bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean
Authors: Skourtanioti Eirini , Ringbauer Harald , Gnecchi Ruscone Guido Alberto , Bianco Raffaela Angelina , Burri Marta , Freund Cäcilia , Furtwängler Anja , Gomes Martins Nuno Filipe , Knolle Florian , Neumann Gunnar U. , Tiliakou Anthi , Agelarakis Anagnostis , Andreadaki-Vlazaki Maria , Betancourt Philip , Hallager Birgitta P. , Jones Olivia A. , Kakavogianni Olga , Kanta Athanasia , Karkanas Panagiotis , Kataki Efthymia , Kissas Konstantinos , Koehl Robert , Kvapil Lynne , Maran Joseph , McGeorge Photini J. P. , Papadimitriou Alkestis , Papathanasiou Anastasia , Papazoglou-Manioudaki Lena , Paschalidis Kostas , Polychronakou-Sgouritsa Naya , Preve Sofia , Prevedorou Eleni-Anna , Price Gypsy , Protopapadaki Eftychia , Schmidt-Schultz Tyede , Schultz Michael , Shelton Kim , Wiener Malcolm H. , Krause Johannes , Jeong Choongwon , Stockhammer Philipp W. 
Published: January 2023

AbstractThe Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean—a region fundamental to Europe’s prehistory—the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans. In contrast, the end of the Neolithic period and the following Early Bronze Age were marked by ‘eastern’ gene flow, which was predominantly of Anatolian origin in Crete. Confirming previous findings for additional Central/Eastern European ancestry in the Greek mainland by the Middle Bronze Age, we additionally show that such genetic signatures appeared in Crete gradually from the seventeenth to twelfth centuries bc, a period when the influence of the mainland over the island intensified. Biological and cultural connectedness within the Aegean is also supported by the finding of consanguineous endogamy practiced at high frequencies, unprecedented in the global ancient DNA record. Our results highlight the potential of archaeogenomic approaches in the Aegean for unravelling the interplay of genetic admixture, marital and other cultural practices.
A modality-independent proto-organization of human multisensory areas
Authors: Setti Francesca , Handjaras Giacomo , Bottari Davide , Leo Andrea , Diano Matteo , Bruno Valentina , Tinti Carla , Cecchetti Luca , Garbarini Francesca , Pietrini Pietro , Ricciardi Emiliano 
Published: January 2023

AbstractThe processing of multisensory information is based upon the capacity of brain regions, such as the superior temporal cortex, to combine information across modalities. However, it is still unclear whether the representation of coherent auditory and visual events requires any prior audiovisual experience to develop and function. Here we measured brain synchronization during the presentation of an audiovisual, audio-only or video-only version of the same narrative in distinct groups of sensory-deprived (congenitally blind and deaf) and typically developed individuals. Intersubject correlation analysis revealed that the superior temporal cortex was synchronized across auditory and visual conditions, even in sensory-deprived individuals who lack any audiovisual experience. This synchronization was primarily mediated by low-level perceptual features, and relied on a similar modality-independent topographical organization of slow temporal dynamics. The human superior temporal cortex is naturally endowed with a functional scaffolding to yield a common representation across multisensory events.
[11C]metomidate PET-CT versus adrenal vein sampling for diagnosing surgically curable primary aldosteronism: a prospective, within-patient trial
Authors: Wu Xilin , Senanayake Russell , Goodchild Emily , Bashari Waiel A. , Salsbury Jackie , Cabrera Claudia P. , Argentesi Giulia , O’Toole Samuel M. , Matson Matthew , Koo Brendan , Parvanta Laila , Hilliard Nick , Kosmoliaptsis Vasilis , Marker Alison , Berney Daniel M. , Tan Wilson , Foo Roger , Mein Charles A. , Wozniak Eva , Savage Emmanuel , Sahdev Anju , Bird Nicholas , Laycock Kate , Boros Istvan , Hader Stefan , Warnes Victoria , Gillett Daniel , Dawnay Anne , Adeyeye Elizabeth , Prete Alessandro , Taylor Angela E. , Arlt Wiebke , Bhuva Anish N. , Aigbirhio Franklin , Manisty Charlotte , McIntosh Alasdair , McConnachie Alexander , Cruickshank J. Kennedy , Cheow Heok , Gurnell Mark , Drake William M. , Brown Morris J. 
Published: January 2023

AbstractPrimary aldosteronism (PA) due to a unilateral aldosterone-producing adenoma is a common cause of hypertension. This can be cured, or greatly improved, by adrenal surgery. However, the invasive nature of the standard pre-surgical investigation contributes to fewer than 1% of patients with PA being offered the chance of a cure. The primary objective of our prospective study of 143 patients with PA (NCT02945904) was to compare the accuracy of a non-invasive test, [11C]metomidate positron emission tomography computed tomography (MTO) scanning, with adrenal vein sampling (AVS) in predicting the biochemical remission of PA and the resolution of hypertension after surgery. A total of 128 patients reached 6- to 9-month follow-up, with 78 (61%) treated surgically and 50 (39%) managed medically. Of the 78 patients receiving surgery, 77 achieved one or more PA surgical outcome criterion for success. The accuracies of MTO at predicting biochemical and clinical success following adrenalectomy were, respectively, 72.7 and 65.4%. For AVS, the accuracies were 63.6 and 61.5%. MTO was not significantly superior, but the differences of 9.1% (95% confidence interval = −6.5 to 24.1%) and 3.8% (95% confidence interval = −11.9 to 9.4) lay within the pre-specified −17% margin for non-inferiority (P = 0.00055 and P = 0.0077, respectively). Of 24 serious adverse events, none was considered related to either investigation and 22 were fully resolved. MTO enables non-invasive diagnosis of unilateral PA.
Molecular residual disease and efficacy of adjuvant chemotherapy in patients with colorectal cancer
Authors: Kotani Daisuke , Oki Eiji , Nakamura Yoshiaki , Yukami Hiroki , Mishima Saori , Bando Hideaki , Shirasu Hiromichi , Yamazaki Kentaro , Watanabe Jun , Kotaka Masahito , Hirata Keiji , Akazawa Naoya , Kataoka Kozo , Sharma Shruti , Aushev Vasily N. , Aleshin Alexey , Misumi Toshihiro , Taniguchi Hiroya , Takemasa Ichiro , Kato Takeshi , Mori Masaki , Yoshino Takayuki 
Published: January 2023

AbstractDespite standard-of-care treatment, more than 30% of patients with resectable colorectal cancer (CRC) relapse. Circulating tumor DNA (ctDNA) analysis may enable postsurgical risk stratification and adjuvant chemotherapy (ACT) treatment decision-making. We report results from GALAXY, which is an observational arm of the ongoing CIRCULATE-Japan study (UMIN000039205) that analyzed presurgical and postsurgical ctDNA in patients with stage II–IV resectable CRC (n = 1,039). In this cohort, with a median follow-up of 16.74 months (range 0.49–24.83 months), postsurgical ctDNA positivity (at 4 weeks after surgery) was associated with higher recurrence risk (hazard ratio (HR) 10.0, P < 0.0001) and was the most significant prognostic factor associated with recurrence risk in patients with stage II or III CRC (HR 10.82, P < 0.001). Furthermore, postsurgical ctDNA positivity identified patients with stage II or III CRC who derived benefit from ACT (HR 6.59, P < 0.0001). The results of our study, a large and comprehensive prospective analysis of ctDNA in resectable CRC, support the use of ctDNA testing to identify patients who are at increased risk of recurrence and are likely to benefit from ACT.
Unsupervised EEG preictal interval identification in patients with drug-resistant epilepsy
Authors: Leal Adriana , Curty Juliana , Lopes Fábio , Pinto Mauro F. , Oliveira Ana , Sales Francisco , Bianchi Anna M. , Ruano Maria G. , Dourado António , Henriques Jorge , Teixeira César A. 
Published: January 2023

AbstractTypical seizure prediction models aim at discriminating interictal brain activity from pre-seizure electrographic patterns. Given the lack of a preictal clinical definition, a fixed interval is widely used to develop these models. Recent studies reporting preictal interval selection among a range of fixed intervals show inter- and intra-patient preictal interval variability, possibly reflecting the heterogeneity of the seizure generation process. Obtaining accurate labels of the preictal interval can be used to train supervised prediction models and, hence, avoid setting a fixed preictal interval for all seizures within the same patient. Unsupervised learning methods hold great promise for exploring preictal alterations on a seizure-specific scale. Multivariate and univariate linear and nonlinear features were extracted from scalp electroencephalography (EEG) signals collected from 41 patients with drug-resistant epilepsy undergoing presurgical monitoring. Nonlinear dimensionality reduction was performed for each group of features and each of the 226 seizures. We applied different clustering methods in searching for preictal clusters located until 2 h before the seizure onset. We identified preictal patterns in 90% of patients and 51% of the visually inspected seizures. The preictal clusters manifested a seizure-specific profile with varying duration (22.9 ± 21.0 min) and starting time before seizure onset (47.6 ± 27.3 min). Searching for preictal patterns on the EEG trace using unsupervised methods showed that it is possible to identify seizure-specific preictal signatures for some patients and some seizures within the same patient.
Imaging features of localized IDH wild-type histologically diffuse astrocytomas: a single-institution case series
Authors: Kibe Yuji , Motomura Kazuya , Ohka Fumiharu , Aoki Kosuke , Shimizu Hiroyuki , Yamaguchi Junya , Nishikawa Tomohide , Saito Ryuta 
Published: January 2023

AbstractIsocitrate dehydrogenase wild-type (IDHwt) diffuse astrocytomas feature highly infiltrative patterns, such as a gliomatosis cerebri growth pattern with widespread involvement. Among these tumors, localized IDHwt histologically diffuse astrocytomas are rarer than the infiltrative type. The aim of this study was to assess and describe the clinical, radiographic, histopathological, and molecular characteristics of this rare type of IDHwt histologically diffuse astrocytomas and thereby provide more information on how its features affect clinical prognoses and outcomes. We retrospectively analyzed the records of five patients with localized IDHwt histologically diffuse astrocytomas between July 2017 and January 2020. All patients were female, and their mean age at the time of the initial treatment was 55.0 years. All patients had focal disease that did not include gliomatosis cerebri or multifocal disease. All patients received a histopathological diagnosis of diffuse astrocytomas at the time of the initial treatment. For recurrent tumors, second surgeries were performed at a mean of 12.4 months after the initial surgery. A histopathological diagnosis of glioblastoma was made in four patients and one of gliosarcoma in one patient. The initial status of IDH1, IDH2, H3F3A, HIST1H3B, and BRAF was “wild-type” in all patients. TERT promoter mutations (C250T or C228T) were detected in four patients. No tumors harbored a 1p/19q codeletion, EGFR amplification, or chromosome 7 gain/10 loss (+ 7/ − 10). We assessed clinical cases of localized IDHwt histologically diffuse astrocytomas that resulted in malignant recurrence and a poor clinical prognosis similar to that of glioblastomas. Our case series suggests that even in patients with histologically diffuse astrocytomas and those who present with radiographic imaging findings suggestive of a localized tumor mass, physicians should consider the possibility of IDHwt histologically diffuse astrocytomas.
The telomerase activator TA-65 protects from cigarette smoke-induced small airway remodeling in mice through extra-telomeric effects
Authors: Tiendrébéogo Arnaud Jean Florent , Soumagne Thibaud , Pellegrin François , Dagouassat Maylis , Tran Van Nhieu Jeanne , Caramelle Philippe , Paul Emmanuel N. , Even Benjamin , Zysman Maeva , Julé Yvon , Samb Abdoulaye , Boczkowski Jorge , Lanone Sophie , Schlemmer Frédéric 
Published: January 2023

AbstractSmall airway remodeling (SAR) is a key phenomenon of airflow obstruction in smokers, leading to chronic obstructive pulmonary disease (COPD). SAR results in an increased thickness of small airway walls, with a combination of peribronchiolar fibrosis with increased fibrous tissue and accumulation of mesenchymal and epithelial cells. SAR pathogenesis is still unclear but recent data suggest that alterations in telomerase activity could represent a possible underlying mechanism of SAR. Our study was dedicated to identify a potential protective role of TA-65, a pharmacological telomerase activator, in a cigarette smoke (CS) model of SAR in mice, and to further precise if extra-telomeric effects of telomerase, involving oxidative stress modulation, could explain it. C57BL/6J mice were daily exposed to air or CS during 4 weeks with or without a concomitant administration of TA-65 starting 7 days before CS exposure. Morphological analyses were performed, and mucus production, myofibroblast differentiation, collagen deposition, as well as transforming growth factor-β1 (TGF-β1) expression in the small airway walls were examined. In addition, the effects of TA-65 treatment on TGF-β expression, fibroblast-to-myofibroblast differentiation, reactive oxygen species (ROS) production and catalase expression and activity were evaluated in primary cultures of pulmonary fibroblasts and/or mouse embryonic fibroblasts in vitro. Exposure to CS during 4 weeks induced SAR in mice, characterized by small airway walls thickening and peribronchiolar fibrosis (increased deposition of collagen, expression of α-SMA in small airway walls), without mucus overproduction. Treatment of mice with TA-65 protected them from CS-induced SAR. This effect was associated with the prevention of CS-induced TGF-β expression in vivo, the blockade of TGF-β-induced myofibroblast differentiation, and the reduction of TGF-β-induced ROS production that correlates with an increase of catalase expression and activity. Our findings demonstrate that telomerase is a critical player of SAR, probably through extra-telomeric anti-oxidant effects, and therefore provide new insights in the understanding and treatment of COPD pathogenesis.
Attention-deficit hyperactivity disorder traits are a more important predictor of internalising problems than autistic traits
Authors: Hargitai Luca D. , Livingston Lucy A. , Waldren Lucy H. , Robinson Ross , Jarrold Christopher , Shah Punit 
Published: January 2023

AbstractAutism Spectrum Disorder (ASD) and Attention-Deficit Hyperactivity Disorder (ADHD) are both linked to internalising problems like anxiety and depression. ASD and ADHD also often co-occur, making their individual statistical contributions to internalising disorders difficult to investigate. To address this issue, we explored the unique associations of self-reported ASD traits and ADHD traits with internalising problems using a large general population sample of adults from the United Kingdom (N = 504, 49% male). Classical regression analyses indicated that both ASD traits and ADHD traits were uniquely associated with internalising problems. Dominance and Bayesian analyses confirmed that ADHD traits were a stronger, more important predictor of internalising problems. However, brief depression and anxiety measures may not provide a comprehensive index of internalising problems. Additionally, we focused on recruiting a sample that was representative of the UK population according to age and sex, but not ethnicity, a variable that may be linked to internalising disorders. Nevertheless, our findings indicate that while ASD and ADHD uniquely predict internalising problems, ADHD traits are a more important statistical predictor than ASD traits. We discuss potential mechanisms underlying this pattern of results and the implications for research and clinical practice concerning neurodevelopmental conditions.
Genetic and ecological drivers of molt in a migratory bird
Authors: Contina Andrea , Bossu Christen M. , Allen Daniel , Wunder Michael B. , Ruegg Kristen C. 
Published: January 2023

AbstractThe ability of animals to sync the timing and location of molting (the replacement of hair, skin, exoskeletons or feathers) with peaks in resource availability has important implications for their ecology and evolution. In migratory birds, the timing and location of pre-migratory feather molting, a period when feathers are shed and replaced with newer, more aerodynamic feathers, can vary within and between species. While hypotheses to explain the evolution of intraspecific variation in the timing and location of molt have been proposed, little is known about the genetic basis of this trait or the specific environmental drivers that may result in natural selection for distinct molting phenotypes. Here we take advantage of intraspecific variation in the timing and location of molt in the iconic songbird, the Painted Bunting (Passerina ciris) to investigate the genetic and ecological drivers of distinct molting phenotypes. Specifically, we use genome-wide genetic sequencing in combination with stable isotope analysis to determine population genetic structure and molting phenotype across thirteen breeding sites. We then use genome-wide association analysis (GWAS) to identify a suite of genes associated with molting and pair this with gene-environment association analysis (GEA) to investigate potential environmental drivers of genetic variation in this trait. Associations between genetic variation in molt-linked genes and the environment are further tested via targeted SNP genotyping in 25 additional breeding populations across the range. Together, our integrative analysis suggests that molting is in part regulated by genes linked to feather development and structure (GLI2andCSPG4) and that genetic variation in these genes is associated with seasonal variation in precipitation and aridity. Overall, this work provides important insights into the genetic basis and potential selective forces behind phenotypic variation in what is arguably one of the most important fitness-linked traits in a migratory bird.
Rapid, multiplex detection of SARS-CoV-2 using isothermal amplification coupled with CRISPR-Cas12a
Authors: Figueiredo Diogo , Cascalheira António , Goncalves Joao 
Published: January 2023

AbstractIn December 2019 an outbreak erupted due to the beta coronavirus Severe Acute Respiratory Syndrome Coronavirus 2 in Wuhan, China. The disease caused by this virus (COVID-19) rapidly spread to all parts of the globe leading to a global pandemic. Efforts to combat the pandemic rely on RT-qPCR diagnostic tests that have high turnaround times (~ 24 h), are easily contaminated, need specialized equipment, facilities, and personnel that end up increasing the overall costs of this method. Loop-mediated isothermal amplification (LAMP) coupled with a reverse transcription step (RT-LAMP) is an alternative diagnostic method that can easily overcome these obstacles, when coupled with CRISPR/Cas it can eliminate false positives. Here we report a fast (~ 40 min), highly sensitive, point-of-care multiplex RT-LAMP and CRISPR/Cas12a assay to detect SARS-CoV-2. This fluorescence-based test achieved 100% specificity and 93% sensitivity using 25 positives and 50 negative patient samples for Ct < 35. Our reported LoD of 3 copies/µL will enable the robust, fast detection of the virus in a dedicated equipment which is a major step towards population-wide accessible testing.
A desire for distraction: uncovering the rates of media multitasking during online research studies
Authors: Drody Allison C. , Pereira Effie J. , Smilek Daniel 
Published: January 2023

AbstractInterpretations of task performance in many cognitive studies rest on the assumption that participants are fully attentive to the tasks they agree to complete. However, with research studies being increasingly conducted online where monitoring participant engagement is difficult, this assumption may be inaccurate. If participants were found to be engaging in off-task behaviours while participating in these studies, the interpretation of study results might be called into question. To investigate this issue, we conducted a secondary data analysis across nearly 3000 participants in various online studies to examine the prevalence of one form of off-task behaviour: media multitasking. Rates of media multitasking were found to be high, averaging 38% and ranging from 9 to 85% across studies. Our findings broadly raise questions about the interpretability of results from online studies and urge researchers to consider the likelihood that participants are simultaneously engaging in off-task behaviours while completing online research tasks.
Monitoring phage-induced lysis of gram-negatives in real time using a fluorescent DNA dye
Authors: Egido Julia E. , Toner-Bartelds Catherine , Costa Ana Rita , Brouns Stan J. J. , Rooijakkers Suzan H. M. , Bardoel Bart W. , Haas Pieter-Jan 
Published: January 2023

AbstractBacteriophages (phages) are viruses that specifically attack bacteria. Their use as therapeutics, which constitutes a promising alternative to antibiotics, heavily relies on selecting effective lytic phages against the pathogen of interest. Current selection techniques are laborious and do not allow for direct visualization of phage infection dynamics. Here, we present a method that circumvents these limitations. It can be scaled for high-throughput and permits monitoring of the phage infection in real time via a fluorescence signal readout. This is achieved through the use of a membrane-impermeant nucleic acid dye that stains the DNA of damaged or lysed bacteria and new phage progeny. We have tested the method on Pseudomonas aeruginosa and Klebsiella pneumoniae and show that an increase in fluorescence reflects phage-mediated killing. This is confirmed by other techniques including spot tests, colony plating, flow cytometry and metabolic activity measurements. Furthermore, we illustrate how our method may be used to compare the activity of different phages and to screen the susceptibility of clinical isolates to phage. Altogether, we present a fast, reliable way of selecting phages against Gram-negative bacteria, which may be valuable in optimizing the process of selecting phages for therapeutic use.