bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of spatially variable genes with graph cuts
Authors: Zhang Ke , Feng Wanwan , Wang Peng 
Published: September 2022

AbstractSingle-cell gene expression data with positional information is critical to dissect mechanisms and architectures of multicellular organisms, but the potential is limited by the scalability of current data analysis strategies. Here, we present scGCO, a method based on fast optimization of hidden Markov Random Fields with graph cuts to identify spatially variable genes. Comparing to existing methods, scGCO delivers a superior performance with lower false positive rate and improved specificity, while demonstrates a more robust performance in the presence of noises. Critically, scGCO scales near linearly with inputs and demonstrates orders of magnitude better running time and memory requirement than existing methods, and could represent a valuable solution when spatial transcriptomics data grows into millions of data points and beyond.
Flexible cue anchoring strategies enable stable head direction coding in both sighted and blind animals
Authors: Asumbisa Kadjita , Peyrache Adrien , Trenholm Stuart 
Published: September 2022

AbstractVision plays a crucial role in instructing the brain’s spatial navigation systems. However, little is known about how vision loss affects the neuronal encoding of spatial information. Here, recording from head direction (HD) cells in the anterior dorsal nucleus of the thalamus in mice, we find stable and robust HD tuning in rd1 mice, a model of photoreceptor degeneration, that go blind by approximately one month of age. In contrast, placing sighted animals in darkness significantly impairs HD cell tuning. We find that blind mice use olfactory cues to maintain stable HD tuning and that prior visual experience leads to refined HD cell tuning in blind rd1 adult mice compared to congenitally blind animals. Finally, in the absence of both visual and olfactory cues, the HD attractor network remains intact but the preferred firing direction of HD cells drifts over time. These findings demonstrate flexibility in how the brain uses diverse sensory information to generate a stable directional representation of space.
Extracellular fibrinogen-binding protein released by intracellular Staphylococcus aureus suppresses host immunity by targeting TRAF3
Authors: Zhang Xiaokai , Xiong Tingrong , Gao Lin , Wang Yu , Liu Luxuan , Tian Tian , Shi Yun , Zhang Jinyong , Zhao Zhuo , Lu Dongshui , Luo Ping , Zhang Weijun , Cheng Ping , Jing Haiming , Gou Qiang , Zeng Hao , Yan Dapeng , Zou Quanming 
Published: September 2022

AbstractMany pathogens secrete effectors to hijack intracellular signaling regulators in host immune cells to promote pathogenesis. However, the pathogenesis of Staphylococcus aureus secretory effectors within host cells is unclear. Here, we report that Staphylococcus aureus secretes extracellular fibrinogen-binding protein (Efb) into the cytoplasm of macrophages to suppress host immunity. Mechanistically, RING finger protein 114, a host E3 ligase, mediates K27-linked ubiquitination of Efb at lysine 71, which facilitates the recruitment of tumor necrosis factor receptor associated factor (TRAF) 3. The binding of Efb to TRAF3 disrupts the formation of the TRAF3/TRAF2/cIAP1 (cellular-inhibitor-of-apoptosis-1) complex, which mediates K48-ubiquitination of TRAF3 to promote degradation, resulting in suppression of the inflammatory signaling cascade. Additionally, the Efb K71R mutant loses the ability to inhibit inflammation and exhibits decreased pathogenicity. Therefore, our findings identify an unrecognized mechanism of Staphylococcus aureus to suppress host defense, which may be a promising target for developing effective anti-Staphylococcus aureus immunomodulators.
Machine learning-based tsunami inundation prediction derived from offshore observations
Authors: Mulia Iyan E. , Ueda Naonori , Miyoshi Takemasa , Gusman Aditya Riadi , Satake Kenji 
Published: September 2022

AbstractThe world’s largest and densest tsunami observing system gives us the leverage to develop a method for a real-time tsunami inundation prediction based on machine learning. Our method utilizes 150 offshore stations encompassing the Japan Trench to simultaneously predict tsunami inundation at seven coastal cities stretching ~100 km along the southern Sanriku coast. We trained the model using 3093 hypothetical tsunami scenarios from the megathrust (Mw 8.0–9.1) and nearby outer-rise (Mw 7.0–8.7) earthquakes. Then, the model was tested against 480 unseen scenarios and three near-field historical tsunami events. The proposed machine learning-based model can achieve comparable accuracy to the physics-based model with ~99% computational cost reduction, thus facilitates a rapid prediction and an efficient uncertainty quantification. Additionally, the direct use of offshore observations can increase the forecast lead time and eliminate the uncertainties typically associated with a tsunami source estimate required by the conventional modeling approach.
Suicide versus homicide firearm injury patterns on trauma systems in a study of the National Trauma Data Bank (NTDB)
Authors: Foote Christopher W. , Doan Xuan-Lan , Vanier Cheryl , Cruz Bianca , Sarani Babak , Palacio Carlos H. 
Published: September 2022

AbstractFirearm related mortality in the USA surpassed all other developed countries. This study hypothesizes that injury patterns, weapon type, and mortality differ between suicide groups as opposed to homicide. The American College of Surgeons National Trauma Database was queried from January 2017 to December 2019. All firearm related injuries were included, and weapon type was abstracted. Differences between homicide and suicide groups by sex, age, race, and injury severity were compared using a Mann–Whitney test for numerical data and Fisher’s exact test for categorical data. The association between weapon type and mortality relative to suicide as opposed to homicide was assessed in Fisher’s exact tests. Significance was defined as p < 0.05. There were 100,031 homicide and 11,714 suicide subjects that met inclusion criteria. Homicides were mostly assault victims (97.6%), male (88%), African–American (62%), had less severe injury (mean (ISS) 12.07) and a median age of 20 years old (IQR: 14, 30, p < 0.01). Suicides were mostly male (83%), white (79%), had more severe injury (mean ISS 20.73), and a median age of 36 years old (IQR: 19, 54, p < 0.01). Suicide group had higher odds of head/neck (OR = 13.6) or face (OR = 5.7) injuries, with lower odds of injury to chest (OR = 0.55), abdominal or pelvic contents (OR = 0.25), extremities or pelvic girdle (OR = 0.15), or superficial soft tissue (OR = 0.32). Mortality rate was higher for suicide group (44.8%; 95% confidence interval (CI) 43.9%, 45.7%) compared to the homicide group (11.5%; 95% CI 11.3%, 11.7%). Suicide had higher mortality, more severe injuries, and more head/neck/facial injuries than homicide. Majority of suicides were with handguns.
Comparison of high-pressure, freeze-thaw cycles and germination-parboiling treatments on lipids digestibility and rancidity of brown rice
Authors: Wang Hao , Wang Qiang , Zhu Jiahong , Hu Guixian 
Published: September 2022

AbstractBrown rice (BR) contains more lipids, as compared with white rice, but its indigestibility and rancidity limit the consumer acceptability. Therefore, the objective of this study was to compare the effect of high-pressure (HP), freeze–thaw cycles (FTC) and germination-parboiling (GP) treatments on lipid in vitro digestibility and rancidity of BR. GP treated BR released the most fatty acids (especially palmitic acid and stearic acid) after in vitro digestion, followed by FTC treated BR. FTC treated BR kept the highest value of fat acidity during storage, while opposite results were observed in GP treated BR. Although HP treatment increased fat acidity value immediately, it slowed down the increase of fat acidity with storage. The results of conjugated dienes and malonaldehydes content in BR stored under accelerated conditions indicated better lipid oxidation stability after HP and GP treatment, and that it’s necessary for FTC treated BR products to be stored under anaerobic conditions.
Homoharringtonine demonstrates a cytotoxic effect against triple-negative breast cancer cell lines and acts synergistically with paclitaxel
Authors: Plett Riley , Mellor Paul , Kendall Stephanie , Hammond S. Austin , Boulet Aren , Plaza Kristine , Vizeacoumar Frederick S. , Vizeacoumar Franco J. , Anderson Deborah H. 
Published: September 2022

AbstractThe lack of targeted therapies for triple-negative breast cancer (TNBC) contributes to their high mortality rates and high risk of relapse compared to other subtypes of breast cancer. Most TNBCs (75%) have downregulated the expression of CREB3L1 (cAMP-responsive element binding protein 3 like 1), a transcription factor and metastasis suppressor that represses genes that promote cancer progression and metastasis. In this report, we screened an FDA-approved drug library and identified four drugs that were highly cytotoxic towards HCC1806 CREB3L1-deficient TNBC cells. These four drugs were: (1) palbociclib isethionate, a CDK4/6 inhibitor, (2) lanatocide C (also named isolanid), a Na+/K+-ATPase inhibitor, (3) cladribine, a nucleoside analog, and (4) homoharringtonine (also named omacetaxine mepesuccinate), a protein translation inhibitor. Homoharringtonine consistently showed the most cytotoxicity towards an additional six TNBC cell lines (BT549, HCC1395, HCC38, Hs578T, MDA-MB-157, MDA-MB-436), and several luminal A breast cancer cell lines (HCC1428, MCF7, T47D, ZR-75-1). All four drugs were then separately evaluated for possible synergy with the chemotherapy agents, doxorubicin (an anthracycline) and paclitaxel (a microtubule stabilizing agent). A strong synergy was observed using the combination of homoharringtonine and paclitaxel, with high cytotoxicity towards TNBC cells at lower concentrations than when each was used separately.
Topic selectivity and adaptivity promote spreading of short messages
Authors: Bojarski Patryk A. , Suchecki Krzysztof , Hołyst Janusz A. 
Published: September 2022

AbstractWhy is the Twitter, with its extremely length-limited messages so popular ? Our work shows that short messages focused on a single topic may have an inherent advantage in spreading through social networks, which may explain the popularity of a service featuring only short messages. We introduce a new explanatory model for information propagation through social networks that includes selectivity of message consumption depending on their content, competition for user’s attention between messages and message content adaptivity through user-introduced changes. Our agent-based simulations indicate that the model displays inherent power-law distribution of number of shares for different messages and that the popular messages are very short. The adaptivity of messages increases the popularity of already popular messages, provided the users are neither too selective nor too accommodating. The distribution of message variants popularity also follows a power-law found in real information cascades. The observed behavior is robust against model parameter changes and differences of network topology.
Boosting algorithm improves the accuracy of juvenile forensic dental age estimation in southern China population
Authors: Shan Weijie , Sun Yunshu , Hu Leyan , Qiu Jie , Huo Miao , Zhang Zikang , Lei Yuting , Chen Qianling , Zhang Yan , Yue Xia 
Published: September 2022

AbstractAge estimation based on the mineralized morphology of teeth is one of the important elements of forensic anthropology. To explore the most suitable age estimation protocol for adolescents in the South China population, 1477 panoramic radiograph images of people aged 2–18 years in the South were collected and staged by the Demirjian mineralization staging method. The dental ages were estimated using the parameters of the Demirjian and Willems. Mathematical optimization and machine learning optimization were also performed in the data processing process in an attempt to obtain a more accurate model. The results show that the Willems method was more accurate in the dental age estimation of the southern China population and the model can be further optimized by reassigning the model through a nonintercept regression method. The machine learning model presented excellent results in terms of the efficacy comparison results with the traditional mathematical model, and the machine learning model under the boosting framework, such as gradient boosting decision tree (GBDT), significantly reduced the error in dental age estimation compared to the traditional mathematical method. This machine learning processing method based on traditional estimation data can effectively reduce the error of dental age estimation while saving arithmetic power. This study demonstrates the effectiveness of the GBDT algorithm in optimizing forensic age estimation models and provides a reference for other regions to use this parameter for age estimation model establishment, and the lightweight nature of machine learning offers the possibility of widespread forensic anthropological age estimation.
Individualized Homeopathic Medicines in Treatment of Hyperuricemia: Evaluation by Double-Blind, Randomized, Placebo-Controlled Trial
Authors: Ghosh Priyanka , Ganguly Subhasish , Mukherjee Shyamal Kumar , Dutta Souvik , Shaikh Abdur Rahaman , Ali Sk Swaif , Singh Navin Kumar , Bhattacharya Pulakendu , Koley Munmun , Saha Subhranil 
Published: September 2022

AbstractIntroduction Hyperuricemia (HU) is a major health issue in India and across the globe. It increases the disease burden and hampers quality of life. This study was aimed at exploring the effects of individualized homeopathic medicines (IHMs) against placebo in the treatment of HU.Methods This double-blind, randomized, placebo-controlled trial was conducted on 60 patients suffering from HU in the outpatient department of D. N. De Homoeopathic Medical College and Hospital, Kolkata. Each patient received either IHMs or identical-looking placebos, along with advice on dietary modifications irrespective of codes. Serum uric acid (SUA) level was the primary outcome measure; the HU quality of life questionnaire (HUQLQ) and the Measure Yourself Medical Outcome Profile version 2 (MYMOP-2) were the secondary outcomes; all measured at baseline, and every month, up to 3 months. Group differences were examined by two-way (split-half) repeated-measures analysis of variance after adjusting for baseline differences. Significance level was set at p ≤0.05, two-tailed.Results The intention-to-treat sample (n = 58) was analyzed. Between-group differences in SUA levels (F 1, 56 = 13.833, p <0.001), HUQLQ scores (F 1, 56 = 32.982, p <0.001) and MYMOP-2 profile scores (F 1, 56 = 23.873, p <0.001) were statistically significant, favoring IHMs against placebos, with medium to large effect sizes. Calcarea carbonica and Pulsatilla nigricans were the most frequently prescribed medicines. No serious adverse events were reported from either of the groups.Conclusion IHMs showed significantly better results than placebos in reducing SUA levels and improving quality of life in patients suffering from HU.Trial registration CTRI/2019/10/021503; UTN: U1111–1241–1431.
4.4.6 Product Subclass 6: Silyltin Reagents
Authors: Yoshida H. 
Published: September 2022

AbstractThis chapter describes the synthesis of silyltin reagents, also frequently called silylstannanes, and their synthetic applications via silicon-tin σ-bond activation. Transition-metal catalysts and non-transition-metal nucleophilic activators can be used for this purpose, leading to a wide range of silicon-installing and tin-installing reactions that provide direct and efficient access to synthetically useful organosilanes and organostannanes.
Disorder of excitons and trions in monolayer MoSe2
Authors: Wang Jue , Manolatou Christina , Bai Yusong , Hone James , Rana Farhan , Zhu X.-Y. 
Published: September 2022

The optical spectra of transition metal dichalcogenide monolayers are dominated by excitons and trions. Here, we establish the dependence of these optical transitions on the disorder from hyperspectral imaging of h-BN encapsulated monolayer MoSe2. While both exciton and trion energies vary spatially, these two quantities are almost perfectly correlated, with spatial variation in the trion binding energy of only ∼0.18 meV. In contrast, variation in the energy splitting between the two lowest energy exciton states is one order of magnitude larger at ∼1.7 meV. Statistical analysis and theoretical modeling reveal that disorder results from dielectric and bandgap fluctuations, not electrostatic fluctuations. Our results shed light on disorder in high quality TMDC monolayers, its impact on optical transitions, and the many-body nature of excitons and trions.
Emotion, psychophysiology, and intersubjectivity
Authors: Peräkylä Anssi , Voutilainen Liisa , Stevanovic Melisa , Henttonen Pentti , Kahri Mikko , Kivioja Maari , Koskinen Emmi , Sams Mikko , Ravaja Niklas 
Published: September 2022

Abstract
Conversation analytical studies on emotion show how
expression of emotion is part of the intersubjective experience.
Emotions, however, are as much physiological as experiential events.
Physiological processes pertaining to emotion involve changes in
cardiovascular activity, in the activation of sweat glands, and in
muscular activity. The dyadic systems theory by Beebe and Lachmann (2002)
suggests that actions that regulate social interaction also serve in
the regulation of internal emotional states of interacting subjects.
Drawing from this theory, our overall research questions was: how is
the expression of emotion in social interaction linked to
physiological responses in the participants? Our main result was
that thorough conversational affiliation, the participants share the
emotional load in the interaction.
Light scattering by plasmonic disks and holes arrays: different or the same?
Authors: Rasskazov Ilia L , Sonwalkar Nishikant , Scott Carney P 
Published: September 2022

Abstract
We suggest a strategy for designing regular 2D arrays of nanoholes (NHs) in metal films with far-field scattering properties similar to that of regular 2D arrays of nanodisks (NDs) with the same periodicity. Full-wave simulations for perfectly conducting, Ag and Au NDs and respectively designed arrays of NHs demonstrate a minor difference between far-field properties either at wavelengths corresponding to Wood–Rayleigh anomalies of the arrays or in a broad wavelength range, depending on the array periodicity and sizes of NDs (NHs). Our results have broad implications in plasmon-enhanced-driven applications, including optoelectronic and photovoltaic devices, where the NH arrays are preferable to be fabricated for nano-structured optics.
Total decay width of

using the infinite-order scale-setting approach based on intrinsic conformality*
Authors: Gao Chu-Tian , Wu Xing-Gang , Huang Xu-Dong , Zeng Jun 
Published: September 2022

Abstract
We conducted a detailed study on the properties of the total decay width of the Higgs decay channel

up to

-order QCD corrections by using the newly suggested infinite-order scale-setting approach, which is based on both the principle of maximum conformality and intrinsic conformality. This approach is called PMC

. By using the PMC

approach, we observed that the conventional renormalization scale ambiguity in perturbative QCD calculation is eliminated, and the residual scale dependence due to unknown higher-order terms can also be highly suppressed. We then obtained an accurate perturbative QCD prediction on the total decay width, e.g.,

keV, where the errors are squared averages of those from all the mentioned error sources.
AKBA inhibits radiotherapy resistance in lung cancer by inhibiting maspin methylation and regulating the AKT/FOXO1/p21 axis
Authors: Gong Chun , Li Wei , Wu Jing , Li Yao-Yao , Ma Yi , Tang Li-Wen 
Published: September 2022

Abstract
Acetyl-keto-b-boswellic acid (AKBA) functions in combating human malignant tumors, including lung cancer. However, the function of AKBA in regulating the radioresistance of lung cancer and its underlying mechanism still need to be elucidated. Radiation-resistant lung cancer cells (RA549) were established. Quantitative real-time polymerase chain reaction (QRT-PCR) and Western blot were employed to examine the messenger RNA (mRNA) and protein expressions. After being treated with AKBA and different doses of X-ray, cell proliferation and survival were examined using colony formation assay and cell-counting kit-8 (CCK-8) assay. The cellular localization of Forkhead box 1 (FOXO1) was measured by immunofluorescence (IF). Flow cytometry was employed to analyze cell cycle and apoptosis. In addition, in vivo experiment was performed to determine the effect of AKBA on the sensitivity of tumors to radiation. Herein, we found that AKBA could enhance the radiosensitivity in RA549, suppress cell proliferation, induce cell apoptosis and arrest cell cycle. It was observed that maspin was lowly expressed and hypermethylated in RA549 cells compared to that in A549 cells, while these changes were all eliminated by AKBA treatment. Maspin knockdown could reverse the regulatory effects of AKBA on radioresistance and cellular behaviors of RA549 cells. In addition, we found that AKBA treatment could repress the phosphorylation of Serine/Threonine Kinase (AKT), and FOXO1, increase the translocation of FOXO1 and p21 level in RA549 cells, which was abolished by maspin knockdown. Moreover, results of tumor xenograft displayed that AKBA could enhance the sensitivity of tumor to radiation through the maspin/AKT/FOXO1/p21 axis. We discovered that AKBA enhanced the radiosensitivity of radiation-resistant lung cancer cells by regulating maspin-mediated AKT/FOXO1/p21 axis.
The influence of host star activity evolution on the population of super-Earths and mini-Neptunes
Authors: Ketzer L , Poppenhaeger K 
Published: September 2022

ABSTRACT
The detected exoplanet population displays a dearth of planets with sizes of about two Earth radii, the so-called radius gap. This is interpreted as an evolutionary effect driven by a variety of possible atmospheric mass-loss processes of exoplanets. For mass loss driven by an exoplanet’s irradiation by stellar X-ray and extreme-UV photons, the time evolution of the stellar magnetic activity is important. It is known from observations of open stellar clusters that stars of the same age and mass do not all follow the same time evolution of activity-induced X-ray and extreme-UV luminosities. Here, we explore how a realistic spread of different stellar activity tracks influences the mass loss and radius evolution of a simulated population of small exoplanets and the observable properties of the radius gap. Our results show qualitatively that different saturation time-scales, i.e. the young age at which stellar high-energy emission starts to decline, and different activity decay tracks over moderate stellar ages can cause changes in the population density of planets in the gap, as well as in the observable width of the gap. We also find that while the first 100 million years of mass loss are highly important to shape the radius gap, significant evolution of the gap properties is expected to take place for at least the first 500–600 million years, i.e. the age of the Hyades cluster. Observations of exoplanet populations with defined ages will be able to shed more light on the radius gap evolution.
The Effect of Two Midwives During the Second Stage of Labour to Reduce Severe Perineal Trauma (Oneplus): A Multicentre, Randomized Controlled Trial in Sweden
Authors: Edqvist Malin , Dahlen Hannah G. , Häggsgård Cecilia , Tern Helena , Ängeby Karin , Teleman Pia , Ajne Gunilla , Rubertsson Christine 
Published: September 2022

(Abstracted from Lancet 2022;399:1242–1253)
In many high-income countries, severe perinatal trauma (SPT), affecting the anal sphincter muscle complex, has been on the rise over the last decade. However, effective strategies to prevent SPT are scarce.