bluuebunny/crossref_metadata_2025_split huggingface dataset:
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling
Authors: Touré Vasundra , Flobak Åsmund , Niarakis Anna , Vercruysse Steven , Kuiper Martin 
Published: December 2020

AbstractCausal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks. Logical regulatory networks can be used to predict biological and cellular behaviors by system perturbations and in silico simulations. Today, broad sets of causal interactions are available in a variety of biological knowledge resources. However, different visions, based on distinct biological interests, have led to the development of multiple ways to describe and annotate causal molecular interactions. It can therefore be challenging to efficiently explore various resources of causal interaction and maintain an overview of recorded contextual information that ensures valid use of the data. This review lists the different types of public resources with causal interactions, the different views on biological processes that they represent, the various data formats they use for data representation and storage, and the data exchange and conversion procedures that are available to extract and download these interactions. This may further raise awareness among the targeted audience, i.e. logical modelers and other scientists interested in molecular causal interactions, but also database managers and curators, about the abundance and variety of causal molecular interaction data, and the variety of tools and approaches to convert them into one interoperable resource.
Application of learning to rank in bioinformatics tasks
Authors: Ru Xiaoqing , Ye Xiucai , Sakurai Tetsuya , Zou Quan 
Published: December 2020

Abstract
Over the past decades, learning to rank (LTR) algorithms have been gradually applied to bioinformatics. Such methods have shown significant advantages in multiple research tasks in this field. Therefore, it is necessary to summarize and discuss the application of these algorithms so that these algorithms are convenient and contribute to bioinformatics. In this paper, the characteristics of LTR algorithms and their strengths over other types of algorithms are analyzed based on the application of multiple perspectives in bioinformatics. Finally, the paper further discusses the shortcomings of the LTR algorithms, the methods and means to better use the algorithms and some open problems that currently exist.
Viral Cultures for Coronavirus Disease 2019 Infectivity Assessment: A Systematic Review
Authors: Jefferson Tom , Spencer Elisabeth A , Brassey Jon , Heneghan Carl 
Published: December 2020

Abstract

Background
We aimed to review the evidence from studies relating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) culture with the results of reverse-transcription polymerase chain reaction (RT-PCR) and other variables that may influence the interpretation of the test, such as time from symptom onset.

Methods
We searched LitCovid, medRxiv, Google Scholar, and the World Health Organization coronavirus disease 2019 (COVID-19) database for COVID-19 up to 10 September 2020. We included studies attempting to culture or observe SARS-CoV-2 in specimens with RT-PCR positivity. Studies were dual-extracted and the data summarized narratively by specimen type. Where necessary, we contacted corresponding authors of included papers for additional information. We assessed quality using a modified Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2) risk-of-bias tool.

Results
We included 29 studies reporting attempts at culturing, or observing tissue infection by, SARS-CoV-2 in sputum, nasopharyngeal or oropharyngeal, urine, stool, blood, and environmental specimens. The quality of the studies was moderate with lack of standardized reporting. The data suggest a relationship between the time from onset of symptom to the timing of the specimen test, cycle threshold (Ct), and symptom severity. Twelve studies reported that Ct values were significantly lower and log copies higher in specimens producing live virus culture. Two studies reported that the odds of live virus culture were reduced by approximately 33% for every 1-unit increase in Ct. Six of 8 studies reported detectable RNA for &gt;14 days, but infectious potential declined after day 8 even among cases with ongoing high viral loads. Four studies reported viral culture from stool specimens.

Conclusions
Complete live viruses are necessary for transmission, not the fragments identified by PCR. Prospective routine testing of reference and culture specimens and their relationship to symptoms, signs, and patient co-factors should be used to define the reliability of PCR for assessing infectious potential. Those with high Ct are unlikely to have infectious potential.
The effects of daily mitotane or diazepam treatment on the formation of chronic stress symptoms in newly captured wild house sparrows
Authors: Fischer Clare P , Romero L Michael 
Published: December 2020

AbstractWild animals brought into captivity frequently experience chronic stress and typically need a period of time to adjust to the conditions of captivity (restraint, artificial lighting, altered diet, human presence, etc.), to which they may never fully acclimate. Changes in mass, the hypothalamic–pituitary–adrenal axis and heart rate parameters have been observed over the first week in newly captive house sparrows (Passer domesticus). In this study, we tested the effects of two drugs, diazepam and mitotane, in preventing the chronic stress symptoms caused by captivity, compared with oil-injected control animals. Diazepam is an anxiolytic that is widely prescribed in humans and other animals and has been shown in some cases to reduce physiological stress. Mitotane is an agent that causes chemical adrenalectomy, reducing the body’s capacity to produce glucocorticoid hormones. Our mitotane treatment did not cause the expected change in corticosterone concentrations. Baseline corticosterone was higher after a week in captivity regardless of the treatment group, while stress-induced corticosterone did not significantly increase above baseline after a week in captivity in any treatment group. However, mitotane treatment did have some physiological effects, as it reduced the resting heart rate and the duration of the heart rate response to a sudden noise. It also prevented the increase in nighttime activity that we observed in control animals. There was no effect of diazepam on corticosterone, resting heart rate, activity or heart rate response to a sudden noise, and no effect of either treatment on the sympathetic vs parasympathetic control of the resting heart rate. Together, these data suggest that mitotane, but not diazepam, can have a modest impact on helping house sparrows adapt to captive conditions. Easing the transition to captivity will likely make conservation efforts, such as initiating captive breeding programs, more successful.
Sugarcane Aphid (Hemiptera: Aphididae) on Sorghum. I. Population Characteristics and Dispersion Patterns in Relation to Different Sample Unit Sizes
Authors: Yang Yubin , Reay-Jones Francis P F , Reagan Thomas E , Beuzelin Julien M , Wilson Blake E , Davis Jeffrey A , Wang Jing 
Published: December 2020

Abstract
The sugarcane aphid, Melanaphis sacchari (Zehntner), has emerged as a serious pest of sorghum in the United States. Field trials were conducted in Louisiana and South Carolina in 2016–2018 to investigate its population characteristics and distribution patterns in relation to four sample unit sizes (three circular and one leaf based). Sugarcane aphid populations usually progressed through a phase of rapid rise followed by a phase of rapid decline within a span of 5–6 wk, with peak density determined by sorghum cultivars and climatic conditions. Peak population densities for susceptible cultivars were 1.9–14.9× that for resistant cultivars on a per plant basis. Melanaphis sacchari tended to concentrate on the lower green leaf nodes early in the infestation, with the distribution shifting toward higher green leaf nodes as the infestation progressed. Aphid densities per cm2 at the basal and middle sections were about twice as high as at the distal section of leaves. The proportions of infested sample units were fitted to the Wilson–Room binomial model that incorporates the effect of density on clumping pattern. For a specific sample unit size, clumping patterns were similar across cultivars, years, and leaf positions, but varied across infestation stages. For a fixed aphid density per sample unit, the proportion of infested sample units decreased with increasing sample unit size. For a fixed aphid density per cm2, proportion infested increased with increasing sample unit size, indicating less clumping with a larger sample unit size. Field sampling time and efficiency between samplers were quantified.
Echocardiographic evaluation of patients undergoing cancer therapy
Authors: Frey Maria Klara , Bergler-Klein Jutta 
Published: December 2020

Abstract
As advances in oncology therapies lead to significant improvement in life expectancy of many cancer entities, short-, and long-term cardiac side effects of oncology treatments gain increasing importance. In search of new screening modalities, echocardiography currently presents the best established and clinically easily feasible tool to detect cardiotoxicity in patients undergoing cancer therapy. This review focusses on the most commonly used oncology therapies and aims to give a practical approach to guide clinicians caring for this growing number of patients.
Analytical methodology to measure periodontal bone morphometry following orthodontic tooth movement in mice
Authors: Fleissig Omer , Hazan-Molina Hagai , Chaushu Stella , Aizenbud Dror , Klein Yehuda , Zini Avraham , Gabet Yankel 
Published: December 2020

Abstract

Introduction
Basic research in orthodontics is commonly conducted in rodents. However, experimental studies on orthodontic tooth movement (OTM) lack a standard method to examine OTM and periodontal changes. This study describes a unifying protocol for the analysis of OTM and associated bone microarchitectural changes in mice using microcomputed tomography (µCT).

Methods
Mice (10 animals/group) were divided into control and OTM groups. OTM was generated by anchoring a nickel–titanium closed-coil spring to the upper incisors to pull the upper left first molar. A third group of TNFα −/− mice was added since these are known to have slower OTM. Using µCT, we implemented and tested a number of methods to measure OTM distance and examine 3D bone morphometric parameters associated with OTM in mice.

Results
In total, we tested five methods to measure the OTM distance in mice. The results indicated that measuring the intermolar diastema, and assessing tooth movement relative to the anterior root of the zygomatic arch, displayed the lowest standard deviation and enabled optimal detection of intergroup differences. We also developed two protocols for µCT analysis of the periradicular bone that yielded no false-positive results. Our results revealed that including the width of the periodontal ligament rather than excluding it from the region of interest in mice detected more statistically significant differences in the morphometric parameters between the OTM and control sides and between WT and TNFα −/− mice despite more subtle differences.

Conclusions
We, therefore, propose new guidelines for a standardized μCT-based method to analyse OTM and the extent of the periradicular bone structural changes in mice.
Immigrant workforce and agriculture productivity: evidence from Italian farm-level data
Authors: Baldoni Edoardo , Coderoni Silvia , Esposti Roberto 
Published: December 2020

AbstractThis paper investigates the farm-level relationship between total factor productivity (TFP) and presence and composition of immigrant workers. A theoretical model expressing how immigrant workforce influences productivity is developed and an explicit and consistent representation of the so-called ‘diversity hypothesis’ is derived. A dynamic panel specification is estimated, and the respective econometric issues are discussed. The analysis is applied to a balanced panel of Italian professional farms extracted from the Farm Accountancy Data Network over the period 2008–2015. The use of micro-level data in such assessment allows to take the wide heterogeneity across farms into account. Results suggest that, when productivity dynamics and farm heterogeneity are accounted for, empirical support to the diversity hypothesis can be found in Italian professional agriculture.
Synthetic biology approaches to copper remediation: bioleaching, accumulation and recycling
Authors: Giachino Andrea , Focarelli Francesca , Marles-Wright Jon , Waldron Kevin J 
Published: December 2020

ABSTRACTOne of the current aims of synthetic biology is the development of novel microorganisms that can mine economically important elements from the environment or remediate toxic waste compounds. Copper, in particular, is a high-priority target for bioremediation owing to its extensive use in the food, metal and electronic industries and its resulting common presence as an environmental pollutant. Even though microbe-aided copper biomining is a mature technology, its application to waste treatment and remediation of contaminated sites still requires further research and development. Crucially, any engineered copper-remediating chassis must survive in copper-rich environments and adapt to copper toxicity; they also require bespoke adaptations to specifically extract copper and safely accumulate it as a human-recoverable deposit to enable biorecycling. Here, we review current strategies in copper bioremediation, biomining and biorecycling, as well as strategies that extant bacteria use to enhance copper tolerance, accumulation and mineralization in the native environment. By describing the existing toolbox of copper homeostasis proteins from naturally occurring bacteria, we show how these modular systems can be exploited through synthetic biology to enhance the properties of engineered microbes for biotechnological copper recovery applications.
Physical Function and All-Cause Mortality in Older Adults Diagnosed With Cancer: A Systematic Review and Meta-Analysis
Authors: Ezzatvar Yasmin , Ramírez-Vélez Robinson , Sáez de Asteasu Mikel L , Martínez-Velilla Nicolás , Zambom-Ferraresi Fabricio , Izquierdo Mikel , García-Hermoso Antonio 
Published: December 2020

Abstract

Background
Physical function is an independent predictor of numerous chronic diseases, but its association with all-cause mortality in older adults diagnosed with cancer has received little attention. The aim of this study was to conduct a systematic review and meta-analysis on the prospective association between physical function and all-cause mortality in older adults diagnosed with cancer.

Methods
Two authors systematically searched MEDLINE, EMBASE, and SPORTDiscus databases. Prospective studies reporting associations of baseline physical function with all-cause mortality in patients aged 60 years or older diagnosed with any type of cancer were included. Hazard ratios (HR) with associated 95% confidence intervals (CI) were extracted from studies for all-cause mortality, and pooled HRs were then calculated using the random-effects inverse-variance model with the Hartung–Knapp–Sidik–Jonkman adjustment.

Results
Data from 25 studies with 8109 adults diagnosed with cancer aged 60 and older were included in the study. Higher levels of physical function (short physical performance battery, HR = 0.44, 95% CI 0.29–0.67; I2 = 16.0%; timed up and go, HR = 0.40, 95% CI 0.31–0.53; I2 = 61.9%; gait speed, HR = 0.41, 95% CI 0.17–0.96; I2 = 73.3%; handgrip strength: HR = 0.61 95% CI 0.43–0.85, I2 = 85.6%; and overall, HR = 0.45 95% CI 0.35–0.57; I2 = 88.6%) were associated with a lower risk of all-cause mortality compared to lower levels of functionality. Neither age at baseline nor length of follow-up had a significant effect on the HR estimates for lower all-cause mortality risk.

Conclusion
Physical function may exert an independent protective effect on all-cause mortality in older adults diagnosed with cancer.
Efficiency of using a neurofeedback device in determining ischaemic early electroencephalography indicators in rabbits with acute brain ischaemia
Authors: Oğuz Sonay 
Published: December 2020

Abstract

OBJECTIVES
Continuous electroencephalography (EEG) monitoring is a useful method in surgical procedures in which brain circulation is at risk. Providing this function using neurofeedback devices reduced to small dimensions may provide ease of use in the early diagnosis of brain ischaemia. The goal of this study was to demonstrate the efficiency of using a neurofeedback device in determining the early EEG indicators of ischaemia in a rabbit model of acute brain ischaemia.

METHODS
Three randomized groups—carotid ischaemia (CI), global ischaemia (GI) and a sham group—each comprising 8 rabbits, were created. In the CI group, the bilateral main carotid artery was clamped; in the GI group, the bilateral subclavian and main carotid arteries were clamped and brain ischaemia was created for 15 min. Brain reperfusion was then achieved for 30 min. In the sham group, the same surgical preparation was performed but no ischaemia occurred. The brain EEG wave activities of all subjects were recorded during the experiment. At the end of the procedure, all brain tissue was removed and apoptotic indexes were determined by histopathological examination. The statistical significance of the histopathological results and the EEG wave activities among the groups was examined.

RESULTS
There was a significant difference between the sham, CI and GI average amplitude ratios, delta (1.02, 0.69, 0.16; P &lt; 0.001) and total wave (0.99, 0.78, 0.49; P &lt; 0.001), respectively. There was no significant difference between the sham and CI groups in delta (sham, CI, 1.01, 0.87; P = 0.1), total wave (sham, CI, 1.22, 0.98; P = 0.2) and amplitude standard deviation rates. However, there was a significant difference in the GI group (P &lt; 0.001). There was a significant difference between all groups in apoptotic index (sham, 17.88; CI, 40.75; GI, 55.88; P &lt; 0.001).

CONCLUSIONS
Significant EEG wave changes resulting from experimental brain ischaemia were analysed with the use of a neurofeedback device. The results indicated that the change in the delta and the total wave standard deviations may be an additional indicator in the formation of permanent brain damage.
A partitioned finite element method for power-preserving discretization of open systems of conservation laws
Authors: Cardoso-Ribeiro Flávio Luiz , Matignon Denis , Lefèvre Laurent 
Published: December 2020

AbstractThis paper presents a structure-preserving spatial discretization method for distributed parameter port-Hamiltonian systems. The class of considered systems are hyperbolic systems of two conservation laws in arbitrary spatial dimension and geometries. For these systems, a partitioned finite element method (PFEM) is derived, based on the integration by parts of one of the two conservation laws written in weak form. The non-linear one-dimensional shallow-water equation (SWE) is first considered as a motivation example. Then, the method is investigated on the example of the non-linear two-dimensional SWE. Complete derivation of the reduced finite-dimensional port-Hamiltonian system (pHs) is provided and numerical experiments are performed. Extensions to curvilinear (polar) coordinate systems, space-varying coefficients and higher-order pHs (Euler–Bernoulli beam equation) are provided.
Severe Acute Respiratory Syndrome Coronavirus 2–Induced Immune Activation and Death of Monocyte-Derived Human Macrophages and Dendritic Cells
Authors: Zheng Jian , Wang Yuhang , Li Kun , Meyerholz David K , Allamargot Chantal , Perlman Stanley 
Published: December 2020

Abstract
Studies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–infected patients and experimentally infected animals indicate a critical role for augmented expression of proinflammatory chemokines and cytokines in severe disease. Here, we demonstrate that SARS-CoV-2 infection of human monocyte-derived macrophages (MDMs) and monocyte-derived dendritic cells was abortive, but induced the production of multiple antiviral and proinflammatory cytokines (interferon-α, interferon-β, tumor necrosis factor, and interleukins 1β, 6, and 10) and a chemokine (CXCL10). Despite the lack of efficient replication in MDMs, SARS-CoV-2 induced profound interferon-mediated cell death of host cells. Macrophage activation and death were not enhanced by exposure to low levels of convalescent plasma, suggesting that antibody-dependent enhancement of infection does not contribute to cell death. Together, these results indicate that infection of macrophages and dendritic cells potentially plays a major role in coronavirus disease 2019 pathogenesis, even in the absence of productive infection.
Police Perspectives of Problem Solving in the Context of Audience Legitimacy
Authors: Phillips Scott W 
Published: December 2020

AbstractThis study examines the police officer’s contemporary views of dealing with minor order-maintenance problems. Their views of problem-solving go beyond situational, neighbourhood and individual variables. Officers might also consider ‘audience legitimacy’ when forming their opinion of problem-solving. A quasi-experimental vignette research design was used to gauge a police officer’s views of rudimentary order-maintenance activity. Police officers of various ranks, and from a range of different sized police agencies, responded to an online survey, resulting in an N of 473. The dependent variable asked respondents their level of agreement with the actions of an officer described in a vignette. Respondents disagreed with an officer’s decision to ignore an order-maintenance problem. The neighbourhood crime characteristics were not related to their judgements about the decisions of the vignette officer. The type of nuisance crime event described in the vignette was related to the respondent’s level of agreement, but only at the 0.10 level. The respondent’s audience legitimacy score was correlated with several officer characteristics, but the relationship disappeared in the regression analysis. The findings are discussed in relation to prior research, and suggestions are made for multidimensional policing research.
Causes of attrition among frontline health workers in rural areas of Bauchi and Cross River States of Nigeria
Authors: Okech M , Okoroafor S C , Ojo O , Mohammed B 
Published: December 2020

ABSTRACT

Background
The situation of frontline health workers in the rural areas of Bauchi and Cross River States has been classified as critical regarding the shortages due to attrition. This affects health service delivery and outcomes.

Methods
We targeted 402 participants, and 389 frontline health workers (nurses, midwives, nurse/midwives, community health officers and community health extension workers) responded. They were drawn from 42 public primary healthcare centers: 23 from Cross River and 19 from Bauchi States. Five focused-group discussions were conducted with 42 facilities in-charges to identify what they perceived as the main causes of attrition in the rural areas.

Results
Our findings indicate that the reasons that had potential to cause attrition of the frontline health workers were either voluntary or involuntary. Out of the 81 nurses in the study, 66 (81 percent) would voluntarily exit the workforce while 15 (19 percent) would leave involuntarily. From a total number of 81 nurses, midwives and nurse/midwives from the two states, 75% would exit due to resignations in search of better prospects in the urban areas. Ninety-nine percent of the community health worker’s attrition had very low intentions of exit, and it would mainly be due to retirements and deaths.

Conclusion
Implementation of tailor-made strategies that reflect their needs is imperative in the two states to reduce attrition among frontline health workers and improve health service outcomes.