bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of heterogeneity in an individual participant data meta‐analysis of prediction models: An overview and illustration
Authors: Steyerberg Ewout W. , Nieboer Daan , Debray Thomas P.A. , van Houwelingen Hans C. 
Published: August 2019

Clinical prediction models aim to provide estimates of absolute risk for a diagnostic or prognostic endpoint. Such models may be derived from data from various studies in the context of a meta‐analysis. We describe and propose approaches for assessing heterogeneity in predictor effects and predictions arising from models based on data from different sources. These methods are illustrated in a case study with patients suffering from traumatic brain injury, where we aim to predict 6‐month mortality based on individual patient data using meta‐analytic techniques (15 studies, n = 11 022 patients). The insights into various aspects of heterogeneity are important to develop better models and understand problems with the transportability of absolute risk predictions.
“I just do what the boys tell me”: Exploring small group student interactions in an integrated STEM unit
Authors: Wieselmann Jeanna R. , Dare Emily A. , Ring‐Whalen Elizabeth A. , Roehrig Gillian H. 
Published: August 2019

AbstractGender equity issues remain a challenge in science, technology, engineering, and mathematics (STEM) fields, where women are highly underrepresented. As integrated STEM instruction becomes increasingly popular in elementary and middle school classrooms, it is important to consider whether the small group activities that are commonplace in STEM instruction support the equitable participation of young girls. This study builds on the existing body of literature to better understand how gender is related to student participation in small group STEM activities and whether students participate differently in science and engineering activities. A single embedded case study was used to explore the experiences of four students aged 10–11 years as they participated in small group work within an integrated STEM unit in their fifth‐grade classroom. Two girls and two boys worked together throughout the unit to explore science content related to electromagnetism and apply their content knowledge to an engineering design challenge. Video and audio of students' small group interactions were analyzed using an observation protocol to code their participation in each 3‐min segment of STEM activity. Student‐ and case‐level analyses were used to identify patterns of interaction based on gender and type of activity (science vs. engineering). Findings suggest that boys and girls participate in small group STEM activities in different ways, adopting distinct roles within their group. In addition, students displayed divergent patterns of interaction in science‐ and engineering‐focused lessons, suggesting that students need additional practice and support in navigating between science and engineering in integrated STEM units.
EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information
Authors: Song Shaoming , Cui Hongfei , Chen Shengquan , Liu Qiao , Jiang Rui 
Published: August 2019

BackgroundTranscription factor is one of the most important regulators in the transcriptional process. Nevertheless, the functional interpretation of transcription factors is still a main challenge due to the poor performance of methods relating to regulatory regions to genes. Epigenetic information, such as chromatin accessibility, contains genome‐wide knowledge about transcription regulation and thus may shed light on the functional interpretation of transcription factors.MethodsWe propose EpiFIT (Epigenetic based Functional Interpretation of Transcription factors), a tool to infer functions of transcription factors from ChIP‐seq data. Briefly, we adopt a variable distance rule to establish associations between regulatory regions and nearby genes. The associations are then filtered to ensure that the remaining regions and associated genes are co‐open. Finally, GO enrichment is applied to all related genes and a ranking list of GO terms is provided as functional interpretation.ResultsWe first examined the chromatin openness correlation between regulatory regions and associated genes. The correlation can help EpiFIT purify regulatory region–gene associations. By evaluating EpiFIT on a set of real data, we demonstrated that EpiFIT outperforms other existing methods for precisely interpreting transcription factor functions. We further verify the efficiency of openness in interpretation and the ability of EpiFIT to build distal region‐gene associations.ConclusionEpiFIT is a powerful tool for interpreting the transcription factor functions. We believe EpiFIT will facilitate the functional interpretation of other regulatory elements, and thus open a new door to understanding the regulatory mechanism.AvailabilityThe application is freely accessible at website: bioinfo.au.tsinghua.edu.cn/openness/EpiFIT/.
Clinicopathological and Prognostic Role of STAT3/p-STAT3 in Breast Cancer Patients in China: A Meta-Analysis
Authors: Li Yang , Wang Yue , Shi Zhixiang , Liu Jinghan , Zheng Shuyun , Yang Jinsong , Liu Yi , Yang Yuhua , Chang Feng , Yu Wenying 
Published: August 2019

AbstractIn order to explore the important factors in the diagnosis of breast cancer in China, meta-analysis of previous studies was performed to understand the association between STAT3/p-STAT3 and breast cancer. Information about STAT3/p-STAT3 expression and clinical data about breast cancer in China in particular were gathered from PubMed, Web of Science, CNKI and WanFang databases. RevMan 5.3 and STATA 14.0 were used to analyze the occurrence, development and metastasis of breast cancer for 2818 patients in 18 studies. STAT3/p-STAT3 expression was higher in breast cancer tissue than in normal ones (OR = 7.48, 95% CI = 5.64–9.94), in highly differentiated breast cancer tissue than in lowly differentiated cancer tissues (OR = 2.13, 95% CI = 1.53–2.98), in III/IV stage breast cancer than in I/II stage breast cancer (OR = 3.58, 95% CI = 2.44–5.25), and in tissue with lymphatic metastasis than in normal tissues (OR = 3.72, 95% CI = 2.59–5.35), respectively. Thus, the expression of STAT3/p-STAT3 plays a clinicopathological and prognostic role in the diagnosis and treatment of Chinese breast cancer patients.
Rhizobacteria AK1 remediates the toxic effects of salinity stress via regulation of endogenous phytohormones and gene expression in soybean
Authors: Khan Muhammad Aaqil , Asaf Sajjad , Khan Abdul Latif , Jan Rahmatullah , Kang Sang-Mo , Kim Kyung-Min , Lee In-Jung 
Published: August 2019

AbstractSalinity stress adversely affects the growth and productivity of different crops. In the present study, we isolated the rhizospheric bacteria Arthrobacter woluwensis AK1 from Pohang beach, South Korea and determined its plant growth-promoting potential under NaCl salt stress (0, 100, and 200 mM). AK1 has phosphate-solubilizing activity and produce siderophores, organic acids, and phytohormones such as gibberellic acid (GA) and indole-3-acetic acid (IAA) that significantly alleviate sodium chloride (NaCl) stress and increase all plant growth attributes. Furthermore, inoculation of AK1 significantly decreased endogenous abscisic acid (ABA) content, extensively regulated the antioxidant activities and mitigated NaCl stress. Similarly, inductively coupled plasma mass spectrometry results showed that soybean plants inoculated with AK1 significantly decreased the amount of sodium (Na+) uptake during NaCl stress after 6 and 12 days. Four genes, auxin resistant 1 (GmLAX1), potassium channel AKT2 (GmAKT2), soybean salt tolerance 1 (GmST1), and salt tolerance-associated gene on chromosome 3 (GmSALT3) were up-regulated, while two genes chloride channel gene (GmNHX1) and Na+/H+ antiporter (GmCLC1) were down-regulated in soybean AK1treated plants. In conclusion, AK1 can mitigate salinity stress, increase plant growth and could be utilized as an eco-friendly bio-fertilizer under salinity stress.
Infections in Neurosurgical Intensive Care Patients: A 3-Year Study in a Tertiary Health Care Center, North India
Authors: Chaturvedi Deepa , Jena Pragnya P. , Tarai Bansidhar , Sandhu Kavita 
Published: August 2019

Abstract
Background In the neurosurgical patient community, infection rate depends on the severity of neurological injuries at the time of presentation, which is measured by the Glasgow coma score (GCS). In addition, associated comorbidities; exposure to invasive devices such as endotracheal tube, central venous catheters, and urinary catheters; and neuroscience-specific devices, such as ventricular/lumbar catheters, increase chances of infection. We share our experience from a dedicated neurosurgical intensive care unit (NSICU) of a super speciality tertiary care hospital in north India.
Patients and Methods This is a 3-year retrospective and observational study from January 2014 to December 2016. Total 2,608 patients were admitted to NSICU during this period; 229 patients were included whose cultures were collected after 48 hours of admission and were positive. We have analyzed patient's risk factors, length of stay (LOS), outcome, organism details, and those health care–associated infections (HAI) that fulfilled the CDC (Centers for Disease Control and Prevention) criteria.
Results Out of 2,608 patients admitted, 229 were culture positive after 48 hours of admission and 53 developed HAIs (53/2,608 [2.03%]). Male-to-female ratio was 2:1. One hundred three patients had a low GCS (5–8) and 126 had a high GCS (9–15). Average LOS in ICU was 6 days, and mortality was 17.4% (40/229). A total of 57 laboratory-confirmed positive cultures were identified in 53 patients. This included 35 from urine, 15 from blood, 2 from surgical wound, and 1 from respiratory tract. Among the HAI, the rate of ventilator-associated pneumonia (VAP) was 0.22, central line-associated bloodstream infection (CLABSI) 3.43, catheter-associated urinary tract infection (CAUTI) 5.93, and surgical site infection (SSI) 0.9%.
Conclusion Neurosurgical patients are particularly vulnerable to infection because of the formidable nature of their illness, frequency of associated trauma, and presence of invasive devices. In our study, lower rate of HAIs was observed because we have a dedicated NSICU, strict infection control practices, an appropriate antimicrobial stewardship program, and early shifting of neurosurgical patients to an appropriately staffed high-dependency unit/ward.
X-ray induced photodynamic therapy with copper-cysteamine nanoparticles in mice tumors
Authors: Shrestha Samana , Wu Jing , Sah Bindeshwar , Vanasse Adam , Cooper Leon N , Ma Lun , Li Gen , Zheng Huibin , Chen Wei , Antosh Michael P. 
Published: August 2019

Significance
Copper-cysteamine nanoparticles can be activated directly by X-rays to produce singlet oxygen. The use of copper-cysteamine nanoparticles (conjugated with pH-low insertion peptide) can enhance the effects of X-ray–induced photodynamic therapy, to lead to improved tumor treatment in mice. The results of this study demonstrate the potential of copper-cysteamine nanoparticles with deeply penetrating X-rays in the treatment of mammalian cancer to overcome current limitations of low penetration, light-induced photodynamic therapy treatment that can only treat superficial cancers.
Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk
Authors: Tengvall Katarina , Huang Jesse , Hellström Cecilia , Kammer Patrick , Biström Martin , Ayoglu Burcu , Lima Bomfim Izaura , Stridh Pernilla , Butt Julia , Brenner Nicole , Michel Angelika , Lundberg Karin , Padyukov Leonid , Lundberg Ingrid E. , Svenungsson Elisabet , Ernberg Ingemar , Olafsson Sigurgeir , Dilthey Alexander T. , Hillert Jan , Alfredsson Lars , Sundström Peter , Nilsson Peter , Waterboer Tim , Olsson Tomas , Kockum Ingrid 
Published: August 2019

SignificanceWe have previously demonstrated an increased autoantibody reactivity to Anoctamin 2 (ANO2), an ion channel expressed in the central nervous system (CNS), in multiple sclerosis (MS). We now show that ANO2 antibodies recognize a fragment of Epstein-Barr virus (EBV) nuclear antigen 1, thereby constituting an example of molecular mimicry. In this way, the immune response toward EBV may take part in and promote CNS inflammation, likely through T cells reactive with the same protein. In our very large case-control cohort, we demonstrate that the presence of ANO2 reactivity associates with a high MS risk, in particular together with HLA risk variants and high EBNA1 antibody titers, which we consider a strong argument for its relevance in MS ethiopathogenesis.
Subjective well-being in China’s changing society
Authors: Clark William A. V. , Yi Daichun , Huang Youqin 
Published: August 2019

Significance
We reevaluate the level of subjective well-being in China with data from the China Household Finance Study. The analysis shows that in contrast to the decline in well-being reported in earlier studies, all groups report increased quality of life in the second decade of the 21st century. The analysis shows that the gap across rural and urban respondents is narrowing. Probit models of the levels of well-being show that social capital, measured as the perceived feelings of safety and security, community participation, and whether society is perceived to be fair, influence reported well-being. Household income, assets, health, being married, and the quality of neighborhood infrastructure, measured by availability of parks, primary schools, and hospitals, contributes positively to subjective well-being.
Retinal and optic nerve degeneration in liver X receptor β knockout mice
Authors: Song Xiao-yu , Wu Wan-fu , Gabbi Chiara , Dai Yu-bing , So Mark , Chaurasiya Surendra P. , Wang Li , Warner Margaret , Gustafsson Jan-Åke 
Published: August 2019

Significance
Optic neuritis, an inflammatory disease of the optic nerve, leads to death of retinal ganglion cells (RGC) and impaired vision. Both LXRα and LXRβ are expressed in the retina and optic nerve. The present study reveals that deletion of LXRβ from the mouse genome leads to loss of RGC. Immunostaining of LXRβ knockout mouse eyes showed that loss of AQP4 expression and activation of microglia in the optic nerve precedes the loss of RGC. The conclusion is that RGC loss is secondary to optic nerve degeneration and that LXRβ is a promising target for the treatment of retinal neurodegenerative diseases.
Phosphatidylserine flipping by the P4-ATPase ATP8A2 is electrogenic
Authors: Tadini-Buoninsegni Francesco , Mikkelsen Stine A. , Mogensen Louise S. , Molday Robert S. , Andersen Jens Peter 
Published: August 2019

Significance
Phospholipid flippases constitute the largest subfamily of P-type ATPases and have in eukaryotic organisms evolved as a central transport system for selective translocation of phospholipids across biological membranes to generate membrane lipid asymmetry, a property essential for numerous cellular processes. The importance of flippases is highlighted by severe neurological disorders and liver diseases caused by flippase dysfunction in humans. The electrogenicity of phospholipid transport by flippases has not previously been explored. We demonstrated that phosphatidylserine translocation by the flippase ATP8A2 generates electrical current, resulting from specific steps in the flippase reaction cycle moving the charged lipid head group between the membrane bilayer leaflets, and that no charged substrate is being countertransported. These findings unravel key features of phospholipid flippases.
We can(’t) do this
Authors: Griebel Tim , Vollmann Erik 
Published: August 2019

AbstractMigration has been a defining topic in the discourse in Germany since the so-called “refugee crisis” in 2015. This corpus-assisted critical discourse analysis systematically reconstructs the discourse about migration in two influential German newspapers, thereby emphasizing the construction of different subject positions for people migrating to Germany. Mass media are an important arena for the fight for hegemony between discursive coalitions of culturalization regimes that are based on openness and closure respectively. The discursive space of the German discourse about migration offers multiple opportunities in this regard. In the left-leaningtaz, we detect a general trend to support an open society although some (but often contested) elements of closure are detected in this medium as well.Die Weltleans much more towards closure and the problematization of migration although it also offers a diverse array of interpellations that depend on the usefulness or threating character of people coming to Germany.
Overview of high temperature fibre Bragg gratings and potential improvement using highly doped aluminosilicate glass optical fibres
Authors: Cavillon Maxime , Lancry Matthieu , Poumellec Bertrand , Wang Yitao , Canning John , Cook Kevin , Hawkins Thomas , Dragic Peter , Ballato John 
Published: August 2019

Abstract
In this paper, various types of high temperature fibre Bragg gratings (FBGs) are reviewed, including recent results and advancements in the field. The main motivation of this review is to highlight the potential of fabricating thermally stable refractive index contrasts using femtosecond (fs) near-infrared radiation in fibres fabricated with non-conventional techniques, such as the molten core method. As a demonstration of this, an yttrium aluminosilicate (YAS) core and pure silica cladding glass optical fibre is fabricated and investigated after being irradiated by an fs laser within the Type II regime. The familiar formation of nanogratings inside both core and cladding regions are identified and studied using birefringence measurements and scanning electron microscopy. The thermal stability of the Type II modifications is then investigated through isochronal annealing experiments (up to T = 1100 °C; time steps, Δt = 30 min). For the YAS core composition, the measured birefringence does not decrease when tested up to 1000 °C, while for the SiO2 cladding under the same conditions, its value decreased by ∼30%. These results suggest that inscription of such ‘Type II fs-IR’ modifications in YAS fibres could be employed to make FBGs with high thermal stability. This opens the door toward the fabrication of a new range of ‘FBG host fibres’ suitable for ultra-high temperature operation.
Initial Characterization of a Subpopulation of Inherent Oscillatory Mammalian Olfactory Receptor Neurons
Authors: Ukhanov Kirill , Bobkov Yuriy V , Martens Jeffrey R , Ache Barry W 
Published: August 2019

Abstract
Published evidence suggests that inherent rhythmically active or “bursting” primary olfactory receptor neurons (bORNs) in crustaceans have the previously undescribed functional property of encoding olfactory information by having their rhythmicity entrained by the odor stimulus. In order to determine whether such bORN-based encoding is a fundamental feature of olfaction that extends beyond crustaceans, we patch-clamped bORN-like ORNs in mice, characterized their dynamic properties, and show they align with the dynamic properties of lobster bORNs. We then characterized bORN-like activity by imaging the olfactory epithelium of OMP-GCaMP6f mice. Next, we showed rhythmic activity is not dependent upon the endogenous OR by patching ORNs in OR/GFP mice. Lastly, we showed the properties of bORN-like ORNs characterized in mice generalize to rats. Our findings suggest encoding odor time should be viewed as a fundamental feature of olfaction with the potential to be used to navigate odor plumes in animals as diverse as crustaceans and mammals.
Implementing Decisions of International Human Rights Institutions – Evidence from the United Nations Human Rights Committee
Authors: Shikhelman Vera 
Published: August 2019

Abstract
In recent years, there has been an increasing amount of research about the implementation of international law. However, there has been almost no empirical research about implementing decisions of international human rights institutions. The decisions of those institutions are usually regarded as soft law, and states do not have a clear legal obligation to implement them. In this article, I bring original empirical data about how and when states implement decisions of the United Nations Human Rights Committee (HRC) in individual communications. I hypothesize that the following factors influence the readiness of states to implement the views of the HRC: (i) the level of democracy and human rights protection in the state; (ii) internal capacity; (iii) strength of civil society; (iv) type of remedy; (v) representation on the HRC; (6) subject matter of the communication. I find that the most important factor for implementing remedies granted by the Committee is the high human rights score of the state. The internal capacity of the state is also significant but to a lesser extent than found in previous studies. Also, I find a certain connection between the state being represented on the HRC and its willingness to implement the remedies.
How can multiple frames enable action on social determinants? Lessons from Australia’s paid parental leave
Authors: Townsend Belinda , Friel Sharon , Baker Phillip , Baum Fran , Strazdins Lyndall 
Published: August 2019

Abstract
How do public health advocates and practitioners encourage policy actors to address the social determinants of health? What strategies can be used to elevate healthy social policies onto government agendas? In this paper, we examine the case of Australia’s first national paid parental leave scheme, announced in 2009 after decades of policy advocacy. This scheme provides job-protected leave and government-funded pay at the minimum wage for 18 weeks for eligible primary care givers on the birth of an infant, and has been shown to reduce health inequities. Drawing on documentary sources and interviews (n = 25) with key policy actors, this paper traces the evolution of this landmark social policy in Australia, focusing on the role of actors, institutions and policy framings in setting the policy agenda. We find that advocates strategically deployed three different framings—for economy, gender equality and health—to drive paid parental leave onto the Government’s agenda. They navigated barriers linked to power, gender ideology and cost, shifting tactics along the way by adopting different frames in various institutional settings and broadening their coalitions. Health arguments varied in different institutional settings and, at times, advocates selectively argued the economic or gender equality framing over health. The case illustrates the successful use of strategic pragmatism to provoke action, and raises broader lessons for advancing action on the social determinants of health. In particular, the case highlights the importance of adopting multiple synergistic policy framings to draw support from non-traditional allies and building coalitions to secure public policy change.