bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards an educational case for social and political issues in the geography curriculum
Authors: Standish Alexander
Published: January 2024

Whilst social and political issues have an important role in the geography curriculum, the long-term erosion of the value and insularity of disciplinary knowledge in society and the curriculum has blurred the distinction between educational aims and political advocacy in classrooms. Increasingly, teachers, policymakers, and nongovernmental organizations (NGOs) instrumentalize the curriculum with respect to their political objectives, including climate change and social injustice. In taking an advocacy approach to pedagogy, they potentially undermine liberal educational objectives, including the development of autonomy and subjectification. Drawing on recent work in philosophy of education (e.g. Biesta; Van Poeck, and Östman) as well as social realist approaches to knowledge, I make a case for teaching about social and political issues on liberal educational grounds. Geography plays a key role in the school curriculum by providing a space for exploring the human condition through the study of people in contrasting environments and cultural systems. Here, we examine how geography teachers can handle issues in a morally careful way and navigate a line between advocacy and educational aims. One key difference examined is the need to treat students as subjects in their own right and to help develop skills of moral enquiry. In practice this means encouraging an open-ended approach, exploring topics (and the values underpinning them) from a range of perspectives, developing sensitivity to difference, and showing tolerance for ideas of which one disapproves. For students to develop agency and moral independence, they must learn how to think about social and political issues rather than be told what to think.
Investigation of polysaccharide from Radix Aconiti Lateralis Preparata (Fuzi) cardio protective effect on doxorubicin-induced chronic cardiotoxicity
Authors: Xiong Fang , Pu Lin , Wang Daibo , Peng Fu , Sun Luyao , Yu Qian , Xie Xiaofang , Peng Cheng
Published: January 2024

Objectives

Doxorubicin (DOX) is a chemotherapy drug for treating malignant tumours. However, its cardiotoxicity has limited its clinical application. The Radix Aconiti Lateralis Preparata, also known as Fuzi, has been used for treating heart failure. Nevertheless, there is still a deficiency of claeity as to whether the Fuzi polysaccharide (FPS) may prevent the side effects of DOX.

Methods

Mice were intraperitoneally administered DOX (15 mg/kg) to establish a mouse model of DOX-induced chronic cardiotoxicity (DICC). The mice were then administered different doses of FPS or enalapril intragastrically.

Key findings

In the DOX group, the activity of CK-MB and LDH and the content of NT-proBNP in serum of mice were increased. Myocardial infiltration of inflammatory cells and cytoplasmic vacuolation occurred. Levels of NLRP3, ASC, Caspase-1, IL-1β, IL-18, IL-6, and Bax increased, whereas levels of Bcl-2, STAT3, and p-STAT3 decreased. After administering FPS (100 mg/kg and 200 mg/kg), there were reductions in CK-MB activity and NT-proBNP levels. Cytoplasmic vacuolation, interstitial infiltration of blood, and infiltration of inflammatory cells were alleviated. The changes in protein expression mentioned above were reversed.

Conclusions

FPS can protect heart function and structure in DICC mice by inhibiting NLRP3 inflammasome-mediated pyroptosis and IL-6/STAT3 pathway-induced apoptosis.
On partial likelihood
Authors: Reid N
Published: January 2024

Partial likelihood, introduced in Cox (1975, Partial likelihood. Biometrika, 62(2),269–276), formalizes the construction of the inference function developed in Cox (1972, Regression models and life-tables (with discussion). Journal of the Royal Statistical Society Series B, 34(2),187–220) and referred there to as a conditional likelihood. Partial likelihood can also be viewed as a version of composite likelihood, a different example of which was studied in Cox, and Reid (2004, A note on pseudolikelihood constructed from marginal densities. Biometrika, 91(3),729–737). In this note, I describe the links between partial and composite likelihood, and the connections to profile, marginal, and conditional likelihood. Somewhat tangentially, two recent applications of the Cox proportional hazards model from the medical literature are briefly discussed, as they highlight the model’s ongoing relevance while also raising some more general questions about inference.
Efficacy and safety of a device that combines multipolar radiofrequency with pulsed electromagnetic field for the treatment of vulvovaginal atrophy: a randomized, sham-controlled trial
Authors: Nappi Rossella E , Martella Silvia , Tiranini Lara , Cucinella Laura , Palacios Santiago
Published: January 2024

Background

Vulvovaginal atrophy (VVA) negatively affects the sexual well-being and quality of life of postmenopausal women, yet it is underreported and undertreated.

Aim

The study sought to investigate the efficacy and safety of a nonablative, noncoagulative multipolar radiofrequency (RF) and pulsed electromagnetic field–based device (PEMF) in treatment of symptoms related to VVA.

Methods

Seventy-six women ≥19 years of age with symptoms associated with VVA were enrolled into this prospective, randomized, sham-controlled, multicenter clinical study. Subjects were randomized to receive 3 RF + PEMF treatments (active group) or sham treatments (sham group) delivered to vaginal tissue at monthly intervals. The Vaginal Health Index (VHI), along with the Female Sexual Function Index (FSFI), subject sexual satisfaction and vaginal laxity (VL) score, treatment-associated pain, and adverse events were assessed at 4 follow-up (FU) visits between 1 and 12 months after treatment.

Outcomes

Changes from baseline VHI, pH, FSFI, VL, and sexual satisfaction scores between the active and sham groups were compared before and after treatment.

Results

Mean VHI scores in the active group were significantly better compared with the sham group after treatment at all but the last FU visit (P < .001). A greater decrease in pH (active over sham) was seen at 1 and 4 months after treatment (P < .05). FSFI improvement was shown in the active group; however, it was not significantly better than sham improvement at all FU visits. Subject sexual satisfaction in the active group showed better improvement over sham at all FU visits (P < .05), while VL evaluations saw greater improvement in the active group at 4, 6, and 12 months posttreatment (P < .05). Treatment satisfaction was greater in the active group and pain was minimal in both groups. No serious adverse effects were reported.

Clinical Implications

As a noninvasive alternative to traditional surgical and topical procedures, 3 sessions of noninvasive combination RF/PEMF safely demonstrated improvement in symptoms related to VVA.

Strengths and Limitations

This study was strengthened by the randomized, sham-controlled design; large sample size; and extended FU period. The study assessments were decreased at later FU visits due to the global COVID pandemic, and this was a key limitation to the study.

Conclusion

Nonablative, noncoagulative multipolar RF/PEMF therapy was safe, improved symptoms associated with VVA, and improved female sexual function while yielding high subject satisfaction.
The identification of a novel compound heterozygous mutation in hereditary human coagulation factor VII deficiency following a bamboo leaf green snake bite
Authors: Qiu Chuanghua , Huang Chunxiu , Chen Xueyan , Gu Dayong
Published: January 2024

Hereditary factor VII (FVII) deficiency is an uncommon autosomal recessive disorder associated with mutations in the F7 gene, and laboratory investigations usually reveal isolated prolongation in prothrombin time (PT)/international normalized ratio (INR). Venom-induced consumptive coagulopathy (VICC) is distinguished by the activation of the coagulation pathway, which is triggered by procoagulant toxins in snake venom. Diagnosing snakebites in patients with hereditary FVII deficiency presents a challenge because prolonged time PT/INR is considered the most valuable diagnostic method for VICC. Therefore, it is possible that certain patients may not promptly receive an accurate diagnosis of hereditary FVII deficiency. We present a pedigree featuring hereditary FVII deficiency, which was diagnosed through Sanger sequencing, following a bamboo leaf green snake bite.
Diagnostic and prognostic value of circulating exosomal glypican-1 in pancreatic cancer: a meta-analysis
Authors: Qiao Zengyun , Wang Enbo , Bao Boyang , Tan Xiaodong , Chen Hailong , Wang Dong , Yuan Liu
Published: January 2024

Background

Pancreatic cancer (PC) is usually detected in the advanced stages. Liquid biopsy has become a revolutionary strategy for cancer diagnosis and prognosis prediction. This study aims to investigate the diagnostic and prognostic value of circulating exosomal glypican-1 (GPC-1) in PC.

Methods

We systematically searched relevant studies. For diagnostic accuracy, pooled sensitivity and specificity and the area under the summary receiver operating characteristic curve (AUC) were calculated. Regarding prognostic value, hazard ratios (HRs) and 95% CIs for overall survival (OS) were summarized by using a random-effects model.

Results

We found 8 studies that examined the diagnostic value of circulating exosomal GPC-1 in PC, and 3 studies that investigated its prognostic value. Pooled sensitivity and specificity were 0.88 (95% CI, 0.65-0.97) and 0.86 (95% CI, 0.72-0.94). The AUC was 0.93 (95% CI, 0.90-0.95). Prognostic analysis showed that higher levels of circulating exosomal GPC-1 were associated with poorer OS in PC patients, and the combined HR for OS was 4.59 (random-effects model, 95% CI = 1.17-18.03, P = .022). The results of both studies were robust and neither had publication bias.

Conclusion

Circulating exosomal GPC-1 may be used as a diagnostic and prognostic biomarker for PC. However, this result needs to be validated by further research using a larger sample size.
The abundance of dark matter haloes down to Earth mass
Authors: Zheng Haonan , Bose Sownak , Frenk Carlos S , Gao Liang , Jenkins Adrian , Liao Shihong , Liu Yizhou , Wang Jie
Published: January 2024

We use the voids-within-voids-within-voids (VVV) simulations, a suite of successive nested N-body simulations with extremely high resolution (denoted, from low to high resolution, by L0 to L7), to test the Press–Schechter (PS), Sheth–Tormen (ST), and extended Press–Schechter (EPS) formulae for the halo abundance over the entire mass range, from minihaloes of 10−6 M⊙, to cluster haloes of 1015 M⊙, at different redshifts, from z = 30 to the present. We find that at z = 0 and z = 2, ST best reproduces the results of L0, which has the mean cosmic density (overdensity δ = 0), at 1011−15 M⊙. The higher resolution levels (L1–L7) are biased underdense regions (δ < −0.6). The EPS formalism takes this into account since it gives the mass function of a region conditioned, in this case, on having a given underdensity. EPS provides good matches to these higher levels, with deviations ≲20 per cent, at 10−6−12.5 M⊙. At z ∼ 7−15, the ST predictions for L0 and the EPS for L1–L7 show somewhat larger deviations from the simulation results. However, at even higher redshifts, z ∼ 30, EPS fits the simulations well again. We confirm our results by picking more subvolumes from the L0 simulation, finding that our conclusions depend only weakly on the size and overdensity of the region. The good agreement of EPS with the higher level simulations implies that PS (or ST) gives an accurate description of the total halo mass function in representative regions of the universe.
Variable white dwarfs in TMTS: asteroseismological analysis of a ZZ Ceti star, TMTS J17184064+2524314
Authors: Guo Jincheng , Chen Yanhui , Yang Yonghui , Wang Xiaofeng , Lin Jie , Ma Xiao-Yu , Xi Gaobo , Mo Jun , Filippenko Alexei V , Brink Thomas G , Zong Weikai , Yan Huahui , Zhao Jingkun , Zeng Xiangyun , Chen Zhihao , Esamdin Ali , Guo Fangzhou , Iskandar Abdusamatjan , Jiang Xiaojun , Li Wenxiong , Liu Cheng , Shi Jianrong , Song Xuan , Wang Letian , Xiang Danfeng , Yan Shengyu , Zhang Jicheng
Published: January 2024

The Tsinghua University-Ma Huateng Telescope for Survey (TMTS) has been constantly monitoring the northern sky since 2020 in search of rapidly variable stars. To find variable white dwarfs (WDs), the TMTS catalogue is cross-matched with the WD catalogue of Gaia EDR3, resulting in over 3000 light curves of WD candidates. The WD TMTS J17184064+2524314 (hereafter J1718) is the second ZZ Ceti star discovered among these common sources. Based on the light curves from TMTS, follow-up photometric observations, and Transiting Exoplanet Survey Satellite, 10 periods and three combination periods are detected. A rotation period of 25.12 ± 0.18 h is derived, according to the identified rotational splitting. Our spectroscopic observation indicates that this WD belongs to DA type with Teff = 11 670 ± 604 K, log g = 8.16 ± 0.36, M = 0.70 ± 0.23 M⊙, and age = 0.51 ± 0.34 Gyr. Based on core-parametrized asteroseismological model grids (≥14 million), we derive the best-fitting solution of Teff = 11 640 ± 20 K, log g = 8.267 ± 0.008, and M = 0.750 ± 0.005 M⊙ for J1718, consistent with the spectral fitting results. For this WD, the corresponding carbon and oxygen abundances in the core are 0.43 and 0.57, respectively. The distance derived from the intrinsic luminosity given by asteroseismology is 64 ± 15 pc, in accord with the distance of 70.1 ± 0.2 pc from Gaia DR3 within the uncertainties.
Finnish perspectives on the business of electricity distribution
Authors: Collan Mikael
Published: January 2024

The profits of the Finnish industry of electricity distribution are driven by a rate of return regulation model. Changes in the model caused a remarkable jump in distribution system operator (DSO) profits. The model rewards large costs and gives the DSOs an incentive to build an extremely weatherproof network, to overinvest. Allowed exceptions to lower costs of network construction may not be fully utilized. Risks connected to demographic changes may influence the forecasted network investment profitability. The emergence of energy communities may also affect the DSOs. There may be differences between public and private DSOs´ financial behavior. The ability of stakeholders to affect regulatory decisions is asymmetric.
On the Writtenness of Political Theory
Authors: Gaonkar Dilip Parameshwar , Topper Keith
Published: January 2024

This volume of essays brings together a group of distinguished and emerging scholars in political theory, philosophy, communication, literature, history, and other areas of the humanities who share an interest in the rhetorical character of political thought and discourse. The essays focus on a wide range of issues regarding the pivotal function of rhetoric in the history of political thought and contemporary political theory. These include, but are not limited to, questions about the performative and constitutive dimensions of political language; the role of affect and emotion in political life; the relationship between logic and style in political argument; the work of persuasion in politics; the play of contingency, experience, and prudence in political judgment; and the rhetorical structure of political texts as evinced in the unavoidable gap between what they say and what they do.
Computer-Supported Collaborative Learning
Authors: Chan Carol , Chen Gaowei , Chen Bodong
Published: January 2024

This chapter discusses the theory, design, and technology of computer-supported collaborative learning (CSCL) for promoting collaborative inquiry and productive discourse, illustrated with several major CSCL research traditions. CSCL, which emerged in the 1990s as an interdisciplinary field, examines how collaboration is supported by technology, focusing on social interactions and computational artifacts. CSCL goes beyond individual learning, emphasizing group cognition and the coordinated processes through which learners negotiate and co-construct shared understandings for knowledge construction. This chapter includes seven sections: (1) Introduction, (2) What is CSCL and theoretical perspectives, (3) CSCL technological affordances, (4) Designing CSCL environments and major research programs, (5) Methodology and analysis of collaboration, (6) Emerging themes and design implications, and (7) Future research directions. After introducing the distinctive features of CSCL, the chapter discusses the theoretical underpinnings of CSCL, including socio-cognitive, socio-cultural, and knowledge-creation perspectives, as well as the technological affordances that inform the design of collaborative learning. Several major CSCL traditions are discussed, ranging from structured to open-ended learning environments, including Collaborative Scripting, Metacognition and Regulation, Argumentation, Dialogism, and Knowledge Building, with a focus on theory-design-technology integration. This chapter also explores the analysis of collaboration and CSCL methods and new technologies, including learning analytics, for examining and supporting collaboration. CSCL is a diverse field, and comparative analyses of these different long-standing research traditions highlight emerging theoretical and design implications. Future directions point to different provocations for developing expanded frameworks and designs that embrace diversity and leverage technological advances to support collaboration, innovation, and creativity.
Tracking Garnet Dissolution Kinetics in 3D Using Deep Learning Grain Shape Classification
Authors: Hartmeier Philip , Lanari Pierre , Forshaw Jacob B , Markmann Thorsten A
Published: January 2024

The kinetics of fluid-driven metamorphic reactions are challenging to study in nature because of the tendency of metamorphic systems to converge towards chemical equilibrium. However, in cases where mineral textures that reflect incomplete reactions are preserved, kinetic processes may be investigated. Atoll garnet, a texture formed by the dissolution of a garnet’s core, has been described in 2D from thin sections of rocks worldwide. Quantifying the extent of this dissolution reaction requires a sample-wide examination of hundreds of individual grains in 3D. In this study, we quantified the distribution of atoll garnet using micro-computed tomography and grain shape analysis. A convolutional neural network was trained on human-labeled garnet grains for automated garnet classification. This approach was applied to a retrogressed mafic eclogite from the Zermatt–Saas Zone (Western Alps). Pervasive atoll-like resorption preferentially affected the larger porphyroblasts, suggesting that compositional zoning patterns exert a first-order control on dissolution rates. A kinetic model shows that the reactivity of metastable garnet to form atolls is favored at pressure–temperature conditions of 560 ± 30°C and 1.6 ± 0.2 GPa. These conditions coincide with the release of water when lawsonite breaks down during the exhumation of mafic eclogites. The model predicts dissolution rates that are three to five times faster for the garnet core than for the rim. This study shows that deep learning algorithms can perform automated textural analysis of crystal shapes in 3D and that these datasets have the potential to elucidate petrological processes, such as the kinetics of fluid-driven metamorphic reactions.
Enhancing international collaboration in science, technology, and innovation to achieve sustainable development goals
Authors: Dominguez Lacasa Iciar , Molina Vogelsang Manuel
Published: January 2024

This paper develops a framework for policymakers supporting sustainable development through international collaboration in science, technology, and innovation (STI). The approach can be applied to derive the national policy strategy for international collaboration in STI. The contribution focuses on the case of Germany in the field of food and agriculture. Accordingly, considering Germany’s current strategic approach for international collaboration in STI, an evidence-based tool for priority setting in the selection of potential partners and technology fields is developed and implemented. More specifically, the approach assesses the opportunity environment for international STI collaboration of Germany with potential partners using patent and economic indicators to capture technological capabilities, technological demand, economic relevance of food, and agriculture in national economies as well as technological and export specialization in food and agriculture. The results present policy strategies enhancing sustainable development.
The Evolution of Multiple Color Mechanisms Is Correlated with Diversification in Sunbirds (Nectariniidae)
Authors: Nicolaï Michaël P J , Van Hecke Bert , Rogalla Svana , Debruyn Gerben , Bowie Rauri C K , Matzke Nicholas J , Hackett Shannon J , D’Alba Liliana , Shawkey Matthew D
Published: January 2024

How and why certain groups become speciose is a key question in evolutionary biology. Novel traits that enable diversification by opening new ecological niches are likely important mechanisms. However, ornamental traits can also promote diversification by opening up novel sensory niches and thereby creating novel inter-specific interactions. More specifically, ornamental colors may enable more precise and/or easier species recognition and may act as key innovations by increasing the number of species-specific patterns and promoting diversification. While the influence of coloration on diversification is well-studied, the influence of the mechanisms that produce those colors (e.g., pigmentary, nanostructural) is less so, even though the ontogeny and evolution of these mechanisms differ. We estimated a new phylogenetic tree for 121 sunbird species and combined color data of 106 species with a range of phylogenetic tools to test the hypothesis that the evolution of novel color mechanisms increases diversification in sunbirds, one of the most colorful bird clades. Results suggest that: (1) the evolution of novel color mechanisms expands the visual sensory niche, increasing the number of achievable colors, (2) structural coloration diverges more readily across the body than pigment-based coloration, enabling an increase in color complexity, (3) novel color mechanisms might minimize trade-offs between natural and sexual selection such that color can function both as camouflage and conspicuous signal, and (4) despite structural colors being more colorful and mobile, only melanin-based coloration is positively correlated with net diversification. Together, these findings explain why color distances increase with an increasing number of sympatric species, even though packing of color space predicts otherwise.
Catch-Up Growth and Inter-industry Productivity Spillovers: Evidence from Trade Data
Authors: Bolhuis Marijn A
Published: January 2024

Where and when does export-led growth work? This paper estimates the importance of inter-industry productivity spillovers for the export-led growth of developing countries. My empirical strategy is based on a standard quantitative trade model that features sector-level gravity in trade flows. Applying the framework to four decades of trade data, I find clear evidence of spillovers, which are larger for skill-intensive sectors. The estimates imply that patterns of sectoral specialization play a quantitatively important role in accounting for the slow convergence of labor productivity in tradable sectors. Quantitative exercises suggest that export-led growth works for poorer countries with an initial comparative advantage in manufacturing, as these countries can use foreign demand from richer countries to reallocate labor towards sectors with high spillovers.
A Western Pocahontas: Myth, Reality, and Memorialization for Spotted Tail’s Daughter, Mni-Akuwin
Authors: Rankin Charles E
Published: January 2024

In March 1866, the Sicangu (Brulé) Lakota chief Spotted Tail brought the body of his seventeen- or eighteen-year-old daughter, Mni-Akuwin, to Fort Laramie. She had died somewhere in the Powder River country. Before she died, she had asked her father to bury her among the Whites at the fort. Her subsequent scaffold burial in the post cemetery was an unusual mix of military display, Christian rites, and Lakota traditions; and the events surrounding it became a dramatic episode in the story of Native-White relations and western settlement. Almost 140 years later she was memorialized at the fort, a National Park Service site, as a symbol of racial reconciliation.

The story of Mni-Akuwin has been told and retold many times through the years, often as a romantic tragedy comparable to the story of early Jamestown and the much-celebrated Pocahontas. The two Native women had a surprising amount in common, including what we know and don’t know about them, what has been ascribed to their motives, and how they have been championed as defenders of European colonists and non-Native settlers. Indian princess mythology, with its insistence on innocence, purity, romantic purpose, and tragedy, has been vital to the persistence of this view—a perspective that has often put reconciliation in the service of White supremacy, dispossession, and rejection of Native culture.

As the Mni-Akuwin story illustrates, reconciliation can be problematic.
Effects of Background Noise and Linguistic Violations on Frontal Theta Oscillations During Effortful Listening
Authors: Mohammadi Yousef , Graversen Carina , Manresa José Biurrun , Østergaard Jan , Andersen Ole Kæseler
Published: January 2024

Objectives:

Background noise and linguistic violations have been shown to increase the listening effort. The present study aims to examine the effects of the interaction between background noise and linguistic violations on subjective listening effort and frontal theta oscillations during effortful listening.

Design:

Thirty-two normal-hearing listeners participated in this study. The linguistic violation was operationalized as sentences versus random words (strings). Behavioral and electroencephalography data were collected while participants listened to sentences and strings in background noise at different signal to noise ratios (SNRs) (−9, −6, −3, 0 dB), maintained them in memory for about 3 sec in the presence of background noise, and then chose the correct sequence of words from a base matrix of words.

Results:

Results showed the interaction effects of SNR and speech type on effort ratings. Although strings were inherently more effortful than sentences, decreasing SNR from 0 to –9 dB (in 3 dB steps), increased effort rating more for sentences than strings in each step, suggesting the more pronounced effect of noise on sentence processing that strings in low SNRs. Results also showed a significant interaction between SNR and speech type on frontal theta event-related synchronization during the retention interval. This interaction indicated that strings exhibited higher frontal theta event-related synchronization than sentences at SNR of 0 dB, suggesting increased verbal working memory demand for strings under challenging listening conditions.

Conclusions:

The study demonstrated that the interplay between linguistic violation and background noise shapes perceived effort and cognitive load during speech comprehension under challenging listening conditions. The differential impact of noise on processing sentences versus strings highlights the influential role of context and cognitive resource allocation in the processing of speech.
Five Retained Soft Contact Lenses in the Upper Fornix: A Case Report in a Patient with Hemifacial Atrophy
Authors: Zhao Minghao , Gu Tianyi , Teng Li , Zhang Chao
Published: January 2024

The displacement of a lost contact lens into the upper fornix is an uncommon occurrence. This case report presents a rare incidence wherein a patient diagnosed with hemifacial atrophy was found to have concealed five soft contact lenses within the left upper fornix during autologous fat injection into the retrobulbar space.
The investigation of dysregulated visual perceptual organization in adults with autism spectrum disorders with phase-amplitude coupling and directed connectivity
Authors: Sun Limin
Published: January 2024

Phase-amplitude coupling (PAC) has been used as a powerful tool to understand the mechanism underlying neural binding by investigating neural synchrony across different frequency bands. This study examined the possibility that dysregulated alpha-gamma modulation may be crucially involved in aberrant brain functioning in autism spectrum disorder (ASD). Magnetoencephalographic data were recorded from 13 adult participants with ASD and 16 controls. The time-coursed sources averaged over a primary visual area 1 and fusiform gyrus area were reconstructed with the minimum-norm estimate method. The alpha-gamma PAC was further calculated based on these sources. The statistical analysis was implemented based on the PAC and directed asymmetry index. The results showed the hyper-activity coupling for ASD at the no-face condition and revealed the importance of alpha-gamma phase modulation in detecting a face. Our data provides novel evidence for the role of the alpha-gamma PAC and suggests that the globe connectivity may be more critical during visual perception.
Data-driven AI system for learning how to run transcript assemblers
Authors: Shen Yihang , Yan Zhiwen , Kingsford Carl
Published: January 2024

We introduce AutoTuneX, a data-driven, AI system designed to automatically predict optimal parameters for transcript assemblers — tools for reconstructing expressed transcripts from the reads in a given RNA-seq sample. AutoTuneX is built by learning parameter knowledge from existing RNA-seq samples and transferring this knowledge to unseen samples. On 1588 human RNA-seq samples tested with two transcript assemblers, AutoTuneX predicts parameters that resulted in 98% of samples achieving more accurate transcript assembly compared to using default parameter settings, with some samples experiencing up to a 600% improvement in AUC. AutoTuneX offers a new strategy for automatically optimizing use of sequence analysis tools.
Nephrectomy and high-salt diet inducing pulmonary hypertension and kidney damage by increasing Ang II concentration in rats
Authors: Jiang Qian , Yang Qifeng , Zhang Chenting , Hou Chi , Hong Wei , Du Min , Shan Xiaoqian , Li Xuanyi , Zhou Dansha , Wen Dongmei , Xiong Yuanhui , Yang Kai , Lin Ziying , Song Jingjing , Mo Zhanjie , Feng Huazhuo , Xing Yue , Fu Xin , Liu Chunli , Peng Fang , Li Bing , Lu Wenju , Yuan Jason X.-J. , Wang Jian , Chen Yuqin
Published: January 2024

Background

Pulmonary hypertension (PH) is a common complication in patients with chronic kidney disease (CKD), affecting prognosis. However, the pathogenesis is not clear, and the lack of a stable animal model is a significant factor.

Methods

In this study, a rat model of chronic kidney disease with pulmonary hypertension (CKD-PH) was developed through 5/6 nephrectomy combined with a high-salt diet. The model’s hemodynamics and pathological changes in multiple organs were dynamically assessed. Lung tissues and serum were collected from the model rats to measure the expression of ACE2, the expression levels of vascular active components related to the renin-angiotensin-aldosterone system (RAAS), and changes in the serum metabolic profile of the model.

Results

After 14 weeks post-surgery, the CKD-PH rat model exhibited significant changes in hemodynamic parameters indicative of pulmonary arterial hypertension, along with alterations such as right ventricular hypertrophy. However, no evidence of pulmonary vascular remodeling was observed. An imbalance in the renin-angiotensin-aldosterone system was identified in the CKD-PH rat models. Downregulation of ACE2 expression was observed in pulmonary tissues. The serum metabolic profile of the CKD-PH rat models showed distinct differences compared to the sham surgery group.

Conclusions

The development of pulmonary arterial hypertension in CKD-PH rats may be primarily attributed to the disruption of the renin-angiotensin-aldosterone system (RAAS), coupled with a decrease in ACE2 expression in pulmonary vascular endothelial tissues and metabolic disturbances.
The Effect of Sensory Reweighting on Postural Control and Cortical Activity in Parkinson’s Disease
Authors: Sadeghi Maryam , Bristow Thomas , Fakorede Sodiq , Liao Ke , Palmer Jacqueline A. , Lyons Kelly E. , Pahwa Rajesh , Huang Chun-Kai , Akinwuntan Abiodun , Devos Hannes
Published: January 2024

Aims

Balance requires the cortical control of visual, somatosensory, and vestibular inputs. The aim of this cross-sectional study was to compare the contributions of each of these systems on postural control and cortical activity using a sensory reweighting approach between participants with Parkinson’s disease (PD) and controls.

Methods

Ten participants with PD (age: 72 ± 9; 3 women; Hoehn & Yahr: 2 [1.5 – 2.50]) and 11 controls (age: 70 ± 3; 4 women) completed a sensory organization test in virtual reality (VR-SOT) while cortical activity was being recorded using electroencephalography (EEG). Conditions 1 to 3 were completed on a stable platform; conditions 4 to 6 on a foam. Conditions 1 and 4 were done with eyes open; conditions 2 and 5 in a darkened VR environment; and conditions 3 and 6 in a moving VR environment. Linear mixed models were used to evaluate changes in center of pressure (COP) displacement and EEG alpha and theta/beta ratio power between the two groups across the postural control conditions. Condition 1 was used as reference in all analyses.

Results

Participants with PD showed greater COP displacement than controls in the anteroposterior (AP) direction when relying on vestibular input (condition 5; p<0.0001). The mediolateral (ML) COP sway was greater in PD than in controls when relying on the somatosensory (condition 2; p = 0.03), visual (condition 4; p = 0.002), and vestibular (condition 5; p < 0.0001) systems. Participants with PD exhibited greater alpha power compared to controls when relying on visual input (condition 2; p = 0.003) and greater theta/beta ratio power when relying on somatosensory input (condition 4; p = 0.001).

Conclusions

PD affects reweighting of postural control, exemplified by greater COP displacement and increased cortical activity. Further research is needed to establish the temporal dynamics between cortical activity and COP displacement.
Cytotoxic CD4+T cells in the bone marrow compromise healthy ageing by enhancing granulopoiesis
Authors: Gabandé-Rodríguez Enrique , Soto-Heredero Gonzalo , Carrasco Elisa , Anerillas Carlos , Escrig-Larena José Ignacio , Delgado-Pulido Sandra , Francos-Quijorna Isaac , Gómez de las Heras Manuel M. , Fernández-Almeida Álvaro , Blanco Eva María , Winand-Osete Elia , Zorita Virginia , Martínez-Cano Jorge , Garrido Amanda , de Cabo Rafael , Mañes Santos , Gorospe Myriam , Mittelbrunn María
Published: January 2024

Neutrophils are the most abundant leukocytes in the blood, with numbers further increasing with age. Despite their essential role as a primary line of defense, neutrophils can contribute to tissue damage and age-related diseases1and a high neutrophil-to-lymphocyte ratio predicts all causes of mortality in the elderly2–5. However, the precise mechanisms driving enhanced neutrophil generation during ageing remain poorly understood. Here, we show that a subset of CD4+T cells with a cytotoxic phenotype (CD4+CTLs) producing the chemokine CCL5 and harbouring dysfunctional mitochondria, infiltrate the bone marrow and induce granulopoiesis in aged mice. During ageing, hematopoietic stem cells upregulate CCR5, the primary receptor for CCL5, and its deficiency limits the T cell-mediated induction of granulopoiesis and neutrophil output. Treatment with the FDA-approved CCR5 inhibitor Maraviroc decreases granulopoiesis and lowers the levels of circulatory and tissue-infiltrating neutrophils, ameliorating multiple ageing biomarkers and improving functional outcomes in aged mice. These findings suggest that age-associated alterations in T cells reduce health outcomes by remodelling the bone marrow niche and enhancing neutrophil generation. Consequently, interventions to disrupt the interplay between T cells and hematopoietic stem cells hold substantial therapeutic potential to ameliorate age-associated diseases.
Persister cancer cells are characterized by H4K20me3 heterochromatin that defines a low inflammatory profile
Authors: Ramponi Valentina , Richart Laia , Kovatcheva Marta , Stephan-Otto Attolini Camille , Capellades Jordi , Lord Alice E. , Yanes Oscar , Ficz Gabriella , Serrano Manuel
Published: January 2024

Anti-cancer therapies may induce proliferative arrest in cancer cells in the form of senescence or drug-tolerant persistency, the latter being a reversible arrest with similarities to embryonic diapause. Here, we use mTOR/PI3K inhibition to develop and characterize a model of persistency/diapause-like arrest in human cancer cells of various origins. We show that persister and senescent cancer cells share an expanded lysosomal compartment and hypersensitivity to BCL-XL inhibition. However, persister cells do not exhibit other features of senescence, such as the loss of Lamin B1, senescence-associated b-galactosidase activity, and an inflammatory phenotype. Compared to senescent cells, persister cells have a profoundly diminished senescence-associated secretory phenotype (SASP), low activation of interferon signaling pathways and lack upregulation of MHC-I presentation. Based on a genome-wide CRISPR/Cas9 screen performed in diapause mouse embryonic stem cells (mESC), we discover that persister human cancer cells are hypersensitive to the inhibition of one-carbon metabolism. This finding led us to uncover that the repressive heterochromatic mark H4K20me3 is enriched at promoters of SASP and interferon response genes in persister cells, but not in senescent cells. Collectively, we define novel features and vulnerabilities of persister cancer cells and we provide insight into the epigenetic mechanisms underlying their low inflammatory and immunogenic activity.
Self-incompatibility based functional genomics for rapid phenotypic characterization of seed metabolism genes
Authors: Azeez Abdul , Bates Philip D.
Published: January 2024

Reverse-genetic characterization of plant gene function through technologies such as CRISPR/Cas, RNAi, or gene overexpression requires the ability to efficiently transform the plant species of interest. However, efficient transformation systems are not available for most plant species.Physaria fendleriis an oilseed plant valued for its unusual hydroxylated fatty acids (HFA, e.g. lesquerolic acid) that accumulates up to 60% of seed oil and is a non-toxic alternative to castor (Ricinus communis) seeds as a source for HFA for the chemical industry. Domestication and improvement ofP. fendleriseed oil requires characterization of genes involved in developing seed metabolism. Tissue culture-based transformation ofP. fendleriis laborious, low-efficiency, and time-consuming (T1 ∼18 months). Additionally,P. fendleriis self-incompatible requiring laborious hand pollination for propagation and seed collection from transgenic lines. We developed a rapid virus-induced gene silencing (VIGS) method to characterize genes within developing seeds. Identification of the self-incompatibility mechanisms inP. fendleriallowed the use of self-compatibility as a novel visual selectable marker by co-targeting the gene of interest (GOI) with the self-incompatibility gene S-locus receptor kinase (SRK). Seeds develop without cross-pollination from silenced SRK and each of those seeds contain the GOI silenced, allowing rapid phenotypic characterization of the seeds in the first generation. Through this methodology we confirmed the in vivo function of two key genes (FAH12, FAE1) involved in lesquerolic acid production. Thus, this self-compatibility based functional genomics approach is a rapid methodology for in vivo reverse-genetic gene characterization in self-incompatible plants.
Integrated Plankton and Trace Metal Analysis as Indicators of Organic Pollution Threats from Carp-Cultured Ponds to Adjacent Ecosystems: Implications for Sustainability
Authors: Mukherjee Manasi , Jarzembowski Paweł , Polechoński Ryszard , Proćków Jarosław
Published: January 2024

Stawy Milickie (Milicz Ponds) is a natural reserve that has a great ecological importance as a Ramsar site and economic importance as one of the largest carp breeding centres in Europe. Continuous anthropogenic pressure on these large ecosystems can lead to a high disturbance on its natural ecology and sustainability. Phytoplankton, one of the most important indicators of any anthropogenic load, especially organic pollution have been studied in the present study. This is the first work ever from Milicz ponds, wherein the diversity, community structure and seasonal variability of phytoplankton with respect to changes in physicochemical parameters and trace metals have been studied. Periodic samples of water and phytoplankton were collected from four selected ponds of various sizes from October 2018 to September 2019. Of the four selected ponds one was unused for carp cultivation. The study reports the presence of 147 phytoplankton species in nine distinct taxonomic groups. The Genera based Algal pollution index indicated presence of organic pollution in both noncultured pond and carp-cultured pond. The heavy metals detected in the concentration order of Cd>Mn>Fe>Zn>Cu>Pb remained much higher than the safe limits of freshwater aquaculture ponds. The probable sources of these pollutants were identified as artificial feed used in the cultivation of carp and inundation from the river basin. This study emphasizes the urgent need for continuous qualitative and quantitative assessment and monitoring of water parameters, including plankton, in these ponds. This study highlights how the structure of microplankton communities, in conjunction with heavy metal analysis, serves as indicators of the spread of organic pollution in non-cultivated aquaculture environments. It strongly advocates for implementing sustainable measures to safeguard this vital ecosystem.
DeepGOMeta: Predicting functions for microbes
Authors: Tawfiq Rund , Niu Kexin , Hoehndorf Robert , Kulmanov Maxat
Published: January 2024

Analyzing microbial samples remains computationally challenging due to their diversity and complexity. The lack of robustde novoprotein function prediction methods exacerbates the difficulty in deriving functional insights from these samples. Traditional prediction methods, dependent on homology and sequence similarity, often fail to predict functions for novel proteins and proteins without known homologs. Moreover, most of these methods have been trained on largely eukaryotic data, and have not been evaluated or applied to microbial datasets. This research introduces DeepGOMeta, a deep learning model designed for protein function prediction, as Gene Ontology (GO) terms, trained on a dataset relevant to microbes. The model is validated using novel evaluation strategies and applied to diverse microbial datasets. Data and code are available athttps://github.com/bio-ontology-research-group/deepgometa
Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients
Authors: Santos Renato , Moreno-Torres Víctor , Pintos Ilduara , Corral Octavio , de Mendoza Carmen , Soriano Vicente , Corpas Manuel
Published: January 2024

Despite advances in identifying genetic markers associated to severe COVID-19, the full genetic characterisation of the disease remains elusive. This study explores the use of imputation in low-coverage whole genome sequencing for a severe COVID-19 patient cohort. We generated a dataset of 79 imputed variant call format files using the GLIMPSE1 tool, each containing an average of 9.5 million single nucleotide variants. Validation revealed a high imputation accuracy (squared Pearson correlation ≈0.97) across sequencing platforms, showing GLIMPSE1’s ability to confidently impute variants with minor allele frequencies as low as 2% in Spanish ancestry individuals. We conducted a comprehensive analysis of the patient cohort, examining hospitalisation and intensive care utilisation, sex and age-based differences, and clinical phenotypes using a standardised set of medical terms developed to characterise severe COVID-19 symptoms. The methods and findings presented here may be leveraged in future genomic projects, providing vital insights for health challenges like COVID-19.
Extraction of naringin dihydrochalcone and its effect on reducing blood lipid levels in vitro
Authors: Tian Mu-yang , Li Si-qi , Qi Jing-wen , Zhang Lei , Yu Xiao-lei
Published: January 2024

Response surface methodology (RSM) was used to optimize the extraction process of naringin. The central component design included three parameters of extraction, namely, temperature (X1), solid-liquid ratio (X2), and extraction time (X3). The optimum extraction temperature was 67℃; the ratio of material to liquid was 54:1mL/g, and the extraction time was 2.8h. According to the best extraction conditions, naringin was processed to verify the accuracy of the model. Five parallel experiments were set up, and a yield of 32.48 mg/g naringin was obtained, that was equivalent to the predicted yield of 32.56 mg/g. Naringin was purified to obtain naringin-refined products using DM101 macroporous adsorption resin. Naringin dihydrochalcone was synthesized following catalytic hydrogenation of purified naringin. The structures of naringin and naringin dihydrochalcone were determined via Fourier infrared spectrometer and nuclear magnetic resonance spectrometry. Evaluate the ability of naringin dihydrochalcone to bind with glycine bile sodium and bovine bile sodium by simulating the gastrointestinal environment in vitro. Further focusing on HepG2 cells, a high cholesterol induced high-fat HepG2 cell model was established. We measured the effects of different concentrations of naringin dihydrochalcone on intracellular lipids in denatured HepG2 cells and further validated the lipid-lowering effect of naringin at the cellular level. The results showed that naringin dihydrochalcone has potential application in functional foods for lowering blood lipids.