bluuebunny/crossref_metadata_2025 huggingface dataset:
Making European performance and impact assessment frameworks glocal
Authors: Melo Ana M.P. , Oliveira Sofia , Oliveira Jorge S. , Martin Corinne S. , Leite Ricardo B.
Published: March 2022

Sustainability of research infrastructures (RIs) is a big challenge for funders, stakeholders and operators, and the development and adoption of adequate management tools is a major concern, namely tools for monitoring and evaluating their performance and impact. BioData.pt is the Portuguese Infrastructure of Biological and Portuguese node of the European Strategy Forum on Research Infrastructures "Landmark" ELIXIR. The foundations of this national research infrastructure were laid under the “Building BioData.pt” project, for four years. During this period, performance and impact indicators were collected and analysed under the light of international guidelines for assessing the performance and impact of European research infrastructures produced by the European Strategy Forum on Research Infrastructures, the Organisation for Economic Co-operation and Development and the EU-funded RI-PATHS project. The exercise shared herein showed that these frameworks can be adopted by national RIs, with the necessary adaptations, namely to reflect the national landscape and specificity of activities, and can be powerful tools in supporting the management of RIs.

“Not everything that counts can be counted, and not everything that can be counted, counts”. Albert Einstein, Theoretical physicist and Nobel Prize winner
A predictive model for daily cumulative COVID-19 cases in Ghana
Authors: Iddrisu Abdul-Karim , A. Amikiya Emmanuel , Otoo Dominic
Published: March 2022

Background: Coronavirus disease 2019 (COVID-19) is a pandemic that has affected the daily life, governments and economies of many countries all over the globe. Ghana is currently experiencing a surge in the number of cases with a corresponding increase in the cumulative confirmed cases and deaths. The surge in cases and deaths clearly shows that the preventive and management measures are ineffective and that policy makers lack a complete understanding of the dynamics of the disease. Most of the deaths in Ghana are due to lack of adequate health equipment and facilities for managing the disease. Knowledge of the number of cases in advance would aid policy makers in allocating sufficient resources for the effective management of the cases.

Methods: A predictive tool is necessary for the effective management and prevention of cases. This study presents a predictive tool that has the ability to accurately forecast the number of cumulative cases. The study applied polynomial and spline models on the COVID-19 data for Ghana, to develop a generalized additive model (GAM) that accurately captures the growth pattern of the cumulative cases.

Results: The spline model and the GAM provide accurate forecast values.

Conclusion: Cumulative cases of COVID-19 in Ghana are expected to continue to increase if appropriate preventive measures are not enforced. Vaccination against the virus is ongoing in Ghana, thus, future research would consider evaluating the impact of the vaccine.
Local ecological knowledge and folk medicine in historical Estonia, Livonia, Courland, and Galicia, 1805-1905
Authors: Anegg Martin , Prakofjewa Julia , Kalle Raivo , Sõukand Renata
Published: March 2022

Background: Historical ethnobotanical data can provide valuable information about past human-nature relationships as well as serve as a basis for diachronic analysis. This data note aims to present a dataset which documented medicinal plant uses, mentioned in a selection of German-language sources from the 19th century covering the historical regions of Estonia, Livonia, Courland, and Galicia.

Methods: Data was mainly obtained by systematic manual search in various relevant historical German-language works focused on the medicinal use of plants. Data about plant and non-plant constituents, their usage, the mode of administration, used plant parts, and their German and local names was extracted and collected into a database in the form of Use Reports.
An optimization of four SARS-CoV-2 qRT-PCR assays in a Kenyan laboratory to support the national COVID-19 rapid response teams
Authors: Mohammed Khadija Said , de Laurent Zaydah R. , Omuoyo Donwilliams O. , Lewa Clement , Gicheru Elijah , Cheruiyot Robinson , Bartilol Brian , Mutua Shadrack , Musyoki Jennifer , Gumba Horace , Mwacharo Jedidah , Riako Debra , Mwangi Shaban J. , Gichuki Bonface M. , Nyamako Lydia , Karani Angela , Karanja Henry , Mugo Daisy , Gitonga John N. , Njuguna Susan , Gumbi Wilson , Tawa Brian , Tendwa Metrine , Cheruiyot Wesley , Sein Yiakon , Nyambu John K. , Patta Shem O. , Thani Thani Suleiman , Maitha Eric K. , Kitole Benson , Mwakinangu Mohamed S. , Muslih Barke S. , Otieno John Ochieng , Nyiro Joyce U. , Kiyuka Patience , Ndwiga Leonard , Wamae Kevin , Kimani Domtila , Makale Johnstone , Morobe John Mwita , Osoti Victor , Lambisia Arnold W. , Odundo Calleb , Mwarumba Salim , Mutunga Martin , Bejon Philip , Tsofa Benjamin , Agoti Charles N. , Ochola-Oyier Lynette Isabella
Published: March 2022

Background: The COVID-19 pandemic relies on real-time polymerase chain reaction (qRT-PCR) for the detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to facilitate roll-out of patient care and infection control measures. There are several qRT-PCR assays with little evidence on their comparability. We report alterations to the developers’ recommendations to sustain the testing capability in a resource-limited setting.

Methods: We used a SARS-CoV-2 positive control RNA sample to generate several 10-fold dilution series that were used for optimization and comparison of the performance of the four qRT-PCR assays: i) Charité Berlin primer-probe set, ii) European Virus Archive – GLOBAL (EVAg) primer-probe set, iii) DAAN premixed commercial kit and iv) Beijing Genomics Institute (BGI) premixed commercial kit. We adjusted the manufacturer- and protocol-recommended reaction component volumes for these assays and assessed the impact on cycle threshold (Ct) values.

Results: The Berlin and EVAg E gene and RdRp assays reported mean Ct values within range of each other across the different titrations and with less than 5% difference. The DAAN premixed kit produced comparable Ct values across the titrations, while the BGI kit improved in performance following a reduction of the reaction components.

Conclusion: We achieved a 2.6-fold and 4-fold increase in the number of tests per kit for the commercial kits and the primer-probe sets, respectively. All the assays had optimal performance when the primers and probes were used at 0.375X, except for the Berlin N gene assay. The DAAN kit was a reliable assay for primary screening of SARS-CoV-2 whereas the BGI kit’s performance was dependent on the volumes and concentrations of both the reaction buffer and enzyme mix. Our recommendation for SARS-CoV-2 diagnostic testing in resource-limited settings is to optimize the assays available to establish the lowest volume and suitable concentration of reagents required to produce valid results.
МЕТАФОРЫ ШЕКСПИРА КАК ПЕРЕВОДЧЕСКАЯ ПРОБЛЕМА (НА МАТЕРИАЛЕ ПЕРЕВОДА ТРАГЕДИИ "РОМЕО И ДЖУЛЬЕТТА" НА РУССКИЙ И ОСЕТИНСКИЙ ЯЗЫКИ)
Authors: BIZIKOEVA L.S. , KOKOEV G.S.
Published: March 2022

Purpose. The goal of the present article is to analyze the original text of the tragedy “Romeo and Juliette” and its translations into the Russian and Ossetian languages to reveal Shakespeare’s metaphors for further analysis of the ways they are translated and possible problems translators might come across while translating. The main methods employed in the research are: the method of contextual analysis, the descriptive-analytical and the contrastive method. Results. The research was based on the theory of Shakespeare’s metaphor introduced by S.M. Mezenin. According to S.M. Mezenin the revealed metaphors were divided into several semantic groups the most numerous of which comprises metaphors with the semantic model “man - nature” that once again proved the idea of Caroline Spurgeon. The analysis of the translations into the Russian and Ossetian languages showed that translators do not always manage to preserve in the translated text unique Shakespeare’s metaphors. Practical implications. The received results can be used in teaching theory and practice of translation, cultural science, comparative lexicology of the Ossetian and Russian languages and the Ossetian and English languages.
Critical thinking
Authors: Nash Kate , Sloam Debra
Published: March 2022

Kate Nash and Debra Sloam explore the benefits of critical thinking and the A-EQUIP model for student midwives
Does training affect understanding of implicit bias and care of black, Asian and minority ethnic babies?
Authors: Chubb Bea , Cockings Rebecca , Valentine Janine , Symonds Emma , Heaslip Vanessa
Published: March 2022

Background

In the UK, there are huge inequities in maternal and neonatal mortality, yet there appears to be very little training to address this for midwives. This quality improvement project aimed to address this by providing training on implicit bias, stereotyping and clinical assessment of babies from black, Asian and minority ethnic families.

Methods

A training package was created and delivered to 67 midwives and students on placement at the Yeovil District NHS Foundation Trust on implicit bias, structural racism and clinical assessment of babies from black, Asian and minority ethnic groups. Pre- and post-training surveys were completed and descriptive statistical analysis alongside thematic analysis was used to analyse the findings.

Results

It was evident that midwives benefited from the training, as pre-session surveys noted that many midwives were unaware of the factors influencing the care of women and babies from black, Asian and minority ethnic families. After the training, they identified a wish to change their practice to be more inclusive.

Conclusions

The training package was well evaluated; however, more training and research is needed to improve the safety of mothers and babies from black, Asian and minority ethnic families.
Survey of photoneutron emitted from 6MV, 10MV, and 15MV medical LINAC using nuclear track detection
Authors:   Department of Radiological Technology, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand, Awikunprasert Panatsada , Sueangamiam Kamonrat ,   Department of Radiological Technology, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand, Tantivatana Thanathip ,   Department of Radiological Technology, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand, Pungkun Vithit ,   Ionising Radiation Metrology Group, Office of Atoms for Peace, Bangkok, Thailand, Dachviriyakij Tanapol ,   Ionising Radiation Metrology Group, Office of Atoms for Peace, Bangkok, Thailand, Rangseevijitprapa Rattapol Rangseevijitprapa ,   Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen Province, Thailand
Published: March 2022

Background: Medical linear accelerators (LINAC) can produce unwanted photoneutrons that might cause tissue damage or cancer in other organs. The efficient techniques and detectors are importantly required to detect these harmful neutrons. Objectives: This study aimed to measure photoneutrons produced from medical LINAC of 6, 10, and 15 megavolts (MV). Materials and methods: Nuclear track detector (CR-39 detectors) were employed to quantify the number of neutrons from LINACs. The X-ray energies, doses, and radiation techniques were varied to compare the number of neutrons. The photoneutron productions inside the LINAC room were also examined. Results: The results showed that there were no neutrons from medical LINAC 6 MV, whereas photoneutrons could be detected from 10 and 15 MV LINAC. Radiotherapeutic techniques with moving multi-leaf collimator (MLC) produced higher photoneutron than techniques without using MLC. The neutrons were detected on the walls of the LINAC room. Conclusion: X-ray energy greater than 10 MeV generated undesired photoneutrons that can penetrate the shielding and increase the patient dose. For the safety of staff to re-enter the treatment room, delaying time should be considered for the neutron decay process
A EDUCAÇÃO HUMANISTA EM PAULO FREIRE: APONTAMENTOS PARA UMA ALFABETIZAÇÃO LIBERTADORA
Authors: Campos Elisabete
Published: March 2022

Resumo: Partindo de estudos sobre educação integral humanista, o objetivo deste ensaio é apresentar os pressupostos político-pedagógicos para uma alfabetização libertadora, com base no pensamento de Paulo Freire. O caráter humanizador, emancipatório e democrático da pedagogia freireana fundamenta uma alfabetização plena e cidadã, na qual o desenvolvimento cognitivo, físico, cultural, emocional, ético e político não se dissociam. Nesse grave momento em que o mundo é atingido por uma pandemia de proporções inimagináveis, as crianças, mais do que nunca, precisam ser ouvidas, acolhidas e respeitadas em suas fragilidades, potencialidades e formas peculiares de viver esse momento inusitado. A alfabetização libertadora promove sua intensa participação como sujeitos na produção criativa do conhecimento. Nas palavras de Freire, a leitura de mundo, que antecede a leitura da palavra, amplia-se nos processos de leitura e escrita e vai se tornando mais crítica para a construção de uma sociedade com justiça social e menos desigualdades.
Deep point cloud landmark localization for fringe projection profilometry
Authors: Wei Shuwen , Kam Michael , Wang Yaning , Opfermann Justin D. , Saeidi Hamed , Hsieh Michael H. , Krieger Axel , Kang Jin U.
Published: March 2022

Point clouds have been widely used due to their information being richer than images. Fringe projection profilometry (FPP) is one of the camera-based point cloud acquisition techniques that is being developed as a vision system for robotic surgery. For semi-autonomous robotic suturing, fluorescent fiducials were previously used on a target tissue as suture landmarks. This not only increases system complexity but also imposes safety concerns. To address these problems, we propose a numerical landmark localization algorithm based on a convolutional neural network (CNN) and a conditional random field (CRF). A CNN is applied to regress landmark heatmaps from the four-channel image data generated by the FPP. A CRF leveraging both local and global shape constraints is developed to better tune the landmark coordinates, reject extra landmarks, and recover missing landmarks. The robustness of the proposed method is demonstrated through ex vivo porcine intestine landmark localization experiments.
Side-lobe reduction by cascading Bragg grating filters on a Si-photonic chip
Authors: Kumar Sushant , Alshamrani Naif , Grieco Andrew , Fainman Yeshaiahu
Published: March 2022

Bragg-grating based cavities and coupler designs present opportunities for flexible allocation of bandwidth and spectrum in silicon photonic devices. Integrated silicon photonic devices are moving toward mainstream, mass adoption, leading to the need for compact Bragg grating based designs. In this work we present a design and experimental validation of a cascaded contra-directional Bragg-grating coupler with a measured main lobe to side-lobe contrast of 12.93 dB. This level of performance is achieved in a more compact size as compared to conventional apodized gratings, and a similar design philosophy can be used to improve side-lobe reduction in grating-based mirror design for on-chip lasers and other cavity-based designs as well.
Simultaneous frequency up/down converting interface based on a single hardware incorporating two phase-correlated photonic mixers
Authors: Zeng Henan , Li Ruoming , Li Wangzhe
Published: March 2022

A novel photonic frequency up/down-converting interface (FCI) with the capability of up-converting an intermediate frequency (IF) signal to a radio frequency (RF) signal and simultaneously down-converting a RF signal to a low IF signal is proposed, and a new application scenario, where both up and down frequency conversion stages of a deramp-on-receive linearly frequency modulated (LFM) continuous wave (CW) radar system are replaced by the FCI, is demonstrated. The five-port photonic FCI can be seen as two ultra-wideband phase-correlated photonic RF mixers incorporated in a single hardware, and the working frequency range of the FCI is up to Ka-band. The FCI is tested by an LFM waveform with 1GHz bandwidth in a deramp-on-receive LFM CW imaging radar system. In the test, the LFM signal can be transmitted and received correctly, and deramp output signals are able to coherently combine among multiple pulses, which generates a clear image of two point-targets with a 3dB range resolution of 15cm.
Continuous spatial self-cleaning in GRIN multimode fiber for self-referenced multiplex CARS imaging
Authors: Wehbi S. , Mansuryan T. , Krupa K. , Fabert M. , Tonello A. , Zitelli M. , Ferraro M. , Mangini F. , Sun Y. , Vergnole S. , Kano H. , Wabnitz S. , Couderc V.
Published: March 2022

We demonstrate how spatial beam self-cleaning and supercontinuum generation in graded-index multimode optical fibers can be directly applied in multiplex coherent anti-Stokes Raman Scattering (M-CARS) spectroscopy. Although supercontinuum generation causes pump depletion mainly in the center of the beam, the partial recovery of the pump brightness due to self-cleaning may enable self-referenced M-CARS, with no additional delay lines to synchronize pump and Stokes waves. As a proof-of-principle, we report examples of imaging of single chemical compounds and polystyrene beads. The new scheme paves the way towards simpler M-CARS systems based on multimode fiber sources.
Local OAM manipulation of a terahertz wave from the air filament by chirping the few-cycle vortex pump laser
Authors: Wang Honggeng , Song Qiying , Cai Yi , Lu Xiaowei , Lin Qinggang , Zeng Xuanke , Shangguan Huangcheng , Xu Shixiang , Chen Yue-Yue , Shen Baifei
Published: March 2022

We propose a scheme to manipulate the local orbital angular momentum (OAM) of the ultra-broadband (0.1–30 THz) terahertz (THz) waves from the laser-induced short air filament via chirping the few-cycle vortex laser pump. The simulation results show that either the THz vortex pulses with linear azimuth-dependent phases or the THz angular accelerating vortex beams (AAVBs) with nonlinear azimuth-dependent phases can be produced by tuning the chirp parameter of the pump. Thus, the dominant physical mechanism for THz generation can be determined. The THz temporal and transverse spatial distributions can be also controlled by the chirp parameter. Furthermore, their local OAM density distributions present very complex structures because most of the modulated azimuthal intensity and the corresponding local angular helicity distributions are not able to cancel out completely. Via analyzing the simulated THz results at the different pump intensities, we classify the initial pump intensity into three cases. For the low intensity case, the Kerr effect comes into prominence, so the generated THz radiation shall be vortex pulses. While for the high intensity case, the leading plasma effect dominates. In contrast, when the pump intensity is at the medium level, the Kerr nonlinearity and the plasma effect may be comparable and competitive. Basically, THz AAVBs are generated for both high and medium intensity cases. Our study will provide the possibility for studying the optically induced rotation technology more intuitively from the perspective of angular momentum transfer.
Integrated photonic devices enabled by silicon traveling wave-like Fabry–Perot resonators
Authors: Liu Qiang , Zeng Desheng , Mei Chenyang , Li Hongwei , Huang Qingzhong , Zhang Xinliang
Published: March 2022

Integrated photonic devices play a key role in modern optical communications, of which optical resonators are important fundamental structures. This work proposes and experimentally demonstrates compact integrated photonic devices based on a traveling wave-like Fabry–Perot (TW-like FP) resonator(s) coupled with waveguides. Add-drop filters based on a single TW-like FP resonator have been realized with a high drop efficiency and the same output direction for the through and drop ports. Particularly, their transmission response can be either symmetric Lorentzian or asymmetric Fano line shape, through adjusting the shift between the two bus waveguides and the waveguide widths. Fano resonance has been demonstrated in a TW-like FP resonator with a very high extinction ratio and large slope rate. The second-order optical filter exhibits low-loss flat-top passbands with small ripples. Owing to the compact size, easy scalability, and large flexibility, TW-like FP cavity-based devices using Fano and Lorentzian resonances will provide new potential applications in integrated photonics.
Real-time measurement and control of nanofiber diameters using a femtowatt photodetector
Authors: Chen Jiao , Zi Xuehui , Zhang Shicheng , Li Xiaolin , Niu Yueping , Gong Shangqing
Published: March 2022

Real-time measurement and control of optical nanofiber diameters are of particular importance in many applications. Here, we propose and demonstrate a novel and simple method to control the nanofiber diameters in real time, which is based on monitoring the intensity of light scattered from the evanescent field using a femtowatt photodetector. Our experimental results show that the ultra-high precision is within 3 nm and accuracy is within 10 nm in the control of diameters ranging from 400 nm to 750 nm. Our method is also universal and can be extended to optical fibers with other wavelengths.
Azimuthally periodic and radially quasi-periodic Bessel-correlated fields
Authors: Luo Meilan , Koivurova Matias , Turunen Jari
Published: March 2022

We introduce a class of partially coherent sources, which are capable of producing beams with radially quasi-periodic and azimuthally fully periodic intensity profiles. The physical properties of the source, as well as the propagation of the intensity distribution and the complex degree of spatial coherence of the ensuing beams are investigated and interpreted. It is shown that the shape and symmetry of the intensity and the degree of spatial coherence are generally adjustable and modulated by the parameters related to the beam source. Moreover, the periodic changes of intensity arise from the discontinuity of the phase. The results provide a method for synthesizing fields with peculiar periodic intensity distributions in polar coordinates.
Quantum entanglement and one-way steering in a cavity magnomechanical system via a squeezed vacuum field
Authors: Zhang Wei , Wang Tie , Han Xue , Zhang Shou , Wang Hong-Fu
Published: March 2022

We propose a simple scheme to generate quantum entanglement and one-way steering between distinct mode pairs in a generic cavity magnomechanical system, which is composed of a microwave cavity and a yttrium iron garnet sphere supporting magnon and phonon modes. The microwave cavity is pumped by a weak squeezed vacuum field, which plays an important role for establishing quantum entanglement and steering. It is found that when the magnon mode is driven by the red-detuned laser, the maximum entanglement between cavity mode and phonon mode and the maximum phonon-to-photon one-way steering can be effectively generated via adjusting the ratio of two coupling rates. While under the much weaker magnomechanical coupling, the quantum entanglement and one-way steering between cavity mode and magnon mode can be achieved, where the steering direction is determined merely by the relative dissipation strength of the cavity to the magnon mode. More interestingly, we reveal that the robustness to the temperature for entanglement and steering between any mode pairs can be evidently enhanced by selecting the squeezing parameter appropriately.
Combined-Vernier effect based on hybrid fiber interferometers for ultrasensitive temperature and refractive index sensing
Authors: Jiang Zejun , Wu Fugen , Yang Jun , Wen Kunhua , Xu Pengbai , Yu Zhangjun , Sun Jiangquan , Wang Yuncai , Qin Yuwen
Published: March 2022

A kind of hybrid fiber interferometer consisting of a fiber Sagnac interferometer (FSI), a closed-cavity Fabry-Perot interferometer (FPI), and an open-cavity FPI is proposed for generating combined-Vernier-effect. Through adjusting the polarization-maintaining fiber (PMF) length of the FSI, the free spectral range (FSR) is tailored to be similar to that of the parallel-connected reference FPI for producing the first Vernier effect, of which the spectrum is used to match the sensing FPI spectrum for obtaining the second Vernier effect. Noticeable lower and upper spectral envelopes are achieved in the first and second Vernier effects, respectively, so called the combined-Vernier spectrum. Accessibly, the upper envelope is only sensitive to the refractive index (RI) owing to the characteristics of the open-cavity FPI, while the lower one is immune to the RI and employed to detect the temperature by taking advantage of the FSI. Most importantly, the sensitivities of RI and temperature can be significantly improved simultaneously without crosstalk. The experimental results show that the RI sensitivity is −19844.67 nm/RIU and the temperature sensitivity is −46.14 nm/°C, which can be used for high-precision temperature and RI simultaneous measurement.
High-precision inversion of dynamic radiography using hydrodynamic features
Authors: Hossain Maliha , Nadiga Balasubramanya T. , Korobkin Oleg , Klasky Marc L. , Schei Jennifer L. , Burby Joshua W. , McCann Michael T. , Wilcox Trevor , De Soumi , Bouman Charles A.
Published: March 2022

While radiography is routinely used to probe complex, evolving density fields in research areas ranging from materials science to shock physics to inertial confinement fusion and other national security applications, complications resulting from noise, scatter, complex beam dynamics, etc. prevent current methods of reconstructing density from being accurate enough to identify the underlying physics with sufficient confidence. In this work, we show that using only features that are robustly identifiable in radiographs and combining them with the underlying hydrodynamic equations of motion using a machine learning approach of a conditional generative adversarial network (cGAN) provides a new and effective approach to determine density fields from a dynamic sequence of radiographs. In particular, we demonstrate the ability of this method to outperform a traditional, direct radiograph to density reconstruction in the presence of scatter, even when relatively small amounts of scatter are present. Our experiments on synthetic data show that the approach can produce high quality, robust reconstructions. We also show that the distance (in feature space) between a testing radiograph and the training set can serve as a diagnostic of the accuracy of the reconstruction.
Laser-induced patterning for a diffraction grating using the phase change material of Ge2Sb2Te5 (GST) as a spatial light modulator in X-ray optics: a proof of concept
Authors: Park Jeongwon , Zalden Peter , Ng Edwin , Johnston Scott , Fong Scott W. , Chang Chieh , Tassone Christopher J. , Van Campen Douglas , Mok Walter , Mabuchi Hideo , Wong H.-S. Philip , Shen Zhi-Xun , Lindenberg Aaron M. , Sakdinawat Anne
Published: March 2022

The proposed X-ray spatial light modulator (SLM) concept is based on the difference of X-ray scattering from amorphous and crystalline regions of phase change materials (PCMs) such as Ge2Sb2Te5 (GST). In our X-ray SLM design, the “on” and “off” states correspond to a patterned and homogeneous state of a GST thin film, respectively. The patterned state is obtained by exposing the homogeneous film to laser pulses. In this paper, we present patterning results in GST thin films characterized by microwave impedance microscopy and X-ray small-angle scattering at the Stanford Synchrotron Radiation Lightsource.
Global dynamics of microbial communities emerge from local interaction rules
Authors: van Vliet Simon , Hauert Christoph , Fridberg Kyle , Ackermann Martin , Dal Co Alma
Published: March 2022

Most microbes live in spatially structured communities (e.g., biofilms) in which they interact with their neighbors through the local exchange of diffusible molecules. To understand the functioning of these communities, it is essential to uncover how these local interactions shape community-level properties, such as the community composition, spatial arrangement, and growth rate. Here, we present a mathematical framework to derive community-level properties from the molecular mechanisms underlying the cell-cell interactions for systems consisting of two cell types. Our framework consists of two parts: a biophysical model to derive the local interaction rules (i.e. interaction range and strength) from the molecular parameters underlying the cell-cell interactions and a graph based model to derive the equilibrium properties of the community (i.e. composition, spatial arrangement, and growth rate) from these local interaction rules. Our framework shows that key molecular parameters underlying the cell-cell interactions (e.g., the uptake and leakage rates of molecules) determine community-level properties. We apply our model to mutualistic cross-feeding communities and show that spatial structure can be detrimental for these communities. Moreover, our model can qualitatively recapitulate the properties of an experimental microbial community. Our framework can be extended to a variety of systems of two interacting cell types, within and beyond the microbial world, and contributes to our understanding of how community-level properties emerge from microscopic interactions between cells.
Effect of malaria and HIV/AIDS co-infection on red blood cell indices and its relation with the CD4 level of patients on HAART in Bench Sheko Zone, Southwest Ethiopia
Authors: Ejigu Solomon , Haile Diresbachew , Solomon Yerukneh
Published: March 2022

Background

Malaria and HIV/AIDS are the two most common infections in sub Saharan Africa (SSA) and worldwide. HIV infected individuals in malaria endemic areas experience severe malaria episodes. The immunological basis of this clinical observation is unclear and the hematologic abnormalities such as anemia in malaria and HIV co infected patients were inconsistent from studies in the past. Ethiopia’s three-fourth of the landmass is malarious and HIV prevalence is high that significantly affect RBC indices and other hematologic profiles.

Objective

This study aimed to compare RBC indices and anemia in HIV patients’ co-infected with malaria and those HIV patients without malaria and correlates these with CD4 level.

Methods

A comparative cross-sectional study was employed on 103 malaria-HIV/AIDS co infected (MHC) and 103 HIV patients without malaria on HAART of the same ART centers in Bench Sheko Zone. Data was collected by structured questionnaire and blood samples were collected from both groups for malaria test and RBC indices measurement. Data was entered and checked in Epi-data and exported to IBM SPSS version 21 software packages for analysis.

Results

There were significant differences in Mean±SD of RBC indices between the two groups (P<0.001). RBC, Hgb, HCT and MCV were lower in MHC patients. In total study participants, significant positive correlation was observed between CD4 count with MCV, CD4 count with MCH and CD4 count with anemia. In the group of malaria-HIV co-infected, CD4 count with RBC and CD4 count with Hgb and in HIV without malaria CD4 count with MCV, CD4 count with MCH and CD4 count with MCHC were positively correlated. Overall anemia prevalence was 45.1%. Anemia prevalence in MHC (Malaria-HIV co-infected) was 63.4%. Anemia prevalence distribution among sex showed that 61.3% in female sex and anemia prevalence distribution among CD4 group showed 55.9% in patients with CD4 count of ≤500 cells/μl. Anemia in MHC patients was higher in those with CD4 count of ≤500 cells/μl (59.3%) while in OH (Only HIV infected) anemia prevalence was similar in those with CD4 count of ≤500 and ≥500 cells/μl (50%). There is significant difference in anemia in MHC and OH infected with different CD4 group (P<0.01).

Conclusion

There was a difference in RBC indices in both groups; RBC, Hgb, HCT and MCV were lower in MHC patients. There was positive correlation between CD4 counts with some RBC indices in combined both groups. However, there was positive correlation between CD4 counts with RBC and Hgb in malaria-HIV co-infected. The combined prevalence of anemia was higher and anemia in MHC was greater than OH infected patients.
Testing and healthcare seeking behavior preceding HIV diagnosis among migrant and non-migrant individuals living in the Netherlands: Directions for early-case finding
Authors: van Bilsen Ward P. H. , Bil Janneke P. , Prins Jan M. , Brinkman Kees , Leyten Eliane , van Sighem Ard , Bedert Maarten , Davidovich Udi , Burns Fiona , Prins Maria
Published: March 2022

Objectives

To assess differences in socio-demographics, HIV testing and healthcare seeking behavior between individuals diagnosed late and those diagnosed early after HIV-acquisition.

Design

Cross-sectional study among recently HIV-diagnosed migrant and non-migrant individuals living in the Netherlands.

Methods

Participants self-completed a questionnaire on socio-demographics, HIV-testing and healthcare seeking behavior preceding HIV diagnosis between 2013–2015. Using multivariable logistic regression, socio-demographic determinants of late diagnosis were explored. Variables on HIV-infection, testing and access to care preceding HIV diagnosis were compared between those diagnosed early and those diagnosed late using descriptive statistics.

Results

We included 143 individuals with early and 101 with late diagnosis, of whom respectively 59/143 (41%) and 54/101 (53%) were migrants. Late diagnosis was significantly associated with older age and being heterosexual. Before HIV diagnosis, 89% of those with early and 62% of those with late diagnosis had ever been tested for HIV-infection (p<0.001), and respectively 99% and 97% reported healthcare usage in the Netherlands in the two years preceding HIV diagnosis (p = 0.79). Individuals diagnosed late most frequently visited a general practitioner (72%) or dentist (62%), and 20% had been hospitalized preceding diagnosis. In these settings, only in respectively 20%, 2%, and 6% HIV-testing was discussed.

Conclusion

A large proportion of people diagnosed late had previously tested for HIV and had high levels of healthcare usage. For earlier-case finding of HIV it therefore seems feasible to successfully roll out interventions within the existing healthcare system. Simultaneously, efforts should be made to encourage future repeated or routine HIV testing among individuals whenever they undergo an HIV test.
Abnormal expression and the significant prognostic value of aquaporins in clear cell renal cell carcinoma
Authors: Li Mingrui , He Minxin , Xu Fangshi , Guan Yibing , Tian Juanhua , Wan Ziyan , Zhou Haibin , Gao Mei , Chong Tie
Published: March 2022

Aquaporins (AQPs) are a kind of transmembrane proteins that exist in various organs of the human body. AQPs play an important role in regulating water transport, lipid metabolism and glycolysis of cells. Clear cell renal cell carcinoma (ccRCC) is a common malignant tumor of the kidney, and the prognosis is worse than other types of renal cell cancer (RCC). The impact of AQPs on the prognosis of ccRCC and the potential relationship between AQPs and the occurrence and development of ccRCC are demanded to be investigated. In this study, we first explored the expression pattern of AQPs by using Oncomine, UALCAN, and HPA databases. Secondly, we constructed protein-protein interaction (PPI) network and performed function enrichment analysis through STRING, GeneMANIA, and Metascape. Then a comprehensive analysis of the genetic mutant frequency of AQPs in ccRCC was carried out using the cBioPortal database. In addition, we also analyzed the main enriched biological functions of AQPs and the correlation with seven main immune cells. Finally, we confirmed the prognostic value of AQPs throughGEPIA and Cox regression analysis. We found that the mRNA expression levels of AQP0/8/9/10 were up-regulated in patients with ccRCC, while those of AQP1/2/3/4/5/6/7/11 showed the opposite. Among them, the expression differences of AQP1/2/3/4/5/6/7/8/9/11 were statistically significant. The differences in protein expression levels of AQP1/2/3/4/5/6 in ccRCC and normal renal tissues were consistent with the change trends of mRNA. The biological functions of AQPs were mainly concentrated in water transport, homeostasis maintenance, glycerol transport, and intracellular movement of sugar transporters. The high mRNA expression levels of AQP0/8/9 were significantly correlated with worse overall survival (OS), while those of AQP1/4/7 were correlated with better OS. AQP0/1/4/9 were prognostic-related factors, and AQP1/9 were independent prognostic factors. In general, this research has investigated the values of AQPs in ccRCC, which could become new survival markers for ccRCC targeted therapy.
Strategic emerging industry layout based on analytic hierarchy process and fuzzy comprehensive evaluation: A case study of Sichuan province
Authors: He Kai , Zhu Nan
Published: March 2022

In the 12th Five-Year Plan period, Sichuan province has selected strategic emerging industries such as new-generation information technology, new energy, high-end equipment manufacturing, new materials, biology, energy conservation and environmental protection. However, its strategic emerging industries are still in the stage of cultivation and development, and there are some problems such as low industrial agglomeration and obvious industrial restructuring. In essence, this is because the focus of the development of strategic emerging industries is not clear enough, and the location advantages are not fully utilized to select the most suitable strategic emerging industries for the development of the region. This paper constructs a regional strategic emerging industries selection decision model, applies ARCGIS to study the spatial distribution of strategic emerging industries in Sichuan province, and uses fuzzy comprehensive evaluation method (FCEM) and analytic hierarchy process (AHP) to solve the priority of developing strategic emerging industries. Conclusions: Firstly, Sichuan province should give priority to the development of new generation information technology industry and new energy vehicle industry, then high-end equipment manufacturing industry, energy-saving and environmental protection industry and new energy industry, and finally biological industry and new material industry. The larger the coefficient of influence is, the higher the comprehensive score is, while the larger the coefficient of sensitivity is, the lower the comprehensive score is. Secondly, the number of enterprises in the new-generation information technology industry and the new energy vehicle industry is still not dominant in Sichuan province. Finally, the study found that the current development of strategic emerging industries in Sichuan province is extremely unbalanced in various regions, and the phenomenon of competition and reconstruction is obvious.
How did the COVID-19 pandemic impact the stress vulnerability of employed and non-employed nursing students in Romania?
Authors: Simionescu Mihaela , Bordea Elena-Nicoleta , Pellegrini Angelo
Published: March 2022

In the light of the current COVID-19 pandemic, being considered a present challenge for public health, the main purpose of this work is to analyze the vulnerability to stress of a sample of nursing students in Romania considering their status on labour market (employed students in the medical system and non-employed students) before and during the COVID-19 pandemic. Employed students were more vulnerable to stress comparing to non-employed ones during the pandemic. In addition to this, the nursing students working in the medical system experienced medium vulnerability to stress during the pandemic comparing to those working before the pandemic who experienced a low vulnerability to stress. Excepting the non-employed students before the pandemic, the females were more vulnerable to stress comparing to the males in the sample and the students living in the country experienced a higher level of stress comparing to those living in the urban area. During the pandemic, most of the employed nursing students expressed their fear of getting infected with COVID-19, this representing the most stressful factor for them, while most of them mentioned the self-control as being the most proper strategy for them to cope with stress. These empirical findings have practical implications for stress control among present and future nurses, for management of medical units and for higher education nursing.
DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age
Authors: Mulcahy Daniel G. , Ibáñez Roberto , Jaramillo Cesar A. , Crawford Andrew J. , Ray Julie M. , Gotte Steve W. , Jacobs Jeremy F. , Wynn Addison H. , Gonzalez-Porter Gracia P. , McDiarmid Roy W. , Crombie Ronald I. , Zug George R. , de Queiroz Kevin
Published: March 2022

Natural history collections are essential to a wide variety of studies in biology because they maintain large collections of specimens and associated data, including genetic material (e.g., tissues) for DNA sequence data, yet they are currently under-funded and collection staff have high workloads. With the advent of aggregate databases and advances in sequencing technologies, there is an increased demand on collection staff for access to tissue samples and associated data. Scientists are rapidly developing large DNA barcode libraries, DNA sequences of specific genes for species across the tree of life, in order to document and conserve biodiversity. In doing so, mistakes are made. For instance, inconsistent taxonomic information is commonly taken from different lending institutions and deposited in data repositories, such as the Barcode of Life Database (BOLD) and GenBank, despite explicit disclaimers regarding the need for taxonomic verification by the lending institutions. Such errors can have profound effects on subsequent research based on these mis-labelled sequences in data repositories. Here, we present the production of a large DNA barcode library of reptiles from the National Museum of Natural History tissue holdings. The library contains 2,758 sequences (2,205 COI and 553 16S) from 2260 specimens (four crocodilians, 37 turtles, and 2,219 lizards, including snakes), representing 583 named species, from 52 countries. In generating this library, we noticed several common mistakes made by scientists depositing DNA barcode data in public repositories (e.g., BOLD and GenBank). Our goal is to raise awareness of these concerns and offer advice to avoid such mistakes in the future to maintain accurate DNA barcode libraries to properly document Earth’s biodiversity.
Kidney injury after lung transplantation: Long-term mortality predicted by post-operative day-7 serum creatinine and few clinical factors
Authors: Doricic Julian , Greite Robert , Vijayan Vijith , Immenschuh Stephan , Leffler Andreas , Ius Fabio , Haverich Axel , Gottlieb Jens , Haller Hermann , Scheffner Irina , Gwinner Wilfried
Published: March 2022

Background

Acute kidney injury (AKI) after lung transplantation (LuTx) is associated with increased long-term mortality. In this prospective observational study, commonly used AKI-definitions were examined regarding prediction of long-term mortality and compared to simple use of the serum creatinine value at day 7 for patients who did not receive hemodialysis, and serum creatinine value immediately before initiation of hemodialysis (d7/preHD-sCr).

Methods

185 patients with LuTx were prospectively enrolled from 2013–2014 at our center. Kidney injury was assessed within 7 days by: (1) the Kidney Disease Improving Global Outcomes criteria (KDIGO-AKI), (2) the Acute Disease Quality Initiative 16 Workgroup classification (ADQI-AKI) and (3) d7/preHD-sCr. Prediction of all-cause mortality was examined by Cox regression analysis, and clinical as well as laboratory factors for impaired kidney function post-LuTx were analyzed.

Results

AKI according to KDIGO and ADQI-AKI occurred in 115 patients (62.2%) within 7 days after LuTx. Persistent ADQI-AKI, KDIGO-AKI stage 3 and higher d7/preHD-sCr were associated with higher mortality in the univariable analysis. In the multivariable analysis, d7/preHD-sCr in combination with body weight and intra- and postoperative platelet transfusions predicted mortality after LuTx with similar performance as models using KDIGO-AKI and ADQI-AKI (concordance index of 0.75 for d7/preHD-sCr vs., 0.74 and 0.73, respectively). Pre-transplant reduced renal function, diabetes, higher BMI, and intraoperative ECMO predicted higher d7/preHD-sCr (r2 = 0.354, p < 0.001).

Conclusion

Our results confirm the importance of AKI in lung transplant patients; however, a simple and pragmatic indicator of renal function, d7/preHD-sCr, predicts long-term mortality equally reliable as more complex AKI-definitions like KDIGO and ADQI.
Clinical efficacy of Chinese herbs for supplementing qi and activating blood circulation combined with N-acetylcysteine in the treatment of idiopathic pulmonary fibrosis: A systematic review and network meta-analysis
Authors: Pang Qinglu , Li Guodong , Cao Fang , Liu Haoge , Wei Wan , Jiao Yang
Published: March 2022

Background

Chinese herbs for supplementing qi and activating blood circulation (CH) combined with N-acetylcysteine (NAC) is widely used for idiopathic pulmonary fibrosis (IPF) in China, but there is a lack of literature to evaluate its efficacy and clinical value.

Purpose

This study compared CH + NAC with other treatments by network meta-analysis to clarify its clinical value.

Methods

Cochrane Library, PubMed, Embase, Web of Science, China National Knowledge Infrastructure, WanFang Data, VIP Database, and China Biology Medicine were searched. Outcomes included lung function (DLCO (%), VC (%), FVC (%), FVC (L)), 6-min walking distance (6MWD), score of St George’s respiratory questionnaire (SGRQ), blood gas analysis (PaO2, PaCO2). The data were analyzed by Review Manager 5.4, Stata 12.0 and ADDIS 1.16.5.

Results

23 studies including 1390 patients (702 in intervention group and 688 in control group) were collected to compare 8 outcome indicators among different treatments involving CH, CH+NAC, CH+PFD, NAC, PFD and PFD+NAC on IPF. Network meta-analysis showed that CH was better than NAC in terms of DLCO (%) (MD = 5.14, 95%CI: 1.01 to 8.68) and 6MWD (MD = 49.17, 95%CI: 25.97 to 71.36) as well as PFD + NAC was better than NAC in terms of FVC (L) (MD = -0.56, 95%CI: -0.83 to -0.31). In rankings results, CH + NAC is the best in terms of FVC (%), SGRQ, PaO2 and PaCO2; CH is the best in terms of DLCO (%), VC (%) and 6MWD; CH + PFD is the best in terms of FVC (L).

Conclusion

CH related treatments may have advantages in the treatment of IPF and CH + NAC may have clinical application value. However, limited by the quality and quantity of researches included, more rational and scientific randomized controlled trials containing large sample sizes need to be conducted to further verify our conclusions.