bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tumor Segmentation using temporal Independent Component Analysis for DCE-MRI
Authors: Lee Joonsang , Zhao Qun , Kent Marc , Platt Simon 
Published: December 2022

AbstractIn this study, we developed the temporal independent component analysis (tICA) to solve the partial volume effect (PVE) in canine brain tumor segmentation. The performance of the tICA is compared to that of spatial ICA (sICA) and an expert manual delineation of tumors based on three criteria: percent volume overlap or Dice coefficient, and percent volume difference. Seven in vivo DCE-MRI datasets of spontaneously occurring canine brain tumors were acquired on a 3 Tesla MRI system. The mean value of percent volume overlap (76.00%) between sICA and manual segmentation is lower than that between tICA and manual segmentation, which is 81.11%. In conclusion, the performance of the two ICA methods for segmenting tumors is very close to that of the expert delineation method. However, the tICA has the advantage over the sICA method in its ability to separate independent tissue signals in a voxel containing different types of tissues.
“Crochet … a little hook to improve attention?”
Authors: Sebastiano Davide Rossi , Muscio Cristina , Duran Dunja , Bonfoco Deborah , Dotta Sara , Anversa Paola , Tiraboschi Pietro , Visani Elisa 
Published: December 2022

AbstractIn this work we compared the short-term effects of crochet on the performance in the well-known Attention Network Test and on the global cortical functioning networks revealed by magnetoencephalography between a group of crocheters and a sex and age-matched control group.Our data revealed that crochet is associated with an increase of the alerting and the orienting networks even after a brief, single work session and that this behavioural effect seems to have a counterpart in the modification seen in the global functional connectivity of the brain, where an increased speed of the information exchange between different brain areas have been seen. Moreover, we discuss the hypothesis that these effects on attentional networks are dissimilar from those determined by meditation, where an improvement in the executive control was previously demonstrated as the main effect.Our results provided for the first time that crochet is associated with an increase in the attentional networks, and namely in alerting and orienting networks, paving the way for the use of textile-related arts in the neurorehabilitation, possibly in combination with meditation, considering that the two practices promote complementary effects on the attentional networks.HighlightsCrocheting positively affects attention, improving alerting and orientingCrocheting speeds up the information exchange between different brain areasCrocheting and meditation promote different effects on the attentional networks
Perilous coexistence:Chilli Leaf Curl VirusandCandidatus Phytoplasma trifoliiinfectingCapsicum annuum, India
Authors: Pandey Vineeta , Srivastava Aarshi , Mall Smriti , Al-Sadi Abdullah M. , Shahid Muhammad Shafiq , Gaur R. K. 
Published: December 2022

AbstractMolecular computing was used to investigate the possible causal agents of chilli crop samples showing mixed symptoms of yellow leaf curl and little leaf type diseases in the Uttar Pradesh province, India. Total genomic DNA was extracted from twenty-five samples and amplified by PCR using a universal primer pair for begomovirus and phytoplasma. Mixed infection samples show positive amplified products for begomovirus (DNA-A and betasatellite) and phytoplasma (16S rRNA and Sec A). The identified begomovirus from chilli samples was identified as a strain isolate of the previously described Chilli Leaf Curl Virus (94.2% nucleotide sequence identity), which is known to infectSolanum lycopersicon, in Oman, whereas the 16S rRNA was identified from the sourceCandidatus Phytoplasma trifolii(99.04% nucleotide sequence identity), which is known to infect Helichrysum flowering plants in India. Subsequently, molecular computing research based on phylogenetic interweaves, putative recombination, amino acid selection, and genetic diversity were investigated, revealing divergent evolutionary patterns with significant variation and recombination events. The majority of the sequence variations observed in begomovirus and phytoplasma were caused via inter- and intra-specific recombination. These findings could be the firstin silicocombined infection analysis of ChiLCV andCa.P.trifoliiin a chilli crop in India, revealing the potential adaption and evolution of begomovirus and phytoplasma to a new geographic range and crop.
Functional characterization of a small gene family coding for putrescine hydroxycinnamoyltransferases in tomato
Authors: Roumani Marwa , Besseau Sébastien , Hehn Alain , Larbat Romain 
Published: December 2022

AbstractPhenolamides are specialized metabolites widely distributed in the plant kingdom. Their structure is composed by the association of hydroxycinnamic acid derivatives to mono-/poly-amine. This association is catalyzed by N-hydroxycinnamoyltransferases enzymes. Tomato plants are accumulating putrescine-derived phenolamides in their vegetative parts. Recently, we identified two genes coding for putrescine-hydroxycinnamoyltransferase (PHT,Solyc11g071470 and Solyc11g071480), which control the accumulation of caffeoylputrescine in tomato leaf submitted to the infestation of leafminer. In this study, we prospected for additional genes implicated in the accumulation of putrescine-derived phenolamides in the tomato vegetative organs. We identified two genes (Solyc06g074710andSolyc11g066640) that we functionally characterized as new PHT. The substrate specificity and the expression patternin plantawas determined for the four tomato PHT. Taken together the results give a comprehensive view of the control of the putrescine-derived phenolamide accumulation in tomato plant through the biochemical specificity and the spatial expression of this small family of PHT.Main conclusionWe identified and functionally characterized two new putrescine hydroxycinnamoyl transferases (PHT) in tomato. These enzymes complete a set a four PHT which control the distribution of putrescine-derived phenolamides in tomato plants.
Home range and dynamic space use reveals age-related differences in risk exposure for reintroduced parrots
Authors: Forrest S. W. , Rodríguez-Recio M. , Seddon P. J. 
Published: December 2022

AbstractIndividual-level differences in animal spatial behaviour can lead to differential exposure to risk. We assessed the risk-exposure of a reintroduced population of kākā (Nestor meridionalis) in a fenced reserve in New Zealand by GPS tracking 10 individuals and comparing the proportion of each individual’s home range beyond the reserve’s fence in relation to age, sex, and fledging origin. To estimate dynamic space use, we used a sweeping window framework to estimate occurrence distributions from temporally overlapping snapshots. For each occurrence distribution, we calculated the proportion outside the reserve’s fence to assess temporal risk exposure, and the area, centroid and overlap to represent the behavioural pattern of space use. Home range area declined significantly and consistently with age, and the space use of juvenile kākā was more dynamic, particularly in relation to positional changes of space use. The wider- ranging and more dynamic behaviour of younger kākā resulted in consistently more time spent outside the reserve, which aligned with a higher number of incidental mortality observations. Quantifying both home range and dynamic space use is an effective approach to assess risk exposure, which can provide guidance for management interventions. We also emphasise the dynamic space use approach, which is flexible and can provide numerous insights towards a species’ spatial ecology.
A prospective evaluation of three saliva qualitative antigen testing kits for the detection of SARS-CoV-2 in Japan
Authors: Terada Norihiko , Akashi Yusaku , Takeuchi Yuto , Ueda Atsuo , Notake Shigeyuki , Nakamura Koji , Suzuki Hiromichi 
Published: December 2022

AbstractIntroductionRapid qualitative antigen testing has been widely used for the laboratory diagnosis of COVID-19 with nasopharyngeal samples. Saliva samples have been used as alternative samples, but the analytical performance of those samples for qualitative antigen testing has not been sufficiently evaluated.MethodsA prospective observational study evaluated the analytical performance of three In Vitro Diagnostics (IVD) approved COVID-19 rapid antigen detection kits for saliva between June 2022 and July 2022 in Japan using real-time reverse transcription polymerase chain reaction (RT-PCR) as a reference. A nasopharyngeal sample and a saliva sample were simultaneously obtained, and RT-PCR was performed.ResultsIn total, saliva samples and nasopharyngeal samples were collected from 471 participants (140 RT-PCR-positive saliva samples and 143 RT-PCR-positive nasopharyngeal samples) for the analysis. The median Ct values were 25.5 (interquartile range [IQR]: 21.9-28.8) for saliva samples and 17.1 (IQR: 15.5-18.7) for nasopharyngeal samples (p<0.001). Compared with saliva samples of RT-PCR, the sensitivity and specificity were 46.4% and 99.7% for ImunoAce SARS-CoV-2 Saliva, 59.3% and 99.1% for Espline SARS-CoV-2 N, and 61.4% and 98.8% for QuickChaser Auto SARS-CoV-2, respectively. The sensitivity is >90% for saliva samples with a moderate-to-high viral load (Ct<25), whereas the sensitivity is <70% for high-viral-load nasopharyngeal samples (Ct<20).ConclusionCOVID-19 rapid antigen detection kits with saliva showed high specificities, but the sensitivities varied among kits, and the analytical performance of saliva qualitative antigen detection kits was much worse than that of kits using nasopharyngeal samples.
A hormone-activated mobile RNAi pathway defends plant stem cells from virus infection
Authors: Incarbone Marco , Bradamante Gabriele , Pruckner Florian , Wegscheider Tobias , Rozhon Wilfried , Nguyen Vu , Gutzat Ruben , Lendl Thomas , MacFarlane Stuart , Nodine Michael , Scheid Ortrun Mittelsten 
Published: December 2022

ABSTRACTStem cells are essential for the development and organ regeneration of multicellular organisms, so their infection by pathogenic viruses must be prevented. Accordingly, mammalian stem cells are highly resistant to viral infection due to dedicated antiviral pathways including RNA interference (RNAi) (1, 2). In plants, a small group of stem cells harbored within the shoot apical meristem (SAM) generates all postembryonic above-ground tissues, including the germline cells. Many viruses do not proliferate in these cells, yet the molecular bases of this exclusion remain only partially understood (3, 4). Here we show that a plant-encoded RNA-dependent RNA polymerase, after activation by the plant hormone salicylic acid, amplifies antiviral RNAi in infected tissues. This provides stem cells with RNA-based virus sequence information, which prevents virus proliferation. Furthermore, we find RNAi to be necessary for stem cell exclusion of several unrelated RNA viruses, despite their ability to efficiently suppress RNAi in the rest of the plant. This work elucidates a molecular pathway of great biological and economic relevance and lays the foundations for our future understanding of the unique systems underlying stem cell immunity.
Unique role for caspase-8 in the release of IL-1β and active caspase-1 from viable human monocytes duringToxoplasma gondiiinfection
Authors: Pandori William J. , Matsuno Stephanie Y. , Kao Tiffany H. , Mallya Sharmila , Batarseh Sarah N. , Lodoen Melissa B. 
Published: December 2022

AbstractMonocytes are among the first cells recruited to sites of infection and major producers of the potent proinflammatory cytokine IL-1β. We previously showed that IL-1β release duringToxoplasma gondiiinfection of primary human monocytes requires the NLRP3 inflammasome and caspase-1 activity but is independent of gasdermin D and pyroptosis. To investigate potential mechanisms of pyroptosis-independent release of IL-1β duringT. gondiiinfection, we constructed caspases-1, -4, -5, or -8 knockout THP-1 monocytic cells. Genetic ablation of caspase-1 or -8, but not caspase-4 or -5, decreased IL-1β release duringT. gondiiinfection without affecting cell death. In contrast, TNF-α and IL-6 secretion were unperturbed in caspase-8 knockout cells duringT. gondiiinfection. Dual pharmacological inhibition of caspase-8 and RIPK1 in primary monocytes also decreased IL-1β release without affecting cell viability or parasite infection efficiency. In addition, caspase-8 was required for the release of active caspase-1 fromT. gondii-infected cells and for IL-1β release during infection with the related apicomplexan parasiteNeospora caninum. Surprisingly, caspase-8 was dispensable for the synthesis and cleavage of IL-1β, but caspase-8 deficiency resulted in theretentionof mature IL-1β within cells. Our data indicate that duringT. gondiiinfection of human monocytes, caspase-8 functions in a novel gasdermin D-independent mechanism controlling IL-1β release from viable cells. This study expands on the known molecular pathways that promote IL-1β in human immune cells and provides the first evidence of a role for caspase-8 in the mechanism of IL-1β release during host defense against infection.
A Genetic and Immunohistochemical Analysis ofH. PyloriPhenotypes and p27 expression in Adenocarcinoma Patients in Jordan
Authors: Al-Sheboul Suhaila A. , Mohammad Ahmad Abdul-Razzak , Shboul Yasemin , Brown Brent , Matalka Ismail I. 
Published: December 2022

AbstractStomach (gastric) cancer is one of the most prevalent and deadly cancers worldwide and the vast majority of gastric cancers are adenocarcinomas. Based on prior research, there is an association betweenHelicobacter pylori (H. pylori)infection and the frequency of duodenal ulcer, distal gastric adenocarcinoma, mucosa-associated lymphoid tissue lymphoma, and antral gastritis.H. pylorivirulence and toxicity factors have been identified to significantly influence the clinical outcomes ofH. pyloriinfection and gastric adenocarcinoma. However, it is unclear exactly how different strains ofH. pyloriinfection affect gastric adenocarcinoma. Current research suggests this involves tumor suppressor genes, like p27, but alsoH. Pyloritoxic proteins. Therefore, we quantified knownH. Pylorigenotypes within adenocarcinoma patients to establish the prevalence of known toxins that include cytotoxin-associated gene A (cagA) and vacuolating cytotoxin A (vacA) within patients of variable diagnosis. This analysis used gastrectomy samples which were validated for DNA viability. The incidence ofH. Pyloriin adenocarcinoma patients in Jordan was established to be 54.5% positive (ureA gene) with cagA genotype occurrence at 57.1% but also vacA gene ratios 24.7%:22.1%: 14.3%:14.3%. (vacAs1:vacAs2: vacAm1:vacAm2). We found statistically significant evidence that p27 was dysregulated and suppressed within nearly allH. PylorivacA genotypes but also that 24.6% ofH. Pylorisamples analyzed had a different bacterial genotype and curiously that p27 protein expression was retained in 12% of tested adenocarcinomaH. Pylorisamples. This is suggestive that p27 could be used as a prognostic indicator but also that an unknown genotype could be contributing to the regulatory effects of p27 protein within this bacterial and cellular environment.Key ContributionIn Jordan, this is the first retrospective study to use validated viable gastrectomy tissue samples rather than tissue biopsies to characterize each of the currently definedH. pyloristrains in patients with variable gastric cancer diagnosis whilst also comparing results with p27 expression within 8 years using these laboratory techniques.ConclusionsBased on these results, a reduction in p27 expression inH. pylori-infected men and women of all ages may be associated with the occurrence of gastric adenocarcinomas. Therefore, p27 may represent a key diagnostic marker and predictor of adenocarcinoma prognosis in such individuals and may find use for guiding subsequent treatment decisions.
Modulation of prey size reveals adaptability and robustness in the cell cycle of an intracellular predator
Authors: Santin Yoann G. , Lamot Thomas , Kaljević Jovana , van Raaphorst Renske , Laloux Géraldine 
Published: December 2022

SummaryDespite the remarkable diversity of bacterial lifestyles, the sophisticated regulatory networks underlying bacterial replication have only been investigated in a limited number of model species so far. In bacteria that do not rely on canonical binary division for proliferation, the coordination of major cellular processes is still mysterious. Moreover, bacterial growth and division remain largely unexplored within spatially confined niches where nutrients are limited. This includes the lifecycle of the model endobiotic predatory bacteriumBdellovibrio bacteriovorus, which grows by filamentation within its host or prey cells and produces a variable number of daughter cells. Here, we examined how the size of the micro-compartment in which predators replicate (i.e., the prey bacterium) impacts their cell cycle progression at the single-cell level. UsingEscherichia coliwith genetically encoded size differences, we show that the duration of the predator cell cycle scales with prey size. As a result, the size of the prey determines the number of predator offspring, through a relationship that is maintained across prey species. Strikingly, the nutritional quality of the prey cell determined the specific growth rate of predators regardless of prey size, reminiscent of the effect of medium composition on the growth of other bacteria. Tuning the predatory cell cycle by modulating prey dimensions also allowed us to reveal invariable temporal connections between key cellular processes. Altogether, our data uncover adaptability and robustness shaping the enclosed replication ofB. bacteriovorus. Consequently, predators optimally exploit the finite prey resources and space while ensuring a strict cell cycle progression. This study opens the way to explore diverse cell cycle control strategies by extending their characterization to intracellular lifestyles, beyond canonical models and growth conditions.
Optimizing tuberculosis treatment efficacy: comparing the standard regimen with Moxifloxacin-containing regimens
Authors: Budak Maral , Cicchese Joseph M. , Maiello Pauline , Borish H. Jacob , White Alexander G. , Chishti Harris B. , Tomko Jaime , Frye L. James , Fillmore Daniel , Kracinovsky Kara , Sakal Jennifer , Scanga Charles A. , Lin Philana Ling , Dartois Véronique , Linderman Jennifer J. , Flynn JoAnne L. , Kirschner Denise E. 
Published: December 2022

AbstractTuberculosis (TB) continues to be one of the deadliest infectious diseases in the world, causing ~1.5 million deaths every year. The World Health Organization initiated anEnd TB Strategythat aims to reduce TB-related deaths in 2035 by 95%. Recent research goals have focused on discovering more effective and more patient-friendly antibiotic drug regimens to increase patient compliance and decrease emergence of resistant TB. Moxifloxacin is one promising antibiotic that may improve the current standard regimen by shortening treatment time. Clinical trials andin vivomouse studies suggest that regimens containing moxifloxacin have better bactericidal activity. However, testing every possible combination regimen with moxifloxacin eitherin vivoor clinically is not feasible due to experimental and clinical limitations. To identify better regimens more systematically, we simulated pharmacokinetics/pharmacodynamics of various regimens (with and without moxifloxacin) to evaluate efficacies, and then compared our predictions to both clinical trials and nonhuman primate studies performed herein. We usedGranSim, our well-established hybrid agent-based model that simulates granuloma formation and antibiotic treatment, for this task. In addition, we established a multiple-objective optimization pipeline usingGranSimto discover optimized regimens based on treatment objectives of interest, i.e., minimizing total drug dosage and lowering time needed to sterilize granulomas. Our approach can efficiently test many regimens and successfully identify optimal regimens to inform pre-clinical studies or clinical trials and ultimately accelerate the TB regimen discovery process.Author summaryTuberculosis (TB) is a top global health concern and treatment for TB requires multiple antibiotics taken for long periods of time, which is challenging for TB patients. Therefore, identifying regimens that are more effective and more patient-friendly than the standard treatment is urgently needed. It is also known that non-compliance leads to the development of drug resistant TB. In this work, we pair computational and experimental models to predict new regimens for the treatment of TB that optimize how fast bacteria are cleared using minimal dosage. We apply novel approaches to this goal and validate our predictions using a non-human primate model. Our findings suggest that systems pharmacological modeling should be employed as a method to narrow the design space for drug regimens for tuberculosis and other diseases as well.
Genome-wide association study of longitudinal urinary albumin excretion in patients with type 1 diabetes
Authors: Hutchinson Anna M , Chen Wei-Min , Onengut-Gumuscu Suna , Benitez-Aguirre Paul , Cameron Fergus J , Chiesa Scott T , Couper Jennifer J , Craig Maria E , Dalton Neil R. , Daneman Denis , Davis Elizabeth A , Deanfield John E , Donaghue Kim C , Jones Timothy W , Mahmud Farid H , Marshall Sally M , Neil Andrew , Rich Stephen S , Marcovecchio M. Loredana , Wallace Chris 
Published: December 2022

AbstractIdentifying genetic determinants for longitudinal changes in albumin excretion in individuals with type 1 diabetes may help identify those that are predisposed to renal, retinal and cardiovascular complications. Most studies have focussed on genetic predisposition to diabetic kidney disease and used cross-sectional measurements of urinary albumin excretion, but with limited success. Here, we utilise the wealth of longitudinal data and bio-samples collected from cohorts of childhood-onset type 1 diabetes followed over the last 30 years to describe a novel trajectory phenotype quantifying urinary albumin excretion changes during childhood and adolescence. We conducted a genome-wide association study and fine-mapping analysis for albumin excretion in 1584 individuals, finding one signal for cross-sectional albumin excretion close toGALNTL6(rs150766792), which validated in a previous independent study, and a novel genome-wide significant signal for albumin excretion trajectory in theCDH18gene region (rs145715205). Our trajectory phenotype quantifies albumin progression and offers a complementary measure to an albumin excretion phenotype based on a single measurement (i.e. most recent data collection) or an average of repeated measurements in longitudinal studies. It can be used to identify genetic or other risk factors which predict better or worse prognosis, thus facilitating the development of new preventive and therapeutic approaches.