bluuebunny/crossref_metadata_2025 huggingface dataset:
Isatin-based spiro indolenine alkaloids from Isatis indigotica Fortune with anti-neuroinflammatory and acetylcholinesterase inhibitory effects
Authors: Bai Ming , Xi Yu-Fei , Mi Si-Hui , Yang Pei-Yuan , Lou Li-Li , Lv Tian-Ming , Zhang Xin , Yao Guo-Dong , Lin Bin , Huang Xiao-Xiao , Song Shao-Jiang
Published: November 2023

Compounds 1a/1b are a pair of enantiomers characterized by an unprecedented 6/5/6/5/6 N,O-heterocyclic scaffold with a unique spiro[4.5] core. Compound 2 is the first 6/5/6/5/5/6 hexacyclic skeleton fused with an unexpected dispiro[4.4.0.4] system.
State monitoring of switching power supply in power system based on time series voltage waveform and image analysis
Authors: Jin Longxing , Yu Weiguo , Wang Shixiang , Li Jin , Zhang Anlong
Published: November 2023

The switching power supply is widely used in the secondary equipment of the power grid. The failure of the switching power supply will cause the protection device to malfunction, leading to a risk of large‐scale power failure. In this paper, a real‐time monitoring method based on only output voltage information is proposed. The experiment shows that this parameter‐reduced approach, relying only on voltage information, outperforms the existing method in detection accuracy.
Sequentially rotated loop and spiral antenna arrays with a coplanar C‐figured feedline
Authors: Hirose Kazuhide , Tsubouchi Susumu , Ito Naonoshin , Urushibata Yuya , Nakano Hisamatsu
Published: November 2023

Using the moment method, two array antennas are investigated to reveal the effects of different radiation elements on the array characteristics. Each array comprises four elements sequentially rotated by 90° and excited by a coplanar C‐figured feedline above the ground plane. It is found that a loop element array has a 3 dB axial ratio bandwidth of 30%, 3.3 times as wide as that of an isolated loop without an array environment. In contrast, a spiral element array shows a 3 dB gain drop bandwidth of 62% (72% for the axial ratio bandwidth, wider than that of an isolated spiral by a factor of 3.0). Almost the same factors of 3.0 and 3.3 for the spiral and loop element arrays are then compared with those in similar studies. It is found that factors are classified into three groups by feedline types. The simulated results are verified by experimental work.
A configuration to double the gain of pyramidal horn antenna using single layer frequency selective surface
Authors: Patnaik Kalyan Mohan , Basavarajappa Gowrish
Published: November 2023

A gain enhancement technique in pyramidal horn antenna using a slot type band pass frequency selective surface (FSS) is presented. The horn antenna without FSS has achieved a measured gain of 10.5 dBi at 10 GHz, while the antenna with the single layer slotted FSS yields an enhanced measured gain of 14.2 dBi (an improvement of 3.7 dB or 134%). Conventionally, such a gain enhancement would 5 times increase in its dimensions (flaring). However, the authors achieve the same with only 2 times increase in dimensions. Another interesting value addition of the proposed idea is that an FSS sheet can be added to the existing horn antenna to increase its gain without altering the antenna itself. Such a scheme is highly beneficial in strategic applications. The proposed gain enhanced horn antenna can be recommended to be utilised in several X‐band applications, such as radar systems (weather, surveillance, traffic control and military), satellite communications and point–point microwave links that require high gain and small form factor.
Construction mode optimal selection method for intelligent sensing system in zero‐carbon parks
Authors: Cheng Mengzeng , Niu Wei , Hu Jingwei , Wang Zongyuan , Chen Jing , Lin Chao
Published: November 2023

The intelligent sensing system is the digital basis for zero‐carbon park operation. Due to the immaturity of its cost‐benefit accounting method and the lack of a special construction mode evaluation system, there is blindness in its investment and construction process. In order to select the suitable construction mode for the intelligent sensing system scientifically and effectively, this paper first establishes the architecture of the intelligent sensing system, and determines a cost‐benefit accounting method of the intelligent sensing system. Then, this paper establishes a construction mode evaluation index system including techno‐economic indicators, and proposes a fuzzy comprehensive evaluation method combing analytic hierarchy process and the decision‐making trial and evaluation laboratory to select the optimal construction mode. The numerical analyses show that the public‐private‐partnership mode of the intelligent sensing system has achieved ideal implementation results.
Einzigartige Arzneiwelten
Authors: Koch Ulrich
Published: November 2023

So wie unsere Patienten einzigartig sind und einen ganz individuellen Ausdruck ihres
In-der-Welt-Seins haben, so sind spiegelbildlich die Entitäten, die
Ausgangsstoffe unserer homöopathischen Arzneien in ihrer Stellung in der
Welt einzigartig. Die homöopathische Behandlungsmethode stellt den
spezifischen Symptomen unserer Patienten die einer Arznei zugeordneten Symptome
gegenüber und arbeitet so die ähnlichste Arznei mit den meisten
Übereinstimmungen auf Symptomebene heraus. Doch den schier unbegrenzten
Individualitäten unserer Patienten steht ein nur sehr beschränkter
Arzneifundus gegenüber, was in der Praxis oft eine große
Herausforderung darstellt, zumal nur ein vergleichsweise kleiner Anteil der
homöopathischen Arzneien qualitativ hochwertig und ausreichend umfangreich
geprüft worden ist. Eine solche Arzneimittelprüfung erfordert zudem
einen großen Zeitaufwand und einige Logistik, um die Rohdaten zu einem
nachvollziehbaren und in der Praxis verifizierbaren Bild zusammenzuführen.
So sind wir auf die praktische Mitarbeit des Homöopathenkollektivs
angewiesen, das durch homöopathische Arzneimittelselbstversuche, Erfahrungen
am Patienten und – falls zutreffend – neue toxikologische
Erkenntnisse die Arzneimittelbilder ergänzen und ihnen eine
größere Tiefenschärfe verleihen kann. Letztendlich
übersetzt jedes Arzneimittelbild die Wirkkräfte der Ausgangssubstanz
auf sehr feine und differenzierte Weise in medizinisch bedeutsame
Handlungsmöglichkeiten und offenbart uns gleichzeitig ein immer tiefer
werdendes Weltverständnis.
Methanediol from cloud-processed formaldehyde is only a minor source of atmospheric formic acid
Authors: Nguyen Thanh Lam , Peeters Jozef , Müller Jean-François , Perera Ajith , Bross David H. , Ruscic Branko , Stanton John F.
Published: November 2023

Atmospheric formic acid is severely underpredicted by models. A recent study proposed that this discrepancy can be resolved by abundant formic acid production from the reaction (
1
) between hydroxyl radical and methanediol derived from in-cloud formaldehyde processing and provided a chamber-experiment-derived rate constant,
k
1
= 7.5 × 10
−12
cm
3
s
−1
. High-level accuracy coupled cluster calculations in combination with
E,J
-resolved two-dimensional master equation analyses yield
k
1
= (2.4 ± 0.5) × 10
−12
cm
3
s
−1
for relevant atmospheric conditions (
T
= 260–310 K and
P
= 0–1 atm). We attribute this significant discrepancy to HCOOH formation from other molecules in the chamber experiments. More importantly, we show that reversible aqueous processes result indirectly in the equilibration on a 10 min. time scale of the gas-phase reaction

HCHO
+

H
2

O
⇌

HOCH
2

OH

(2) with a HOCH
2
OH to HCHO ratio of only
ca
. 2%. Although HOCH
2
OH outgassing upon cloud evaporation typically increases this ratio by a factor of 1.5–5, as determined by numerical simulations, its in-cloud reprocessing is shown using a global model to strongly limit the gas-phase sink and the resulting production of formic acid. Based on the combined findings in this work, we derive a range of 1.2–8.5 Tg/y for the global HCOOH production from cloud-derived HOCH
2
OH reacting with OH. The best estimate, 3.3 Tg/y, is about 30 times less than recently reported. The theoretical equilibrium constant
K
eq
(2) determined in this work also allows us to estimate the Henry’s law constant of methanediol (8.1 × 10
5
M atm
−1
at 280 K).
How does a hyperuniform fluid freeze?
Authors: Lei Yusheng , Ni Ran
Published: November 2023

All phase transitions can be categorized into two different types: continuous and discontinuous phase transitions. Discontinuous phase transitions are normally accompanied with significant structural changes, and nearly all of them have the kinetic pathway of nucleation and growth, if the system does not suffer from glassy dynamics. Here, in a system of barrier-controlled reactive particles, we find that the discontinuous freezing transition of a nonequilibrium hyperuniform fluid into an absorbing state does not have the kinetic pathway of nucleation and growth, and the transition is triggered by long-wavelength fluctuations. The transition rate decreases with increasing the system size, which suggests that the metastable hyperuniform fluid could be kinetically stable in an infinitely large system. This challenges the common understanding of metastability in discontinuous phase transitions. Moreover, we find that the “metastable yet kinetically stable” hyperuniform fluid features a scaling in the structure factor

S

(
k
→
0
)

∼

k

1.2

in 2D, which is the third dynamic hyperuniform state in addition to the critical hyperuniform state with

S

(
k
→
0
)

∼

k

0.45

and the nonequilibrium hyperuniform fluid with

S

(
k
→
0
)

∼

k
2

.
Gasdermin D is the only Gasdermin that provides protection against acute
Salmonella
gut infection in mice
Authors: Fattinger Stefan A. , Maurer Luca , Geiser Petra , Bernard Elliott M. , Enz Ursina , Ganguillet Suwannee , Gül Ersin , Kroon Sanne , Demarco Benjamin , Mack Vanessa , Furter Markus , Barthel Manja , Pelczar Pawel , Shao Feng , Broz Petr , Sellin Mikael E. , Hardt Wolf-Dietrich
Published: November 2023

Gasdermins (GSDMs) share a common functional domain structure and are best known for their capacity to form membrane pores. These pores are hallmarks of a specific form of cell death called pyroptosis and mediate the secretion of pro-inflammatory cytokines such as interleukin 1β (IL1β) and interleukin 18 (IL18). Thereby, Gasdermins have been implicated in various immune responses against cancer and infectious diseases such as acute
Salmonella
Typhimurium (
S.
Tm) gut infection. However, to date, we lack a comprehensive functional assessment of the different Gasdermins (GSDMA-E) during
S
.Tm infection in vivo. Here, we used epithelium-specific ablation, bone marrow chimeras, and mouse lines lacking individual Gasdermins, combinations of Gasdermins or even all Gasdermins (GSDMA1-3C1-4DE) at once and performed littermate-controlled oral
S
.Tm infections in streptomycin-pretreated mice to investigate the impact of all murine Gasdermins. While GSDMA, C, and E appear dispensable, we show that GSDMD i) restricts
S
.Tm loads in the gut tissue and systemic organs, ii) controls gut inflammation kinetics, and iii) prevents epithelium disruption by 72 h of the infection. Full protection requires GSDMD expression by both bone-marrow-derived lamina propria cells and intestinal epithelial cells (IECs). In vivo experiments as well as 3D-, 2D-, and chimeric enteroid infections further show that infected IEC extrusion proceeds also without GSDMD, but that GSDMD controls the permeabilization and morphology of the extruding IECs, affects extrusion kinetics, and promotes overall mucosal barrier capacity. As such, this work identifies a unique multipronged role of GSDMD among the Gasdermins for mucosal tissue defense against a common enteric pathogen.
Linear motif specificity in signaling through p38α and ERK2 mitogen–activated protein kinases
Authors: Torres Robles Jaylissa , Lou Hua Jane , Shi Guangda , Pan Pauline Lining , Turk Benjamin E.
Published: November 2023

Mitogen-activated protein kinase (MAPK) cascades are essential for eukaryotic cells to integrate and respond to diverse stimuli. Maintaining specificity in signaling through MAPK networks is key to coupling distinct inputs to appropriate cellular responses. Docking sites—short linear motifs found in MAPK substrates, regulators, and scaffolds—can promote signaling specificity through selective interactions, but how they do so remains unresolved. Here, we screened a proteomic library for sequences interacting with the MAPKs extracellular signal-regulated kinase 2 (ERK2) and p38α, identifying selective and promiscuous docking motifs. Sequences specific for p38α had high net charge and lysine content, and selective binding depended on a pair of acidic residues unique to the p38α docking interface. Finally, we validated a set of full-length proteins harboring docking sites selected in our screens to be authentic MAPK interactors and substrates. This study identifies features that help define MAPK signaling networks and explains how specific docking motifs promote signaling integrity.
The construction of philosophical ideas in the paratexts of the German translation of the
Zhuangzi by Richard Wilhelm
Authors: Nana Pang , Mengye Liang
Published: November 2023

Among the numerous German translations of the traditional Chinese cultural classic Zhuangzi, the
version by the missionary Richard Wilhelm, Dschuang Dsi. Das wahre Buch vom südlichen Blütenland (1912), is of great significance as the first direct translation from Chinese. The work
contributed greatly to the popularity of Taoism in Germany. However, studies on the German versions of the
Zhuangzi are limited, and most focus on the text itself, whereas the research value of the paratexts has been
neglected. This study explores the role of paratexts of Wilhelm’s translation in the construction of Zhuang Zhou’s philosophical
ideas. We find there is a noticeable presence of the translator’s voice in the paratexts of Wilhelm’s translation. Moreover, the
interpretative role of the paratexts can enhance readers’ understanding of Wilhelm’s construction of the philosophical ideas
conveyed by the text. Based on the analysis of paratexts, we conclude that Wilhelm’s translation is characterized by Western
cultural interventions, such as analogies between Zhuang Zhou and Western philosophers and the adoption of Christian claims. This
may be attributed to the goal of Wilhelm’s translation (i.e., to introduce the Zhuangzi to general
German-speaking readers), his cultural background of Western education (especially at the Tübingen Seminary), and the sinological
tradition of studying and translating Chinese classics from the perspective of Western culture at the time.
Uncertainty-guided cross learning via CNN and transformer for semi-supervised honeycomb lung lesion segmentation
Authors: Zi-an Zhao , Xiu-fang Feng , Xiao-qiang Ren , Yun-yun Dong
Published: November 2023

Objective. Deep learning networks such as convolutional neural networks (CNN) and Transformer have shown excellent performance on the task of medical image segmentation, however, the usual problem with medical images is the lack of large-scale, high-quality pixel-level annotations, which is a very time-consuming and laborious task, and its further leads to compromised the performance of medical image segmentation under limited annotation conditions. Approach. In this paper, we propose a new semi-supervised learning method, uncertainty-guided cross learning, which uses a limited number of annotated samples along with a large number of unlabeled images to train the network. Specifically, we use two networks with different learning paradigms, CNN and Transformer, for cross learning, and use the prediction of one of them as a pseudo label to supervise the other, so that they can learn from each other, fully extract the local and global features of the images, and combine explicit and implicit consistency regularization constraints with pseudo label methods. On the other hand, we use epistemic uncertainty as a guiding message to encourage the model to learn high-certainty pixel information in high-confidence regions, and minimize the impact of erroneous pseudo labels on the overall learning process to improve the performance of semi-supervised segmentation methods. Main results. We conducted honeycomb lung lesion segmentation experiments using a honeycomb lung CT image dataset, and designed several sets of comparison experiments and ablation experiments to validate the effectiveness of our method. The final experimental results show that the Dice coefficient of our proposed method reaches 88.49% on the test set, and our method achieves state-of-the-art performance in honeycomb lung lesion segmentation compared to other semi-supervised learning methods. Significance. Our proposed method can effectively improve the accuracy of segmentation of honeycomb lung lesions, which provides an important reference for physicians in the diagnosis and treatment of this disease.
Effects of N/Si ratio on mechanical properties of amorphous silicon nitride coating
Authors: Zhou Huasi , Persson Cecilia , Xia Wei , Engqvist Håkan
Published: November 2023

The utilization of silicon nitride coatings has been proposed as an effective method to enhance wear resistance and mitigate the release of metallic ions from biomedical implants. However, the relatively high dissolution rate of low-density coatings remains an obstacle to their implementation. Here, chemical vapour deposition techniques may have advantages over the typically used physical vapour deposition (PVD) methods. Therefore, in this study, silicon nitride coatings were obtained by low-pressure chemical vapor deposition (LPCVD). Since the nitrogen-to-silicon (N/Si) ratio and deposition temperature have been reported as major factors affecting the performance of the coatings, the effects of ammonia (NH3) to dichlorosilane (SiH2Cl2) flow ratio and deposition temperature were systemically investigated in the form of microstructure, mechanical and tribological properties of the coatings. The results revealed that the coatings exhibited a dense structure. As the ammonia flow ratio increased, the surface became smoother, and the hardness and elastic modulus increased and reached the maximum at a flow ratio of 4, giving a hardness of around 27 GPa and an elastic modulus of 290 GPa, respectively. The higher mechanical properties of the coatings deposited at a flow ratio of 4 are attributed to the stronger covalent Si-N bonding, as confirmed by XPS results. However, the coatings deposited at a flow ratio of 2 exhibited the lowest wear rate, at 9.5

×

10−7 mm3 Nm−1, around one-third of the value of the coatings deposited at a flow ratio of 6, likely due to the high silicon content of these coatings. Increasing the temperature resulted in an increased deposition rate, higher hardness and elastic modulus as well as a lower wear rate, likely due to incomplete reactions at lower temperatures. The generally high hardness and low wear rate indicate that the coatings deposited by LPCVD are promising for application in spinal implants.
Screen printable PANI/carbide-derived carbon supercapacitor electrode ink with chitosan binder
Authors: Yesilyurt Ezgi Inci , Pionteck Jürgen , Keskinen Jari , Kattainen Aapo , Punkari Timo , Simon Frank , Mäntysalo Matti , Voit Brigitte
Published: November 2023

Polyaniline (PANI)/carbide-derived carbon (CDC) was synthesized by using in-situ chemical oxidative polymerization of PANI in presence of CDC. Conductive electrode ink materials were prepared by using eco-friendly chitosan binder in water media. In the following, symmetrical supercapacitors (SCs) were fabricated by both doctor blade coating and screen printing technique. The electrical conductivity, morphology, specific capacitance, and energy density of these composites were evaluated for their applicability as SC electrodes. Pure PANI with chitosan binder was not printable because of its brittleness, however, the presence of CDC allows the preparation of smooth films which are suitable for electrode preparation. The fabricated composite electrode has a higher specific capacitance (up to 419 F g−1) and higher energy density (up to 6.7 W h kg−1) compared to the pristine CDC electrode. The capacitance of screen-printed SCs was 440–470 mF with an equivalent series resistance of about 27 Ω.
Religion in 21st-Century Political Philosophy
Authors: Lægaard Sune
Published: November 2023

Discussions of religion in political philosophy concern normative questions such as whether religious reasons can be appealed to in political justification, whether the state can support the church, how the state should regulate religious symbols in public space, and how freedom of religion and religious discrimination should be understood. Debates about religion in political philosophy can be separated into two different main framings. One framing represents the issues in terms of a relation between different spheres, such as religion and politics. Another framing represents the issues in terms of the regulation of specific acts and activities, such as observing religious beliefs by wearing religious dress. All these issues, however framed, raise questions about what counts as religion and why it is normatively relevant. However, religion can denote quite different things which are normatively relevant for different reasons in different respects.
Cognitive Behavior Therapy for Psychosis (CBTp)
Authors: Morrison Anthony P. , Wood Lisa J.
Published: November 2023

Cognitive behavior therapy (CBT) is an evidence-based psychological therapy that has been shown to have small to medium effects in improving outcomes for people experiencing psychosis. CBT’s theoretical model, drawing together cognitive and behavioral theories, outlines that it is the appraisal and response to an event which maintains distress rather than the event itself. CBT for psychosis (CBTp) specifically aims to modify appraisals and responses to psychotic experiences in order to reduce distress. CBTp has a substantial evidence base and is the most frequently offered psychological treatment for psychosis. There have been significant advancements in the field, with process-oriented therapies and digital interventions showing promise; however, more large-scale trials are required. Moreover, service users report positive experiences with CBTp and value the normalizing therapeutic relationship, improved personal understanding, and acquisition of new coping strategies. Improving dissemination and adapting CBTp so that it is appropriate for all populations is an ongoing priority for future research. Moreover, the evidence base requires more user-centered research to ensure CBTp is meeting the needs of service users.
Real-Time Transaction Data for Nowcasting and Short-Term Economic Forecasting
Authors: Galbraith John W.
Published: November 2023

Transaction data from consumer purchases is used for monitoring, nowcasting, or short-term forecasting of important macroeconomic aggregates such as personal consumption expenditure and national income. Data on individual purchase transactions, recorded electronically at point of sale or online, offer the potential for accurate and rapid estimation of retail sales expenditure, itself an important component of personal consumption expenditure and therefore of national income. Such data may therefore allow policymakers to base actions on more up-to-date estimates of the state of the economy. However, while transaction data may be obtained from a number of sources, such as national payments systems, individual banks, or financial technology companies, data from each of these sources contain limitations.

Data sets will differ in the forms of information contained in a record, the degree to which the samples are representative of the relevant population of consumers, and the different types of payments that are observed and captured in the record. As well, the commercial nature of the data may imply constraints on the researcher’s ability to make data sets available for replication. Regardless of the source, the data will generally require filtering and aggregation in order to provide a clear signal of changes in economic activity.

The resulting series may be incorporated into any of a variety of model types, along with other data, for nowcasting and short-term forecasting.
Detroit
Authors: Pettengill Ryan S.
Published: November 2023

From its earliest origins through the 21st century, Detroit was a capitalist venture that was tied to the global economy. Throughout the pre-Columbian period, Detroit served as a meeting point where a diverse confederation of Native Americans came together to conduct business and diplomacy. Later, the city became a contested territorial holding that the Western imperial powers of France, Spain, Great Britain, and the United States fought over, as it represented a critical gateway that opened up trade to the central and western regions of North America. Between 1835 and 1929, capitalists built wharfs, railroad lines, factories, warehouses, and other forms of industrial infrastructure, attracting throngs of working-class job seekers and causing Detroit’s population to boom from approximately 1,100 in 1819 to more than one million in 1930. The population peaked at nearly two million in 1950 and, by 2020, it had declined to approximately 700,000.

Detroit’s history might be thought of in three distinct periods: a pre-Columbian period where the region consisted of a preindustrial space that was occupied by Anishinaabeg peoples, later to be claimed by European colonists; a long industrial era in which businessmen, such as Henry Ford, centralized production within the city; and a slow period of economic decline as the city struggled to adapt to different trends in a global economy. As Detroit entered the 21st century, the city faced a declining population, rising budget deficits, and a crumbling infrastructure. Still, as several multinational corporations based their operations out of Detroit, the city remained a capitalist venture fundamentally tied to the global economy.
Pronominal and Expletive Subjects in Germanic
Authors: De Vogelaer Gunther
Published: November 2023

The syntax ofGermanic subject pronouns is only minimally different from nominal subjects. Germanic has to a large extent dispensed with null subjects, leading to a tendency to also use pronouns to refer to highly accessible subjects and the frequent use of expletive subjects, for instance with weather verbs or in other impersonal constructions. Correspondingly, all Germanic languages at least show some tendency to formally reduce subject pronouns in unstressed positions, and some languages have encoded a more systematic distinction between strong and weak forms, with weak forms developing proper formal and distributional properties. Additional differences between Germanic languages regarding subject pronouns concern the emergence and use of honorifics and the degree to which pronominal reference still reflects nouns’ grammatical gender rather than being replaced with a semantic system encoding biological gender and individuation. Regards expletives, most derive from neuter pronouns esor deictic adverbsder. The main difference within Germanic with respect to their use is whether they function as first-position placeholders (e.g., Icelandic) vis-à-vis languages in which they are generally used in impersonal constructions, also in a post-verbal position (e.g., Dutch). Both the constraints on referential null subjects and the use of expletives in impersonal constructions are typologically rare and have been related to other aspects of Germanic grammar, such as the verb-second property and widespread leveling in the verbal agreement paradigm. Research has also addressed the relationship between subject pronouns and their antecedent, as well as the semantic and pragmatic conditions under which weak pronouns and expletives are used.
Demographic confounders distort inference of gene regulatory and gene co-expression networks in cancer
Authors: Ketteler Anna , Blumenthal David B
Published: November 2023

Gene regulatory networks (GRNs) and gene co-expression networks (GCNs) allow genome-wide exploration of molecular regulation patterns in health and disease. The standard approach for obtaining GRNs and GCNs is to infer them from gene expression data, using computational network inference methods. However, since network inference methods are usually applied on aggregate data, distortion of the networks by demographic confounders might remain undetected, especially because gene expression patterns are known to vary between different demographic groups. In this paper, we present a computational framework to systematically evaluate the influence of demographic confounders on network inference from gene expression data. Our framework compares similarities between networks inferred for different demographic groups with similarity distributions obtained for random splits of the expression data. Moreover, it allows to quantify to which extent demographic groups are represented by networks inferred from the aggregate data in a confounder-agnostic way. We apply our framework to test four widely used GRN and GCN inference methods as to their robustness w. r. t. confounding by age, ethnicity and sex in cancer. Our findings based on more than $ {44000}$ inferred networks indicate that age and sex confounders play an important role in network inference for certain cancer types, emphasizing the importance of incorporating an assessment of the effect of demographic confounders into network inference workflows. Our framework is available as a Python package on GitHub: https://github.com/bionetslab/grn-confounders.
Predicting gene regulatory links from single-cell RNA-seq data using graph neural networks
Authors: Mao Guo , Pang Zhengbin , Zuo Ke , Wang Qinglin , Pei Xiangdong , Chen Xinhai , Liu Jie
Published: November 2023

Single-cell RNA-sequencing (scRNA-seq) has emerged as a powerful technique for studying gene expression patterns at the single-cell level. Inferring gene regulatory networks (GRNs) from scRNA-seq data provides insight into cellular phenotypes from the genomic level. However, the high sparsity, noise and dropout events inherent in scRNA-seq data present challenges for GRN inference. In recent years, the dramatic increase in data on experimentally validated transcription factors binding to DNA has made it possible to infer GRNs by supervised methods. In this study, we address the problem of GRN inference by framing it as a graph link prediction task. In this paper, we propose a novel framework called GNNLink, which leverages known GRNs to deduce the potential regulatory interdependencies between genes. First, we preprocess the raw scRNA-seq data. Then, we introduce a graph convolutional network-based interaction graph encoder to effectively refine gene features by capturing interdependencies between nodes in the network. Finally, the inference of GRN is obtained by performing matrix completion operation on node features. The features obtained from model training can be applied to downstream tasks such as measuring similarity and inferring causality between gene pairs. To evaluate the performance of GNNLink, we compare it with six existing GRN reconstruction methods using seven scRNA-seq datasets. These datasets encompass diverse ground truth networks, including functional interaction networks, Loss of Function/Gain of Function data, non-specific ChIP-seq data and cell-type-specific ChIP-seq data. Our experimental results demonstrate that GNNLink achieves comparable or superior performance across these datasets, showcasing its robustness and accuracy. Furthermore, we observe consistent performance across datasets of varying scales. For reproducibility, we provide the data and source code of GNNLink on our GitHub repository: https://github.com/sdesignates/GNNLink.
Multi-faith Chaplaincy’s Outcomes-Based Measures: The Tail that Wags the Dog
Authors: Tenorio Addison S
Published: November 2023

The current manner of practicing chaplaincy in health care is one which prizes the multi-faith chaplain. When one asks multi-faith chaplain, “To whom are you beholden?” they will respond, “The patient.” This is evident in the way that chaplaincy is currently practiced and taught, which prizes the use of psychology over recourse to theology. Chaplaincy’s recourse to practices whose aims are directed toward the efficient rather than the eternal challenges its original telos. This paper looks at this question by blending a Catholic and Engelhardtian approach to conclude that chaplains should recognize that they are beholden to God, rather than to patients’ autonomy.
Chaplaincy as a “Living Human Web”
Authors: Thornton Andrea
Published: November 2023

Engelhardt’s critiques of “generic chaplaincy” rely on the argument that chaplains are secular; however, professionally certified chaplains must maintain ordination with an ecclesial body. Engelhardt’s concerns are better directed at the academic subfield that supports and trains chaplains: pastoral theology. That field is somewhat guilty of forced ecumenism because it attempts a universal theology rooted in experience and the social sciences rather than the authority of creeds, ecclesial bodies, or traditions. Pastoral theology makes too many sacrifices to the authority of the behavioral sciences without sufficient appreciation for sacramental theology and the spiritual bonds that rituals effect in communities of shared belief. In this model, ritual is reduced to its instrumental value in addressing the emotional needs of patients rather than viewed as efficacious spiritual care. Chaplains should take a holistic approach to theology so that they can better identify the duties and scope of interfaith spiritual care.
Multi-dimensional opinion chaos synchronization based on multi-layer complex networks
Authors: Liu Shan , Tao Ruixing
Published: November 2023

In complex networks, the interactions of opinions are significantly affected by network structure. Moreover, multi-layer networks, which contain multiple subsystems and different types of interactions, are considered to have a stronger ability to simulate various real-world systems than traditional single-layer complex networks. Based on this motivation, this article attempts to show how to achieve complete synchronization of multi-dimensional opinions in a multi-layer network topology where the opinions of nodes have Rössler chaotic dynamics. A first step in investigating the synchronization of multi-layer complex networks is to propose a multi-dimensional opinion evolution model. In this article, the multi-layer complex network model combining the Rössler oscillation system is built, which provides us a tool for insight into the nodes complexity in multi-layer networks. Furthermore, a general criterion for globally exponentially asymptotic synchronization of multi-layer complex networks is provided using multiple Lyapunov stability theories. We illustrate the reliability of the model and the correctness of the criterion by Runge-Kutta (RK4) simulation. These findings shed new light on some interesting phenomena in society and help decision-makers predict the prevalence of hot topics and public opinions.
Educational attainment of children with congenital heart disease in the United Kingdom
Authors: Cave Daniel G W , Wands Zoë E , Cromie Kirsten , Hough Amy , Johnson Kathryn , Mon-Williams Mark , Bentham James R , Feltbower Richard G , Glaser Adam W
Published: November 2023

Background

Educational attainment in children with congenital heart disease (CHD) within the UK has not been reported, despite the possibility of school absences and disease-specific factors creating educational barriers.

Methods and results

Children were prospectively recruited to the Born in Bradford birth cohort between March 2007 and December 2010. Diagnoses of CHD were identified through linkage to the congenital anomaly register and independently verified by clinicians. Multivariable regression accounted for relevant confounders. Our primary outcome was the odds of ‘below expected’ attainment in maths, reading, and writing at ages 4–11 years.

Educational records of 139 children with non-genetic CHD were compared with 11 188 age-matched children with no major congenital anomaly. Children with CHD had significantly higher odds of ‘below expected’ attainment in maths at age 4–5 years [odds ratio (OR) 1.64, 95% confidence interval (CI) 1.07–2.52], age 6–7 (OR 2.03, 95% CI 1.32–3.12), and age 10–11 (OR 2.28, 95% CI 1.01–5.14). Odds worsened with age, with similar results for reading and writing. The odds of receiving special educational needs support reduced with age for children with CHD relative to controls [age 4–5: OR 4.84 (2.06–11.40); age 6–7: OR 3.65 (2.41–5.53); age 10–11: OR 2.73 (1.84–4.06)]. Attainment was similar for children with and without exposure to cardio-pulmonary bypass. Lower attainment was strongly associated with the number of pre-school hospital admissions.

Conclusion

Children with CHD have lower educational attainment compared with their peers. Deficits are evident from school entry and increase throughout primary school.
Patterns of Evolution of TRIM Genes Highlight the Evolutionary Plasticity of Antiviral Effectors in Mammals
Authors: Fernandes Alexandre P , OhAinle Molly , Esteves Pedro J
Published: November 2023

The innate immune system of mammals is formed by a complex web of interacting proteins, which together constitute the first barrier of entry for infectious pathogens. Genes from the E3-ubiquitin ligase tripartite motif (TRIM) family have been shown to play an important role in the innate immune system by restricting the activity of different retrovirus species. For example, TRIM5 and TRIM22 have both been associated with HIV restriction and are regarded as crucial parts of the antiretroviral machinery of mammals. Our analyses of positive selection corroborate the great significance of these genes for some groups of mammals. However, we also show that many species lack TRIM5 and TRIM22 altogether. By analyzing a large number of mammalian genomes, here we provide the first comprehensive view of the evolution of these genes in eutherians, showcasing that the pattern of accumulation of TRIM genes has been dissimilar across mammalian orders. Our data suggest that these differences are caused by the evolutionary plasticity of the immune system of eutherians, which have adapted to use different strategies to combat retrovirus infections. Altogether, our results provide insights into the dissimilar evolution of a representative family of restriction factors, highlighting an example of adaptive and idiosyncratic evolution in the innate immune system.
Risky Gravity
Authors: Juvenal Luciana , Santos Monteiro Paulo
Published: November 2023

We consider the canonical trade model with heterogeneous firms, love for variety and trade costs, and integrate it in the consumption CAPM model. This yields a structural gravity equation that includes an additional factor related to risk premia. Empirical evidence based on firm-level data confirms the importance of cross-sectional heterogeneity in risk and time-varying risk premia to shape bilateral trade flows. The structural gravity model augmented to account for fluctuations in risk premia offers a compelling explanation for trade collapses during abrupt economic downturns.
The utility of alpine cave fossil assemblages for zoological census: an example from northern Utah, United States
Authors: O’Brien Kaedan , Irmis Randall B , Brenner Coltrain Joan , Dalmas Daniel Martin , Derieg Katrina M , Evans Thomas , Richards Eric S , Richards Fumiko M , Rickart Eric A , Faith J Tyler
Published: November 2023

Assemblages of mammal skeletal remains provide a powerful tool for censusing wildlife populations to establish zoological baselines required for evaluating biogeographic trends over varying timescales. Caves provide an ideal depositional setting to preserve these skeletal remains despite potential time averaging and taphonomic filtering. We describe a Holocene paleontological assemblage from Boomerang Cave in the Bear River Range of Cache County, northern Utah, United States, at an elevation of 2,231 m, and at the boundary between the Great Basin and Rocky Mountain biogeographic provinces. We analyzed 1,228 surface-collected specimens from six areas within the cave, and identified a minimum of 22 nonoverlapping mammalian taxa, comprising all size classes present in the region. Compared to museum records for mammals from the Bear River Range and individuals trapped or observed in the vicinity of the cave, specimen-based rarefaction demonstrates that our assemblage captures most of the mammalian diversity expected in the area. This is particularly apparent for carnivorans and soricids, which are particularly well-represented in the Boomerang Cave assemblage, with the former clade represented by at least nine taxa. This high level of diversity can be attributed to the relatively random nature of natural trap cave deposition, reducing accumulation biases due to size or diet. We also record the first occurrence of Merriam’s Shrew (Sorex merriami) from the Bear River Range. Our analysis does not indicate any mammalian changes between late Holocene and present-day communities, but these data establish a new zoological baseline for an alpine community at the interface between two key biogeographic provinces in western North America. Our work highlights the value of collecting skeletal remains from cave assemblages as a convenient and fast method for censusing terrestrial mammalian communities.
Lactate regulates major zygotic genome activation by H3K18 lactylation in mammals
Authors: Li Jingyu , Hou Weibo , Zhao Qi , Han Wei , Cui Hongdi , Xiao Songling , Zhu Ling , Qu Jiadan , Liu Xiaoyu , Cong Weitao , Shen Jingling , Zhao Yuzheng , Gao Shaorong , Huang Guoning , Kong Qingran
Published: November 2023

Lactate is present at a high level in the microenvironment of mammalian preimplantation embryos in vivo and in vitro. However, its role in preimplantation development is unclear. Here, we report that lactate is highly enriched in the nuclei of early embryos when major zygotic genome activation (ZGA) occurs in humans and mice. The inhibition of its production and uptake results in developmental arrest at the 2-cell stage, major ZGA failure, and loss of lactate-derived H3K18lac, which could be rescued by the addition of Lac-CoA and recapitulated by overexpression of H3K18R mutation. By profiling the landscape of H3K18lac during mouse preimplantation development, we show that H3K18lac is enriched on the promoter regions of most major ZGA genes and correlates with their expressions. In humans, H3K18lac is also enriched in ZGA markers and temporally concomitant with their expressions. Taken together, we profile the landscapes of H3K18lac in mouse and human preimplantation embryos, and demonstrate the important role for H3K18lac in major ZGA, showing that a conserved metabolic mechanism underlies preimplantation development of mammalian embryos.
Exogeneous metal ions as therapeutic agents in cardiovascular disease and their delivery strategies
Authors: Hong Xiaoqian , Tian Geer , Zhu Yang , Ren Tanchen
Published: November 2023

Metal ions participate in many metabolic processes in the human body, and their homeostasis is crucial for life. In cardiovascular diseases (CVDs), the equilibriums of metal ions are frequently interrupted, which are related to a variety of disturbances of physiological processes leading to abnormal cardiac functions. Exogenous supplement of metal ions has the potential to work as therapeutic strategies for the treatment of CVDs. Compared with other therapeutic drugs, metal ions possess broad availability, good stability and safety and diverse drug delivery strategies. The delivery strategies of metal ions are important to exert their therapeutic effects and reduce the potential toxic side effects for cardiovascular applications, which are also receiving increasing attention. Controllable local delivery strategies for metal ions based on various biomaterials are constantly being designed. In this review, we comprehensively summarized the positive roles of metal ions in the treatment of CVDs from three aspects: protecting cells from oxidative stress, inducing angiogenesis, and adjusting the functions of ion channels. In addition, we introduced the transferability of metal ions in vascular reconstruction and cardiac tissue repair, as well as the currently available engineered strategies for the precise delivery of metal ions, such as integrated with nanoparticles, hydrogels and scaffolds.
Diversity and Clonality in Populations of Phytophthora citrophthora and P. syringae Causing Brown Rot of Citrus in California
Authors: Riley Nathan , Förster Helga , Adaskaveg James E.
Published: November 2023

Phytophthora citrophthora and P. syringae are currently the primary causal organisms of brown rot of citrus fruits in California. To possibly find an explanation for the prevalence of the previously minor species P. syringae, we determined the population structures of both pathogens in California using next-generation sequencing and population genomics analyses. Whole-genome sequencing and aligning with newly assembled reference genomes identified 972,266 variants in 132 isolates of P. citrophthora and 422,208 variants in 154 isolates (including 24 from noncitrus tree crops) of P. syringae originating from three major growing regions. The resulting data sets were visualized using principal component analysis, discriminant analysis of principal components, unweighted pair-group method with arithmetic mean dendrograms, fastStructure, and minimum spanning networks, and we obtained the index of association, diversity summary statistics, and genetic distance statistics values GST, G′′ ST, and Jost's D. Subpopulations of both species were mostly defined by their geographic origin indicating restricted dispersal of inoculum. Except for five isolates, the population structure of P. citrophthora (that is heterothallic and unlikely to reproduce sexually) was clonal to semi-clonal, with very little genetic diversity within and among subgroups. In contrast, the population structure of P. syringae was also clonal to semi-clonal, but isolates were placed into four main clusters of much higher diversity. Clonality in both species can be explained by a high level of asexual reproduction. The higher diversity in the homothallic P. syringae is likely due to commonly occurring sexual reproduction. One distinct cluster of P. syringae consisted solely of isolates from noncitrus hosts; therefore, the origin of P. syringae in citrus could not be resolved.
Iron inhibits glioblastoma cell migration and polarization
Authors: Shenoy Ganesh , Kheirabadi Sina , Ataie Zaman , Sahu Aurosman Pappus , Palsa Kondaiah , Wade Quinn , Khunsriraksakul Chachrit , Khristov Vladimir , Slagle‐Webb Becky , Lathia Justin D. , Wang Hong‐Gang , Sheikhi Amir , Connor James R.
Published: November 2023

Glioblastoma is one of the deadliest malignancies facing modern oncology today. The ability of glioblastoma cells to diffusely spread into neighboring healthy brain makes complete surgical resection nearly impossible and contributes to the recurrent disease faced by most patients. Although research into the impact of iron on glioblastoma has addressed proliferation, there has been little investigation into how cellular iron impacts the ability of glioblastoma cells to migrate—a key question, especially in the context of the diffuse spread observed in these tumors. Herein, we show that increasing cellular iron content results in decreased migratory capacity of human glioblastoma cells. The decrease in migratory capacity was accompanied by a decrease in cellular polarization in the direction of movement. Expression of CDC42, a Rho GTPase that is essential for both cellular migration and establishment of polarity in the direction of cell movement, was reduced upon iron treatment. We then analyzed a single‐cell RNA‐seq dataset of human glioblastoma samples and found that cells at the tumor periphery had a gene signature that is consistent with having lower levels of cellular iron. Altogether, our results suggest that cellular iron content is impacting glioblastoma cell migratory capacity and that cells with higher iron levels exhibit reduced motility.
Ending the HIV Epidemic
Authors: Kirton Carl A.
Published: November 2023

Despite progress, there is still much work to be done.