bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alterations in gene expression in the spinal cord of mice lacking Nfix
Authors: Matuzelski Elise , Essebier Alexandra , Harris Lachlan , Gronostajski Richard M. , Harvey Tracey J. , Piper Michael 
Published: September 2020

Abstract
Objective
Nuclear Factor One X (NFIX) is a transcription factor expressed by neural stem cells within the developing mouse brain and spinal cord. In order to characterise the pathways by which NFIX may regulate neural stem cell biology within the developing mouse spinal cord, we performed an microarray-based transcriptomic analysis of the spinal cord of embryonic day (E)14.5 Nfix−/− mice in comparison to wild-type controls.

Data description
Using microarray and differential gene expression analyses, we were able to identify differentially expressed genes in the spinal cords of E14.5 Nfix−/− mice compared to wild-type controls. We performed microarray-based sequencing on spinal cords from n = 3 E14.5 Nfix−/− mice and n = 3 E14.5 Nfix+/+ mice. Differential gene expression analysis, using a false discovery rate (FDR) p-value of p < 0.05, and a fold change cut-off for differential expression of >  ± 1.5, revealed 1351 differentially regulated genes in the spinal cord of Nfix−/− mice. Of these, 828 were upregulated, and 523 were downregulated. This resource provides a tool to interrogate the role of this transcription factor in spinal cord development.
Microbial dark matter filling the niche in hypersaline microbial mats
Authors: Wong Hon Lun , MacLeod Fraser I. , White Richard Allen , Visscher Pieter T. , Burns Brendan P. 
Published: September 2020

Abstract
Background
Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been shown to possess a substantial abundance of uncultivable microorganisms. These enigmatic microbes, jointly coined as ‘microbial dark matter’ (MDM), are hypothesised to play key roles in modern microbial mats.

Results
We reconstructed 115 metagenome-assembled genomes (MAGs) affiliated to MDM, spanning 42 phyla. This study reports for the first time novel microorganisms (Zixibacterial order GN15) putatively taking part in dissimilatory sulfate reduction in surface hypersaline settings, as well as novel eukaryote signature proteins in the Asgard archaea. Despite possessing reduced-size genomes, the MDM MAGs are capable of fermenting and degrading organic carbon, suggesting a role in recycling organic carbon. Several forms of RuBisCo were identified, allowing putative CO2 incorporation into nucleotide salvaging pathways, which may act as an alternative carbon and phosphorus source. High capacity of hydrogen production was found among Shark Bay MDM. Putative schizorhodopsins were also identified in Parcubacteria, Asgard archaea, DPANN archaea, and Bathyarchaeota, allowing these members to potentially capture light energy. Diversity-generating retroelements were prominent in DPANN archaea that likely facilitate the adaptation to a dynamic, host-dependent lifestyle.

Conclusions
This is the first study to reconstruct and describe in detail metagenome-assembled genomes (MAGs) affiliated with microbial dark matter in hypersaline microbial mats. Our data suggests that these microbial groups are major players in these systems. In light of our findings, we propose H2, ribose and CO/CO2 as the main energy currencies of the MDM community in these mat systems.
Deep learning-based question answering system for intelligent humanoid robot
Authors: Budiharto Widodo , Andreas Vincent , Gunawan Alexander Agung Santoso 
Published: September 2020

AbstractBackgroundThe development of Intelligent Humanoid Robot focuses on question answering systems that can interact with people is very limited. In this research, we would like to propose an Intelligent Humanoid Robot with the self-learning capability for accepting and giving responses from people based on Deep Learning and Big Data knowledge base. This kind of robot can be used widely in hotels, universities, and public services. The Humanoid Robot should consider the style of questions and conclude the answer through conversation between robot and user. In our scenario, the robot will detect the user’s face and accept commands from the user to do an action.FindingsThe question from the user will be processed using deep learning, and the result will be compared to the knowledge base on the system. We proposed our Deep Learning approach, based on Recurrent Neural Network (RNN) encoder, Convolution Neural Network (CNN) encoder, with Bidirectional Attention Flow (BiDAF).ConclusionsOur evaluation indicates that using RNN based encoder with BiDAF gives a higher score, than CNN encoder with the BiDAF. Based on our experiment, our model get 82.43% F1 score and the RNN based encoder will give a higher EM/F1 score than using the CNN encoder.
The relationship between immune status as measured by stimulated ex-vivo tumour necrosis factor alpha levels and the acquisition of nosocomial infections in critically ill mechanically ventilated patients
Authors: Levin Gabrielle , Boyd J. Gordon , Day Andrew , Hunt Miranda , Maslove David M. , Norman Patrick , O’Callaghan Nicole , Sibley Stephanie , Muscedere John 
Published: September 2020

Abstract
Introduction
Immunological dysfunction is common in critically ill patients but its clinical significance and the optimal method to measure it are unknown. The level of tumor necrosis factor alpha (TNF-α) after ex-vivo whole blood stimulation with lipopolysaccharide (LPS) has been proposed as a possible method to quantify immunological function. We hypothesized that in a cohort of critically ill patients, those with a lower post-stimulation TNF-α level would have increased rates of nosocomial infections (NIs) and worse clinical outcomes.

Methods
A secondary analysis of a phase 2 randomized, multi-centre, double-blinded placebo-controlled trial. As there was no difference between treatment and control arms in outcomes and NI rate, all the patients were analyzed as one cohort. On enrolment, day 4, 7, and weekly until day 28, whole blood was incubated with LPS ex-vivo and subsequent TNF-α level was measured. Patients were grouped in tertiles according to delta and peak TNF-α level. The primary outcome was the association between NIs and tertiles of TNF-α level post LPS stimulation; secondary outcomes included ICU and 90-day mortality, and ICU and hospital length of stay.

Results
Data was available for 201 patients. Neither the post LPS stimulation delta TNF-α group nor the peak TNF-α post-stimulation group were associated with the development of NIs or clinical outcomes. Patients in the highest tertile for post LPS stimulation delta TNF-α compared to the lowest tertile were younger [61.1 years ± 15.7 vs. 68.6 years ± 12.8 standard deviations (SD) in the lowest tertile], had lower acuity of illness (APACHE II 25.0 ± 9.7 vs. 26.7 ± 6.1) and had lower baseline TNF-α (9.9 pg/mL ± 19.0 vs. 31.0 pg/mL ± 68.5). When grouped according to peak post-stimulation TNF-α levels, patients in the highest tertile had higher serum TNF-α at baseline (21.3 pg/mL ± 66.7 compared to 6.5 pg/mL ± 9.0 in the lowest tertile).

Conclusion
In this prospective multicenter study, ex-vivo stimulated TNF-α level was not associated with the occurrence of NIs or clinical outcomes. Further study is required to better ascertain whether TNF levels and ex-vivo stimulation can be used to characterize immune function in critical illness and if other assays might be better suited to this task.
The roles of miRNA, lncRNA and circRNA in the development of osteoporosis
Authors: Yang Yang , Yujiao Wang , Fang Wang , Linhui Yuan , Ziqi Guo , Zhichen Wei , Zirui Wang , Shengwang Wang 
Published: September 2020

AbstractOsteoporosis is a common metabolic bone disease, influenced by genetic and environmental factors, that increases bone fragility and fracture risk and, therefore, has a serious adverse effect on the quality of life of patients. However, epigenetic mechanisms involved in the development of osteoporosis remain unclear. There is accumulating evidence that epigenetic modifications may represent mechanisms underlying the links of genetic and environmental factors with increased risk of osteoporosis and bone fracture. Some RNAs, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), have been shown to be epigenetic regulators with significant involvement in the control of gene expression, affecting multiple biological processes, including bone metabolism. This review summarizes the results of recent studies on the mechanisms of miRNA-, lncRNA-, and circRNA-mediated osteoporosis associated with osteoblasts and osteoclasts. Deeper insights into the roles of these three classes of RNA in osteoporosis could provide unique opportunities for developing novel diagnostic and therapeutic approaches to this disease.
Roles of fibrinolytic factors in the alterations in bone marrow hematopoietic stem/progenitor cells during bone repair
Authors: Okada Kiyotaka , Nishioka Minoru , Kaji Hiroshi 
Published: September 2020

AbstractIn bone tissues, metabolic turnover through bone resorption by osteoclasts and bone formation by osteoblasts, termed bone remodeling, is strictly controlled and maintains homeostasis. Fibrinolytic factors are expressed in osteoclasts and osteoblasts, and are involved in bone remodeling through bone resorption and formation. The repair/regeneration process after bone injury is divided into the acute inflammatory, repair, and remodeling stages. Osteoblasts, osteoclasts, chondrocytes, and macrophages involved in the bone repair process originate from hematopoietic stem/progenitor cells (HSPCs) and mesenchymal stem cells (MSCs) in the bone marrow. Therefore, stem cells in the bone marrow may be strongly influenced by bone injury. The urokinase-type PA (u-PA)/plasminogen (Plg) system functions in macrophage accumulation/phagocytosis through chemokines in the acute inflammatory stage, and Plg increases blood vessel-related growth factor expression, being involved in vascularization in mice. Plasminogen activator inhivitor-1 (PAI-1) causes bone loss and delayed bone repair through the inhibition of osteoblast differentiation in a drug-induced diabetes model in mice. Plg is considered to induce transforming growth factor-β (TGF-β) production in macrophages in the bone repair process, TGF-β release from the extracellular matrix through the activation of matrix metalloproteinase-9 (MMP-9), and stromal cell-derived factor-1 (SDF-1) expression in endosteal preosteoblasts, leading to the induction of bone marrow HSPCs in mice. Based on the above, establishment of a fibrinolytic factor-targeting method efficiently promoting bone repair/regeneration and fracture healing, and development of a new osteoporosis treatment method and diagnostic marker are awaited.
Placard in Hand: A Simple, Inexpensive Intervention to Improve On-Treatment Visit Compliance in a Safety Net Radiation Oncology Patient Population
Authors: Moeller Alexander R. , Clancy Pauline E. , Qureshi Muhammad Mustafa , Guill Jacklyn R. , Dyer Michael A. , Hirsch Ariel E. , Truong Minh-Tam , Mak Kimberley S. 
Published: September 2020

PURPOSE: On-treatment visits (OTVs) for patients undergoing radiotherapy (RT) should occur every five fractions. Compliance with OTVs was identified as a potential issue in a safety-net patient population. This study determined if brightly colored placards given to patients improved OTV compliance. MATERIALS AND METHODS: A retrospective analysis of all patients with lung cancer receiving RT from October 1, 2015 to September 30, 2017 evaluated OTV compliance before (No Placard) and after (Placard) the placard was introduced in the clinic. Analysis of variance, χ2 tests, and Fisher’s exact tests were performed to assess differences in continuous and categorical patient and treatment variables, respectively. RESULTS: The No Placard group included 48 patients who were scheduled for 151 OTVs. The Placard group included 50 patients who were scheduled for 187 OTVs. The percentage of missed OTVs in the No Placard group was 9.3% (14/151), versus 2.1% (4/187) in the Placard group ( P = .004). Patients in the No Placard group were more likely to speak English (97.9% v 86.0%; P = .060), were less likely to have stage I-III disease (75% v 88%; P = .097), and received lower mean RT doses (48.2 Gy v 55.6 Gy; P = .007). On multivariate analysis adjusting for language, stage, and RT dose, the adjusted mean rate of missed OTVs in the No Placard group was 7.1%, versus 1.4% in the Placard group ( P = .019). CONCLUSION: A significant increase in compliance of OTVs was observed with the introduction of brightly colored placards. This represents a simple, inexpensive method to improve OTV compliance in a safety-net setting and may be applicable to other patient populations.
Mental health status and quality of life among Cambodian migrant workers in Thailand
Authors: Chamroen Pall , Samphors Sim , Rachutorn Thiwakorn , S. Dewey Rebecca , Pisey Vong 
Published: September 2020

Background: Migrant workers have become a major issue for Thailand. Most of the migrants are from Myanmar, Cambodia, and Laos. Most are employed in jobs referred to as the “3 Ds”; difficult, dangerous and dirty. However, little is known concerning the living and working conditions, or health-related quality of life of these migrant workers. This study aims to determine factors influencing the quality of life of Cambodian migrant workers in Thailand. Methods: A cross-sectional study was conducted among 1,211 Cambodian migrant workers in Thailand, using multistage random sampling from eight districts of the two provinces (Sa Kaeo and Surin) with a structured questionnaire interview. The WHOQOL-BREF was used to measure Quality of Life (QOL) with Cronbach’s alpha of 0.77. Mental health status was assessed using the Perceived Stress Scale (PSS) and Center for Epidemiological Studies-Depression (CES-D) scale with Cronbach’s alpha of 0.83. Descriptive statistics provide participant characteristics. Multilevel logistic regression (MLR) were used to determine which factors significantly impacted the outcome measures in terms of the adjusted odds ratio (AOR). P<0.05 was considered statistically significant. Results: About one third of these migrant workers had a poor quality of life (34.52%; 95%CI: 31.84-37.20), and had moderate-to-high levels of stress (67.96%; 95%CI: 65.33-70.59), and symptoms of depression (69.69%; 95%CI: 67.10-72.29). After controlling other covariate factors, the factors associated with poor QOL were a high level perceived of stress (AOR=3.64; 95%CI: 2.41-5.49; p<0.001); living with family and relatives (AOR=3.63; 95%CI: CI 2.42-5.45; p<0.001); and housing being provided by their employer (AOR=2.66; 95%CI: 1.74-4.08; p<0.001). Conclusion: Stress was strongly associated with QOL. The living environment was found to be the next most influential factor on QOL. Mental health programs aimed at helping migrant workers to cope with stress and to improve their living conditions will help improve QOL in the target group.
Natural Gas Energy Consumption Strategy by Iron and Steel Industry Enterprises
Authors: Koksharov V. , Kirshina I. 
Published: September 2020

The existing modern conceptual approaches to the formation of an assessment of the natural gas consumption strategy in the steel industry do not allow assessing comprehensively all the processes that occur in the enterprise affecting the efficiency of natural gas consumption. Due to the fact that natural gas acts an important role as a universal energy resource, both in the economy and in international politics, the modern strategy for assessing the consumption of natural gas in the steel industry is becoming a key factor in increasing competitiveness and guaranteeing sustainable economic growth of the country's steel industry.
The article proposes a conceptual approach to the development of the model in order to assess the strategy of natural gas consumption at iron and steel enterprises, which allows timely management decisions to be taken to increase the organization of efficient energy consumption at the enterprise.
Based on the proposed conceptual approach to assessing the strategy of natural gas consumption at the iron and steel industry, it can be stated that this assessment is interconnected with the assessment of the integral criterion for the implementation of the goals of organizing effective energy management.
Przydrożne sacrum w pamięci lokalnej
Authors: Cichoń Stanisław Szczepan 
Published: September 2020

A Roadside Sacrum in Local Memory. Study of the Myślenice Land
The article analyses selected examples of roadside shrines typical for the area of the Myślenice land, Poland. The author points at the characteristic elements of small architecture that reflects spiritual values cultivated by past generations living in the region. The current population scattered across the Myślenice land cultivates with care the individual and collective memory of their ancestors embraced in well-shaped stone blocks of the shrines.
La lectura entre els infants i els joves a catalunya (2018-2019)
Authors: Centelles Jaume 
Published: September 2020

En aquest capítol es fa palès un cert estancament del grau d’assoliment de les competències lectores per part dels infants i joves, i es reflexiona sobre algunes de les possibles causes d’aquesta inèrcia conformista que ens porta a un «anar fent» que ens impedeix aprofitar el potencial humà del país. També es relacionen alguns plans institucionals de suport a la lectura, la consolidació d’activitats reeixides —jornades, congressos, grups de treball— que mostren interès de fer de la lectura una pedra angular de l’educació i s’apunten algunes idees o situacions que ens allunyen de l’optimisme que hauria de motivar-nos, si és que ens volem constituir definitivament com a societat lectora.
Affects, activisms and resistances facing the impacts of Capitaloceno: an embodied learning experience in Chile
Authors: Aedo María Paz , Cabaña Gabriela 
Published: September 2020

The planetary transformations of Capitalocene affect us in multiple and heterogeneous forms. In this context, activisms emerging as embodied, experiential and situated manifestations of affectation. This article is an exploration of the activisms and resistances against impacts that Capitalocene -specifically, the extractivism- has had in Chilean society, from the perspective and experience of our own trajectories as global south academics and activists, committed to the entanglements that emerge constantly in the face of the impacts. Our work refers to the affects and resistances that we as authors have had the chance to experience in spaces of training and companionship of activists who resist in territories affected by the mining, agro-export and energy industry; and those who studied the Diploma in Social Ecology and Political Ecology from the Group of Agroecology and the Environment at the University of Santiago, offered between 2013 and 2017. Based on these experiences, we argue that the "affective turn" offers an indispensable perspective about hegemony, resistances and political changes in the current crisis.
Racial and Ethnic Differences in Behavioral Problems and Medication Use Among Children With Autism Spectrum Disorders
Authors: Quebles Irina , Solomon Olga , Smith Kathryn A. , Rao Sowmya R. , Lu Frances , Azen Colleen , Anaya Grace , Yin Larry 
Published: September 2020

Abstract
We examined racial and ethnic differences in the prevalence of behavioral problems measured by the Child Behavioral Checklist (CBCL), sleep disturbances measured by the Child Sleep Habits Questionnaire (CSHQ), and medication use among children with Autism Spectrum Disorders (ASD). We analyzed data from the Autism Treatment Network (ATN) dataset for 2,576 children ages 6 to 18 years of age diagnosed with ASD. Multivariable logistic regression accounting for age, gender, Diagnostic and Statistical Manual of Mental Disorders (4th Edition – Text Revision), diagnosis (Autistic Disorder, PDD-NOS, Asperger's Disorder), and parents' education did not show any racial or ethnic differences in behavioral challenges, conduct problems, or sleep disturbances for any of the groups, but Black children had lower odds of Total Problem Behaviors and Asian children had lower odds of Hyperactivity compared to White children. As a group, children from racial and ethnic minorities had lower odds of Total Problem Behaviors and Conduct Problems compared to White children. Hispanic children had lower odds of medication use for Behavioral Challenges, Total Problem Behaviors, Hyperactivity, and Conduct Problems. Asian children had lower odds of medication use for Behavioral Challenges, Total Problem Behaviors, and Hyperactivity; and had close to lower odds in medication use for Conduct Problems. Black children had lower odds for medication use for Total Problem Behaviors only. As a group, children from racial and ethnic minorities had lower odds for medication use for Behavioral Challenges, Total Problem Behaviors, Hyperactivity, and Conduct problems, but not for Sleep Disturbances. While these results are consistent with previous studies showing that White children are significantly more likely to receive psychotropic medication compared to children from racial and ethnic minority groups, we found no such differences for sleep challenges, suggesting that they are more consistently identified and equitably treated than other behavioral problems associated with ASD. We draw upon Andersen's (1995) Behavioral Model of Healthcare Use to suggest predisposing, enabling, and needs factors that may contribute to this pattern of racial and ethnic differences in the use of medications among children ASD.
3D printed waveguides based on photonic crystal fiber designs for complex fiber-end photonic devices
Authors: Bertoncini Andrea , Liberale Carlo 
Published: September 2020

Optical waveguide segments based on geometrically unbound photonic crystal fiber (PCF) designs could be exploited as building blocks to realize miniaturized complex devices that implement advanced photonic operations. Here, we show how to fabricate optical waveguide segments with PCF designs by direct high-resolution 3D printing and how the combination of these segments can realize complex photonic devices. We demonstrate the unprecedented precision and flexibility of our method by fabricating the first-ever fiber polarizing beam splitter based on PCFs. The device was directly printed in one step on the end-face of a standard single-mode fiber and was 210 µm long, offering broadband operation in the optical telecommunications C-band. Our approach harnesses the potential of high-resolution 3D printing and of PCF designs paving the way for the development of novel miniaturized complex photonic systems, which will positively impact and advance optical telecommunications, sensor technology, and biomedical devices.