bluuebunny/crossref_metadata_2025 huggingface dataset:
Prooftexting from Other People’s Scriptures? “Prophets and Patriarchs” in Acts of Philip 5–7
Authors: Snyder Julia
Published: February 2023

What role has the “Old Testament” played in the self-understanding of Christians over the centuries, and what can we learn from the fact that Israel’s scriptures are often cited in early Christian texts? Using the Acts of Philip as a case study, this article argues that we should not assume all early Christian writers thought of these as “my own scriptures.” When we encounter citations from Israel’s scriptures in Christian texts, a variety of interpretive options should be considered, including the possibility that some writers saw Israel’s scriptures as “other people’s scriptures, not ours,” or would have consigned them a limited role in the Christian life, treating them as relevant for apologetics and evangelism—or for talking about apologetics and evangelism—but not for ongoing Christian discipleship. The article offers a new interpretation of Acts Phil. 5–7 and also examines Qur’anic citations in the Dialogue of Timothy I and the Caliph.
Partners with Benefits: When Multinational Corporations Succeed in Authoritarian Courts
Authors: Chen Frederick R. , Xu Jian
Published: February 2023

Scholars often assume that courts in authoritarian regimes cannot credibly protect foreign investors’ interests because these institutions lack judicial independence. In this article, we construct a novel data set on multinational corporations’ litigation activities in Chinese courts from 2002 to 2017. This supports the first systematic case-level analysis of foreign firms’ lawsuit outcomes in an authoritarian judiciary. We find that foreign companies frequently engage in litigation in authoritarian courts. Moreover, we theoretically and empirically distinguish between two types of government–business ties in terms of their effectiveness in incentivizing the host state to protect foreign investors’ interests. We argue that ad hoc, personal political connections deliver only trivial lawsuit success for multinational enterprises, while formal corporate partnerships with regime insiders can lead the state to structurally internalize foreign investors’ interests. In particular, we demonstrate that joint venture partnerships with state-owned enterprises help foreign firms obtain more substantial monetary compensation than other types of multinational enterprises. By contrast, the personal political connections of foreign firms’ board members do not foster meaningful judicial favoritism. These findings are robust to tests of alternative implications, matching procedures, and subsample robustness checks. This article advances our understanding of multinational corporations’ political risk in host countries, government–business relations, and authoritarian judicial institutions.
Cerebral blood flow in striatum is increased by partial dopamine agonism in initially antipsychotic-naïve patients with psychosis
Authors: Bojesen Kirsten Borup , Glenthøj Birte Yding , Sigvard Anne Korning , Tangmose Karen , Raghava Jayachandra Mitta , Ebdrup Bjørn Hylsebeck , Rostrup Egill
Published: February 2023

Background

Resting cerebral blood flow (rCBF) in striatum and thalamus is increased in medicated patients with psychosis, but whether this is caused by treatment or illness pathology is unclear. Specifically, effects of partial dopamine agonism, sex, and clinical correlates on rCBF are sparsely investigated. We therefore assessed rCBF in antipsychotic-naïve psychosis patients before and after aripiprazole monotherapy and related findings to sex and symptom improvement.

Methods

We assessed rCBF with the pseudo-Continuous Arterial Spin Labeling (PCASL) sequence in 49 first-episode patients (22.6 ± 5.2 years, 58% females) and 50 healthy controls (HCs) (22.3 ± 4.4 years, 63% females) at baseline and in 29 patients and 49 HCs after six weeks. RCBF in striatum and thalamus was estimated with a region-of-interest (ROI) approach. Psychopathology was assessed with the positive and negative syndrome scale.

Results

Baseline rCBF in striatum and thalamus was not altered in the combined patient group compared with HCs, but female patients had lower striatal rCBF compared with male patients (p = 0.009). Treatment with a partial dopamine agonist increased rCBF significantly in striatum (p = 0.006) in the whole patient group, but not significantly in thalamus. Baseline rCBF in nucleus accumbens was negatively associated with improvement in positive symptoms (p = 0.046), but baseline perfusion in whole striatum and thalamus was not related to treatment outcome.

Conclusions

The findings suggest that striatal perfusion is increased by partial dopamine agonism and decreased in female patients prior to first treatment. This underlines the importance of treatment effects and sex differences when investigating the neurobiology of psychosis.
Relating the prosody of infant-directed speech to children’s vocabulary size
Authors: HAN Mengru , DE JONG Nivja H. , KAGER René
Published: February 2023

This study examines correlations between the prosody of infant-directed speech (IDS) and children’s vocabulary size. We collected longitudinal speech data and vocabulary information from Dutch mother-child dyads with children aged 18 (N = 49) and 24 (N = 27) months old. We took speech context into consideration and distinguished between prosody when mothers introduce familiar vs. unfamiliar words to their children. The results show that IDS mean pitch predicts children’s vocabulary growth between 18 and 24 months. In addition, the degree of prosodic modification when mothers introduce unfamiliar words to their children correlates with children’s vocabulary growth during this period. These findings suggest that the prosody of IDS, especially in word-learning contexts, may serve linguistic purposes.
Hijacking the Familiar: The Work of Big Telly Theatre Company
Authors: SEATON ZOЁ
Published: February 2023

The following is a transcript of the Q&A with Zoё Seaton on 2 August 2022.
Re-Reading Morant Bay: Protest, Inquiry, and Colonial Rule
Authors: Connolly Jonathan
Published: February 2023

The 1865 Morant Bay Rebellion figures prominently in scholarship on modern Britain, colonial Jamaica, and the British Empire, as a milestone of post-emancipation protest, a turning point in British race-thinking, and a focal point for debates on martial law and British justice. This article presents a new interpretation of the rebellion’s legal and political significance. Focused on processes of formal inquiry, I argue that legal analysis reshaped the political “moral” of the event. For the rebellion’s participants and some British observers, Morant Bay challenged the practice of colonial rule. But beginning with the royal commission of inquiry called to investigate the suppression, formal inquiry displaced the systemic critique that had largely motivated the uprising. Focused increasingly on the nature of martial law and culminating in the criminal prosecution of Jamaica’s colonial governor, legal debate and analysis transformed the scandal’s moral center and turned Morant Bay into a new justification for further and more centralized imperial control. In developing these arguments, the article examines law’s capacity to read, write, and exclude competing narratives of empire. In so doing, it contributes to scholarship on scandal and legitimation, and offers a new interpretation of a seminal nineteenth-century debate on the use of martial law.
Schizophrenia as a risk factor for cardiovascular and metabolic health outcomes: a comparative risk assessment
Authors: Ali S. , Santomauro D. , Ferrari A. J , Charlson F.
Published: February 2023

Aims

Cardiometabolic diseases are responsible for the majority of premature deaths in people with schizophrenia. This study aimed to quantify the fatal burden of ischaemic heart disease (IHD), stroke and diabetes attributable to schizophrenia.

Methods

Comparative Risk Assessment methodology from the Global Burden of Disease (GBD) study was used to calculate attributable burden; pooled relative risks (RRs) for IHD, stroke and diabetes were estimated via meta-regression, which were combined with GBD schizophrenia prevalence estimates to calculate the deaths and years of life lost (YLLs) caused by these health outcomes that were attributable to schizophrenia. The proportion of explained all-cause fatal burden and corresponding unexplained burden was also calculated.

Results

The pooled RRs for IHD, stroke and diabetes mortality were 2.36 [95% uncertainty interval (UI) 1.77 to 3.14], 1.86 (95% UI 1.36 to 2.54) and 4.08 (95% UI 3.80 to 4.38) respectively. Schizophrenia was responsible for around 50 000 deaths and almost 1.5 million YLLs globally in 2019 from these health outcomes combined. IHD, stroke and diabetes together explained around 13% of all deaths and almost 11% of all YLLs attributable to schizophrenia, resulting in 320 660 (95% UI 288 299 to 356 517) unexplained deaths and 12 258 690 (95% UI 10 925 426 to 13 713 646) unexplained YLLs.

Conclusions

Quantifying the physical disease burden attributable to schizophrenia provides a means of capturing the substantial excess mortality associated with this disorder within the GBD framework, contributing to an important evidence base for healthcare planning and practice.
Hubble Detects the Start of a New Saturn Ring Spoke Season
Authors: Simon Amy A. , Hedman Matthew M. , Nicholson Philip D. , Tiscareno Matthew S. , Showalter Mark R. , McDonald Troy , Callos Samantha
Published: February 2023

Saturn's ring spokes typically appear over an 8‐year duration centered on equinox. Hubble Space Telescope observations in 2021 indicate the beginning of a new spoke season as Saturn approaches equinox in 2025. The spokes show increased contrast and longevity in 2022, persisting for up to 11 hours. The spokes are visible from UV to near‐IR and are slightly bluer (i.e., less red) than the rings, but we find no significant wavelength dependence in the spectral contrast, which approximates their optical depth). Spoke rotation rates are between 606 and 626 min, consistent with either Keplerian rotation or possibly the variable rotation rate of Saturn's kilometric radiation. Spoke activity is expected to increase over the next several years.
Large‐Scale Disturbances in the Upper Thermosphere Induced by the 2022 Tonga Volcanic Eruption
Authors: Li Ruoxi , Lei Jiuhou , Kusche Jürgen , Dang Tong , Huang Fuqing , Luan Xiaoli , Zhang Shun‐Rong , Yan Maodong , Yang Ziyi , Liu Feifan , Dou Xiankang
Published: February 2023

The effects of volcanic eruptions on the ionosphere have been well studied, however, evidence for the anticipated upper atmospheric neutral variations and their exact extents of change are rarely available. Here, we report dramatic thermospheric disturbances following the 15 January 2022 Tonga eruption. The GRACE‐FO and Swarm‐C observations from the accelerometers exhibited three successive thermospheric density waves at ∼500 km altitudes propagating concentrically across the globe at 200–450 m/s phase speed and two of the three waves converged at the antipode of the epicenter. A large‐scale and long‐lasting neutral density depletion within a radius of approximately 10,000 km around the epicenter occurred, along with the density enhancement around the antipode of the epicenter. Such an enhancement is comparable in the relative intensity with respect to the no‐eruption condition, to the effect of a moderate geomagnetic storm. This study offers observational evidence of substantial global upper thermospheric perturbations well above their origin near the Earth's surface due to a volcanic eruption.
Hourly Periodic Variations of Ultralow‐Frequency (ULF) Waves in Jupiter's Magnetosheath
Authors: Gu W. D. , Yao Z. H. , Pan D. X. , Xu Y. , Zhang B. , Delamere P. A. , Fu S. Y. , Xie L. , Ye S. Y. , Chen Y. N. , Dunn W. R. , Wei Y.
Published: February 2023

Periodic variations are widely identified in the Jovian system, varying from 10 s of seconds to several days or even longer. These processes are strongly influenced by solar wind conditions, planetary rotation and Io's volcanic activity. Ultralow‐frequency (ULF) waves at 10 s of minutes, which are the typical time scale of field‐line resonance, are considered as a crucial process in driving the Jovian energy circulation. The longer time‐scale periodicities are likely associated with global mass circulation. In this study, we focus on multihour variations of the ULF wave energy, which are difficult to identify within the magnetosphere due to the rapid planetary rotation modulation. Using the magnetic field observations from Juno and Galileo in Jupiter's magnetosheath, we found multiple significant multihour periodicities, widely distributed from 2 to 10 hr, peaked at different values from case to case. The most common periodicities were between 3 and 5 hr, existing in both the dawn and dusk sides. These common periodicities are likely associated with the energy transport from the inside to the magnetosheath.
ERdj5 protects goblet cells from endoplasmic reticulum stress-mediated apoptosis under inflammatory conditions
Authors: Jeong Hyunjin , Hong Eun-Hye , Ahn Jae-Hee , Cho Jaewon , Jeong Jae-Hyeon , Kim Chae-Won , Yoon Byung-Il , Koo Ja Hyun , Park Yun-Yong , Yang Yoon Mee , Iwawaki Takao , Vallance Bruce A. , Chang Sun-Young , Ko Hyun-Jeong
Published: February 2023

Endoplasmic reticulum stress is closely associated with the onset and progression of inflammatory bowel disease. ERdj5 is an endoplasmic reticulum-resident protein disulfide reductase that mediates the cleavage and degradation of misfolded proteins. Although ERdj5 expression is significantly higher in the colonic tissues of patients with inflammatory bowel disease than in healthy controls, its role in inflammatory bowel disease has not yet been reported. In the current study, we used ERdj5-knockout mice to investigate the potential roles of ERdj5 in inflammatory bowel disease. ERdj5 deficiency causes severe inflammation in mouse colitis models and weakens gut barrier function by increasing NF-κB-mediated inflammation. ERdj5 may not be indispensable for goblet cell function under steady-state conditions, but its deficiency induces goblet cell apoptosis under inflammatory conditions. Treatment of ERdj5-knockout mice with the chemical chaperone ursodeoxycholic acid ameliorated severe colitis by reducing endoplasmic reticulum stress. These findings highlight the important role of ERdj5 in preserving goblet cell viability and function by resolving endoplasmic reticulum stress.
Association of maternal snuff use and smoking with Sudden Infant Death Syndrome: a national register study
Authors: Gunnerbeck Anna , Lundholm Cecilia , Rhedin Samuel , Mitha Ayoub , Chen Ruoqing , D’Onofrio Brian M. , Almqvist Catarina
Published: February 2023

Background

The aim was to study whether non-combustible nicotine (Swedish snuff) use in pregnancy is associated with elevated risk of post neonatal mortality, Sudden Infant Death Syndrome (SIDS), and Sudden Unexpected Infant Death (SUID) and to study how cessation before the antenatal booking influenced these risks.

Methods

This was a population-based register study of all infants with information on tobacco exposure in early pregnancy born in Sweden 1999–2019, n = 2,061,514. Self-reported tobacco use in early pregnancy was categorized as nonuse, snuff use, and moderate and heavy smoking. Multiple logistic regression models were used to estimate crude and adjusted odds ratios (aORs) with 95% confidence intervals (CIs).

Results

Maternal snuff use was associated with increased risks of post neonatal mortality, SIDS, and SUID. The risks of snuff use and moderate smoking were of similar magnitude. Heavy smoking was associated with the highest risks. Cessation of smoking and snuff use before the antenatal booking was associated with lower risks of SIDS and SUID compared to that of continuous usage.

Conclusions

Maternal snuff use was associated with increased risks of post neonatal mortality, SIDS, and SUID. Nicotine is the common substance in cigarette smoke and snuff. These findings support the hypothesis that nicotine contributes to an elevated risk of SIDS.

Impact

Maternal snuff use and smoking in early pregnancy were associated with increased risks of post neonatal mortality, SIDS, and SUID.

Cessation of smoking and snuff use before the first antenatal visit was associated with reduced risks of SIDS and SUID.

The common substance in cigarette smoke and snuff is nicotine. Our findings suggest that nicotine contributes to an elevated risk of SIDS and SUID.

The implication of our findings is that all forms of nicotine should be avoided in pregnancy.
Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission
Authors: Shapiro Julie Teresa , Zorea Alvah , Kav Aya Brown , Ontiveros Vicente J , Mizrahi Itzhak , Pilosof Shai
Published: February 2023

Antimicrobial resistance (AMR) is a significant threat to public health. Plasmids are principal vectors of AMR genes, significantly contributing to their spread and mobility across hosts. Nevertheless, little is known about the dynamics of plasmid genetic exchange across animal hosts. Here, we use theory and methodology from network and disease ecology to investigate the potential of gene transmission between plasmids using a data set of 21 plasmidomes from a single dairy cow population. We constructed a multilayer network based on pairwise plasmid genetic similarity. Genetic similarity is a signature of past genetic exchange that can aid in identifying potential routes and mechanisms of gene transmission within and between cows. Links between cows dominated the transmission network, and plasmids containing mobility genes were more connected. Modularity analysis revealed a network cluster where all plasmids contained a mobM gene, and one where all plasmids contained a beta-lactamase gene. Cows that contain both clusters also share transmission pathways with many other cows, making them candidates for super-spreading. In support, we found signatures of gene super-spreading in which a few plasmids and cows are responsible for most gene exchange. An agent-based transmission model showed that a new gene invading the cow population will likely reach all cows. Finally, we showed that edge weights contain a non-random signature for the mechanisms of gene transmission, allowing us to differentiate between dispersal and genetic exchange. These results provide insights into how genes, including those providing AMR, spread across animal hosts.
Immortal-time bias in older vs younger age groups: a simulation study with application to a population-based cohort of patients with colon cancer
Authors: Pilleron Sophie , Maringe Camille , Morris Eva J. A. , Leyrat Clémence
Published: February 2023

Background

In observational studies, the risk of immortal-time bias (ITB) increases with the likelihood of early death, itself increasing with age. We investigated how age impacts the magnitude of ITB when estimating the effect of surgery on 1-year overall survival (OS) in patients with Stage IV colon cancer aged 50–74 and 75–84 in England.

Methods

Using simulations, we compared estimates from a time-fixed exposure model to three statistical methods addressing ITB: time-varying exposure, delayed entry and landmark methods. We then estimated the effect of surgery on OS using a population-based cohort of patients from the CORECT-R resource and conducted the analysis using the emulated target trial framework.

Results

In simulations, the magnitude of ITB was larger among older patients when their probability of early death increased or treatment was delayed. The bias was corrected using the methods addressing ITB. When applied to CORECT-R data, these methods yielded a smaller effect of surgery than the time-fixed exposure approach but effects were similar in both age groups.

Conclusion

ITB must be addressed in all longitudinal studies, particularly, when investigating the effect of exposure on an outcome in different groups of people (e.g., age groups) with different distributions of exposure and outcomes.
Johann Gregor Mendel: the victory of statistics over human imagination
Authors: Raudenska Martina , Vicar Tomas , Gumulec Jaromir , Masarik Michal
Published: February 2023

In 2022, we celebrated 200 years since the birth of Johann Gregor Mendel. Although his contributions to science went unrecognized during his lifetime, Mendel not only described the principles of monogenic inheritance but also pioneered the modern way of doing science based on precise experimental data acquisition and evaluation. Novel statistical and algorithmic approaches are now at the center of scientific work, showing that work that is considered marginal in one era can become a mainstream research approach in the next era. The onset of data-driven science caused a shift from hypothesis-testing to hypothesis-generating approaches in science. Mendel is remembered here as a promoter of this approach, and the benefits of big data and statistical approaches are discussed.
2022 Renal denervation therapy for the treatment of hypertension: a statement from the Thai Hypertension Society
Authors: Roubsanthisuk Weranuj , Kunanon Sirisawat , Chattranukulchai Pairoj , Panchavinnin Pariya , Wongpraparut Nattawut , Chaipromprasit Jarkarpun , Pienvichitr Pavit , Ayudhya Rapeephon Kunjara Na , Sukonthasarn Apichard ,   on behalf of Thai Hypertension Society
Published: February 2023

Hypertension remains a significant risk factor for major cardiovascular events worldwide. Poor adherence to treatment is extremely common in clinical practice, leading to uncontrolled hypertension. However, some patients with resistant hypertension still have uncontrolled blood pressure despite good medical compliance. A specific group of patients also develop adverse reactions to many blood pressure-lowering medications. These scenarios indicate that innovative strategies to lower blood pressure in challenging cases of hypertension are needed. The blood pressure-lowering efficacy of catheter-based renal denervation therapy to decrease sympathetic tone has been confirmed in many publications in recent years. Apart from both the invasiveness and the expensiveness of this technology, appropriate case selection to undergo this procedure is still developing. The utilization of renal denervation therapy for hypertension treatment in Thailand has lasted for 10 years with a good response in most cases. Currently, only certain interventionists at a few medical schools in Thailand can perform this procedure. However, more physicians are now interested in applying this technology to their patients. The Thai Hypertension Society Committee has reviewed updated information to provide principles for the appropriate utilization of renal denervation therapy. The blood pressure-lowering mechanism, efficacy, suitable patient selection, pre- and postprocedural assessment and procedural safety of renal denervation are included in this statement.
Interfacial solute flux promotes emulsification at the water|oil interface
Authors: Colón-Quintana Guillermo S. , Clarke Thomas B. , Dick Jeffrey E.
Published: February 2023

Emulsions are critical across a broad spectrum of industries. Unfortunately, emulsification requires a significant driving force for droplet dispersion. Here, we demonstrate a mechanism of spontaneous droplet formation (emulsification), where the interfacial solute flux promotes droplet formation at the liquid-liquid interface when a phase transfer agent is present. We have termed this phenomenon fluxification. For example, when HAuCl4 is dissolved in an aqueous phase and [NBu4][ClO4] is dissolved in an oil phase, emulsion droplets (both water-in-oil and oil-in-water) can be observed at the interface for various oil phases (1,2-dichloroethane, dichloromethane, chloroform, and nitrobenzene). Emulsification occurs when AuCl4– interacts with NBu4+, a well-known phase-transfer agent, and transfers into the oil phase while ClO4– transfers into the aqueous phase to maintain electroneutrality. The phase transfer of SCN– and Fe(CN)63– also produce droplets. We propose a microscopic mechanism of droplet formation and discuss design principles by tuning experimental parameters.
Mitotic DNA synthesis in response to replication stress requires the sequential action of DNA polymerases zeta and delta in human cells
Authors: Wu Wei , Barwacz Szymon A. , Bhowmick Rahul , Lundgaard Katrine , Gonçalves Dinis Marisa M. , Clausen Malgorzata , Kanemaki Masato T. , Liu Ying
Published: February 2023

Oncogene activation creates DNA replication stress (RS) in cancer cells, which can generate under-replicated DNA regions (UDRs) that persist until cells enter mitosis. UDRs also have the potential to generate DNA bridges in anaphase cells or micronuclei in the daughter cells, which could promote genomic instability. To suppress such damaging changes to the genome, human cells have developed a strategy to conduct ‘unscheduled’ DNA synthesis in mitosis (termed MiDAS) that serves to rescue under-replicated loci. Previous studies have shown that MiDAS proceeds via a POLD3-dependent pathway that shows some features of break-induced replication. Here, we define how human cells utilize both DNA gap filling (REV1 and Pol ζ) and replicative (Pol δ) DNA polymerases to complete genome duplication following a perturbed S-phase. We present evidence for the existence of a polymerase-switch during MiDAS that is required for new DNA synthesis at UDRs. Moreover, we reveal that, upon oncogene activation, cancer cell survival is significantly compromised when REV1 is depleted, suggesting that REV1 inhibition might be a feasible approach for the treatment of some human cancers.
Field programmable spin arrays for scalable quantum repeaters
Authors: Wang Hanfeng , Trusheim Matthew E. , Kim Laura , Raniwala Hamza , Englund Dirk R.
Published: February 2023

The large scale control over thousands of quantum emitters desired by quantum network technology is limited by the power consumption and cross-talk inherent in current microwave techniques. Here we propose a quantum repeater architecture based on densely-packed diamond color centers (CCs) in a programmable electrode array, with quantum gates driven by electric or strain fields. This ‘field programmable spin array’ (FPSA) enables high-speed spin control of individual CCs with low cross-talk and power dissipation. Integrated in a slow-light waveguide for efficient optical coupling, the FPSA serves as a quantum interface for optically-mediated entanglement. We evaluate the performance of the FPSA architecture in comparison to a routing-tree design and show an increased entanglement generation rate scaling into the thousand-qubit regime. Our results enable high fidelity control of dense quantum emitter arrays for scalable networking.
Visualizing RNA conformational and architectural heterogeneity in solution
Authors: Ding Jienyu , Lee Yun-Tzai , Bhandari Yuba , Schwieters Charles D. , Fan Lixin , Yu Ping , Tarosov Sergey G. , Stagno Jason R. , Ma Buyong , Nussinov Ruth , Rein Alan , Zhang Jinwei , Wang Yun-Xing
Published: February 2023

RNA flexibility is reflected in its heterogeneous conformation. Through direct visualization using atomic force microscopy (AFM) and the adenosylcobalamin riboswitch aptamer domain as an example, we show that a single RNA sequence folds into conformationally and architecturally heterogeneous structures under near-physiological solution conditions. Recapitulated 3D topological structures from AFM molecular surfaces reveal that all conformers share the same secondary structural elements. Only a population-weighted cohort, not any single conformer, including the crystal structure, can account for the ensemble behaviors observed by small-angle X-ray scattering (SAXS). All conformers except one are functionally active in terms of ligand binding. Our findings provide direct visual evidence that the sequence-structure relationship of RNA under physiologically relevant solution conditions is more complex than the one-to-one relationship for well-structured proteins. The direct visualization of conformational and architectural ensembles at the single-molecule level in solution may suggest new approaches to RNA structural analyses.
Enhanced charge density wave with mobile superconducting vortices in La1.885Sr0.115CuO4
Authors: Wen J.-J. , He W. , Jang H. , Nojiri H. , Matsuzawa S. , Song S. , Chollet M. , Zhu D. , Liu Y.-J. , Fujita M. , Jiang J. M. , Rotundu C. R. , Kao C.-C. , Jiang H.-C. , Lee J.-S. , Lee Y. S.
Published: February 2023

Superconductivity in the cuprates is found to be intertwined with charge and spin density waves. Determining the interactions between the different types of order is crucial for understanding these important materials. Here, we elucidate the role of the charge density wave (CDW) in the prototypical cuprate La1.885Sr0.115CuO4, by studying the effects of large magnetic fields (H) up to 24 Tesla. At low temperatures (T), the observed CDW peaks reveal two distinct regions in the material: a majority phase with short-range CDW coexisting with superconductivity, and a minority phase with longer-range CDW coexisting with static spin density wave (SDW). With increasing magnetic field, the CDW first grows smoothly in a manner similar to the SDW. However, at high fields we discover a sudden increase in the CDW amplitude upon entering the vortex-liquid state. Our results signify strong coupling of the CDW to mobile superconducting vortices and link enhanced CDW amplitude with local superconducting pairing across the H − T phase diagram.
A CpG island-encoded mechanism protects genes from premature transcription termination
Authors: Hughes Amy L. , Szczurek Aleksander T. , Kelley Jessica R. , Lastuvkova Anna , Turberfield Anne H. , Dimitrova Emilia , Blackledge Neil P. , Klose Robert J.
Published: February 2023

Transcription must be tightly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, by dissecting the function of the SET1 chromatin-modifying complexes that bind to CpG island-associated gene promoters, we discover that they play a specific and essential role in enabling the expression of low to moderately transcribed genes. Counterintuitively, this effect can occur independently of SET1 complex histone-modifying activity and instead relies on an interaction with the RNA Polymerase II-binding protein WDR82. Unexpectedly, we discover that SET1 complexes enable gene expression by antagonising premature transcription termination by the ZC3H4/WDR82 complex at CpG island-associated genes. In contrast, at extragenic sites of transcription, which typically lack CpG islands and SET1 complex occupancy, we show that the activity of ZC3H4/WDR82 is unopposed. Therefore, we reveal a gene regulatory mechanism whereby CpG islands are bound by a protein complex that specifically protects genic transcripts from premature termination, effectively distinguishing genic from extragenic transcription and enabling normal gene expression.
Multi-omics and machine learning reveal context-specific gene regulatory activities of PML::RARA in acute promyelocytic leukemia
Authors: Villiers William , Kelly Audrey , He Xiaohan , Kaufman-Cook James , Elbasir Abdurrahman , Bensmail Halima , Lavender Paul , Dillon Richard , Mifsud Borbála , Osborne Cameron S.
Published: February 2023

The PML::RARA fusion protein is the hallmark driver of Acute Promyelocytic Leukemia (APL) and disrupts retinoic acid signaling, leading to wide-scale gene expression changes and uncontrolled proliferation of myeloid precursor cells. While known to be recruited to binding sites across the genome, its impact on gene regulation and expression is under-explored. Using integrated multi-omics datasets, we characterize the influence of PML::RARA binding on gene expression and regulation in an inducible PML::RARA cell line model and APL patient ex vivo samples. We find that genes whose regulatory elements recruit PML::RARA are not uniformly transcriptionally repressed, as commonly suggested, but also may be upregulated or remain unchanged. We develop a computational machine learning implementation called Regulatory Element Behavior Extraction Learning to deconvolute the complex, local transcription factor binding site environment at PML::RARA bound positions to reveal distinct signatures that modulate how PML::RARA directs the transcriptional response.
A method for an unbiased estimate of cross-ancestry genetic correlation using individual-level data
Authors: Momin Md. Moksedul , Shin Jisu , Lee Soohyun , Truong Buu , Benyamin Beben , Lee S. Hong
Published: February 2023

Cross-ancestry genetic correlation is an important parameter to understand the genetic relationship between two ancestry groups. However, existing methods cannot properly account for ancestry-specific genetic architecture, which is diverse across ancestries, producing biased estimates of cross-ancestry genetic correlation. Here, we present a method to construct a genomic relationship matrix (GRM) that can correctly account for the relationship between ancestry-specific allele frequencies and ancestry-specific allelic effects. Through comprehensive simulations, we show that the proposed method outperforms existing methods in the estimations of SNP-based heritability and cross-ancestry genetic correlation. The proposed method is further applied to anthropometric and other complex traits from the UK Biobank data across ancestry groups. For obesity, the estimated genetic correlation between African and European ancestry cohorts is significantly different from unity, suggesting that obesity is genetically heterogenous between these two ancestries.
Photonic Majorana quantum cascade laser with polarization-winding emission
Authors: Han Song , Chua Yunda , Zeng Yongquan , Zhu Bofeng , Wang Chongwu , Qiang Bo , Jin Yuhao , Wang Qian , Li Lianhe , Davies Alexander Giles , Linfield Edmund Harold , Chong Yidong , Zhang Baile , Wang Qi Jie
Published: February 2023

Topological cavities, whose modes are protected against perturbations, are promising candidates for novel semiconductor laser devices. To date, there have been several demonstrations of topological lasers (TLs) exhibiting robust lasing modes. The possibility of achieving nontrivial beam profiles in TLs has recently been explored in the form of vortex wavefront emissions enabled by a structured optical pump or strong magnetic field, which are inconvenient for device applications. Electrically pumped TLs, by contrast, have attracted attention for their compact footprint and easy on-chip integration with photonic circuits. Here, we experimentally demonstrate an electrically pumped TL based on photonic analogue of a Majorana zero mode (MZM), implemented monolithically on a quantum cascade chip. We show that the MZM emits a cylindrical vector (CV) beam, with a topologically nontrivial polarization profile from a terahertz (THz) semiconductor laser.
Identification of potential biomarkers in Barrett’s esophagus derived esophageal adenocarcinoma
Authors: Yi Nan , Zhao Hailiang , He Juan , Xie Xike , Liang Liexin , Zuo Guowen , Xiong Mingyue , Liang Yunxiao , Yi Tingzhuang
Published: February 2023

Almost 50% of esophageal adenocarcinoma (EAC) patients progressed from Barrett’s esophagus (BE). EAC is often diagnosed at late stages and is related to dismal prognosis. However, there are still no effective methods for stratification and therapy in BE and EAC. Two public datasets (GSE26886 and GSE37200) were analyzed to identify differentially expressed genes (DEGs) between BE and EAC. Then, a series of bioinformatics analyses were performed to explore potential biomarkers associated with BE-EAC. 27 up- and 104 down-regulated genes were observed between GSE26886 and GSE37200. The GO and KEGG enrichment analysis indicated that the DEGs were highly involved in tumorigenesis. Subsequently, Weighted Gene Co-Expression Network Analysis (WGCNA) were performed to explore the potential genes related to BE-EAC, which were validated in The Cancer Genome Atlas (TCGA) database,and 5 up-regulated genes (MYO1A,ACE2,COL1A1,LGALS4, andADRA2A) and 3 down-regulated genes (AADAC,RAB27A, andP2RY14) were found in EAC. Meanwhile,ADRA2AandAADACcould contribute to EAC pathogenesis and progression.MYO1A,ACE2,COL1A1,LGALS4,ADRA2A, AADAC,RAB27A, andP2RY14could be potential novel diagnostic and prognostic biomarkers in BE-EAC.
Factors influencing satisfaction with male circumcision in Taiwan
Authors: Chen Chia Hung , Cheng Wei-Ming , Fan Yu-Hua , Chang Tung-Ping
Published: February 2023

We aimed to investigate patient satisfaction with male circumcision in Taiwan. An online, questionnaire-based, cross-sectional study involving 376 circumcised men 20 to 40 years of age in Taiwan was conducted. Circumcision-related satisfaction was defined as a visual analogue scale score ≥ 6 (range, 1–10). Pearson’s chi-square test was performed to compare differences between satisfied and unsatisfied participants. Factors predictive of participant satisfaction were analysed using multivariate logistic regression. Statistical significance was set at P < 0.05. Among 376 circumcised men, 249 (66.2%) reported satisfaction with circumcision. Satisfied participants had higher levels of education, underwent circumcision for phimosis or balanitis, underwent circumcision during adulthood, reported a larger penile size, and had fewer long-term complaints. Furthermore, 89.4% had various long-term complaints, including skin colour mismatch, changes in masturbation methods, hypertrophic scarring, excessive shortening of the prepuce, and redundant prepuce. Multivariate analysis revealed that adult circumcision and the absence of long-term conditions were predictive of satisfaction. Two-thirds of participants were satisfied with their circumcision outcome, especially those who underwent circumcision for phimosis or balanitis during adulthood. Proper preoperative patient selection and postoperative symptom prevention would improve patient satisfaction.
Sedimentary structures of microbial carbonates in the fourth member of the Middle Triassic Leikoupo Formation, Western Sichuan Basin, China
Authors: Wang Yuanchong , Shi Kaibo , Liu Bo
Published: February 2023

In recent years, abundant natural gas has been found in microbial carbonates in the fourth member of the Leikoupo Formation in Western Sichuan Basin. In this study, from the observation of 626 microbial thin sections, four types of microbial carbonates are classified based on the differences of mesostructures. Among them, thrombolites and stromatolites are subdivided into eight types based on the differences of microstructures. Six types of microbial microstructure association (MSA) are identified, and are mainly developed in microbial mounds. The energy of sedimentary environment and hydrodynamic conditions of them from low to high is MSA-5, MSA-1, MSA-6, MSA-3, MSA-4 and MSA-2. Because of the arid climate in the Annie Period, a restricted platform are developed in the upper sub-member of the Leikoupo Formation in Western Sichuan Basin, and the sedimentary facies are lagoon (gypsiferous lagoon or salt lake in evaporate conditions), microbial mounds, shoals, inner platform shoals and open sea from the east to the west. Microbial microstructures not only affect the pore evolution of microbial carbonate reservoirs, but also affect the diagenesis of microbial carbonate reservoirs of the fourth member of the Leikoupo Formation.
Agricultural spider decline: long-term trends under constant management conditions
Authors: Samu F. , Szita É. , Botos E. , Simon J. , Gallé-Szpisjak N. , Gallé R.
Published: February 2023

There is widespread evidence for a worldwide trend of insect decline, but we have much fewer data about recent temporal trends in other arthropod groups, including spiders. Spiders can be hypothesised to similarly decline because of trophic dependence on insects and being equally sensitive to local and global environmental changes. Background trends in arthropod populations can be verified if we decouple large-scale environmental transitions, such as climate change, from local factors. To provide a case study on baseline spider community trends, we observed changes in the spider community of an unsprayed alfalfa field and its margin 23 years apart under largely unchanged local conditions. We aimed to determine whether there are changes in spider abundance, species richness and mean species characteristics. Spider abundance per unit effort decreased dramatically, by 45% in alfalfa and by 59% in the margin, but species richness and most characteristics remained unchanged. Community composition in both habitats shifted and became more similar by the current study period. The population decline was especially marked in certain farmland species. We propose that in the absence of local causative factors, spider abundance decline in our study indicates a reduction of spider populations at landscape and regional scales.
Experimenter familiarization is a crucial prerequisite for assessing behavioral outcomes and reduces stress in mice not only under chronic pain conditions
Authors: Segelcke Daniel , Talbot Steven R. , Palme Rupert , La Porta Carmen , Pogatzki-Zahn Esther , Bleich André , Tappe-Theodor Anke
Published: February 2023

Rodent behavior is affected by different environmental conditions. These do not only comprise experimental and housing conditions but also familiarization with the experimenter. However, specific effects on pain-related behavior and chronic pain conditions have not been examined. Therefore, we aimed to investigate the impact of different housing conditions, using individually ventilated and standard open top cages, inverted day-night cycles, and experimenter familiarization on male mice following peripheral neuropathy using the spared nerve injury (SNI) model. Using a multimodal approach, we evaluated evoked pain-related- using von Frey hair filaments, measured gait pattern with the CatWalk system, assessed anxiety- and depression-like behavior with the Elevated plus maze and tail suspension test, measured corticosterone metabolite levels in feces and utilized an integrative approach for relative-severity-assessment. Mechanical sensitivity differed between the cage systems and experimenter familiarization and was affected in both sham and SNI mice. Experimenter familiarization and an inverted day-night cycle reduced mechanical hypersensitivity in SNI and sham mice. SNI mice of the inverted day-night group displayed the slightest pronounced alterations in gait pattern in the Catwalk test. Anxiety-related behavior was only found in SNI mice of experimenter-familiarized mice compared to the sham controls. In addition, familiarization reduced the stress level measured by fecal corticosteroid metabolites caused by the pain and the behavioral tests. Although no environmental condition significantly modulated the severity in SNI mice, it influenced pain-affected phenotypes and is, therefore, crucial for designing and interpreting preclinical pain studies. Moreover, environmental conditions should be considered more in the reporting guidelines, described in more detail, and discussed as a potential influence on pain phenotypes.
Seroprevalence of four endemic human coronaviruses and, reactivity and neutralization capability against SARS-CoV-2 among children in the Philippines
Authors: Sayama Yusuke , Okamoto Michiko , Saito Mayuko , Saito-Obata Mariko , Tamaki Raita , Joboco Christine Dahlia , Lupisan Socorro , Oshitani Hitoshi
Published: February 2023

Four endemic human coronaviruses (HCoV), HCoV-229E, HCoV-NL63, HCoV-HKU1, and HCoV-OC43, are closely related to SARS-CoV-2. These coronaviruses are known to infect humans living in temperate areas, including children under 5 years old; however, the seroprevalence of four HCoVs among children in tropical areas, including the Philippines, remains unclear. This study aimed to assess the prevalence of antibodies against four HCoVs and to determine the reactivity and neutralization of these antibodies against SARS-CoV-2 among children in the Philippines. A total of 315 serum samples collected from 2015 to 2018, before the emergence of SARS-CoV-2, in Biliran island, Philippines, were tested for the presence of antibodies against four HCoVs and SARS-CoV-2 using recombinant spike ectodomain proteins by IgG-enzyme-linked immunosorbent assay (ELISA). Reactivity to and neutralization of SARS-CoV-2 were also investigated. The seroprevalence of the four HCoVs was 63.8% for HCoV-229E, 71.4% for HCoV-NL63, 76.5% for HCoV-HKU1, and 83.5% for HCoV-OC43 by ELISA. Age group analysis indicated that seropositivity to all HCoVs reached 80% by 2–3 years of age. While 69/315 (21.9%) of the samples showed reactive to SARS-CoV-2, almost no neutralization against SARS-CoV-2 was detected using neutralization assay. Reactivity of antibodies against SARS-CoV-2 spike protein obtained by ELISA may not correlate with neutralization capability.
Electron tomography unravels new insights into fiber cell wall nanostructure; exploring 3D macromolecular biopolymeric nano-architecture of spruce fiber secondary walls
Authors: Fernando Dinesh , Kowalczyk Michael , Guindos Pablo , Auer Manfred , Daniel Geoffrey
Published: February 2023

Lignocellulose biomass has a tremendous potential as renewable biomaterials for fostering the “bio-based society” and circular bioeconomy paradigm. It requires efficient use and breakdown of fiber cell walls containing mainly cellulose, hemicellulose and lignin biopolymers. Despite their great importance, there is an extensive debate on the true structure of fiber walls and knowledge on the macromolecular nano-organization is limited and remains elusive in 3D. We employed dual-axis electron tomography that allows visualization of previously unseen 3D macromolecular organization/biopolymeric nano-architecture of the secondary S2 layer of Norway spruce fiber wall. Unprecedented 3D nano-structural details with novel insights into cellulose microfibrils (~ 2 nm diameter), macrofibrils, nano-pore network and cell wall chemistry (volume %) across the S2 were explored and quantified including simulation of structure related permeability. Matrix polymer association with cellulose varied between microfibrils and macrofibrils with lignin directly associated with MFs. Simulated bio-nano-mechanical properties revealed stress distribution within the S2 and showed similar properties between the idealized 3D model and the native S2 (actual tomogram). Present work has great potential for significant advancements in lignocellulose research on nano-scale understanding of cell wall assembly/disassembly processes leading to more efficient industrial processes of functionalization, valorization and target modification technologies.