bluuebunny/crossref_metadata_2025 huggingface dataset:
Feature selection in single-cell RNA sequencing data: a comprehensive evaluation
Authors: Paplomatas Petros , Lazaros Konstantinos , Dimitrakopoulos Georgios N. , Vrahatis Aristidis
Published: September 2024

Single-cell RNA sequencing (scRNA-seq) has revolutionized biological and medical research, providing unique insights into the intricate cell-type compositions within various tissues. Unlike bulk RNA sequencing, scRNA-seq allows for examining gene expression at the individual cell level, revealing cellular heterogeneity and identifying rare cell types. However, the high dimensionality and inherent noise in scRNA-seq data pose significant analytical challenges. This study focuses on dimensionality reduction and cell-type identification in scRNA-seq data analysis. We developed the GenesRanking package, which offers 20 techniques for dimensionality reduction, including filter-based and embedding machine learning–based methods. By integrating feature selection methods from both statistics and machine learning, we provide a robust framework for improving data interpretation. Our comprehensive evaluation across five diverse scRNA-seq datasets demonstrates that although some methods show consistent performance, the technique should be chosen according to specific datasets for obtaining optimal results. Our findings underscore the enduring necessity for further refinement and continuous innovation in the field of scRNA-seq analysis, aiming to enhance the accuracy of cell-type identification and improve overall data interpretation.
Levinas ve Derrida’da Dostluk
Authors: Aydoğan Emine
Published: September 2024

Bu çalışmada Çağdaş felsefenin iki önemli siması olan Fransız düşünürler Emmanuel Levinas ve Jacques Derrida’nın dostluk meselesine yaklaşımları ele alınmaya çalışılacaktır. Felsefe ile yakın bir bağı olan bir kavram olarak dostluk, İlkçağdan Çağdaş felsefeye her dönem bazı problematikler çerçevesinde sürekli yinelenen bir tema olarak karşımıza çıkar. Özellikle Çağdaş felsefede yaşam deneyiminin temel gönderenlerinden biri olarak dışımızdakileri, başkalarını hatırlatan ve bu anlamda ben-öteki problematiği çerçevesinde çokça tartışılan bir temadır. Dolayısıyla dostluk teması için bu iki ismin seçilmesi tesadüf değildir. Öznelerarasılığın ve ötekinin yeniden tartışılmaya başlandığı Kıta Avrupası Felsefesinde, ihmale uğramış dostluk meselesi de bu isimlerle birlikte tekrar felsefe sahnesine taşınmıştır. Bu anlamda iki isimden ilk olarak öteki filozofu olarak görülen ve felsefeye etikle başlangıç yapan Levinas’ın ötekiye öncelik verirken dostluk meselesindeki tavrı ve dostlukla ilgili yaklaşımlara yön verip vermediği tartışmaya açılacaktır. Diğer taraftan Dostluk Politikası başlıklı eseriyle öne çıkan Derrida’nın dostluk meselesini yine öteki üzerinden kimlik ve farklılık problemleriyle nasıl ilişkilendirdiği açıklanmaya çalışılacaktır.
Ockham’s Flying Soul An Argument Against Henry of Ghent on the Powers of the Soul
Authors: Bobovnik Nena
Published: September 2024

Medieval thinkers unanimously believed a human soul has various powers. Yet, the latter point is also nearly the only one they agreed upon. In the paper, I focus on two contrary opinions maintained by Henry of Ghent and William of Ockham. Whereas Henry of Ghent held powers of the soul are defined with respect to the activities they are powers-for, Ockham refuted such a contention. To make his point Ockham launches a thought experiment: if God created an intellective soul without creating anything else, wouldn’t the powers in this soul still exist fully? Upon succinctly presenting Henry of Ghent’s view on the powers of the soul, I provide a detailed analysis of Ockham’s counterargument. I argue Henry could still reply to Ockham’s rebuttal, and show how the latter bares a remote resemblance to Avicenna’s flying man argument.
The parodic character of posthistory
Authors:   Lobachevsky State University of Nizhny Novgorod, Fatenkov Aleksey
Published: September 2024

The philosophical understanding of the end of human history has a long tradition and, de­spite many different interpretations, gravitates towards two opposite versions. The opti­mistic version is symbolically presented in G.W.F. Hegel’s concept, while the pessimistic one can be found in the latest conceptual essays of the “late” V.S. Solovyov. This text is structured in a tonality that partly echoes that of the latter. Methodologically, it is based on the subject-centered strategy of existential philosophy and the variation of dialectics associated with it. Thematically, it aims to reflect on the state of posthistory, a term that, according to the author, by virtue of its prefix “post-”, captures not only temporal shades of meaning (“after”), but also parodic ones. Every post-something parodies its own root, speculatively enhancing some meaningful aspects of it and hiding others. Posthistory di­minishes the social for the sake of the socio-technical and hypertrophies the political, which is already dominant in the historical process and its standard perception. The author focuses on the intellectual support of well-defined trends in modern social life and criti­cally analyzes theoretical constructions that fully (B. Latour) or partially (J.O. de La Met­trie) legitimize the reduction of the social to the socio-technical and subordinate, directly (K. Schmitt) or indirectly (S. Newman), the social to the political. While recognizing the weakness of modern society and agreeing with the importance of individual resistance to the negative tendencies that dominate it, the author emphasizes the positive signifi­cance of the individual’s self-identity – in contrast to post-structuralism and post-anar­chism – resulting from the individual’s power over himself. At the same time, the indivi­dual effort is considered insufficient to address the human condition. The prognosis for the posthistorical future is therefore pessimistic. But fortunately, earthly life – human life itself – is not limited to history and posthistory.
Information concepts of consciousness: D.I. Dubrovsky and D. Chalmers
Authors:   Lomonosov Moscow State University, Zhudina Anastasia
Published: September 2024

The article is devoted to the study of the grounds for comparative analysis of the ideas of D.I. Dubrovsky and representatives of analytic philosophy of mind, in particular, D. Chalmers. D.I. Dubrovsky began to develop the information concept of consciousness several decades be­fore analytic philosophers. However, a conceptual work is necessary to establish thematic unity. D.I. Dubrovsky is known for his critical attitude to analytic philosophy of mind. The article explores the grounds for D.I. Dubrovsky’s criticism of the concepts of philosophers of mind, in particular, D. Chalmers. Constructive criticism is possible provided that the terms of the concept being criti­cized are understood. The main question of the article concerns the extent to which the terms of Dubrovsky’s theory are similar in meaning to the terms of analytic philosophy of consciousness, in particular, the concept of D. Chalmers. The possibility of “translating” the terms of D.I. Dub­rovsky’s theory into the language of philosophy of mind in order to include his ideas in the field of research of analytic philosophers is evaluated. Since D.I. Dubrovsky’s position was formed in the 1960s, the historical and philosophical context is taken into account when considering the pro­visions of his theory. Some provisions of the philosophy of dialectical materialism are given, which may allow modern thinkers who are not sufficiently familiar with Soviet philosophy to understand D.I. Dubrovsky’s ideas more deeply. The article analyzes the understanding of D.I. Dubrovsky and D. Chalmers of such terms as “mind/consciousness”, “qualia”, “information”, “materialism/physica­lism”, which form the basis of the concepts of each of the philosophers. It is demonstrated that the same terms conceal different contents, which leads to mutual misunderstanding of the parties – D.I. Dubrovsky and representatives of analytic philosophy of mind – which is aggravated by the dif­ference of methodological approaches. It is argued that D.I. Dubrovsky’s theory in the context of ana­lytic philosophy of mind represents a variant of the identity theory and can allow to solve easy prob­lems, while taking into account the specificity of first-person consciousness.
Emile Boutroux on Kant’s Philosophy
Authors:   Institute of Philosophy, Russian Academy of Sciences, Blauberg Irina
Published: September 2024

This article precedes the publication of the Russian translation of the work by Emile Boutroux, a famous French spiritualist philosopher, epistemologist and historian of philosophy, “Kant’s Morals and Modernity”. The interpretation of Kant’s teachings proposed by Boutroux is considered. Based on some of Kant’s ideas and criticizing others, Boutroux sought to update meta - physics through reflection on science and scientific knowledge. Noting aspects of his concept that gave reason to attribute it to French neo-Kantianism, the author of the article also highlights significant points that are determined by Boutroux’s own philosophical position and do not allow him to be considered a faithful follower of the Königsberg thinker: the denial of dualism and the necessary nature of scientific knowledge.
Metaphysics of Maximus the Confessor: Dynamics of Actualization and Transformation of the Cosmos
Authors:   Lomonosov Moscow State University, Surkov Ivan ,   Institute of Philosophy, Russian Academy of Sciences
Published: September 2024

The review introduces readers to a new monograph by the Norwegian historian of philosophy T.T. Tollefsen. In the new book, the author summarizes his many years of research into the legacy of St. Maximus the Confessor, one of the most important and sophisticated Byzantine thinkers. The metaphysics of St. Maximus is described as a large philosophical system, as coherent and rational as other systems of late Antiquity. Its distinctive feature is its emphasized dynamism, which consists in the movement of the entire sensual and intelligible cosmos towards the goal of comprehensive actualization and deification. Tollefsen describes the philosophical system of Maximus the Confessor in the following topics: epistemology, the doctrine of creation, the doctrine of logoi, divine activity (energy), the problem of universals, and the question of Incarnation and deification. In addition, the scholar makes an attempt to apply the metaphysics of St. Maximus to the philosophical problems of our time.
Ethical Theories of Immanuel Kant and Christian Wolff: Similarities and Differences
Authors:   Institute of Philosophy, Russian Academy of Sciences, Povecherova Anastasia
Published: September 2024

The article compares the ethical concepts of Christian Wolff and Immanuel Kant and identifies not only coincidences, but also, mainly, their fundamental differences. On the one hand, Wolff denies the possibility of attributing good or evil to an action depending on the will of God. On the other hand, the Creator is the one who actualizes the existing relationship between things, and therefore moral assessment is still inseparable from him. For Kant, the divine will is completely excluded as a source of moral law, but at the same time it is a natural result of the consistent fulfillment of the moral dictates of reason. The concept of freedom is equally important for both thinkers. Wolff insists on its necessity, but hardly justifies its possibility, since he attributes any immoral action not to freedom of choice, but to a lack of knowledge. The philosopher does not assume a mismatch of will and reason. In addition, the thinker assumes a universal determinism of nature, the latter expresses itself in a natural law, which also coincides with the divine law. The basic principle of Wolfian ethics is perfection, which is not strictly defined and which Kant himself considers unclear. Thus, the moral character of an action, according to Wolff, depends not only on these laws, but also on the principle of perfection. At the same time, for Kant, the morality of an action depends on compliance with the moral law, and first of all, the intention preceding the action or inaction is evaluated. In Wolff'’s case, the consequence arising from the act is subject to evaluation, which is the opposite of Kant’s ideas.
The Stoic Notion of ἁμάρτημα in SVF III, 500: Alternative Interpretations
Authors:   Institute of Philosophy, Russian Academy of Sciences, Seregin Andrei
Published: September 2024

The paper offers a detailed analysis of the Stoic notion of ἁμάρτημα (morally wrong activity) as defined in SVF III, 500: “that which is done contrary to right reason, or that in which something appropriate has been omitted by a rational animal”. The author seeks to clarify how this formulation relates to alternative interpretations of early Stoic ethics, one of which suggests that appropriate acts may also fall under the notion of ἁμάρτημα, while another implies that ἁμάρτημα extensionally coincides with inappropriate acts. The author demonstrates that, for a number of reasons, primarily the presence of the conjunction “or” in the text, this definition is highly ambiguous and more or less compatible with both of these interpretations, the first of which seems preferable in itself on the basis of much other evidence.
Evolutionary, cognitive and semiotic foundations of learning in virtual reality
Authors:   Kuban State Agrarian University, Sukhoverkhov Anton , DeWitt Dorothy ,   University of Malaya
Published: September 2024

The article addresses the classical epistemological debate on direct and indirect realism from educational perspectives relating to the studies of Virtual Reality (VR) and Augmented Real­ity (AR). Recently, D. Hoffman introduced the Interface Theory of Perception stating that senses and thoughts mediate and represent reality similar to interface of computer represent­ing hidden process in a computer. Hoffman goes further and compares the nature of cogni­tion with production of virtual reality. Studies of VR partly confirmed such statements. For instance, due to an interaction of our mind with computer-generated objects (signs), move­ment and acceleration in VR during a virtual free fall from a parachute experienced as real. By using the Interface Theory of Perception and semiotic theory, the paper examines how the signs and interactions in VR scenarios can replace/construct studied realities and be used for learning. It is argued that VR allows building for learners ‘developmental niches’ to ex­perience and acquire new skills or conceptual knowledge. Overlays or signs augmented on these VR environments give ‘semiotic scaffolding’ for learners who re-construct studied social realities or receive instructions for the acquisition of professional skills. These results were investigated in three types of VR environments with different degrees of semiotic scaf­folding and evaluated by experts in cultural education. It is shown that VR provides learning environments similar to the real world and provided semiotic scaffolding reduced the cogni­tive loads in these developmental niches. VR environments for professional learning as well as for general education can benefit from using semiotic scaffoldings in virtual apprentice­ship and professional instruction. Augmented Reality could also scaffold and speed-up sci­entific discoveries through the effective integration of researchers into the ‘collective me­mory’ (global databases) and technically scaffolded processes of recognition.
Herbarium specimens reveal a cryptic invasion of tetraploid Centaurea stoebe in Europe
Authors: Rosche Christoph , Broennimann Olivier , Novikov Andriy , Mrázová Viera , Boiko Ganna V. , Danihelka Jiří , Gastner Michael , Guisan Antoine , Kožić Kevin , Müller-Schärer Heinz , Nagy Dávid , Remelgado Ruben , Ronikier Michał , Selke Julian , Shiyan Natalia , Suchan Tomasz , Thoma Arpad , Zdvořák Pavel , Mráz Patrik , Lehnert Marcus
Published: September 2024

Numerous plant species are expanding their native ranges due to anthropogenic environmental change. Because cytotypes of polyploid complexes show often similar morphologies, there may be unnoticed range expansions (i.e., cryptic invasions) of one cytotype into regions where only the other cytotype is native. We critically revised 13,078 herbarium specimens of diploid and tetraploid Centaurea stoebe, collected across Europe between 1790 and 2023. Based on their distribution in relictual habitats, we suggest that diploids are native across their entire European range, whereas tetraploids are native only to South-Eastern Europe and have recently expanded their range toward Central Europe. The proportion of tetraploids exponentially increased over time in their expanded but not in their native range. This cryptic invasion took predominantly place in ruderal habitats and enlarged the climatic niche of tetraploids toward a more oceanic climate. Our differentiation between native and expanded ranges conflicts with dozens of previous studies on C. stoebe. Thus, herbarium specimens can prevent erroneous assumptions on the native ranges of species, which has fundamental implications for designing research studies and assessing biodiversity trends. Moreover, we demonstrate the value of spatio-temporally explicit data in formulating and testing hypotheses regarding the superior colonization abilities of polyploids in ruderal habitats.
Augmented Repair Technique for Patellar Tendon Rupture Using Two Suture Anchors and Three Transosseous Sutures: a retrospective cohort study
Authors: Li Ding , He Yuchen , Xu Zhenmu , Chen Yueming , Jiang Kai , Zhou Ding , Liu Qian , Zhu Weihong
Published: September 2024

Background
Patellar tendon rupture is an uncommon injury that usually requires surgical repair, but no consensus exists regarding the ideal repair technique. Suture anchor repair and the transosseous suture method have be widely used, but the suture anchor technique may cause anchor pull-out, while the transosseous suture method may result in insufficient suture strength. Therefore, we propose and evaluate the efficacy of augmented repair technique with two suture anchors and three transosseous sutures for patellar tendon repairs.
Methods
We conducted a retrospective cohort study of patients who received surgery for patellar tendon rupture between January 2016 and December 2020. All patients underwent a standardized integrated knee extensor mechanism augmentation repair technique by the same surgeon with 2 suture anchors and 3 transosseous sutures. Radiology, complications, and patient-reported outcomes were recorded. Clinical outcomes were measured using range of motion (ROM), patient satisfaction, Visual Analog Scale (VAS) pain scores, Knee Society Function Score (KSS-F), International Knee Documentation Committee (IKDC) score, Lysholm score, and Tegner score.
Results
Totally 40 patients were enrolled with an average age of 33.95 years. Mean follow-up duration was 60 months (range: 36 to 72 months). All cases were diagnosed with patellar tendon rupture at the patellar attachment and received the surgery. The risk of complications was 7.5% (3/40). Mean postoperative ROM improved from 45.65 ± 10.66 to 127.25 ± 3.99 (mean ± SD, p < 0.001). Mean postoperative VAS pain score, KSS-F score, IKDC score, Lysholm score and Tegner score significantly improved (p < 0.001). The median Caton Deschamps Index significantly decreased from 1.71 ± 0.22 to 1.07 ± 0.07 (p < 0.001). Postoperative MRI revealed evident healing between the patellar tendon and the inferior pole of the patella.
Conclusions
The integrated knee extensor mechanism augmentation repair technique is reliable and effective for patellar tendon rupture. 5-year-follow up results verified its favorable outcomes.
Observation of exciton-vibron coupling in cold dense nitrogen
Authors: Lei Li , Wu Binbin , Liu Jingyi , Tao Yu
Published: September 2024

Cold dense matter (CDM) exhibits unique quantum states or effects, and the quantum correlation effects in dense nitrogen become significant at low temperatures, which provides an opportunity to explore the matter under cold dense conditions. The optical band gap (Eg) of dense nitrogen gradually closes with increasing pressure, eventually leading to the metallization. At the same time, the exciton energy (Ex) also gradually decreases as the Eg decreases, this process may trigger a new quantum correlation transition correlated with the exciton coupling. Here we designed a state-of-the-art isothermal-compression Raman spectroscopy technology to probe vibrational properties in cold dense nitrogen, and clearly observed vibron fluctuations and phonon stiffening when we isothermally compressed the solid nitrogen above 130 GPa at below 150 K. This phenomenon is believed to be related to the pressure-driven exciton-vibron coupling in cold dense nitrogen due to the excitonic interaction can enhanced at low temperature, and the exciton binding energies and their lifetimes can be modified. We defined the exciton-vibron coupling state as the new μ-N2 phase, and also identified its pressure-temperature (P-T) phase boundaries. Our finding not only provides experimental basis for the existence of exciton-vibron coupling in cold dense nitrogen, but also provides a clear and manageable context for exploring complex interactions under extreme conditions.
Impact of COVID-19 on a Medium-Sized Travel Medicine Clinic in Eastern Pennsylvania, USA
Authors: Palwai Pravallika , Gareca Marcelo , Rao Sowmya R. , Knouse Mark C.
Published: September 2024

Background:
The COVID-19 pandemic (COVID) disrupted international travel. We sought to determine the impact of the COVID-19 pandemic on patient volume, traveler demographics, and income of our travel clinic in Pennsylvania, USA.
Methods:
We extracted de-identified pre-travel data on 3,510 pre-travel consultations for adults during: Pre-COVID-19 (January 2018-December 2019), Early COVID-19 (April 2020-March 2022) and Late COVID-19 (April 2022-March 2023). We compared traveler demographics, destinations, purpose of travel, medical conditions, and number of vaccinations administered over time, and we obtained our clinic’s revenue from our financial database (TruSource) from the Pre-COVID-19 period to the Early and Late COVID-19 periods.
Results:
We observed 84% and 85% relative decreases in traveler volume and revenue respectively from the Pre-COVID-19 to the Early COVID-19 period. The proportional decrease in volume was highest for travelers over 65 years of age, decreasing from 16–11%. Of those that sought care during Early COVID-19, proportionally fewer travelers had multiple co-morbid conditions and were taking chronic medications. Trip length increased and there was a significant proportional increase in travel to Africa. Travel to visit friends or family and for service work also proportionally increased during Early-COVID-19 versus Pre-COVID-19. Clinic volume and revenue began to increase in Late COVID-19 but did not return to Pre-COVID levels.
Conclusions:
The COVID pandemic resulted in a large reduction in patient volume and revenue in our academic-based Pennsylvania travel clinic. We saw substantial changes in our traveler demographics, destinations, as well as reasons and durations of travel.
CaMK2A overexpression activates CREB signaling-dependent mitophagy and induces neuronal apoptosis in diabetes retinopathy
Authors: Yang Xiaochun , zhang yuxin , zhou yikun , liu mingzhi , zhao haiyan , yang yang , su jianyun
Published: September 2024

Background
Diabetic retinopathy (DR) is a common complication of diabetes mellitus, characterized by progressive neurodegeneration and vision impairment. The Ca2+/calmodulin-dependent protein kinase II alpha (CaMK2A) and cAMP response element-binding protein (CREB) signaling pathway has been implicated in various neurological disorders. However, its role in DR pathogenesis remains elusive.
Methods
We established a DR mouse model by streptozotocin administration and performed histological, biochemical, and molecular analyses to investigate the involvement of CaMK2A/CREB signaling and its interplay with mitophagy. Additionally, we employed in vitro high-glucose (HG) treatment in immortalized RGC-5 cell line to dissect the underlying mechanisms. Pharmacological and genetic modulations were utilized to target CaMK2A/CREB pathway and mitophagy.
Results
In the DR model, we observed retinal degeneration, increased apoptosis, and reduced neurotransmitter production, accompanied by enhanced mitophagy and activation of the CaMK2A/CREB pathway. HG induction in RGC-5 cells recapitulated these findings, and autophagy inhibition partially rescued cell death but failed to suppress CaMK2A/CREB activation, suggesting mitophagy as a downstream consequence. CaMK2A knockdown or CREB phosphorylation inhibition attenuated HG-induced mitophagy, apoptosis, and neurotransmitter depletion, while CREB activation exacerbated these effects. CaMK2A silencing mitigated DR progression, oxidative stress, inflammation, and neuronal loss, akin to dopamine/carbidopa administration in DR mouse model.
Conclusion
Our findings unveil a pivotal role of CaMK2A/CREB signaling in driving mitophagy and neurodegeneration in DR. Targeting this pathway represents a potential therapeutic strategy for DR management.
Mapping Green space, Roads & Built-up Areas with Optical Remote Sensing and Polarimetric SAR (A Novel Approach)
Authors: Aghlmand Majid , Onur Mehmet İnanç , Talaei Reza
Published: September 2024

Recent progress in remote sensing and Geographical Information System (GIS) has revolutionized the research studies on urban space. Satellites that image on daily basis and cloud platforms that increase mathematical modelling precision and speed have given rise to extraction of high-quality data. In this study, we propose a novel approach in extracting information on green space, buildings, and roads in Ankara and Eskişehir cities in Türkiye. In this approach, optical and SAR images are utilized. Modelling is also fulfilled in google earth engine cloud platform using machine learning algorithm. We show how optical and SAR images with varying indexes may lead to a Land use/Land cover map with the highest overall accuracy (98.94 for Ankara and 93.97 for Eskişehir). Additionally, techniques offered in this study can help to extract other classes other than the present study ones. Land use/Land cover map is the basis of many studies and can benefit urban management, planning, urban policy making, protection and renovation, and environmental sustainment.
Distribution, Scaling, and Depiction of the Temporal Branches of the Facial Nerve
Authors: Hunt Bradley , Johson Santos A. , Klukkert Zachary S.
Published: September 2024

Purpose. Iatrogenic injury to the temporal branches of the facial nerve (CN VII) is the leading postoperative complication of the preauricular surgical approach to the temporomandibular joint (TMJ). Many of the anatomical illustrations vary greatly in how the anatomy of the temporal branches of the facial nerve are depicted. Additionally, there are few studies that discuss this variation. This study aims to provide more accurate data on this discrepancy.
Methods. Here, the distribution of temporal branches of the facial nerve was examined in 20 cadaveric donors. A count of branches and the location of each was mapped as they crossed the zygomatic arch, with attention paid to variation in the breadth of the nerve free “preauricular window” which is pertinent to the surgical access to the TMJ. Comparable measures were collected from published anatomical illustrations and tested for accuracy.
Results. Preauricular window breadth measurements were found to be comparable to previous studies, but the mean value was lower here. Patterns in the nerve distribution fit a proportional model whereby the zygomatic length (ZL) is divided into five equal segments, the most posterior of which was found to be free of CN VII branches in all donors. In anatomic illustrations, the number of nerve branches crossing ZL was undercounted and the breadth of the preauricular window was overestimated.
Conclusion. Results suggest that controlling for face size could reduce the variation observed in the breadth of the facial nerve-free zone near the TMJ. Non-cadaveric reference illustrations do not represent the anatomy accurately.
Enhancing Flash Flood Susceptibility Modeling in Arid Regions: Integrating Digital Soil Mapping and Machine Learning Algorithms
Authors: Sheikh Zahra , Zolfaghari Ali Asghar , Raeesi Maryam , Soltani Azadeh
Published: September 2024

Flash floods in arid regions are among the most dangerous and destructive disasters worldwide, with their frequency increasing due to intensified climate change and anthropogenic activities. This study aims to identify susceptibility areas to flash floods in arid regions, characterized by high vulnerability, numerous complexities, and unknown mechanisms. 19-flash flood causative physiographic, climatic, geological, hydrological, and environmental parameters were considered. Using the Boruta wrapper-based feature selection algorithm, temperature, distance to the river, and elevation were identified as the most effective parameters. Four standalone and hybrid machine learning models (Random Forest (RF), Support Vector Regression (SVR), GLMnet, TreeBag, and Ensemble) were employed to model and determine flash flood susceptibility maps. Based on performance evaluation metrics (accuracy, precision, recall, and Areas Under Curve (AUC) indexes), the RF and Ensemble models exhibited the best performance with values of (0.94, 0.93), (0.97, 1), (0.92, 0.88), (0.94, 0.94), respectively. The findings highlighted the previously overlooked role of soil in flood susceptibility mapping studies, particularly in arid areas with high levels of silt and clay soils. This study introduced digital soil mapping for the first time in flood susceptibility studies, providing an effective approach for the spatial prediction of soil properties using easily accessible remote sensing data to generate soil maps in areas with limited available data. It emphasizes the importance of examining the role of soil in arid areas during flash flood modeling and recommends using Ensemble and RF models for their high flexibility in such studies.
Tomographic diffractometry of laser-induced plasma formations
Authors: Fleischer Sharly , Ostrovsky Ivan , Hurvitz Gilad , Bograd Eli , Flaxer Eli , Hazra Soumitra
Published: September 2024

A sensitive optical diffractometry method is developed and utilized for advanced tomography of laser-induced air plasma formations. Using transverse diffractometry and Supergaussian plasma distribution modelling we extract the main parameters of the plasma being the plasma density, width and shape with 20𝜇𝑚 spatial resolution throughout the plasma formation. The experimentally recorded diffraction patterns fitted by the Supergaussian plasma model are found to capture unprecedentedly delicate traits in the evolution of the plasma from its effective birth and on. Key features in the spatial evolution of the plasma such as the 'escape position', the 'turning point' and the refocusing dynamics of the beam are identified and explored in details. Our work provides experimental and theoretical access into the highly nonlinear dynamics of laser-induced air plasma.
Identification of three QTLs that additively affect heading time in bread wheat (Triticum aestivum L.) by QTL-seq approach
Authors: Komura Shoya , Kobayashi Fuminori , Oono Youko , Handa Hirokazu , Inoue Yoshihiro , Yoshida Kentaro
Published: September 2024

Optimizing the timing of heading is crucial for achieving stable production in bread wheat (Triticum aestivum L.). We analyzed a breeding line, ‘B1-0393’, that headed 5 days earlier than the Japanese elite cultivar ‘Kitahonami’. To identify quantitative trait loci (QTLs) responsible for this difference, we conducted QTL-seq using F3 progeny of a cross between ‘Kitahonami’ and ‘B1-0393’. We detected QTLs on chromosomes 2D (QDth.kupg-2D), 3D (QDth.kupg-3D), and 4A (QDth.kupg-4A), explaining 10.25%, 2.00%, and 8.24%, respectively, of phenotypic variance. The QDth.kupg-2D locus corresponded to the major photoperiod-regulating gene Photoperiod-D1 (Ppd-D1). ‘Kitahonami’ had the photoperiod-sensitive Ppd-D1b allele and ‘B1-0393’ had the insensitive Ppd-D1a allele. QDth.kupg-4A overlapped with previously reported QTLs, while QDth.kupg-3D was a novel QTL. Segregation analysis using F2 and F3 plants confirmed that alleles from ‘B1-0393’ at all three loci accelerated heading and that the three QTLs had additive effects on days to heading. Our findings could be valuable for regulating heading time to optimize wheat yield.
Multi-omics analysis Identifies PTTG1 as a prognostic biomarker associated with immunotherapy and chemotherapy resistance
Authors: Wei Handong , Ma Yaxin , Chen Shuxing , Zou Chunlin , Wang Lihui
Published: September 2024

Background
Pituitary tumor-transforming gene 1 (PTTG1) is an important gene in tumour development. However, the relevance of PTTG1 in tumour prognosis, immunotherapy response, and medication sensitivity in human pan-cancer has to be determined.
Methods
TIMER, GEPIA, the human protein atlas, GEPIA, TISCH2, and cBioportal examined the gene expression, protein expression, prognostic value, and genetic modification landscape of PTTG1 in 33 malignancies based on the TCGA cohort. The association between PTTG1 and tumour immunity, tumour microenvironment, immunotherapy response, and anticancer drug sensitivity was investigated using GSCA, TIDE, and CellMiner CDB. Molecular docking was used to validate the possible chemotherapeutic medicines for PTTG1. Additionally, siRNA-mediated knockdown was employed to confirm the probable role of PTTG1 in paclitaxel-resistant cells.
Results
PTTG1 is overexpressed and associated with poor survival in most tumors. Functional enrichment study revealed that PTTG1 is involved in the cell cycle and DNA replication. A substantial connection between PTTG1 expression and immune cell infiltration points to PTTG1's possible role in the tumour microenvironment. High PTTG1 expression is associated with tumour immunotherapy resistance. The process could be connected to PTTG1, which mediates T cell exhaustion and promotes cytotoxic T lymphocyte malfunction. Furthermore, PTTG1 was found to be substantially linked with sensitivity to several anticancer medications. Suppressing PTTG1 with siRNA reduced clone formation and migration, implying that PTTG1 may play a role in paclitaxel resistance.
Conclusion
PTTG1 shows potential as a cancer diagnostic, prognostic, and chemosensitivity marker. Increased PTTG1 expression is linked to resistance to cancer treatment. The mechanism could be linked to PTTG1's role in promoting cytotoxic T lymphocyte dysfunction and mediating T cell exhaustion. It is feasible to consider PTTG1, which is expressed on Treg and Tprolif cells, as a new therapeutic target for overcoming immunotherapy resistance.
Developing intervention fidelity strategies for a behaviour change intervention delivered in primary care dental practices: The RETURN Fidelity Strategy
Authors: Lowers Victoria , Young Bridget , Harris Rebecca Vera
Published: September 2024

Background
Behaviour change interventions delivered in real-world settings could be vulnerable to threats to internal and external validity if methodological considerations are overlooked. Intervention fidelity strategies are an important mechanism to improve the scientific rigor of such studies. Feasibility studies provide a vital opportunity to refine and optimise research processes and implementation strategies before embarking on larger scale projects. This paper sets out the development of a comprehensive intervention fidelity strategy guided by The National Institutes of Health Behavior Change Consortium (NIH BCC) recommendations.
Method
Using observations (53 hours) and qualitative interviews (17 participant interviews and 2 staff interviews) conducted during the delivery of the RETURN fidelity study (InteRventions to rEduce inequaliTies in the Uptake of Routine deNtal care), an intervention fidelity strategy was developed for use in the RETURN main trial.
Results
A comprehensive intervention fidelity strategy was developed, structured around the five domains of the NIH BCC's recommendations (design, training, delivery, receipt, enactment) and attending to the goals pertaining to each of those domains. This paper sets out the fidelity strategy implemented in the RETURN main trial.
Implications and Conclusions:
The RETURN fidelity strategy was influenced by the unique research environment the primary dental care setting presents. The strategy could serve as a blueprint to other researchers conducting research in similar settings. It is also intended that this strategy is read alongside the RETURN results upon their publication.
T cell exhaustion-related exosome genes for predicting survival and immunotherapy efficacy in colorectal cancer
Authors: Wang Yilin , Su Peizhu , Lu Qinghua , Huang Huiwen , Li Zhaotao
Published: September 2024

Background
Treatment options for colorectal cancer are limited. T cell exhaustion is one of the barriers to tumor immunotherapy. No comprehensive analysis of T cell exhaustion-related exosome prognostic models for colorectal cancer (CRC) has been conducted.
Method
Samples were collected from the Cancer Genome Atlas (TCGA) database, exoRBase database and Gene Expression Omnibus (GEO) database. The single sample gene set enrichment analysis (ssGSEA) algorithm screened out T cell exhaustion-related exosome differential expression genes, signature genes were screened by univariate Cox regression and Lasso regression, and risk score models were constructed and validated. A nomogram containing risk scores and clinical parameters was established and evaluated. In addition, single cell analysis and tumor immune microenvironment assessment were also performed.
Results
Sixteen signature genes were identified, based on which the risk score model was constructed and validated. This model can predict the overall survival (OS) of TCGA and GEO queues well. Scores were identified as independent risk factors for OS and correlated with certain clinicopathological features. A nomogram was developed that integrated clinical parameters and risk scores and showed higher predictive accuracy. Finally, significant differences in immune microenvironment were found between the high- and low-risk groups. Thus, scores can also be used to predict the response to immunotherapy.
Conclusions
In general, we screened out T cell exhaustion-related exosome genes of CRC, constructed a risk score model which could predict survival and immunotherapy efficacy, and found correlations between risk scores and clinicopathologic features and immune microenvironment.
KN-VLM: KNowledge-guided Vision-and-Language Model for Visual Abductive Reasoning
Authors: Tan Kuo , Qi Zhaobo , Zhong Jianping , Xu Yuanrong , Zhang Weigang
Published: September 2024

Visual abductive reasoning strives to deduce the most suitable hypothesis that effectively explains the underlying visual context, garnering considerable attention in the academic community. However, recent efforts are inherently limited by their exclusive reliance on visual information, overlooking the invaluable com-monsense and the semantic/causal relationships, leading to inaccurate abductive reasoning outcomes. To tackle the above issue, we propose a simple but powerful KNowledge-guided Vision-and-Language Model (KN-VLM), which primarily consists of a visual reasoning branch and a knowledge reasoning branch. The visual reasoning branch utilizes a powerful visual embedding model followed by a visual-Qformer to capture visual features. The knowledge reasoning branch aims to acquire two complementary types of knowledge commonsense knowledge and complemented knowledge. The former aims to extract the intricate and detailed conceptual knowledge embedded within the observed video, which deepens the model’s comprehension of the presented video content. The latter utilizes the external knowledge base to further augment the understanding of the interconnec-tions and causal relationships among these concepts, thereby strengthening the model’s abductive reasoning capability. After that, the effective fusion of the two branches completes the abductive reasoning task, which generates descriptions for the observed and explanation events. Experimental results on the VAR and CookReasoning dataset show that our model achieves promising performance.
Biogeographical origin of Andrographis Wall. ex Nees (Acanthaceae) in eastern peninsular India based on molecular phylogenetics
Authors: Surveswaran Siddharthan , Kalaimani Yuvasri
Published: September 2024

The genus Andrographis is predominantly peninsular Indian distribution after the resurrection of Haplanthus which is predominantly southeast Asian in distribution. Previous study have shown its close phylogenetic affinity with Haplanthodes and Haplanthus. In this study we constructed a most comprehensive phylogeny of the tribe Andrographideae using five plastid regions, rbcL, matK, trnLF, psbA-trnH and trnGR. The results show polyphyly between Andrographis, Haplanthodes and Haplanthus, resulting in a Andrographis sensu lato (s.l.) clade. Within this earliest splitting clade consisted of Andrographis and Haplanthus ovatus. The next split was with Haplanthodes followed by Andrographis sensu stricto (s.s) clade. Within the Andrographis clade, we observed two clades one was western in distribution and the other was eastern in distribution in peninsular India. Biogeographical analysis suggested an eastern peninsular Indian origin of Andrographis and followed by dispersal into the relative wetter western peninsular India. We deduced the time of diversification of the clades of Andrographis. We discuss the role of south Asian winter monsoon in the diversification of Andrographis which has adapted to aridity.
Transcriptome profiling reveals genes associated with inflammation and fibrosis among 10 - 15-year-old children with Schistosoma mansoni and Plasmodium falciparum coinfection along the Albert Nile in Uganda
Authors: Namulondo Joyce , Nyangiri Oscar Asanya , Kimuda Magambo Phillip , Nambala Peter , Nassuuna Jacent , Kabagenyi Joyce , Egesa Moses , Nerima Barbara , Biryomumaisho Savino , Mugasa Claire Mack , Elliott Alison , Noyes Harry , Tweyongyere Robert , Matovu Enock , Mulindwa Julius
Published: September 2024

Background Malaria and schistosomiasis are significant parasitic diseases in Uganda and coinfections with the two are not uncommon in areas endemic to both parasites. The aim of this study was to determine the effect of P. falciparum and S. mansoni coinfection on the gene expression in peripheral blood of school age children aged between 10–15 years.Methods A cross sectional study of children aged 10–15 years, was conducted in selected sites along the Albert Nile in Pakwach District in northwest Uganda. Quantitative PCR (qPCR) was used to test for S. mansoni and P. falciparum infection. Furthermore samples that were sequenced using Illumina NovaSeq S4 and the reads aligned to the GRCh38 human genome were matched with those with S. mansoni and P. falciparum qPCR results. Differential gene expression analysis was done using DESeq2.Results Of the 210 study particpants, 76.2% (160/210) were P. falciparum positive, 91% (191/210) were S. mansoni positive and 150 (71%) had coinfection with both P. falciparum and S. mansoni, which was slightly fewer coinfections than expected by chance (Fisher exact test p-value of 0.02). RNAseq data was obtained for 33 participants of which 17 had P. falciparum and S. mansoni coinfection, 4 S. mansoni infection only, 1 had P. falciparum infection only while 11 were uninfected. Principal component analysis revealed clustering of gene expression by gender and infection status when S. mansoni and P. falciparum coinfected children were compared with uninfected children. We observed 15 DEGs of which 2 (CEPT1 and RETREG1) were downregulated and 13 (GAS6, DEXI, PALMD, SAMD15 AC138028.4, GFOD1-AS1, AC034102.6, AC005153.1, AC020914.1, AC017028.2, AC244502.3, AC013486.1, AC106760.1) upregulated when S. mansoni and P. falciparum coinfected children were compared with uninfected children. The differentially expressed genes are associated with inflammation and fibrosis and also included regulatory long noncoding RNA.Conclusions By molecular detection, this study observed a high prevalence of P. falciparum among the school age children (10–15 years) living in the S. mansoni endemic hotspots along the Albert-Nile region of Pakwach district, northwestern Uganda. The study shows differential expression of genes associated with inflammation and fibrosis among coinfected when compared to the uninfected children.
Application of polidocanol foam injection sclerotherapy in patients with antithrombotic therapy combined with mixed hemorrhoid bleeding: A single-center experience and literature review
Authors: Li Zhen , Liu Hailong , Ding Wenjing , Wang Song , Lv Liang , Li Xiaobin , Ding Haibo
Published: September 2024

Objective To explore the single-center clinical experience of polydocanol foam in the antithrombotic treatment of mixed hemorrhoid patients with bleeding and review the related literature.Methods From March 2018 to May 2023, we retrospectively analyzed the clinical data of 7 patients who were admitted to the General Surgery Department of Yangpu Hospital affiliated to Tongji University. Patients with antithrombotic therapy combined with mixed hemorrhoid bleeding who failed to receive conservative treatment need to be treated with polydocanol foam injection sclerotherapy. We summarized the single-center clinical application experience of polydocanol foam injection sclerotherapy in the treatment of patients receiving antithrombotic therapy combined with mixed hemorrhoid bleeding. Through a literature search, the related literature results concerning the application of polydocanol foam sclerotherapy in the antithrombotic treatment of patients with mixed hemorrhoid bleeding were reviewed.Results Seven patients were successfully treated with polydocanol foam sclerotherapy, and the bleeding stopped. The operation time ranged from 10–30 minutes, and no serious complications occurred. At the 4-week postoperative follow-up evaluation, none of the patients had bleeding again, and hemoglobin significantly increased (Hb: 106.0 ± 17.4 g/L vs Hb: 70.9 ± 19.7 g/L). Four weeks after surgery, the overall clinical efficacy rate reached 100%, with a satisfaction rate of 100%. Through a literature review, three studies were ultimately included for analysis.Conclusion Polydocanol foam injection sclerotherapy is a safe and effective method for patients receiving antithrombotic therapy combined with mixed hemorrhoid bleeding. However, larger multicenter prospective studies are needed before this is the preferred treatment for such patients.