bluuebunny/crossref_metadata_2025 huggingface dataset:
A scoping review protocol of evidence-based guidance and guidelines published by general practitioner professional organisations
Authors: O'Brien Emer , Clyne Barbara , Smith Susan M. , O'Herlihy Noirin , Harkins Velma , Wallace Emma
Published: February 2022

Introduction:General practitioners (GPs) strive to use a patient centered approach to achieve shared decision making by integrating clinical evidence, clinical judgement, and patient priorities. In order to achieve this standard of care, GPs require relevant, up to date and high quality evidence. Currently there is a gap in the literature regarding the role of GP professional organisations internationally in producing and publishing evidence based guidance and clinical guidelines for GPs. This protocol outlines a scoping review to identify what evidence-based guidance is produced by general practitioner professional organisations internationally in terms of topic content, the structure and methods used to develop guidance and ways of disseminating this guidance, to support general practice clinical decision making.

Methods:This scoping review will be conducted using the framework proposed by the Joanna Briggs Institute and the Preferred Reporting Items for Systematic Reviews and Meta-analysis extension for scoping reviews (PRISMA-ScR), will be used to guide the reporting. Two researchers will search electronic databases (Medline, Embase, Cochrane Library and Scopus), grey literature sources and contact international GP professional organisations directly to identify appropriate studies for inclusion. Key information will be categorised and classified to generate a summary of the methods used internationally to develop and implement evidence-based guides for general practitioners and a narrative synthesis will be conducted.

Conclusions:This scoping review will examine current practice internationally regarding the role of General Practice professional organisations in producing and publishing clinical guidelines and evidence based guidance to support general practitioner’s clinical decision making to benefit patient care.
Immunohistochemistry localises myosin-7a to cochlear efferent boutons
Authors: Sirko Piotr , Kozlov Andrei S.
Published: February 2022

Background: Myosin 7a is an actin-binding motor protein involved in the formation of hair-cell stereocilia both in the cochlea and in the vestibular system. Mutations in myosin 7a are linked to congenital hearing loss and are present in 50% of Type-1 Usher syndrome patients who suffer from progressive hearing loss and vestibular system dysfunction.

Methods: Myosin 7a is often used to visualise sensory hair cells due to its well characterised and localised expression profile. We thus conducted myosin-7a immunostaining across all three turns of the adult rat organ of Corti to visualise hair cells.

Results: As expected, we observed myosin 7a staining in both inner and outer hair cells. Unexpectedly, we also observed strong myosin 7a staining in the medial olivocochlear efferent synaptic boutons contacting the outer hair cells. Efferent bouton myosin-7a staining was present across all three turns of the cochlea. We verified this localisation by co-staining with a known efferent bouton marker, the vesicular acetylcholine transporter.

Conclusions: In addition to its role in stereocilia formation and maintenance, myosin 7a or certain myosin-7a expression variants might play a role in efferent synaptic transmission in the cochlea and thus ultimately influence cochlear gain regulation. Our immunohistochemistry results should be validated with other methods to confirm these serendipitous findings.
The genome sequence of the blue-tailed damselfly, Ischnura elegans (Vander Linden, 1820)
Authors: Price Benjamin W. , Winter Martin , Brooks Stephen J. ,   Natural History Museum Genome Acquisition Lab,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life programme,   Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: February 2022

We present a genome assembly from an individual female Ischnura elegans (the blue-tailed damselfly; Arthropoda; Insecta; Odonata; Coenagrionidae). The genome sequence is 1,723 megabases in span. The majority of the assembly (99.55%) is scaffolded into 14 chromosomal pseudomolecules, with the X sex chromosome assembled.
Kanonicy regularni od pokuty prowincji litewskiej na ziemiach byłego Wielkiego Księstwa Litewskiego w pierwszych latach po rozbiorach Rzeczypospolitej
Authors: Prašmantaitė Aldona
Published: February 2022

CANONS REGULAR OF PENANCE OF THE LITHUANIAN PROVINCE ON THE TERRITORY OF THE FORMER GRAND DUCHY OF LITHUANIA IN EARLY YEARS AFTER THE PARTITION OF POLISH LITHUANIAN COMMONWEALTH The history of Canons Regular of Penance (Ordo Canonicorum S. Mariae de Metro [or Demetri] de Urbe de Poenitentia Beatorum Martyrum) on the territory of the Grand Duchy of Lithuania began in the end of the 14th century. The king of Poland and Grand Duke of Lithuania Władysław Jagiełło brought Canons of Penance from Cracow to the just christened Lithuania and founded for them two monasteries in the parishes of the diocese of Vilnius. Over centuries, new communities of the convent arose in the Vilnius diocese with their number reaching almost twenty in certain periods. Towards the end of the 17th century, the new Lithuanian Province was established. Partitions of Polish-Lithuanian Commonwealth in the end of the 18th century caused serious transformations within the Catholic Church of the Grand Duchy of Lithuania, which affected Canons Regular, as well. The Vilnius diocese, where the communities of the Lithuanian Province stayed, found itself under power of the Russian Empire. Repressions against the Catholic Church led to cassation of the Canon’s convents of the Lithuanian Province after the November Uprising (1830-31). On the ground of the literature and sources related to the Canons Regular of Penance of the Lithuanian Province, the research concerning their history in the early years after partition has been undertaken. The analysis proved the initial hypothesis that in the early years after partition, Canons Regular of the Lithuanian Province were still vital. Nothing indicated that their end was coming. The rule of the convent strongly emphasized pastoral work. The majority of its members were priests, active in parishes as parish-priests or vicars. Even though the number of vocations started to decrease after the partitions – there were even years when nobody joined the community – the convent functioned successfully enough. According to the rule, the priority was given to pastoral work and all 15 convents had their own parishes in the said period. A typical representative of the convent during the early stage after partitions was middle-aged and ordained, usually a parish priest or his auxiliary in the parish belonging to the convent on a given territory. Usually, a monk appointed to a certain office would hold it for several terms. The presented research demonstrates that the convent of Canons Regular had a relatively big influence upon the spiritual life of the Vilnius diocese during the said period.
Juridinių asmenų nemokumo procesas: Monografija
Authors: Jokubauskas Remigijus
Published: February 2022

This book focuses on the issues related to effectiveness of corporate insolvency proceedings. In Lithuania the latest reform of corporate insolvency proceedings was implemented in 2019 following the adoption of the Law on Insolvency of Enterprises (thereinafter – LIE) which reformed restructuring and bankruptcy proceedings and replaced the Law on Bankruptcy proceedings of Enterprises (thereinafter – LBE) and the Law on Restructuring of Enterprises (thereinafter – LRE). Therefore, the legislator repealed two laws governing insolvency proceedings and established single insolvency proceedings for bankruptcy and restructuring. According to the regulation of insolvency proceedings established in Lithuania, only judicial methods of resolving insolvency disputes are recognized, since both restructuring and bankruptcy (except for the out-of-court bankruptcy of a company) cases are heard in the court. Also, the recent case law of Lithuanian courts shows that in insolvency disputes the courts shall ensure, by available means, efficiency of the proceedings and, in exceptional circumstances, intervene in matters falling within the competence of creditors.
A Convex Reformulation and an Outer Approximation for a Large Class of Binary Quadratic Programs
Authors: Rostami Borzou , Errico Fausto , Lodi Andrea
Published: February 2022

Binary Quadratic Program with Variable Partitioning Constraints

The binary quadratic program with variable partitioning constraints is a very general class of optimization problems that is very difficult to solve because of the nonconvexity and integrality of the variables and is ubiquitous, among others, in network design, computer vision, and transportation and logistics. In their article, “A convex reformulation and an outer approximation for a large class of binary quadratic programs,” Rostami et al. show how to transform such a nonconvex challenging problem into a convex bilinear program with decomposable structure. The authors develop a branch-and-cut algorithm based on outer approximation cuts, in which the cuts are generated on the fly by efficiently solving separation subproblems. The results of their computational experiments on different problems confirm the efficacy of the solution methods in solving large-scale problem instances.
Photon transport mediated by a trimer QED system with PT-symmetry
Authors: Li Haozhen , Zeng Ran , Zhou Xuefang , Hu Miao , Xia Xiuwen , Cheng Mu-Tian , Xu Jingping , Yang Yaping
Published: February 2022

The photon transport in a pair of parallel waveguides mediated by a parity-time- (PT-) symmetric trimer QED system is investigated. We demonstrate that the transport behaviors of the incident photons transferring between different waveguides can be actively controlled by the PT symmetry. The efficiency of such photon transport can be tuned to be much larger than 100% when the optical gain is introduced, and the transfer intensity is robust against the weak coupling among the atom, the cavity modes, their corresponding coupling mismatch, as well as the atomic dissipation. Furthermore, we demonstrate that when the system is excited by two input fields, the relative phase of the two input signals can serve as a sensitive control parameter for manipulating the photon transport, and controllable directional amplification of the incident signal photons with a fixed frequency can be realized by modulating the relative phase. The obtained results can be useful for designing phase-dependent active nonreciprocal devices, i.e., a phase-sensitive directional amplifier.
Widely tunable and switchable multiwavelength erbium-doped fiber laser based on a single ring cavity
Authors: Mirza Jawad , Ghafoor Salman , Atieh Ahmad , Kanwal Benish , Qureshi Khurram Karim
Published: February 2022

In this paper, we propose and demonstrate through numerical simulations a novel, to the best of our knowledge, widely tunable and switchable multiwavelength erbium-doped fiber laser (EDFL) operating in the 1524–1650 nm wavelength range covering the C-, L-, and U-bands. The EDFL is based on a single ring cavity and a single forward pump source operating at 980 nm wavelength. The length of the erbium-doped fiber and pumping configuration is optimized, enabling a wide tuning of 126 nm with an average lasing power of 15 dBm. Switchable multiple wavelengths are generated from the EDFL through an intracavity tunable optical filter (TOF) and a specially designed out-of-cavity comb filter (CF). Forty-nine wavelengths having average optical power and linewidth of around −10 dBm and 0.01 nm, respectively, are obtained at the output of the CF. Moreover, the free spectral range among the multiple wavelengths is adjusted easily by simply varying the frequency of sinusoidal radio frequency signal used to modulate the lasing signal obtained by tuning the intracavity TOF at a particular wavelength with the help of a dual-drive Mach–Zehnder modulator. The proposed EDFL is low cost, efficient, and highly stable with an average output power of around 15 dBm for 10% output coupling ratio over a 126 nm wide tuning range covering C-, L- and U-bands.
Two-color second-order sideband generation via magnon Kerr nonlinearity in a cavity magnonical system
Authors: Liu Yilou , Ling Li , Shui Tao , Ji Ning , Liu Shaopeng , Yang Wen-Xing
Published: February 2022

We investigate the enhanced generation of the optical second-order sideband (OSS) via magnon Kerr nonlinearity from a cavity magnonical hybrid system consisting of a single small yttrium iron garnet (YIG) crystal sphere and a three-dimensional (3D) rectangular cavity driven with a weak probe and a strong control field. Beyond the linear approximation, we solve the nonlinear Heisenberg–Langevin equations for achieving the analytical solutions by employing the perturbation technique. Using the experimentally achievable parameter settings, we demonstrate that the OSS generation can be significantly enhanced via increasing the magnon Kerr nonlinearity even if the coupling between the cavity and magnon is weak. Interestingly, two-color OSS generation can be observed when the cavity-magnon coupling is in the strong-coupling regime, which results from the magnonical polaritons induced by the hybrid of cavity and magnon modes. The present results illustrate the potential to utilize magnon Kerr nonlinearity for enhancing optical higher-order sidebands and controlling optical frequency combs, as well as to guide the design of experimental implementation.
High-order continuous-variable coherence of phase-dependent squeezed state
Authors: Guo Yanqiang , Zhang Haojie , Guo Xiaomin , Zhang Yuchi , Zhang Tiancai
Published: February 2022

We study continuous variable coherence of phase-dependent squeezed state based on an extended Hanbury Brown-Twiss scheme. High-order coherence is continuously varied by adjusting squeezing parameter r, displacement α, and squeezing phase θ. We also analyze effects of background noise γ and detection efficiency η on the measurements. As the squeezing phase shifts from 0 to π, the photon statistics of the squeezed state continuously change from the anti-bunching (g(n) < 1) to super-bunching (g(n) > n!) which shows a transition from particle nature to wave nature. The experiment feasibility is also examined. It provides a practical method to generate phase-dependent squeezed states with high-order continuous-variable coherence by tuning squeezing phase θ. The controllable coherence source can be applied to sensitivity improvement in gravitational wave detection and quantum imaging.
Efficient wavefront sensorless adaptive optics based on large dynamic crosstalk-free holographic modal wavefront sensing
Authors: Liu Ming , Dong Bing
Published: February 2022

The correction of wavefront sensorless adaptive optics (WFSless AO) can be significantly accelerated by using a holographic modal wavefront sensor (HMWFS). The HMWFS is realized by a computer-generated hologram (CGH) into which all aberration modes to be detected are encoded and only a single-shot image is required for simultaneous measurement of multiple modes. The conventional HMWFS suffers from a quite limited dynamic range and severe inter-modal crosstalk which deteriorates the sensing accuracy. We proposed a novel HMWFS with a large dynamic range and no crosstalk and validated its performance by simulation and experiment. In the improved HMWFS scheme, the aberration is represented by Lukosz modes whose gradients are orthogonal and the modal coefficients can be estimated independently. Instead of using a binary CGH in conventional HMWFS, a kinoform CGH with high diffraction efficiency is adopted in the improved HMWFS. The kinoform CGH is produced by a phase-only liquid-crystal spatial light modulator (LCSLM) which also serves as a wavefront corrector in our WFSless AO system.
Broadband second-harmonic generation in step-chirped periodically poled lithium niobate waveguides
Authors: Wu Xiao , Zhang Li , Hao Zhenzhong , Zhang Ru , Ma Rui , Bo Fang , Zhang Guoquan , Xu Jingjun
Published: February 2022

Periodically poled lithium niobate (PPLN) structures on a chip enable efficient second-order nonlinear optical effects, benefiting from the tight light confinement and the utilization of d33. Here, we report a broadband second-harmonic (SH) generation in a step-chirped PPLN waveguide on X-cut lithium niobate on insulator (LNOI). The high fidelity of the poling period is demonstrated over the whole length of 7 mm using a non-destructive technique of piezoresponse force microscopy. The SH signal was continuously observed in the step-chirped PPLN waveguides while scanning the wavelength of the pump laser from 1550 nm to 1660 nm. The SH conversion efficiency was measured to be 9.6 % W-1 cm-2 at 1642 nm. This work will benefit wavelength conversions of light sources with wideband spectra.
Transflective spatial terahertz wave modulator
Authors: Tao ShiNa , Shen ZhiXiong , Yu HongGuan , Wang HuaCai , Ge ShiJun , Hu Wei
Published: February 2022

Spatial light modulators can digitally manipulate the amplitude, phase, and polarization of light. Their counterparts in the terahertz band are highly pursued to meet the requirements of numerous applications such as wireless communications and biomedical detection. Here, we propose a spatial terahertz wave modulator based on a liquid-crystal-integrated metadevice. The modulator consists of 8 × 8 pixels. The liquid crystal layer is sandwiched between an asymmetric split ring resonator array and pixelated interdigital electrodes. Fano resonance occurs for the transmitted wave, while the reflected wave is perfectly absorbed. By separately driving the liquid crystal with pixelated interdigital electrodes, both the Fano resonance and absorption peak can be continuously tuned due to the variation in the environmental refractive index. This work provides a transflective spatial terahertz wave modulator that can dynamically reconfigure a terahertz wavefront.
Photoacoustic computational ghost imaging
Authors: Torke Paul R. , Nuster Robert , Paltauf Guenther
Published: February 2022

Photoacoustic imaging with optical resolution usually requires a single-pixel raster scan. An alternative approach based on illumination with patterns obtained from a Hadamard matrix, measurement of the generated ultrasound wave with a single detector, followed by a reconstruction known from computational ghost imaging is demonstrated here. Since many pixels on the object are illuminated at the same time, thereby contributing to the recorded signal, this approach gives a better contrast-to-noise ratio compared to the raster scan, as demonstrated in a phantom experiment. Furthermore, exploiting the temporal information for depth-resolved imaging is possible. The proposed method will be beneficial in situations where the radiant exposure of a sample is limited due to either safety precautions or the properties of the available light source.
Integrated room temperature single-photon source for quantum key distribution
Authors: Zeng Helen Zhi Jie , Ngyuen Minh Anh Phan , Ai Xiaoyu , Bennet Adam , Solntsev Alexander S. , Laucht Arne , Al-Juboori Ali , Toth Milos , Mildren Richard P. , Malaney Robert , Aharonovich Igor
Published: February 2022

High-purity single-photon sources (SPS) that can operate at room
temperature are highly desirable for a myriad of applications,
including quantum photonics and quantum key distribution. In this
work, we realize an ultra-bright solid-state SPS based on an atomic
defect in hexagonal boron nitride (hBN) integrated with a solid
immersion lens (SIL). The SIL increases the source efficiency by a
factor of six, and the integrated system is capable of producing over
ten million single photons per second at room temperature. Our results
are promising for practical applications of SPS in quantum
communication protocols.
Reducing the noise of fiber supercontinuum sources to its limits by exploiting cascaded soliton and wave breaking nonlinear dynamics
Authors: Sierro Benoît , Hänzi Pascal , Spangenberg Dirk , Rampur Anupamaa , Heidt Alexander M.
Published: February 2022

The low-noise and phase-coherent nonlinear transformation of a narrowband laser into a broadband supercontinuum (SC) in an optical fiber forms the basis of extremely precise applications ranging from optical frequency comb technology to ultrafast photonics and biomedical imaging. A major challenge of this process is the avoidance of incoherent nonlinear effects that amplify random quantum noise, requiring careful birefringence and dispersion engineering of the fiber. However, fundamental trade-offs exist between working in normal or anomalous dispersion regimes. Here, we combine the benefits of nonlinear dynamics in both regimes by cascading soliton compression and optical wave breaking in a hybrid fiber, formed by joining two widely available, commercial, polarization-maintaining step-index fibers exhibiting anomalous and all-normal dispersion, respectively. We experimentally demonstrate that this hybrid approach results in an ultra-low-noise fiber SC source covering the 930–2130 nm range with phase coherence near unity, spectrally resolved relative intensity noise (RIN) as low as 0.05%, and averaging 0.1% over a bandwidth of 750 nm, approaching the theoretical limits close to the pump laser noise. This corresponds to a doubling of the generated spectral bandwidth and a decrease of RIN by up to 1 order of magnitude compared to direct pumping of the individual fibers, where modulational polarization instabilities play a limiting role. Owing to its simplicity and its scalability to high repetition rates, our hybrid scheme is readily applicable to various laser platforms and could enhance the performance of applications such as hyperspectral nonlinear microscopy, coherent optical communications, and photonic signal processing.
A DNA replication-independent function of pre-replication complex genes during cell invasion in C. elegans
Authors: Lattmann Evelyn , Deng Ting , Walser Michael , Widmer Patrizia , Rexha-Lambert Charlotte , Prasad Vibhu , Eichhoff Ossia , Daube Michael , Dummer Reinhard , Levesque Mitchell P. , Hajnal Alex
Published: February 2022

Cell invasion is an initiating event during tumor cell metastasis and an essential process during development. A screen ofC.elegansorthologs of genes overexpressed in invasive human melanoma cells has identified several components of the conserved DNA pre-replication complex (pre-RC) as positive regulators of anchor cell (AC) invasion. The pre-RC genes function cell-autonomously in the G1-arrested AC to promote invasion, independently of their role in licensing DNA replication origins in proliferating cells. While the helicase activity of the pre-RC is necessary for AC invasion, the downstream acting DNA replication initiation factors are not required. The pre-RC promotes the invasive fate by regulating the expression of extracellular matrix genes and components of the PI3K signaling pathway. Increasing PI3K pathway activity partially suppressed the AC invasion defects caused by pre-RC depletion, suggesting that the PI3K pathway is one critical pre-RC target. We propose that the pre-RC, or a part of it, acts in the postmitotic AC as a transcriptional regulator that facilitates the switch to an invasive phenotype.
LRRK2 dynamics analysis identifies allosteric control of the crosstalk between its catalytic domains
Authors: Weng Jui-Hung , Aoto Phillip C. , Lorenz Robin , Wu Jian , Schmidt Sven H. , Manschwetus Jascha T. , Kaila-Sharma Pallavi , Silletti Steve , Mathea Sebastian , Chatterjee Deep , Knapp Stefan , Herberg Friedrich W. , Taylor Susan S.
Published: February 2022

The 2 major molecular switches in biology, kinases and GTPases, are both contained in the Parkinson disease–related leucine-rich repeat kinase 2 (LRRK2). Using hydrogen–deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations, we generated a comprehensive dynamic allosteric portrait of the C-terminal domains of LRRK2 (LRRK2RCKW). We identified 2 helices that shield the kinase domain and regulate LRRK2 conformation and function. One helix in COR-B (COR-B Helix) tethers the COR-B domain to the αC helix of the kinase domain and faces its activation loop, while the C-terminal helix (Ct-Helix) extends from the WD40 domain and interacts with both kinase lobes. The Ct-Helix and the N-terminus of the COR-B Helix create a “cap” that regulates the N-lobe of the kinase domain. Our analyses reveal allosteric sites for pharmacological intervention and confirm the kinase domain as the central hub for conformational control.
RecPD: A Recombination-aware measure of phylogenetic diversity
Authors: Bundalovic-Torma Cedoljub , Desveaux Darrell , Guttman David S.
Published: February 2022

A critical step in studying biological features (e.g., genetic variants, gene families, metabolic capabilities, or taxa) is assessing their diversity and distribution among a sample of individuals. Accurate assessments of these patterns are essential for linking features to traits or outcomes of interest and understanding their functional impact. Consequently, it is of crucial importance that the measures employed for quantifying feature diversity can perform robustly under any evolutionary scenario. However, the standard measures used for quantifying and comparing the distribution of features, such as prevalence, phylogenetic diversity, and related approaches, either do not take into consideration evolutionary history, or assume strictly vertical patterns of inheritance. Consequently, these approaches cannot accurately assess diversity for features that have undergone recombination or horizontal transfer. To address this issue, we have devised RecPD, a novel recombination-aware phylogenetic-diversity statistic for measuring the distribution and diversity of features under all evolutionary scenarios. RecPD utilizes ancestral-state reconstruction to map the presence / absence of features onto ancestral nodes in a species tree, and then identifies potential recombination events in the evolutionary history of the feature. We also derive several related measures from RecPD that can be used to assess and quantify evolutionary dynamics and correlation of feature evolutionary histories. We used simulation studies to show that RecPD reliably reconstructs feature evolutionary histories under diverse recombination and loss scenarios. We then applied RecPD in two diverse real-world scenarios including a preliminary study type III effector protein families secreted by the plant pathogenic bacterium Pseudomonas syringae and growth phenotypes of the Pseudomonas genus and demonstrate that prevalence is an inadequate measure that obscures the potential impact of recombination. We believe RecPD will have broad utility for revealing and quantifying complex evolutionary processes for features at any biological level.
Targeting EDEM protects against ER stress and improves development and survival in C. elegans
Authors: Ghenea Simona , Chiritoiu Marioara , Tacutu Robi , Miranda-Vizuete Antonio , Petrescu Stefana Maria
Published: February 2022

EDEM-1, EDEM-2 and EDEM-3 are key players for the quality control of newly synthesized proteins in the endoplasmic reticulum (ER) by accelerating disposal and degradation of misfolded proteins through ER Associated Degradation (ERAD). Although many previous studies reported the role of individual ERAD components especially in cell-based systems, still little is known about the consequences of ERAD dysfunction under physiological and ER stress conditions in the context of a multicellular organism. Here we report the first individual and combined characterization and functional interplay of EDEM proteins in Caenorhabditis elegans using single, double, and triple mutant combinations. We found that EDEM-2 has a major role in the clearance of misfolded proteins from ER under physiological conditions, whereas EDEM-1 and EDEM-3 roles become prominent under acute ER stress. In contrast to SEL-1 loss, the loss of EDEMs in an intact organism induces only a modest ER stress under physiological conditions. In addition, chronic impairment of EDEM functioning attenuated both XBP-1 activation and up-regulation of the stress chaperone GRP78/BiP, in response to acute ER stress. We also show that pre-conditioning to EDEM loss in acute ER stress restores ER homeostasis and promotes survival by activating ER hormesis. We propose a novel role for EDEM in fine-tuning the ER stress responsiveness that affects ER homeostasis and survival.
From viability to cell death: Claims with insufficient evidence in high-impact cell culture studies
Authors: Özkaya Ali Burak , Geyik Caner
Published: February 2022

Background

Reliability of preclinical research is of critical concern. Prior studies have demonstrated the low reproducibility of research results and recommend implementing higher standards to improve overall quality and robustness of research. One understudied aspect of this quality issue is the harmony between the research hypotheses and the experimental design in published work.

Methods and findings

In this study we focused on highly cited cell culture studies and investigated whether commonly asserted cell culture claims such as viability, cytotoxicity, proliferation rate, cell death and apoptosis are backed with sufficient experimental evidence or not. We created an open access database containing 280 claims asserted by 103 different high-impact articles as well as the results of this study. Our findings revealed that only 64% of all claims were sufficiently supported by evidence and there were concerning misinterpretations such as considering the results of tetrazolium salt reduction assays as indicators of cell death or apoptosis.

Conclusions

Our analysis revealed a discordance between experimental findings and the way they were presented and discussed in the manuscripts. To improve quality of pre-clinical research, we require clear nomenclature by which different cell culture claims are distinctively categorized; materials and methods sections to be written more meticulously; and cell culture methods to be selected and utilized more carefully. In this paper we recommend a nomenclature for selected cell culture claims as well as a methodology for collecting evidence to support those claims.
Using mass spectrometry to investigate fluorescent compounds in squirrel fur
Authors: Hughes Bryan , Bowman Jeff , Stock Naomi L. , Burness Gary
Published: February 2022

While an array of taxa are capable of producing fluorescent pigments, fluorescence in mammals is a novel and poorly understood phenomenon. A first step towards understanding the potential adaptive functions of fluorescence in mammals is to develop an understanding of fluorescent compounds, or fluorophores, that are present in fluorescent tissue. Here we use Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) of flying squirrel fur known to fluoresce under ultraviolet (UV) light to identify potentially fluorescent compounds in squirrel fur. All of the potentially fluorescent compounds we identified were either present in non-fluorescent fur or were not present in all species of fluorescent flying squirrel. Therefore, we suggest that the compounds responsible for fluorescence in flying squirrels may also be present in non-fluorescent mammal fur. Some currently unexplained factor likely leads to excitation of fluorophores in flying squirrel fur. A recently suggested hypothesis that fluorescence in mammals is widely caused by porphyrins is consistent with our findings.
Relationships between the hard and soft dimensions of the nose in Pan troglodytes and Homo sapiens reveal the positions of the nasal tips of Plio-Pleistocene hominids
Authors: Campbell Ryan M. , Vinas Gabriel , Henneberg Maciej
Published: February 2022

By identifying homogeneity in bone and soft tissue covariation patterns in living hominids, it is possible to produce facial approximation methods with interspecies compatibility. These methods may be useful for producing facial approximations of fossil hominids that are more realistic than currently possible. In this study, we conducted an interspecific comparison of the nasomaxillary region in chimpanzees and modern humans with the aim of producing a method for predicting the positions of the nasal tips of Plio-Pleistocene hominids. We addressed this aim by first collecting and performing regression analyses of linear and angular measurements of nasal cavity length and inclination in modern humans (Homo sapiens;n= 72) and chimpanzees (Pan troglodytes;n= 19), and then performing a set of out-of-group tests. The first test was performed on four subjects that belonged to the same genus as the training sample, i.e.,Homo(n= 2) andPan(n= 2), and the second test, which functioned as an interspecies compatibility test, was performed onPan paniscus(n= 1),Gorilla gorilla(n= 3),Pongo pygmaeus(n= 1),Pongo abelli(n= 1),Symphalangus syndactylus(n= 3), andPapio hamadryas(n= 3). We identified statistically significant correlations in both humans and chimpanzees with slopes that displayed homogeneity of covariation. Prediction formulae combining these data were found to be compatible with humans and chimpanzees as well as all other African great apes, i.e., bonobos and gorillas. The main conclusion that can be drawn from this study is that our set of regression models for approximating the position of the nasal tip are homogenous among humans and African apes, and can thus be reasonably extended to ancestors leading to these clades.
Manifestations, responses, and consequences of mistreatment of sick newborns and young infants and their parents in health facilities in Kenya
Authors: Abuya Timothy , Warren Charlotte E. , Ndwiga Charity , Okondo Chantalle , Sacks Emma , Sripad Pooja
Published: February 2022

Background

Despite efforts to incorporate experience of care for women and newborns in global quality standards, there are limited efforts to understand experience of care for sick newborns and young infants. This paper describes the manifestations, responses, and consequences of mistreatment of sick young infants (SYIs), drivers, and parental responses in hospital settings in Kenya.

Methods

A qualitative formative study to inform the development of strategies for promoting family engagement and respectful care of SYI was conducted in five facilities in Kenya. Data were collected from in-depth interviews with providers and policy makers (n = 35) and parents (n = 25), focus group discussions with women and men (n = 12 groups), and ethnographic observations in each hospital (n = 64 observation sessions). Transcribed data were organized using Nvivo 12 software and analyzed thematically.

Results

We identified 5 categories of mistreatment: 1) health system conditions and constraints, including a) failure to meet professional standards, b) delayed provision of care; and c) limited provider skills; 2) stigma and discrimination, due to provider perception of personal hygiene or medical condition, and patient feelings of abandonment; 3) physically inappropriate care, including providers taking blood samples and inserting intravenous lines and nasogastric tubes in a rough manner; or parents being pressured to forcefully feed infants or share unsterile feeding cups to avoid providers’ anger; 4) poor parental-provider rapport, expressed as ineffective communication, verbal abuse, perceived disinterest, and non-consented care; and 5) no organized form of bereavement and posthumous care in the case of infant’s death. Parental responses to mistreatment were acquiescent or non-confrontational and included feeling humiliated or accepting the situation. Assertive responses were rare but included articulating disappointment by expressing anger, and/or deciding to seek care elsewhere.

Conclusion

Mistreatment for SYIs is linked to poor quality of care. To address mistreatment in SYI, interventions that focus on building better communication, responding to the developmental needs of infants and emotional needs for parents, strengthen providers competencies in newborn care, as well as a supportive, enabling environments, will lead to more respectful quality care for newborns and young infants.
Hydraulic mechanisms of the uneven enrichment of soil organic carbon in sediments during rain-induced overland flow
Authors: Liu Lin , Li Zhongwu , Jiao Panpan
Published: February 2022

Organic carbon (OC) can be unevenly enriched in different-sized sediment particles under low-intensity, rain-induced overland flows, but its hydraulic mechanisms are not completely understood. Hence, in this study, the hydraulic transport mechanisms of unevenly enriched OC between different-sized sediment particles were investigated through simulated rainfall experiments at gradients of 5°, 10°, and 15° and typical regional rainfall intensities of 45, 90, and 120 mm h−1. Results showed that the critical flow velocity of aggregate transport through loess soil was approximately 0.08 m s−1. When the flow velocity was larger than this critical value, the aggregate loss amount increased quickly and exponentially. Flow velocities lower than 0.08 m s−1were determined to be essential conditions for uneven OC enrichment between sediment particles. At such velocities, even when the runoff depth was greater than 0.0018 m, the enrichment ratio of soil organic carbon (SOC;ERoc) values in all size classes of sediment particles was larger than 1.0. Small runoff depths caused preferential OC enrichment in silt and clay, whereas large runoff depths promoted OC enrichment in the >0.25 mm size class of sediment particles. The critical flow velocity and transport way differ between these high-OC-concentration clay and silt and large light organic particles. The interaction between flow velocity and runoff depth onERocsin <0.05 mm particles was larger than that of >0.05 mm particles. Under the transport limit erosion, the flow velocity and stream power positively correlated with unevenERocsin different size sediment particles through distinct laws. Slope and rainfall intensity could not be ignored in predicting uneven OC enrichment in sediments by interacting with hydraulic factor and effecting aggregate stripping, respectively. Hydraulic factors mainly affected the uneven OC enrichment by controlling particle selective detachment and transport process. Owing to the different hydraulic mechanisms of OC enrichment in different size particles, the obtained regression functions for uneven OC enrichment could be divided into two types. One was for calculating the OC concentrations in sediment particles with sizes of <2 mm (R2> 0.844,P< 0.005), and the other was for calculating the OC concentrations in large macroaggregates (>2 mm;R2= 0.805,P< 0.005). The findings provide an important reference for understanding SOC transport mechanisms and its mineralization potential under the effect of water erosion and improving SOC dynamic models.
Body fat prediction through feature extraction based on anthropometric and laboratory measurements
Authors: Fan Zongwen , Chiong Raymond , Hu Zhongyi , Keivanian Farshid , Chiong Fabian
Published: February 2022

Obesity, associated with having excess body fat, is a critical public health problem that can cause serious diseases. Although a range of techniques for body fat estimation have been developed to assess obesity, these typically involve high-cost tests requiring special equipment. Thus, the accurate prediction of body fat percentage based on easily accessed body measurements is important for assessing obesity and its related diseases. By considering the characteristics of different features (e.g. body measurements), this study investigates the effectiveness of feature extraction for body fat prediction. It evaluates the performance of three feature extraction approaches by comparing four well-known prediction models. Experimental results based on two real-world body fat datasets show that the prediction models perform better on incorporating feature extraction for body fat prediction, in terms of the mean absolute error, standard deviation, root mean square error and robustness. These results confirm that feature extraction is an effective pre-processing step for predicting body fat. In addition, statistical analysis confirms that feature extraction significantly improves the performance of prediction methods. Moreover, the increase in the number of extracted features results in further, albeit slight, improvements to the prediction models. The findings of this study provide a baseline for future research in related areas.
Personal attributes and attitudes to substance use disorder: A study among Jordanian undergraduate medical majors students
Authors: Abuhammad Sawsan , Hatamleh Reem , Alrawashdeh Mohammad , Alrabadi Nasr , Mukattash Tareq , Abuhammad Mai , Howard Kimberly
Published: February 2022

Background

Emerging health professionals in undergraduate programs should be equipped to provide care to people with substance use disorder (SUD). The students’ personal attributes may impact their attitude toward those with SUD. This study aims to evaluate the impact of personal attributes of Jordanian undergraduate health students on their attitudes toward SUD and examine the relationship between the personal attributes and their devaluation and discriminatory (stigmatory) behaviour toward those with SUD.

Method

A cross-sectional descriptive design was used to examine the attitudes and stigmatory behaviours. The data were collected between May to October 2017 with a structured questionnaire that consisted of three parts: 1) a data sheet to collect the socio-demographic characteristics of the participants, 2) the Acute Mental Health Scale (ATAMHS), and 3) the Devaluation-Discrimination Scale (DDS).

Findings

Younger and females demonstrated a positive attitude toward those with SUD compared to older or male students. Age, gender, and previous experience with SUD are significant factors that affect their attitude.

Conclusion

Identifying the attitude to people with SUD and personal attributes of emerging health professionals in Jordan will help identify the need to educate them prior to their entry into practice.
Household decision-making and the mental well-being of marriage-based immigrant women in South Korea
Authors: Lee Eunji , Kim Soo In , Jung-Choi Kyunghee , Kong Kyoung Ae
Published: February 2022

Objective

We assessed the association between household decision-making and mental well-being among Asian immigrant women residing in Korea. We also investigated if the impact varies by the regional origin and examined potential factors for joint decision-making.

Methods

We conducted a cross-sectional study using the Korean National Survey of Multicultural Families 2015 and logistic regression. We analyzed data from 11,188 married immigrant women ages 20 to 59 who were originally from East Asia or Southeast/South Asia and co-living with their spouses. We defined households as joint-decision, wife-decision, or husband-decision based on who decides how living expenses are spent. Mental well-being encompassed a depressive mood for two consecutive weeks, and life and marital satisfaction.

Results

After controlling for covariates, we showed that immigrant women in husband-decision households were more likely to have depressive mood (odds ratio [OR] 1.26, 95% confidence interval [CI]: 1.14–1.38), poorer life satisfaction (OR 1.49, 95% CI: 1.24–1.78), and poorer marital satisfaction (OR 1.81, 95% CI: 1.47–2.22) than women in joint-decision households. Immigrant women in wife-decision households had a similar but slightly lower odds of poor mental well-being. This association was less prominent for Southeast/South Asian origin than East Asian origin, while the age-adjusted prevalence rates of poor mental well-being among them were higher than their East Asian counterparts. Factors that restricted the odds of husband-decision did not necessarily guarantee wife-decision.

Conclusions

This study suggests one-sided decision-making can be a risk factor for immigrant women’s poor mental well-being, while joint decision-making is protective. Differences across regional origins suggest domestic decision-making might be a less important predictor for mental well-being in immigrants more occupied with adapting to the host society. Factors for joint decision-making should be addressed to improve the mental well-being of immigrant women.
Determinants of acceptance of Coronavirus disease-2019 (COVID-19) vaccine among Lebanese health care workers using health belief model
Authors: Youssef Dalal , Abou-Abbas Linda , Berry Atika , Youssef Janet , Hassan Hamad
Published: February 2022

Since Health care workers (HCWs) are at high occupational risk for COVID-19, they are prioritized for immunization. This study aimed to assess the acceptance rate of the COVID-19 vaccine among HCWs and to identify its determinants. A web-based cross-sectional study was conducted between10 and 31 December 2020 among Lebanese HCWs. The Health Belief Model (HBM) was used as a theoretical framework. Multivariable logistic analyses were carried out to identify the factors associated with the acceptance of the COVID-19 vaccine among HCWs. A total of 1800 HCWs have completed the survey. Around half (58.10%) of them were frontline HCWs and aged between (30–49) years old. Over two-thirds (67.33%) of the participants have received the seasonal influenza vaccine. The acceptance rate of the COVID-19 vaccine among surveyed HCWs was 58%. HCWs who were male (aOR = 1.99, 95% CI (1.41–2.80)), working in the frontlines (aOR = 1.61, 95% CI (1.17–2.21), and those who have received influenza vaccination for the current year (aOR = 1.38, 95% CI(0.99–1.92)) were more willing to get the COVID-19 vaccine. However, factors such as living in rural areas (aOR = 0.61, 95% CI (0.44–0.84)), and being previously diagnosed with COVID-19 (aOR = 0.66, 95%CI (0.45–0.96) were found negatively associated with vaccine acceptance. In terms of health beliefs items, concerns related to the novelty of vaccine (aOR = 0.42, 95% CI (0.25–0.71)), side effects/vaccine safety (aOR = 0.41, 95% CI (0.23–0.73), reliability of manufacturer (aOR = 0.43, 95% CI (0.30–0.63)), and the number of required doses (aOR = 0.58, 95% CI (0.40–0.84)) were also negatively associated with the willingness to get vaccinated against COVID-19. Remarkably, concerns such as the limited accessibility (aOR = 1.68, 95% CI (1.14–2.47)), and availability of vaccines (aOR = 2.16, 95% CI (1.46–3.20)) were associated with an increased likelihood of willingness to receive the COVID-19 vaccine. With regards to cues of action, receiving reliable and adequate information about the vaccine (aOR = 1.98, 95% CI (1.36–2.88)), recommendation by health authorities (aOR = 1.93, 95% CI(1.33–2.81)), and recommendations from health facilities (aOR = 2.68, 95% CI(1.80–3.99)) were also positively associated with vaccine acceptance. Lastly, perception of COVID-19 vaccine benefits by HCWs in terms of protecting them and their close contacts (patients, family members, and friends) from COVID-19 infection (aOR = 4.21, 95% CI (2.78–7.11)) was associated with an increased likelihood of vaccine uptake. The moderate acceptance rate of the COVID-19 vaccine among HCWs found in our study could have broader extents. Understanding and pointing out factors impairing vaccine acceptance such as concerns about the novelty of vaccine and manufacturers’ reliability are required to reach a higher vaccination rate.