. , Toschi Nicola , Napadow Vitaly 
Published: January 2022

AbstractPatient–clinician concordance in behavior and brain activity has been proposed as a potential key mediator of mutual empathy and clinical rapport in the therapeutic encounter. However, the specific elements of patient–clinician communication that may support brain-to-brain concordance and therapeutic alliance are unknown. Here, we investigated how pain-related, directional facial communication between patients and clinicians is associated with brain-to-brain concordance. Patient–clinician dyads interacted in a pain-treatment context, during synchronous assessment of brain activity (fMRI hyperscanning) and online video transfer, enabling face-to-face social interaction. In-scanner videos were used for automated individual facial action unit (AU) time-series extraction. First, an interpretable machine-learning classifier of patients’ facial expressions, from an independent fMRI experiment, significantly distinguished moderately painful leg pressure from innocuous pressure stimuli. Next, we estimated neural-network causality of patient-to-clinician directional information flow of facial expressions during clinician-initiated treatment of patients’ evoked pain. We identified a leader–follower relationship in which patients predominantly led the facial communication while clinicians responded to patients’ expressions. Finally, analyses of dynamic brain-to-brain concordance showed that patients’ mid/posterior insular concordance with the clinicians’ anterior insula cortex, a region identified in previously published data from this study1, was associated with therapeutic alliance, and self-reported and objective (patient-to-clinician-directed causal influence) markers of negative-affect expressivity. These results suggest a role of patient-clinician concordance of the insula, a social-mirroring and salience-processing brain node, in mediating directional dynamics of pain-directed facial communication during therapeutic encounters.
microRNA-124-3p attenuates myocardial injury in sepsis via modulating SP1/HDAC4/HIF-1α axis
Authors: Wu Mei , Huang Zehong , Huang Wenfang , Lin Mengyu , Liu Weifeng , Liu Kexuan , Li Cai 
Published: January 2022

AbstractSepsis-induced cardiac dysfunction can lead to death in sepsis. In this case, we targeted to explore in detail the relative mechanism of microRNA (miR)-124-3p in sepsis-induced myocardial injury via the specific protein 1/histone deacetylase 4/hypoxia-inducing factor 1α (SP1/HDAC4/HIF-1α) axis. Septic rats were modeled by cecal ligation puncture while in vitro septic cardiomyocyte H9C2 were induced by lipopolysaccharide (LPS). miR-124-3p/SP1/HDAC4/HIF-1α expression levels in myocardial tissues of septic rats and LPS-treated H9C2 cells were measured. miR-124-3p overexpression and SP1 silencing assays were implemented on LPS-treated H9C2 cells to explore theirs actions in inflammation, oxidative stress and cell apoptosis. The interactions of miR-124-3p, SP1, and HDAC4 were testified. miR-124-3p was lowly expressed while SP1, HDAC4, and HIF-1α were highly expressed in sepsis. Upregulation of miR-124-3p ameliorated inflammation, oxidative stress, and apoptosis of LPS-treated H9C2 cells. Silencing SP1 improved LPS-induced damage to cardiomyocytes. miR-124-3p targeted SP1 and HDAC4 interacted with SP1. SP1 overexpression antagonized miR-124-3p upregulation-induced improvements in LPS-induced cardiomyocyte damage. This study illustrates that miR-124-3p improves myocardial injury in septic rats through targeted regulation of SP1 to mediate HDAC4/HIF-1α.
KLF2 up-regulates IRF4/HDAC7 to protect neonatal rats from hypoxic-ischemic brain damage
Authors: Wu Fan , Li Chunlin 
Published: January 2022

AbstractNeonatal brain hypoxic ischemic injury is a devastating event causing permanent brain damage. The current study set out to explore the role of Kruppel-like factor 2 (KLF2) and its downstream molecular mechanism on hypoxic-ischemic brain damage (HIBD) in neonatal rats. First, we adopted a modified Rice method to develop a HIBD model in postnatal day seven Sprague Dawley (SD) rat pups. Next, neuronal damage, morphological changes, and neuronal apoptosis were documented in the vulnerable hippocampal CA1 region and evaluated using Nissl staining, H&E staining, and TUNEL assay, respectively. Meanwhile, a hypoxic-ischemic model using the oxygen-glucose deprivation (OGD) method was established in cortical neurons isolated from day one SD rat pups, followed by MTT and flow cytometry detections of the cell survival rate and apoptotic ability. Experimental findings revealed that KLF2 was poorly-expressed in the brain tissues of HIBD rats and in the OGD-induced neurons. We found that KLF2 overexpression inhibited neuron apoptosis in vitro and in vivo, which was also observed to inhibit brain injury in the HIBD rats and alleviate neuronal damage of OGD-treated neurons. Besides, as dual luciferase reporter gene assay and chromatin immunoprecipitation established that KLF2 bound to the interferon regulatory factor 4 (IRF4) promoter, which promoted the binding of IRF4 in the promoter of histone deacetylase 7 (HDAC7) to augment its expression, thereby inhibiting neuronal apoptosis and brain damage. In conclusion, our findings indicated that KLF2 could increase the expression of IRF4 to up-regulate the expression of HDAC7, which protects against HIBD in neonatal rats.
Characterizing cellular heterogeneity in fibrotic hypersensitivity pneumonitis by single-cell transcriptional analysis
Authors: Wang Junyi , Zhang Lei , Luo Li , He Ping , Xiong Anying , Jiang Manling , Liu Yao , Liu Shengbin , Ran Qin , Wu Dehong , Xiong Ying , He Xiang , Li Guoping 
Published: January 2022

AbstractFibrotic hypersensitivity pneumonitis (FHP) remains one of fatal interstitial pulmonary disease. Comprehensively dissecting the cellular heterogeneity of FHP paves the way for developing general gene therapeutic solutions for FHP. Here, utilizing an integrated strategy based on scRNA-seq, scTCR-seq, and bulk RNA-seq analysis of FHP profiles, we identified ten major cell types and 19 unique subtypes. FHP exhibited higher features of EMT and inflammation-promoting than normal control. In distinct subsets of lung macrophages in FHP, FN1high, PLA2G7high, and MS4A6Ahigh macrophages with predominant M2 phenotype exhibited higher activity of inflammatory responses and para-inflammation than other macrophages. KRT17high basal-like epithelial cells were significantly increased in FHP, and showed higher ability to induce EMT. We identified roles for ACTA2high, COL1A1high, and PLA2G2Ahigh fibroblasts in FHP, which were significantly related to interstitial fibrosis. NK cells and KLRG1+ effector CD8+ T cells had greater activity in inflammation-promoting. Our results provide a comprehensive portrait of cellular heterogeneity in FHP, and highlight the indispensable role of cell subpopulations in shaping the complexity and heterogeneity of FHP. These subpopulations are potentially key players for FHP pathogenesis.
Mature but not developing Schwann cells promote axon regeneration after peripheral nerve injury
Authors: Endo Takeshi , Kadoya Ken , Suzuki Tomoaki , Suzuki Yuki , Terkawi Mohamad Alaa , Kawamura Daisuke , Iwasaki Norimasa 
Published: January 2022

AbstractSince Schwann cells (SCs) support axonal growth at development as well as after peripheral nerve injury (PNI), developing SCs might be able to promote axon regeneration after PNI. The purpose of the current study was to elucidate the capability of developing SCs to induce axon regeneration after PNI. SC precursors (SCPs), immature SCs (ISCs), repair SCs (RSCs) from injured nerves, and non-RSCs from intact nerves were tested by grafting into acellular region of rat sciatic nerve with crush injury. Both of developing SCs completely failed to support axon regeneration, whereas both of mature SCs, especially RSCs, induced axon regeneration. Further, RSCs but not SCPs promoted neurite outgrowth of adult dorsal root ganglion neurons. Transcriptome analysis revealed that the gene expression profiles were distinctly different between RSCs and SCPs. These findings indicate that developing SCs are markedly different from mature SCs in terms of functional and molecular aspects and that RSC is a viable candidate for regenerative cell therapy for PNI.
Development of a sensitive, quantitative assay with broad subtype specificity for detection of total HIV-1 nucleic acids in plasma and PBMC
Authors: Kibirige C. N. , Manak M. , King D. , Abel B. , Hack H. , Wooding D. , Liu Y. , Fernandez N. , Dalel J. , Kaye Steve , Imami N. , Jagodzinski L. , Gilmour J. 
Published: January 2022

AbstractAn LTR-based quantitative PCR (qPCR) assay was modified and optimized for the quantification of total HIV-1 nucleic acids in plasma and PBMC. TaqMan qPCR primers and probes were designed against the NCBI/LANL HIV-1 compendium database by analyzing sequences used in assays for sensitive cross-clade detection of HIV-1 as reported in the literature and elucidating regions of improved cross-subtype specificity. Inosine and mixed nucleotide bases were included at polymorphic sites. Real-time RT-qPCR and qPCR were performed on plasma viral RNA and cellular lysates. A step-up amplification approach to allow binding of primers across polymorphic regions showed improved sensitivity compared to universal cycling. Unlike a lead competing laboratory-developed assay, all major HIV-1 subtypes, and a wide range of recombinants from a 127-member diversity panel were detected and accurately quantified in spiked plasmas. Semi-nested PCR increased detection sensitivity even further. The assay was able to detect down to 88 copies/mL of HIV-1 in plasma with 95% efficiency or the equivalent of a single infected cell. The PCR assay will be valuable in studies that monitor very low viral levels including residual or break through HIV-1 in patients receiving antiretroviral therapy, in HIV-1 cure, and in other research studies.
Local impacts on road networks and access to critical locations during extreme floods
Authors: Loreti Simone , Ser-Giacomi Enrico , Zischg Andreas , Keiler Margreth , Barthelemy Marc 
Published: January 2022

AbstractFloods affected more than 2 billion people worldwide from 1998 to 2017 and their occurrence is expected to increase due to climate warming, population growth and rapid urbanization. Recent approaches for understanding the resilience of transportation networks when facing floods mostly use the framework of percolation but we show here on a realistic high-resolution flood simulation that it is inadequate. Indeed, the giant connected component is not relevant and instead, we propose to partition the road network in terms of accessibility of local towns and define new measures that characterize the impact of the flooding event. Our analysis allows to identify cities that will be pivotal during the flooding by providing to a large number of individuals critical services such as hospitalization services, food supply, etc. This approach is particularly relevant for practical risk management and will help decision makers for allocating resources in space and time.
Entangled states shaping with CV states of definite parity
Authors: Kuts Dmitry A. , Podoshvedov Sergey A. 
Published: January 2022

AbstractWe present a new method to entangle continuous variable (CV) states of certain parity and photonic states for the purpose of generating optical hybrid cluster (HC) states. To do it we introduce two families of the CV states of definite parity which stems from single mode squeezed vacuum (SMSV) state. Potential to apply the CV states of certain parity is high. We report on the generation of the even/odd Schrödinger cat state like (SCS-like) states whose fidelities with even/odd SCS of amplitude of $$4.2$$

4.2

are more of $$0.99$$

0.99

, when 30,31 photons are detected in auxiliary mode of input SMSV state initially mixed with single photon. We show that the quantum efficiency of a photon number resolving (PNR) detector is crucial to maintaining the success rate of even/odd SCSs generator at an acceptable level. The scheme with delocalized photon implements deterministic imperfect entanglement operation between macro and micro states. We show that the beam splitter implements the two-qubits operation $$control-Z$$

c
o
n
t
r
o
l
-
Z

(CZ) for input CV states of definite parity and photonic states, provided that certain result is detected in measurement mode. An extension of the entangling operation for two entangled delocalized photons (TEDP) allows one to realize three-qubit HC state. Seven-qubit HC state is the result of conjunction of two three-qubit HC states through TEDP state.
Training load responses modelling and model generalisation in elite sports
Authors: Imbach Frank , Perrey Stephane , Chailan Romain , Meline Thibaut , Candau Robin 
Published: January 2022

AbstractThis study aims to provide a transferable methodology in the context of sport performance modelling, with a special focus to the generalisation of models. Data were collected from seven elite Short track speed skaters over a three months training period. In order to account for training load accumulation over sessions, cumulative responses to training were modelled by impulse, serial and bi-exponential responses functions. The variable dose-response (DR) model was compared to elastic net (ENET), principal component regression (PCR) and random forest (RF) models, while using cross-validation within a time-series framework. ENET, PCR and RF models were fitted either individually ($$M_{I}$$

M
I

) or on the whole group of athletes ($$M_{G}$$

M
G

). Root mean square error criterion was used to assess performances of models. ENET and PCR models provided a significant greater generalisation ability than the DR model ($$p = 0.018$$

p
=
0.018

, $$p < 0.001$$

p
<
0.001

, $$p = 0.004$$

p
=
0.004

and $$p < 0.001$$

p
<
0.001

for $$ENET_{I}$$

E
N
E

T
I

, $$ENET_{G}$$

E
N
E

T
G

, $$PCR_{I}$$

P
C

R
I

and $$PCR_{G}$$

P
C

R
G

, respectively). Only $$ENET_{G}$$

E
N
E

T
G

and $$RF_{G}$$

R

F
G

were significantly more accurate in prediction than DR ($$p < 0.001$$

p
<
0.001

and $$p < 0.012$$

p
<
0.012

). In conclusion, ENET achieved greater generalisation and predictive accuracy performances. Thus, building and evaluating models within a generalisation enhancing procedure is a prerequisite for any predictive modelling.
Using deep learning models to analyze the cerebral edema complication caused by radiotherapy in patients with intracranial tumor
Authors: Chao Pei-Ju , Chang Liyun , Kang Chen-Lin , Lin Chin-Hsueh , Shieh Chin-Shiuh , Wu Jia-Ming , Tseng Chin-Dar , Tsai I-Hsing , Hsu Hsuan-Chih , Huang Yu-Jie , Lee Tsair-Fwu 
Published: January 2022

AbstractUsing deep learning models to analyze patients with intracranial tumors, to study the image segmentation and standard results by clinical depiction complications of cerebral edema after receiving radiotherapy. In this study, patients with intracranial tumors receiving computer knife (CyberKnife M6) stereotactic radiosurgery were followed using the treatment planning system (MultiPlan 5.1.3) to obtain before-treatment and four-month follow-up images of patients. The TensorFlow platform was used as the core architecture for training neural networks. Supervised learning was used to build labels for the cerebral edema dataset by using Mask region-based convolutional neural networks (R-CNN), and region growing algorithms. The three evaluation coefficients DICE, Jaccard (intersection over union, IoU), and volumetric overlap error (VOE) were used to analyze and calculate the algorithms in the image collection for cerebral edema image segmentation and the standard as described by the oncologists. When DICE and IoU indices were 1, and the VOE index was 0, the results were identical to those described by the clinician.The study found using the Mask R-CNN model in the segmentation of cerebral edema, the DICE index was 0.88, the IoU index was 0.79, and the VOE index was 2.0. The DICE, IoU, and VOE indices using region growing were 0.77, 0.64, and 3.2, respectively. Using the evaluated index, the Mask R-CNN model had the best segmentation effect. This method can be implemented in the clinical workflow in the future to achieve good complication segmentation and provide clinical evaluation and guidance suggestions.
Impact of vaccination on the COVID-19 pandemic in U.S. states
Authors: Chen Xiao , Huang Hanwei , Ju Jiandong , Sun Ruoyan , Zhang Jialiang 
Published: January 2022

AbstractGovernments worldwide are implementing mass vaccination programs in an effort to end the novel coronavirus (COVID-19) pandemic. Here, we evaluated the effectiveness of the COVID-19 vaccination program in its early stage and predicted the path to herd immunity in the U.S. By early March 2021, we estimated that vaccination reduced the total number of new cases by 4.4 million (from 33.0 to 28.6 million), prevented approximately 0.12 million hospitalizations (from 0.89 to 0.78 million), and decreased the population infection rate by 1.34 percentage points (from 10.10 to 8.76%). We built a Susceptible-Infected-Recovered (SIR) model with vaccination to predict herd immunity, following the trends from the early-stage vaccination program. Herd immunity could be achieved earlier with a faster vaccination pace, lower vaccine hesitancy, and higher vaccine effectiveness. The Delta variant has substantially postponed the predicted herd immunity date, through a combination of reduced vaccine effectiveness, lowered recovery rate, and increased infection and death rates. These findings improve our understanding of the COVID-19 vaccination and can inform future public health policies.