bluuebunny/crossref_metadata_2025 huggingface dataset:
Plio/Pleistocene-induced climatic oscillations drive cladogenesis in a high-altitude freshwater crab, Potamonautes mariepskoppie (Decapoda: Potamonautidae), in South Africa
Authors: Gunkel Kallyn G R , Daniels Savel R
Published: November 2024

In this study, we explored the phylogeographical history of the mountain-dwelling freshwater crab Potamonautes mariepskoppie to understand evolutionary processes and identify possible hidden lineages. DNA sequence data from mitochondrial loci (COI, 12S rRNA, and 16S rRNA) and a nuclear locus (histone 3) were analysed using both maximum likelihood and Bayesian inference. Species delimitation was tested with four methods: ASAP, bPTP, bGMYC, and STACEY. Divergence time estimation and ecological niche modelling with ENMEval and Maxent were used to study species distribution and elucidate abiotic factors affecting evolution. Phylogenetic analyses showed three distinct clades, corresponding to geographical regions: Limpopo, Mpumalanga, and Mount Sheba. These clades had no shared haplotypes and exhibited moderate genetic differentiation. Divergence time estimates indicated that these clades diverged during the Plio/Pleistocene, a period of significant climatic shifts in southern Africa. All four species delimitation methods consistently supported the recognition of these clades as distinct species; however, discriminant function analyses of carapace characteristics showed significant overlap between the three clades. Ecological niche modelling indicated that rainfall is a key factor in the species distribution. The present study highlights the need for further investigation of the high-elevation plateaus throughout Limpopo and Mpumalanga, because fine-scale sampling might unmask considerable hitherto-undocumented biodiversity.
A cross-sectional evaluation of knowledge and attitudes of medical interns regarding social service practices in healthcare institutions
Authors: Şevik İrem , Kuyucu Simge , Torcu Özgün , Çiçeklioğlu Meltem
Published: November 2024

Interprofessional collaboration is essential for holistic healthcare, yet social work remains under-integrated in medical curricula, particularly in Türkiye. Neoliberal policies have weakened community-based services, increasing the need to address gaps in medical education regarding social work’s role in addressing social determinants of health. This is especially critical given Türkiye’s demographic shifts, such as an aging population and rising social inequalities. This study aimed to assess the knowledge and attitudes of intern doctors at a university in Izmir, Türkiye, regarding social work practices in healthcare and to identify associated factors. A sample of 181 was selected through simple random sampling. Data analysis included descriptive statistics, t-test, Spearman correlation, and factor analyses. The Cronbach’s alpha for the attitude scale was 0.87. A significant portion (34.8 percent) had not heard of the social work profession, and 56.4 percent were unaware of social workers in their institution. Female students and those encountering underserved patients showed higher knowledge scores. There was a weak positive correlation between knowledge and attitudes. Factors influencing attitudes included gender, familiarity with social work, encountering underserved patients and financial status. Changes in medical education are needed to enhance interprofessional collaboration, with further research recommended on gender roles and attitudes towards social work.
Loss of tissue-type plasminogen activator causes multiple developmental anomalies
Authors: Uguen Kevin , Frey Tanja , Muthaffar Osama , Décarie Jean-Claude , Ameziane Najim , Boissel Sarah , Baradaran-Heravi Yalda , Rauch Anita , Oprea Gabriela , Rad Aboulfazl , Steindl Katharina , Michaud Jacques L
Published: November 2024

Hydrocephalus and Dandy–Walker malformation are amongst the most common congenital brain anomalies. We identified three consanguineous families with both obstructive hydrocephalus and Dandy–Walker malformation. To understand the molecular basis of these anomalies, we conducted genome-wide sequencing in these families. We identified three homozygous truncating variants in the PLAT gene in the four affected family members. All of them showed tetraventricular hydrocephalus. In two individuals, a membrane at the inferior aspect of the fourth ventricle was likely the cause of their hydrocephalus. Three cases exhibited Dandy–Walker malformation, whereas the two oldest individuals displayed intellectual disability. PLAT encodes the tissue-type plasminogen activator, a serine protease whose main function is to cleave the proenzyme plasminogen to produce active plasmin. Interestingly, plasminogen deficiency has also been shown to cause obstructive hydrocephalus and Dandy–Walker malformation, suggesting that loss of PLAT causes these defects by disrupting plasmin production. In summary, we describe a recessive disorder characterized by obstructive hydrocephalus, Dandy–Walker malformation and intellectual disability in individuals with loss-of-function variants in PLAT. This discovery further strengthens the involvement of the plasminogen pathway in the pathogenesis of these developmental disorders.
Cerebral white matter myelination is associated with longitudinal changes in processing speed across the adult lifespan
Authors: Gong Zhaoyuan , Bilgel Murat , An Yang , Bergeron Christopher M , Bergeron Jan , Zukley Linda , Ferrucci Luigi , Resnick Susan M , Bouhrara Mustapha
Published: November 2024

Myelin’s role in processing speed is pivotal, as it facilitates efficient neural conduction. Its decline could significantly affect cognitive efficiency during ageing. In this work, myelin content was quantified using our advanced MRI method of myelin water fraction mapping. We examined the relationship between myelin water fraction at the time of MRI and retrospective longitudinal change in processing speed among 121 cognitively unimpaired participants, aged 22–94 years, from the Baltimore Longitudinal Study of Aging and the Genetic and Epigenetic Signatures of Translational Aging Laboratory Testing (a mean follow-up duration of 4.3 ± 6.3 years) using linear mixed-effects models, adjusting for demographics. We found that higher myelin water fraction values correlated with longitudinally better-maintained processing speed, with particularly significant associations in several white matter regions. Detailed voxel-wise analysis provided further insight into the specific white matter tracts involved. This research underscores the essential role of myelin in preserving processing speed and highlights its potential as a sensitive biomarker for interventions targeting age-related cognitive decline, thereby offering a foundation for preventative strategies in neurological health.
Excessive Data Collection and (Mis)use of Data: A Comparative Law and Economics Study on the Chinese Didi Case and the German Facebook Case
Authors: Li Qian
Published: November 2024

The excessive data collection and (mis)use of data can result in the coexistence of two market failures—namely, market dominance and information asymmetry—which in turn interact with each other in digital markets and trigger simultaneous concerns about competition law and data protection law. This article establishes a law and economics framework to study the divergence in response to the concerns caused by excessive data collection and (mis)use of data by dominant technology undertakings in the European Union and China. The German competition authority, the Bundeskartellamt, found that Facebook, a dominant social network platform, abused its dominant position by excessively collecting and misusing user data without consent, whereas the Cyberspace Administration of China addressed similar concerns caused by Didi, a dominant ride-hailing undertaking, via data protection law. Based on the comparative analysis of the German Facebook case and the Chinese Didi case, a competition law approach to deal with excessive data collection and the (mis)use of data by a dominant technology undertaking results in high enforcement costs due to the prerequisites of market definition and dominance determination under abuse of dominance, while contributing to minimizing error costs, especially false negatives in the absence of data protection enforcement. In contrast, a data protection approach would be a cost-effective way to intervene in the market ex-ante by decreasing the likelihood of excessive collection and misuse of data, reducing the exclusionary and/or exploitative effects of competition and lowering the market entry barrier that benefits from the collection and processing of significant amounts of data.
Acute kidney injury following CAR-T cell therapy: a nephrologist’s perspective
Authors: Kanbay Mehmet , Mizrak Berk , Alper Ezgi N , Copur Sidar , Ortiz Alberto
Published: November 2024

Chimeric antigen receptor T (CAR-T) cell therapy, an emerging personalized immunotherapy for various haematologic malignancies, autoimmune diseases and other conditions, involves the modification of patients’ T cells to express a chimeric antigen receptor that recognizes tumour or autoimmune cell antigens, allowing CAR-T cells to destroy cancerous and other target cells selectively. Despite remarkable clinical improvements in patients, multiple adverse effects have been associated with CAR-T cell therapy. Among the most recognized adverse effects are cytokine release syndrome, immune effector cell–associated neurotoxicity syndrome and tumour lysis syndrome. Even though less recognized, the incidence of acute kidney injury (AKI) ranges from 5 to 33%. The wide range of reported AKI incidence rates might depend on patient population characteristics and comorbidities and specific CAR-T cell therapy features. Even though the exact pathophysiology remains unknown, several key mechanisms, including cytokine release syndrome, tumour lysis syndrome and other factors such as direct renal toxicity of CAR-T cell therapy, conditioning regimens or other medications (e.g. antibiotics), and infectious complications (e.g. sepsis) have been proposed. Risk factors for CAR-T-related AKI include lower baseline glomerular filtration rate, higher rates of allopurinol or rasburicase use, intravenous contrast material exposure, elevated baseline lactate dehydrogenase and grade 3 or higher cytokine release syndrome. Future prospective studies with larger patient populations are needed to gain insights into the pathophysiology of CAR-T-related AKI and, more importantly, to be able to prevent as well as to develop novel and more efficient treatment modalities. In this narrative review, we discuss the underlying pathophysiology, risk factors, potential interventions and future directions related to AKI following CAR-T cell therapy.
Complications on the feeding artery after an arterio-venous fistula closure in patients after kidney transplantation – a national cohort study
Authors: Zrimšek Matej , Vajdič-Trampuž Barbara , Jelenc Matija , Kšela Juš , Gubenšek Jakob
Published: November 2024

Background

Arteriovenous fistulas (AVFs) in kidney transplant recipients are sometimes closed, either as a policy or due to complications. We collected data on the incidence of complications after AVF closure in a national cohort of transplanted patients.

Methods

Patients who received a kidney transplant between 2000 and 2015 and had a functional AVF that was later ligated or extirpated were included. Medical records were searched for arterial complications on the arm with the closed AVF. Furthermore, all patients who were still alive in January 2023 were invited for a follow-up arterial ultrasound exam.

Results

Sixty patients were included; mean follow-up was 9.3 ± 3.8 years. There were five (8% cumulative incidence) patients with symptomatic arterial thrombosis and three (5% incidence) with a symptomatic feeding artery aneurysm. Prospective ultrasound exams were performed in 50 patients; the mean diameter of the brachial artery was almost doubled on the arm with the closed AVF (8.1 ± 3.2 versus 4.7 ± 0.7 mm; P < .001). Additional asymptomatic complications were found in nine patients (18% incidence): seven cases (14% incidence) of arterial thrombosis, some extending up to the axillary artery, and three (6% incidence) brachial artery aneurysms. All patients in whom the thrombosis spread to the brachial artery had large brachial arteries (>10 mm) or an aneurysm.

Conclusion

We observed a high cumulative incidence of arterial thrombosis (20%) and brachial artery aneurysms (10%), sometimes developing several years after AVF closure. These complications should be taken into account when contemplating closure of a well-developed AVF and an AVF-preserving approach with flow reduction surgery might be preferred in some cases.
A comparison of artificial intelligence–enhanced electrocardiography approaches for the prediction of time to mortality using electrocardiogram images
Authors: Sau Arunashis , Zeidaabadi Boroumand , Patlatzoglou Konstantinos , Pastika Libor , Ribeiro Antônio H , Sabino Ester , Peters Nicholas S , Ribeiro Antonio Luiz P , Kramer Daniel B , Waks Jonathan W , Ng Fu Siong
Published: November 2024

Aims

Most artificial intelligence-enhanced electrocardiogram (AI-ECG) models used to predict adverse events including death require that the ECGs be stored digitally. However, the majority of clinical facilities worldwide store ECGs as images.

Methods and results

A total of 1 163 401 ECGs (189 539 patients) from a secondary care data set were available as both natively digital traces and PDF images. A digitization pipeline extracted signals from PDFs. Separate 1D convolutional neural network (CNN) models were trained on natively digital or digitized ECGs, with a discrete-time survival loss function to predict time to mortality. A 2D CNN model was trained on 310 × 868 px ECG images. External validation was performed in 958 954 ECGs (645 373 patients) from a Brazilian primary care cohort and 1022 ECGs (1022 patients) from a Chagas disease cohort. The image 2D CNN model and digitized 1D CNN model performed comparably to natively digital 1D CNN model in internal [C-index 0.780 (0.779–0.781), 0.772 (0.771–0.774), and 0.775 (0.774–0.776), respectively] and external validation. Models trained on natively digital 1D ECGs had comparable performance when applied to digitized 1D ECGs [C-index 0.773 (0.771–0.774)].

Conclusion

Both the image 2D CNN and digitized 1D CNN enable mortality prediction from ECG images, with comparable performance to natively digital 1D CNN. Models trained on natively digital 1D ECGs can also be applied to digitized 1D ECGs, without any significant loss in performance. This work allows AI-ECG mortality prediction to be applied in diverse global settings lacking digital ECG infrastructure.
Whole-genome sequencing confirms multiple species of Galapagos giant tortoises
Authors: Gaughran Stephen J , Gray Rachel , Ochoa Alexander , Jones Menna , Fusco Nicole , Miller Joshua M , Poulakakis Nikos , de Queiroz Kevin , Caccone Adalgisa , Jensen Evelyn L
Published: November 2024

Galapagos giant tortoises are endemic to the Galapagos Archipelago, where they are found in isolated populations. While these populations are widely considered distinguishable in morphology, behavior, and genetics, the recent divergence of these taxa has made their status as species controversial. Here, we apply multispecies coalescent methods for species delimitation to whole-genome resequencing data from 38 tortoises across all 13 extant taxa to assess support for delimiting these taxa as species. In contrast to previous studies based solely on divergence time, we find strong evidence to reject the hypothesis that all Galapagos giant tortoises belong to a single species. Instead, a conservative interpretation of model-based and divergence-based results indicates that these taxa form a species complex consisting of a minimum of 9 species, with most analyses supporting 13 species. There is mixed support for the species status of taxa living on the same island, with some methods suggesting multiple populations of a single species per island. These results make clear that Galapagos giant tortoise taxa represent different stages in the process of speciation, with some taxa further along in that evolutionary process than others. Our study provides insight into the complex process of speciation on islands, which is urgently needed given the threatened status of island species around the world.
Genome-based analysis of biosynthetic potential from antimycotic Streptomyces rochei strain A144
Authors: Zhang Li-juan , Wang Ning , Huang Wei , Wu Long-yuan , Song Bo , Wang Su-ling , Sheng Jian-dong , Wang Wei
Published: November 2024

Streptomyces rochei is a species of Streptomyces with a diverse range of biological activities. Streptomyces rochei strain A144 was isolated from desert soils and exhibits antagonistic activity against several plant pathogenic fungi. The genome of S. rochei A144 was sequenced and revealed the presence of one linear chromosome and one plasmid. The chromosome length was found to be 8 085 429 bp, with a GC content of 72.62%, while the Plas1 length was 177 399 bp, with a GC content (proportion of guanine and cytosine in DNA sequences) of 69.08%. Comparative genomics was employed to analyse the S. rochei group. There is a high degree of collinearity between the genomes of S. rochei strains. Based on pan-genome analysis, S. rochei has 10 315 gene families, including 4051 core and 2322 unique genes. AntiSMASH was used to identify the gene clusters for secondary metabolites, identifying 33 secondary metabolite genes on the A144 genome. Among them, 18 clusters were found to be >70% identical to known biosynthetic gene clusters (BGCs), indicating that A144 has the potential to synthesize secondary metabolites. The majority of the BGCs were found to be conserved within the S. rochei group, including those encoding polyketide synthases, terpenes, non-ribosomal peptide synthetases, other ribosomally synthesized and post-translationally modified peptides, nicotianamine-iron transporters, lanthipeptides, and a few other types. The S. rochei group can be a potential genetic source of useful secondary metabolites with applications in medicine and biotechnology.
Chromosome-Scale Genomes of the Flightless Caterpillar Hunter Beetles Calosoma tepidum and Calosoma wilkesii From British Columbia (Coleoptera: Carabidae)
Authors: Gauthier Jérémy , Blanc Mickael , Toussaint Emmanuel F A
Published: November 2024

The giant ground beetle genus Calosoma (Coleoptera, Carabidae) comprises ca. 120 species distributed worldwide. About half of the species in this genus are flightless due to a process of wing reduction likely resulting from the colonization of remote habitats such as oceanic islands, highlands, and deserts. This clade is emerging as a new model to study the genomic basis of wing evolution in insects. In this framework, we present the de novo assemblies and annotations of two Calosoma species genomes from British Columbia, Calosoma tepidum and Calosoma wilkesii. Combining PacBio HiFi and Hi-C sequencing, we produce high-quality reference genomes for these two species. Our annotation using long-read RNAseq and existing Coleoptera protein evidence identified a total of 21,976 genes for C. tepidum and 26,814 genes for C. wilkesii. Using synteny analyses, we provide an in-depth comparison of genomic architectures in these two species. We infer an overall pattern of chromosome-scale conservation between the two species, with only minor rearrangements within chromosomes. These new reference genomes represent a major step forward in the study of this group, providing high-quality references that open the door to different approaches such as comparative genomics or population scale resequencing to study the implications of flight evolution.
Associations Between Deficit Accumulation Frailty and Baseline Markers of Lifestyle in the U.S. POINTER Trial
Authors: Espeland Mark A , Demesie Yitbarek N , Olson KayLoni , Lockhart Samuel N , Farias Sarah E Tomaszewski , Cleveland Maryjo L , Tangney Christy C , Crivelli Lucia , Snyder Heather M , York Michele K , Baker Laura D , Whitmer Rachel A , Wing Rena R , Garcia Katelyn R , Callahan Kathryn E
Published: November 2024

Background

Multidomain lifestyle interventions may have the potential to slow biological aging as captured by deficit accumulation frailty indices. We describe the distribution and composition of the 49-component frailty index developed by the U.S. POINTER clinical trial team of investigators and assess its cross-sectional associations with sociodemographic factors and markers chosen to be representative of behaviors targeted by the trial’s multidomain interventions.

Methods

We draw baseline data from the 2 111 volunteers enrolled in U.S. POINTER who were ages 60–79 years and at increased risk for cognitive decline. Frailty components were grouped into 9 domains. Associations that frailty index scores and their domains had with behavioral markers were described with correlations and canonical correlation.

Results

The 25th, 50th, and 75th percentiles of the frailty index score distribution were 0.153, 0.189, and 0.235. Higher frailty scores tended to occur among individuals who were older, male, and living in areas of greater deprivation (all p < .001). They were also associated with poorer self-reported diet, less physical activity, and higher Framingham risk scores (all p < .001). Associations were diffusely distributed among the frailty component domains, indicating that no individual domain was dominating associations.

Conclusions

The U.S. POINTER deficit accumulation frailty index had expected relationships with sociodemographic factors and sensitivity to the behaviors targeted by the trial’s interventions. Our analysis supports its use as a secondary outcome to assess whether the multidomain interventions differentially impact an established marker of biological aging. ClinicalTrials.gov Identifier: NCT03688126.
Integrating deep learning and discrete cosine transform for surface waves full-waveform inversion
Authors: Rincón Felipe , Berti Sean , Aleardi Mattia , Tognarelli Andrea , Stucchi Eusebio
Published: November 2024

Accurate estimations of near-surface S-wave velocity (Vs) models hold particular significance in geological and engineering investigations. On the one hand, the popular multichannel analysis of surface waves (MASWs) is limited to the 1-D and the plane wave assumptions. On the other hand, the more advanced and computationally expensive full-waveform inversion (FWI) approach is often solved within a deterministic framework that hampers an accurate uncertainty assessment and makes the final predictions heavily reliant on the starting model. Here we combine deep learning with discrete cosine transform (DCT) to solve the FWI of surface waves and to efficiently estimate the inversion uncertainties. Our neural network approach effectively learns the inverse non-linear mapping between DCT-compressed seismograms and DCT-compressed S-velocity models. The incorporation of DCT into the deep learning framework provides several advantages: it notably reduces parameter space dimensionality and alleviates the ill-conditioning of the problem. Additionally, it decreases the complexity of the network architecture and the computational cost for the training phase compared to training in the full domain. A Monte Carlo simulation is also used to propagate the uncertainties from the data to the model space. We first test the implemented inversion method on synthetic data to showcase the generalization capabilities of the trained network and to explore the implications of incorrect noise assumptions in the recorded seismograms and inaccurate wavelet estimations. Further, we demonstrate the applicability of the implemented method to field data. In this case, available borehole information is used to validate our predictions. In both the synthetic and field applications, the predictions provided by the proposed method are compared with those of a deterministic FWI and the outcomes of a network trained in the full data and model spaces. Our experiments confirm that the implemented deep-learning inversion efficiently and successfully solves the FWI problem and yields more accurate and stable results than a network trained without the DCT compression. This opens the possibility to efficiently train a neural network that provides accurate instantaneous predictions of Vs near-surface models and related uncertainties.
High-precision identification and prediction of low-voltage load characteristics in smart grids based on hybrid deep learning framework
Authors: Cui Ziti , Wang Wei , Jiang Wei , Guo Jun , Liu Yang
Published: November 2024

This paper proposes a hybrid deep learning framework (HDLF) that combines improved convolutional neural networks (CNNs), long short-term memory (LSTM) networks, and transformer models. First, feature selection and dimensionality reduction are performed using XGBoost and principal component analysis, respectively. Secondly, CNN is enhanced by multiscale convolution, residual connection, and attention mechanism. Then, the bidirectional LSTM is combined with temporal convolutional network to improve the LSTM. Then, an improved dynamic focusing mechanism of transformer is introduced. The experimental results show that the HDLF has an accuracy of 0.945 in identifying low-pressure load characteristics.
Beyond Seeing and Listening: Children Born from Conflict-Related Sexual Violence
Authors: Távara Gabriela
Published: November 2024

This essay discusses some points made by the three books under review regarding how children born of conflict-related sexual violence have not been seen and listened to by those working in the field of transitional justice. To this end, it explores some of the reasons behind this oversight, including generalized assumptions about their relationships with their mothers, families and communities. It also discusses some of the limitations of the current transitional justice framework to address the plight of these children. Finally, the essay emphasizes the importance of analyzing more deeply the particular context in which these children are embedded. To this end it draws from some of the frameworks presented in the three books under review, which allow for a more capacious comprehension of the situation of children born of conflict-related sexual violence.
Inoculation with PGPR co-fermented broths promotes growth, yields, and quality of pepper by increasing soil nutrients and changing soil bacterial community
Authors: Han Yujie , Tian Lei , Luo Yu , Han Lizhen
Published: November 2024

Aims

The purpose of this study was to explore impacts of different combinations of co-fermentation plant growth-promoting rhizobacteria (PGPR) broth on the growth and yield of pepper.

Methods and results

The effects of co-fermentation broth containing a random combination of two PGPR strains on the growth of pepper were analyzed. All inoculation treatments promoted growth, yield, and quality of peppers. The relative abundance of the dominant Proteobacteria and Sphingomonas was significantly higher in the planted soil at the seedling and fruiting stages, and the soil available nitrogen, phosphorus, and potassium contents were correspondingly higher. In addition, the co-fermented broth of Bacillus velezensis HP9 and Burkholderia pyrrocinia P10 treatment had the most pronounced effect on plant growth, while the combination of Bacillus flexus HGD12 and P10 had the greatest impact on fruit nutritional indices. This is consistent with the highest enrichment of beneficial bacterial genera at the seedling stage in the HP9 and P10 treatment and at the fruiting stage in the P10 and HGD12 treatment groups, respectively.

Conclusions

Different combinations of co-fermented bacterial broths increased soil nutrient contents and changed the bacterial community, which in turn promoted the growth, yield, and quality of pepper.
An efficient deep learning method for amino acid substitution model selection
Authors: Tinh Nguyen Huy , Vinh Le Sy
Published: November 2024

Amino acid substitution models play an important role in studying the evolutionary relationships among species from protein sequences. The amino acid substitution model consists of a large number of parameters; therefore, it is estimated from hundreds or thousands of alignments. Both general models and clade-specific models have been estimated and widely used in phylogenetic analyses. The maximum likelihood method is normally used to select the best-fit model for a specific protein alignment under the study. A number of studies have discussed theoretical concerns as well as the computational burden of the maximum likelihood methods in model selection. Recently, machine learning methods have been proposed for selecting nucleotide models. In this article, we propose a method to measure substitution rates among amino acids (called summary statistics) from protein alignments to efficiently train a deep learning network of so-called ModelDetector for detecting amino acid substitution models. The ModelDetector network was trained from 2,246,400 alignments on a computer with eight cores (without GPU) in about 3.3 hr. Experiments on simulation data showed that the accuracy of the ModelDetector was comparable with that of the maximum likelihood method ModelFinder. It was orders of magnitude faster than the maximum likelihood method in inferring amino acid substitution models and able to analyze genome alignments with millions of sites in minutes. The results indicate that the deep learning network can play as a promising tool for amino acid substitution model selection.
Pancreaticoduodenectomy after Roux-en-Y gastric bypass and novel endoscopic ultrasound-directed transgastric ERCP procedure
Authors: Orsi Carolina , Davis Tyler , Moudy Paige , Ismael Hishaam
Published: November 2024

Performing a pancreaticoduodenectomy (PD) in patients having undergone a Roux-en-Y gastric bypass (RNYGB) poses a significant surgical challenge. We present a patient with a history of RNYGB and endoscopic ultrasound-directed transgastric ERCP (EDGE) procedure who underwent a successful PD. This 77-year-old female with history of open RNYBG presented with resectable pancreatic adenocarcinoma. A preoperative EDGE procedure was required for biliary decompression. A PD was performed by removing the entire biliopancreatic limb for oncologic resection. The reconstructive technique here involved utilizing the old common channel for the hepaticojejunostomy, pancreaticojejunostomy, and remnant gastrojejunostomy. The case also included Axios stent placement during a preoperative EDGE procedure. This case describes the first reported successful PD in a patient with prior RNYGB and EDGE procedure. Although the optimal technique for this clinical scenario remains unestablished, this unique case contributes to the literature by demonstrating an effective approach for practicing surgeons.
Preliminary Description of the Jewish Arabic Dialect of Ghardaïa (Central Algeria) with Elements of Phonology, Socio-Phonetics, and Morphology
Authors: Gębski Wiktor
Published: November 2024

Ghardaïa, situated in the centre of Saharan Algeria, is renowned for its well-preserved medieval architecture tracing back to its establishment by the puritanical Ibāḍiyyah sect in the 11th century CE. The city has been home to a Jewish community for centuries, although its exact origins remain debated. Evidence suggests migrations from Djerba, Marrakesh, and Tafilalt shaping a unique Jewish dialect that reflects ties to both Tunisia and Morocco. This paper presents a preliminary linguistic analysis of the Jewish dialect of Ghardaïa, shedding light on its historical layers and socio-linguistic dynamics. Through comparative analysis with neighbouring Muslim dialects, Jewish Djerba, and Jewish Marrakesh, it unravels the complexities of this distinct linguistic heritage, providing insights into its origins and evolution. Additionally, it delves into the nuanced variations between male and female lects within the Jewish community of Ghardaïa, elucidating socio-phonetic features that contribute to the rich diversity of the dialect.
Phytochrome-interacting factors PIF4 and PIF5 directly regulate autophagy during leaf senescence in Arabidopsis
Authors: Lee Juhyeon , Kang Myeong Hoon , Choi Da-Min , Marmagne Anne , Park Jeehye , Lee Heeho , Gwak Eunha , Lee Jong-Chan , Kim Jeong-Il , Masclaux-Daubresse Céline , Lim Pyung Ok
Published: November 2024

During leaf senescence, autophagy plays a critical role by removing damaged cellular components and participating in nutrient remobilization to sink organs. However, how AUTOPHAGY (ATG) genes are regulated during natural leaf senescence remains largely unknown. In this study, we attempted to identify upstream transcriptional regulator(s) of ATG genes and their molecular basis during leaf senescence in Arabidopsis through the combined analyses of promoter binding, autophagy flux, and genetic interactions. We found that PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and PIF5 directly bind to the promoters of ATG5, ATG12a, ATG12b, ATG8a, ATG8e, ATG8f, and ATG8g, inducing their transcription. These target ATG genes are down-regulated in pif4, pif5, and pif4pif5 mutants, resulting in decreased autophagic activity and slower degradation of chloroplast proteins and chlorophyll. Conversely, overexpression of ATG8 genes accelerated protein degradation with early leaf senescence. Moreover, our data suggested partial suppression of the pif4pif5 phenotype by ATG8a overexpression. PIF4/PIF5 also influence senescence induced by nutrient starvation, another hallmark of the autophagy pathway. Furthermore, we observed that the PIF4/PIF5–ATG regulatory module may contribute to seed maturation. Our study not only unveils transcriptional regulators of autophagy in natural leaf senescence but also underscores the potential role of PIF4/PIF5 as functional regulators in leaf senescence and nutrient remobilization.
A search for H i absorption in distant star-forming galaxies with ASKAP-FLASH – I. Selection and analysis of the radio sample
Authors: Eden Sophie L , Sadler Elaine M , Pimbblet Kevin A , Mahony Elizabeth K , Yoon Hyein
Published: November 2024

We present and discuss two catalogues of ultraviolet (UV)-selected (near-UV (NUV)$\lt 22.8$ mag) galaxies that lie within a 200 deg$^2$ area of sky covered by the ASKAP First Large Absorption Survey in H i (FLASH) and have an impact parameter of less than 20 arcsec to a FLASH radio continuum source. These catalogues are designed to enable a future search for 21 cm H i absorption in and around star-forming galaxies at redshift $0.4\lt z\lt 1$. We outline the production of this UV-bright data set, which has optical spectroscopy from the WiggleZ and Sloan Digital Sky Survey (SDSS) surveys and a median redshift of ${\sim} 0.6$. Analysis of the optical spectra, using multiple diagnostic diagrams, shows that galaxies with an impact parameter of less than 5 arcsec are likely to be physically associated with the radio source and are five times more likely to be an active galactic nucleus than objects without a radio match. Conversely, objects with impact factors between 5 and 20 arcsec are largely (>80 per cent) star-forming and resemble the overall WiggleZ population. The ($g - i$) colour evolution with redshift is consistent with a history of active star formation, but the radio-associated objects are typically redder and have colours similar to high-excitation radio galaxies. The redshift distribution of the two catalogues matches the overall distribution for WiggleZ galaxies, despite their otherwise rare radio properties. These catalogues can be expanded in future as new radio data become available, and a forthcoming paper will present the H i absorption results.
Characterizing long-term astroclimate parameters at the Muztagh-Ata site in the Pamir plateau with ERA5 and MERRA-2 data
Authors: Zhang Jicheng , Zhao Yong , Gao Jian , Esamdin Ali , Zhang Wenzhao , Yuan Haibo , Feng Guojie , Niu Hubiao , Gu Wenbo , Zhang Xuan , Bai Chunhai
Published: November 2024

The Muztagh-Ata site, an excellent high-altitude ground-based astronomical observing site was discovered and monitored in the eastern part of the Pamir Plateau in the southwestern Xinjiang Uygur Autonomous Region of China. This site has been systematically monitored using various observational parameters since the spring of 2017. Yet, the site lacks long-term monitoring and statistical characterization of key variables such as: precipitable water vapour (PWV) and air temperature. These factors directly influence whether a site is suitable for hosting large ground-based telescopes across optical, infrared, submillimeter, and millimeter wavelengths in later stages. In this study, we utilized atmospheric reanalysis data sets from the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2) and ERA5, the fifth edition of the European Centre for Medium-Range Weather Forecasts (ECMWF). These data sets were combined with local observations from the weather station at the Muztagh-Ata site. Following the validation of ground-based and satellite data, we conducted a comparative analysis of PWV and temperature trends at the Muztagh-Ata site over a period of 24 yr. The weighted annual mean nighttime temperature and PWV increase at rates of 0.18 $\sim$ 0.38$^{\circ }$C decade$^{-1}$ and 0.02 $\sim$ 0.15 mm decade$^{-1}$, respectively. The nighttime PWV slightly decrease during the winter with rates of $-$0.01 $\sim \, -$0.03 mm decade$^{-1}$. This findings reveal that the PWV and temperature variation patterns at the Muztagh-Ata site are consistently stable, particularly in the results derived from the ERA5 data set. The comprehensive conditions at this site are highly suitable and advantageous for hosting large optical, infrared, submillimeter, and millimeter wavelengths telescope installations.
Battle of the CH motions: aliphatic versus aromatic contributions to astronomical PAH emission and exploration of the aliphatic, aromatic, and ethynyl CH stretches
Authors: Esposito Vincent J , Bejaoui Salma , Billinghurst Brant E , Boersma Christiaan , Fortenberry Ryan C , Salama Farid
Published: November 2024

Strong anharmonic coupling between vibrational states in polycyclic aromatic hydrocarbons (PAH) produces highly mixed vibrational transitions that challenge the current understanding of the nature of the astronomical mid-infrared PAH emission bands. Traditionally, PAH emission bands have been characterized as either aromatic or aliphatic, and this assignment is used to determine the fraction of aliphatic carbon in astronomical sources. In reality, each of the transitions previously utilized for such an attribution is highly mixed with contributions from both aliphatic and aromatic CH motions as well as non-CH motions such as CC stretches. High-resolution gas-phase IR absorption measurements of the spectra of the aromatic molecules indene and 2-ethynyltoluene at the Canadian Light Source combined with high-level anharmonic quantum chemical computations reveal the complex nature of these transitions, implying that the use of these features as a marker for the aliphatic fraction in astronomical sources is not uniquely true or actually predictive. Further, the presence of aliphatic, aromatic, and ethynyl CH groups in 2-ethynyltoluene provides an internally consistent opportunity to simultaneously study the spectroscopy of all three astronomically important groups. Finally, this study makes an explicit connection between fundamental quantum mechanical principles and macroscopic astronomical chemical physics, an important link necessary to untangle the lifecycle of stellar and planetary systems.
Accurate Inference of the Polyploid Continuum Using Forward-Time Simulations
Authors: Dunn Tamsen , Sethuraman Arun
Published: November 2024

Multiple rounds of whole-genome duplication (WGD) followed by diploidization have occurred throughout the evolutionary history of angiosperms. Much work has been done to model the genomic consequences and evolutionary significance of WGD. While researchers have historically modeled polyploids as either allopolyploids or autopolyploids, the variety of natural polyploids span a continuum of differentiation across multiple parameters, such as the extent of polysomic versus disomic inheritance, and the degree of genetic differentiation between the ancestral lineages. Here we present a forward-time polyploid genome evolution simulator called SpecKS. SpecKS models polyploid speciation as originating from a 2D continuum, whose dimensions account for both the level of genetic differentiation between the ancestral parental genomes, as well the time lag between ancestral speciation and their subsequent reunion in the derived polyploid. Using extensive simulations, we demonstrate that changes in initial conditions along either dimension of the 2D continuum deterministically affect the shape of the Ks histogram. Our findings indicate that the error in the common method of estimating WGD time from the Ks histogram peak scales with the degree of allopolyploidy, and we present an alternative, accurate estimation method that is independent of the degree of allopolyploidy. Lastly, we use SpecKS to derive tests that infer both the lag time between parental divergence and WGD time, and the diversity of the ancestral species, from an input Ks histogram. We apply the latter test to transcriptomic data from over 200 species across the plant kingdom, the results of which are concordant with the prevailing theory that the majority of angiosperm lineages are derived from diverse parental genomes and may be of allopolyploid origin.
Intercellular mosaic methylation in fast-growing Mycobacterium tuberculosis clinical isolates
Authors: Ahmadi Jeshvaghane Maryam , Modlin Samuel J , Conkle-Gutierrez Derek , Espinoza Monica E , Valafar Faramarz
Published: November 2024

Orphan DNA adenine methyltransferases (MTases) of Mycobacterium tuberculosis (Mtb) exhibit diversity across clinical isolates, but the forces driving this variation are not entirely clear. Recently, we observed several isolates exhibiting anomalous hypomethylation by Type I MTase Mycobacterial Adenine Methyltransferase C (MamC) despite a wild-type mamC genotype (‘MamC-anomalous’ isolates). Investigating this hypomethylation through multiple analyses revealed three key findings. First, heterogeneity analysis revealed intercellular mosaic methylation (IMM) in MamC-anomalous isolates. While they often exhibit phase-variable heterogeneity, this is the first report of IMM by a prokaryotic Type I MTase. Second, MamC-anomalous isolates exhibited a large, stable difference in chromosome copy number along the replication axis (a proxy for bacterial growth rate), suggesting a distinct growth phase accompanied by MamC hypomethylation. Third, MamC methylation efficiency decreased progressively with distance from the origin of replication on both strands, with a marked exaggeration in MamC-anomalous isolates. In contrast, other Mtb MTases (MamA and MamB) exhibited lower methylation levels away from the origin only on the lagging strand, and without exaggeration in MamC-anomalous isolates. We conclude that, among Mtb MTases, MamC DNA methylation is uniquely linked to growth dynamics.
Machine learning prediction of brain metastasis invasion pattern on brain magnetic resonance imaging scans
Authors: Najafian Keyhan , Rehany Benjamin , Nowakowski Alexander , Ghazimoghadam Saba , Pierre Kevin , Zakarian Rita , Al-Saadi Tariq , Reinhold Caroline , Babajani-Feremi Abbas , Wong Joshua K , Guiot Marie-Christine , Lacasse Marie-Constance , Lam Stephanie , Siegel Peter M , Petrecca Kevin , Dankner Matthew , Forghani Reza
Published: November 2024

Background

Brain metastasis invasion pattern (BMIP) is an emerging biomarker associated with recurrence-free and overall survival in patients, and differential response to therapy in preclinical models. Currently, BMIP can only be determined from the histopathological examination of surgical specimens, precluding its use as a biomarker prior to therapy initiation. The aim of this study was to investigate the potential of machine learning (ML) approaches to develop a noninvasive magnetic resonance imaging (MRI)-based biomarker for BMIP determination.

Methods

From an initial cohort of 329 patients, a subset of 132 patients met the inclusion criteria for this retrospective study. We evaluated the ability of an expert neuroradiologist to reliably predict BMIP. Thereafter, the dataset was randomly divided into training/validation (80% of cases) and test subsets (20% of cases). The ground truth for BMIP was the histopathologic evaluation of resected specimens. Following MRI sequence co-registration, advanced feature extraction techniques deriving hand-crafted radiomic features with traditional ML classifiers and convolution-based deep learning (CDL) models were trained and evaluated. Different ML approaches were used individually or using ensembling techniques to determine the model with the best performance for BMIP prediction.

Results

Expert evaluation of brain MRI scans could not reliably predict BMIP, with an accuracy of 44%–59% depending on the semantic feature used. Among the different ML and CDL models evaluated, the best-performing model achieved an accuracy of 85% and an F1 score of 90%.

Conclusions

ML approaches can effectively predict BMIP, representing a noninvasive MRI-based approach to guide the management of patients with brain metastases.
A tactile perception method with flexible grating structural color
Authors: Qiu Yuze , Yan Chunfei , Zhang Yan , Yang Shengxuan , Yao Xiang , Ai Fawen , Zheng Jinjin , Zhang Shiwu , Yu Xinge , Dong Erbao
Published: November 2024

Affordable high-resolution cameras and state-of-the-art computer vision techniques have led to the emergence of various vision-based tactile sensors. However, current vision-based tactile sensors mainly depend on geometric optics or marker tracking for tactile assessments, resulting in limited performance. To solve this dilemma, we introduce optical interference patterns as the visual representation of tactile information for flexible tactile sensors. We propose a novel tactile perception method and its corresponding sensor, combining structural colors from flexible blazed gratings with deep learning. The richer structural colors and finer data processing foster the tactile estimation performance. The proposed sensor has an overall normal force magnitude accuracy of 6 mN, a planar resolution of 79 μm and a contact-depth resolution of 25 μm. This work presents a promising tactile method that combines wave optics, soft materials and machine learning. It performs well in tactile measurement, and can be expanded into multiple sensing fields.
Influence of global warming and human activity on mercury accumulation patterns in wetlands across the Qinghai–Tibet Plateau
Authors: Feng Xinbin , Wang Xun , Jia Longyu , Yuan Wei , Lu Meng , Liu Nantao , Wu Fei , Cai Xinyuan , Wang Feiyue , Lin Che-Jen
Published: November 2024

Wetlands in the Qinghai–Tibet Plateau are a unique and fragile ecosystem undergoing rapid changes. We show two unique patterns of mercury (Hg) accumulation in wetland sediments. One is the ‘surface peak’ in monsoon-controlled regions and the other is the ‘subsurface peak’ in westerly-controlled regions. The former is attributed to the combined effects of increasing anthropogenic emissions and climate-induced changes in the cryosphere and wetland hydrology in the last 100−150 years. The climate changes in westerly-controlled regions in the last 50−70 years led to a fluctuation in hydrology and Hg peak in the sediment subsurface. The increase in legacy Hg input from soil erosion has largely enhanced the Hg accumulation rate in wetlands since the 1950s, especially in the proglacial wetlands. We highlight that accelerated glacier melting and permafrost thawing caused by global warming have altered geomorphology and hydrology, and affected Hg transport and accumulation in wetlands.