bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strength Analysis of Metro Kapsul Knuckle Plate and Tie Rod using Finite Element Method
Authors: Budiwantoro B , Raditya Y D , Harjandi Y A 
Published: November 2019

Abstract
Metro Kapsul is a public transportation system developed to solve traffic problems and save travel time in Bandung. It is categorized as a light rail train with a capacity of 70 passengers per capsule. Before it operates, analysis is needed to ensure the vehicle’s safety. Two crucial parts to be analysed are the knuckle plate and the tie rod of the train. The knuckle plate and the tie rod must meet the requirements of the standards based on PM 175 2015. Forces on each component are calculated using equations from free body diagrams. Static and fatigue analysis are then conducted using ANSYS with Finite Element Method based on load cases in UIC Code 615-4 standard. The maximum stresses that occurred are 195.64 MPa for the knuckle plate and 118.54 MPa for the tie rod. In terms of fatigue, based on the modified Goodman failure criteria, the knuckle plate and tie rod are proven to be safe.
Influence of Heat Treatment on Structure and Corrosion Resistance of 8090 Aluminium Alloy for Ethanol Fuel Tank Application
Authors: Astaghfari Garimahdi , Soegijono Bambang 
Published: November 2019

Abstract
Investigation was carried out to understand the influence of heat treatment on structure and corrosion resistance of 8090 aluminium alloy in ethanol solution for ethanol fuel tank application. Heat treatments were subjected to solutionizing at temperature 525ºC for 4 hours to infiltrate the aluminium crystal by copper atoms and aging at temperature 190ºC with different time to bring copper and lithium atoms out of aluminium crystal during aging process. X-ray diffraction was performed to investigate the phase of each sample with different aging time. Electrochemical experiments were conducted to investigate the corrosion resistance in 3, 5% and 7% NaCl solution and 70% and 96% of ethanol solution. The results show different corrosion behaviour of this material. Heat treatment on this material shows significant different results.
Why philosophy of biology?
Authors: Okasha Samir 
Published: November 2019

Abstract
Philosophy has long been intertwined with the natural sciences. Many of the greatest philosophers of the last 400 years were influenced by the science of their day and some made important scientific contributions of their own. ‘Why philosophy of biology?’ explains that the birth of science gave rise to a new type of philosophical enquiry, which asks questions about the methods of science itself. Philosophy of biology emerged in the 1970s as a distinct field of enquiry from the interplay of three factors: the need for a less physics-centric picture of science; the presence of conceptual issues within biology itself; and the naturalistic turn in general philosophy.
Evolution and natural selection
Authors: Okasha Samir 
Published: November 2019

Abstract
In 1859 Charles Darwin published On the Origin of Species, in which he set out his theory of evolution. The book marked a turning point in our understanding of the natural world and revolutionized biology. ‘Evolution and natural selection’ outlines the theory of evolution by natural selection, explaining its unique status in biology and its philosophical significance. It considers how Darwin’s theory undermined the ‘argument from design’, a traditional philosophical argument for the existence of God; how the integration of Darwin’s theory with genetics, in the early 20th century, gave rise to neo-Darwinism; and why, despite evolutionary theory being a mainstay of modern biology, in society at large there is a marked reluctance to believe in evolution.
Function and adaptation
Authors: Okasha Samir 
Published: November 2019

Abstract
A striking feature of the biological sciences is their frequent appeal to the notion of function. Why do biologists make such liberal use of function-talk, and what exactly does it mean? ‘Function and adaptation’ explores the concept of biological function and asks how it should be understood. There are two rival philosophical theories of function: the aetiological theory and the ‘causal role’ theory. The aetiological theory emphasizes that function attributions are often answers to the ultimate question ‘why does it exist?’ whereas the causal role theory draws attention to a proximate question, namely ‘how does it work?’.
Why it happened
Authors: Doyle William 
Published: November 2019

Abstract
Describing why the French Revolution happened poses challenges. The French Revolution was not a single event; it was a series of developments that stretched over a number of years beginning between 1787 and 1789. ‘Why it happened’ attempts to outline the causes of the French Revolution by looking at the events leading up to the end of the 1780s. This was a period of uncertainty and confusion. What role did the monarchy have in causing the initial disquiet? Were the seeds of disorder already present in French society in the late 18th century? How important was France’s financial difficulties in causing a crisis?
A fast and memory-efficient implementation of the transfer bootstrap
Authors: Lutteropp Sarah , Kozlov Alexey M , Stamatakis Alexandros 
Published: November 2019

Abstract

Motivation
Recently, Lemoine et al. suggested the transfer bootstrap expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support for taxon-rich datasets. However, the original TBE implementation in the booster tool is compute- and memory-intensive.

Results
We developed a fast and memory-efficient TBE implementation. We improve upon the original algorithm by Lemoine et al. via several algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10× to 40× memory savings compared with booster.

Availability and implementation
Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallel version that also computes additional TBE-related statistics is available at: https://github.com/lutteropp/raxml-ng/tree/tbe.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Human Dynamic Clamp Reveals the Fronto-Parietal Network Linking Real-Time Social Coordination and Cognition
Authors: Dumas G , Moreau Q , Tognoli E , Kelso J A S 
Published: November 2019

Abstract
How does the brain allow us to interact with others? Social neuroscience has already provided some answers to these questions but has tended to treat high-level, cognitive interpretations of social behavior separately from the sensorimotor mechanisms upon which they rely. The goal here is to identify the underlying neural processes and mechanisms linking sensorimotor coordination and intention attribution. We combine the human dynamic clamp, a novel paradigm for studyingrealistic social behavior, with high-resolution electroencephalography. The collection of humanness and intention attribution reports, kinematics, and neural data affords an opportunity to relate brain activity to the ongoing social behavior. Behavioral results demonstrate that sensorimotor coordination influences the judgments of cooperativeness and humanness. Analysis of brain dynamics reveals two distinct networks related to the integration of visuo-motor information from self and other which overlap over the right parietal region. Furthermore, judgment of humanness and cooperation of others modulate the functional connectivity between this right parietal hub and the prefrontal cortex. These results reveal how distributed neural dynamics integrates information from “low-level” sensorimotor mechanisms and “high-level” social cognition to support the realistic social behaviors that play out in real time during interactive scenarios.
Preventing unwanted situations and gaining trust: a qualitative study of older people and families’ experiences with advance care planning in the daily practice of primary care
Authors: Glaudemans Jolien J , Willems Dick L , Wind Jan , Onwuteaka Philipsen Bregje D 
Published: November 2019

Abstract

Background
Using advance care planning (ACP) to anticipate future decisions can increase compliance with people’s end-of-life wishes, decrease inappropriate life-sustaining treatment and reduce stress, anxiety and depression. Despite this, only a minority of older people engage in ACP, partly because care professionals lack knowledge of approaches towards ACP with older people and their families.

Objective
To explore older people’s and their families’ experiences with ACP in primary care.

Methods
We conducted qualitative, semi-structured, face-to-face interviews with 22 older people (aged &gt;70 years, v/m: 11/11), with experience in ACP, and eight of their family members (aged 40–79 years, f/m: 7/1). Transcripts were inductively analysed using a grounded theory approach.

Results
We distinguished three main themes. (i) Openness and trust: Respondents were more open to ACP if they wanted to prevent specific future situations and less open if they lacked trust or had negative thoughts regarding general practitioners’ (GPs’) time for and interest in ACP. Engaging in ACP appeared to increase trust. (ii) Timing and topics: ACP was not initiated too early. Quality of ACP seemed to improve if respondents’ views on their current life and future, a few specific future care scenarios and expectations and responsibilities regarding ACP were discussed. (iii) Roles of family: Quality of ACP appeared to improve if family was involved in ACP.

Conclusions
Quality and accessibility of ACP may improve if GPs and nurses involve family, explain GPs’ interest in ACP and discuss future situations older people may want to prevent, and views on their current life and future.
Generalized stiffness reduction method to remove the artificial edge-effects for seismic wave modelling in elastic anisotropic media
Authors: Zhou Bing , Won Moosoo , Greenhalgh Stewart , Liu Xu 
Published: November 2019

SUMMARYIn seismic wave modelling, the boundary reflections caused by the computational grid edges should be reduced to produce accurate simulation results. The perfectly matched layer (PML) method is one of the popular techniques to suppress such artificial reflections, because it can be easily applied to the first-order wave equation in many numerical methods. However, one issue of the PML method is that the stability condition might be violated in complex elastic anisotropic media. In these cases, the PML method will not attenuate the boundary reflections but rather introduce strong artefacts in the simulation results. To tackle this problem, we propose a generalized stiffness reduction method (GSRM) as a substitute for the PML method. We first derive the stability conditions of the PML method and analyse the suitable conditions for their application to time- and frequency-domain seismic wave modelling. Then, we develop a simple and effective numerical implementation of the GSRM to attenuate the boundary reflections and apply it to seismic wave modelling in elastic anisotropic media. We give some numerical experiments to demonstrate the feasibility and advantages of the GSRM compared to the PML method. Numerical examples show the GSRM is conceptually simpler, more computationally efficient and more straightforward in terms of numerical implementation than the PML method for seismic modelling using either first- or second-order time- and frequency-domain wave equations.
Addressing food insecurity in Australia through education for sustainability
Authors: Nuttman Sonia , Patrick Rebecca , Townsend Mardie 
Published: November 2019

Abstract
Within Australia food insecurity affects an estimated 4 million people annually. Health promotion degrees traditionally prepare pre-service graduates to address food insecurity from a social determinants perspective, little consideration of integrating ecological determinants, however, has been noted. This is a significant problem considering unprecedented environmental challenges facing future food production. Education for sustainability (EfS) is purported to develop graduates who can respond to significant sustainability issues in the 21st century. This study examined the potential for health promotion degrees to utilize EfS to address food insecurity through an ecological lens. The study also illustrates why it might be valuable for academics to use such an approach. Semi-structured interviews with 15 Australian health and sustainability academics and document analysis of 26 associated teaching units was undertaken. Thematic analysis informed the data analysis process to provide meaning and insight into emerging themes. Academics were unaware of EfS or its potential for developing ecologically literate graduates. A lack of university commitment towards sustainability and knowledge and skills to implement EfS were identified as potential barriers. Academics, however, were ascribing to the central tenets used in EfS such as interdisciplinary thinking and reflective practice, demonstrating its potential use in health promotion. EfS, as a framework for incorporating an ecological perspective into health promotion degrees has not been fully realized. This study suggests capacity building of academics with regard to the use of EfS as an approach within health promotion degrees to address significant sustainability issues in the 21st century, such as food insecurity.
Frontotemporal dementia non-sense mutation of progranulin rescued by aminoglycosides
Authors: Kuang Lisha , Hashimoto Kei , Huang Eric J , Gentry Matthew S , Zhu Haining 
Published: November 2019

Abstract
Frontotemporal dementia (FTD) is an early onset dementia characterized by progressive atrophy of the frontal and/or temporal lobes. FTD is highly heritable with mutations in progranulin accounting for 5–26% of cases in different populations. Progranulin is involved in endocytosis, secretion and lysosomal processes, but its functions under physiological and pathological conditions remains to be defined. Many FTD-causing non-sense progranulin mutations contain a premature termination codon (PTC), thus progranulin haploinsufficiency has been proposed as a major disease mechanism. Currently, there is no effective FTD treatment or therapy. Aminoglycosides are a class of antibiotics that possess a less-known function to induce eukaryotic ribosomal readthrough of PTCs to produce a full-length protein. The aminoglycoside-induced readthrough strategy has been utilized to treat multiple human diseases caused by PTCs. In this study, we tested the only clinically approved readthrough small molecule PTC124 and 11 aminoglycosides in a cell culture system on four PTCs responsible for FTD or a related neurodegenerative disease amyotrophic lateral sclerosis. We found that the aminoglycosides G418 and gentamicin rescued the expression of the progranulin R493X mutation. G418 was more effective than gentamicin (~50% rescue versus &lt;10%), and the effect was dose- and time-dependent. The progranulin readthrough protein displayed similar subcellular localization as the wild-type progranulin protein. These data provide an exciting proof-of-concept that aminoglycosides or other readthrough-promoting compounds are a therapeutic avenue for familial FTD caused by progranulin PTC mutations.
Bounded Volume Denominators and Bounded Negativity
Authors: Bauer Thomas , Harbourne Brian , Küronya Alex , Nickel Matthias 
Published: November 2019

AbstractIn this paper, we study the question of whether on smooth projective surfaces the denominators in the volumes of big line bundles are bounded. In particular, we investigate how this condition is related to bounded negativity (i.e., the boundedness of self-intersections of irreducible curves). Our 1st result shows that boundedness of volume denominators is equivalent to primitive bounded negativity, which in turn is implied by bounded negativity. We connect this result to the study of semi-effective orders of divisors: our 2nd result shows that negative classes exist, which become effective only after taking an arbitrarily large multiple.
Levels of Human Immunodeficiency Virus DNA Are Determined Before ART Initiation and Linked to CD8 T-Cell Activation and Memory Expansion
Authors: Martin Genevieve E , Pace Matthew , Shearer Freya M , Zilber Eva , Hurst Jacob , Meyerowitz Jodi , Thornhill John P , Lwanga Julianne , Brown Helen , Robinson Nicola , Hopkins Emily , Olejniczak Natalia , Nwokolo Nneka , Fox Julie , Fidler Sarah , Willberg Christian B , Frater John 
Published: November 2019

AbstractInitiation of antiretroviral therapy (ART) in early compared with chronic human immunodeficiency virus (HIV) infection is associated with a smaller HIV reservoir. This longitudinal analysis of 60 individuals who began ART during primary HIV infection (PHI) investigates which pre- and posttherapy factors best predict HIV DNA levels (a correlate of reservoir size) after treatment initiation during PHI. The best predictor of HIV DNA at 1 year was pre-ART HIV DNA, which was in turn significantly associated with CD8 memory T-cell differentiation (effector memory, naive, and T-bet−Eomes− subsets), CD8 T-cell activation (CD38 expression) and T-cell immunoglobulin and mucin-domain containing-3 (Tim-3) expression on memory T cells. No associations were found for any immunological variables after 1 year of ART. Levels of HIV DNA are determined around the time of ART initiation in individuals treated during PHI. CD8 T-cell activation and memory expansion are linked to HIV DNA levels, suggesting the importance of the initial host-viral interplay in eventual reservoir size.
The Colonization of Carbapenem-Resistant Klebsiella pneumoniae: Epidemiology, Resistance Mechanisms, and Risk Factors in Patients Admitted to Intensive Care Units in China
Authors: Qin Xiaohua , Wu Shi , Hao Min , Zhu Jing , Ding Baixing , Yang Yang , Xu Xiaogang , Wang Minggui , Yang Fan , Hu Fupin 
Published: November 2019

Abstract

Background
Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a threat to public health, most notably as a superbug causing nosocomial infections. Patients in the intensive care unit (ICU) are at increased risk of hospital-acquired K pneumoniae infection, especially CRKP. This study was conducted to investigate the frequency of gastrointestinal and nasopharyngeal K pneumoniae colonization and its contribution to infections in ICU patients.

Methods
A 3-month prospective cohort study was performed in which 243 ICU patients were screened for intestinal and nasopharyngeal carriage of K pneumoniae at admission and once per week thereafter. The colonization and clinical infection isolates were analyzed by antimicrobial susceptibility testing to identify CRKP and were characterized by multilocus sequence typing (MLST) and whole-genome sequencing combined with epidemiological data to investigate the resistance mechanisms and assess the possible transmitted infection.

Results
Twenty-eight percent (68 of 243) of patients tested positive for carriage of K pneumoniae immediately upon admission to ICU, 54% (37 of 68) of which were nonduplicate CRKP isolates. Patients with carbapenem-susceptible K pneumoniae (CSKP) colonization at admission were more likely to acquire CRKP colonization during the ICU stay compared with patients without K pneumoniae colonization at admission. The incidence of subsequent CRKP infection in the baseline CSKP (32.3%, 10 of 31) and CRKP (45.9%, 17 of 37) carrier group was significantly higher than that of the baseline non-KP carrier group (8.6%, 15 of 175). The risk factors associated with acquired CRKP colonization during the ICU stay among negative CRKP colonization at admission included previous exposure to carbapenem, tigecycline or β-lactam/β-lactamases inhibitor, and invasive processes or surgical operations. Sixty-four percent (27 of 42) of patients with K pneumoniae infection were colonized by clonally related K pneumoniae strains according to enterobacterial repetitive intergenic consensus sequence-polymerase chain reaction analysis. ST11 (72%, 53 of 74) was the most predominant MLST type of clonally related CRKP isolate colonizing these patients, followed by ST15 (26%, 19 of 74).

Conclusions
The colonization of K pneumoniae may increase the incidence of corresponding K pneumoniae infection in critically ill patients in the ICU. High prevalence of ST11 CRKP (due to blaKPC-2) carriage and infection in ICU was observed.
Incidence and Clearance of Anal Human Papillomavirus (HPV)-16 and HPV-18 Infection, and Their Determinants, Among Human Immunodeficiency Virus-Infected Men Who Have Sex With Men in France
Authors: Alberts Catharina J , Heard Isabelle , Canestri Ana , Marchand Lucie , Fléjou Jean-François , Piroth Lionel , Ferry Tristan , Didelot Jean-Michel , Siproudhis Laurent , Henno Sébastien , Poizot-Martin Isabelle , Darragh Teresa M , Clifford Gary M , Combes Jean-Damien , Etienney Isabelle ,   for the ANRS EP57 APACHES Study group, Arvieux C , Canestri A , Clifford G M , Combes J D , Costes-Martineau V , Del Grande J , Didelot J M , Etienney I , Falguières M , Ferry T , Fischer H , Flejou J F , Heard I , Henno S , Hoyau N , Landon M , Laude H , Le Breton F , Lesage A C , Lion A , Maincent G , Marchand L , Njatonirina H , Patey O , Petrov Sanchez V , Pialoux V , Piroth L , Poizot-Martin I , Zaegel-Faucher O , Ressiot E , Radenne S , Reynes J , Siproudhis L , Tamalet C , Tattevin P 
Published: November 2019

AbstractBackgroundProspective data on the natural history of anal human papillomavirus (HPV) infection are scarce in human immunodeficiency virus (HIV)-infected men who have sex with men (MSM).MethodsWe analyzed incidence and clearance of HPV-16 and HPV-18 in a French cohort of HIV-infected MSM, aged ≥35 years, followed-up annually (n = 438, 2014–2018).ResultsHuman papillomavirus-16 and HPV-18 incidence were similar (~10% incident infections at 24 months). Human papillomavirus-16 incidence was higher among high-grade versus no lesion at baseline (adjusted incidence rate ratio = 3.0; 95% confidence interval, 1.07–8.18). Human papillomavirus-16 cleared significantly slower than HPV-18 (32% versus 54% by 24 months).ConclusionsIn conclusion, anal HPV-16 is more persistent than HPV-18, and its incidence correlates with a prior detection of high-grade lesions.