bluuebunny/crossref_metadata_2025 huggingface dataset:
Packing topological entropy for amenable group actions
Authors: DOU DOU , ZHENG DONGMEI , ZHOU XIAOMIN
Published: October 2021

Packing topological entropy is a dynamical analogy of the packing dimension, which can be viewed as a counterpart of Bowen topological entropy. In the present paper we give a systematic study of the packing topological entropy for a continuous G-action dynamical system
$(X,G)$
, where X is a compact metric space and G is a countable infinite discrete amenable group. We first prove a variational principle for amenable packing topological entropy: for any Borel subset Z of X, the packing topological entropy of Z equals the supremum of upper local entropy over all Borel probability measures for which the subset Z has full measure. Then we obtain an entropy inequality concerning amenable packing entropy. Finally, we show that the packing topological entropy of the set of generic points for any invariant Borel probability measure
$\mu $
coincides with the metric entropy if either
$\mu $
is ergodic or the system satisfies a kind of specification property.
Triadic resonances in internal wave modes with background shear
Authors: Patibandla Ramana , Mathur Manikandan , Roy Anubhab
Published: October 2021

In this paper, we use asymptotic theory and numerical methods to study resonant triad interactions among discrete internal wave modes at a fixed frequency (

$\omega$

) in a two-dimensional, uniformly stratified shear flow. Motivated by linear internal wave generation mechanisms in the ocean, we assume the primary wave field as a linear superposition of various horizontally propagating vertical modes at a fixed frequency

$\omega$

. The weakly nonlinear solution associated with the primary wave field is shown to comprise superharmonic (frequency

$2\omega$

) and zero frequency wave fields, with the focus of this study being on the former. When two interacting primary modes

$m$

and

$n$

are in triadic resonance with a superharmonic mode

$q$

, it results in the divergence of the corresponding superharmonic secondary wave amplitude. For a given modal interaction

$(m, n)$

, the superharmonic wave amplitude is plotted on the plane of primary wave frequency

$\omega$

and Richardson number

$Ri$

, and the locus of divergence locations shows how the resonance locations are influenced by background shear. In the limit of weak background shear (

$Ri\to \infty$

), using an asymptotic theory, we show that the horizontal wavenumber condition

$k_m + k_n = k_q$

is sufficient for triadic resonance, in contrast to the requirement of an additional vertical mode number condition (

$q = |m-n|$

) in the case of no shear. As a result, the number of resonances for an arbitrarily weak shear is significantly larger than that for no shear. The new resonances that occur in the presence of shear include the possibilities of resonance due to self-interaction and resonances that occur at the seemingly trivial limit of

$\omega \approx 0$

, both of which are not possible in the no shear limit. Our weak shear limit conclusions are relevant for other inhomogeneities such as non-uniformity in stratification as well, thus providing an understanding of several recent studies that have highlighted superharmonic generation in non-uniform stratifications. Extending our study to finite shear (finite

$Ri$

) in an ocean-like exponential shear flow profile, we show that for cograde–cograde interactions, a significant number of divergence curves that start at

$Ri\to \infty$

will not extend below a cutoff

$Ri$

$\sim O(1)$

. In contrast, for retrograde–retrograde interactions, the divergence curves extend all the way from

$Ri\to \infty$

to

$Ri = 0.5$

. For mixed interactions, new divergence curves appear at

$\omega = 0$

for

$Ri\sim O(10)$

and extend to other primary wave frequencies for smaller

$Ri$

. Consequently, the total (

$\text {cograde} + \text {retrograde} + \text {mixed}$

) number of resonant triads is of the same order for small

$Ri\approx 0.5$

as in the limit of weak shear (

$Ri\to \infty$

), although it attains a maximum at

$Ri\sim O(10)$

.
No Excuses: A Brief History of Playing Through Risk in College Football
Authors: Bachynski Kathleen
Published: October 2021

Celebrations of playing through risk, skepticism of athletes perceived as faking injuries, unregulated training regimens, the mythos of amateurism, and lack of accountability for preventable health harms have long characterized many college football programs. Setting policies that effectively prioritize player health will require taking this history into account.
THE IMPACT OF ORTHOGRAPHY ON LEXICAL ACCESS
Authors: Opitz Andreas , Bordag Denisa
Published: October 2021

Previous research has shown that orthographic marking may have a function beyond identifying orthographic word forms. In two visual priming experiments with native speakers and advanced learners of German (Czech natives) we tested the hypothesis that orthography can convey word-class cues comparable to morphological marking. We examined the effect of initial letter capitalization of nouns (a specific property of German orthography) on the processing of five homonymous and grammatically ambiguous forms. Both populations showed the same pattern of results: deverbal nouns (conversions) patterned together with countable nouns while in a previous study (with eliminated orthographic word-class cues) they patterned together with infinitives. Together, findings suggest that orthographic cues can trigger word-class-specific lexical retrieval/access. They also suggest a lexical entry structure in which conversion nouns, infinitives, and inflected verbal forms share a category-neutral parent node and that specified subnodes are accessed only when specifying cues are available and/or necessary for processing.
Martian Atmospheric CO2 and Pressure Profiling With Differential Absorption Lidar: System Consideration and Simulation Results
Authors: Lin B. , Liu Z.
Published: October 2021

This study explores a new concept of Martian differential absorption Lidar operating at the 2‐μm CO2 absorption band for atmospheric CO2 and pressure observations. For the considered system, two or more closely spaced wavelengths are selected, so that environmental factors such as surface reflection, atmospheric scattering, and absorptions from other trace gases on the lidar return signals are very similar for all selected wavelengths, but the difference in CO2 absorption is substantial. Thus, Martian CO2 amount and air pressure could be retrieved from the measured CO2 differential absorption optical depth at the selected wavelengths. Simulations based on Mars's environmental conditions and technically feasible lidar systems show that lidar returns from the surface could have sufficient signal strengths that allow surface air pressure measurements with 1 Pa precision after a horizontally 5‐km averaging when dust optical depth is smaller than 1.5. Even when the dust optical depth increases to 3, the uncertainty in the air pressure and column CO2 amount measurements with a random error is still smaller than 1%. In the presence of moderate dust aerosol loads and with the optimal selection of offline and online wavelengths, atmospheric CO2 and pressure profiles could also be retrieved from the surface up to an ∼13‐km altitude with the random error smaller than 1% for a horizontal resolution of 100 km and a vertical resolution of 100 m during night or 400 m during day. These CO2 and pressure measurements would significantly improve weather and climate modeling and prediction.
The Energy Spectra of Electron Microbursts Between 200 keV and 1 MeV
Authors: Johnson A. T. , Shumko M. , Sample J. , Griffith B. , Klumpar D. , Spence H. , Blake J. B.
Published: October 2021

This study investigates the energy spectrum of electron microbursts observed by the Focused Investigations of Relativistic Electron Burst Intensity, Range, and Dynamics II (FIREBIRD‐II, henceforth FIREBIRD) CubeSats. FIREBIRD is a pair of CubeSats, launched in January 2015 into a low Earth orbit, which focuses on studying electron microbursts. High‐resolution electron data from FIREBIRD‐II consist of 5 differential energy channels between 200 keV and 1 MeV and a 1 MeV integral channel. This covers an energy range that has not been well studied from low Earth orbit with good energy and time resolution. This study aims to improve the understanding of the scattering mechanism behind electron microbursts by investigating their spectral properties and their relationship with the equatorial electron population under different geomagnetic conditions. Microbursts are identified in the region of the North Atlantic where FIREBIRD only observes electrons in the bounce loss cone. The electron flux and exponential energy spectrum of each microburst are calculated using a FIREBIRD instrument response modeled in GEANT4 (GEometry ANd Tracking) and compared with the near‐equatorial electron spectra measured by the Van Allen Probes. Microbursts occurring when the Auroral Electrojet (AE) index is enhanced tend to carry more electrons with relatively higher energies. The microburst scattering mechanism is more efficient at scattering electrons with lower energies; however, the difference in scattering efficiency between low and high energy is reduced during periods of enhanced AE.
Troposphere‐Mesosphere Coupling by Convectively Forced Gravity Waves During Southern Hemisphere Monsoon Season as Viewed by AIM/CIPS
Authors: Forbes Jeffrey M. , Zhang Xiaoli , Randall Cora E. , France Jeff , Harvey V. Lynn , Carstens Justin , Bailey Scott M.
Published: October 2021

A new data set consisting of Rayleigh Albedo Anomaly variance data resulting from measurements by the Cloud Imaging and Particle Size instrument on the Aeronomy for Ice in the Mesosphere satellite is introduced, and is used to illustrate the lower‐mesospheric (50–55 km) gravity wave (GW) response to tropospheric convection during Southern Hemisphere monsoon season (December‐February). The correspond to GWs with vertical wavelengths 15 km and horizontal wavelengths between about 23 and 600 km. It is shown that these scales encompass most of the convectively generated GW spectrum at 50–55 km altitude due to both plume overshoot and diabatic heating, and include those GWs most likely to impact the overlying ionosphere‐thermosphere‐mesosphere system. The GWs originate from convective sources associated with the African and South American land masses, the maritime continent/Australia, and the South Pacific Convergence Zone. The regions of enhanced convection are identified according to half‐hourly rainfall rate (RR) distributions from the Global Precipitation Measurement mission. The GW exhibits spatial, inter‐monthly, and inter‐annual variabilities connected with RR and propagation conditions. A ∼ southward shift of longitudinal structures in with respect to RR longitudinal structures is interpreted in terms of wave focusing toward the middle atmosphere summer easterly jet core. For the South American Monsoon System, a linear regression analysis shows variability to be expressible in terms of upper‐stratosphere zonal wind speeds (correlation coefficient R = −0.91) with magnitude of RR playing a much lesser role (R = 0.16).
A Global and Seasonal Perspective of Martian Water Vapor From ExoMars/NOMAD
Authors: Crismani M. M. J. , Villanueva G. L. , Liuzzi G. , Smith M. D. , Knutsen E. W. , Daerden F. , Neary L. , Mumma M. J. , Aoki S. , Trompet L. , Thomas I. R. , Ristic B. , Bellucci G. , Piccialli A. , Robert S. , Mahieux A. , Lopez Moreno J.‐J. , Sindoni G. , Giuranna M. , Patel M. R. , Vandaele A. C.
Published: October 2021

Slightly less than a Martian Year of nominal science (March 2018–January 2020) with the ExoMars Trace Gas Orbiter has furthered the ongoing investigation of dayside water vapor column abundance. These dayside observations span latitudes between 75°S and 75°N, and all longitudes, which can provide global snapshots of the total water column abundances. In addition to tracking the seasonal transport of water vapor between poles, geographic enhancements are noted, particularly in the southern hemisphere, both in Hellas Basin, and in other regions not obviously correlated to topography. We report consistent water vapor climatology with previous spacecraft observations, however, note a difference in total water vapor content is noted. Finally, we are unable to find evidence for substantial diurnal variation in the total dayside water vapor column.
Changes in Paleovegetation and Climate Seasonality in Central China Over Last Two Glacial Cycles: A Stable Isotope Perspective From Land Snails
Authors: Qin Ben , Wu Yan , Cui Linlin , Wu Naiqin , Du Shuisheng , Wang Xu , Ding Zhongli
Published: October 2021

Modern investigations have shown that oxygen and carbon isotopes of land snail shells are useful indicators of climate and vegetation in monsoonal regions. However, stable isotope studies on snail fossil shells have seldom been done, and the reliability of those indicators needs further verification. Moreover, intrashell stable isotope analysis of individual snails is rather scarce, and seasonal variation in the glacial‐interglacial monsoonal climate remains unclear. Therefore, we performed δ18O and δ13C analyses on fossil shells of cold‐aridiphilous Cathaica pulveratrix and subhumidiphilous Metodontia yantaiensis from the loess section over the last two glacial cycles at the Beiyao site on the southern Chinese Loess Plateau. The δ18O values of fossil shells reflected monsoonal rainfall amounts and more rainfall during MIS3 and MIS7 than during MIS4 and MIS6. Meanwhile, the δ13C values of fossil shells indicated the relative abundance of C3/C4 plants and more C4 biomass during MIS3 and MIS7 than during MIS4 and MIS6. The δ18O and δ13C values of the two species from the same horizon are significantly different, reflecting differences in their growing season and/or physiological habits. Intrashell variations in stable isotopes showed that climatic seasonality was much stronger during the glacial periods than during the interglacials. Our findings provide an environmental background for explaining past human activities at the Beiyao site. The investigation of stone artifacts showed that ancient human activities were relatively strong during MIS3 and MIS7. During these stages, the warm and humid climate with smaller seasonal contrast was favorable for the regional expansion of human activities.
XBP1 regulates the protumoral function of tumor-associated macrophages in human colorectal cancer
Authors: Zhao Yahui , Zhang Weina , Huo Miaomiao , Wang Peng , Liu Xianghe , Wang Yu , Li Yinuo , Zhou Zhixiang , Xu Ningzhi , Zhu Hongxia
Published: October 2021

Macrophages are among the most abundant immune cells in colorectal cancer (CRC). Re-educating tumor-associated macrophages (TAMs) to switch from protumoral to anti-tumoral activity is an attractive treatment strategy that warrants further investigation. However, little is known about the key pathway that is activated in TAMs. In this study, infitrating CD206+ TAMs in CRC were sorted and subjected to RNA-seq analysis. Differentially expressed genes were found to be enriched in unfolded protein response/endoplasmic reticulum stress response processes, and XBP1 splicing/activation was specifically observed in TAMs. XBP1 activation in TAMs promoted the growth and metastasis of CRC. Ablation of XBP1 inhibited the expression of the pro-tumor cytokine signature of TAMs, including IL-6, VEGFA, and IL-4. Simultaneously, XBP1 depletion could directly inhibit the expression of SIRPα and THBS1, thereby blocking “don’t eat me” recognition signals and enhancing phagocytosis. Therapeutic XBP1 gene editing using AAV2-sgXBP1 enhanced the anti-tumor activity. Together, XBP1 activation in TAMs drives CRC progression by elevating pro-tumor cytokine expression and secretion, as well as inhibiting macrophage phagocytosis. Targeting XBP1 signaling in TAMs may be a potential strategy for CRC therapy.
Mapping global prevalence of depression among postpartum women
Authors: Wang Ziyi , Liu Jiaye , Shuai Huan , Cai Zhongxiang , Fu Xia , Liu Yang , Xiao Xiong , Zhang Wenhao , Krabbendam Elise , Liu Shuo , Liu Zhongchun , Li Zhihui , Yang Bing Xiang
Published: October 2021

Postpartum depression (PPD) is the most common psychological condition following childbirth, and may have a detrimental effect on the social and cognitive health of spouses, infants, and children. The aim of this study was to complete a comprehensive overview of the current literature on the global epidemiology of PPD. A total of 565 studies from 80 different countries or regions were included in the final analysis. Postpartum depression was found in 17.22% (95% CI 16.00–18.51) of the world’s population. Meta-regression analysis showed that study size, country or region development, and country or region income were the causes of heterogeneity. Multivariable meta-regression analysis found that study size and country or area development were the most important predictors. Varied prevalence rates were noted in geographic regions with the highest rate found in Southern Africa (39.96%). Of interested was a significantly lower rate of PPD in developed countries or high-income countries or areas. Furthermore, the findings showed that there was a substantial difference in rates of PPD when marital status, educational level, social support, spouse care, violence, gestational age, breast feeding, child mortality, pregnancy plan, financial difficulties, partnership, life stress, smoking, alcohol intake, and living conditions were considered in the pooled estimates. Our results indicated that one out of every five women experiences PPD which is linked to income and geographic development. It is triggered by a variety of causes that necessitate the attention and committed intervention of primary care providers, clinicians, health authorities, and the general population.
LncRNA SNHG17 interacts with LRPPRC to stabilize c-Myc protein and promote G1/S transition and cell proliferation
Authors: Liu Jin-Yu , Chen Ya-Jing , Feng Huan-Hui , Chen Zhan-Li , Wang Yun-Long , Yang Jin-E , Zhuang Shi-Mei
Published: October 2021

Oncogenic c-Myc is a master regulator of G1/S transition. Long non-coding RNAs (lncRNAs) emerge as new regulators of various cell activities. Here, we found that lncRNA SnoRNA Host Gene 17 (SNHG17) was elevated at the early G1-phase of cell cycle. Both gain- and loss-of function studies disclosed that SNHG17 increased c-Myc protein level, accelerated G1/S transition and cell proliferation, and consequently promoted tumor cell growth in vitro and in vivo. Mechanistically, the 1-150-nt of SNHG17 physically interacted with the 1035-1369-aa of leucine rich pentatricopeptide repeat containing (LRPPRC) protein, and disrupting this interaction abrogated the promoting role of SNHG17 in c-Myc expression, G1/S transition, and cell proliferation. The effect of SNHG17 in stimulating cell proliferation was attenuated by silencing c-Myc or LRPPRC. Furthermore, silencing SNHG17 or LRPPRC increased the level of ubiquitylated c-Myc and reduced the stability of c-Myc protein. Analysis of human hepatocellular carcinoma (HCC) tissues revealed that SNHG17, LRPPRC, and c-Myc were significantly upregulated in HCC, and they showed a positive correlation with each other. High level of SNHG17 or LRPPRC was associated with worse survival of HCC patients. These data suggest that SNHG17 may inhibit c-Myc ubiquitination and thus enhance c-Myc level and facilitate proliferation by interacting with LRPPRC. Our findings identify a novel SNHG17-LRPPRC-c-Myc regulatory axis and elucidate its roles in G1/S transition and tumor growth, which may provide potential targets for cancer therapy.
Elaiophylin reduces body weight and lowers glucose levels in obese mice by activating AMPK
Authors: Bao Ruoxuan , Meng Yongmei , Zhang Haibo , Yang Chen , Li Wei , Zhang Cheng , Zhang Jinye , Sun Renqiang , Li Zengxia , Jiang Wei , Zhang Chensong , Zhang Changsheng , Yuan Hai-Xin , Dang Yongjun
Published: October 2021

Obesity is an epidemic affecting 13% of the global population and increasing the risk of many chronic diseases. However, only several drugs are licensed for pharmacological intervention for the treatment of obesity. As a master regulator of metabolism, the therapeutic potential of AMPK is widely recognized and aggressively pursued for the treatment of metabolic diseases. We found that elaiophylin (Ela) rapidly activates AMPK in a panel of cancer-cell lines, as well as primary hepatocytes and adipocytes. Meanwhile, Ela inhibits the mTORC1 complex, turning on catabolism and turning off anabolism together with AMPK. In vitro and in vivo studies showed that Ela does not activate AMPK directly, instead, it increases cellular AMP/ATP and ADP/ATP ratios, leading to AMPK phosphorylation in a LKB1-dependent manner. AMPK activation induced by Ela caused changes in diverse metabolic genes, thereby promoting glucose consumption and fatty acid oxidation. Importantly, Ela activates AMPK in mouse liver and adipose tissue. As a consequence, it reduces body weight and blood glucose levels and improves glucose and insulin tolerance in both ob/ob and high-fat diet-induced obese mouse models. Our study has identified a novel AMPK activator as a candidate drug for the treatment of obesity and its associated chronic diseases.
Structural and functional analysis of target recognition by the lymphocyte adaptor protein LNK
Authors: Morris Rhiannon , Zhang Yaoyuan , Ellyard Julia I. , Vinuesa Carola G. , Murphy James M. , Laktyushin Artem , Kershaw Nadia J. , Babon Jeffrey J.
Published: October 2021

The SH2B family of adaptor proteins, SH2-B, APS, and LNK are key modulators of cellular signalling pathways. Whilst SH2-B and APS have been partially structurally and biochemically characterised, to date there has been no such characterisation of LNK. Here we present two crystal structures of the LNK substrate recognition domain, the SH2 domain, bound to phosphorylated motifs from JAK2 and EPOR, and biochemically define the basis for target recognition. The LNK SH2 domain adopts a canonical SH2 domain fold with an additional N-terminal helix. Targeted analysis of binding to phosphosites in signalling pathways indicated that specificity is conferred by amino acids one- and three-residues downstream of the phosphotyrosine. Several mutations in LNK showed impaired target binding in vitro and a reduced ability to inhibit signalling, allowing an understanding of the molecular basis of LNK dysfunction in variants identified in patients with myeloproliferative disease.
Emergence and control of photonic band structure in stacked OLED microcavities
Authors: Allemeier David , Isenhart Benjamin , Dahal Ekraj , Tsuda Yuki , Yoshida Tsukasa , White Matthew S.
Published: October 2021

We demonstrate an electrically-driven metal-dielectric photonic crystal emitter by fabricating a series of organic light emitting diode microcavities in a vertical stack. The states of the individual microcavities are shown to split into bands of hybridized photonic energy states through interaction with adjacent cavities. The propagating photonic modes within the crystal depend sensitively on the unit cell geometry and the optical properties of the component materials. By systematically varying the metallic layer thicknesses, we show control over the density of states and band center. The emergence of a tunable photonic band gap due to an asymmetry-introduced Peierls distortion is demonstrated and correlated to the unit cell configuration. This work develops a class of one dimensional, planar, photonic crystal emitter architectures enabling either narrow linewidth, multi-mode, or broadband emission with a high degree of tunability.
IHC-based Ki67 as response biomarker to tamoxifen in breast cancer window trials enrolling premenopausal women
Authors: Joosten Stacey E. P. , Wellenstein Marius , Koornstra Rutger , van Rossum Annelot , Sanders Joyce , van der Noort Vincent , Ferrandez Maria C. , Harkes Rolf , Mandjes Ingrid A. M. , Rosing Hilde , Huitema Alwin , Beijnen Jos H. , Wesseling Jelle , van Diest Paul J. , Horlings Hugo M. , Linn Sabine C. , Zwart Wilbert
Published: October 2021

Window studies are gaining traction to assess (molecular) changes in short timeframes. Decreased tumor cell positivity for the proliferation marker Ki67 is often used as a proxy for treatment response. Immunohistochemistry (IHC)-based Ki67 on tissue from neo-adjuvant trials was previously reported to be predictive for long-term response to endocrine therapy for breast cancer in postmenopausal women, but none of these trials enrolled premenopausal women. Nonetheless, the marker is being used on this subpopulation. We compared pathologist assessed IHC-based Ki67 in samples from pre- and postmenopausal women in a neo-adjuvant, endocrine therapy focused trial (NCT00738777), randomized between tamoxifen, anastrozole, or fulvestrant. These results were compared with (1) IHC-based Ki67 scoring by AI, (2) mitotic figures, (3) mRNA-based Ki67, (4) five independent gene expression signatures capturing proliferation, and (5) blood levels for tamoxifen and its metabolites as well as estradiol. Upon tamoxifen, IHC-based Ki67 levels were decreased in both pre- and postmenopausal breast cancer patients, which was confirmed using mRNA-based cell proliferation markers. The magnitude of decrease of Ki67 IHC was smaller in pre- versus postmenopausal women. We found a direct relationship between post-treatment estradiol levels and the magnitude of the Ki67 decrease in tumors. These data suggest IHC-based Ki67 may be an appropriate biomarker for tamoxifen response in premenopausal breast cancer patients, but anti-proliferative effect size depends on estradiol levels.
Direct observation of polarization-induced two-dimensional electron/hole gases at ferroelectric-insulator interface
Authors: Huyan Huaixun , Addiego Christopher , Yan Xingxu , Gadre Chaitanya A. , Melville Alexander , Schlom Darrell G. , Pan Xiaoqing
Published: October 2021

Two-dimensional electron gas or hole gas (2DEG or 2DHG) and their functionalities at artificial heterostructure interfaces have attracted extensive attention in recent years. Many theoretical calculations and recent experimental studies have shown the formation of alternating 2DEG and 2DHG at ferroelectric/insulator interfaces, such as BiFeO3/TbScO3, depending on the different polarization states. However, a direct observation based on the local charge distribution at the BiFeO3/TbScO3 interface has yet to be explored. Herein we demonstrate the direct observation of 2DHG and 2DEG at BiFeO3/TbScO3 interface using four-dimensional scanning transmission electron microscopy and Bader charge analysis. The results show that the measured charge state of each Fe/O columns at the interface undergoes a significant increase/reduction for the polarization state pointing away/toward the interface, indicating the existence of 2DHG/2DEG. This method opens up a path of directly observing charge at atomic scale and provides new insights into the design of future electronic nanodevices.
The interaction of lipids and inflammatory markers predict negative symptom severity in patients with schizophrenia
Authors: Goldsmith David R. , Massa Nicholas , Miller Brian J. , Miller Andrew H. , Duncan Erica
Published: October 2021

Finding biological predictors and novel mechanisms underlying negative symptoms of schizophrenia is of significant importance given the lack of effective treatments. Increasing data support a role for metabolic dysfunction and inflammation in reward processing deficits in psychiatric illness. Herein, we found an interaction between lipids and inflammation as a predictor of worse negative symptom severity in individuals with schizophrenia. Future studies may seek to further elucidate this relationship and thereby reveal novel treatment targets for negative symptoms.
NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding
Authors: Wang Kanix , Stevens Robert , Alachram Halima , Li Yu , Soldatova Larisa , King Ross , Ananiadou Sophia , Schoene Annika M. , Li Maolin , Christopoulou Fenia , Ambite José Luis , Matthew Joel , Garg Sahil , Hermjakob Ulf , Marcu Daniel , Sheng Emily , Beißbarth Tim , Wingender Edgar , Galstyan Aram , Gao Xin , Chambers Brendan , Pan Weidi , Khomtchouk Bohdan B. , Evans James A. , Rzhetsky Andrey
Published: October 2021

Machine reading (MR) is essential for unlocking valuable knowledge contained in millions of existing biomedical documents. Over the last two decades1,2, the most dramatic advances in MR have followed in the wake of critical corpus development3. Large, well-annotated corpora have been associated with punctuated advances in MR methodology and automated knowledge extraction systems in the same way that ImageNet4was fundamental for developing machine vision techniques. This study contributes six components to an advanced, named entity analysis tool for biomedicine: (a) a new, Named Entity Recognition Ontology (NERO) developed specifically for describing textual entities in biomedical texts, which accounts for diverse levels of ambiguity, bridging the scientific sublanguages of molecular biology, genetics, biochemistry, and medicine; (b) detailed guidelines for human experts annotating hundreds of named entity classes; (c) pictographs for all named entities, to simplify the burden of annotation for curators; (d) an original, annotated corpus comprising 35,865 sentences, which encapsulate 190,679 named entities and 43,438 events connecting two or more entities; (e) validated, off-the-shelf, named entity recognition (NER) automated extraction, and; (f) embedding models that demonstrate the promise of biomedical associations embedded within this corpus.
Triglycerides and low HDL cholesterol predict coronary heart disease risk in patients with stable angina
Authors: Caselli Chiara , De Caterina Raffaele , Smit Jeff M , Campolo Jonica , El Mahdiui Mohammed , Ragusa Rosetta , Clemente Alberto , Sampietro Tiziana , Clerico Aldo , Liga Riccardo , Pelosi Gualtiero , Rocchiccioli Silvia , Parodi Oberdan , Scholte Arthur , Knuuti Jhuani , Neglia Danilo ,   EVINCI and SMARTool
Published: October 2021

We assessed whether high triglycerides (TG) and low high-density lipoprotein cholesterol (HDL-C) levels, expressed by an increased TG/HDL-C ratio, predict coronary atherosclerotic disease (CAD) outcomes in patients with stable angina. We studied 355 patients (60 ± 9 years, 211 males) with stable angina who underwent coronary computed tomography angiography (CTA), were managed clinically and followed for 4.5 ± 0.9 years. The primary composite outcome was all-cause mortality and non-fatal myocardial infarction. At baseline, the proportion of males, patients with metabolic syndrome, diabetes and obstructive CAD increased across TG/HDL-C ratio quartiles, together with markers of insulin resistance, hepatic and adipose tissue dysfunction and myocardial damage, with no difference in total cholesterol or LDL-C. At follow-up, the global CTA risk score (HR 1.06, 95% confidence interval (CI) 1.03–1.09, P = 0.001) and the IV quartile of the TG/HDL-C ratio (HR 2.85, 95% CI 1.30–6.26, P < 0.01) were the only independent predictors of the primary outcome. The TG/HDL-C ratio and the CTA risk score progressed over time despite increased use of lipid-lowering drugs and reduction in LDL-C. In patients with stable angina, high TG and low HDL-C levels are associated with CAD related outcomes independently of LDL-C and treatments.

Trial registration. EVINCI study: ClinicalTrials.gov NCT00979199, registered September 17, 2009; SMARTool study: ClinicalTrials.gov NCT04448691, registered June 26, 2020.
Comprehensive investigations of mixed convection of Fe–ethylene-glycol nanofluid inside an enclosure with different obstacles using lattice Boltzmann method
Authors: Fu Chenqi , Rahmani Amin , Suksatan Wanich , Alizadeh S. M. , Zarringhalam Majid , Chupradit Supat , Toghraie Davood
Published: October 2021

In the present paper, nanofluid mixed convection is investigated in a square cavity with an adiabatic obstacle by using the Lattice Boltzmann method (LBM). This enclosure contains Fe–ethylene-glycol nanofluid and three constant temperature thermal sources at the left wall and bottom of the enclosure through a lateral wall. The fluid is incompressible, laminar, and Newtonian. The obtained results are presented in the constant Ra = 104and a Pr = 0.71 for different Ri = 0.1, 1, and 10. The effects of the slope of the enclosure, volume fraction of nanoparticles$$\left( \varphi \right)$$φ, the location of adiabatic obstacles, and nanoparticle diameter in the fluid are investigated on the value of heat transfer. A change in the attack angle of the enclosure leads to changes in the movement distance for fluid between hot and cold sources and passing fluid through case E, which affects the flow pattern strongly. In each attack angle, on colliding with an obstacle, the fluid heat transfers between two sources, which leads to uniform heat transfer in the enclosure. By increasing the velocity of the lid, the Richardson number decreases leading to improvement of the convective heat transfer coefficient and Nusselt number enhancement. The results so obtained reveal that by augmenting$$\varphi$$φvalue the effect of Richardson number reduction can augment Nusselt number and the amount of absorbed heat from the hot surface. Consequently, in each state where a better flow mixture and lower depreciation of fluid velocity components, due to the penetration of lid movement and buoyancy force, occurs higher heat transfer rate is accomplished. Furthermore, it is shown that when Ri = 0.1, the effect of cavity angle is more important but when Ri = 10, the effect of the position of obstacle is more visible.
Vitamin D epimers are associated with circulating haemoglobin levels independently of C-reactive protein
Authors: Chailurkit La-or , Sritara Piyamitr , Vathesatogkit Prin , Yamwong Sukit , Thongmung Nisakron , Ongphiphadhanakul Boonsong
Published: October 2021

Vitamin D deficiency has been shown to be associated with anaemia. Circulating 25(OH)D consists of both epimeric and nonepimeric forms. However, the relative roles of epimeric and nonepimeric vitamin D in regulating anaemia and haemoglobin levels remain unknown. Therefore, in this study, we examined the effect of vitamin D, including its epimers, on haemoglobin levels, independently of its effect on circulating high-sensitivity C-reactive protein (hsCRP). This was a cross-sectional study of 1655 subjects from a long-term follow-up cohort at the Electricity Generating Authority of Thailand. Venous blood sample were collected for determination of vitamin D [25(OH)D2, 25(OH)D3, 3′-epi-25(OH)D2, and 3′-epi-25(OH)D3], haemoglobin, and hsCRP levels. Data are presented as mean ± standard deviation. Age, sex, and body mass index (BMI) were significantly associated with circulating haemoglobin levels, while no association was found between total serum 25(OH)D and haemoglobin levels. However, when total 25(OH)D was separated into 3′-epimeric and non-3′-epimeric forms, 3′-epi-25(OH)D was significantly associated with haemoglobin levels, independently of age, sex, and BMI (P < 0.01). No association was found between non-3′-epi-25(OH)D and haemoglobin. When hsCRP was added to the model, the effect 3′-epi-25(OH)D on haemoglobin levels remained significant (P < 0.01). In conclusion, vitamin D epimers are associated with circulating haemoglobin levels, which supports the role of vitamin D in red blood cell and iron physiology.
Effect of straw biochar amendment on tobacco growth, soil properties, and rhizosphere bacterial communities
Authors: Zheng Jiayu , Zhang Jixu , Gao Lin , Wang Rui , Gao Jiaming , Dai Yanchen , Li Wei , Shen Guoming , Kong Fanyu , Zhang Jiguang
Published: October 2021

Biochar is an effective soil conditioner. However, we have limited understanding of biochar effects on the tobacco growth and bacterial communities in rhizosphere. The aim of this study was to investigate the effects of different straw biochar amendment (0, 2, 10, and 50 g/kg dry soil) on tobacco growth, soil properties, and bacterial communities in rhizosphere by pot trials. Most of tobacco agronomic traits increased when the application rate varied from 0 to 10 g/kg, but were inhibited by 50 g/kg of biochar application. Soil pH, SOC, available nutrients and soil urease, invertase, and acid phosphatase activities were all increased with the biochar application, whereas catalase activity decreased or remained unchanged. The OTUs and bacterial community diversity indices differed with the biochar application doses in rhizosphere and non-rhizosphere soils. And significant differences in bacterial communities were found between the rhizosphere and non-rhizosphere soils despite the biochar addition.Firmicutes,Proteobacteria,Acidobacteria,Bacteroidetes, andActinobacteriawere the dominant phyla in all soil samples, but they had different abundances in different treatment influenced by the rhizosphere and biochar effect. The high dose of biochar (50 g/kg) decreased the similarity of soil bacterial community structure in rhizosphere compared with those in non-rhizosphere soil. These results provide a better understanding of the microecological benefits of straw biochar in tobacco ecosystem.
Calophyllaceae plastomes, their structure and insights in relationships within the clusioids
Authors: Trad Rafaela Jorge , Cabral Fernanda Nunes , Bittrich Volker , Silva Saura Rodrigues da , Amaral Maria do Carmo Estanislau do
Published: October 2021

A complete chloroplast genome is not yet available for numerous species of plants. Among the groups that lack plastome information is the clusioid clade (Malpighiales), which includes five families: Bonnetiaceae, Calophyllaceae, Clusiaceae, Hypericaceae, and Podostemaceae. With around 2200 species, it has few published plastomes and most of them are from Podostemaceae. Here we assembled and compared six plastomes from members of the clusioids: five from Calophyllaceae (newly sequenced) and one from Clusiaceae. Putative regions for evolutionary studies were identified and the newly assembled chloroplasts were analyzed with other available chloroplasts for the group, focusing on Calophyllaceae. Our results mostly agree with recent studies which found a general conserved structure, except for the two Podostemaceae species that have a large inversion (trnK-UUU–rbcL) and lack one intron from ycf3. Within Calophyllaceae we observed a longer LSC and reduced IRs in Mahurea exstipulata, resulting in some genic rearrangement, and a short inversion (psbJ–psbE) in Kielmeyera coriacea. Phylogenetic analyses recovered the clusioids and the five families as monophyletic and revealed that conflicts in relationships reported in the literature for the group agree with nodes concentrating uninformative or conflicting gene trees. Our study brings new insights about clusioid plastome architecture and its evolution.
Neurocraft: software for microscale brain network dynamics
Authors: Sakellariou Dimitris Fotis , Vakrinou Angeliki , Koutroumanidis Michalis , Richardson Mark Phillip
Published: October 2021

The brain operates at millisecond timescales but despite of that, the study of its functional networks is approached with time invariant methods. Equally, for a variety of brain conditions treatment is delivered with fixed temporal protocols unable to monitor and follow the rapid progression and therefore the cycles of a disease. To facilitate the understanding of brain network dynamics we developed Neurocraft, a user friendly software suite. Neurocraft features a highly novel signal processing engine fit for tracking evolving network states with superior time and frequency resolution. A variety of analytics like dynamic connectivity maps, force-directed representations and propagation models, allow for the highly selective investigation of transient pathophysiological dynamics. In addition, machine-learning tools enable the unsupervised investigation and selection of key network features at individual and group-levels. For proof of concept, we compared six seizure-free and non seizure-free focal epilepsy patients after resective surgery using Neurocraft. The network features were calculated using 50 intracranial electrodes on average during at least 120 epileptiform discharges lasting less than one second, per patient. Powerful network differences were detected in the pre-operative data of the two patient groups (effect size = 1.27), suggesting the predictive value of dynamic network features. More than one million patients are treated with cardiac and neuro modulation devices that are unable to track the hourly or daily changes in a subject’s disease. Decoding the dynamics of transition from normal to abnormal states may be crucial in the understanding, tracking and treatment of neurological conditions. Neurocraft provides a user-friendly platform for the research of microscale brain dynamics and a stepping stone for the personalised device-based adaptive neuromodulation in real-time.
Comparison of cognitive performance between patients with Parkinson’s disease and dystonia using an intraoperative recognition memory test
Authors: Shi Lin , Yuan Tianshuo , Fan Shiying , Diao Yu , Qin Guofan , Liu Defeng , Zhu Guanyu , Qin Kai , Liu Huanguang , Zhang Hua , Yang Anchao , Meng Fangang , Zhang Jianguo
Published: October 2021

Neuroscientific studies on the function of the basal ganglia often examine the behavioral performance of patients with movement disorders, such as Parkinson’s disease (PD) and dystonia (DT), while simultaneously examining the underlying electrophysiological activity during deep brain stimulation surgery. Nevertheless, to date, there have been no studies comparing the cognitive performance of PD and DT patients during surgery. In this study, we assessed the memory function of PD and DT patients with the Montreal Cognitive Assessment (MoCA) and the Mini-Mental State Examination (MMSE). We also tested their cognitive performance during the surgery using a continuous recognition memory test. The results of the MoCA and MMSE failed to reveal significant differences between the PD and DT patients. Additionally, no significant difference was detected by the intraoperative memory test between the PD and DT patients. The intraoperative memory test scores were highly correlated with the MMSE scores and MoCA scores. Our data suggest that DT patients perform similarly to PD patients in cognitive tests during surgery, and intraoperative memory tests can be used as a quick memory assessment tool during surgery.
Optimizing drug selection from a prescription trajectory of one patient
Authors: Aguayo-Orozco Alejandro , Haue Amalie Dahl , Jørgensen Isabella Friis , Westergaard David , Moseley Pope Lloyd , Mortensen Laust Hvas , Brunak Søren
Published: October 2021

It is unknown how sequential drug patterns convey information on a patient’s health status and treatment guidelines rarely account for this. Drug-agnostic longitudinal analyses of prescription trajectories in a population-wide setting are needed. In this cohort study, we used 24 years of data (1.1 billion prescriptions) from the Danish prescription registry to model the risk of sequentially redeeming a drug after another. Drug pairs were used to build multistep longitudinal prescription trajectories. These were subsequently used to stratify patients and calculate survival hazard ratios between the stratified groups. The similarity between prescription histories was used to determine individuals’ best treatment option. Over the course of 122 million person-years of observation, we identified 9 million common prescription trajectories and demonstrated their predictive power using hypertension as a case. Among patients treated with agents acting on the renin-angiotensin system we identified four groups: patients prescribed angiotensin converting enzyme (ACE) inhibitor without change, angiotensin receptor blockers (ARBs) without change, ACE with posterior change to ARB, and ARB posteriorly changed to ACE. In an adjusted time-to-event analysis, individuals treated with ACE compared to those treated with ARB had lower survival probability (hazard ratio, 0.73 [95% CI, 0.64–0.82]; P < 1 × 10−16). Replication in UK Biobank data showed the same trends. Prescription trajectories can provide novel insights into how individuals’ drug use change over time, identify suboptimal or futile prescriptions and suggest initial treatments different from first line therapies. Observations of this kind may also be important when updating treatment guidelines.
Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production
Authors: Song Chi , Fu Fangfang , Yang Lulu , Niu Yan , Tian Zhaoyang , He Xiangxiang , Yang Xiaoming , Chen Jie , Sun Wei , Wan Tao , Zhang Han , Yang Yicheng , Xiao Tian , Dossa Komivi , Meng Xiangxiao , Cao Fuliang , Van de Peer Yves , Wang Guibin , Chen Shilin
Published: October 2021

Taxol, a natural product derived from Taxus, is one of the most effective natural anticancer drugs and the biosynthetic pathway of Taxol is the basis of heterologous bio-production. Here, we report a high-quality genome assembly and annotation of Taxus yunnanensis based on 10.7 Gb sequences assembled into 12 chromosomes with contig N50 and scaffold N50 of 2.89 Mb and 966.80 Mb, respectively. Phylogenomic analyses show that T. yunnanensis is most closely related to Sequoiadendron giganteum among the sampled taxa, with an estimated divergence time of 133.4−213.0 MYA. As with most gymnosperms, and unlike most angiosperms, there is no evidence of a recent whole-genome duplication in T. yunnanensis. Repetitive sequences, especially long terminal repeat retrotransposons, are prevalent in the T. yunnanensis genome, contributing to its large genome size. We further integrated genomic and transcriptomic data to unveil clusters of genes involved in Taxol synthesis, located on the chromosome 12, while gene families encoding hydroxylase in the Taxol pathway exhibited significant expansion. Our study contributes to the further elucidation of gymnosperm relationships and the Taxol biosynthetic pathway.
Mitigating the non-specific uptake of immunomagnetic microparticles enables the extraction of endothelium from human fat
Authors: Antonyshyn Jeremy A. , Mazzoli Vienna , McFadden Meghan J. , Gramolini Anthony O. , Hofer Stefan O. P. , Simmons Craig A. , Santerre J. Paul
Published: October 2021

Endothelial cells are among the fundamental building blocks for vascular tissue engineering. However, a clinically viable source of endothelium has continued to elude the field. Here, we demonstrate the feasibility of sourcing autologous endothelium from human fat – an abundant and uniquely dispensable tissue that can be readily harvested with minimally invasive procedures. We investigate the challenges underlying the overgrowth of human adipose tissue-derived microvascular endothelial cells by stromal cells to facilitate the development of a reliable method for their acquisition. Magnet-assisted cell sorting strategies are established to mitigate the non-specific uptake of immunomagnetic microparticles, enabling the enrichment of endothelial cells to purities that prevent their overgrowth by stromal cells. This work delineates a reliable method for acquiring human adipose tissue-derived microvascular endothelial cells in large quantities with high purities that can be readily applied in future vascular tissue engineering applications.
Photochemical bromination and iodination of peptides and proteins by photoexcitation of aqueous halides
Authors: Luo Pan , Liu Zheyi , Zhang Tingting , Wang Xiaolei , Liu Jing , Liu Yiqiang , Zhou Xiaohu , Chen Yang , Hou Guangjin , Dong Wenrui , Xiao Chunlei , Jin Yan , Yang Xueming , Wang Fangjun
Published: October 2021

Laser excitation of aqueous halides at wavelengths shorter than 200 nm for structure-selective photochemical halogenation of native proteins.