bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential enrichment of yeast DNA in SARS-CoV-2 and related genomes supports synthetic origin hypothesis
Authors: Lisewski Andreas Martin
Published: September 2021

Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should be also considered.   

Results: Here we show that genomes from SARS-CoV-2 and from closely related coronaviruses are differentially enriched with short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for virus replication, host cell invasion, and host immune response. Specifically, for SARS-CoV-2, we identify two sites: one at the start of the viral replicase domain, and the other at the end of the spike gene past its critical domain junction; for SARS-CoV-1, one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain. As yeast is not a natural host for this virus family, we propose a directed passage model for viral constructs, including virus replicase, in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential sequence homology data across yeast chromosomes congruent with chromosomes harboring specific auxotrophic markers further support this passage model. Model and data together allow us to infer a hypothetical tripartite genome assembly scheme for the synthetic biogenesis of SARS-CoV-2 and SARS-CoV-1.  

Conclusions: These results provide evidence that the genome sequences of SARS-CoV-1, SARS-CoV-2, but not that of RaTG13 and all other closest SARS coronavirus family members identified, are carriers of distinct homology signals that might point to large-scale genomic editing during a passage of directed replication and chromosomal integration inside genetically modified yeast cells.
Modelling temporal data in knowledge graphs: a systematic review protocol
Authors: Hooshafza Sepideh , Orlandi Fabrizio , Flynn Rachel , McQuaid Louise , Stephens Gaye , O'Connor Laura
Published: September 2021

Background: The benefits of having high-quality healthcare data are well established. However, high-dimensionality and irregularity of healthcare data pose challenges in their management. Knowledge graphs have gained increasing popularity in many domains, as a method for representing data to overcome such challenges. However, little is known about their suitability for use with healthcare data.

One important factor in representing data is “time”.Data with time related attributes are considered, temporal data. Temporal data are frequently observed in healthcare and the management of rapidly changing patient data is an ongoing challenge. Traditionally, data models have focused on presenting static data and do not account for temporal data. Temporal data models ensure time consistency in data models and assist analysing the history of data and predicting the future trends in data. Knowledge graphs can include temporal data models and are therefore of interest to the field of healthcare data management.

As such, the herein aim is to outline a protocol for an inter-disciplinary systematic review of approaches, applications and challenges in modelling temporal data in knowledge graphs so that we can inform the application of knowledge graphs to healthcare data.

Method: The research questions is, what are the existing approaches in modelling temporal data in knowledge graphs. Two sub-questions on applications, and challenges will also be evaluated. ACM digital library, IEEEXplore and ScienceDirect will be searched for this review. The search will be limited to peer-reviewed literature referring to knowledge graphs based on Resource Description Framework (RDF). A narrative synthesis of the papers will be conducted.

Conclusion: The findings of this systematic review will be useful for data engineers to better represent data and perform analytics through temporal data modelling. They can be applied in the context of healthcare data and the current challenges faced in managing rapidly changing patient data.
Child labor in Colombia: factors affecting the selection of economic activity
Authors: Ramoni-Perazzi Josefa , Orlandoni-Merli Giampaolo , Castillo-Paredes Laura , Peña Guillén Jesús Alberto
Published: September 2021

The aim of this research was to determine whether child labor in Colombia’s urban areas shows specific characteristics and backgrounds once it is divided by economic activity. The descriptive analysis was based on basic statistics and multiple correspondence analysis, and the probability of working was modeled through a logit model. Finally, a multinomial logit model was applied to consider the six most common economic activity sectors these children work at. The evidence suggests that the probability of a particular type of work is affected by personal characteristics and lifestyles.
Reconstruction of finite deep sub-wavelength nanostructures by Mueller-matrix scattered-field microscopy
Authors: Wang Cai , Chen Xiuguo , Chen Chao , Sheng Sheng , Song Lixuan , Gu Honggang , Jiang Hao , Zhang Chuanwei , Liu Shiyuan
Published: September 2021

Computational super-resolution is a novel approach to break the diffraction limit. The Mueller matrix, which contains full-polarization information about the morphology and structure of a sample, can add super-resolution information and be a promising way to further enhance the resolution. Here we proposed a new approach called Mueller-matrix scattered-field microscopy (MSM) that relies on a computational reconstruction strategy to quantitatively determine the geometrical parameters of finite deep sub-wavelength nanostructures. The MSM adopts a high numerical-aperture objective lens to collect a broad range of spatial frequencies of the scattered field of a sample in terms of Mueller-matrix images. A rigorous forward scattering model is established for MSM, which takes into account the vectorial nature of the scattered field when passing through the imaging system and the effect of defocus in the measurement process. The experimental results performed on a series of isolated Si lines have demonstrated that MSM can resolve a feature size of λ/16 with a sub-7 nm accuracy. The MSM is fast and has a great measurement accuracy for nanostructures, which is expected to have a great potential application for future nanotechnology and nanoelectronics manufacturing.
Freeform optical design of beam shaping systems with variable illumination properties
Authors: Yang Lin , Shen Fanqi , Ding Zhanghao , Tao Xiao , Zheng Zhenrong , Wu Fei , Li Yong , Wu Rengmao
Published: September 2021

Freeform optics constitutes a new technology that is currently driving substantial changes in beam shaping. Most of the current beam shaping systems are elaborately tailored for fixed optical properties, which means the output light distribution of a beam shaping system usually cannot be changed. What we present here is a class of beam shaping systems, the optical properties of which can be changed to meet the requirements for different applications. The proposed beam shaping system is composed of a freeform lens and a non-classical zoom system which is designed by ray aiming and the conservation of energy instead of aberration control. The freeform lens includes two elaborately designed freeform optical surfaces, by which both the intensity distribution and wave-front of an incident light beam are manipulated in a desired manner. The light beam after propagating through the non-classical zoom system produces an illumination pattern on a fixed observation plane with a variable pattern size and an unchanged irradiance distribution at different zoom positions. Two design examples are presented to demonstrate the effectiveness of the proposed beam shaping systems.
Strong UV laser absorption source near 355 nm in fused silica and its origination
Authors: Feng Qingyi , Deng Hongxiang , Huang Sizhao , Li Bo , Xiang Xia , Li Li , Wang Biyi , Zheng Wanguo , Yuan Xiaodong , Li Sean , Yang Hongdong , Zu Xiaotao
Published: September 2021

As a high-performance optical material, fused silica is widely applied in high-power laser and photoelectric systems. However, laser induced damage (LID) of fused silica severely limits the output power and performance of these systems. Due to the values in strong field physics and improving the load capacity and performance of high power systems at UV laser, LID at 355 nm of fused silica has attracted much attention. It has been found that, even be treated by advanced processing technologies, the actual damage threshold of fused silica at 355 nm is far below the intrinsic threshold. It means that there is an absorption source near 355 nm in fused silica. However, to date, the absorption source is still unknown. In this paper, a absorption source near 355 nm is found by first-principles calculations. We find that the absorption source near 355 nm is neutral oxygen-vacancy defect (NOV, ≡Si-Si≡) and this defect originates from the oxygen deficiency of fused silica. Our results indicate that NOV defect can be taken as a damage precursor for 355 nm UV laser, and this precursor can be obviously reduced by increasing the ratio of oxygen to silicon. Present work is valuable for exploring damage mechanisms and methods to improve the damage threshold of fused silica at UV laser.
Modified dual Mach-Zehnder interferometers with new locating algorithm for intrusion detection
Authors: Ho Hsin-Ren , Hsieh Cheng-Yu , Hsu Yung-Cheng , Wang Likarn
Published: September 2021

A new type of dual Mach-Zehnder interferometer (DMZI) scheme is presented to eliminate the polarization induced fading usually encountered in fiber-optic intrusion detection systems that use DMZIs. With such a new optical scheme, two identical signal waveforms with only a time delay that corresponds to the location of intrusion can always be obtained without using a polarization control loop. In the study, we also present a new algorithm for locating the intrusion-induced disturbance on the fiber. The experiments carried out in our lab have demonstrated that locating errors of <26 m can be obtained with the presented system used for detecting an intrusion point on a 250 meter long fiber cable. Also, the proposed DMZI system has been tested for years without changing any optical components except the laser type and the length of the sensing fiber. Notably, the thresholds for determining the intrusion have never been altered since the laser type was changed in 2018. In addition, detections of the clockwise and counter-clockwise signals have maintained a condition of high interference visibility, and the locating capability has remained at the same level.
Generation of an optical needle beam with a laser inscribed Pancharatnam-Berry phase element under imperfect conditions
Authors: Gotovski Pavel , Šlevas Paulius , Orlov Sergej , Ulčinas Orestas , Urbas Antanas
Published: September 2021

Beams exhibiting long focal lines and small focal spot sizes are desired in a variety of applications and are called optical needles, with Bessel beams being a common example. Conical prisms are regularly used to generate Bessel beams, however, this method is usually plagued by an appearance of on-axis oscillations. In this work, we consider an optical element based on the space-domain Pancharatnam-Berry phase (PBP) to generate a high-power optical needle with a smooth and constant on-axis intensity profile. The phase in PBP elements is not introduced through optical path differences but results from the geometric phase that accompanies space-variant polarization manipulation. Our implementation is based on a type 2 modification of bulk transparent glass material, resulting in the formation of nanogratings with slow axes aligned perpendicular to the grating corrugation. We investigate both numerically and experimentally the stability of an optical needle generation under imperfect conditions. Influences of misalignments in the optical schema are investigated numerically and experimentally.
Temperature dependencies of the refractive index for Al-Ga-In-As metamorphic layers
Authors: Emelyanov V. M. , Levina S. A. , Kalyuzhnyy N. A. , Mintairov S. A. , Nakhimovich M. V. , Shvarts M. Z.
Published: September 2021

Temperature dependencies of the refractive indices,

n

, for

I
n

x

G
a

1
−
x

A
s

and

I
n

x

A
l

1
−
x

A
s

metamorphic layers with

x
=

0.06

−

0.25

have been determined. For this purpose, we performed variable-temperature (80 to 400 K) measurements of the specular reflection coefficient using custom distributed-Bragg-reflector structures in the spectral range from 0.8 µm to 2.2 µm. All the compositions exhibited a nearly linear temperature dependence of

n

. For

I
n

x

G
a

1
−
x

A
s

, the temperature coefficient (

d
n

/

d
T

) increases from

2.0

⋅

10

−
4

K

−
1

for

x
=

0.06

to

4.5

⋅

10

−
4

K

−
1

at

x
=

0.25

. In turn, the temperature coefficient of the

I
n

x

A
l

1
−
x

A
s

refractive index stays at the level of

(

1.7

−

2.0

)
⋅

10

−
4

K

−
1

at the considered indium contents.
Controlling the surface charge of simple viruses
Authors: Duran-Meza A. L. , Villagrana-Escareño M. V. , Ruiz-García J. , Knobler C. M. , Gelbart W. M.
Published: September 2021

The vast majority of plant viruses are unenveloped, i.e., they lack a lipid bilayer that is characteristic of most animal viruses. The interactions between plant viruses, and between viruses and surfaces, properties that are essential for understanding their infectivity and to their use as bionanomaterials, are largely controlled by their surface charge, which depends on pH and ionic strength. They may also depend on the charge of their contents, i.e., of their genes or–in the instance of virus-like particles–encapsidated cargo such as nucleic acid molecules, nanoparticles or drugs. In the case of enveloped viruses, the surface charge of the capsid is equally important for controlling its interaction with the lipid bilayer that it acquires and loses upon leaving and entering host cells. We have previously investigated the charge on the unenveloped plant virus Cowpea Chlorotic Mottle Virus (CCMV) by measurements of its electrophoretic mobility. Here we examine the electrophoretic properties of a structurally and genetically closely related bromovirus, Brome Mosaic Virus (BMV), of its capsid protein, and of its empty viral shells, as functions of pH and ionic strength, and compare them with those of CCMV. From measurements of both solution and gel electrophoretic mobilities (EMs) we find that the isoelectric point (pI) of BMV (5.2) is significantly higher than that of CCMV (3.7), that virion EMs are essentially the same as those of the corresponding empty capsids, and that the same is true for the pIs of the virions and of their cleaved protein subunits. We discuss these results in terms of current theories of charged colloidal particles and relate them to biological processes and the role of surface charge in the design of new classes of drug and gene delivery systems.
Hemorrhagic and thrombotic manifestations in the central nervous system in COVID-19: A large observational study in the Brazilian Amazon with a complete autopsy series
Authors: Santana Monique Freire , Frank Carlos Henrique Michiles , Almeida Taynná Vernalha Rocha , Jeronimo Christiane Maria Prado , de Araújo Pinto Rebecca Augusta , Martins Yasmin Ferreira , de Farias Maria Eduarda Leão , Dutra Bruna Guimarães , Brito-Sousa José Diego , Baía-da-Silva Djane Clarys , Xavier Mariana Simão , Lacerda Marcus Vinicius Guimarães , Almeida Val Fernando Fonseca , Monteiro Gisely Cardoso , Sampaio Vanderson de Souza , Monteiro Wuelton Marcelo , Ferreira Luiz Carlos de Lima
Published: September 2021

SARS-CoV-2 affects mainly the lungs, however, other manifestations, including neurological manifestations, have also been described during the disease. Some of the neurological findings have involved intracerebral or subarachnoid hemorrhage, strokes, and other thrombotic/hemorrhagic conditions. Nevertheless, the gross pathology of hemorrhagic lesions in the central nervous system has not been previously described in Brazilian autopsy cases. This study aimed to describe gross and microscopic central nervous system (CNS) pathology findings from the autopsies and correlate them with the clinical and laboratory characteristics of forty-five patients with COVID-19 from Manaus, Amazonas, Brazil. Forty-four patients were autopsied of which thirty-eight of these (86.36%) were positive by RT-PCR for COVID-19, and six (13.3%) were positive by the serological rapid test. Clinical and radiological findings were compatible with the infection. The patients were classified in two groups: presence (those who had hemorrhagic and/or thrombotic manifestations in the CNS) and absence (those who did not present hemorrhagic and/or thrombotic manifestations in the CNS). For risk assessment, relative risk and respective confidence intervals were estimated. Macroscopic or microscopic hemorrhages were found in twenty-three cases (52,27%). The postmortem gross examination of the brain revealed a broad spectrum of hemorrhages, from spots to large and confluent areas and, under microscopy, we observed mainly perivascular discharge. The association analyses showed that the use of corticosteroid, anticoagulant and antibiotic had no statistical significance with a risk of nervous system hemorrhagic manifestations. However, it is possible to infer a statistical tendency that indicates that individuals with diabetes had a higher risk for the same outcome (RR = 1.320, 95% CI = 0.7375 to 2.416, p = 0.3743), which was not observed in relation to other comorbidities. It is unknown whether the new variants of the virus can cause different clinical manifestations, such as those observed or indeed others. As a result, more studies are necessary to define clinical and radiologic monitoring protocols and strategic interventions for patients at risk of adverse and fatal events, such as the extensive hemorrhaging described here. It is imperative that clinicians must be aware of comorbidities and the drugs used to treat patients with COVID-19 to prevent CNS hemorrhagic and thrombotic events.
Identifying indicator species in ecological habitats using Deep Optimal Feature Learning
Authors: Tsai Yiting , Baldwin Susan A. , Gopaluni Bhushan
Published: September 2021

Much of the current research on supervised modelling is focused on maximizing outcome prediction accuracy. However, in engineering disciplines, an arguably more important goal is that of feature extraction, the identification of relevant features associated with the various outcomes. For instance, in microbial communities, the identification of keystone species can often lead to improved prediction of future behavioral shifts. This paper proposes a novel feature extractor based on Deep Learning, which is largely agnostic to underlying assumptions regarding the training data. Starting from a collection of microbial species abundance counts, the Deep Learning model first trains itself to classify the selected distinct habitats. It then identifies indicator species associated with the habitats. The results are then compared and contrasted with those obtained by traditional statistical techniques. The indicator species are similar when compared at top taxonomic levels such as Domain and Phylum, despite visible differences in lower levels such as Class and Order. More importantly, when our estimated indicators are used to predict final habitat labels using simpler models (such as Support Vector Machines and traditional Artificial Neural Networks), the prediction accuracy is improved. Overall, this study serves as a preliminary step that bridges modern, black-box Machine Learning models with traditional, domain expertise-rich techniques.
Elevated C-reactive protein in early COVID-19 predicts worse survival among hospitalized geriatric patients
Authors: Villoteau Adeline , Asfar Marine , Otekpo Marie , Loison Jocelyne , Gautier Jennifer , Annweiler Cédric ,   on behalf of the GERIA-COVID study group
Published: September 2021

Background

The objective of this cohort study was to determine whether elevated CRP in early COVID-19 was associated with 14-day mortality in geriatric patients.

Methods

Plasma CRP levels at hospital admission and 14-day all-cause mortality were assessed in geriatric inpatients hospitalized for COVID-19. Potential confounders were age, sex, functional abilities, history of malignancies, hypertension, cardiomyopathy, albuminemia, number of acute health issues, use of antibiotics and respiratory treatments.

Results

Ninety-five participants (mean±SD 88.0±5.5years; 49.5%women; mean CRP, 76.7±77.5mg/L; mean albuminemia, 32.9±6.0g/L) were included. Sixteen participants who did not survive at day 14 exhibited higher CRP level at baseline than the others (120.3±71.2 versus 67.9±76.1 mg/L, P = 0.002). There was no difference in albuminemia (P = 0.329). Plasma CRP level was directly associated with 14-day mortality (fully adjusted HR = 1.11, P = 0.025). The cut-off for CRP associated with 14-day mortality was set at 35mg/L (sensitivity = 0.88; specificity = 0.56). Those with CRP<35mg/L had longer survival time than the others (log-rank P<0.001).

Conclusions

Elevated CRP levels were associated with poorer 14-day survival in hospitalized geriatric COVID-19 patients.
Chirality and asymmetry increase the potency of candidate ADRM1/RPN13 inhibitors
Authors: Anchoori Ravi K. , George Logan , Tseng Ssu-Hsueh , Lam Brandon , Polkampally Srinidhi , Amiano Anjali D. , Foran Palmer , Tsingine Hannah , Samanapally Harideep , Carrizo Velasquez Fernanda , Das Samarjit , Xing Deyin , Bin Salam Ahmad , Karanam Balasubramanyam , Hung Chien-Fu , Roden Richard B. S.
Published: September 2021

Bortezomib and the other licensed 20S proteasome inhibitors show robust activity against liquid tumors like multiple myeloma, but have disappointed against solid tumors including ovarian cancer. Consequently, interest is mounting in alternative non-peptide based drugs targeting the proteasome’s 19S regulatory particle subunit, including its ubiquitin receptor RPN13. RA183 and RA375 are more potent analogs of the prototypic inhibitor of RPN13 (iRPN13) called RA190, and they show promise for the treatment of ovarian cancer. Here we demonstrate that rendering these candidate RPN13 inhibitors chiral and asymmetric through the addition of a single methyl to the core piperidone moiety increases their potency against cancer cell lines, with the S-isomer being more active than the R-isomer. The enhanced cancer cell cytotoxicities of these compounds are associated with improved binding to RPN13 in cell lysates, ATP depletion by inhibition of glycolysis and mitochondrial electron chain transport, mitochondrial depolarization and perinuclear clustering, oxidative stress and glutathione depletion, and rapid accumulation of high molecular weight polyubiquitinated proteins with a consequent unresolved ubiquitin proteasome system (UPS) stress response. Cytotoxicity was associated with an early biomarker of apoptosis, increased surface annexin V binding. As for cisplatin, BRCA2 and ATM deficiency conferred increased sensitivity to these iRPN13s. Ubiquitination plays an important role in coordinating DNA damage repair and the iRPN13s may compromise this process by depletion of monomeric ubiquitin following its sequestration in high molecular weight polyubiquitinated protein aggregates. Indeed, a synergistic cytotoxic response was evident upon treatment of several ovarian cancer cell lines with either cisplatin or doxorubicin and our new candidate iRPN13s, suggesting that such a combination approach warrants further exploration for the treatment of ovarian cancer.
Traditional practices influencing the use of maternal health care services in Indonesia
Authors: Aryastami Ni Ketut , Mubasyiroh Rofingatul
Published: September 2021

Background

Maternal Mortality Ratio (MMR) in Indonesia is still high, 305, compared to 240 deaths per 100,000 in South East Asian Region. The use of Traditional Birth Attendance (TBA) as a cascade for maternal health and delivery, suspected to be the pocket of the MMR problem. The study aimed to assess the influence of traditional practices on maternal health services in Indonesia.

Methods

We used two data sets of national surveys for this secondary data analysis. The samples included 14,798 mothers whose final delivery was between January 2005 and August 2010. The dependent variables were utilization of maternal healthcare, including receiving antenatal care (ANC≥4), attended by skilled birth attendance (SBA), and having a facility-based delivery (FBD). The independent variables were the use of traditional practices, type of family structure, and TBA density. We run a Multivariate logistic regression for the analysis by controlling all the covariates.

Results

Traditional practices and high TBA density have significantly inhibited the mother’s access to maternal health services. Mothers who completed antenatal care were 15.6% lost the cascade of facility-based delivery. The higher the TBA population, the lower cascade of the use of Maternal Health Services irrespective of the economic quintile. Mothers in villages with a high TBA density had significantly lower odds (AOR = 0.30; CI = 0.24–0.38; p<0.01) than mothers in towns with low TBA density. Moreover, mothers who lived in an extended family had positively significantly higher odds (AOR = 1.33, CI = 1.17–1.52; p<0.01) of using maternal health services.

Discussion

Not all mothers who have received proper antenatal delivered the baby in health care facilities or preferred a traditional birth attendance instead. Traditional practices influenced the ideal utilization of maternal health care. Maternal health care utilization can be improved by community empowerment through the maternal health policy to easier mothers get delivery in a health care facility.
The impact of the 2014 Ebola epidemic on HIV disease burden and outcomes in Liberia West Africa
Authors: Moses Soka J. , Wachekwa Ian , Van Ryn Collin , Grandits Greg , Pau Alice , Badio Moses , Kennedy Stephen B. , Sneller Michael C. , Higgs Elizabeth S. , Lane H. Clifford , Fallah Mosoka , Migueles Stephen A. , Reilly Cavan
Published: September 2021

Background

Detailed longitudinal studies of HIV-positive individuals in West Africa are lacking. Here the HIV prevalence, incidence, all-cause mortality, and the proportion of individuals receiving treatment with cART in two cohorts of participants in Ebola-related studies are described.

Setting

Individuals of all ages were enrolled and followed at four sites in the area of Monrovia, Liberia.

Methods

Two cohorts identified in response to the Ebola epidemic are described to provide insights into the current state of the HIV epidemic. HIV testing was performed at baseline for participants in both cohorts and during follow-up in one cohort.

Results

Prevalence and incidence of HIV (prevalence of 3.1% for women and 1.4% for men and incidence of 3.3 per 1,000) were higher in these cohorts compared to 2018 national estimates (prevalence of 1.3% and incidence of 0.39 per 1,000). Most participants testing positive did not know their status prior to testing. Of those who knew they were HIV positive, 7.9% reported being on antiretroviral treatment. The death rate among those with HIV was 12.3% compared to 1.9% in HIV-negative individuals (adjusted odds ratio of 6.87). While higher levels of d-dimer were associated with increased mortality, this was not specific to those with HIV, however lower hemoglobin levels were associated with increased mortality among those with HIV.

Conclusion

These findings point to a need to perform further research studies aimed at fulfilling these knowledge gaps and address current shortcomings in the provision of care for those living with HIV in Liberia.
Acetylcholine esterase inhibitory activity of green synthesized nanosilver by naphthopyrones isolated from marine-derived Aspergillus niger
Authors: Abdelwahab Ghada Mahmoud , Mira Amira , Cheng Yuan-Bin , Abdelaziz Tarek A. , Lahloub Mohamed Farid I. , Khalil Ashraf Taha
Published: September 2021

Aspergillus niger metabolites exhibited a wide range of biological properties including antioxidant and neuro-protective effects and some physical properties as green synthesis of silver nanoparticles AgNP. The present study presents a novel evidence for the various biological activities of green synthesized AgNPs. For the first time, some isolated naphtho-γ-pyrones from marine-derived Aspergillus niger, flavasperone (1), rubrofusarin B (2), aurasperone A (3), fonsecinone A (4) in addition to one alkaloid aspernigrin A (7) were invistigated for their inhibitory activity of acetylcholine esterase AChE, a hallmark of Alzheimer’s disease (AD). The ability to synthesize AgNPs by compounds 3, 4 and 7 has been also tested for the first time. Green synthesized AgNPs were well-dispersed, and their size was ranging from 8–30 nm in diameter, their morphology was obviously spherical capped with the organic compounds. Further biological evaluation of their AChE inhibitory activity was compared to the parent compounds. AgNps dramatically increased the inhibitory activity of Compounds 4, 3 and 7 by 84, 16 and 13 fold, respectively to be more potent than galanthamine as a positive control with IC50 value of 1.43 compared to 0.089, 0.311 and 1.53 of AgNPs of Compounds 4, 3 and 7, respectively. Also compound 2 showed moderate inhibitory activity. This is could be probably explained by closer fitting to the active sites or the synergistic effect of the stabilized AgNPs by the organic compouds. These results, in addition to other intrinsic chemical and biological properties of naphtho-γ-pyrones, suggest that the latter could be further explored with a view towards other neuroprotective studies for alleviating AD.
Coupling coordination relationship between ecosystem services and water-land resources for the Daguhe River Basin, China
Authors: Sun Baodi , Tang Jingchao , Yu Dehu , Song Zhiwen
Published: September 2021

Water and land resource utilization is an important driving force of changes in ecosystem services; therefore, research on multi-parameter coupling systems that consider “ecosystem services, water resources, and land resources” together has key significance for river basins. This study aims to reveal the interaction and mutual influence of ecosystem services and water and land resources in the Daguhe River Basin, China, based on the coupling coordination degree model. The results showed that during the period from 2000 to 2010, the coupling coordination degree values for the years 2000, 2005, and 2010 were 0.6005, 0.7292, and 0.8037. The corresponding coupling coordination classifications were categorized as “primary coordinated development”, “intermediate coordinated development,” and “well-coordinated development”, respectively. These results reflected the fact that the relationship between water and land resource utilization and the environment tends to evolve in the direction of coordinated development (an improvement in one part corresponds to an improvement in another part) with variation in water and land utilization types, and eventually pushes the whole resource, as well as ecological and environmental systems, from low to high levels of coupling coordination degrees as observed in case of the Daguhe River Basin, China. Our research provides an overview of the interaction between ecosystem services and water and land resources in the Daguhe Basin and even in the Shandong Province. With our results, we offer new perspectives on river basin management and for planning future eco-environmental policies (the policy is specifically designed for the ecological environment) by combining water and land resource utilization.
A fairer way to compare researchers at any career stage and in any discipline using open-access citation data
Authors: Bradshaw Corey J. A. , Chalker Justin M. , Crabtree Stefani A. , Eijkelkamp Bart A. , Long John A. , Smith Justine R. , Trinajstic Kate , Weisbecker Vera
Published: September 2021

The pursuit of simple, yet fair, unbiased, and objective measures of researcher performance has occupied bibliometricians and the research community as a whole for decades. However, despite the diversity of available metrics, most are either complex to calculate or not readily applied in the most common assessment exercises (e.g., grant assessment, job applications). The ubiquity of metrics like the h-index (h papers with at least h citations) and its time-corrected variant, the m-quotient (h-index ÷ number of years publishing) therefore reflect the ease of use rather than their capacity to differentiate researchers fairly among disciplines, career stage, or gender. We address this problem here by defining an easily calculated index based on publicly available citation data (Google Scholar) that corrects for most biases and allows assessors to compare researchers at any stage of their career and from any discipline on the same scale. Our ε′-index violates fewer statistical assumptions relative to other metrics when comparing groups of researchers, and can be easily modified to remove inherent gender biases in citation data. We demonstrate the utility of the ε′-index using a sample of 480 researchers with Google Scholar profiles, stratified evenly into eight disciplines (archaeology, chemistry, ecology, evolution and development, geology, microbiology, ophthalmology, palaeontology), three career stages (early, mid-, late-career), and two genders. We advocate the use of the ε′-index whenever assessors must compare research performance among researchers of different backgrounds, but emphasize that no single index should be used exclusively to rank researcher capability.
A novel noninvasive formula for predicting cirrhosis in patients with chronic hepatitis C
Authors: Atsukawa Masanori , Tsubota Akihito , Kondo Chisa , Uchida-Kobayashi Sawako , Takaguchi Koichi , Tsutsui Akemi , Nozaki Akito , Chuma Makoto , Hidaka Isao , Ishikawa Tsuyoshi , Iwasa Motoh , Tamai Yasuyuki , Tobari Maki , Matsuura Kentaro , Nagura Yoshihito , Abe Hiroshi , Kato Keizo , Suzuki Kenta , Okubo Tomomi , Arai Taeang , Itokawa Norio , Toyoda Hidenori , Enomoto Masaru , Tamori Akihiro , Tanaka Yasuhito , Kawada Norifumi , Takei Yoshiyuki , Iwakiri Katsuhiko
Published: September 2021

Evaluating liver fibrosis is crucial for disease severity assessment, treatment decisions, and hepatocarcinogenic risk prediction among patients with chronic hepatitis C. In this retrospective multicenter study, we aimed to construct a novel model formula to predict cirrhosis. A total of 749 patients were randomly allocated to training and validation sets at a ratio of 2:1. Liver stiffness measurement (LSM) was made via transient elastography using FibroScan. Patients with LSM ≥12.5 kPa were regarded as having cirrhosis. The best model formula for predicting cirrhosis was constructed based on factors significantly and independently associated with LSM (≥12.5 kPa) using multivariate regression analysis. Among the 749 patients, 198 (26.4%) had LSM ≥12.5 kPa. In the training set, multivariate analysis identified logarithm natural (ln) type IV collagen 7S, ln hyaluronic acid, and ln Wisteria floribunda agglutinin positive Mac-2-binding protein (WFA+-Mac-2 BP) as the factors that were significantly and independently associated with LSM ≥12.5 kPa. Thus, the formula was constructed as follows: score = −6.154 + 1.166 × ln type IV collagen 7S + 0.526 × ln hyaluronic acid + 1.069 × WFA+-Mac-2 BP. The novel formula yielded the highest area under the curve (0.882; optimal cutoff, −0.381), specificity (81.5%), positive predictive values (62.6%), and predictive accuracy (81.6%) for predicting LSM ≥12.5 kPa among fibrosis markers and indices. These results were almost similar to those in the validated set, indicating the reproducibility and validity of the novel formula. The novel formula scores were significantly, strongly, and positively correlated with LSM values in both the training and validation data sets (correlation coefficient, 0.721 and 0.762; p = 2.67 × 10−81 and 1.88 × 10−48, respectively). In conclusion, the novel formula was highly capable of diagnosing cirrhosis in patients with chronic hepatitis C and exhibited better diagnostic performance compared to conventional fibrosis markers and indices.
Transforming the German ICD-10 (ICD-10-GM) into Injury Severity Score (ISS)—Introducing a new method for automated re-coding
Authors: Niemann Marcel , Märdian Sven , Niemann Pascal , Tetteh Liv , Tsitsilonis Serafeim , Braun Karl F. , Stöckle Ulrich , Graef Frank
Published: September 2021

Background

While potentially timesaving, there is no program to automatically transform diagnosis codes of the ICD-10 German modification (ICD-10-GM) into the injury severity score (ISS).

Objective

To develop a mapping method from ICD-10-GM into ICD-10 clinical modification (ICD-10-CM) to calculate the abbreviated injury scale (AIS) and ISS of each patient using the ICDPIC-R and to compare the manually and automatically calculated scores.

Methods

Between January 2019 and June 2021, the most severe AIS of each body region and the ISS were manually calculated using medical documentation and radiology reports of all major trauma patients of a German level I trauma centre. The ICD-10-GM codes of these patients were exported from the electronic medical data system SAP, and a Java program was written to transform these into ICD-10-CM codes. Afterwards, the ICDPIC-R was used to automatically generate the most severe AIS of each body region and the ISS. The automatically and manually determined ISS and AIS scores were then tested for equivalence.

Results

Statistical analysis revealed that the manually and automatically calculated ISS were significantly equivalent over the entire patient cohort. Further sub-group analysis, however, showed that equivalence could only be demonstrated for patients with an ISS between 16 and 24. Likewise, the highest AIS scores of each body region were not equal in the manually and automatically calculated group.

Conclusion

Though achieving mapping results highly comparable to previous mapping methods of ICD-10-CM diagnosis codes, it is not unrestrictedly possible to automatically calculate the AIS and ISS using ICD-10-GM codes.
Trends in wildlife rehabilitation rescues and animal fate across a six-year period in New South Wales, Australia
Authors: Kwok Alan B. C. , Haering Ron , Travers Samantha K. , Stathis Peter
Published: September 2021

Globally, millions of animals are rescued and rehabilitated by wildlife carers each year. Information gathered in this process is useful for uncovering threats to native wildlife, particularly those from anthropogenic causes. However, few studies using rehabilitation data include a diverse range of fauna, cover large geographical areas, and consider long-term trends. Furthermore, few studies have statistically modelled causes of why animals come into care, and what are their chances of survival. This study draws on 469,553 rescues reported over six years by wildlife rehabilitators for 688 species of bird, reptile, and mammal from New South Wales, Australia. For birds and mammals, ‘abandoned/orphaned’ and ‘collisions with vehicles’ were the dominant causes for rescue, however for reptiles this was ‘unsuitable environment’. Overall rescue numbers were lowest in winter, and highest in spring, with six-times more ‘abandoned/orphaned’ individuals in spring than winter. Of the 364,461 rescues for which the fate of an animal was known, 92% fell within two categories: ‘dead’, ‘died or euthanased’ (54.8% of rescues with known fate) and animals that recovered and were subsequently released (37.1% of rescues with known fate). Modelling of the fate of animals indicated that the likelihood of animal survival (i.e. chance of: being released, left and observed, or permanent care), was related to the cause for rescue. In general, causes for rescue involving physical trauma (collisions, attacks, etc.) had a much lower likelihood of animals surviving than other causes such as ‘unsuitable environment’, ‘abandoned/orphaned’, and this also showed some dependence upon whether the animal was a bird, reptile, or mammal. This suggests rehabilitation efforts could be focused on particular threats or taxa to maximise success, depending on the desired outcomes. The results illustrate the sheer volume of work undertaken by rehabilitation volunteers and professionals toward both animal welfare and to the improvement of wildlife rehabilitation in the future.
Postural sway in the moving room scenario: New evidence for functional dissociation between self-motion perception and postural control
Authors: Horiuchi Kentaro , Imanaka Kuniyasu , Ishihara Masami
Published: September 2021

Postural control in quiet standing is often explained by a reflexive response to optical flow, the apparent motion of environmental objects in a visual scene. However, moving room experiments show that even small-amplitude body sway can evoke odd sensations or motion sickness, indicating that a consciousness factor may also be involved. Studies targeting perception of self-motion, vection, typically use rapid visual stimuli moving in a single direction to maintain a constant feeling of vection, and there are few studies of vection using low-speed sinusoidal visual stimuli similar to human pendular movement. In the present study we searched for changes in postural control during periods of vection during quiet standing. Participants (N = 19, age = 20.4 ±1.1 years) were shown dynamic visual stimuli in the form of sinusoidally expanding and contracting random dots, and the stimuli speed and visual field were manipulated. Posture was continually evaluated using Center of Pressure (CoP) measurements. Participants were also asked to report feelings of vection, both by pressing a button during the trial and through an overall rating at the end of each trial. Using repeated-measures ANOVA, we assessed changes in the CoP and vection variables between experimental conditions, as well as possible interactions between the variables. The results show that postural reaction and vection were both affected by the visual stimuli and varied with speed. The peripheral visual field was found to couple to stronger feeling of vection and better quality of postural control. However, no significant relationship between postural control and vection, nor evidence of vection interaction to the relationship between optical flow and postural control, was found. Based on our results we conclude that for postural stability during quiet standing, visual cues dominate over any potential consciousness factor arising due to vection.
Increased levels of circulating LPS during Tuberculosis prevails in patients with advanced pulmonary involvement
Authors: Gallucci Georgina , Santucci Natalia , Díaz Ariana , Bongiovanni Bettina , Bértola Diego , Gardeñez Walter , Rassetto Mauricio , Bay María Luisa , Bottasso Oscar , D’Attilio Luciano
Published: September 2021

Our earlier studies in tuberculosis (TB) patients indicate that in those where the process evolves to a larger pulmonary involvement, the immune endocrine response may promote an unfavorable environment. Chronic infectious diseases, and their persistent proinflammatory response, may affect mucosal barriers integrity favoring the translocation of gastrointestinal bacteria, leading to an increase of circulating lipopolysaccharides (LPS). Consequently, we quantified LPS levels in TB patients, with different degrees of pulmonary involvement, and controls (Co) and analyzed the possible relationship between LPS and inflammatory mediators i.e., C reactive protein (CRP), interleukin 6 (IL-6) and Interferon-gamma (IFN-γ), Erythrocyte Sedimentation Rate (ESR), steroid hormones (Cortisol and Dehydroepiandrosterone, DHEA), and inflammatory transcripts from peripheral blood mononuclear cells (IL-1β, IL-6, IFN-γ). LPS was assessed by the Limulus amoebocyte lysate assay and the ELISA technique was used to quantify hormones and cytokines in the plasma samples. Cytokine transcripts from PBMC were evaluated by qRT-PCR. Non-parametric tests were used. LPS levels were increased in TB patients, as did levels of CRP, IL-6, IFN-γ, cortisol and ESR. Severe patients had the highest amounts of circulating LPS; with moderate and severe cases showing much higher levels of CRP, ESR, IL-6, IFN-γ and cortisol/DHEA ratio, as an endocrine imbalance. Only in PBMC from severe cases was mRNA for IL-1β increased. Correlation analysis showed that levels of LPS from severe patients were positively associated with IL-6 and IFN-γ plasma concentrations and with IL-1β transcripts, while IL-6 had a positive correlation with the cortisol/DHEA ratio. The higher levels of circulating LPS during progressive TB may emerge as a contributing factor for the persistence of the greater immune endocrine imbalance distinctive of advanced disease, which might suggest a vicious cycle among LPS, inflammation and endocrine imbalance.
Multi-criteria optimization for planning volumetric-modulated arc therapy for prostate cancer
Authors: Park Jongmoo , Park Jaehyeon , Oh Sean , Yea Ji Woon , Lee Jeong Eun , Park Jae Won
Published: September 2021

We aimed to compare the volumetric-modulated arc therapy (VMAT) plans with or without multi-criteria optimization (MCO) on commercial treatment-planning systems (Eclipse, Varian Medical System, Palo Alto, CA, USA) for patients with prostate cancer. We selected 25 plans of patients with prostate cancer who were previously treated on the basis of a VMAT plan. All plans were imported into the Eclipse Treatment Planning System version 15.6, and re-calculation and re-optimization were performed. The MCO plan was then generated. The dosimetric quality of the plans was evaluated using dosimetric parameters and dose indices that account for target coverage and sparing of the organs at risk (OARs). We defined the rectum, bladder, and bilateral femoral heads. The VMAT-MCO plan offers an improvement of gross treatment volume coverage with increased minimal dose and reduced maximal dose. In the planning treatment volume, the Dmean and better gradient, homogeneity, and conformity indexes improved despite the increasing hot and cold spots. When implemented through the MCO plan, a steeper fall off the adjacent OARs in the overlap area was achieved to obtain lower dose parameters. MCO generated better sparing of the rectum and bladder through a tradeoff of the increasing dose to the bilateral femoral heads within the tolerable dose constraints. Compared with re-optimization and re-calculation, respectively, significant dose reductions were observed in the bladder (241 cGy and 254 cGy; p<0.001) and rectum (474 cGy and 604 cGy, p<0.001) with the MCO. Planning evaluation and dosimetric measurements showed that the VMAT-MCO plan using visualized navigation can provide sparing of OAR doses without compromising the target coverage in the same OAR dose constraints.