bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of plasma-activated water forEscherichia colidecontamination and shelf-life extension of kale
Authors: Wang Hexiang , Li Yingxia , Xi Qian , Han Rongwei , Cullen Patrick J , Du Qijing , Yang Yongxin , Forghani Fereidoun , Zhang Jiacheng , Wang Jun 
Published: June 2022

AbstractThe aim of this study was to examine the effectiveness of plasma-activated water (PAW) for inactivating Escherichia coli (E. coli) and retention of key quality factors for kale. Different plasma discharge times (1, 2, 3, 4, 5, and 10 min) and different exposure times (2, 4, 6, 8, 10, and 15 min) were used to investigate the inactivation effect of E. coli spot-inoculated on kale. The influence of different exposure times on the pH, hardness and color of kale was studied post-treatment. In addition, the effects of PAW on the shelf-life of kale over 12 d of storage at 4 °C were investigated. The results showed that after the treatment of 5-PAW-8 (8 min treatment by PAW generated by 5 min plasma discharge), the population of E. coli on kale was reduced by approximately 1.55 log colony-forming units (CFU)/g and the changes in pH, hardness and color of kale were not significant (P&gt;0.05). During the storage period after 5-PAW-8 treatment, the hardness, weight loss, color, surface morphology and ascorbic acid were found to be better than those of the two control groups (P&lt;0.05). Furthermore, no significant changes were observed in pH values, the content of total phenols, or 1,1-dipheny1-2-picrylhydrazyl radical scavenging capacity (P&gt;0.05). It is indicated that PAW treatment is a promising method for improving microbiological safety and extending the shelf-life of kale.
The Evolution of Offspring Size: A Metabolic Scaling Perspective
Authors: Pettersen Amanda K , Schuster Lukas , Metcalfe Neil B 
Published: June 2022

AbstractSize at the start of life reflects the initial per offspring parental investment—including both the embryo and the nutrients supplied to it. Initial offspring size can vary substantially, both within and among species. Within species, increasing offspring size can enhance growth, reproduction, competitive ability, and reduce susceptibility to predation and starvation later in life, that can ultimately increase fitness. Previous work has suggested that the fitness benefits of larger offspring size may be driven by energy expenditure during development—or how offspring metabolic rate scales with offspring size. Despite the importance of early-life energy expenditure in shaping later life fitness trajectories, consideration of among-species scaling of metabolic rate at the time of birth as a potential source of general metabolic scaling patterns has been overlooked by theory. Here, we review the patterns and processes of energy expenditure at the start of life when mortality is often greatest. We compile existing data on metabolic rate and offspring size for 191 ectotherm species spanning eight phyla and use phylogenetically controlled methods to quantify among-species scaling patterns. Across a 109-fold mass range, we find that offspring metabolic rate scales hypometrically with size, with an overall scaling exponent of 0.66. This exponent varies across ontogenetic stage and feeding activity, but is consistently hypometric, including across environmental temperatures. Despite differences in parental investment, life history and habitat, large-offspring species use relatively less energy as a proportion of size, compared with small-offspring species. Greater residual energy can be used to fuel the next stages of life, particularly in low-resource environments. Based on available evidence, we conclude that, while large knowledge gaps remain, the evolution of offspring size is likely shaped by context-dependent selection acting on correlated traits, including metabolic rates maintaining hypometric scaling, which operates within broader physical constraints.
Neuropathologic Findings in Elderly HIV-Positive Individuals
Authors: Magaki Shino D , Vinters Harry V , Williams Christopher K , Mareninov Sergey , Khanlou Negar , Said Jonathan , Nemanim Natasha , Gonzalez Jessica , Morales Jose G , Singer Elyse J , Yong William H 
Published: June 2022

Abstract
The elderly HIV-positive population is growing due to the widespread use of combination antiretroviral therapy (cART), but the effects of longstanding HIV infection on brain aging are unknown. A significant proportion of HIV-positive individuals develop HIV-associated neurocognitive disorder (HAND) even on cART, but the pathogenesis of HAND is unknown. Although neuroinflammation is postulated to play an important role in aging and neurodegenerative diseases such as Alzheimer disease (AD), it is unclear whether HIV accelerates aging or increases the risk for AD. We examined the brains of 9 elderly HIV-positive subjects on cART without co-infection by hepatitis C virus compared to 7 elderly HIV-negative subjects. Microglial and astrocyte activation and AD pathologic change in association with systemic comorbidities and neurocognitive assessment were evaluated. There was no difference in microglial or astrocyte activation between our HIV-positive and HIV-negative cohorts. One HIV-positive subject and 2 HIV-negative subjects demonstrated significant amyloid deposition, predominantly in the form of diffuse senile plaques, but these individuals were cognitively normal. Neurofibrillary tangles were sparse in the HIV-positive cohort. There was a high prevalence of cardiovascular comorbidities in all subjects. These findings suggest that multiple factors likely contribute to aging and cognitive impairment in elderly HIV-positive individuals on cART.
A low appendiceal mucinous neoplasm lesion in an inflamed appendix within an inguinal hernia
Authors: Arenas Daniel J , Hernandez Paul T , Hwang Jasmine , Agarwal Divyansh , Warshauer Alexander K , Holena Daniel N 
Published: June 2022

Abstract
Amyand’s hernia, an incarcerated appendix inside an inguinal hernia, accounts for &lt;1% of hernias in children and even less in adults. Similarly, low-grade appendiceal mucinous (LAMN) lesions are only found in &lt;1% of removed appendices. We present the case of a 72-year-old man with a 15-year history of a large right inguinoscrotal hernia that presented with right lower quadrant pain, was found by computed tomography imaging to have an incarcerated appendix with a large fluid collection, and was post-operatively diagnosed with an LAMN lesion. Although our case is rare due to the simultaneity of the Amyand’s hernia and LAMN conditions, each separate condition is prevalent enough for most surgical providers to encounter at least one of these. For our case, we discuss the decisions made in the pre-operative and post-operative management and relevant literature.
Gastrointestinal tract Candida spp colonization shows mostly a monoclonal pattern: an intra-patient pilot study
Authors: Mesquida Aina , Álvarez-Uría Ana , Vicente Teresa , Muñoz Patricia , Guinea Jesús , Escribano Pilar 
Published: June 2022

Abstract

Gastrointestinal tract Candida genotypes may associate with isolates later causing infections. We genotyped Candida spp isolates (n = 200 individual colonies) from rectal swabs to assess whether gastrointestinal gut colonization is caused by a single genotype (monoclonal pattern) or a combination of them (polyclonal pattern). C. glabrata showed a sheer monoclonal pattern. C. parapsilosis and C. tropicalis showed a monoclonal pattern involving the presence of either exclusively identical genotypes or a combination of clonally-related genotypes; in the latter case, a dominant genotype was always found. C. albicans showed mostly a polyclonal pattern involving a combination of dominant clonally-related genotypes and unrelated genotypes.

Lay Summary
We genotyped C. albicans, C. parapsilosis, C. tropicalis, and C. glabrata isolates prospectively from rectal swabs to study the gastrointestinal colonization pattern in the patients. Gastrointestinal tract colonization is mostly monoclonal and commonly dominated by one genotype.
The Dark Energy Survey supernova program: cosmological biases from supernova photometric classification
Authors: Vincenzi M , Sullivan M , Möller A , Armstrong P , Bassett B A , Brout D , Carollo D , Carr A , Davis T M , Frohmaier C , Galbany L , Glazebrook K , Graur O , Kelsey L , Kessler R , Kovacs E , Lewis G F , Lidman C , Malik U , Nichol R C , Popovic B , Sako M , Scolnic D , Smith M , Taylor G , Tucker B E , Wiseman P , Aguena M , Allam S , Annis J , Asorey J , Bacon D , Bertin E , Brooks D , Burke D L , Rosell A Carnero , Carretero J , Castander F J , Costanzi M , da Costa L N , Pereira M E S , De Vicente J , Desai S , Diehl H T , Doel P , Everett S , Ferrero I , Flaugher B , Fosalba P , Frieman J , García-Bellido J , Gerdes D W , Gruen D , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , James D J , Kuehn K , Kuropatkin N , Lahav O , Li T S , Lima M , Maia M A G , Marshall J L , Miquel R , Morgan R , Ogando R L C , Palmese A , Paz-Chinchón F , Pieres A , Malagón A A Plazas , Reil K , Roodman A , Sanchez E , Schubnell M , Serrano S , Sevilla-Noarbe I , Suchyta E , Tarle G , To C , Varga T N , Weller J , Wilkinson R D ,   (DES Collaboration)
Published: June 2022

ABSTRACT
Cosmological analyses of samples of photometrically identified type Ia supernovae (SNe Ia) depend on understanding the effects of ‘contamination’ from core-collapse and peculiar SN Ia events. We employ a rigorous analysis using the photometric classifier SuperNNova on state-of-the-art simulations of SN samples to determine cosmological biases due to such ‘non-Ia’ contamination in the Dark Energy Survey (DES) 5-yr SN sample. Depending on the non-Ia SN models used in the SuperNNova training and testing samples, contamination ranges from 0.8 to 3.5 per cent, with a classification efficiency of 97.7–99.5 per cent. Using the Bayesian Estimation Applied to Multiple Species (BEAMS) framework and its extension BBC (‘BEAMS with Bias Correction’), we produce a redshift-binned Hubble diagram marginalized over contamination and corrected for selection effects, and use it to constrain the dark energy equation-of-state, w. Assuming a flat universe with Gaussian ΩM prior of 0.311 ± 0.010, we show that biases on w are &lt;0.008 when using SuperNNova, with systematic uncertainties associated with contamination around 10 per cent of the statistical uncertainty on w for the DES-SN sample. An alternative approach of discarding contaminants using outlier rejection techniques (e.g. Chauvenet’s criterion) in place of SuperNNova leads to biases on w that are larger but still modest (0.015–0.03). Finally, we measure biases due to contamination on w0 and wa (assuming a flat universe), and find these to be &lt;0.009 in w0 and &lt;0.108 in wa, 5 to 10 times smaller than the statistical uncertainties for the DES-SN sample.
Nanomolar affinity of EF-hands in neuronal calcium sensor 1 for bivalent cations Pb2+, Mn2+, and Hg2+
Authors: Alam Md Shofiul , Azam Samiol , Pham Khoa , Leyva Dennys , Fouque Kevin Jeanne Dit , Fernandez-Lima Francisco , Miksovska Jaroslava 
Published: June 2022

Abstract
Abiogenic metals Pb and Hg are highly toxic since chronic and/or acute exposure often leads to severe neuropathologies. Mn2+ is an essential metal ion but in excess can impair neuronal function. In this study, we address in vitro the interactions between neuronal calcium sensor 1 (NCS1) and divalent cations. Results showed that non-physiological ions (Pb2+ and Mn2+) bind to EF-hands in NCS1 with nanomolar affinity and lower equilibrium dissociation constant than the physiological Ca2+ ion. (Kd, Pb2+ = 7.0 ± 1.0 nM; Kd, Mn2+ = 34.0 ± 6.0 nM; K). Native ultra-high resolution mass spectrometry (FT-ICR MS) and trapped ion mobility spectrometry—mass spectrometry (nESI-TIMS-MS) studies provided the NCS1-metal complex compositions—up to four Ca2+ or Mn2+ ions and three Pb2+ ions (M⋅Pb1-3Ca1-3, M⋅Mn1-4Ca1-2, and M⋅Ca1-4) were observed in complex—and similarity across the mobility profiles suggests that the overall native structure is preserved regardless of the number and type of cations. However, the non-physiological metal ions (Pb2+, Mn2+, and Hg2+) binding to NCS1 leads to more efficient quenching of Trp emission and a decrease in W30 and W103 solvent exposure compared to the apo and Ca2+ bound form, although the secondary structural rearrangement and exposure of hydrophobic sites are analogous to those for Ca2+ bound protein. Only Pb2+ and Hg2+ binding to EF-hands leads to the NCS1 dimerization whereas Mn2+ bound NCS1 remains in the monomeric form, suggesting that other factors in addition to metal ion coordination, are required for protein dimerization.
CircadiOmics: circadian omic web portal
Authors: Samad Muntaha , Agostinelli Forest , Sato Tomoki , Shimaji Kohei , Baldi Pierre 
Published: June 2022

Abstract
Circadian rhythms are a foundational aspect of biology. These rhythms are found at the molecular level in every cell of every living organism and they play a fundamental role in homeostasis and a variety of physiological processes. As a result, biomedical research of circadian rhythms continues to expand at a rapid pace. To support this research, CircadiOmics (http://circadiomics.igb.uci.edu/) is the largest annotated repository and analytic web server for high-throughput omic (e.g. transcriptomic, metabolomic, proteomic) circadian time series experimental data. CircadiOmics contains over 290 experiments and over 100 million individual measurements, across &gt;20 unique tissues/organs, and 11 different species. Users are able to visualize and mine these datasets by deriving and comparing periodicity statistics for oscillating molecular species including: period, amplitude, phase, P-value and q-value. These statistics are obtained from BIO_CYCLE and JTK_CYCLE and are intuitively aggregated and displayed for comparison. CircadiOmics is the most up-to-date and cutting-edge web portal for searching and analyzing circadian omic data and is used by researchers around the world.
Noncanonical amino acid mutagenesis in response to recoding signal-enhanced quadruplet codons
Authors: Chen Yan , He Xinyuan , Ma Bin , Liu Kun , Gao Tianyu , Niu Wei , Guo Jiantao 
Published: June 2022

Abstract
While amber suppression is the most common approach to introduce noncanonical amino acids into proteins in live cells, quadruplet codon decoding has potential to enable a greatly expanded genetic code with up to 256 new codons for protein biosynthesis. Since triplet codons are the predominant form of genetic code in nature, quadruplet codon decoding often displays limited efficiency. In this work, we exploited a new approach to significantly improve quadruplet UAGN and AGGN (N = A, U, G, C) codon decoding efficiency by using recoding signals imbedded in mRNA. With representative recoding signals, the expression level of mutant proteins containing UAGN and AGGN codons reached 48% and 98% of that of the wild-type protein, respectively. Furthermore, this strategy mitigates a common concern of reading-through endogenous stop codons with amber suppression-based system. Since synthetic recoding signals are rarely found near the endogenous UAGN and AGGN sequences, a low level of undesirable suppression is expected. Our strategy will greatly enhance the utility of noncanonical amino acid mutagenesis in live-cell studies.
ATRT-09. Outcome and therapeutic interventions in relapsed and refractory ATRT – The EU-RHAB perspective
Authors: Steinbügl Mona , Nemes Karolina , Gruhle Miriam , Johann Pascal , Gil-da-Costa Maria Joao , Ebinger Martin , Sehested Astrid , Hauser Peter , Reinhard Harald , Hettmer Simone , Jakob Marcus , Rutkowski Stefan , Driever Pablo Hernáiz , Fleischhack Gudrun , Kerl Kornelius , Witt Olaf , Gerss Joachim , Siebert Reiner , Schüller Ulrich , Hasselblatt Martin , Frühwald Michael C 
Published: June 2022

Abstract
Currently an internationally accepted consensus treatment for relapsed/refractory ATRT is missing. Little is known about relapse patterns, prognostic factors and outcome. In a recently published cohort of 143 ATRTs from the EU-RHAB registry, progression on therapy or relapse occurred in 64% (n=91). Previously published strategies for treatment failure have been restricted to individual, mostly clinically guided, attempts or early phase trials with limited sample sizes. We present a cohort of 55 patients with relapsed/refractory ATRT identified between 2015 and 2021 (total ATRT recruited n=147). Median age was 19 months; in 27.3% (n=15) a germline mutation was identified. A total of 43/55 tumors were subgrouped [60.5% SHH (n=26), 14.0% MYC (n=6), 23.3% TYR (n=10), one patient with SHH+TYR]. Salvage therapy was applied to 83.6% (46/55). Sixty therapy attempts with 17 different regimens subclassified into conventional chemotherapy, epigenetic, targeted or metronomic therapy were applied to 40/55 patients. Median overall survival (OS) was 20±1.8 weeks following the first event, median time to progression was 11±1.8 weeks. 12 months OS was 23.1%. No significant differences in survival were noted between different molecular subgroups; neither was germline mutation in SMARCB1 prognostic. Patients &lt;12 months (n=9;16.4%) had a significantly reduced OS compared to older patients. (9±6.0wks vs. 22±3.2wks, p&lt;0.05) Those who received therapy according to metronomic approaches such as MEMMAT (8/55;14.5%) survived longer than patients treated with other regimens, including epigenetic and targeted therapy. (72±36.8wks vs. 25±6.2wks, p&lt;0.05) Our data provide valuable insights into a vulnerable group of patients deserving evidence based clinical management and access to clinical trials of all phases. Prospectively we aim to merge the results with data from other, international cohorts to generate more robust and valuable results.
ATRT-18. Atypical Teratoid/Rhabdoid Tumor in Children: Case Reports from Indonesia
Authors: Ramadhan Diko Anugrah , Gautami Wanda , Rahmartani Ludi Dhyani , Rafli Ahmad , Gunawan Kevin , Amal Mohamad Yanuar , Susanto Eka , Handoko Handoko 
Published: June 2022

Abstract
Atypical teratoid/rhabdoid tumor (AT/RT) of the central nervous system is a sporadic and highly malignant tumor that usually affects very young children and is typically deadly despite very aggressive treatment. The optimal treatment for AT/RT remains unclear, including surgery, radiotherapy, and chemotherapy. Here we report cases of AT/RT in Indonesia. Case 1: A three-year-old girl came with worsening intermittent headaches with projectile vomiting, progressive and insidious right spastic hemiparesis, and slowly progressive weight loss three months before admission. She had septate multiloculated hydrocephalus. Head MRI demonstrates a solid lobulated mass with heterogeneous enhancement and MRS shows an aggressive metabolite pattern, arising from posterior fossa extending into the cerebellum and cerebellopontine angle, causing severe obstructive hydrocephalus. She underwent tumor resection with a midline suboccipital approach, then continued with craniospinal irradiation with dose of 36 Gy in 20 fractions then followed by 18 Gy in 10 fractions booster to posterior fossa, making the total dose to posterior fossa (the tumor) to be 54 Gy. Case 2: A twenty-month-old baby with a history of recurrent seizures, tremors, and less activity in the last two months. She had spasticity with hyperreflexia. She has been referred to our center for further evaluation and management after biopsy and VP shunt surgery at the previous hospital. Head CT scan demonstrates a large solid heterogeneous mass in the right hemisphere cerebral, causing midline shift and hydrocephalus. After the VP shunt was repaired, she underwent Head Start III chemotherapy protocol cycle 1. Both pathology examinations of the patients revealed a hypercellular tumor with prominent hyperchromatic nucleoli and loss of INI-1 staining on immunohistochemistry consistent with an ATRT diagnosis. Unfortunately, both patients died due to severe sepsis after treatment. Although AT/RT has become increasingly recognized, prognosis of ATRT is generally unfavorable, especially in developing countries.
ATRT-19. Functional genomics reveal distinct modulators of response to CDK4/6 inhibitors in ATRTs
Authors: Merk Daniel , Hirsch Sohpie , Tsiami Foteini , Walter Bianca , Haeusser Lara , Babaei Sepideh , Admard Jakob , Casadei Nicolas , Roggia Cristiana , Spohn Michael , Schittenhelm Jens , Singer Stephan , Schüller Ulrich , Piccioni Federica , Persky Nicole , Root David , Claassen Manfred , Tatagiba Marcos , Tabatabai Ghazaleh 
Published: June 2022

Abstract
Brain tumors are the leading cause of cancer-related deaths in children, and atypical teratoid rhabdoid tumors (ATRTs) are among the most common aggressive brain tumors in infants. With no standard-of-care treatment so far, ATRTs continue to have relatively low survival estimates, illustrating the urgent need for more efficacious treatment options. We have previously used genome-wide CRISPR/Cas9 knockout screens in combination with small-molecule drug assays to identify targetable vulnerabilities in ATRTs. CDK4/6 inhibitors, among the most promising drugs in our study with direct translational potential, are capable of inhibiting tumor growth due to mutual exclusive dependency of ATRTs on either CDK4 or CDK6. We here used genome-wide loss-of-function and gain-of-function strategies to identify modulators of response to CDK4/6 inhibition in ATRTs. Of note, while some well-known resistance mechanisms such as loss of RB1 or FBXW7 are shared by ATRT cell lines, we have also identified modulators of response to CDK4/6 inhibition with opposing effects across ATRT cell lines. As such, loss of AMBRA1, a recently described master regulator of D type cyclins, can either oppose the effects of or synergize with CDK4/6 inhibitors based on the cellular background. We are currently using a proteomics approach to further delineate the mechanism driving this functional heterogeneity of AMBRA1 in ATRTs. Our study will therefore provide deeper insights into the response of ATRTs to CDK4/6 inhibitors, which represent one of the most promising class of targeted agents for the treatment of ATRTs.
ATRT-25. CERVICAL ATYPICAL TERATOID RHABDOID TUMOR IN PEDIATRIC PATIENTS: A STUDY OF THE LAST DECADE
Authors: Fonseca Rodrigues Amanda Cyntia Lima , Louro Letícia dos Santos , Kostakis Maria Eduarda Geddo , Fialho Milena Henriques , Ruiz Kananda Oliveira Garcia , Costa Beatriz Patriota Saraiva , Gomes Monique Benemérita Vilela 
Published: June 2022

Abstract
BACKGROUND: Atypical rhabdoid teratoid tumor (AT/RT) is an extremely rare primary tumor of the central nervous system (CNS) with a high incidence in children under 3 years of age. The existing literature involving this tumor is scarce, even though AT/RT is considered one of the most malignant brain tumors due to its aggressive course and short survival time, which generally does not exceed 1 year. METHODS: The “PubMed” database was used for this study using the MeSH Terms “Child” and “Atypical Teratoid Rhabdoid Tumor” and the filter “Case Reports” in order to carry out a study with the clinical cases of the last decade and the involvement of this tumor in the cervical region of pediatric patients. 96 articles were found, however, only 10 articles were selected for this review. RESULTS: It is possible to affirm that the cases of AT/RT are found in greater numbers in children under 3 years of age and are predominantly located in the cervical region when they affect the spinal cord. In addition, MRI usually shows a solid heterogeneous mass that results in the appearance of symptoms, since the mass compresses the conus medullaris and consequently generates pain in the spine. The prognosis is reported to be a difficult one and the median patient survival time is less than one year. CONCLUSION: Therefore, AT/RT is rare, fatal, primary and malignant in the CNS that have a high degree of recurrence and dissemination. The diagnosis is made through anatomopathological examination and the loss of INI-1 expression constitutes an important finding for its conclusion. Treatment is multimodal and may combine surgery, chemotherapy and radiotherapy.