Miracle-dz/UniFAR-FTUs huggingface dataset:
Multivariate Faunal Analyses of the Turonian Bissekty Formation: Variation in the Degree of Marine Influence in Temporally and Spatially Averaged Fossil Assemblages

Abstract The Bissekty Formation, exposed on the Dzharakuduk escarpment (Kyzylkum Desert) in Uzbekistan, contains the richest and most abundant Turonian terrestrial fauna known from Eurasia. This study utilizes ordination analyses to identify spatial or temporal patterns (i.e., biofacies) in the distribution of spatially averaged skeletal elements (i.e., mix of unequivocally marine faunal elements with terrestrial ones) within the laterally extensive intraformational conglomerates (IFCs) of the Bissekty Formation. Ordination analyses were used to determine similarities among the IFCs based on their absolute taxonomic abundance and presence or absence. To determine the primary factor(s) driving the ordination pattern, taxonomic abundance, richness, environmental restrictions (aquatic, semi-aquatic, and terrestrial), and skeletal element size were examined. Relative Sørensen and Sørensen in combination with Euclidean and city block metrics were used in the analysis and results were consistent across methodologies. Ordination patterns were driven by aquatic taxa, which were dominated in abundance and richness by marine and brackish-tolerant taxa. By mapping the abundance of terrestrial, semi-aquatic, and aquatic taxa of individual IFCs onto ordination space, the relative position of the coastline with reference to the Dzharakuduk escarpment during the deposition of the Bissekty Formation can be inferred. These results indicate that ordination analyses are useful tools for examining taphonomically biased samples and should be utilized more frequently in vertebrate studies.
Incarcerated umbilical hernia in a patient with cirrhotic ascites in combination with chronic lymphocytic leukemia: a case report

Umbilical hernia is a common type of extra-abdominal hernia in adults. However, chronic granulocytic leukemia in combination with cirrhotic ascites and renal insufficiency is less common. The patient reported here had both indications and contraindications for emergency surgery; therefore, the treatment options were subject to debate. We report the case of a man in his 60s who had a strangulated umbilical hernia, with overlying purple-colored infected and necrotic skin. The area was painful, but his bowel movements were normal. Patients underwent comprehensive conservative management, and remote follow-ups via telephone and video conferencing for a period of 60 days, during which the incarcerated contents of the hernia eventually retracted and his pain was relieved, such that there were no longer indications for emergency surgery. In addition, his skin infection disappeared and his quality of life improved, and therefore the treatment outcomes were good. Thus, we provide evidence that not all incarcerated umbilical hernias require emergency surgery, but may respond well to conservative treatment when the contents do not include intestinal loops or other critical organs.
MiRiQ Database: A Platform for In Silico Rice Mutant Screening

Abstract Genetic studies using mutant resources have significantly contributed to elucidating plant gene function. Massive mutant libraries sequenced by next-generation sequencing technology facilitate mutant identification and functional analysis of genes of interest. Here, we report the creation and release of an open-access database (https://miriq.agr.kyushu-u.ac.jp/index.php), called Mutation-induced Rice in Kyushu University (MiRiQ), designed for in silico mutant screening based on a whole-genome-sequenced mutant library. This database allows any user to easily find mutants of interest without laborious efforts such as large-scale screening by PCR. The initial version of the MiRiQ database (version 1.0) harbors a total of 1.6 million single-nucleotide variants (SNVs) and InDels of 721 M1 plants that were mutagenized by N-methyl-N-nitrosourea treatment of the rice cultivar Nipponbare (Oryza sativa ssp. japonica). The SNVs were distributed among 87% of all 35,630 annotated protein-coding genes of the Nipponbare genome and were predicted to induce missense and nonsense mutations. The MiRiQ database provides built-in tools, such as a search tool by keywords and JBrowse for mutation searches. Users can request mutant seeds in the M2 or M3 generations from a request form linked to this database. We believe that the availability of a wide range of gene mutations in this database will benefit the plant science community and breeders worldwide by accelerating functional genomic research and crop improvement.
Real-Life Effectiveness of Smoking Cessation Delivery Modes: A Comparison Against Telephone Counseling and the Role of Individual Characteristics and Health Conditions in Quit Success

Abstract Introduction Professional behavioral counseling for smoking cessation can be delivered in many forms, which may not work equally well for everyone. We aim to explore in a real-world setting whether different delivery modes yield different rates of quit success and whether quit success varies based on gender, age, educational level, and being treated for a health condition. Aims and Methods We used monitoring data (n = 13 747) from a smoking cessation counseling provider in the Netherlands (September 2018 to August 2021) to compare differences in quit success immediately after the end of counseling and at 12-month follow-up between telephone and other modes of counseling. Participants chose which mode of counseling they received. At the 12-month follow-up, we also examined differences in quit success based on demographic characteristics and whether one is being treated for various health conditions. Results Participants of in-person group counseling and online in-company group counseling were significantly more likely to have quit immediately after the counseling compared with telephone counseling (OR = 1.25, 95% CI = 1.08–1.44; OR = 1.63, 95% CI = 1.18–2.24). Analyses revealed no significant differences in quit success between telephone and other modes of counseling after 12 months. Those treated for a respiratory or psychological condition were less likely to have maintained quit success, as were women, and participants with a lower educational level. Conclusions When chosen by oneself, the mode of smoking cessation counseling received does not appear to be important for long-term quit success. However, certain groups warrant extra support to prevent excessive program attrition and unsuccessful quit attempts. Implications Our findings suggest that when chosen by oneself, the delivery mode of smoking cessation counseling does not appear to be important for long-term quit success. This finding is of particular relevance for those who are unable to attend in-person cessation counseling due to, for instance, reduced accessibility or mobility. We also found that women, lower educated, and younger participants were more likely to dropout of the cessation program or to not have maintained a quit attempt, signaling that disparities in smoking cessation persist when standardized counseling is given, and therefore more tailored counseling may be necessary for these groups.
Thiazides do not affect mortality but may reduce CV events vs. nondiuretic antihypertensive drugs at up to 5 y

SOURCE CITATION Reinhart M, Puil L, Salzwedel DM, et al. First-line diuretics versus other classes of antihypertensive drugs for hypertension. Cochrane Database Syst Rev. 2023;7:CD008161. 37439548.
Sedimentological and marine eogenetic control on porosity distribution in Upper Cretaceous carbonate turbidites (central Albania)

Results of a detailed petrographic and stable isotope study illustrate that sedimentological differences and eogenetic dissolution/precipitation processes controlled porosity distribution within carbonate turbidites of the Ionian basin (central Albania). Based on lithology characteristics and porosity distribution observed in outcrop, individual turbidite beds can be subdivided into four distinct intervals, i.e. from base to top: (A) a non‐porous wackestone/floatstone or packstone followed by (B) porous packstone–grainstone that grades into (C) wackestone and (D) non‐porous mudstone with pelagic foraminifera. Wackestone interval C is characterized by an alternation of porous and non‐porous laminae. Changes in turbidity current flow regime controlled the initial presence of matrix micrite giving rise to both matrix‐ and grain‐supported lithologies within turbidite sequences. These are non‐porous and porous, respectively. Four eogenetic diagenetic processes (dissolution, cementation, neomorphism and compaction) acted shortly after deposition and modified primary porosity characteristics and distribution. Alteration by meteoric water is excluded based on the continuous burial until the Oligocene of the studied deep marine carbonates. Moreover, the stable isotope data with values between −2·1‰ and +0·7‰ for δ18OV‐PDB and between +1‰ and +3‰ for δ13CV‐PDB, favour alteration by marine‐derived pore‐waters. Compaction and aggrading neomorphism occurred dominantly in intervals characterized by higher matrix micrite content, i.e. the floatstone base and the wackestone–mudstone upper turbidite part. Framework‐stabilizing cementation occurred dominantly in the packstone–grainstone middle part of the turbidite beds. In the latter porous lithologies, matrix micrite was not compacted because of the grain fabric and the framework‐stabilizing cements. Here, neomorphism of micrite into microrhombic euhedral calcite occurred and microporosity was preserved.
CLAVATA signaling in plant–environment interactions

Abstract Plants must rapidly and dynamically adapt to changes in their environment. Upon sensing environmental signals, plants convert them into cellular signals, which elicit physiological or developmental changes that allow them to respond to various abiotic and biotic cues. Because plants can be simultaneously exposed to multiple environmental cues, signal integration between plant cells, tissues, and organs is necessary to induce specific responses. Recently, CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides and their cognate CLAVATA-type receptors received increased attention for their roles in plant–environment interactions. CLE peptides are mobile signaling molecules, many of which are induced by a variety of biotic and abiotic stimuli. Secreted CLE peptides are perceived by receptor complexes on the surface of their target cells, which often include the leucine-rich repeat receptor-like kinase CLAVATA1. Receptor activation then results in cell-type and/or environment-specific responses. This review summarizes our current understanding of the diverse roles of environment-regulated CLE peptides in modulating plant responses to environmental cues. We highlight how CLE signals regulate plant physiology by fine-tuning plant–microbe interactions, nutrient homeostasis, and carbon allocation. Finally, we describe the role of CLAVATA receptors in the perception of environment-induced CLE signals and discuss how diverse CLE-CLAVATA signaling modules may integrate environmental signals with plant physiology and development.
Probing neurodynamics of experienced emotions—a Hitchhiker’s guide to film fMRI

Abstract Film functional magnetic resonance imaging (fMRI) has gained tremendous popularity in many areas of neuroscience. However, affective neuroscience remains somewhat behind in embracing this approach, even though films lend themselves to study how brain function gives rise to complex, dynamic and multivariate emotions. Here, we discuss the unique capabilities of film fMRI for emotion research, while providing a general guide of conducting such research. We first give a brief overview of emotion theories as these inform important design choices. Next, we discuss films as experimental paradigms for emotion elicitation and address the process of annotating them. We then situate film fMRI in the context of other fMRI approaches, and present an overview of results from extant studies so far with regard to advantages of film fMRI. We also give an overview of state-of-the-art analysis techniques including methods that probe neurodynamics. Finally, we convey limitations of using film fMRI to study emotion. In sum, this review offers a practitioners’ guide to the emerging field of film fMRI and underscores how it can advance affective neuroscience.
Incidence and predictors of stroke and silent cerebral embolism following very high-power short-duration atrial fibrillation ablation

Abstract Aims Cerebral thrombo-embolism is a dreaded complication of pulmonary vein isolation (PVI) for atrial fibrillation; its surrogate, silent cerebral embolism (SCE) can be detected by diffusion-weighted brain magnetic resonance imaging (bMRI). Initial investigations have raised a concern that very high-power, short-duration (vHPSD; 90 W/4 s) temperature-controlled PVI with the QDOT Micro catheter may be associated with a higher incidence of SCE compared with low-power long-duration ablation. We aimed to assess the incidence of procedural complications of vHPSD PVI with an emphasis on cerebral safety. Methods and results We enrolled 328 consecutive patients undergoing their PVI procedure using vHPSD. A subgroup of 61 consecutive patients underwent diffusion-weighted bMRI within 24 h of the procedure, and incidence and predictors of SCE were studied. The mean procedure time and left atrial dwell time for the overall cohort were 69.6 ± 24.1 and 46.5 ± 21.5 min, respectively. First-pass isolation was achieved in 82%. No stroke or transient ischaemic attack occurred. Silent cerebral embolism was identified in 5 of 61 patients (8.2%). Silent cerebral embolism following procedures was significantly associated with lower baseline generator impedance (105.8 vs. 112.6 Ω, P < 0.0001) and with intermittent loss of catheter–tissue contact during ablation (14.1% vs. 6.1%, P < 0.0001). Conclusion Very high-power, short-duration PVI is a safe technique with an excellent acute success rate. Silent cerebral embolism incidence in our cohort was below the previously reported range, with no clinically overt cerebral complications. Lower baseline generator impedance and loss of contact during ablation may contribute to a higher risk of SCEs.
Industrial clusters and districts in the new economy: some perspectives and cases

There is currently a popular view that the world is undergoing profound changes in the fundamental relationships upon which it is organised. In particular, there is widespread talk of a ‘globalised' economy, facilitated by and associated with ‘new' technologies and practices. There is a further consensus that within this ‘globalised', ‘new' economy, regionalisation in some form is important. The aim of this volume is to address these topical issues, presenting perspectives from which they can be analysed and exploring specific aspects in greater detail. The contributors provide a framework for understanding current trends, and suggest approaches that highlight appropriate ways forward in the context of both opportunities and dangers. In doing so, they discuss specific cases and explore detailed policy possibilities, including the prospect of stimulating change through multinational engagement and debate.
Description of Aphelenchoides persicus sp. n. (Nematoda: Aphelenchoididae) from Iran

Abstract During a survey on the soil nematodes, a population of the genus Aphelenchoides was collected around the rhizosphere of persimmon in Guilan Province, Iran. The morphological and molecular characters confirmed the new species, namely A. persicus sp. n. The new species is characterized by a female body length (699–1068 μm), lip region offset from the rest of the body by a slight constriction, lateral fields with six incisures, stylet 12–13.5 μm long, with a clear basal swelling, excretory pore ca 1.5 metacorpal length posterior to base of the metacorpus, post uterine sac elongate, about 4–7 times than the vulval body diameter; conical female tail with a single centrally located mucron with tiny projection close to the tail tip, male body length (663–908 μm), and spicule well developed with rounded condylus, blunt conical rostrum, and a hook-like tip of dorsal limb. The new species belongs to the Group 2 category of Aphelenchoides species and was similar to seven known species with six lateral field incisures, including A. allius, A. chinensis, A. meghalayensis, A. nechaleos, A. paranechaleos, A. parasexlineatus, and A. sexlineatus. The molecular phylogeny based on 28S rDNA revealed that the new species stands close to A. hamospiculatus (MN931591; MN931592) and two unidentified Aphelenchoides (KY769057; LC583315). The measurements, line illustrations, LM photographs, and phylogenetic analysis are given for the new species.
An Integral R-Banded Karyotype Analysis System of Bone Marrow Metaphases Based on Deep Learning.

CONTEXT. — Conventional karyotype analysis, which provides comprehensive cytogenetic information, plays a significant role in the diagnosis and risk stratification of hematologic neoplasms. The main limitations of this approach include long turnaround time and laboriousness. Therefore, we developed an integral R-banded karyotype analysis system for bone marrow metaphases, based on deep learning. OBJECTIVE. — To evaluate the performance of the internal models and the entire karyotype analysis system for R-banded bone marrow metaphase. DESIGN. — A total of 4442 sets of R-banded normal bone marrow metaphases and karyograms were collected. Accordingly, 4 deep learning-based models for different analytic stages of karyotyping, including denoising, segmentation, classification, and polarity recognition, were developed and integrated as an R-banded bone marrow karyotype analysis system. Five-fold cross validation was performed on each model. The whole system was implemented by 2 strategies of automatic and semiautomatic workflows. A test set of 885 metaphases was used to assess the entire system. RESULTS. — The denoising model achieved an intersection-over-union (IoU) of 99.20% and a Dice similarity coefficient (DSC) of 99.58% for metaphase acquisition. The segmentation model achieved an IoU of 91.95% and a DSC of 95.79% for chromosome segmentation. The accuracies of the segmentation, classification, and polarity recognition models were 96.77%, 98.77%, and 99.93%, respectively. The whole system achieved an accuracy of 93.33% with the automatic strategy and an accuracy of 99.06% with the semiautomatic strategy. CONCLUSIONS. — The performance of both the internal models and the entire system is desirable. This deep learning-based karyotype analysis system has potential in clinical application.
Cultural poetics of illness and healing

This issue of Transcultural Psychiatry presents selected papers from the McGill Advanced Study Institute on “Cultural Poetics of Illness and Healing. ” The meeting addressed the cognitive science of language, metaphor, and poiesis from embodied and enactivist perspectives; how cultural affordances, background knowledge, discourse, and practices enable and constrain poiesis; the cognitive and social poetics of symptom and illness experience; and the politics and practice of poetics in healing ritual, psychotherapy, and recovery. This introductory essay outlines an approach to illness experience and its transformation in healing practices that emphasizes embodied processes of metaphor as well as the social processes of self-construal and positioning through material and discursive engagements with the cultural affordances that constitute our local worlds. The approach has implications for theory building, training, and clinical practice in psychiatry.
PGP-14 establishes a polar lipid permeability barrier within the C. elegans pharyngeal cuticle

The cuticles of ecdysozoan animals are barriers to material loss and xenobiotic insult. Key to this barrier is lipid content, the establishment of which is poorly understood. Here, we show that the p-glycoprotein PGP-14 functions coincidently with the sphingomyelin synthase SMS-5 to establish a polar lipid barrier within the pharyngeal cuticle of the nematode C. elegans. We show that PGP-14 and SMS-5 are coincidentally expressed in the epithelium that surrounds the anterior pharyngeal cuticle where PGP-14 localizes to the apical membrane. pgp-14 and sms-5 also peak in expression at the time of new cuticle synthesis. Loss of PGP-14 and SMS-5 dramatically reduces pharyngeal cuticle staining by Nile Red, a key marker of polar lipids, and coincidently alters the nematode’s response to a wide-range of xenobiotics. We infer that PGP-14 exports polar lipids into the developing pharyngeal cuticle in an SMS-5-dependent manner to safeguard the nematode from environmental insult.
Paired box 6 gene delivery preserves beta cells and improves islet transplantation efficacy

Loss of pancreatic beta cells is the central feature of all forms of diabetes. Current therapies fail to halt the declined beta cell mass. Thus, strategies to preserve beta cells are imperatively needed. In this study, we identified paired box 6 (PAX6) as a critical regulator of beta cell survival. Under diabetic conditions, the human beta cell line EndoC‐βH1, db/db mouse and human islets displayed dampened insulin and incretin signalings and reduced beta cell survival, which were alleviated by PAX6 overexpression. Adeno‐associated virus (AAV)‐mediated PAX6 overexpression in beta cells of streptozotocin‐induced diabetic mice and db/db mice led to a sustained maintenance of glucose homeostasis. AAV‐PAX6 transduction in human islets reduced islet graft loss and improved glycemic control after transplantation into immunodeficient diabetic mice. Our study highlights a previously unappreciated role for PAX6 in beta cell survival and raises the possibility that ex vivo PAX6 gene transfer into islets prior to transplantation might enhance islet graft function and transplantation outcome.
Molecular basis for SOX2-dependent regulation of super-enhancer activity

Abstract Pioneer transcription factors (TFs) like SOX2 are vital for stemness and cancer through enhancing gene expression within transcriptional condensates formed with coactivators, RNAs and mediators on super-enhancers (SEs). Despite their importance, how these factors work together for transcriptional condensation and activation remains unclear. SOX2, a pioneer TF found in SEs of pluripotent and cancer stem cells, initiates SE-mediated transcription by binding to nucleosomes, though the mechanism isn’t fully understood. To address SOX2’s role in SEs, we identified mSE078 as a model SOX2-enriched SE and p300 as a coactivator through bioinformatic analysis. In vitro and cell assays showed SOX2 forms condensates with p300 and SOX2-binding motifs in mSE078. We further proved that SOX2 condensation is highly correlated with mSE078’s enhancer activity in cells. Moreover, we successfully demonstrated that p300 not only elevated transcriptional activity but also triggered chromatin acetylation via its direct interaction with SOX2 within these transcriptional condensates. Finally, our validation of SOX2-enriched SEs showcased their contribution to target gene expression in both stem cells and cancer cells. In its entirety, this study imparts valuable mechanistic insights into the collaborative interplay of SOX2 and its coactivator p300, shedding light on the regulation of transcriptional condensation and activation within SOX2-enriched SEs.