bluuebunny/crossref_metadata_2025_split huggingface dataset:
MedFuseNet: An attention-based multimodal deep learning model for visual question answering in the medical domain
Authors: Sharma Dhruv , Purushotham Sanjay , Reddy Chandan K. 
Published: October 2021

AbstractMedical images are difficult to comprehend for a person without expertise. The scarcity of medical practitioners across the globe often face the issue of physical and mental fatigue due to the high number of cases, inducing human errors during the diagnosis. In such scenarios, having an additional opinion can be helpful in boosting the confidence of the decision maker. Thus, it becomes crucial to have a reliable visual question answering (VQA) system to provide a ‘second opinion’ on medical cases. However, most of the VQA systems that work today cater to real-world problems and are not specifically tailored for handling medical images. Moreover, the VQA system for medical images needs to consider a limited amount of training data available in this domain. In this paper, we developMedFuseNet, an attention-based multimodal deep learning model, for VQA on medical images taking the associated challenges into account. OurMedFuseNetaims at maximizing the learning with minimal complexity by breaking the problem statement into simpler tasks and predicting the answer. We tackle two types of answer prediction—categorization and generation. We conducted an extensive set of quantitative and qualitative analyses to evaluate the performance ofMedFuseNet. Our experiments demonstrate thatMedFuseNetoutperforms the state-of-the-art VQA methods, and that visualization of the captured attentions showcases the intepretability of our model’s predicted results.
Molecular mechanism of oil induced growth inhibition in diatoms using Thalassiosira pseudonana as the model species
Authors: Kamalanathan Manoj , Mapes Savannah , Hillhouse Jessica , Claflin Noah , Leleux Joshua , Hala David , Quigg Antonietta 
Published: October 2021

AbstractThe 2010 Deepwater Horizon oil-spill exposed the microbes of Gulf of Mexico to unprecedented amount of oil. Conclusive evidence of the underlying molecular mechanism(s) on the negative effects of oil exposure on certain phytoplankton species such as Thalassiosira pseudonana is still lacking, curtailing our understanding of how oil spills alter community composition. We performed experiments on model diatom T. pseudonana to understand the mechanisms underpinning observed reduced growth and photosynthesis rates during oil exposure. Results show severe impairment to processes upstream of photosynthesis, such as light absorption, with proteins associated with the light harvesting complex damaged while the pigments were unaffected. Proteins associated with photosynthetic electron transport were also damaged, severely affecting photosynthetic apparatus and depriving cells of energy and carbon for growth. Negative growth effects were alleviated when an organic carbon source was provided. Further investigation through proteomics combined with pathway enrichment analysis confirmed the above findings, while highlighting other negatively affected processes such as those associated with ferroxidase complex, high-affinity iron-permease complex, and multiple transmembrane transport. We also show that oxidative stress is not the primary route of negative effects, rather secondary. Overall, this study provides a mechanistic understanding of the cellular damage that occurs during oil exposure to T. pseudonana.
Identification of candidate genes from androgenic gland in Macrobrachium nipponense regulated by eyestalk ablation
Authors: Jin Shubo , Fu Yin , Hu Yuning , Fu Hongtuo , Jiang Sufei , Xiong Yiwei , Qiao Hui , Zhang Wenyi , Gong Yongsheng , Wu Yan 
Published: October 2021

AbstractThe eyestalk of crustaceans, such as Macrobrachium nipponense, contains many neurosecretory hormones affecting the process of reproduction, molting, metabolism of glucose, and other functions. In this study, important metabolic pathways and candidate genes involved in male sexual development were selected from M. nipponense. The methodology involved performing long-read and next generation transcriptome sequencing of genes from the androgenic gland after eyestalk ablation. qPCR analysis revealed that the mRNA expression of Mn-IAG was significantly increased after ablation of both the single-side (SS) and double-side (DS) eyestalk, compared with the control group (CG). The long-read transcriptome generated 49,840 non-redundant transcripts. A total of 1319, 2092 and 4351 differentially expressed genes (DEGs) were identified between CG versus SS, SS versus DS and CG versus DS, respectively. These data indicated that ablation of the double-sided eyestalk played stronger regulatory roles than the single-side ablation on male sexual development in M. nipponense. This was consistent with the qPCR analysis. Cell Cycle, Cellular Senescence, Oxidative Phosphorylation, Glycolysis/Gluconeogenesis and Steroid Hormone Biosynthesis were the primary enriched metabolic pathways in all three comparisons, and the important genes from these metabolic pathways were also selected. qPCR permitted secondary confirmation of ten DEGs identified through RNA-seq. RNAi-mediated silencing analyses of Hydroxysteroid dehydrogenase like 1 (HSDL1) revealed that HSDL1 has a positive regulatory effect on testes development. This study provides valuable insight into male sexual development in M. nipponense, including metabolic pathways and genes, paving the way for advanced studies on male sexual development in this species and in other crustaceans.
Evolution﻿ of spin freezing transition and structural, magnetic phase diagram of Dy$$_{2-\textit{x}}$$La$$_\textit{x}$$Zr$$_{2}$$O$$_{7}$$ (0 $$\le$$ $$\textit{x}$$ $$\le$$ 2.0)
Authors: Sheetal  , Yadav C. S. 
Published: October 2021

AbstractDy$$_{2}$$

2

Zr$$_{2}$$

2

O$$_{7}$$

7

a disordered pyrochlore system, exhibits the spin freezing behavior under the application of the magnetic field. We have performed detailed magnetic studies of Dy$$_{2-\textit{x}}$$

2
-
x

La$$_\textit{x}$$

x

Zr$$_{2}$$

2

O$$_{7}$$

7

to understand the evolution of the magnetic spin freezing in the system. Our studies suggest the stabilization of the pyrochlore phase with the substitution of non-magnetic La along with the biphasic mixture of fluorite and pyrochlore phases for the intermediate compositions. We observed that the spin freezing (T$$_{f}$$

f

$$\sim$$
∼
17 K) at higher La compositions (1.5 $$\le$$
≤
$$\textit{x}$$
x
$$\le$$
≤
1.99) is similar to the field-induced spin freezing for low La compositions (0 $$\le$$
≤
$$\textit{x}$$
x
$$\le$$
≤
0.5) and the well-known spin ice systems Dy$$_{2}$$

2

Ti$$_{2}$$

2

O$$_{7}$$

7

and Ho$$_{2}$$

2

Ti$$_{2}$$

2

O$$_{7}$$

7

. The low-temperature magnetic state for higher La compositions (1.5 $$\le$$
≤
$$\textit{x}$$
x
$$\le$$
≤
1.99) culminates into a spin-glass like state below 6 K. Cole–Cole plot and Casimir-du Pr$$\acute{e}$$

e
´

fit shows the narrow distribution of spin relaxation time in these compounds.
Effective Landé factors for an electrostatically defined quantum point contact in silicene
Authors: Rzeszotarski Bartłomiej , Mreńca-Kolasińska Alina , Peeters François M. , Szafran Bartłomiej 
Published: October 2021

AbstractThe transconductance and effective Landé $$g^*$$

g
∗

factors for a quantum point contact defined in silicene by the electric field of a split gate is investigated. The strong spin–orbit coupling in buckled silicene reduces the $$g^*$$

g
∗

factor for in-plane magnetic field from the nominal value 2 to around 1.2 for the first- to 0.45 for the third conduction subband. However, for perpendicular magnetic field we observe an enhancement of $$g^*$$

g
∗

factors for the first subband to 5.8 in nanoribbon with zigzag and to 2.5 with armchair edge. The main contribution to the Zeeman splitting comes from the intrinsic spin–orbit coupling defined by the Kane–Mele form of interaction.
Host response transcriptomic analysis of Crimean-Congo hemorrhagic fever pathogenesis in the cynomolgus macaque model
Authors: Arnold Catherine E. , Shoemaker Charles J. , Smith Darci R. , Douglas Christina E. , Blancett Candace D. , Graham Amanda S. , Minogue Timothy D. 
Published: October 2021

AbstractCrimean-Congo hemorrhagic fever virus (CCHFV) is a highly pathogenic tick-borne RNA virus prevalent in Asia, Europe, and Africa, and can cause a hemorrhagic disease (CCHF) in humans with mortality rates as high as 60%. A general lack of both effective medical countermeasures and a comprehensive understanding of disease pathogenesis is partly driven by an historical lack of viable CCHF animal models. Recently, a cynomolgous macaque model of CCHF disease was developed. Here, we document the targeted transcriptomic response of non-human primates (NHP) to two different CCHFV strains; Afghan09-2990 and Kosova Hoti that both yielded a mild CCHF disease state. We utilized a targeted gene panel to elucidate the transcriptomic changes occurring in NHP whole blood during CCHFV infection; a first for any primate species. We show numerous upregulated genes starting at 1 day post-challenge through 14 days post-challenge. Early gene changes fell predominantly in the interferon stimulated gene family with later gene changes coinciding with an adaptive immune response to the virus. There are subtle differences between viral strains, namely duration of the differentially expressed gene response and biological pathways enriched. After recovery, NHPs showed no lasting transcriptomic changes at the end of sample collection.
Efflux transporters in rat placenta and developing brain: transcriptomic and functional response to paracetamol
Authors: Koehn L. M. , Huang Y. , Habgood M. D. , Nie S. , Chiou S. Y. , Banati R. B. , Dziegielewska K. M. , Saunders N. R. 
Published: October 2021

AbstractAdenosine triphosphate binding cassette (ABC) transporters transfer lipid-soluble molecules across cellular interfaces either directly or after enzymatic metabolism. RNAseq analysis identified transcripts for ABC transporters and enzymes in rat E19, P5 and adult brain and choroid plexus and E19 placenta. Their functional capacity to efflux small molecules was studied by quantitative analysis of paracetamol (acetaminophen) and its metabolites using liquid scintillation counting, autoradiography and ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS). Animals were treated acutely (30 min) and chronically (5 days, twice daily) with paracetamol (15 mg/kg) to investigate ability of brain and placenta barriers to regulate ABC transport functionality during extended treatment. Results indicated that transcripts of many efflux-associated ABC transporters were higher in adult brain and choroid plexus than at earlier ages. Chronic treatment upregulated certain transcripts only in adult brain and altered concentrations of paracetamol metabolites in circulation of pregnant dams. Combination of changes to metabolites and transport system transcripts may explain observed changes in paracetamol entry into adult and fetal brains. Analysis of lower paracetamol dosing (3.75 mg/kg) indicated dose-dependent changes in paracetamol metabolism. Transcripts of ABC transporters and enzymes at key barriers responsible for molecular transport into the developing brain showed alterations in paracetamol pharmacokinetics in pregnancy following different treatment regimens.
Pilot investigation on the dose-dependent impact of irradiation on primary human alveolar osteoblasts in vitro
Authors: Amler Anna-Klara , Schlauch Domenic , Tüzüner Selin , Thomas Alexander , Neckel Norbert , Tinhofer Ingeborg , Heiland Max , Lauster Roland , Kloke Lutz , Stromberger Carmen , Nahles Susanne 
Published: October 2021

AbstractRadiotherapy of head and neck squamous cell carcinoma can lead to long-term complications like osteoradionecrosis, resulting in severe impairment of the jawbone. Current standard procedures require a 6-month wait after irradiation before dental reconstruction can begin. A comprehensive characterization of the irradiation-induced molecular and functional changes in bone cells could allow the development of novel strategies for an earlier successful dental reconstruction in patients treated by radiotherapy. The impact of ionizing radiation on the bone-forming alveolar osteoblasts remains however elusive, as previous studies have relied on animal-based models and fetal or animal-derived cell lines. This study presents the first in vitro data obtained from primary human alveolar osteoblasts. Primary human alveolar osteoblasts were isolated from healthy donors and expanded. After X-ray irradiation with 2, 6 and 10 Gy, cells were cultivated under osteogenic conditions and analyzed regarding their proliferation, mineralization, and expression of marker genes and proteins. Proliferation of osteoblasts decreased in a dose-dependent manner. While cells recovered from irradiation with 2 Gy, application of 6 and 10 Gy doses not only led to a permanent impairment of proliferation, but also resulted in altered cell morphology and a disturbed structure of the extracellular matrix as demonstrated by immunostaining of collagen I and fibronectin. Following irradiation with any of the examined doses, a decrease of marker gene expression levels was observed for most of the investigated genes, revealing interindividual differences. Primary human alveolar osteoblasts presented a considerably changed phenotype after irradiation, depending on the dose administered. Mechanisms for these findings need to be further investigated. This could facilitate improved patient care by re-evaluating current standard procedures and investigating faster and safer reconstruction concepts, thus improving quality of life and social integrity.
Heterozygosity of the major histocompatibility complex predicts later self-reported pubertal maturation in men
Authors: Arnocky Steven , Hodges-Simeon Carolyn , Davis Adam C. , Desmarais Riley , Greenshields Anna , Liwski Robert , Quillen Ellen E. , Cardenas Rodrigo , Breedlove S. Marc , Puts David 
Published: October 2021

AbstractIndividual variation in the age of pubertal onset is linked to physical and mental health, yet the factors underlying this variation are poorly understood. Life history theory predicts that individuals at higher risk of mortality due to extrinsic causes such as infectious disease should sexually mature and reproduce earlier, whereas those at lower risk can delay puberty and continue to invest resources in somatic growth. We examined relationships between a genetic predictor of infectious disease resistance, heterozygosity of the major histocompatibility complex (MHC), referred to as the human leukocyte antigen (HLA) gene in humans, and self-reported pubertal timing. In a combined sample of men from Canada (n = 137) and the United States (n = 43), MHC heterozygosity predicted later self-reported pubertal development. These findings suggest a genetic trade-off between immunocompetence and sexual maturation in human males.
Maintenance of prior behaviour can enhance cultural selection
Authors: Walker Bradley , Segovia Martín José , Tamariz Monica , Fay Nicolas 
Published: October 2021

AbstractMany cultural phenomena evolve through a Darwinian process whereby adaptive variants are selected and spread at the expense of competing variants. While cultural evolutionary theory emphasises the importance of social learning to this process, experimental studies indicate that people’s dominant response is to maintain their prior behaviour. In addition, while payoff-biased learning is crucial to Darwinian cultural evolution, learner behaviour is not always guided by variant payoffs. Here, we use agent-based modelling to investigate the role of maintenance in Darwinian cultural evolution. We vary the degree to which learner behaviour is payoff-biased (i.e., based on critical evaluation of variant payoffs), and compare three uncritical (non-payoff-biased) strategies that are used alongside payoff-biased learning: copying others, innovating new variants, and maintaining prior variants. In line with previous research, we show that some level of payoff-biased learning is crucial for populations to converge on adaptive cultural variants. Importantly, when combined with payoff-biased learning, uncritical maintenance leads to stronger population-level adaptation than uncritical copying or innovation, highlighting the importance of maintenance to cultural selection. This advantage of maintenance as a default learning strategy may help explain why it is a common human behaviour.
Temporal activity patterns suggesting niche partitioning of sympatric carnivores in Borneo, Malaysia
Authors: Nakabayashi Miyabi , Kanamori Tomoko , Matsukawa Aoi , Tangah Joseph , Tuuga Augustine , Malim Peter T. , Bernard Henry , Ahmad Abdul Hamid , Matsuda Ikki , Hanya Goro 
Published: October 2021

AbstractTo propose proper conservation measures and to elucidate coexistence mechanisms of sympatric carnivore species, we assessed temporal activity patterns of the sympatric carnivore species using 37,379 photos collected for more than 3 years at three study sites in Borneo. We categorized activity patterns of nine carnivore species (one bear, three civets, two felids, one skunk, one mustelid, one linsang) by calculating the photo-capturing proportions at each time period (day, night, twilight). We then evaluated temporal activity overlaps by calculating the overlap coefficients. We identified six nocturnal (three civets, one felid, one skunk, one linsang), two diurnal (one felid, one mustelid), and one cathemeral (bear) species. Temporal activity overlaps were high among the nocturnal species. The two felid species possessing morphological and ecological similarities exhibited clear temporal niche segregation, but the three civet species with similar morphology and ecology did not. Broad dietary breadth may compensate for the high temporal niche overlaps among the nocturnal species. Despite the high species richness of Bornean carnivores, almost half are threatened with extinction. By comparing individual radio-tracking and our data, we propose that a long-term study of at least 2 or 3 years is necessary to understand animals’ temporal activity patterns, especially for sun bears and civets, by camera-trapping and to establish effective protection measures.
Survival and recurrence with or without axillary dissection in patients with invasive breast cancer and sentinel node metastasis
Authors: Sanvido Vanessa Monteiro , Elias Simone , Facina Gil , Bromberg Silvio Eduardo , Nazário Afonso Celso Pinto 
Published: October 2021

AbstractTo evaluate overall survival and locoregional recurrence between patients with invasive breast tumours and sentinel node metastasis undergoing sentinel lymph node dissection (SLND) alone and those undergoing complete axillary lymph node dissection (ALND). In this retrospective cohort study, we reviewed the medical records of patients with invasive breast carcinoma who underwent lumpectomy at a public university hospital in Brazil between 2008 and 2018. We evaluated the overall survival and the locoregional recurrence using Kaplan–Meier and Cox regression analyses, respectively. Overall, 97 participants who underwent lumpectomy were enroled; 41 in the ALND group, and 56 in the SLND group, according to Z0011 criteria. Only 17% of the patients in the ALND group had an additional biopsy-proven axillary disease, and 83% were treated with complete dissection unnecessarily. The 5-year survival rates were 80.1% and 87.5% for SLND and ALND, respectively (p = 0.376). Locoregional recurrence was rare (1.7% and 7.3% in the SLND and ALND, respectively; p = 0.3075). Overall survival and locoregional recurrence were similar between the two groups. The de-escalation of ALND to SLND in women with metastasis in the sentinel lymph node treated with conservative surgery and radiotherapy that meet the Z0011 criteria is feasible even in developing countries.
Centromere size scales with genome size across Eukaryotes
Authors: Plačková Klára , Bureš Petr , Zedek František 
Published: October 2021

AbstractPrevious studies on grass species suggested that the total centromere size (sum of all centromere sizes in a cell) may be determined by the genome size, possibly because stable scaling is important for proper cell division. However, it is unclear whether this relationship is universal. Here we analyze the total centromere size using the CenH3-immunofluorescence area as a proxy in 130 taxa including plants, animals, fungi, and protists. We verified the reliability of our methodological approach by comparing our measurements with available ChIP-seq-based measurements of the size of CenH3-binding domains. Data based on these two independent methods showed the same positive relationship between the total centromere size and genome size. Our results demonstrate that the genome size is a strong predictor (R-squared = 0.964) of the total centromere size universally across Eukaryotes. We also show that this relationship is independent of phylogenetic relatedness and centromere type (monocentric, metapolycentric, and holocentric), implying a common mechanism maintaining stable total centromere size in Eukaryotes.
Drug repositioning by merging active subnetworks validated in cancer and COVID-19
Authors: Lucchetta Marta , Pellegrini Marco 
Published: October 2021

AbstractComputational drug repositioning aims at ranking and selecting existing drugs for novel diseases or novel use in old diseases. In silico drug screening has the potential for speeding up considerably the shortlisting of promising candidates in response to outbreaks of diseases such as COVID-19 for which no satisfactory cure has yet been found. We describe DrugMerge as a methodology for preclinical computational drug repositioning based on merging multiple drug rankings obtained with an ensemble of disease active subnetworks. DrugMerge uses differential transcriptomic data on drugs and diseases in the context of a large gene co-expression network. Experiments with four benchmark diseases demonstrate that our method detects in first position drugs in clinical use for the specified disease, in all four cases. Application of DrugMerge to COVID-19 found rankings with many drugs currently in clinical trials for COVID-19 in top positions, thus showing that DrugMerge can mimic human expert judgment.
A systematic analysis of genetic interactions and their underlying biology in childhood cancer
Authors: Daub Josephine T. , Amini Saman , Kersjes Denise J. E. , Ma Xiaotu , Jäger Natalie , Zhang Jinghui , Pfister Stefan M. , Holstege Frank C. P. , Kemmeren Patrick 
Published: October 2021

AbstractChildhood cancer is a major cause of child death in developed countries. Genetic interactions between mutated genes play an important role in cancer development. They can be detected by searching for pairs of mutated genes that co-occur more (or less) often than expected. Co-occurrence suggests a cooperative role in cancer development, while mutual exclusivity points to synthetic lethality, a phenomenon of interest in cancer treatment research. Little is known about genetic interactions in childhood cancer. We apply a statistical pipeline to detect genetic interactions in a combined dataset comprising over 2,500 tumors from 23 cancer types. The resulting genetic interaction map of childhood cancers comprises 15 co-occurring and 27 mutually exclusive candidates. The biological explanation of most candidates points to either tumor subtype, pathway epistasis or cooperation while synthetic lethality plays a much smaller role. Thus, other explanations beyond synthetic lethality should be considered when interpreting genetic interaction test results.