bluuebunny/crossref_metadata_2025 huggingface dataset:
Information seeking behaviors of environmental journalists
Authors: Gilbert Stacy , White Philip B. , Tallman Kathryn
Published: June 2021

Journalists and librarians share a common goal of providing information to the public, yet very little is known about how journalists’ information seeking behavior intersects with libraries. This case study seeks to understand the information seeking behavior of environmental journalists by investigating how their information needs intersect with the library and how their information seeking behavior changed over the course of their 9-month fellowship at the University of Colorado Boulder. Semi-structured interviews were conducted with seven environmental journalists at the beginning and end of their fellowship, while an open coding approach was used to identify themes. Generally, study participants conducted research by (1) identifying a story idea and conducting a preliminary search, (2) expanding their knowledge on the topic through scientific articles and interviews with experts, (3) conducting field research, and (4) completing research when information is redundant and they are confident with their knowledge. This process, and their growing feelings of confidence as they conducted research, were similar to, but not exactly, Kuhlthau’s Information Search Process model. Their interactions with the library were mostly limited to accessing books and articles. Overall, there was little change in the participants’ information seeking behavior, possibly due to limited time to learn new resources, reliance on preexisting research habits, professional competence, and lack of awareness of library services (e.g. librarians, workshops, and public academic library access). An understanding of journalists’ information seeking behavior can help librarians conduct instruction and outreach efforts that address journalists’ information needs.
Thermal behavior of N-Methylaniline modified phenolic friction composites
Authors: Fakhraddin Yusubov Fikrat
Published: June 2021

This article discusses observations on thermal stability, decomposition properties and degradation of organic components of friction composite materials fabricated by powder metallurgy techniques. N-Methylaniline modified phenolic resin used as a binder material in the preparation of composite materials. Thermogravimetry method was used to study the thermal properties of the samples. The experiments were performed on a TGA Q50 (TA Instrument) in an oxygen atmosphere. In order to better assess the thermal characteristics of the composites, the analyses were carried out by separating thermographs into three parts according to the degradation mechanism. The obtained results helped to assess the thermal stability of the friction materials. The degradation of phenolic resin was observed in the temperature range of 312–362°C. It was found that barite and copper-graphite particles improve the thermal characteristics of the samples.
Prevalence and Social Risk Factors of Infertility in Vietnam
Authors: Kim Nam Il , Chamchan Chalermpol , Tangchonlatip Kanchana
Published: June 2021

Despite of significant social meaning of childlessness in Vietnam, there have been less scientific interests and social concerns about infertility during the past decades. This study aimed to measure infertility prevalence rate among Vietnamese married women and identifies the risk factors associated with vulnerability of infertility in social perspectives. A total of 11,715 married women aged between 20 and 44 years were selected from two rounds of Vietnam Multiple Indicator Cluster Survey in 2011 and 2014. The study applied a demographic definition of infertility; refers to an absence of live birth in the past 24 months among married women having desire of child and not using any contraceptive method. Primary infertility prevalence was decreased from 1.6% in 2011 to 1.1% in 2014, while secondary infertility increased from 3.5% to 3.7% during the same period. Multinomial logistic regression analysis revealed that age of women and husband, education, wealth index and age at first marriage were significantly associated with primary infertility, while education, wealth index and age at first marriage were significantly associated with secondary infertility. Despite some limitations, this study is helpful to understand infertility dynamics and some influencing factors increasing the risk of infertility in social context of the Vietnam.
Experimental study on the damage process of marble under true triaxial pre-peak unloading conditions
Authors: Gao Yaohui , Wang Zhaofeng
Published: June 2021

Stress-induced instability is associated with rock damage. Here, the progressive brittle fracturing process in Jinping marble is studied by introducing two types of true triaxial pre-peak unloading tests, namely, the incrementally cyclic loading-unloading minimum principal stress test (ICM test) and the incrementally cyclic loading-unloading maximum and minimum principal stress test (ICMM test). By comprehensively analysing the irreversible strains, dissipated energy, acoustic emission (AE) characteristics and scanning electron microscopy (SEM) results, the rock damage evolution can be quantified and divided into two distinctive damage stages. At the boundary point, the irreversible strain increments reach their minimum values. In the gentle damage stage, the normalized irreversible strains increase linearly, and this process is associated with a small number of AE hits with low amplitude. The rapid damage stage is characterized by a nonlinear increase in the normalized irreversible strains, and this process is associated with a large number of AE hits with high amplitude. The dissipated energy mainly increases in the rapid damage stage. In addition, the rapid damage stage in the ICMM test mainly occurs in the last five cycles, due to the differences in the deviatoric stresses in each cycle. In both of these tests, the failure mode is principally characterized by tensile failure. Moreover, the precursory signals of rock fracturing and the influence of the loading paths on the strength are discussed.
The Attorneys’ Gender: Exploring Counsel Success before the U.S. Supreme Court
Authors: Hack Jonathan S. , Jenkins Clinton M.
Published: June 2021

Stereotypes are powerful heuristics structuring decision-making, with research suggesting that gender-based stereotypes place women at a professional disadvantage. This paper tests whether attorneys’ gender influences Supreme Court outcomes. We construct an attorney-focused data set combining personal and professional attributes with case-level characteristics from 1946 to 2016. Our approach brings clarity to previous findings, enabling a longitudinal analysis of women participation before the Court. We find that attorney gender does not influence party success. In doing so, we show that a more nuanced approach is needed when studying the intersection between judicial outcomes and attorney traits.
The end of global pluralism?
Authors: Reus-Smit Christian
Published: June 2021

The liberal international order is a fragmented institutional complex, comprising often disparate elements. One of these is a distinctive institutional approach to the global organization of cultural difference. This approach combines universal Westphalian sovereignty (and the pluralist interstate order it facilitates) with international human rights norms that seek to protect the cultural freedoms of individuals. I term this institutional amalgam “global pluralism”. Like many elements of the liberal order, such pluralism is now under challenge, confronted by resurgent ethno-nationalism, politicized religion, and civilizational chauvinism. The key question is whether global pluralism has the adaptive capacities to withstand such challenges. This article develops a theoretical framework for comprehending these institutional capacities. Conceiving global pluralism as a “diversity regime,” I argue that such regimes always rest on social “recognition contracts,” and that these give them certain structural characteristics: configurations of political authority and modes of cultural recognition. Focusing on these characteristics, I compare global pluralism with past Western and non-Western diversity regimes, and clarify the adaptive strengths and weaknesses of different institutional forms. This contractual-structural analysis exposes the historical uniqueness of global pluralism but also its structural vulnerabilities. While global pluralism has distinct advantages over past diversity regimes—principally, that it does not itself generate unstable cultural cleavages and hierarchies—it requires complex forms of social contracting to sustain, and its individualist mode of recognition struggles to accommodate collectivist cultural claims. Such contracting is essential, however, if global pluralism is to withstand current challenges, all of which involve collectivist claims.
Discrimination by politicians against religious minorities: Experimental evidence from the UK
Authors: Crawfurd Lee , Ramli Ukasha
Published: June 2021

Are Labour party politicians anti-Semitic, and are Conservative party politicians Islamophobic? In this correspondence study we measure the responsiveness of elected local representatives in the United Kingdom to requests from putative constituents from minority religious groups. We send short email requests to 10,268 local government representatives from each of the main political parties, from stereotypically Islamic, Jewish, and Christian names. Response rates are six to seven percentage points lower to stereotypically Muslim or Jewish names. The two major political parties both show equal bias towards the two minority group names. Results suggest that the bias in response may be implicit. Bias is lower in more dense and diverse locations.
Nonlinear hysteretic parameter identification using improved artificial bee colony algorithm
Authors: Yao Renzhi , Chen Yanmao , Wang Li , Lu Zhongrong
Published: June 2021

Hysteresis is a common phenomenon arising in many engineering applications. It describes a memory-based relation between the restoring force and the displacement. Identification of the hysteretic parameters is central to practical application of the hysteretic models. To proceed so, a noteworthy thing is that the hysteretic models are often complex and non-differentiable so that getting the gradients is never straightforward and therefore, the swarm-based algorithm is often preferable to inverse hysteretic parameter identification. Along these lines, an improved artificial bee colony algorithm is developed in this paper for general hysteretic parameter identification. On the one hand, several hysteretic models along with the extensions to tackle the degradation and pinching behaviours are considered and how to model a structure with hysteretic components is also elaborated. As a result, the governing equation for the direct problem is established. On the other hand, the differential evolution mechanism is introduced to improve the original artificial bee colony algorithm. Numerical examples are conducted to testify the feasibility and accuracy of the proposed method in nonlinear hysteretic parameter identification.
Cardiovascular disease in people born to unmarried mothers in two historical periods: The Helsinki Birth Cohort Study 1934–1944
Authors: Mikkonen H. Maiju , Salonen Minna K. , Häkkinen Antti , Osmond Clive , Eriksson Johan G. , Kajantie Eero
Published: June 2021

Aims:Socio-economic conditions in early life are important contributors to cardiovascular disease – the leading cause of mortality globally – in later life. We studied coronary heart disease (CHD) and stroke in adulthood among people born out of wedlock in two historical periods: before and during World War II in Finland. Methods: We compared offspring born out of wedlock before (1934–1939) and during (1940–1944) World War II with the offspring of married mothers in the Helsinki Birth Cohort Study. The war affected the position of unmarried mothers in society. We followed the study subjects from 1971 to 2014 and identified deaths and hospital admissions from CHD and stroke. Data were analysed using a Cox regression, adjusting for other childhood and adulthood socio-economic circumstances. Results: The rate of out-of-wedlock births was 240/4052 (5.9%) before World War II and 397/9197 (4.3%) during World War II. Among those born before World War II, out-of-wedlock birth was associated with an increased risk of stroke (hazard ratio (HR)=1.44; 95% confidence interval (CI) 1.00–2.07) and CHD (HR=1.37; 95% CI 1.02–1.86). Among those born out of wedlock during World War II, the risks of stroke (HR=0.89; 95% CI 0.58–1.36) and CHD (HR=0.70; 95% CI 0.48=1.03) were similar to those observed for the offspring of married mothers. The p-values for interaction of unmarried×World War II were ( p=0.015) for stroke and ( p=0.003) for CHD. Conclusions: In a society in which marriage is normative, being born out of wedlock is an important predictor of lifelong health disadvantage. However, this may change rapidly when societal circumstances change, such as during a war.
A Bayesian optimized framework for successful application of unscented Kalman filter in parameter identification of MDOF structures
Authors: Sheibani Mohamadreza , Ou Ge
Published: June 2021

The success of the unscented Kalman filter can be jeopardized if the required initial parameters are not identified carefully. These parameters include the initial guesses and the levels of uncertainty in the target parameters and the process and measurement noise parameters. While a set of appropriate initial target parameters give the unscented Kalman filter a head start, the uncertainty levels and noise parameters set the rate of convergence in the process. Therefore, due to the coupling effect of these parameters, an inclusive approach is desired to maintain the chance of convergence for expensive experimental tests. In this paper, a framework is proposed that, via a virtual emulation prior to the experiment, determines a set of initial conditions to ensure a successful application of the online parameter identification. A Bayesian optimization method is proposed, which considers the level of confidence in the initial guesses for the target parameters to suggest the appropriate noise covariance matrices. The methodology is validated on a five-story shear frame tested on a shake table. The results indicate that, indeed, a trade-off can be made between the robustness of the online updating and the final parameter accuracy.
Dreaming Marx, Engels, Durkheim, and Simmel
Authors: Harding Sandra
Published: June 2021

An account of how my philosophical and sociological interests have both clashed and collaborated, beginning with my doctoral work.
Can one artist name an unnamed road after himself?
Authors: Xu Weilin
Published: June 2021

Process of rapid urbanisation in China during recent years have created the need for names to be given to new urban roads. However, due to the inattention of institutions charged with responsibilities for place-naming, some roads remain unnamed. Although these unnamed roads have been overlooked by China’s municipal authorities and by toponymic scholars, they have attracted the attention of Yulu Ge. In 2013, Ge named an unnamed road in Beijing after himself as a work of public art, aiming to urge the government to improve urban governance and to raise public awareness about the necessity of civic engagement. While there are many studies on the critical toponymy and geographies of public art, little attention has been paid to place-naming as a work of public art and the popular responses to it. This article considers how Ge conducted his public art and the attitudes of city residents who had knowledge of it. It is argued that Ge’s artistic practice has brought convenience to residents’ everyday lives and has led city authorities and urban communities to pay greater attention to unnamed roads. However, questions remain over the role of the artist as a disruptive presence in the city’s orderly structure. Therefore, this article argues that the disputes over the Geyu Road remind artists and scholars to consider how place-naming as an artistic practice can intervene in urban lives in a more appropriate way, and the extent to which authorities and urban society can accommodate creative and effective interventions such as Ge’s place-naming practices.
Technical possibilities for recycling plastics from agribusiness
Authors: Cadena Francisco , Aldás María Belén , Aguilar Alex Darío , Inga Allyson , Cando Daniel
Published: June 2021

Plastic waste generated by the Ecuadorian agro-industrial sector represents one of the main environmental impacts, particularly in floricultural and banana production, as a result of its use as a greenhouse cover and as a protective element for the fruit cluster, respectively. The situation become more complicated because of the level of degradation caused by environmental exposure and the degree of contamination due to the use of agrochemicals that plastics present once their useful life has expired. The current research was divided into two stages: characterization of plastic waste and conditioning prior to reprocessing. The results revealed the plastic waste of the floricultural and banana sector, whose predominant material corresponds to LDPE and HDPE, respectively, presents a level of contamination that allows them to be considered as “non-hazardous” waste, which allows them to be recycled, but their processes must be properly controlled and carried out by qualified people. The level of degradation in the exposed banana bags showed losses of mechanical properties of tensile less than 50%, which means that the material is not degraded and it is feasible to recycle it directly. Additionally, the FTIR-ATR spectra on both sides of the film in the samples did not register representative bands of oxidation. On the other hand, in the greenhouse waste, the losses of mechanical properties of tensile strength above 50% as well as the noticeable formation of carbonyl groups in the structure of the material showed the degradation of the plastic. Therefore, the feasibility of recycling will depend on the incorporation of virgin material. The conditioning of the waste for subsequent recycling revealed the need of a washing process consisting of four stages: initial cleaning, pre-wash, washing, and air-drying.
Becoming Anti-Racist Occupational Therapy Practitioners: A Scoping Study
Authors: Sterman Julia , Njelesani Janet
Published: June 2021

The ongoing racism pandemic in the United States negatively impacts the health, safety, and occupations of Black, Indigenous, and/or People of Color. Although occupational therapy (OT) practitioners have a pressing obligation to actively address racism’s causes and consequences, they lack guidance on what to do. This scoping study sought to identify and synthesize existing knowledge on ways OT practitioners and the profession can engage in anti-racist actions. Six databases were searched for content related to OT and anti-racism. The 31 included articles indicated that OT practitioners should: engage in reflexivity on ways their power and privilege impact therapeutic relationships, use inclusive models, consider how racism can impact client occupations and health care access, and address structural racism through advocacy and occupations as means. Although being anti-racist is a lifelong process, strategies within this study can support OT practitioners and the profession to initiate concrete anti-racist actions.
Venoarterial Extracorporeal Membrane Oxygenation via Direct Axillary Artery Cannulation
Authors: Shah Aakash , Madathil Ronson J. , Griffith Bartley P. , Kaczorowski David J.
Published: June 2021

Venoarterial extracorporeal membrane oxygenation (VA-ECMO) is an effective means of support for patients awaiting cardiac or cardiopulmonary transplantation. Typically, peripheral cannulation via the femoral vessels is preferred. However, an alternative is use of the axillary or subclavian artery, which is typically performed via a graft. Here we present the case of a patient who required VA-ECMO for cardiogenic shock with severe pulmonary hypertension as a bridge to heart-lung transplantation. Initially cannulated via the femoral artery, he was converted to a direct axillary cannulation strategy with a distal perfusion catheter and successfully bridged to transplantation. This technique avoids the use of an interposition graft and mitigates problems associated with it.
Will Tanzania’s Wildlife Sector Survive the COVID-19 Pandemic?
Authors: Kideghesho Jafari R. , Kimaro Houssein S. , Mayengo Gabriel , Kisingo Alex W.
Published: June 2021

The COVID-19 pandemic presents a potential threat to wildlife resources in Africa. In this review, using Tanzania as a case, we examine the impacts and risks that wildlife sectors in Africa are facing or are likely to face as a result of this pandemic. We recognize loss of revenues from tourism as a major impact that could negatively influence the management of wildlife species and habitats. Loss of tourism revenues reduces capacity of the conservation agencies to fund conservation operations and support the benefit sharing schemes. Furthermore, it undermines the efficacy of conservation to compete with alternative economic activities which are ecologically damaging. Increased unemployment and household poverty due to closure of businesses may exacerbate wildlife crime and unsustainable activities. Additionally, contributions from donor-funding organizations and development partners cannot be guaranteed as revenues may be diverted to support other sectors including health. In order to address and minimize the impacts and reduce the risks to the wildlife sector, the following policy measures are recommended: ensure adequate budget for conservation; develop a crisis management plan; reconsider protocols for conducting wildlife trade; develop a comprehensive tourism recovery plan; promote scientific studies focusing on zoonoses and adopt a One-Health Approach as a matter of urgency in dealing with COVID-19 and future pandemics.
Affordances-Based Brand Relations: An Inquire on Memetic Brands on Instagram
Authors: Caliandro Alessandro , Anselmi Guido
Published: June 2021

In this article, we argue that, in an era of platformization of culture, social media users tend to relate with brands through modalities that are more informed by platforms’ affordances (i.e., by the technical architecture of and participatory cultures thriving on social media platforms), rather than shared systems of values and meanings promulgated within brand communities or influencers’ fandoms. Our argument grounds on an analysis of 757,776 Instagram posts related to six global brands, through which we show how users create branded content by following and reproducing a memetic logic. Drawing on our empirical results and Limor Shifman’s theory of Internet memes, we introduce the notion of memetic brands. Memetic brands are collections of branded social media posts, which derive from a standard branded template that repeats from user to user with small compositional changes at every iteration and on top of which users attach expressions of their vernacular creativity. In the process, memetic brands vehiculate a hypersignification, that is, an implicit discourse on fluid and situational consumption. Through the concepts of affordances-based brand relations and memetic brands, the article contributes (from a theoretical and methodological point of view) to the emerging literature on platformization of culture.
Communicating to Non-Speaking Critically Ill Patients: Augmentative and Alternative Communication Technique as an Essential Strategy
Authors: Al-Yahyai, RN, BSN Asaad Nasser Salim , Arulappan, RN, RM, BSC (N), MSC (N), PhD (N), DNSc Judie , Matua Gerald Amandu , Al-Ghafri, RN, BSN Sultan Marhoon , Al-Sarakhi, RN, BSN Sami Hamood , Al-Rahbi, RN, BSN Khalid Khalfan Said , Jayapal Sathish Kumar
Published: June 2021

Introduction

Communication with hospitalized patients is crucial to improve the quality and safety of health care.

Methods

The study assessed the communication methods used by nurses while communicating to non-speaking critically ill patients. The participants included staff nurses working in ICU, CICU, HD units of neuro- surgical, orthopedic, medical and oncology wards. Purposive sampling technique was used to recruit a total number of 194 nurses. The communication methods used were assessed by a questionnaire comprised of a list of 21 strategies used to communicate with non-speaking patients.

Results

The most commonly used strategies were reading the patient’s mouthing words, encouraging the patient by telling them that they are doing well and nurses helping them to get better, assessing the patients for their communication ability, “thumps up” to indicate “yes”, “shake head” indicating “no”, use OK, or point to body parts, speaking slowly and waiting for the patient’s response, spending time to listen patiently to what the patient say and touching the non-speaking critically ill patient when the nurse speaks with the patient.

Conclusion

The study reported that the nurses used variety of communication strategies while communicating to non- speaking critically ill patients. However very few nurses used Augmentative and alternative communication strategies to communicate to non-speaking critically ill patients. The study recommends the importance of establishing Augmentative and Alternative Communication strategies in the hospitals.
Using Civil Law Approaches to Hate Crimes in the United States for Illicit Antiquities and Fine Art Cases
Authors: Burmon Kate Melody
Published: June 2021

The current legal system is not designed to pursue satisfying action in criminal court for hate crimes or fine art crimes. However, the civil court system in the United States might provide a more fruitful avenue in combatting these crimes. The burden of proof is lessened to preponderance of evidence. Compensatory and punitive damages awarded in civil cases against hate groups appear to create a more significant financial impact than reparations in criminal cases. Known forprofit entities engage in both of these types of crimes. Due to the limitations of criminal legal solutions in the United States, pursuing a civil legal approach might prove more effective in combatting cases involving hate crime as well as illicit antiquities and fine art.
Clearance of circulating tumor DNA in a high-risk stage-IV rectal carcinoma patient with synchronous liver metastases after conversion surgery is correlated with pathologic complete response
Authors: Huang Yingying , Jia Wenzhuo , Wang Lijun , Ou Qiuxiang , Wu Xue , Xing Baocai
Published: June 2021

Colorectal cancer is the third most common cancer worldwide, and its incidence continues to grow. Approximately one-third of patients with colorectal cancer develop liver metastases during the natural course of disease. Complete surgical resection is associated with very low mortality in colorectal liver metastasis patients, but only a small fraction of colorectal liver metastasis patients fulfill the selection criteria for surgical treatment. We herein describe a high-risk stage-IV rectal carcinoma patient who was initially unresectable according to the National Comprehensive Cancer Network guidelines with a clinical risk score of 4 but received conversion surgery combined with systemic chemotherapy and achieved a favorable long-term clinical outcome (pathologic complete response) of approximately 28 months. Furthermore, serial circulating tumor DNA monitoring using next-generation sequencing provided a comprehensive view of the patient’s clinical and pathologic status for better clinical decision support over the course of the disease. The absence of circulating tumor DNA/cells after conversion surgery was correlated with pathologic complete response. This case study not only demonstrated that a curative oncosurgical approach could be considered for high-risk colorectal liver metastasis patients under specific circumstances but also highlighted the role of circulating tumor DNA monitoring to gain further insight into the evolution of a patient’s response over time.
Regulation of RNA polymerase II activity is essential for terminal erythroid maturation
Authors: Murphy Zachary C. , Murphy Kristin , Myers Jacquelyn , Getman Michael , Couch Tyler , Schulz Vincent P. , Lezon-Geyda Kimberly , Palumbo Cal , Yan Hongxia , Mohandas Narla , Gallagher Patrick G. , Steiner Laurie A.
Published: June 2021

The terminal maturation of human erythroblasts requires significant changes in gene expression in the context of dramatic nuclear condensation. Defects in this process are associated with inherited anemias and myelodysplastic syndromes. The progressively dense appearance of the condensing nucleus in maturing erythroblasts led to the assumption that heterochromatin accumulation underlies this process, but despite extensive study, the precise mechanisms underlying this essential biologic process remain elusive. To delineate the epigenetic changes associated with the terminal maturation of human erythroblasts, we performed mass spectrometry of histone posttranslational modifications combined with chromatin immunoprecipitation coupled with high-throughput sequencing, Assay for Transposase Accessible Chromatin, and RNA sequencing. Our studies revealed that the terminal maturation of human erythroblasts is associated with a dramatic decline in histone marks associated with active transcription elongation, without accumulation of heterochromatin. Chromatin structure and gene expression were instead correlated with dynamic changes in occupancy of elongation competent RNA polymerase II, suggesting that terminal erythroid maturation is controlled largely at the level of transcription. We further demonstrate that RNA polymerase II “pausing” is highly correlated with transcriptional repression, with elongation competent RNA polymerase II becoming a scare resource in late-stage erythroblasts, allocated to erythroid-specific genes. Functional studies confirmed an essential role for maturation stage-specific regulation of RNA polymerase II activity during erythroid maturation and demonstrate a critical role for HEXIM1 in the regulation of gene expression and RNA polymerase II activity in maturing erythroblasts. Taken together, our findings reveal important insights into the mechanisms that regulate terminal erythroid maturation and provide a novel paradigm for understanding normal and perturbed erythropoiesis.
Exploring the pathways to chronic lymphocytic leukemia
Authors: Stevenson Freda K. , Forconi Francesco , Kipps Thomas J.
Published: June 2021

In chronic lymphocytic leukemia (CLL), increasing knowledge of the biology of the tumor cells has led to transformative improvements in our capacity to assess and treat patients. The dependence of tumor cells on surface immunoglobulin receptor signaling, survival pathways, and accessory cells within the microenvironment has led to a successful double-barreled attack with designer drugs. Studies have revealed that CLL should be classified based on the mutational status of the expressed IGHV sequences into 2 diseases, either unmutated (U) or mutated (M) CLL, each with a distinctive cellular origin, biology, epigenetics/genetics, and clinical behavior. The origin of U-CLL lies among the natural antibody repertoire, and dominance of IGHV1-69 reveals a superantigenic driver. In both U-CLL and M-CLL, a calibrated stimulation of tumor cells by self-antigens apparently generates a dynamic reiterative cycle as cells, protected from apoptosis, transit between blood and tissue sites. But there are differences in outcome, with the balance between proliferation and anergy favoring anergy in M-CLL. Responses are modulated by an array of microenvironmental interactions. Availability of T-cell help is a likely determinant of cell fate, the dependency on which varies between U-CLL and M-CLL, reflecting the different cells of origin, and affecting clinical behavior. Despite such advances, cell-escape strategies, Richter transformation, and immunosuppression remain as challenges, which only may be met by continued research into the biology of CLL.
Machine learning integrates genomic signatures for subclassification beyond primary and secondary acute myeloid leukemia
Authors: Awada Hassan , Durmaz Arda , Gurnari Carmelo , Kishtagari Ashwin , Meggendorfer Manja , Kerr Cassandra M. , Kuzmanovic Teodora , Durrani Jibran , Shreve Jacob , Nagata Yasunobu , Radivoyevitch Tomas , Advani Anjali S. , Ravandi Farhad , Carraway Hetty E. , Nazha Aziz , Haferlach Claudia , Saunthararajah Yogen , Scott Jacob , Visconte Valeria , Kantarjian Hagop , Kadia Tapan , Sekeres Mikkael A. , Haferlach Torsten , Maciejewski Jaroslaw P.
Published: June 2021

Although genomic alterations drive the pathogenesis of acute myeloid leukemia (AML), traditional classifications are largely based on morphology, and prototypic genetic founder lesions define only a small proportion of AML patients. The historical subdivision of primary/de novo AML and secondary AML has shown to variably correlate with genetic patterns. The combinatorial complexity and heterogeneity of AML genomic architecture may have thus far precluded genomic-based subclassification to identify distinct molecularly defined subtypes more reflective of shared pathogenesis. We integrated cytogenetic and gene sequencing data from a multicenter cohort of 6788 AML patients that were analyzed using standard and machine learning methods to generate a novel AML molecular subclassification with biologic correlates corresponding to underlying pathogenesis. Standard supervised analyses resulted in modest cross-validation accuracy when attempting to use molecular patterns to predict traditional pathomorphologic AML classifications. We performed unsupervised analysis by applying the Bayesian latent class method that identified 4 unique genomic clusters of distinct prognoses. Invariant genomic features driving each cluster were extracted and resulted in 97% cross-validation accuracy when used for genomic subclassification. Subclasses of AML defined by molecular signatures overlapped current pathomorphologic and clinically defined AML subtypes. We internally and externally validated our results and share an open-access molecular classification scheme for AML patients. Although the heterogeneity inherent in the genomic changes across nearly 7000 AML patients was too vast for traditional prediction methods, machine learning methods allowed for the definition of novel genomic AML subclasses, indicating that traditional pathomorphologic definitions may be less reflective of overlapping pathogenesis.
Hepatitis B and C virus infection among healthcare workers in Africa: a systematic review and meta-analysis
Authors: Atlaw Daniel , Sahiledengle Biniyam , Tariku Zerihun
Published: June 2021

Background

Healthcare workers are at risk of acquiring hepatitis B and C virus infections through patients’ blood and bodily fluids exposure. So far, there is no pooled data that shows the prevalence of HBV and HCV among health care workers in Africa. This study aimed to determine the pooled prevalence of hepatitis B and C infections among health care workers in Africa.

Methods

Studies reporting the prevalence of HBV and HCV were identified from major databases and gray literature. PubMed, CINAHL, POPLINE, ScienceDirect, African Journals Online (AJOL), and Google Scholar were systematically searched to identify relevant studies. A random-effect model was used to estimate the pooled prevalence of hepatitis B and C among health care workers in Africa. The heterogeneity of studies was assessed using Cochran Q statistics and I2 tests. Publication bias was assessed using Begg’s tests.

Result

In total, 1885 articles were retrieved, and 44 studies met the inclusion criteria and included in the final analysis. A total of 17,510 healthcare workers were included. The pooled prevalence of hepatitis B virus infection among health care workers in Africa is estimated to be 6.81% (95% CI 5.67–7.95) with a significant level of heterogeneity (I2 = 91.6%; p < 0.001). While the pooled prevalence of hepatitis C virus infection using the random-effects model was 5.58% (95% CI 3.55–7.61) with a significant level of heterogeneity (I2 = 95.1%; p < 0.001).

Conclusion

Overall, one in fifteen and more than one in twenty healthcare workers were infected by HBV and HCV, respectively. The high burden of HBV and HCV infections remains a significant problem among healthcare workers in Africa.
On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Authors: Senczuk Gabriele , Mastrangelo Salvatore , Ajmone-Marsan Paolo , Becskei Zsolt , Colangelo Paolo , Colli Licia , Ferretti Luca , Karsli Taki , Lancioni Hovirag , Lasagna Emiliano , Marletta Donata , Persichilli Christian , Portolano Baldassare , Sarti Francesca M. , Ciani Elena , Pilla Fabio
Published: June 2021

Background

During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach.

Results

Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools.

Conclusions

This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.
A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations
Authors: Jia Hao , Park Sung-Joon , Nakai Kenta
Published: June 2021

Background

Understanding the functional effects of non-coding variants is important as they are often associated with gene-expression alteration and disease development. Over the past few years, many computational tools have been developed to predict their functional impact. However, the intrinsic difficulty in dealing with the scarcity of data leads to the necessity to further improve the algorithms. In this work, we propose a novel method, employing a semi-supervised deep-learning model with pseudo labels, which takes advantage of learning from both experimentally annotated and unannotated data.

Results

We prepared known functional non-coding variants with histone marks, DNA accessibility, and sequence context in GM12878, HepG2, and K562 cell lines. Applying our method to the dataset demonstrated its outstanding performance, compared with that of existing tools. Our results also indicated that the semi-supervised model with pseudo labels achieves higher predictive performance than the supervised model without pseudo labels. Interestingly, a model trained with the data in a certain cell line is unlikely to succeed in other cell lines, which implies the cell-type-specific nature of the non-coding variants. Remarkably, we found that DNA accessibility significantly contributes to the functional consequence of variants, which suggests the importance of open chromatin conformation prior to establishing the interaction of non-coding variants with gene regulation.

Conclusions

The semi-supervised deep learning model coupled with pseudo labeling has advantages in studying with limited datasets, which is not unusual in biology. Our study provides an effective approach in finding non-coding mutations potentially associated with various biological phenomena, including human diseases.
A multi-task CNN learning model for taxonomic assignment of human viruses
Authors: Ma Haoran , Tan Tin Wee , Ban Kenneth Hon Kim
Published: June 2021

Background

Taxonomic assignment is a key step in the identification of human viral pathogens. Current tools for taxonomic assignment from sequencing reads based on alignment or alignment-free k-mer approaches may not perform optimally in cases where the sequences diverge significantly from the reference sequences. Furthermore, many tools may not incorporate the genomic coverage of assigned reads as part of overall likelihood of a correct taxonomic assignment for a sample.

Results

In this paper, we describe the development of a pipeline that incorporates a multi-task learning model based on convolutional neural network (MT-CNN) and a Bayesian ranking approach to identify and rank the most likely human virus from sequence reads. For taxonomic assignment of reads, the MT-CNN model outperformed Kraken 2, Centrifuge, and Bowtie 2 on reads generated from simulated divergent HIV-1 genomes and was more sensitive in identifying SARS as the closest relation in four RNA sequencing datasets for SARS-CoV-2 virus. For genomic region assignment of assigned reads, the MT-CNN model performed competitively compared with Bowtie 2 and the region assignments were used for estimation of genomic coverage that was incorporated into a naïve Bayesian network together with the proportion of taxonomic assignments to rank the likelihood of candidate human viruses from sequence data.

Conclusions

We have developed a pipeline that combines a novel MT-CNN model that is able to identify viruses with divergent sequences together with assignment of the genomic region, with a Bayesian approach to ranking of taxonomic assignments by taking into account both the number of assigned reads and genomic coverage. The pipeline is available at GitHub via https://github.com/MaHaoran627/CNN_Virus.
Mendelian randomization studies of brain MRI yield insights into the pathogenesis of neuropsychiatric disorders
Authors: Song Weichen , Qian Wei , Wang Weidi , Yu Shunying , Lin Guan Ning
Published: June 2021

Background

Observational studies have identified various associations between neuroimaging alterations and neuropsychiatric disorders. However, whether such associations could truly reflect causal relations remains still unknown.

Results

Here, we leveraged genome-wide association studies (GWAS) summary statistics for (1) 11 psychiatric disorders (sample sizes varied from n = 9,725 to 1,331,010); (2) 110 diffusion tensor imaging (DTI) measurement (sample size n = 17,706); (3) 101 region-of-interest (ROI) volumes, and investigate the causal relationship between brain structures and neuropsychiatric disorders by two-sample Mendelian randomization. Among all DTI-Disorder combinations, we observed a significant causal association between the superior longitudinal fasciculus (SLF) and the risk of Anorexia nervosa (AN) (Odds Ratio [OR] = 0.62, 95 % confidence interval: 0.50 ~ 0.76, P = 6.4 × 10− 6). Similar significant associations were also observed between the body of the corpus callosum (fractional anisotropy) and Alzheimer’s disease (OR = 1.07, 95 % CI: 1.03 ~ 1.11, P = 4.1 × 10− 5). By combining all observations, we found that the overall p-value for DTI − Disorder associations was significantly elevated compared to the null distribution (Kolmogorov-Smirnov P = 0.009, inflation factor λ = 1.37), especially for DTI − Bipolar disorder (BP) (λ = 2.64) and DTI − AN (λ = 1.82). In contrast, for ROI-Disorder combinations, we only found a significant association between the brain region of pars triangularis and Schizophrenia (OR = 0.48, 95 % CI: 0.34 ~ 0.69, P = 5.9 × 10− 5) and no overall p-value elevation for ROI-Disorder analysis compared to the null expectation.

Conclusions

As a whole, we show that SLF degeneration may be a risk factor for AN, while DTI variations could be causally related to some neuropsychiatric disorders, such as BP and AN. Also, the white matter structure might have a larger impact on neuropsychiatric disorders than subregion volumes.
Direct effects of mast cell proteases, tryptase and chymase, on bronchial epithelial integrity proteins and anti-viral responses
Authors: Ramu Sangeetha , Akbarshahi Hamid , Mogren Sofia , Berlin Frida , Cerps Samuel , Menzel Mandy , Hvidtfeldt Morten , Porsbjerg Celeste , Uller Lena , Andersson Cecilia K.
Published: June 2021

Background

Mast cells (MCs) are known to contribute to both acute and chronic inflammation. Bronchial epithelial cells are the first line of defence against pathogens and a deficient anti-viral response has been suggested to play a role in the pathogenesis of asthma exacerbations. However, effects of MC mediators on bronchial epithelial immune response have been less studied. The aim of this study is to investigate the direct effects of stimulation with MC proteases, tryptase and chymase, on inflammatory and anti-viral responses in human bronchial epithelial cells (HBECs).

Method

Cultured BEAS-2b cells and primary HBECs from 3 asthmatic patients were stimulated with tryptase or chymase (0.1 to 0.5 μg/ml) for 1, 3, 6 and 24 h. To study the effects of MC mediators on the anti-viral response, cells were stimulated with 10 μg/ml of viral mimic Poly (I:C) for 3 and 24 h following pre-treatment with 0.5 μg/ml tryptase or chymase for 3 h. Samples were analysed for changes in pro-inflammatory and anti-viral mediators and receptors using RT-qPCR, western blot and Luminex.

Results

Tryptase and chymase induced release of the alarmin ATP and pro-inflammatory mediators IL-8, IL-6, IL-22 and MCP-1 from HBECs. Moreover, tryptase and chymase decreased the expression of E-cadherin and zonula occludens-1 expression from HBECs. Pre-treatment of HBECs with tryptase and chymase further increased Poly (I:C) induced IL-8 release at 3 h. Furthermore, tryptase significantly reduced type-I and III interferons (IFNs) and pattern recognition receptor (PRR) expression in HBECs. Tryptase impaired Poly (I:C) induced IFN and PRR expression which was restored by treatment of a serine protease inhibitor. Similar effects of tryptase on inflammation and anti-viral responses were also confirmed in primary HBECs from asthmatic patients.

Conclusion

MC localization within the epithelium and the release of their proteases may play a critical role in asthma pathology by provoking pro-inflammatory and alarmin responses and downregulating IFNs. Furthermore, MC proteases induce downregulation of epithelial junction proteins which may lead to barrier dysfunction. In summary, our data suggests that mast cells may contribute towards impaired anti-viral epithelial responses during asthma exacerbations mediated by the protease activity of tryptase.