bluuebunny/crossref_metadata_2025 huggingface dataset:
Ex vivo Improvement of a von Willebrand Disease Type 2A Phenotype Using an Allele-Specific Small-Interfering RNA
Authors: de Jong Annika , Dirven Richard J. , Boender Johan , Atiq Ferdows , Anvar Seyed Yahya , Leebeek Frank W. G. , van Vlijmen Bart J. M. , Eikenboom Jeroen
Published: August 2020

Von Willebrand disease (VWD) is the most common inherited bleeding disorder and is mainly caused by dominant-negative mutations in the multimeric protein von Willebrand factor (VWF). These mutations may either result in quantitative or qualitative defects in VWF. VWF is an endothelial protein that is secreted to the circulation upon endothelial activation. Once secreted, VWF multimers bind platelets and chaperone coagulation factor VIII in the circulation. Treatment of VWD focuses on increasing VWF plasma levels, but production and secretion of mutant VWF remain uninterrupted. Presence of circulating mutant VWF might, however, still affect normal hemostasis or functionalities of VWF beyond hemostasis. We hypothesized that inhibition of the production of mutant VWF improves the function of VWF overall and ameliorates VWD phenotypes. We previously proposed the use of allele-specific small-interfering RNAs (siRNAs) that target frequent VWF single nucleotide polymorphisms to inhibit mutant VWF. The aim of this study is to prove the functionality of these allele-specific siRNAs in endothelial colony-forming cells (ECFCs). We isolated ECFCs from a VWD type 2A patient with an intracellular multimerization defect, reduced VWF collagen binding, and a defective processing of proVWF to VWF. After transfection of an allele-specific siRNA that specifically inhibited expression of mutant VWF, we showed amelioration of the laboratory phenotype, with normalization of the VWF collagen binding, improvement in VWF multimers, and enhanced VWF processing. Altogether, we prove that allele-specific inhibition of the production of mutant VWF by siRNAs is a promising therapeutic strategy to improve VWD phenotypes.
A robust and interpretable end-to-end deep learning model for cytometry data
Authors: Hu Zicheng , Tang Alice , Singh Jaiveer , Bhattacharya Sanchita , Butte Atul J.
Published: August 2020

Significance

Cytometry technologies are able to profile immune cells at single-cell resolution. They are widely used for both clinical diagnosis and biological research. We developed a deep learning model for analyzing cytometry data. We demonstrated that the deep learning model accurately diagnoses the latent cytomegalovirus (CMV) in healthy individuals. In addition, we developed a method for interpreting the deep learning model, allowing us to identify biomarkers associated with latent CMV infection. The deep learning model is widely applicable to other cytometry data related to human diseases.
Coupled transmembrane mechanisms control MCU-mediated mitochondrial Ca
2+
uptake
Authors: Vais Horia , Payne Riley , Paudel Usha , Li Carmen , Foskett J. Kevin
Published: August 2020

Significance

Control of the level of calcium inside mitochondria is important because mitochondrial calcium regulates metabolism, cell death, and cellular signaling. The main pathway for mitochondrial calcium uptake is a calcium-selective ion channel complex in the inner mitochondrial membrane called the mitochondrial calcium uniporter (MCU). How the activity of the MCU ion channel is regulated is controversial. Here we employed electrophysiology of single isolated mitochondria to record MCU calcium and sodium ionic currents. We found that MCU ion channel activity is controlled by distinct Ca
2+
-regulated mechanisms on both sides of the inner mitochondrial membrane that are coupled to each other. These mechanisms allow for enhanced cellular regulation of mitochondrial calcium homeostasis.
Universal free-energy landscape produces efficient and reversible electron bifurcation
Authors: Yuly J. L. , Zhang P. , Lubner C. E. , Peters J. W. , Beratan D. N.
Published: August 2020

Significance

Electron bifurcation is an efficient and reversible redox reaction at the heart of key bioenergetic and biocatalytic reaction pathways used in nature. Electron bifurcation oxidizes a two-electron donor, using the electrons to reduce cofactors on two separate electron-transfer redox chains. The coupling of these redox reactions allows one of the electrons to move thermodynamically uphill, leveraging the downhill flow of the other electron. Thus, electron bifurcation may generate strong oxidants or reductants with minimal free-energy loss (i.e., reversibly). Not surprisingly, life harnesses electron bifurcation in biochemical pathways that perform challenging chemical reactions, including proton translocation across membranes, nitrogen fixation, and CO
2
reduction. We predict that there is one universal free-energy landscape that supports efficient electron bifurcation reactions.
Evidence for topological superconductivity: Topological edge states in Bi2Te3/FeTe heterostructure*
Authors: Guo Bin , Shi Kai-Ge , Qin Hai-Lang , Zhou Liang , Chen Wei-Qiang , Ye Fei , Mei Jia-Wei , He Hong-Tao , Pan Tian-Luo , Wang Gan
Published: August 2020

Majorana fermions have been predicted to exist at the edge states of a two-dimensional topological superconductor. We fabricated single quintuple layer (QL) Bi2Te3/FeTe heterostructure with the step-flow epitaxy method and studied the topological properties of this system by using angle-resolved photoemission spectroscopy and scanning tunneling microscopy/spectroscopy. We observed the coexistence of robust superconductivity and edge states on the single QL Bi2Te3 islands which can be potential evidence for topological superconductor.
Transit Oriented Development (TOD) Policies and Station Area Development in Asian Cities
Authors: Kidokoro Tetsuo
Published: August 2020

Many metropolitan cities of Asia are planning and implementing extensive investment in mass transit network and thus, are now at the threshold of whether they become transit cities or car traffic saturation cities. Promotion of Transit Oriented development (TOD) policies will be a key to move forward to transit cities. TOD should consider: transit oriented regional growth management plan, station area zoning regulations (mixed-use, minimum density, maximum parking, etc.), joint development among local governments, transit agencies, private developers, institutional mechanism for the public and private cooperation in station area development. In this paper, the cases from the cities in Japan, United States and the Southeast Asia are examined including Toyama in Japan, Kuala Lumpur in Malaysia and Jakarta in Indonesia. In conclusion, the following are discussed as the factors for successful Implementation of TOD in Asian Cities. Shift from highway-based zoning to transit oriented zoning: Creation of institutional mechanism for the public and private cooperation in the station area development, balance between public benefit and private benefit, connection of transit service and affordable housing, and, multi-modal connection planning including walking.
Dealing with Private and Public Space Interface Problem in TOD Area. Case study of Batuceper Station, Tangerang
Authors: Abadi Agustinus Adib , Nugraha Marestu Rizki
Published: August 2020

The Indonesian government has implemented the new strategy of Transit-Oriented Development (TOD) in dealing with urban issues, especially to overcome some of the urbanization effects such as housing deficiency, traffic jams, and private car usage. Under the PPP scheme, national private companies have initiated developing apartments in TOD of Batuceper station, located at the most populated district in the city of Tangerang. The mixture of residences with other public activities at TOD creates problems of privacy as the concern of accessibility and connectivity in the development principles. An in-depth study to examine this problem is required. Thus, this paper reviews various research related to the private and public spatial interface in the mix facilities area. This paper analyses the possible private and private space interface strategy between an apartment and other functions or activities at TOD Batuceper station development. The findings of this paper suggested that apartment design at the TOD area is a complex problem, and the proper strategy to solve such spatial interface problems depends on its linking hierarchy with other activities in the development area.
Re-orienting TOD concept and implementation in Jakarta
Authors: Suryani Sri , Harun Ismet B. , Astuti Wahyu K.
Published: August 2020

Since the 1990s, Jakarta city planning has introduced Transit-Oriented Development (TOD) as solution to dominant auto-mobility and sprawl to regional cities in Bogor, Depok, Tangerang, and Bekasi (JABODETABEK) by improving accessibility and inter-connectivity in urban mobility. Nevertheless, less has been investigated to what extent the on-going implementation in TOD projects departs from the means of TOD as planning approach in response to the urban problems. This paper aims to investigate TOD concept and implementation in Jakarta by proposing a comparative study on TOD in Japan and JABODETABEK, by using desk study in the planning documents and TOD projects. In each case, the investigation focuses on three sections; planning, implementation, and output. This paper reveals that the current TOD projects in Jakarta are based on single land development within proximity of TOD stations that maximizes private development benefits. Therefore, it concludes that the “TOD” projects in Jakarta have not yet met the TOD principles as a planning approach in response to the urban sprawls and integrated development.
Transit Passengers-Oriented Built Environment: An Evaluation of Mode Shift and Street Network and Design
Authors: Prayogi Luthfi , Aqli Wafirul
Published: August 2020

Recently there have been efforts on designing a built environment that encourages its residents to take transit more and use personal motorised vehicles less, commonly known as transit-oriented development (TOD). The outcome of such efforts can be evaluated by the mode shift from using a private motorised vehicle to taking transit occurring among the residents of the built environment. This article explores the mode shift that occurred among Transjakarta BRT corridor 1 passenger that is triggered by the street network and design around the Transjakarta corridor 1 bus stops. This article also evaluates the qualities of the street network and design around the mentioned bus stops to complement the passengers’ mode shift explanation. This article is written using a qualitative approach and inductive rationalization. Information regarding the passengers’ mode shift is obtained through an indirect interview, while evaluation on the qualities of the street network and design is carried out using space syntax analysis. This article finds that the magnitude of mode shift to taking Transjakarta corridor 1 due to the qualities of the street network and design around the bus stops is not significant. In line with that, the integration and connectivity of the streets around the observed segment of Transjakarta corridor 1 is relatively low. This article concludes that even though mode shift to taking Transjakarta corridor 1 is occurring, the street network and design around the Transjakarta bus stops have not contributed significantly in triggering the mode shift. This article proposes a relatively new approach in evaluating TOD, which is by simultaneously assessing the citizens’ habit and preference and the built environment.
Patterns of Sustainable Shophouse Development for Transit-Oriented Areas
Authors: Sidi Boedi Darma , Samsirina  , Putri Tika Novis , Rahmi Marlisa
Published: August 2020

Shophouse is a combination between commercial and residential functions in one building that commonly found in numerous cities in Indonesia. In the development of TOD area, shophouses become one of the TOD developers’ marketing strategy in attracting more potential consumers, due to its economic value. Apparently, in its development and utilization, the existence of shophouses are causing several problem that related to environmental sustainability. This paper describe two sustainability problems that occur in the development of shop houses. Firstly, the ineffective utilization of living spaces in shophouses, which is the main focus of the discussion in this paper. Secondly, the shophouse facades were frequently changed by the shopkeepers or tenants to adjust their business representation, in which opposing the principle of sustainability. These two phenomena describe the inconsistency in sustainability principle of the shophouses in a transit-oriented development. Thus, the development of shophouses in transit-oriented area need to acquire a different pattern from the current pattern of shophouses. The residential function in a shophouses in a transit-oriented area should be vertically separated from the business function, or to be part of the Mixed-Use Concept. Therefore, hopefully the development of shophouses could support the sustainability principle of transit-oriented areas in the future.
A Review of Urban Visual Environment in Transit-Oriented Development (TOD): Visual Comfort and Disturbance
Authors: Febrian Dhini Dwi Rizky , Wonorahardjo Surjamanto
Published: August 2020

Transit-Oriented Development (TOD) is one solution that widely applied to control the density of cities. Seeing the precedent, areas adjacent to public transit will be dominated by high-rise buildings. The issues raised in this paper related to how the phenomenon of high-rise development impacts the urban visual environment. The literature review method is used to determine aspects of the urban environment through visual comfort and visual disturbance. Literature review results in several factors influencing the urban visual environment, consist of the natural landscape, vegetation, exterior building and views, dimension, urban screen, visibility, colors, and materials. It was found that the difference between comfort and disturbance indicators tends to be thin because there is an acceptable disturbance. This situation occurs where visual disturbance can be tolerated as long as psychologically, there is a pleasantness increase. Related to TOD, development around transit areas must be considered for its impact on the urban visual environment. It is expected that through the achievement of a comfortable urban visual environment, the level of satisfaction will increase along with the increasing role of the transit area in supporting the use of public transportation and walkability, which are the goals of the TOD in an urban area.
Mix-strata Housing Plan through Vertical Extension Remodeling for Aged Apartments
Authors: Choi Jae Pil , Choi Jun Ho , Baek Soo Yeon , Kim Jung Woo , Ai Lian Shu
Published: August 2020

A large number of apartments in the 1st phase new towns that were built in the vicinity of Seoul during the 1990s are now facing problems associated with aging. To solve this issue of deterioration, the Korean government has encouraged remodeling, in particular allowing general sales for housing where vertical extensions have been added through remodeling. In this study, a mix-strata housing plan through vertical extension remodeling has been proposed for aged apartments in Korea’s Bundang new town, with a focus on public transportation. By considering a previous study, various floor plans which cater to the specific characteristics of the residents — including single household, elderly couples, newlyweds, and the young generation—have been examined in this study, and how these residents would be able to form a community with existing residents has been suggested. The authors hope that the results of this study would not only resolve the physical deterioration of aged apartment complexes in TOD areas but also establish a new form of remodeling that retains new social sustainability.
Affordable Residential in TOD Area
Authors: Poerbo Heru W.
Published: August 2020

Transit Oriented Development (TOD) areas in Jakarta are formed with the operation of the first MRT line, followed by the LRT network. However, with the development of mass rapid transit arise the problem of providing affordable housing units within the TOD area. This problem is particularly noticeable in central city TOD areas. This paper describes the process of inquiry in the effort of providing affordable housing in central city TOD areas. The study begins with literature research and case study to find the percentage of affordable housing that should be provided within the TOD area. Discussion with stakeholders and expert of TOD planning will reveal what problems are faced by the provision of housing within TOD area in Jakarta, as well as some possible solution to these problems. The most difficult problem is the land price that prohibits the provision of affordable flats or apartment units there. Changes in regulation regarding the central city mixed use development as well as building codes might be necessary in order to build affordable apartment units in central TOD areas.
Transit-induced Gentrification in Bangkok, Thailand: A Review
Authors: Margono Romi Bramantyo , Zuraida Siswanti , Abadi Agustinus Adib
Published: August 2020

As many of the developing megacities, Bangkok has also implemented a TOD system to tackle the increase of traffic congestion and the availability of transportation issues. However, the TOD projects in Bangkok are not supported by an appropriate provision in affordable housing. In recent years, as the improved accessibility and transit proximity are often capitalized into housing and land prices, it resulted in the low-income population displacement, a condition that refers to the term transit-induced gentrification. This paper uses Bangkok, Thailand, as a case study to review the impact of TOD especially in the displacement of populations. The review concludes that the gentrification in Bangkok is initiated by the increase of the value and rent price of the property due to the presence of the transit station. The case in Bangkok is one of the precedents that have a combination of characteristics from the early period and the latest period definition of gentrification. It has the characteristics that the case is concentrated in the city center and the subject is working class and wealthy residents, which from the early definition. While it still represents the characteristics of the latest definition, such as indirect and direct displacement that appear at the same time.
Critical Review of Advanced Material for Transit-Oriented Development in a Hot-Humid Climate
Authors: Rahmah Nadiya , Wonorahardjo Surjamanto
Published: August 2020

Building material applied in a Transit-Oriented Development (TOD) area should meet high requirements such as having heavy-duty capacity, high durability, low maintenance, cost-effectiveness, and environmental-friendliness. In a tropical-rainforest or hot-humid climate, some of those requirements are intensified, especially those which are related to solar radiation and rainwater. Most existing urban development in a hot-humid climate must endure problems caused by uncontrolled stormwater and urban heat island (UHI). The idea of adopting a transit-oriented paradigm into the existing cities, convey a question whether the shift will be determining the liveability of the area; whether it could solve the existing problem or, on the contrary, generate additional problems. To overcome problems of an existing urban area and anticipate the requirements of a TOD area, the researcher progressively develops numerous materials under the term such as ‘advanced material’, ‘green material’, and ‘smart material’. This review covers current trends in material research which is relevant for TOD in a hot-humid climate. The identified trends are analyzed to generate discussion in which the TOD planning in hot-humid climate should consider and anticipate the prospect of advanced material.
TOD Model through Low Carbon City Concept in Urban Design (case study: Palembang, Indonesia)
Authors: Asriana Nova , Donny Koerniawan Mochamad
Published: August 2020

Nowadays, Indonesia confronts urbanization, which raises many problems in the urban area, one of them is carbon emissions. Many researches have been done to address the issue of carbon emissions, TOD (Transit-Oriented Development) is one of them. This paper focuses entirely on how to develop the Transit-Oriented Development (TOD) design through low carbon city concepts in Indonesia. The concept of low-carbon cities is potentially implemented for high-energy efficiency in the areas of transport and housing will be able to reduce carbon footprint by decreasing trip frequencies, greater public transportation use for residents, increasing of walking level and higher accessibility. The city has to stimulate compact development with the high mobility movement of space in which space, building and infrastructure will be incorporated into a complex to authorise for living varied, commercial and social space to merge in environmentally sustainability. The development of a design strategy for the stakeholders is needed to develop and promote design ideas to optimise the spatial structure of cities. This paper aims to improve low carbon city model by adding integration between the urban spatial structure and land use to promote urban mixed, mobility, walkability, urban connectivity, and accessibility. These strategies will be used in a new development city in Palembang. Palembang is selected as representative of the rising megapolitan city in Indonesia where it still has capabilities for new spatial development planning to be improved the quality of life, well-planned new connectivity and sustainable cities. In this issue the TOD approach will be harmonized with the low carbon city concept.
The Implementation of Transit-Oriented Development Concepts on Pedestrian Pathways in the City of Bandung
Authors: Gaputra Agara Dama , Widiastuti Indah , Dwi Estika Nita
Published: August 2020

As a form of urban development, transit-oriented development (TOD) maximizes the amount of residential, business, and leisure space within walking distance of public transport facilities. TOD places more emphasis on design that increases interest in walking, by providing a scale that is appropriate for pedestrians. The Bandung City Government for the period of 2013-2018 has applied TOD in the city of Bandung by building various kinds of public facilities, also restoration and construction of infrastructure to improve the walkability aspect of Bandung. The developments that took place in Bandung then increased its livability, among others through the emergence of various types of thematic parks and various pedestrian infrastructures. The scope of this paper is to critically discuss how TOD was implemented in Bandung mainly through the observation on revitalized pedestrian pathways, while the author’s views on TOD which focused on pedestrian pathways is also formulated. Based on analysis carried out, it was found how TOD, specifically the revitalization of pedestrian pathways, was implemented partially with an emphasis on aesthetic aspects. Furthermore, this study described how Bandung has the potential to exploit pathways within kampung kota in heed of context-based TOD.
Building Material in The Perspective of Energy Efficiency and Thermal Environment in TOD Area
Authors: Muhammad Fadhil , Wonorahardjo Surjamanto
Published: August 2020

The development of urban area such as a Transit Oriented Development (TOD) involves a lot of building materials that are forming the physical environment which rises problems of urban heat island (UHI) and energy consumption. The TOD forming urban corridors that rise urban canyon issues with high air temperature, poor air quality, high energy consumption for air cooling and purifying (HVAC). The common heavyweight building materials that dominate the physical environment of TOD and other urban areas have low specific heat and high heat capacity. Another thermal property of concrete and brick storing the heat energy influence the air temperature during the night. The lightweight modern building materials that are cheap in construction cost show the worse phenomenon in the UHI perspective due to its lower specific heat. This review paper discusses the role of building material in the urban thermal environment such as the TOD area in the energy and environment perspective. The early result shows that both heavyweight and lightweight modern building material have a bad performance for the environment and should be mitigated otherwise our future will become worse. The energy consumption that rises uncontrollably due to bad air quality and high temperature will decrease the liveability level of the urban area.
Study of TODs Tall Building Fire Evacuation: Refuge Floor Utilities
Authors: Hutomo Cahyo Septianto , Tambunan Lily
Published: August 2020

Life safety has to be prior objective due to TODs tall buildings increment, for instance, mixed-use tower or integrated superblock estate, may cause fire accident. Refuge floor provision often met spatial issues according to define its configuration. Refuge floors are more relevant to the RSET factor because of the objectives. This study focused on identification of affecting factor using refuge floors with help of RSET factor from certain relevant three case studies of TODs tall buildings increment. The highlighted findings from certain case study plays important role to clarify the RSET factor on using refuge floor. Building height shows significant utility for refuge floor occupancies in accordance to refuge due to density control inside vertical egress.
Improving Undergraduate Epidemiology Education: An Example Using Instructional Teams
Authors: Brown Heidi E , Cox Jonathan
Published: August 2020

Epidemiology is a core component of the undergraduate public health curriculum and a critical component of a healthy community and a comprehensive education. Evidence-based, collaborative instructional practices improve student success, reach diverse student populations, and improve learning outcomes. Here we describe the pedagogical approach of an instructional team with which we observed an 18% greater learning gain (95% confidence interval: 6.5, 29.5; t = −3.08; P = 0.002), based on pre-/posttesting in a large (approximately 120 students) undergraduate course, than with the prior course offering. There were no differences in DEW rates (defined as receiving a grade of D (scoring 60%–69%) or E (scoring <60%) or withdrawing (W)) between the 2 offerings, but the ratio of “A” to “B” grades was higher (by approximately 10%) after deployment of the instructional team (Pearson’s χ2 (1 degree of freedom) = 4.17, P = 0.041). In addition, students reported greater satisfaction with the course deploying an instructional team (80.4% positive sentiment in course evaluation comments compared with 76.1% in the prior offering). As students and faculty become more familiar with effective evidence-based instructional practices, improvements in student learning can be achieved and the goal of creating an educated citizenry ready to build a healthy society will be more attainable.
Aldosterone, Inflammation, Immune System, and Hypertension
Authors: Ferreira Nathanne S , Tostes Rita C , Paradis Pierre , Schiffrin Ernesto L
Published: August 2020

Aldosterone is a mineralocorticoid hormone that controls body fluid and electrolyte balance. Excess aldosterone is associated with cardiovascular and metabolic diseases. Inflammation plays a critical role on vascular damage promoted by aldosterone and aggravates vascular abnormalities, including endothelial dysfunction, vascular remodeling, fibrosis and oxidative stress, and other manifestations of end-organ damage that are associated with hypertension, other forms of cardiovascular disease, and diabetes mellitus and the metabolic syndrome. Over the past few years, many studies have consistently shown that aldosterone activates cells of the innate and adaptive immune systems. Macrophages and T cells accumulate in the kidneys, heart, and vasculature in response to aldosterone, and infiltration of immune cells contributes to end-organ damage in cardiovascular and metabolic diseases. Aldosterone activates various subsets of innate immune cells such as dendritic cells and monocytes/macrophages, as well as adaptive immune cells such as T lymphocytes, and, by activation of mineralocorticoid receptors stimulates proinflammatory transcription factors and the production of adhesion molecules and inflammatory cytokines and chemokines. This review will briefly highlight some of the studies on the involvement of aldosterone in activation of innate and adaptive immune cells and its impact on the cardiovascular system. Since aldosterone plays a key role in many cardiovascular and metabolic diseases, these data will open up promising perspectives for the identification of novel biomarkers and therapeutic targets for prevention and treatment of diseases associated with increased levels of aldosterone, such as arterial hypertension, obesity, the metabolic syndrome, and heart failure.
Egg spottiness reflects female condition, physiological stress, and ornament expression in a common rallid species
Authors: Minias Piotr , Gómez Jesús , Włodarczyk Radosław
Published: August 2020

Lay Summary

• There is equivocal support for direct associations between maternal quality and deposition of protoporphyrin pigmentation (dark spots and blotches) in avian eggshells.

• Research on protoporphyrin eggshell pigmentation has primarily focused on a single avian order (Passeriformes).

• We examined associations of protoporphyrin-based eggshell pigmentation with female phenotypic and genetic traits in a non-passerine species, the Eurasian Coot.

• Deposition of protoporphyrin in eggshells (total number per area of egg spots) positively correlated with female condition and expression of a putative bare-part ornament (frontal shield), while it was negatively associated with the level of physiological stress.

• Protoporphyrin-based eggshell pigmentation acts as a reliable signal of female phenotypic (but not genetic) traits in the Eurasian Coot.

• Signaling properties of protoporphyrin-based egg coloration are likely to largely differ between different evolutionary lineages of birds.
A spectral clustering with self-weighted multiple kernel learning method for single-cell RNA-seq data
Authors: Qi Ren , Wu Jin , Guo Fei , Xu Lei , Zou Quan
Published: August 2020

Single-cell RNA-sequencing (scRNA-seq) data widely exist in bioinformatics. It is crucial to devise a distance metric for scRNA-seq data. Almost all existing clustering methods based on spectral clustering algorithms work in three separate steps: similarity graph construction; continuous labels learning; discretization of the learned labels by k-means clustering. However, this common practice has potential flaws that may lead to severe information loss and degradation of performance. Furthermore, the performance of a kernel method is largely determined by the selected kernel; a self-weighted multiple kernel learning model can help choose the most suitable kernel for scRNA-seq data. To this end, we propose to automatically learn similarity information from data. We present a new clustering method in the form of a multiple kernel combination that can directly discover groupings in scRNA-seq data. The main proposition is that automatically learned similarity information from scRNA-seq data is used to transform the candidate solution into a new solution that better approximates the discrete one. The proposed model can be efficiently solved by the standard support vector machine (SVM) solvers. Experiments on benchmark scRNA-Seq data validate the superior performance of the proposed model. Spectral clustering with multiple kernels is implemented in Matlab, licensed under Massachusetts Institute of Technology (MIT) and freely available from the Github website, https://github.com/Cuteu/SMSC/.
The Impact of Intersectionality of Multiple Identities on the Digital Health Divide, Quality of Life and Loneliness amongst Older Adults in the UK
Authors: Liu Ben Chi-Pun
Published: August 2020

The study measures the digital divide between digital/internet users and non-digital/internet users and the intersectional impact of multiple identities, i.e. gender, race and social status, on older adults in the UK. The analysis interviewed 9,246 adults aged fifty-five plus years in 2012 and 8,484 in 2014 in the English Longitudinal Study on Ageing. The digital health divide was evaluated both by CASP-19 (quality of life, QoL) and UCLA-Loneliness Scale with the intersectional effect of respondents’ multiple identities and digital/internet use. The results suggested a reduction in the digital divide amongst elders in the UK. Generalised estimating equations found that, amongst regular internet users having good social status, white females attained good QoL and little loneliness (CASP-19: β = 2.921, p <0.001; Loneliness: β=–0.631, p <0.001); and white and BME (black and minority ethnic) males both scored low on the loneliness scale (white: β=–0.809, p < 0.001 BME: β= –0.549, p <0.05). BME females with poor social status despite regular internet use got lower QoL and greater loneliness scores (CASP-19: β=–3.107, p <0.05; Loneliness: β=0.935, p <0.001), showing inequalities in their health outcomes. The intersectional perspective of cumulative disadvantages can help social workers better understand how the multiplicative effect of multiple identities socially excludes the vulnerable adults. Implications for research and practice are discussed.
Body-first versus brain-first biological subtyping of Parkinson’s disease
Authors: Bohnen Nicolaas I , Postuma Ronald B
Published: August 2020

This scientific commentary refers to ‘Brain-first versus body-first Parkinson’s disease: a multi-modal imaging case-control study’, by Horsager etal. (doi:10.1093/brain/awaa238).
Detection of 2D and 3D Video Transitions Based on EEG Power
Authors: Manshouri Negin , Melek Mesut , Kayıkcıoglu Temel
Published: August 2020

Despite the long and extensive history of 3D technology, it has recently attracted the attention of researchers. This technology has become the center of interest of young people because of the real feelings and sensations it creates. People see their environment as 3D because of their eye structure. In this study, it is hypothesized that people lose their perception of depth during sleepy moments and that there is a sudden transition from 3D vision to 2D vision. Regarding these transitions, the EEG signal analysis method was used for deep and comprehensive analysis of 2D and 3D brain signals. In this study, a single-stream anaglyph video of random 2D and 3D segments was prepared. After watching this single video, the obtained EEG recordings were considered for two different analyses: the part involving the critical transition (transition state) and the state analysis of only the 2D versus 3D or 3D versus 2D parts (steady state). The main objective of this study is to see the behavioral changes of brain signals in 2D and 3D transitions. To clarify the impacts of the human brain’s power spectral density (PSD) in 2D-to-3D (2D_3D) and 3D-to-2D (3D_2D) transitions of anaglyph video, nine visual healthy individuals were prepared for testing in this pioneering study. Spectrogram graphs based on short time Fourier transform (STFT) were considered to evaluate the power spectrum analysis in each EEG channel of transition or steady state. Thus, in 2D and 3D transition scenarios, important channels representing EEG frequency bands and brain lobes will be identified. To classify the 2D and 3D transitions, the dominant bands and time intervals representing the maximum difference of PSD were selected. Afterward, effective features were selected by applying statistical methods such as standard deviation, maximum (max) and Hjorth parameters to epochs indicating transition intervals. Ultimately, k-nearest neighbors, support vector machine and linear discriminant analysis (LDA) algorithms were applied to classify 2D_3D and 3D_2D transitions. The frontal, temporal and partially parietal lobes show 2D_3D and 3D_2D transitions with a good classification success rate. Overall, it was found that Hjorth parameters and LDA algorithms have 71.11% and 77.78% classification success rates for transition and steady state, respectively.
An Opinion Spread Prediction Model With Twitter Emotion Analysis During Algeria’s Hirak
Authors: Drif Ahlem , Hadjoudj Khalil
Published: August 2020

Social media is believed to have played a central role in the mobilization of Algerian citizens to peaceful protest against their country’s corrupt regime. Since no one foresaw these protests (called ‘The Revolution of Smiles’ or ‘The Hirak Movement’), this research conducted social media analysis to elicit vital insights about both the intensity of sentiment and the influence of social media on this unexpected instigation of political protest. This work built a deep learning model and analysed the influence of content, sentiment and user features on information spread. The model used the learning capability of a long short-term memory network to predict ‘retweetability’. Experiments were conducted on two real-world datasets (Hirak and Brexit) collected from Twitter. User features were found to be a key element in the diffusion of information. The strongest feelings about event context actively influenced the spread of tweets. The Twitter emotion corpus was found to improve the predictive ability of the model developed in this study.
Food Resource Sharing of Alder Leaf Beetle Specialists (Coleoptera: Chrysomelidae) as Potential Insect–Plant Interface for Horizontal Transmission of Endosymbionts
Authors: Cardoso Anabela , Gómez-Zurita Jesús
Published: August 2020

Recent studies suggest that endosymbionts of herbivore insects can be horizontally transferred to other herbivores feeding on the same host plants, whereby the plant acts as an intermediate stage in the chain of transmission. If this mechanism operates, it is also expected that insect communities sharing the same host plant will have higher chances to share their endosymbionts. In this study, we use a high-throughput 16S rRNA metabarcoding approach to investigate the presence, diversity, and potential sharing of endosymbionts in several species of leaf beetles (Coleoptera: Chrysomelidae) of a local community specialized on an alder diet in North America. Rickettsia and Wolbachia were predominant in the sample, with strong evidence for each species having their own dominant infection, of either or both types of bacteria. However, all species shared a much lower proportion of a particular Wolbachia type, compatible with the same strain dominant in one of the species of leaf beetles. Crucially, the same 16S rRNA haplotype of Wolbachia was found on alder leaf extracts. The combined evidence and the absence of this strain in a syntopic species of leaf beetle feeding on a different host plant support the hypothesis that at least the initial stages of the mechanism that would allow horizontal transmission of endosymbionts across species feeding on the same plant is possible. The accessibility and characteristics of endosymbiont associations of this system make it suitable for deeper analyses of their diversity and transmission in natural conditions.
The US–Chinese trade war: an event study of stock-market responses
Authors: Egger Peter H , Zhu Jiaqing
Published: August 2020

At the beginning of 2018, President Trump started taking protective tariff measures against products from China in a sequence of events which started a ‘trade war’ between the United States and China. As the value of trade flows affected on both sides rose to a significant amount, this episode will become an interesting research object in the future. A thorough analysis of many outcomes of interest is at this point in time – and even will be in the next few years – impossible due to a lack of data which will only become available at a later point. However, as is customary with historical preferential liberalizations in trade agreements and potentially the opposite of it through Brexit, it is possible to gauge consequences of this ‘trade war’ or ‘trade dispute’ when focusing on the stocks of listed companies around related tariff-change announcements or implementations by the United States and China in the relevant time span. This paper proposes such an analysis and finds, very much consistent with the rumours from business, that the associated protectionist tariffs appear to have done to a large extent the opposite of what was intended: they hurt domestic firms in targeted and also other, untargeted sectors of an acting country, and they affect third countries and territories which are not even party to the ‘trade war’ or ‘dispute’.
Estimating Forest Productivity Using Site Characteristics, Multipoint Measures, and a Nonparametric Approach
Authors: Hemingway Halli , Kimsey Mark
Published: August 2020

Understanding the productivity of forestland is essential in sustainable management of forest ecosystems. The most common measure of site productivity is breast height–age site index (BHASI). BHASI has limitations as a productivity measure and can compound error in predictive models. We explored the accuracy of productivity predictions using an alternative productivity measure (10-meter site index) and a nonparametric approach. An orthogonal sampling design ensured samples were collected across the range of conditions known to influence Douglas-fir (Pseudotsuga menziesii var. glauca) height-growth rates. Using climate, soil, and topographic data along with 10-meter site index measurements, we compared five possible models to estimate forest productivity. Model parameters, performance, and predictions were compared. Twelve validation sites were used to test the accuracy of model predictions. Model performance was significantly improved when smoothing span values were optimized and elevation was added as a predictor. A four-predictor nonparametric model with a bias-corrected Akaike information criterion–optimized smoothing span value produced the most accurate results and was used to produce forest productivity maps for the study area. The low resolution of currently available climatic data and the complex nature of the study area landscape necessitate a topographic variable for accurate productivity predictions.

Study Implications

Defining and understanding forest productivity is of interest to a wide variety of natural resource professionals including ecologists, climate change experts, forest biometricians, and forest managers. A new method of defining forest productivity using multipoint height-age pairs at 10 and 20 meters and calculated growth rates combined with an appropriate landscape-scale stratification and a nonparametric approach provides accurate productivity estimates. This method is more widely applicable and more precise for specific locations than previous productivity estimation methods. Better productivity and tree growth information will provide more accurate estimates of future forest condition and structure.
Quality and Intensity of Light in the In Vitro Development of Microstumps of Eucalyptus urophylla in a Photoautotrophic System
Authors: Miranda Natane A , Xavier Aloisio , Otoni Wagner C , Gallo Ricardo , Gatti Kellen C , de Moura Luciana C , Souza Denys M S C , Maggioni Joane H , Santos Suellen S de O
Published: August 2020

The quality and quantity of light are important factors in controlling in vitro plant growth in photoautotrophic systems. The aim of this study was to evaluate the influence of light quality (fluorescent, white, red, blue, red/blue, and distant red) on microstumps of a Eucalyptus urophylla clone in an in vitro photoautotrophic system, as well as the intensity of fluorescent light (60, 85, 100, and 140 μmol m–2 s–1) in the growth and production of microcutting. The number of shoots and microcutting, the size of the largest shoot, the stomatal density, chlorophyll, and carotenoid content were analyzed. Light quality altered plant growth, and fluorescent light intensity did not affect the microstumps’ production during the evaluation period. In white light-emitting diode (LED) light, there was higher production of carotenoids, with a lower initial production of microcuttings. A smaller number of shoots were obtained in blue LED. In general, the different qualities and light intensities tested allowed for the growth of the Eucalyptus urophylla clone grown in vitro, making it possible to obtain microcuttings under photoautotrophic cultivation.

Study Implications

In vitro propagation is a stressful process for plants and has limitations for commercial-scale Eucalyptus production. Fluorescent lamps, closed containers, and high sucrose concentrations are traditionally used. To reduce costs and improve production, the use of efficient light sources and photoautotrophic cultivation systems become alternatives. This study investigated the influence of light on the in vitro growth of a Eucalyptus clone in a photoautotrophic system. The quality was more important than the intensity of light. Foresters will be able to indicate the use of LEDs (light-emitting diodes) as a replacement for fluorescent lamps. This approach is useful in enhancing micropropagation techniques.
A novel fluorescent lung-marking technique using the photodynamic diagnosis endoscope system and vitamin B2
Authors: Tanaka Nobuhiro , Waseda Ryuichi , Saito Daisuke , Ohsima Masahiro , Matsumoto Isao , Takemura Hirofumi
Published: August 2020

OBJECTIVES

For small pulmonary nodules that are unidentifiable by palpation or in endoscopic surgeries wherein palpation is not feasible, visualizing their location is necessary when performing pulmonary sublobar resection procedures, such as wedge resection or segmentectomy. We invented a new transbronchial lung-marking technique using the photodynamic diagnosis endoscope system and vitamin B2 and examined its feasibility and safety via porcine studies.

METHODS

We established the marking procedure in pigs and examined the marking clarity and size, fluorescence intensity and duration and possible complications. In another study, sublobar resection for virtual target lesions was performed in pigs based on the fluorescent markings. The procedure duration, marking visibility, surgical margin from the lesions and technique-related complications were assessed.

RESULTS

All 36 markings in 6 pigs were identifiable and were widely distributed over the right lung. The median diameter and fluorescence intensity at 60 min after marking were 6.0 (5.5–6.7) mm and 137.5 (122–168), respectively. All 18 markings for the 6 virtual target lesions (3 markings for each target) were clearly identified, and all target lesions were found in the resected specimens. The median duration per marking was 244 (194–255) seconds. The shortest median surgical margin from a target lesion was 11.5 (9.3–13.5) mm. No procedure-related complications were observed.

CONCLUSIONS

This novel transbronchial fluorescent lung-marking technique was useful and safe in sublobar resections for small non-palpable pulmonary lesions.