bluuebunny/crossref_metadata_2025 huggingface dataset:
The private versus public contribution to the biomedical literature during the COVID-19, Ebola, H1N1, and Zika public health emergencies
Authors: Beall Reed F. , Moradpour Javad , Hollis Aidan
Published: October 2021

Background

The private versus public contribution to developing new health knowledge and interventions is deeply contentious. Proponents of commercial innovation highlight its role in late-stage clinical trials, regulatory approval, and widespread distribution. Proponents of public innovation point out the role of public institutions in forming the foundational knowledge undergirding downstream innovation. The rapidly evolving COVID-19 situation has brought with it uniquely proactive public involvement to characterize, treat, and prevent this novel health treat. How has this affected the share of research by industry and public institutions, particularly compared to the experience of previous pandemics, Ebola, H1N1 and Zika?

Methods

Using Embase, we categorized all publications for COVID-19, Ebola, H1N1 and Zika as having any author identified as affiliated with industry or not. We placed all disease areas on a common timeline of the number of days since the WHO had declared a Public Health Emergency of International Concern with a six-month lookback window. We plotted the number and proportion of publications over time using a smoothing function and plotted a rolling 30-day cumulative sum to illustrate the variability in publication outputs over time.

Results

Industry-affiliated articles represented 2% (1,773 articles) of publications over the 14 months observed for COVID-19, 7% (278 articles) over 7.1 years observed for Ebola, 5% (350 articles) over 12.4 years observed for H1N1, and 3% (160 articles) over the 5.7 years observed for Zika. The proportion of industry-affiliated publications built steadily over the time observed, eventually plateauing around 7.5% for Ebola, 5.5% for H1H1, and 3.5% for Zika. In contrast, COVID-19’s proportion oscillated from 1.4% to above 2.7% and then declined again to 1.7%. At this point in the pandemic (i.e., 14 months since the PHEIC), the proportion of industry-affiliated articles had been higher for the other three disease areas; for example, the proportion for H1N1 was twice as high.

Conclusions

While the industry-affiliated contribution to the biomedical literature for COVID is extraordinary in its absolute number, its proportional share is unprecedentedly low currently. Nevertheless, the world has witnessed one of the most remarkable mobilizations of the biomedical innovation ecosystem in history.
Carnivorous Nepenthes x ventrata plants use a naphthoquinone as phytoanticipin against herbivory
Authors: Dávila-Lara Alberto , Rahman-Soad Asifur , Reichelt Michael , Mithöfer Axel
Published: October 2021

Carnivorous plants feed on animal prey, mainly insects, to get additional nutrients. This carnivorous syndrome is widely investigated and reported. In contrast, reports on herbivores feeding on carnivorous plants and related defenses of the plants under attack are rare. Here, we studied the interaction of a pitcher plant,Nepenthes x ventrata, with a generalist lepidopteran herbivore,Spodoptera littoralis, using a combination of LC/MS-based chemical analytics, choice and feeding assays. Chemical defenses inN.x ventrataleaves were analyzed uponS.littoralisfeeding. A naphthoquinone, plumbagin, was identified inNepenthesdefense against herbivores and as the compound mainly responsible for the finding thatS.littoralislarvae gained almost no weight when feeding onNepenthesleaves. Plumbagin is constitutively present but further 3-fold increased upon long-term (> 1 day) feeding. Moreover, in parallelde novoinduced trypsin protease inhibitor (TI) activity was identified. In contrast to TI activity, enhanced plumbagin levels were not phytohormone inducible, not even by defense-related jasmonates although upon herbivory their level increased more than 50-fold in the case of the bioactive jasmonic acid-isoleucine. We conclude thatNepenthesis efficiently protected against insect herbivores by naphthoquinones acting as phytoanticipins, which is supported by additional inducible defenses. The regulation of these defenses remains to be investigated.
Bringing the social into vaccination research: Community-led ethnography and trust-building in immunization programs in Sierra Leone
Authors: Enria Luisa , Bangura Joseph S. , Kanu Hassan M. , Kalokoh Joseph A. , Timbo Alie D. , Kamara Mohamed , Fofanah Maligie , Kamara Alhassan N. , Kamara Adikalie I. , Kamara Morlai M. , Suma Ibrahim Sorie , Kamara Osman M. , Kamara Alusine M. , Kamara Alhajie O. , Kamara Abu B. , Kamara Emmah , Lees Shelley , Marchant Mark , Murray Mariama
Published: October 2021

Background

Vaccine hesitancy is a complex, contested social phenomenon and existing research highlights the multifaceted role of trust in strengthening vaccine confidence. However, understanding public engagement with vaccination through the lens of (mis)trust requires more contextual evidence on trust’s qualitative determinants. This includes expanding the geographic focus beyond current studies’ focus on High Income Countries. Furthermore, obstacles remain in effectively integrating social science findings in the design of vaccine deployment strategies, and in ensuring that those who implement interventions and are affected by them are directly involved in producing knowledge about vaccination challenges.

Methods

We piloted a community-led ethnographic approach, training Community Health Workers (CHWs) in Kambia District, Sierra Leone, in qualitative social science methods. Methods included participant observation, participatory power mapping and rumour tracking, focus group discussions and key stakeholder interviews. CHWs, with the support of public health officials and professional social scientists, conducted research on vaccination challenges, analysed data, tested new community engagement strategies based on their findings and elicited local perspectives on these approaches.

Results

Our findings on vaccine confidence in five border communities highlighted three key themes: the impact of prior experiences with the health system on (mis)trust; relevance of livelihood strategies and power dynamics for vaccine uptake and access; and the contextual nature of knowledge around vaccines. Across these themes, we show how expressions of trust centered on social proximity, reliability and respect and the role of structural issues affecting both vaccine access and confidence. The pilot also highlighted the value and practical challenges to meaningfully co-designed research.

Conclusion

There is scope for broader application of a community-led ethnographic approach will help redesign programming that is responsive to local knowledge and experience. Involving communities and low-cadre service providers in generating knowledge and solutions can strengthen relationships and sustain dialogue to bolster vaccine confidence.
Influence of the H1N1 influenza pandemic on the humoral immune response to seasonal flu vaccines
Authors: Jang Hyesun , Ross Ted M.
Published: October 2021

In this study, we hypothesized that the humoral response to trivalent seasonal influenza virus vaccines was influenced by rapid antigenic switching of H1 HA. We tested archived sera and peripheral blood mononuclear cells (PBMC) collected at prior to vaccination at day 0, as well as days 30 and 90 after vaccination during the 2009/2010 and 2010/2011 influenza virus seasons. During the 2009/2010 season, vaccination successfully induced antibodies with hemagglutinin inhibition (HAI) activity against both H1N1 and H3N2 vaccine components. For the 2010/2011 season, the A/California/04/2009 (CA/09) H1N1 elicited seroconversion (HAI titer = 1:40) and novel memory B cell (Bmem) responses from most individuals. However, the H3N2 influenza virus component of the vaccine, A/Perth/16/2009 (Perth/09), back-boosted and elicited antibodies with HAI activity and Bmem response to historical H3N2 influenza virus strains. Following stratification of the pre-existing antibody with HAI against the CA/09 H1N1, there was a negative correlation with HAI seroconversion to other vaccine strains. Overall, strong immune responses against CA/09 H1N1 influenza virus negatively influenced the induction of novel humoral responses.
Healthcare worker stress, anxiety and burnout during the COVID-19 pandemic in Singapore: A 6-month multi-centre prospective study
Authors: Teo Irene , Chay Junxing , Cheung Yin Bun , Sung Sharon C. , Tewani Komal G. , Yeo Li Fang , Yang Grace Meijuan , Pan Fang Ting , Ng Jin Ying , Abu Bakar Aloweni Fazila , Ang Hui Gek , Ayre Tracy Carol , Chai-Lim Crystal , Chen Robert Chun , Heng Ai Ling , Nadarajan Gayathri Devi , Ong Marcus Eng Hock , See Brian , Soh Chai Rick , Tan Boon Kiat Kenneth , Tan Bien Soo , Tay Kenny Xian Khing , Wijaya Limin , Tan Hiang Khoon
Published: October 2021

Aim

The long-term stress, anxiety and job burnout experienced by healthcare workers (HCWs) are important to consider as the novel coronavirus disease (COVID-19) pandemic stresses healthcare systems globally. The primary objective was to examine the changes in the proportion of HCWs reporting stress, anxiety, and job burnout over six months during the peak of the pandemic in Singapore. The secondary objective was to examine the extent that objective job characteristics, HCW-perceived job factors, and HCW personal resources were associated with stress, anxiety, and job burnout.

Method

A sample of HCWs (doctors, nurses, allied health professionals, administrative and operations staff; N = 2744) was recruited via invitation to participate in an online survey from four tertiary hospitals. Data were gathered between March-August 2020, which included a 2-month lockdown period. HCWs completed monthly web-based self-reported assessments of stress (Perceived Stress Scale-4), anxiety (Generalized Anxiety Disorder-7), and job burnout (Physician Work Life Scale).

Results

The majority of the sample consisted of female HCWs (81%) and nurses (60%). Using random-intercept logistic regression models, elevated perceived stress, anxiety and job burnout were reported by 33%, 13%, and 24% of the overall sample at baseline respectively. The proportion of HCWs reporting stress and job burnout increased by approximately 1·0% and 1·2% respectively per month. Anxiety did not significantly increase. Working long hours was associated with higher odds, while teamwork and feeling appreciated at work were associated with lower odds, of stress, anxiety, and job burnout.

Conclusions

Perceived stress and job burnout showed a mild increase over six months, even after exiting the lockdown. Teamwork and feeling appreciated at work were protective and are targets for developing organizational interventions to mitigate expected poor outcomes among frontline HCWs.
Micronutrient intake status and associated factors among children aged 6–23 months in the emerging regions of Ethiopia: A multilevel analysis of the 2016 Ethiopia demographic and health survey
Authors: Gebremedhin Tsegaye , Aschalew Andualem Yalew , Tsehay Chalie Tadie , Dellie Endalkachew , Atnafu Asmamaw
Published: October 2021

Background

Micronutrient (MN) deficiency among children is recognised as a major public health problem in Ethiopia. The scarcity of MNs in Ethiopia, particularly in pastoral communities, might be severe due to poor diets mitigated by poor healthcare access, drought, and poverty. To reduce MNs deficiency, foods rich in vitamin A (VA) and iron were promoted and programs like multiple micronutrient powder (MNP), iron and vitamin A supplements (VAS) and or deworming have been implemented. Nationally for children aged 6–23 months, consumption of four or more food groups from diet rich in iron and VA within the previous 24 hours, MNP and iron supplementation within seven days, and VAS and >75% of deworming within the last 6 months is recommend; however, empirical evidence is scarce. Therefore, this study aimed to assess the recommended MN intake status of children aged 6–23 months in the emerging regions of Ethiopia.

Methods

Data from the Ethiopia Demographic and Health Survey 2016 were used. A two-stage stratified sampling technique was used to identify 1009 children aged 6–23 months. MN intake status was assessed using six options: food rich in VA or iron consumed within the previous 24 hours, MNP or iron supplementation with the previous seven days, VAS or deworming within six months. A multilevel mixed-effect logistic regression analysis was computed, and a p-value of < 0.05 and Adjusted Odds Ratio (AOR) with 95% Confidence Interval (CI) were used to identify the individual and community-level factors.

Results

In this analysis, 37.3% (95% CI: 34.3–40.3) of children aged 6–23 months had not received any to the recommended MNs sources. The recommended MNs resulted; VAS (47.2%), iron supplementation (6.0%), diet rich in VA (27.7%), diet rich in iron (15.6%), MNP (7.5%), and deworming (7.1%). Antenatal care visit (AOR: 1.9, 95% CI: 1.4–2.8), work in the agriculture (AOR: 2.2, 95% CI: 1.3–3.8) and children aged 13 to 23 months (AOR: 1.7, 95% CI: 1.2–2.4) were the individual-level factors and also Benishangul (AOR: 2.2, 95% CI: 1.3–4.9) and Gambella regions (AOR: 1.9, 95% CI: 1.0–3.4) were the community-level factors that increased micronutrient intake whereas residence in rural (AOR: 0.4, 95% CI: 0.1–0.9) was the community-level factors that decrease micronutrient intake.

Conclusions

Micronutrient intake among children aged 6–23 months in the pastoral community was low when compared to the national recommendation. After adjusting for individual and community level factors, women’s occupational status, child’s age, antenatal visits for recent pregnancy, residence and region were significantly associated with the MN intake status among children aged 6–23 months.
The expanding movement of primary care physicians operating at the first line of healthcare delivery systems in sub-Saharan Africa: A scoping review
Authors: Bello Kéfilath , De Lepeleire Jan , Kabinda M. Jeff , Bosongo Samuel , Dossou Jean-Paul , Waweru Evelyn , Apers Ludwig , Zannou Marcel , Criel Bart
Published: October 2021

Introduction

In sub-Saharan Africa (SSA), the physicians’ ratio is increasing. There are clear indications that many of them have opted to work at the first-line of healthcare delivery systems, i.e. providing primary care. This constitutes an important change in African healthcare systems where the first line has been under the responsibility of nurse-practitioners for decades. Previous reviews on primary care physicians (PCPs) in SSA focused on the specific case of family physicians in English-speaking countries. This scoping review provides a broader mapping of the PCPs’ practices in SSA, beyond family physicians and including francophone Africa. For this study, we defined PCPs as medical doctors who work at the first-line of healthcare delivery and provide generalist healthcare.

Methods

We searched five databases and identified additional sources through purposively selected websites, expert recommendations, and citation tracking. Two reviewers independently selected studies and extracted and coded the data. The findings were presented to a range of stakeholders.

Findings

We included 81 papers, mostly related to the Republic of South Africa. Three categories of PCPs are proposed: family physicians,“médecins généralistes communautaires”, and general practitioners. We analysed the functioning of each along four dimensions that emerged from the data analysis: professional identity, governance, roles and activities, and output/outcome. Our analysis highlighted several challenges about the PCPs’ governance that could threaten their effective contribution to primary care. More research is needed to investigate better the precise nature and performance of the PCPs’ activities. Evidence is particularly needed for PCPs classified in the category of GPs and, more generally, PCPs in African countries other than the Republic of South Africa.

Conclusions

This review sheds more light on the institutional, organisational and operational realities of PCPs in SSA. It also highlighted persisting gaps that remain in our understanding of the functioning and the potential of African PCPs.
Reduced utilitarian willingness to violate personal rights during the COVID-19 pandemic
Authors: Antoniou Rea , Romero-Kornblum Heather , Young J. Clayton , You Michelle , Kramer Joel H. , Chiong Winston
Published: October 2021

The COVID-19 pandemic poses many real-world moral dilemmas, which can pit the needs and rights of the many against the needs and rights of the few. We investigated moral judgments in the context of the contemporary global crisis among older adults, who are at greatest personal risk from the pandemic. We hypothesized that during this pandemic, individuals would give fewer utilitarian responses to hypothetical dilemmas, accompanied by higher levels of confidence and emotion elicitation. Our pre-registered analysis (https://osf.io/g2wtp) involved two waves of data collection, before (2014) and during (2020) the COVID-19 pandemic, regarding three categories of moral dilemmas (personal rights, agent-centered permissions, and special obligations). While utilitarian responses considered across all categories of dilemma did not differ, participants during the 2020 wave gave fewer utilitarian responses to dilemmas involving personal rights; that is, they were less willing to violate the personal rights of others to produce the best overall outcomes.
Engineering well-expressed, V2-immunofocusing HIV-1 envelope glycoprotein membrane trimers for use in heterologous prime-boost vaccine regimens
Authors: Crooks Emma T. , Almanza Francisco , D’Addabbo Alessio , Duggan Erika , Zhang Jinsong , Wagh Kshitij , Mou Huihui , Allen Joel D. , Thomas Alyssa , Osawa Keiko , Korber Bette T. , Tsybovsky Yaroslav , Cale Evan , Nolan John , Crispin Max , Verkoczy Laurent K. , Binley James M.
Published: October 2021

HIV-1 vaccine immunofocusing strategies may be able to induce broadly-reactive neutralizing antibodies (NAbs). Here, we engineered a panel of diverse, membrane-resident native HIV-1 trimers vulnerable to two broad targets—the V2 apex and fusion peptide (FP). Selection criteria included i) high expression and ii) infectious function, so that trimer neutralization sensitivity can be profiled in pseudovirus (PV) assays. Initially, we boosted the expression of 17 candidate trimers by truncating gp41 and introducing a gp120-gp41 SOS disulfide to prevent gp120 shedding. "Repairs" were made to fill glycan holes and eliminate other strain-specific aberrations. A new neutralization assay allowed PV infection when our standard assay was insufficient. Trimers with exposed V3 loops, a target of non-NAbs, were discarded. To try to increase V2-sensitivity, we removed clashing glycans and modified the C-strand. Notably, a D167N mutation improved V2-sensitivity in several cases. Glycopeptide analysis of JR-FL trimers revealed near complete sequon occupation and that filling the N197 glycan hole was well-tolerated. In contrast, sequon optimization and inserting/removing glycans at other positions frequently had global "ripple" effects on glycan maturation and sequon occupation throughout the gp120 outer domain and gp41. V2 MAb CH01 selectively bound to trimers with small high mannose glycans near the base of the V1 loop, thereby avoiding clashes. Knocking in a rare N49 glycan was found to perturb gp41 glycans, increasing FP NAb sensitivity—and sometimes improving expression. Finally, a biophysical analysis of VLPs revealed that i) ~25% of particles bear Env spikes, ii) spontaneous particle budding is high and only increases 4-fold upon Gag transfection, and iii) Env+ particles express ~30–40 spikes. Taken together, we identified 7 diverse trimers with a range of sensitivities to two targets to allow rigorous testing of immunofocusing vaccine concepts.
‘I’m not a doctor, but I can sew a mask’: The face mask home sewing movement as a means of control during the COVID-19 pandemic of 2020
Authors: Martindale Addie K. , Armstead Charity , McKinney Ellen
Published: October 2021

As the COVID-19 pandemic emerged, a widespread shortage of personal protective equipment (PPE) specifically N95 face masks were exposed. This need was quickly answered by home sewers who did not hesitate to answer the request of medical professionals to help fill the PPE shortage. As the United States entered a national quarantine, home sewers turned to social media, specifically Instagram to share their participation and communicate the need to recruit others to join them in their mask sewing efforts. This research aimed to interpret the Instagram post messages shared to understand the motivations of participation in mask sewing efforts. Social media hashtags were used to identify the messages related to home sewing face masks for the pandemic. A netnographic qualitative research approach uncovered five overarching themes: this is helping me, call to action, do it right, rising to the occasion and I’m ready for this.
Older adults’ philanthropic crafting of face masks during COVID-19
Authors: Schnittka Christine Guy
Published: October 2021

During the early months of the COVID-19 pandemic, people of all ages began sewing fabric face masks. Organized through separate grassroots movements, oftentimes using social media platforms, people pooled their resources to make masks for front line workers and others in desperate need. While some people sold these face masks, many participated in philanthropic crafting, donating them to hospitals and other health care centres. Older adults were identified early on as being particularly vulnerable to the effects of the virus, and so their response to mitigate the impacts of the pandemic through crafting was salient. This study investigated the experience of philanthropic hand crafting by older adults who were living through the COVID-19 pandemic. Twenty-seven older adults of age 60–87 who sewed masks for others were interviewed. A comprehensive data analysis of these interviews yielded 39 descriptive codes that were collapsed into eight themes: emotions, engagement, meaning, relationships, accomplishment, intellect, moral values and agency. One finding was that there were psychological, relational and existential benefits for the crafters. Making masks allowed participants to help other people, and it gave the participants a feeling of value, worthiness and purpose. Additionally, participants felt more in control in a chaotic world as they made masks to protect themselves, their loved ones, as well as strangers. The philanthropic crafting enhanced older adults’ well-being in many ways, and lessons learned from this study could be extended into ‘normal times’. For example, more older adults would be able to participate in craft-based philanthropy if they had access to the tools and materials. They would be more motivated if they received thank you notes and pictures of the recipients using their handmade gifts, and if they could express their creativity more. Finally, creating a physical or virtual community for older adults around craft philanthropy would help older adults feel more connected to and supported by their peers, and the community at large.
A Real-Time Photogrammetric System for Acquisition and Monitoring of Three-Dimensional Human Body Kinematics
Authors: Chen Long , Wu Bo , Zhao Yao , Li Yuan
Published: October 2021

Real-time acquisition and analysis of three-dimensional (3D) human body kinematics are essential in many applications. In this paper, we present a real-time photogrammetric system consisting of a stereo pair of red-green-blue (RGB) cameras. The system incorporates a multi-threaded and
graphics processing unit (GPU)-accelerated solution for real-time extraction of 3D human kinematics. A deep learning approach is adopted to automatically extract two-dimensional (2D) human body features, which are then converted to 3D features based on photogrammetric processing, including
dense image matching and triangulation. The multi-threading scheme and GPU-acceleration enable real-time acquisition and monitoring of 3D human body kinematics. Experimental analysis verified that the system processing rate reached ∼18 frames per second. The effective detection distance
reached 15 m, with a geometric accuracy of better than 1% of the distance within a range of 12 m. The real-time measurement accuracy for human body kinematics ranged from 0.8% to 7.5%. The results suggest that the proposed system is capable of real-time acquisition and monitoring of 3D human
kinematics with favorable performance, showing great potential for various applications.
Escola, educação integral e a Educação em Direitos Humanos
Authors: Klein Ana Maria , Bressan Marina Scaramuzza , Santos Paula Toledo Lara dos
Published: October 2021

O presente ensaio aborda a crescente importância da escola em sociedades cada vez mais complexas e a consequente necessidade de uma educação integral que conceba o ser humano em sua multidimensionalidade e volte-se para a humanização dos estudantes. Propõe-se a formação ética e para a cidadania por meio da Educação em Direitos Humanos. Este tipo de educação, obrigatória em todos os níveis e modalidades de ensino no país, estrutura-se a partir de conhecimentos sobre os Direitos Humanos, valores como igualdade, liberdade e solidariedade  e práticas que gerem ações e instrumentos em favor da promoção, da proteção e da defesa dos direitos humanos, bem como da reparação de suas violações. Este conhecimento desenvolve-se pela problematização da realidade contribuindo para a inserção social e cidadã crítica em relação às violações de direitos que ocorrem no país.
Clasificación de parámetros y criterios al ensamblar la ráfaga
Authors: Jiménez-Pinzón Neil Andrés , López-Perafán José Giovanny
Published: October 2021

Este artículo presenta una clasificación de algunos de los algoritmos o mecanismos para ensamblar la ráfaga de datos existentes en la literatura científica de las redes de conmutación óptica de ráfagas, basándose en los diferentes parámetros y criterios que inciden en el proceso de ensamblaje. Resaltando, que dicha clasificación es el resultado de la etapa de revisión del estado del arte en el trabajo de grado titulado “Algoritmo Adaptativo basado en la Lógica Difusa y PSO para el Ensamble de Ráfagas en una red OBS Distribuida”, a nivel de maestría. La forma en que se ensambla la ráfaga es de gran importancia ya que es el proceso que gestiona la carga de tráfico entrante a una red y de esta manera gestiona el desempeño de toda la red.

En algunos casos, el desempeño es analizado en cuanto a la probabilidad de bloqueo y en el retardo de extremo a extremo de las ráfagas transmitidas, entre otros parámetros. Los resultados ayudaran a los nuevos investigadores, interesados en las redes ópticas y más en el proceso de ensamblaje, tener una introducción general de las redes de conmutación óptica, conocer y diferenciar los parámetros y criterios que inciden a la hora de ensamblar una ráfaga de datos, señalando algunas de las combinaciones que se han aplicado en otros trabajos. Además, poder identificar algunos de los problemas potenciales abiertos en este tema.
BRIDGING TOGETHER AUTHORITARIAN RIGHT-WING POLITICS AND NEOLIBERAL URBAN POLITICS: ISTANBUL’S BID FOR 2020 SUMMER OLYMPICS
Authors: YAVUZ YAVUZ
Published: October 2021

This study aims to analyse the political impact of sports mega-events through urban lenses. Sports mega-events often come along with drastic transformations in the built environment of the city where they are held. Contemporary urban impact of the sports mega-events, with the increased role rested by local and/or national governments on the private sector in the organization, is highly interconnected with the neoliberal measures of selling out the urban space, undertaken for hosting the event. In terms of the hosts, there is an increasing shift towards the countries where right-wing authoritarian parties are in power. I argue that the promises of these governments guaranteeing more swift urban transformations to meet the infrastructure requirements of hosting these events cause this shift and in turn, right-wing authoritarian governments use these events as platforms for disseminating their ideologies.  This research aims to trace this trend, based on the example of İstanbul’s failed bid to host the 2020 Summer Olympics and the neoliberal urban policies in Turkey under the Justice and Development Party (AKP). By using the city master plan presented during the bidding process and the statements made by AKP officials, I aim to demonstrate how hosting international sports events in Turkey is undertaken as part of a neoliberal urban policy and how this is incorporated into a wider conservative-Islamist political project by the AKP.
Fast augmentation algorithms for network kernel density visualization
Authors: Chan Tsz Nam , Li Zhe , U Leong Hou , Xu Jianliang , Cheng Reynold
Published: October 2021

Network kernel density visualization, or NKDV, has been extensively used to visualize spatial data points in various domains, including traffic accident hotspot detection, crime hotspot detection, disease outbreak detection, and business and urban planning. Due to a wide range of applications for NKDV, some geographical software, e.g., ArcGIS, can also support this operation. However, computing NKDV is very time-consuming. Although NKDV has been used for more than a decade in different domains, existing algorithms are not scalable to million-sized datasets. To address this issue, we propose three efficient methods in this paper, namely aggregate distance augmentation (ADA), interval augmentation (IA), and hybrid augmentation (HA), which can significantly reduce the time complexity for computing NKDV. In our experiments, ADA, IA and HA can achieve
at least
5x to 10x speedup, compared with the state-of-the-art solutions.
Comprehensible counterfactual explanation on Kolmogorov-Smirnov test
Authors: Cong Zicun , Chu Lingyang , Yang Yu , Pei Jian
Published: October 2021

The Kolmogorov-Smirnov (KS) test is popularly used in many applications, such as anomaly detection, astronomy, database security and AI systems. One challenge remained untouched is how we can obtain an explanation on why a test set fails the KS test. In this paper, we tackle the problem of producing counterfactual explanations for test data failing the KS test. Concept-wise, we propose the notion of most comprehensible counterfactual explanations, which accommodates both the KS test data and the user domain knowledge in producing explanations. Computation-wise, we develop an efficient algorithm MOCHE (for MOst CompreHensible Explanation) that avoids enumerating and checking an exponential number of subsets of the test set failing the KS test. MOCHE not only guarantees to produce the most comprehensible counterfactual explanations, but also is orders of magnitudes faster than the baselines. Experiment-wise, we present a systematic empirical study on a series of benchmark real datasets to verify the effectiveness, efficiency and scalability of most comprehensible counterfactual explanations and MOCHE.
On the algebra of data sketches
Authors: Lemiesz Jakub
Published: October 2021

We consider the problem of designing a distributed data sketch for scenario in which data stream is observed by many independent network nodes. We require that a sketch apart from being computationally and memory efficient should also be mergeable in a way that mimics set theory operations on related data sets.

For example, when monitoring network traffic, one may consider how many distinct packets passed through a given node (sum of sets for different time windows) or passed through two given nodes (intersection of sets from two locations) and what is their total size (intersection of weighted sets).

In this paper we propose a sketch that allows to efficiently summarize sets constructed from a sequence of set theory operations. We also provide an analytical control over the trade-off between the accuracy and storage/computational requirements. In comparison to the previous works the proposed solution 1) allows the weights of elements, 2) allows performing set theory operations simultaneous on a large number of sketches, 3) does not require computationally expensive numerical calculations and guarantees low overheads.
Massively parallel algorithms for personalized pagerank
Authors: Hou Guanhao , Chen Xingguang , Wang Sibo , Wei Zhewei
Published: October 2021

Personalized PageRank (PPR) has wide applications in search engines, social recommendations, community detection, and so on. Nowadays, graphs are becoming massive and many IT companies need to deal with large graphs that cannot be fitted into the memory of most commodity servers. However, most existing state-of-the-art solutions for PPR computation only work for single-machines and are inefficient for the distributed framework since such solutions either
(i)
result in an excessively large number of communication rounds, or
(ii)
incur high communication costs in each round.

Motivated by this, we present
Delta-Push
, an efficient framework for single-source and top-
k
PPR queries in distributed settings. Our goal is to reduce the number of rounds while guaranteeing that the load, i.e., the maximum number of messages an executor sends or receives in a round, can be bounded by the capacity of each executor. We first present a non-trivial combination of a redesigned parallel push algorithm and the Monte-Carlo method to answer single-source PPR queries. The solution uses pre-sampled random walks to reduce the number of rounds for the push al6gorithm. Theoretical analysis under the
Massively Parallel Computing (MPC)
model shows that our proposed solution bounds the communication rounds to [EQUATION] under a load of
O
(
m/p
), where
m
is the number of edges of the input graph,
p
is the number of executors, and ϵ is a user-defined error parameter. In the meantime, as the number of executors increases to
p'
= γ ·
p
, the load constraint can be relaxed since each executor can hold
O
(γ ·
m/p'
) messages with invariant local memory. In such scenarios, multiple queries can be processed in batches simultaneously. We show that with a load of
O
(γ ·
m/p'
), our Delta-Push can process γ queries in a batch with [EQUATION] rounds, while other baseline solutions still keep the same round cost for each batch. We further present a new top-
k
algorithm that is friendly to the distributed framework and reduces the number of rounds required in practice. Extensive experiments show that our proposed solution is more efficient than alternatives.
Endothelial cell-derived SSAO can increase MLC20 phosphorylation in VSMCs
Authors: Zhang Yuxing , Zhang Xiliang , Cao Zhen , Huang Yun , Zheng Yuexin , Yang Xiaodong
Published: October 2021

Vascular hyporesponsiveness in the shock decompensation period is an important factor leading to death. Myosin light chain 20 (MLC20) is the main effector protein that regulates vascular reactivity. However, whether the change in semicarbazide-sensitive amine oxidase (SSAO) expression during hypoxia can change the MLC20 phosphorylation level, and its underlying mechanism were not clear. The amine oxidase copper containing 3 (AOC3) overexpressing adenovirus vector was constructed and transfected into rat intestinal microvascular endothelial cells (RIMECs) to overexpress SSAO, and the RIMECs were co-cultured with rat intestinal microvascular smooth muscle cells (RIMSCs). The changes in SSAO/inducible nitric oxide synthase (iNOS)/Rho associate coiled-coil containing protein kinase 1 (ROCK1) expression levels and MLC20 phosphorylation level were detected. Here we found that the increased SSAO by AOC3 overexpression can decrease the iNOS expression level and its activity after hypoxia. In addition, RIMSCs co-cultured with RIMECs overexpressed with AOC3 gene had significantly higher ROCK1 protein level and MLC20 phosphorylation level than RIMSCs co-cultured with normal RIMECs. Our study demonstrated that SSAO overexpression can significantly inhibit iNOS activity, promote RhoA/ROCK pathway activation, and increase the phosphorylation level of MLC20, which might be the potential mechanism in relieving the vascular hyporesponsiveness during shock decompensation.
Automated identification of diagnostic labelling errors in medicine
Authors: Hautz Wolf E. , Kündig Moritz M. , Tschanz Roger , Birrenbach Tanja , Schuster Alexander , Bürkle Thomas , Hautz Stefanie C. , Sauter Thomas C. , Krummrey Gert
Published: October 2021

Objectives

Identification of diagnostic error is complex and mostly relies on expert ratings, a severely limited procedure. We developed a system that allows to automatically identify diagnostic labelling error from diagnoses coded according to the international classification of diseases (ICD), often available as routine health care data.

Methods

The system developed (index test) was validated against rater based classifications taken from three previous studies of diagnostic labeling error (reference standard). The system compares pairs of diagnoses through calculation of their distance within the ICD taxonomy. Calculation is based on four different algorithms. To assess the concordance between index test and reference standard, we calculated the area under the receiver operating characteristics curve (AUROC) and corresponding confidence intervals. Analysis were conducted overall and separately per algorithm and type of available dataset.

Results

Diagnoses of 1,127 cases were analyzed. Raters previously classified 24.58% of cases as diagnostic labelling errors (ranging from 12.3 to 87.2% in the three datasets). AUROC ranged between 0.821 and 0.837 overall, depending on the algorithm used to calculate the index test (95% CIs ranging from 0.8 to 0.86). Analyzed per type of dataset separately, the highest AUROC was 0.924 (95% CI 0.887–0.962).

Conclusions

The trigger system to automatically identify diagnostic labeling error from routine health care data performs excellent, and is unaffected by the reference standards’ limitations. It is however only applicable to cases with pairs of diagnoses, of which one must be more accurate or otherwise superior than the other, reflecting a prevalent definition of a diagnostic labeling error.
Performance assessment of a balloon assisted micro airborne wind turbine system
Authors: Noronha Naveen Prakash , Munishamaih Krishna
Published: October 2021

This study intends to examine the performance of a balloon-assisted micro airborne wind turbine in a low wind speed location. The influence of the balloon separation gap on the airborne wind energy system (AWES) performance is also explored. A micro-AWES with a diameter of 3 m and a power output of 1 kW was fabricated and tested at 50, 100, 150, 200, and 250 m. Further, the optimum separation spacing of 13 m was maintained between the balloon and the ducted turbine to reduce balloon turbulence on the turbine. The airborne wind turbine achieved a maximum power output of 250 W at 250 m height while the average wind speed remained 6 m/s. The maximum power coefficient obtained was 0.25 while annual energy production (AEP) remained 1200 kWh. The low power coefficient is credited to the turbulence and drifting in the airborne system and the drag caused by the airborne structure. While a cost-effective commercial model of micro AWES is still being developed, the present work attempts to harvest wind energy at high elevations in low wind speed areas.
Study of twisted Bargmann transform via Bargmann transform
Authors: Bais Shubham R. , D Venku Naidu
Published: October 2021

In the present article, we give an alternate and easier proof for the image characterization of

L
2

⁢

(

ℝ

2
⁢
n

)

{L^{2}(\mathbb{R}^{2n})}

under the twisted Bargmann transform which was earlier studied by Krontz, Thangavelu and Xu. As a consequence, we study some properties of the twisted Bergman spaces for

0
<
p
≤
∞

{0<p\leq\infty}

and the

L
p

{L^{p}}

-boundedness of the twisted Bargmann transform,

1
≤
p
≤
∞

{1\leq p\leq\infty}

. We also study

L
p

{L^{p}}

-boundedness of the twisted Bargmann projection

P
t

{P_{t}}

and the duality relations between the spaces

B
t
p

⁢

(

ℂ

2
⁢
n

)

{B_{t}^{p}(\mathbb{C}^{2n})}

,

1
<
p
<
∞

{1<p<\infty}

.
Regenerating Former Military Sites in Italy. The Dichotomy between ‘Profit-Driven Spaces’ and ‘Urban Commons’
Authors: Camerin Federico
Published: October 2021

Within the last decades, the reorganisation of the Armed Force left many voids in the territories. Being located in highly lucrative and desirable locations, former military sites can be redeveloped into either profit-driven spaces or proper urban commons. This paper focuses the attention on the Italian case and scrutinises former military barracks in the dichotomies between the generation of profit-driven spaces and urban commons. Also, the analysis questions the actual role of these voids in guaranteeing the right to the city, especially in times of severe shortage of public resources to undertake urban regeneration processes.
Synthesis of greener silver nanoparticle-based chitosan nanocomposites and their potential antimicrobial activity against oral pathogens
Authors: Rajeshkumar Shanmugam , Tharani Munusamy , Rajeswari Vijayarangan Devi , Alharbi Naiyf S. , Kadaikunnan Shine , Khaled Jamal M. , Gopinath Kasi , Vijayakumar Natesan , Govindarajan Marimuthu
Published: October 2021

In the present investigation, silver nanoparticles (AgNPs) and silver nanoparticle-based chitosan nanocomposite were synthesized using Cissus arnottiana leaf extract. The biosynthesized nanoparticles and nanocomposites were characterized using SEM, TEM, and AFM to uncover the morphological characteristics such as size and shape. The SEM image depicts the size of the nanocomposite to be 30–40 nm and shape as spherical. The TEM results reveal the shape of the nanocomposite to be spherical and size around 10–60 nm. The XRD results show the crystalline nature of the AgNPs-based chitosan nanocomposite. The SAED analysis pattern seems to be concordant with the XRD results. The AFM image ensured the precise surface morphology of the synthesized silver nanocomposite in the 3-dimensional pattern. The antimicrobial efficacy of the biosynthesized AgNPs, AgNP nanocomposite, and chitosan nanoparticles was tested against oral pathogens. The results revealed a potential antimicrobial effect, which states that it must be converted into nanomedicine to meet future biomedical needs.
The effects of thyroid dysfunction on DNA damage and apoptosis in liver and heart tissues of rats
Authors: Guler Gulnur , Dasdelen Dervis , Baltaci Saltuk Bugra , Sivrikaya Abdullah , Baltaci Abdulkerim Kasim , Mogulkoc Rasim
Published: October 2021

Objectives

Thyroid hormones affect many enzymes, organs, and systems. They also play a role in complex biological events including development and growth. The main objective of this study was to analyze the effects of thyroid dysfunction on DNA damage and apoptosis in liver and heart tissues as well as the treatment of these disorders.

Methods

Thirty-eight Wistar-albino male rats were randomly divided into five groups: 1. Control group (n=6): The rats were sacrificed without any application and liver and heart samples were collected. 2. Hypothyroidism group (n=8): Prophyltiouracil (PTU)-10 mg/kg/day was applied to induce hypothyroidism by intraperitoneal route for two weeks. 3. Hypothyroidism + Thyroxine group (n=8): After one week of PTU application (10 mg/kg/day), a high dose of l-thyroxine (1.5 mg/kg/day) was applied by intraperitoneal route for one week. 4. Hyperthyroidism group (n=8): l-thyroxine (0.3 mg/kg/day) was applied intraperitoneally to induce hyperthyroidism for two weeks. 5. Hyperthyroidism + PTU group (n=8): After one week of high dose l-thyroxine application, PTU (10 mg/kg/day) was applied for one week.

Results

Liver and heart tissues were collected to evaluate 8-hydroxy-2 deoxyguanosine (8-OHdG), caspase-8 and caspase-9 levels. Hypothyroidism caused DNA damage in the liver, while hyperthyroidism caused DNA damage in the heart tissue. Hyperthyroidism also led to a significant increase in levels of caspase-8 and caspase-9 in liver tissue.

Conclusions

The results of the study show that DNA damage and caspase levels in the heart and liver are affected differently in experimental hypothyroidism and hyperthyroidism.
Specifications of standards in systems and synthetic biology: status and developments in 2021
Authors: Schreiber Falk , Gleeson Padraig , Golebiewski Martin , Gorochowski Thomas E. , Hucka Michael , Keating Sarah M. , König Matthias , Myers Chris J. , Nickerson David P. , Sommer Björn , Waltemath Dagmar
Published: October 2021

This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2021 special issue presents four updates of standards: Synthetic Biology Open Language Visual Version 2.3, Synthetic Biology Open Language Visual Version 3.0, Simulation Experiment Description Markup Language Level 1 Version 4, and OMEX Metadata specification Version 1.2. This document can also be consulted to identify the latest specifications of all COMBINE standards.
The gut-cardiovascular connection: new era for cardiovascular therapy
Authors: Cheng Chak Kwong , Huang Yu
Published: October 2021

Our gut microbiome is constituted by trillions of microorganisms including bacteria, archaea and eukaryotic microbes. Nowadays, gut microbiome has been gradually recognized as a new organ system that systemically and biochemically interact with the host. Accumulating evidence suggests that the imbalanced gut microbiome contributes to the dysregulation of immune system and the disruption of cardiovascular homeostasis. Specific microbiome profiles and altered intestinal permeability are often observed in the pathophysiology of cardiovascular diseases. Gut-derived metabolites, toxins, peptides and immune cell-derived cytokines play pivotal roles in the induction of inflammation and the pathogenesis of dysfunction of heart and vasculature. Impaired crosstalk between gut microbiome and multiple organ systems, such as gut-vascular, heart-gut, gut-liver and brain-gut axes, are associated with higher cardiovascular risks. Medications and strategies that restore healthy gut microbiome might therefore represent novel therapeutic options to lower the incidence of cardiovascular and metabolic disorders.
Genetically-engineered hamster models: applications and perspective in dyslipidemia and atherosclerosis-related cardiovascular disease
Authors: Liu George , Lai Pingping , Guo Jiabao , Wang Yuhui , Xian Xunde
Published: October 2021

Cardiovascular disease is the leading cause of morbidity and mortality in both developed and developing countries, in which atherosclerosis triggered by dyslipidemia is the major pathological basis. Over the past 40 years, small rodent animals, such as mice, have been widely used for understanding of human atherosclerosis-related cardiovascular disease (ASCVD) with the advantages of low cost and ease of maintenance and manipulation. However, based on the concept of precision medicine and high demand of translational research, the applications of mouse models for human ASCVD study would be limited due to the natural differences in metabolic features between mice and humans even though they are still the most powerful tools in this research field, indicating that other species with biological similarity to humans need to be considered for studying ASCVD in future. With the development and breakthrough of novel gene editing technology, Syrian golden hamster, a small rodent animal replicating the metabolic characteristics of humans, has been genetically modified, suggesting that gene-targeted hamster models will provide new insights into the precision medicine and translational research of ASCVD. The purpose of this review was to summarize the genetically-modified hamster models with dyslipidemia to date, and their potential applications and perspective for ASCVD.