Miracle-dz/UniFAR-FTUs huggingface dataset:
A New Hypothesis for the Origin of Dune Ridges

In support of a new hypothesis concerning the origin of dune ridges, fieldwork was carried out on the Long Beach Peninsula, SW Washington State, between 1997 and 2002. Procedures included coring, profiling, measuring and recording cross-section stratigraphy, and collected data analyzed and compiled at Western Washington University. The proposed hypothesis envisions coseismic subsidence, formation of a berm or beach ridge, subsequent uplift, and eolian deposition on the berm or beach ridge to form a new dune ridge. Geomorphic and stratigraphic evidence from the Long Beach Peninsula is presented and compared to the standard models outlined in the literature. Most of the scientific work done on dune ridge and beach ridge topography around the world has been done in tectonically inactive regions. Normal processes found on passive margin coasts produce dune ridges by variations in sediment supply and sea level. Long Beach Peninsula, situated within the Cascadia Subduction Zone margin, is affected by large subduction zone earthquakes that drop the elevation of the coast by 0.5 to 2.0 m, followed by rebound. Stratigraphic evidence from within the ridges shows wave deposited sands at elevations up to 2 m above present day beach deposits, and elevations above those within the intervening swales. The higher elevation deposits in the ridges are possibly the result of post-earthquake deposition in a higher relative sea level environment.
A vertebrobasilar junction aneurysm successfully treated with a combination of surgical clipping and flow diverter placement based on the results of computational fluid dynamics analysis: illustrative case

BACKGROUND The treatment of vertebrobasilar junction (VBJ) aneurysms is challenging. Although flow diverters (FDs) are a possible treatment option, geometrical conditions hinder intervention. VBJ aneurysms possess dual inflow vessels from the bilateral vertebral arteries (VAs), one of which is ideally occluded prior to FD treatment. However, it remains unclear which VA should be occluded. OBSERVATIONS A 75-year-old male with a growing VBJ complex aneurysm exhibiting invagination toward the brainstem and causing perifocal edema required intervention. Preoperative computational fluid dynamics (CFD) analysis demonstrated that left VA occlusion would result in more stagnant flow and less impingement of flow than right VA occlusion. According to the simulated strategy, surgical clipping of the left VA just proximal to the aneurysm was performed, followed by FD placement from the basilar artery trunk to the right VA. The patient demonstrated tolerance of the VA occlusion, and follow-up computed tomography angiography at 18 months after FD treatment confirmed the disappearance of the aneurysm. LESSONS Preoperative flow dynamics simulations using CFD analysis can reveal an optimal treatment strategy involving a hybrid surgery that combines FD placement and direct surgical occlusion for a VBJ complex aneurysm.
Comments on ``Regional Impacts of Irrigation in Mexico and the Southwestern United States on Hydrometeorological Fields in the North American Monsoon Region''

AbstractFor their investigation of the impact of irrigated agriculture on hydrometeorological fields in the North American monsoon (NAM) region, Mahalov et al. used the Weather Research and Forecasting (WRF) Model to simulate weather over the NAM region in the summer periods of 2000 and 2012, with and without irrigation applied to the regional croplands. Unfortunately, while the authors found that irrigated agriculture may indeed influence summer precipitation, the magnitude, location, and seasonality of their irrigation inputs were substantially inaccurate because of 1) the assumption that pixels classified as “irrigated cropland” are irrigated during the summer and 2) an outdated land cover map that misrepresents known agricultural districts. The combined effects of these errors are 1) an overestimation of irrigated croplands by a factor of 3–10 along the coast of the Gulf of California and by a factor of 1.5 near the Colorado River delta and 2) a large underestimation of irrigation by a factor of 7–10 .
A novel predictive model of lymphovascular space invasion in early-stage endometrial cancer

Objective: To predict lymphovascular space invasion (LVSI) positivity in early-stage (stage 1-2) endometrial cancer (EC) using a predictive model with prognostic factors of EC. Materials and Methods: We included 461 patients who underwent total hysterectomy and bilateral salpingo-oophorectomy with pelvic-paraaortic lymphadenectomy as the primary treatment for presumed early-stage EC at our clinic between 2010 and 2020. Moreover, all surgical specimens were examined histopathologically for the positivity or negativity of LVSI, and the patients were divided into two groups based on these pathologic outcomes. Age, menopausal status, histological type (type 1-2), histological grade (grades 1-2-3), depth of myometrial invasion, and peritoneal cytology results were recorded and analyzed as clinicopathological and demographic characteristics of the patients. The Loess algorithm determined the relationship between the observed and predicted outcomes. The distinction between the algorithms was evaluated by calculating the C-index. Results: LVSI positivity was significantly associated with advanced age, menopause, type 2 EC, advanced histological grade, malignant peritoneal cytology, cervical involvement, and a tumor exceeding 50% of the myometrial depth (p<0.001, respectively). Remarkably, LVSI was most strongly associated with three explanatory variables: 1- More than 50% myometrial invasion [odds ratio (OR): 3.78; 95% confidence interval (CI): 1.80-7.60], 2- Advanced histological grade [OR=1.98 (1.20-3.20) 95% CI], 3- Malignant peritoneal cytology [OR= 3.06 (1.40-6.30) 95% CI]. The penalized maximum likelihood estimation model correctly classified 87% of the included patients (C-index: 0.876). Conclusion: Our predictive model may help predict LVSI based on different prognostic factors. The prognostic factors included in the nomogram were significantly associated with LVSI, particularly myometrial invasion depth of more than 50%, advanced histological grade, and malignant peritoneal cytology.
Geodynamic models of Archean continental collision and the formation of mantle lithosphere keels

The processes responsible for the formation of thick, strong and cold Archean sub‐continental lithospheric mantle (mantle keels) beneath Archean cratons remain elusive. Here, the dynamics of some such processes are studied by forward numerical modeling of the thermo‐mechanical evolution of continental lithosphere undergoing collision and orogenesis under Neoarchean‐like conditions. The numerical experiments illustrate that depending on the composition of the crust and the degree of radioactive heat production (RHP) in the crust, three dominant modes of mantle lithosphere deformation evolve: (1) pure‐shear thickening; (2) imbrication; (3) and a mode best described as underplating. All three modes of deformation result in the thickening and emplacement of plate‐like mantle lithosphere to depths between 200 km and 350 km. The transition from pure‐shear thickening to imbrication is largely dependent on the degree of RHP in the crust, while the transition from the imbrication style to the underplating style is dependent on the composition of the lower crust.
Genomic Resources and Annotations for a Colonial Ascidian, the Light-Bulb Sea Squirt Clavelina lepadiformis

Abstract Ascidian embryos have been studied since the birth of experimental embryology at the end of the 19th century. They represent textbook examples of mosaic development characterized by a fast development with very few cells and invariant cleavage patterns and lineages. Ascidians belong to tunicates, the vertebrate sister group, and their study is essential to shed light on the emergence of vertebrates. Importantly, deciphering developmental gene regulatory networks has been carried out mostly in two of the three ascidian orders, Phlebobranchia and Stolidobranchia. To infer ancestral developmental programs in ascidians, it is thus essential to carry out molecular embryology in the third ascidian order, the Aplousobranchia. Here, we present genomic resources for the colonial aplousobranch Clavelina lepadiformis: a transcriptome produced from various embryonic stages, and an annotated genome. The assembly consists of 184 contigs making a total of 233.6 Mb with a N50 of 8.5 Mb and a L50 of 11. The 32,318 predicted genes capture 96.3% of BUSCO orthologs. We further show that these resources are suitable to study developmental gene expression and regulation in a comparative framework within ascidians. Additionally, they will prove valuable for evolutionary and ecological studies.
Sparse Action Tube Detection

Action tube detection is a challenging task as it requires not only to locate action instances in each frame, but also link them in time. Existing action tube detection methods often employ multi-stage pipelines with complex designs and time-consuming linking procedure. In this paper, we present a simple end-to-end action tube detection method, termed as Sparse Tube Detector (STDet). Unlike those dense action detectors, our core idea is to use a set of learnable tube queries and directly decode them into action tubes (i.e., a set of tracked boxes with action label) from video content. This sparse detection paradigm shares several advantages. First, the large number of hand-crafted anchor candidates in dense action detectors is greatly reduced to a small number of learnable tubes, which results in a more efficient detection framework. Second, our learnable tube queries directly attend the whole video content, which endows our method with the capacity of capturing long-range information for action detection. Finally, our action detector is an end-to-end tube detection without requiring the linking procedure, which directly and explicitly predicts the action boundary instead of depending on the linking strategy. Extensive experiments shows that our STDet outperforms the previous state-of-the-art methods on two challenging untrimmed video action detection datasets of UCF101-24 and MultiSports. We hope our method will be an simple end-to-end tube detection baseline and can inspire new ideas in this direction.
Modeling Fe(II) Complexes Using Neural Networks

We report a Fe(II) data set of more than 23000 conformers in both low-spin (LS) and high-spin (HS) states. This data set was generated to develop a neural network model that is capable of predicting the energy and the energy splitting as a function of the conformation of a Fe(II) organometallic complex. In order to achieve this, we propose a type of scaled electronic embedding to cover the long-range interactions implicitly in our neural network describing the Fe(II) organometallic complexes. For the total energy prediction, the lowest MAE is 0.037 eV, while the lowest MAE of the splitting energy is 0.030 eV. Compared to baseline models, which only incorporate short-range interactions, our scaled electronic embeddings improve the accuracy by over 70% for the prediction of the total energy and the splitting energy. With regard to semiempirical methods, our proposed models reduce the MAE, with respect to these methods, by 2 orders of magnitude.
De-escalation of surgical radicality for non-fertility preserving management in patients with early-stage cervical cancer: a systematic review.

OBJECTIVE We sought to evaluate the oncologic outcomes of simple hysterectomy in patients with low-risk early-stage cervical cancer (tumors ≤2 cm with limited stromal invasion). METHODS This study was registered in PROSPERO (registration number CRD42023433840) following the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) checklist. MEDLINE (through Ovid), EmMBASEbase, and Cochrane Central Register of Controlled Trials were searched from inception until June 2023. Randomized controlled trials and observational studies with two arms of comparison (simple hysterectomy with lymph node assessment vs radical hysterectomy with lymph node assessment) in patients with low-risk early-stage cervical cancer were considered. RESULTS The search identified 1270 articles; eighteen studies were considered potentially eligible after removing duplicates, and four met the selection criteria. Three studies were randomized controlled trials, and the other was a retrospective cohort study. In total, 981 patients were included. There were 485 (49.4%) and 496 (50.6%) patients in the simple hysterectomy and radical hysterectomy groups, respectively. Simple hysterectomy with lymph node assessment was not associated with a higher risk of death at 5 years (RR 0.98, 95% CI: 0.31 to 3.10; I2=0%, two randomized controlled trials, 141 patients, for an absolute risk reduction of zero percentage points [95% CI -9.0 to 9.0]), pelvic recurrence at 3 years (97.5% and 97.8% for simple hysterectomy and radical hysterectomy, respectively, p=0.79), and overall recurrence at 3 years (95 %% and 100% for simple hysterectomy and radical hysterectomy, respectively, p=0.30). CONCLUSION Simple hysterectomy with lymph node evaluation for low-risk early-stage cervical cancer is not associated with a detrimental effect on oncologic outcomes and has a better morbidity profile.
The effectiveness and tolerability of trauma‐focused psychotherapies for psychotic symptoms: A systematic review of trauma‐focused psychotherapies

Abstract Introduction Psychological trauma is an established risk factor for psychosis. Trauma‐focused psychotherapies (TFPT) have been suggested as a potential treatment for reducing psychotic symptoms in those who have experienced trauma. We therefore sought to investigate the effectiveness, tolerability, and acceptability of TFPT for psychotic symptoms. Methods We conducted a systematic review of studies of any form of TFPT that measured psychotic symptoms across a broad range of diagnoses. Results From 2584 papers initially identified, 17 studies (857 participants) met eligibility criteria. TFPT were found to be well tolerated, with very few adverse events. Acceptability was also high, with a mean dropout rate of 20%. Conclusions Whilst the evidence of effectiveness for TFPT in reducing psychotic symptoms is weak, we found tentative evidence in favour of exposure‐based interventions. Methodologically rigorous trials investigating the efficacy of TFPT for the treatment of psychotic symptoms are needed to assess this promising intervention.
Lipid-Binding Regions within PKC-Related Serine/Threonine Protein Kinase N1 (PKN1) Required for Its Regulation

PKC-related serine/threonine protein kinase N1 (PKN1) is a protease/lipid-activated protein kinase that acts downstream of the RhoA and Rac1 pathways. PKN1 comprises unique regulatory, hinge region, and PKC homologous catalytic domains. The regulatory domain harbors two homologous regions, i.e., HR1 and C2-like. HR1 consists of three heptad repeats (HR1a, HR1b, and HR1c), with PKN1-(HR1a) hosting an amphipathic high-affinity cardiolipin-binding site for phospholipid interactions. Cardiolipin and C18:1 oleic acid are the most potent lipid activators of PKN1. PKN1-(C2) contains a pseudosubstrate sequence overlapping that of C20:4 arachidonic acid. However, the cardiolipin-binding site(s) within PKN1-(C2) and the respective binding properties remain unclear. Herein, we reveal (i) that the primary PKN1-(C2) sequence contains conserved amphipathic cardiolipin-binding motif(s); (ii) that trimeric PKN1-(C2) predominantly adopts a β-stranded conformation; (iii) that two distinct types of cardiolipin (or phosphatidic acid) binding occur, with the hydrophobic component playing a key role at higher salt levels; (iv) the multiplicity of C18 fatty acid binding to PKN1-(C2); and (v) the relevance of our lipid-binding parameters for PKN1-(C2) in terms of kinetic parameters previously determined for the full-length PKN1 enzyme. Thus, our discoveries create opportunities to design specific mammalian cell inhibitors that disrupt the localization of membrane-associated PKN1 signaling molecules.
Projection Mapping under Environmental Lighting by Replacing Room Lights with Heterogeneous Projectors.

Projection mapping (PM) is a technique that enhances the appearance of real-world surfaces using projected images, enabling multiple people to view augmentations simultaneously, thereby facilitating communication and collaboration. However, PM typically requires a dark environment to achieve high-quality projections, limiting its practicality. In this paper, we overcome this limitation by replacing conventional room lighting with heterogeneous projectors. These projectors replicate environmental lighting by selectively illuminating the scene, excluding the projection target. Our contributions include a distributed projector optimization framework designed to effectively replicate environmental lighting and the incorporation of a large-aperture projector, in addition to standard projectors, to reduce high-luminance emitted rays and hard shadows-undesirable factors for collaborative tasks in PM. We conducted a series of quantitative and qualitative experiments, including user studies, to validate our approach. Our findings demonstrate that our projector-based lighting system significantly enhances the contrast and realism of PM results even under environmental lighting compared to typical lights. Furthermore, our method facilitates a substantial shift in the perceived color mode from the undesirable aperture-color mode, where observers perceive the projected object as self-luminous, to the surface-color mode in PM.
Trypanosomiasis Control and African Rural Development

John Ford I in a paper published post- humously, stated that tsetse control should not be carried out except as an integral part of the general resource management of an African country. Anthony Jordan continues in this tradition in assessing the validity of trypanosomiasis control, not as so many others have done, as an end in itself, but as a part of the process of rural development. There are two parts to the book: the first ten chapters discuss the reasons for trypanosomiasis control and the methods by which it is carried out; the final four 'chapters which constitute the most novel
BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework

Abstract Motivation Removal of batch effect between multiple datasets from different experimental platforms has become an urgent problem, since single-cell RNA sequencing (scRNA-seq) techniques developed rapidly. Although there have been some methods for this problem, most of them still face the challenge of under-correction or over-correction. Specifically, handling batch effect in highly nonlinear scRNA-seq data requires a more powerful model to address under-correction. In the meantime, some previous methods focus too much on removing difference between batches, which may disturb the biological signal heterogeneity of datasets generated from different experiments, thereby leading to over-correction. Results In this article, we propose a novel multi-layer adaptation autoencoder with dual-channel framework to address the under-correction and over-correction problems in batch effect removal, which is called BERMAD and can achieve better results of scRNA-seq data integration and joint analysis. First, we design a multi-layer adaptation architecture to model distribution difference between batches from different feature granularities. The distribution matching on various layers of autoencoder with different feature dimensions can result in more accurate batch correction outcome. Second, we propose a dual-channel framework, where the deep autoencoder processing each single dataset is independently trained. Hence, the heterogeneous information that is not shared between different batches can be retained more completely, which can alleviate over-correction. Comprehensive experiments on multiple scRNA-seq datasets demonstrate the effectiveness and superiority of our method over the state-of-the-art methods. Availability and implementation The code implemented in Python and the data used for experiments have been released on GitHub (https://github.com/zhanglabNKU/BERMAD) and Zenodo (https://zenodo.org/records/10695073) with detailed instructions.
SOCIOLOGÍA -S- DE LA COMUNICACIÓN Y LA CULTURA, EN MÉXICO. Jorge A. González y el proyecto de Colima. Intelectuales, frentes, culturas urbanas e identidades múltiples y plurales

This article of the text Culture (s), (1) reviews the history of the author, the references to his work and the prospect of Cultural Fronts work as an excuse, to track the contribution of the grain popular in cultural studies and their conceptualizations, in structuring hazy knowledge of the communications field in Mexico and Latin America, in the eighties of last century.
Increasing manually annotated resources for Galician: the Parallel Universal Dependencies Treebank

This paper presents the development of the Parallel Universal Dependencies (PUD) treebank for Galician. PUD treebanks were originally created for the CoNLL 2017 Shared Task on Multilingual Parsing, and have subsequently been used both to develop NLP tools and to perform cross-linguistic analysis using parallel resources. The Galician PUD consists of 1000 sentences manually reviewed by professional translators and aligned with the other 23 available PUD treebanks. The linguistic annotation was first carried out using state-of-the-art NLP tools for Galician, and then reviewed by two experts, achieving a high inter-annotator agreement. We describe the process of translating, pre-processing, and reviewing the corpus, and discuss the annotation of some linguistic phenomena in comparison with other PUD tree-banks. The release of Galician PUD will double the size of the available treebanks for this linguistic variety, as only 1000 reviewed sentences were available to date. It will also be useful for carrying out cross-linguistic analyses including Galician, and as an additional test corpus for machine translation systems.
Question Answering for Dialogue State Tracking in Portuguese

Dialogue State Tracking (DST) is a component of task-oriented dialogue systems, used to track the progress of a conversation while maintaining a representation of the current state. We explore DST in Portuguese dialogues, marking the first known application specific to this language. We introduce a new task-oriented dialogue dataset in Portuguese, adapted from the widely-used MultiWOZ, and propose to leverage available question-answering (QA) models for slot filling. Predefined questions are made to user’s utterance, in a process that does not require training in dialogue data. We evaluate two QA models, based on BERT-base and on T5, select suitable thresholds on their scores, and test both intent recognition, as a preliminary step, and post-processing for matching categorical slots. Performance is still far from the state-of-the-art for English, but incorporating intent recognition and post-processing significantly improves performance. These findings not only advance DST within Portuguese-speaking communities but also create opportunities for new dialogue systems in Portuguese.