bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors That Contribute to Cost Differences Based on ICU of Admission in Neonates Undergoing Congenital Heart Surgery: A Novel Decomposition Analysis
Authors: Johnson Joyce T. , Sullivan Kirsen L. , Nelson Richard E. , Sheng Xiaoming , Greene Tom H. , Bailly David K. , Eckhauser Aaron W. , Marino Bradley S. , Minich L. LuAnn , Pinto Nelangi M. 
Published: August 2020

Objectives:
We leveraged decomposition analysis, commonly used in labor economics, to understand determinants of cost differences related to location of admission in children undergoing neonatal congenital heart surgery.

Design:
A retrospective cohort study.

Setting:
Pediatric Health Information Systems database.

Patients:
Neonates (<30 d old) undergoing their index congenital heart surgery between 2004 and 2013.

Measurements and Main Results:
A decomposition analysis with bootstrapping determined characteristic (explainable by differing covariate levels) and structural effects (if covariates are held constant) related to cost differences. Covariates included center volume, age at admission, prematurity, sex, race, genetic or major noncardiac abnormality, Risk Adjustment for Congenital Heart Surgery-1 score, payor, admission year, cardiac arrest, infection, and delayed sternal closure.
Of 19,984 infants included (10,491 [52%] to cardiac ICU/PICU and 9,493 [48%] to neonatal ICU), admission to the neonatal ICU had overall higher average costs ($24,959 ± $3,260; p < 0.001) versus cardiac ICU/PICU admission. Characteristic effects accounted for higher costs in the neonatal ICU ($28,958 ± $2,044; p < 0.001). Differing levels of prematurity, genetic syndromes, hospital volume, age at admission, and infection contributed to higher neonatal ICU costs, with infection rate providing the most significant contribution ($13,581; p < 0.001). Aggregate structural effects were not associated with cost differences for those admitted to the neonatal ICU versus cardiac ICU/PICU (p = 0.1). Individually, prematurity and age at admission were associated with higher costs due to structural effects for infants admitted to the neonatal ICU versus cardiac ICU/PICU.

Conclusions:
The difference in cost between neonatal ICU and cardiac ICU/PICU admissions is largely driven by differing prevalence of risk factors between these units. Infection rate was a modifiable factor that accounted for the largest difference in costs between admitting units.
Intergender Hand Transplant
Authors: MT Friji , Sivakumar Dinesh Kumar , Mohapatra Deviprasad , Chittoria Ravikumar 
Published: August 2020

Abstract
Hand and upper-extremity transplantation restore severely damaged limbs that cannot be repaired with conventional surgical techniques. Over the past 20 years, more than 200 vascularized composite allotransplantations have been performed worldwide, among them 7 were cases of sex unmatched hand transplants. The long term effects of recipient sex hormones and nerve regeneration on the sexually dimorphic physical features of donor upper extremity have not been described previously. We report a case of sex congruent transformation of hand morphology in an intergender hand transplant.
From bioinformatics user to bioinformatics engineer: a report
Authors: de Araújo Gilderlanio Santana 
Published: August 2020

AbstractTeaching computer programming is not a simple task and it is challenging to introduce the concepts of programming in graduate programs of other fields. Little efforts have been made on engaging students in computational development after programming trainings. An emerging need is to establish subjects of bioinformatics and programming languages in genetics and molecular biology graduate programs, when students in these degree programs are immersed in a sea of genomic and transcriptomic data, which demands proficient computational treatment. I report an empirical guideline to introduce programming languages and recommend Python as first language for graduate programs in which students were from genetics and molecular biology backgrounds. Including the development of programming solutions related to graduate students' research activities may improve programming skills and better engagement. These results suggest that the applied approach leads to enhanced learning of introductory to autonomy in highly advanced programming concepts by graduate students. This guide should be extended for other research programs.
Binding Ligands that Straddle an Important Contact Site on the RBD of the Covid-19 Spike Protein
Authors: Boyarsky Abraham 
Published: August 2020

AbstractThe receptor binding domain (RBD) of the spike protein of the Covid-19 virus is responsible for attachment to human ACE2. A number of recent articles have studied monoclonal antibody blocking [8-11] and peptide inhibitors [12-16] of the Covid-19 virus. Here we report virtual ligand-based screening that targets pockets on each side of an important binding site with residues 502-504 on the RBD that contact residues 353-357 [15] of hACE2. These ligands are intended as pre-exposure therapy for Covid-19 infection.
Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors
Authors: Iketani Sho , Forouhar Farhad , Liu Hengrui , Hong Seo Jung , Lin Fang-Yu , Nair Manoj S. , Zask Arie , Huang Yaoxing , Xing Li , Stockwell Brent R. , Chavez Alejandro , Ho David D. 
Published: August 2020

AbstractWe report the identification of three structurally diverse compounds – compound 4, GC376, and MAC-5576 – as inhibitors of the SARS-CoV-2 3CL protease. Structures of each of these compounds in complex with the protease revealed strategies for further development, as well as general principles for designing SARS-CoV-2 3CL protease inhibitors. These compounds may therefore serve as leads for the basis of building effective SARS-CoV-2 3CL protease inhibitors.
Synthetic Lethal Interactions Prediction Based on Multiple Similarity Measures Fusion
Authors: Wen Yu-Qi , Wu Lian-Lian , Yang Xiao-Xi , Yan Bo-Wei , He Song , Bo Xiao-Chen 
Published: August 2020

AbstractThe synthetic lethality (SL) relationship arises when a combination of deficiencies in two genes leads to cell death, whereas a deficiency in either one of the two genes does not. The survival of the mutant tumor cells depends on the SL partner genes of the mutant gene, so the cancer cells could be selectively killed by inhibiting the SL partners of the oncogenic genes but normal cells not. Therefore, developing SL pairs identification methods is increasingly needed for cancer targeted therapy. In this paper, we proposed a new approach based on similarity fusion to predict SL pairs. Multiple types of gene similarity measures are integrated and k-NN algorithm are applied to achieve the similarity-based classification task between gene pairs. As a similarity-based method, our method demonstrated excellent performance in multiple experiments. Besides the effectiveness of our method, the ease of use and expansibility can also make our method more widely used in practice.
KDM4 Orchestrates Epigenomic Remodeling of Senescent Cells and Potentiates the Senescence-Associated Secretory Phenotype
Authors: Zhang Boyi , Long Qilai , Wu Shanshan , Song Shuling , Xu Qixia , Han Liu , Qian Min , Ren Xiaohui , Jiang Jing , Fu Qiang , Guo Jianming , Zhang Xiaoling , Chang Xing , Lam Eric W-F , Campisi Judith , Kirkland James L. , Sun Yu 
Published: August 2020

AbstractCellular senescence restrains the expansion of neoplastic cells through several layers of regulation, including epigenetic decoration of chromatin structure and functional modulation of bioactive components. Here we report that expression of the histone H3-specific demethylase KDM4 is upregulated in human stromal cells upon cellular senescence. In clinical oncology, upregulated KDM4 and diminished H3K9/H3K36 methylation are correlated with adverse survival of cancer patients post-chemotherapy. Global chromatin accessibility mappingviaATAC-seq and expression profiling through RNA-seq reveal extensive reorganization of chromosomes and spatiotemporal reprogramming of the transcriptomic landscape, events responsible for development of the senescence-associated secretory phenotype (SASP). Selectively targeting KDM4 dampens the SASP of senescent stromal cells and enhances the apoptotic index of cancer cells in the treatment-damaged tumor microenvironment (TME), together prolonging overall survival of experimental animals. Our study supports the dynamic change of H3K9/H3K36 methylation marks during cellular senescence, identifies an unusually permissive chromatin state, unmasks KDM4 as a key modulator of the SASP, and presents a novel therapeutic avenue to manipulate cellular senescence and curtail age-related pathologies.
Ventral Pallidum GABA Neurons Mediate Motivation Underlying Risky Choice
Authors: Farrell M.R. , Esteban J.S.D. , Faget L. , Floresco S.B. , Hnasko T.S. , Mahler S.V. 
Published: August 2020

AbstractPursuing rewards while avoiding danger is an essential function of any nervous system. Here, we examine a new mechanism helping rats negotiate the balance between risk and reward when making high-stakes decisions. Specifically, we focus on GABA neurons within an emerging mesolimbic circuit nexus—the ventral pallidum (VP). These neurons play a distinct role from other VP neurons in simple motivated behaviors in mice, but their roles in more complex motivated behaviors is unknown. Here, we interrogate the behavioral functions of VPGABAneurons in male and female transgenic GAD1:Cre rats (and wildtype littermates), using a reversible chemogenetic inhibition approach. Employing a behavioral assay of risky decision making, and of the food-seeking and shock-avoidance components of this task, we show that engaging inhibitory Gi/osignaling specifically in VPGABAneurons suppresses motivation to pursue highly salient palatable foods, and possibly also motivation to avoid being shocked. In contrast, inhibiting these neurons did not affect seeking of low-value food, free consumption of palatable food, or unconditioned affective responses to shock. Accordingly, when rats considered whether to pursue food despite potential for shock in a risky decision-making task, inhibiting VPGABAneurons caused them to more readily select a small but safe reward over a large but dangerous one—an effect not seen in the absence of shock threat. Together, results indicate that VPGABAneurons are critical for high-stakes adaptive responding that is necessary for survival, but which may also malfunction in psychiatric disorders.Significance StatementIn a dynamic world, it is essential to implement appropriate behaviors under circumstances involving rewards, threats, or both. Here, we demonstrate a crucial role for VPGABAneurons in high-stakes motivated behavior of several types. We show that this VPGABArole in motivation impacts decision making, as inhibiting these neurons yields a conservative, risk-averse strategy not seen when the task is performed without threat of shock. These new roles for VPGABAneurons in behavior may inform future strategies for treating addiction, and other disorders of maladaptive decision making.
SubFeat: Feature Subspacing Ensemble Classifier for Function Prediction of DNA, RNA and Protein Sequences
Authors: Haque H.M.Fazlul , Arifin Fariha , Adilina Sheikh , Rafsanjani Muhammod , Shatabda Swakkhar 
Published: August 2020

AbstractThe information of a cell is primarily contained in Deoxyribonucleic Acid (DNA). There is a flow of information of DNA to protein sequences via Ribonucleic acids (RNA) through transcription and translation. These entities are vital for the genetic process. Recent developments in epigenetic also show the importance of the genetic material and knowledge of their attributes and functions. However, the growth in known attributes or functionalities of these entities are still in slow progression due to the time consuming and expensivein vitroexperimental methods. In this paper, we have proposed an ensemble classification algorithm calledSubFeatto predict the functionalities of biological entities from different types of datasets. Our model uses a feature subspace based novel ensemble method. It divides the feature space into sub-spaces which are then passed to learn individual classifier models and the ensemble is built on this base classifiers that uses a weighted majority voting mechanism.SubFeattested on four datasets comprising two DNA, one RNA and one protein dataset and it outperformed all the existing single classifiers and as well as the ensemble classifiers.SubFeatis made availalbe as a Python-based tool. We have made the packageSubFeatavailable online along with a user manual. It is freely accessible from here:https://github.com/fazlulhaquejony/SubFeat.
Environmental enrichment reverses memory impairment in B3-ARKO mice
Authors: Ravache Thais Terpins , Nunes Gabriela G. , Batistuzzo Alice , Lorena Fernanda B. , do Nascimento Bruna P. P. , Bernardi Martha , Ribeiro Miriam O. 
Published: August 2020

ABSTRACTNorepinephrine plays an important role in modulating the processes of memory consolidation and evocation through its beta-adrenergic receptors (Adrβ), which are expressed in the hippocampus and amygdala. Several studies have shown that all three subtypes of Adrβ (β1, β2and β3) play an important role in cognition. Environmental enrichment (EE), a technique initially used to decrease the stress of animals held in captive environments, has also been shown to produce cognitive benefits in both healthy and sick animals. In this study, we hypothesized that EE would reverse the memory impairment induced by the absence or Adrβ3. To test this, 21- and 86-day-old Adrβ3KO mice were exposed to an EE protocol for 8 weeks. The study showed that the EE protocol is able to correct the memory impairment when applied to Adrβ3KO animals immediately after weaning but has no effect when applied to adult animals. We also found that aging worsens the memory of Adrβ3KO mice. Our results suggest that a richer and more diverse environment helps to correct memory impairment in Adrβ3KO animals. They also reinforce the idea that noradrenergic signaling is involved in the cognitive impairment observed late in life, as aging led to a worsening in the memory of the Adrβ3KO animals that was not corrected by the environmental enrichment protocol.
Accurate brain age prediction using recurrent slice-based networks
Authors: Lam Pradeep K. , Santhalingam Vigneshwaran , Suresh Parth , Baboota Rahul , Zhu Alyssa H. , Thomopoulos Sophia I. , Jahanshad Neda , Thompson Paul M. 
Published: August 2020

ABSTRACTBrainAge (a subject’s apparent age predicted from neuroimaging data) is an important biomarker of brain aging. The deviation of BrainAge from true age has been associated with psychiatric and neurological disease, and has proven effective in predicting conversion from mild cognitive impairment (MCI) to dementia. Conventionally, 3D convolutional neural networks and their variants are used for brain age prediction. However, these networks have a larger number of parameters and take longer to train than their 2D counterparts. Here we propose a 2D slice-based recurrent neural network model, which takes in an ordered sequence of sagittal slices as input to predict the brain age. The model consists of two components: a 2D convolutional neural network (CNN), which encodes the relevant features from the slices, and a recurrent neural network (RNN) that learns the relationship between slices. We compare our method to other recently proposed methods, including 3D deep convolutional regression networks, information theoretic models, and bag-of-features (BoF) models (such as BagNet) - where the classification is based on the occurrences of local features, without taking into consideration their global spatial ordering. In our experiments, our proposed model performs comparably to, or better than, the current state of the art models, with nearly half the number of parameters and a lower convergence time.
Inflammasome- and gasdermin D-independent IL-1β production mobilizes neutrophils to inhibit antitumor immunity
Authors: Kiss Máté , Vande Walle Lieselotte , Lebegge Els , Van Damme Helena , Murgaski Aleksandar , Qian Junbin , Ehling Manuel , Pretto Samantha , Bolli Evangelia , Keirsse Jiri , Elkrim Yvon , Martins Maria Solange , Fossoul Amelie , Lambrechts Diether , Mazzone Massimiliano , Wullaert Andy , Lamkanfi Mohamed , Van Ginderachter Jo A. , Laoui Damya 
Published: August 2020

ABSTRACTInterleukin-1β (IL-1β) is a central mediator of inflammation whose secretion typically requires proteolytic maturation by the inflammasome and formation of membrane pores by gasdermin D (GSDMD). Emerging evidence suggests an important role for IL-1β in promoting cancer progression in patients, but the underlying mechanisms are little understood. Here, we show a key role for IL-1β in driving tumor progression in two distinct mouse tumor models. Notably, inflammasome activation and GSDMD were dispensable for the production of intratumoral bioactive IL-1β, which promoted systemic mobilization and infiltration of neutrophils into tumors. Neutrophils recruited via IL-1β suppressed the acquisition of an effector T-cell phenotype and subsequent antitumor immune response. Moreover, IL-1β was essential for neutrophil accumulation upon antiangiogenic therapy, thereby contributing to therapy-induced immunosuppression. Antitumor immunity in the absence of IL-1β-dependent neutrophil recruitment relied on immunostimulatory macrophages which promoted the infiltration and activation of cytotoxic T-cells. Overall, these results support a tumor-promoting role for IL-1β through establishing an immunosuppressive microenvironment and show that inflammasome activation is not essential for its release in tumors.
Five patterns of cell signaling pathways associated with cell behavior
Authors: Takeda Yuji , Kawano Kazuharu , Ma Rui , Saitoh Shinichi , Asao Hironobu 
Published: August 2020

AbstractCell signaling pathway is complex systems. Here, we present a concept for a new approach to analyze cell signaling pathway associated with cell behavior. In theoretically, cell behavior is recognized by energy and fluctuation. In this study, we measured phosphorylation level of signal transducers in a cell and fluctuation of the phosphorylation level in the cell population using flow cytometry. Flow cytometric data of mean fluorescence intensity (MFI) and coefficient variation (CV) were considered to the energy and the fluctuation, respectively. Topologically, the changes of MFI and CV were categorized into five patterns (we tentatively named as attractive, subsequent, passive, counter, and negative arbiter). In this study, we clarified the relationship between the cell behavior and the five patterns. Furthermore, combining the five patterns can define the signaling pathways, such as simple activated signal, oscillating signal, regulatory signal, robust signal, or homeostatic signal. These observations provide a proof of concept for general strategy to use the five patterns for connection between cell signaling pathway and cell behavior.
Fibre-specific laterality of white matter in left and right language dominant people
Authors: Verhelst Helena , Dhollander Thijs , Gerrits Robin , Vingerhoets Guy 
Published: August 2020

AbstractDespite the typical symmetrical appearance of the human brain, several functional and structural asymmetries have been reported. Language is the most commonly described lateralised cognitive function, relying relatively more on the left hemisphere in over 90% of the population. This is in line with white matter studies which have revealed leftwards lateralisation of the arcuate fasciculus, a white matter tract that connects important language-related regions. Most research to date examining the structure-function relationship of language lateralisation only included people showing a left language hemisphere dominance. As such, the reported correlations do not allow for inferences of relationships between the directions of functional and structural lateralisation of language.In this work, we applied a state-of-the-art “fixel-based” analysis approach, which allows to statistically analyse white matter micro- and macrostructure on a fibre-specific level. To study lateralisation using this framework, we defined a bespoke fibre-specific laterality index which allowed us to examine whole-brain white matter asymmetries in samples of participants with left and right language dominance (LLD and RLD respectively). Both groups showed similar extensive and intricate patterns of significant white matter lateralisation. Few group differences were found between both groups, with a similar leftwards lateralisation of the arcuate fasciculus, regardless of functional language lateralisation of the participants. A significant group difference of lateralisation was detected in the forceps minor, with a leftwards lateralisation in LLD and rightwards lateralisation for the RLD group.In conclusion, we showed that fixel-based analysis of fibre-specific lateralisation indices is an effective approach to study white matter asymmetries. Our results suggest that the lateralisation of language functioning and the arcuate fasciculus are driven by independent biases. The exact relationship between forceps minor asymmetry and language dominance could be an interesting subject of future studies.
Robotic assembly for tight tolerant cascaded peg-in-hole process with incomplete constraints
Authors: Cheng Hongtai , Liu Tianzhuo , Zhang Wei , Hao Lina 
Published: August 2020

Purpose
Installing a tight tolerant stepped shaft is not a trivial task for an industrial robot. If all peg-hole constraints are complete, the cascaded peg-in-hole task can be simplified into several independent stages and accomplished one by one. However, if some of the constraints are incomplete, the cross stage interference will bring additional difficulties. This paper aims to discuss the cascaded peg-in-hole problem with incomplete constraints.

Design/methodology/approach
In this paper, the problem is formulated according to geometric parameters of the stepped shaft and completeness of the corresponding hole. The possible jamming type is modeled and analyzed. A contact modeling and control strategy is proposed to compensate the peg postures under incomplete constraints.

Findings
The above methods are implemented on an experiment platform and the results verify the effectiveness of the proposed robotic assembly strategy.

Originality/value
Based on force/torque sensor, a hybrid control strategy for incomplete constraints cascaded peg-in-hole assembly problem is proposed.