bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection of the high efficient sgRNA for CRISPR-Cas9 to edit herbicide related genes, PDS, ALS, and EPSPS in tomato
Authors: Yang So Hee , Kim Euyeon , Park Hyosun , Koo Yeonjong 
Published: February 2022

AbstractHerbicide resistance is one of the main crop traits that improve farming methods and crop productivity. CRISPR-Cas9 can be applied to the development of herbicide-resistant crops based on a target site resistance mechanism, by editing genes encoding herbicide binding proteins. The sgRNAs capable of editing the target genes of herbicides, pds (phytoene desaturase), ALS (acetolactate synthase), and EPSPS (5-Enolpyruvylshikimate-3-phosphate synthase), were designed to use with the CRISPR-Cas9 system in tomato (Solanum lycopersicum cv. Micro-Tom). The efficiency of the sgRNAs was tested using Agrobacterium mediated transient expression in the tomato cotyledons. One sgRNA designed for editing the target site of PDS had no significant editing efficiency. However, three different sgRNAs designed for editing the target site of ALS had significant efficiency, and one of them, ALS2-P sgRNA, showed over 0.8% average efficiency in the cotyledon genome. The maximum efficiency of ALS2-P sgRNA was around 1.3%. An sgRNA for editing the target site of EPSPS had around 0.4% editing efficiency on average. The sgRNA efficiency testing provided confidence that editing of the target sites could be achieved in the transformation process. We confirmed that 19 independent transgenic tomatoes were successfully edited by ALS2_P or ALS1_W sgRNAs and two of them had three base deletion mutations, which are expected to have altered herbicide resistance. In this study, we demonstrated the usefulness of performing an sgRNA efficiency test before crop transformation, and confirmed that the CRISPR-Cas9 system is a valuable tool for breeding herbicide-resistant crops.
Charcoal or black stone? Reconstructions as a tool to study the behaviour of dry underdrawing materials within the paint structure of sixteenth century panel paintings
Authors: Melo H. P. , Valadas Sara , Cruz António João , Candeias António 
Published: February 2022

Abstract
Reconstructions were used as a tool to investigate the use of charcoal and black stone as underdrawing materials in sixteenth century panel paintings with white or off-white preparatory layers. Research was based on the examination of a group of sixteenth century panel paintings by the Portuguese Mannerist painter Francisco João (doc. 1558–1595) and his workshop. Analysis of the original underdrawing material in cross-sections, using microscopic and spectroscopic techniques was not always conclusive. Based on materials thought to be employed by Francisco João and on data collected from sixteenth and seventeenth century European technical treatises along with published analytical studies of panel paintings with white or off-white preparatory layers from this period, reconstructions were performed using charcoal (untreated and oiled—as described in contemporary literature) and natural black stone over different preparatory surfaces. Microscopic analyses of cross-sections from reconstructions were made to assist the discussion of the behaviour of the dry underdrawing media within the paint structure. Results revealed that whereas charcoal could be easily removed if drawn directly over gesso, it would remain fixed when drawn over a ground treated with an oil-based intermediate layer, even when the latter was completely dry to the touch. The persistence of a charcoal drawing when applied over oil challenged the widely disseminated assumption that naturally occurring black stone, which makes a permanent mark, had been employed more frequently than charcoal since the latter appeared to be easily disturbed and hence transitory. The very lengthy curing time for a drying oil could be responsible for fixing the friable media. Reconstructions further showed that oiled charcoal is easily prepared and agreeable to use on any type of surface, where it remains without smudging. Finally, research suggests that the painter’s choice of underdrawing material is closely dependent on the nature of the binder of intermediate layers and on the position of the underdrawing layout within the paint structure.
Data agreement analysis and correction of comparative geomagnetic vector observations
Authors: He Zhaobo , Hu Xingxing , Teng Yuntian , Zhang Xiuxia , Shen Xiaoyu 
Published: February 2022

AbstractGeomagnetism, similar to other areas of geophysics, is an observation-based science. Data agreement between comparative geomagnetic vector observations is one of the most important evaluation criteria for high-quality geomagnetic data. The main influencing factors affecting the agreement between comparative observational data are the attitude angle, scale factor, long-term time drift, and temperature. In this paper, we propose a method based on a genetic algorithm and linear regression to correct for these effects and use the distribution pattern of points in Bland–Altman plots with a 95% confidence interval length to qualitatively and quantitatively evaluate the agreement between the comparative observational data. In Bland–Altman plots with better agreement, that is, with the corrected data, more than 95% of the points are distributed within the 95% confidence interval and there is no obvious pattern in the distribution of the points. Meanwhile, the length of 95% confidence interval decreased significantly after the correction. The method presented here has positive effects on the vector instrumentation detection and would enhance the robustness of geomagnetic observatory by bringing the data quality of the backup variometer data in line with the primary variometer.
Graphical Abstract
Seismic reflection imaging of deep crustal structures via reverse time migration using offshore wide-angle seismic data on the eastern margin of the Sea of Japan
Authors: Shiraishi Kazuya , No Tetsuo , Fujie Gou 
Published: February 2022

AbstractWe applied reverse time migration (RTM) to offshore wide-angle seismic data acquired with airgun shots and sparsely deployed ocean bottom seismographs (OBSs) for reflection imaging of the Moho discontinuity in the eastern margin of the Sea of Japan. While seismic tomography is generally applied to wide-angle seismic data for estimating regional velocity, reflection imaging is uncommon due to the low folds from wide-spacing OBS deployment. The long offset reflection data obtained by airgun-OBS surveys are promising for profiling deep crustal structures, which may be able to add constraints on the velocity structures estimated by tomographic inversion. Furthermore, reflection imaging from wide-angle seismic data is useful when only airgun-OBS data are acquired without any MCS data due to weather conditions or restrictions of using streamer cables. In this study, we validated the feasibility of RTM, which is an effective reflection imaging method based on wavefield modelling with the two-way wave equation, using offshore wide-angle seismic data acquired along two crossing survey lines off Niigata–Yamagata. Airgun shot intervals were 200 m in both surveys, and the OBS spacings were 5 km along a 297-km-long line and 8 km or 16 km along a 366-km-long line, except for OBSs near the coast. By applying RTM with velocity models estimated by traveltime tomography of the same OBS data, we successfully imaged clear reflections around depths of 20–30 km. We confirmed that reflections observed in the long offset range were effective in imaging the deep structures that were not imaged by the MCS survey in this region. The depths of reflectors were traced from approximately 20 km in the offshore area to approximately 30 km near the coast, which corresponds to the Moho discontinuity. The depth variation is consistent with the crustal classification that was inferred based on tomography analyses: thick oceanic crust in the Yamato Basin and rifted continental or island arc crust beneath the areas from the Sado Ridge to the coast. Our results from two surveys with different OBS spacings suggested the high potential of the application to a wide variety of wide-angle seismic data for crustal-scale seismic exploration.
Graphic Abstract
High levels of monocytic myeloid-derived suppressor cells are associated with favorable outcome in patients with pneumonia and sepsis with multi-organ failure
Authors: Schrijver Irene T. , Karakike Eleni , Théroude Charlotte , Baumgartner Pétra , Harari Alexandre , Giamarellos-Bourboulis Evangelos J. , Calandra Thierry , Roger Thierry 
Published: February 2022

Abstract
Background
Myeloid-derived suppressor cells (MDSCs) are immature myeloid cells with immunosuppressive functions sub-classified into monocytic and polymorphonuclear MDSCs (M-MDSCs and PMN-MDSCs). Clinical studies reported increased levels of MDSCs that were associated with poor outcome in sepsis patients. Since sepsis patients exhibit signs of inflammation and immunosuppression, MDSCs may provide benefit by dampening deleterious inflammation in some patients. To test this hypothesis, we measured MDSCs in critically ill sepsis patients with pneumonia and multi-organ dysfunctions and a high likelihood of death.

Methods
This was a prospective multicenter observational cohort study performed in eight ICUs in Athens and Thessaloniki, Greece, enrolling critically ill patients with pneumonia and sepsis with multi-organ dysfunctions. A flow cytometry approach using blood collected at study inclusion in tubes containing lyophilized antibodies combined to unsupervised clustering was developed to quantify M-MDSCs and PMN-MDSCs.

Results
Forty-eight patients were included, of whom 34 died within 90 days. At study inclusion, M-MDSCs and PMN-MDSCs were increased in sepsis patients when compared to healthy subjects (3.07% vs 0.96% and 22% vs 2.1% of leukocytes, respectively; p < 10–4). Increased PMN-MDSCs were associated with secondary infections (p = 0.024) and new sepsis episodes (p = 0.036). M-MDSCs were more abundant in survivors than in patients who died within 28 days (p = 0.028). Stratification of patients according to M-MDSC levels revealed that high levels of M-MDSC were associated with reduced 90-day mortality (high vs low M-MDSCs: 47% vs 84% mortality, p = 0.003, hazard ratio [HR] = 3.2, 95% CI 1.4–7.2). Combining high M-MDSC levels with low Acute Physiology and Chronic Health Evaluation (APACHE) II score improved patient stratification (M-MDSCshigh/APACHE IIlow vs M-MDSCslow/APACHE IIlow: 20% vs 80% 90-day mortality, p = 0.0096, HR = 7.2, 95% CI 1.6–32). In multivariate analyses high M-MDSCs remained correlated with improved survival in patients with low APACHE II score (p = 0.05, HR = 5.26, 95% CI 1.0–27.8).

Conclusion
This is the first study to associate high levels of M-MDSCs with improved survival in sepsis patients.
Wave-shaped microfluidic chip assisted point-of-care testing for accurate and rapid diagnosis of infections
Authors: Yin Bin-Feng , Wan Xin-Hua , Yang Ming-Zhu , Qian Chang-Cheng , Sohan A. S. M. Muhtasim Fuad 
Published: February 2022

Abstract
Background
Early diagnosis and classification of infections increase the cure rate while decreasing complications, which is significant for severe infections, especially for war surgery. However, traditional methods rely on laborious operations and bulky devices. On the other hand, point-of-care (POC) methods suffer from limited robustness and accuracy. Therefore, it is of urgent demand to develop POC devices for rapid and accurate diagnosis of infections to fulfill on-site militarized requirements.

Methods
We developed a wave-shaped microfluidic chip (WMC) assisted multiplexed detection platform (WMC-MDP). WMC-MDP reduces detection time and improves repeatability through premixing of the samples and reaction of the reagents. We further combined the detection platform with the streptavidin–biotin (SA-B) amplified system to enhance the sensitivity while using chemiluminescence (CL) intensity as signal readout. We realized simultaneous detection of C-reactive protein (CRP), procalcitonin (PCT), and interleukin-6 (IL-6) on the detection platform and evaluated the sensitivity, linear range, selectivity, and repeatability. Finally, we finished detecting 15 samples from volunteers and compared the results with commercial ELISA kits.

Results
Detection of CRP, PCT, and IL-6 exhibited good linear relationships between CL intensities and concentrations in the range of 1.25–40 μg/ml, 0.4–12.8 ng/ml, and 50–1600 pg/ml, respectively. The limit of detection of CRP, PCT, and IL-6 were 0.54 μg/ml, 0.11 ng/ml, and 16.25 pg/ml, respectively. WMC-MDP is capable of good adequate selectivity and repeatability. The whole detection procedure takes only 22 min that meets the requirements of a POC device. Results of 15 samples from volunteers were consistent with the results detected by commercial ELISA kits.

Conclusions
WMC-MDP allows simultaneous, rapid, and sensitive detection of CRP, PCT, and IL-6 with satisfactory selectivity and repeatability, requiring minimal manipulation. However, WMC-MDP takes advantage of being a microfluidic device showing the coefficients of variation less than 10% enabling WMC-MDP to be a type of point-of-care testing (POCT). Therefore, WMC-MDP provides a promising alternative to POCT of multiple biomarkers. We believe the practical application of WMC-MDP in militarized fields will revolutionize infection diagnosis for soldiers.
A help or hindrance? Highly educated refugees’ perceptions of the role of civic integration programmes in accessing the labour market in Oslo, Malmö and Munich
Authors: Mozetič Katarina 
Published: February 2022

AbstractResearch often focuses on individual-level factors shaping refugee labour market participation. Less research has been conducted on the implications of the roles of employers, integration programmes, migrant support organisations and similar. This article contributes to the literature by seeking to understand highly educated refugees’ perceptions of how civic integration programmes shape opportunity structures for their labour market participation. It is particularly concerned with how the programmes’ characteristics of malleability and comprehensiveness inform integration processes. Accordingly, the article analyses identification contestations that transpire within civic integration programmes, as perceived by the participants, and compares how these unfold in three different contexts. A total of 41 semi-structured interviews with highly educated refugees in Oslo, Malmö, and Munich were analysed. The findings suggest that the civic integration programmes were thought to either foster or hinder the participants’ employment pathways depending on whether the participants were perceived as highly educated individuals or reduced to the general category of ‘refugee’. The differences were traced back to each civic integration programme’s capacity to provide malleable integration support, calling attention to the importance of the programmes’ acknowledgment of refugees’ heterogeneous needs and the pitfalls associated with undifferentiated refugee categorisation.
Predictive value of erythrocyte sedimentation rate and C-reactive protein in Behcet's disease activity and manifestations: a cross-sectional study
Authors: Parsaei Amirhossein , Moradi Soroush , Masoumi Maryam , Davatchi Fereydoun , Najafi Anahita , Kooshki Ashkan Mohammadi , Hajighadery Abdolkarim , Akhlaghi Massoomeh , Faezi Tahereh , Kavosi Hoda 
Published: February 2022

Abstract
Background
Behcet’s disease (BD) as a chronic inflammatory condition that affects the eyes, skin, central nervous system, gastrointestinal tract and vessels. According to the literature, the exact value of C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) in predicting active manifestations of BD remains controversial. In this study, we aim to assess and compare values of ESR and CRP between BD patients with active/inactive BD and active/inactive manifestations of the disease. Moreover, we try to determine the predictive value of ESR and CRP for disease activity.

Methods
Participants (n = 514) were drug-naïve BD patients; Based on last two visits, ESR and CRP values, disease activity, and active manifestations were recorded. The Man-Whitney U test measured the associations, and the binomial logistic regression evaluated the predictive value of ESR and CRP for active disease and each active manifestation. The sensitivity and specificity and the area under the curve (AUC) for each model were determined using receiver operating characteristic curves (ROC). Multiple regressions were run to predict BD activity score from ESR and CRP.

Result
Patients with active oral, genital, joint and dermal manifestations had higher ESR and CRP values (Mann–Whitney U test, p < 0.05 for all). Binomial logistic regressions showed that ESR had valuable predictive value for active BD (OR = 1.09 [1.04–1.13], AUC = 0.79 [0.74–0.83], p < 0.001) and active vascular manifestations (1.03 [1.01–1.05], AUC = 0.85 [0.79–0.92], p < 0.001). CRP had good predictive value for active vascular manifestations (OR 1.98 [1.45–2.72], AUC = 0.86 [0.8–0.91], p < 0.001). The optimal value of ESR ≥ 10.5 and ESR ≥ 42.5 could predict active BD and active vascular manifestations with sensitivity, specificity = 71%, 75% and = 81%, 83% respectively.

Conclusions
ESR and CRP are both associated with active BD and most manifestations of the diseases. They can be used for the prediction of active BD and active vascular manifestations in BD patients. Further studies can help to confirm the findings of the current research.
Mass spectrometry and two-dimensional electrophoresis in prenatal diagnosis of mucopolysaccharidosis type VI
Authors: Aboulnasr Aly A. , Gaber Khaled R. , Abdel Sameea Gamal , Gouda Amr S. , Ibrahim Mona M. , Shalabi Taghreed A. , Elnouri Amr 
Published: February 2022

Abstract
Background
Mucopolysaccharidosis VI (MPS VI) or Maroteaux–Lamy syndrome is an autosomal recessive lysosomal storage disorder. Clinical manifestations are related to progressive accumulation of dermatan sulfate (DS). Two-dimensional electrophoresis has traditionally been used for the diagnosis of MPS disorders. The method is only qualitative and is time consuming. For prenatal diagnosis of MPS, 6–8 ml of amniotic fluid is required and 5 working days to complete. It needs personal experience to do the test and to interpret the results. Mass spectrometry (MS) is now available as a quantitative method and for prenatal diagnosis of MPS it needs less amniotic fluid and takes only 2 working days. It is more accurate, less person dependent, but it costs more. Our aim was to introduce quantitative determination of dermatan sulfate using mass spectrometry in the prenatal diagnosis of MPS VI in Egypt and to compare this technique to the classical qualitative diagnosis using two-dimensional electrophoresis (2-DEP) of the glycosaminoglycans (GAGs) in amniotic fluid. Thirty pregnant females each with single fetus were subjected to amniocentesis at 16 weeks gestation. Ten with a previously affected MPS VI infant and twenty served as controls. Prenatal diagnosis (PD) was done by both MS and 2-DEP.

Results
MS verified 2-DEP results which showed 5 affected and 5 non-affected fetuses with MPS VI.

Conclusion
Two-dimensional electrophoresis of the GAGs in amniotic fluid is a good qualitative method and MS was an accurate quantitative method for prenatal diagnosis of MPS type VI. Quantitative determination of GAGs in AF by mass spectrometry is quicker. Where prenatal diagnosis is recommended for at risk pregnancies, mass spectrometry could be used more in the future as it gives rapid and accurate results.
Accuracy of MRI (TLICS vs AOSIS) in assessment of thoracolumbar spine injuries for guiding treatment
Authors: Nagi Mona Ali Mohamed Ali , Sakr Mai Mohamed Sedik 
Published: February 2022

Abstract
Background
The thoracic segment represents the most common area fractured in the whole spine. Complete neurological deficits are commonly associated with thoracic injuries possibly due to a relatively small canal diameter as compared to the cervical or lumbar spine. Magnetic resonance is the gold standard of imaging, especially in patients suffering from neurological deficits as well as in soft tissue assessment mainly the disc, ligaments, and neural elements. The thoracolumbar injury classification and severity score system (TLICS) and the thoracolumbar AO Spine injury score (TLAOSIS), are two scoring systems designed to help surgeons in management plans of thoraco-lumbar injuries. The aim of our study is to compare these two main thoracolumbar injury classification systems in deciding the management strategies in thoraco-lumbar injuries. This study is a retrospective study that included 70 patients (42 males and 28 females) who suffered acute traumatic vertebral fractures. All patients underwent MRI including T1WI, T2W and STIR sequences. The MRI was viewed by two independent radiologists of 5- and 10-years’ experience and compared to surgical decisions.

Results
Out of 70 patients included in our study, the TL AOSIS matched treatment recommendation in 62 patients (88.6%), and the TLICS matched in 60 patients (85.7%). The TL AOSIS achieved sensitivity 95%, specificity 80%, while the TLICS achieved sensitivity 72.2%, specificity 100%.

Conclusion
Both TL AOSIS and TLICS have very close results in their reliability for guiding treatment strategy, yet TL AOSIS matched treatment recommendation more than TLICS, with sensitivity more than TLICS, while TLICS had more specificity.
Ultrafast modulation of valley dynamics in multiple WS2 − Ag gratings strong coupling system
Authors: Zhao Le-Yi , Wang Hai , Wang Hai-Yu , Zhou Qiang , Zhang Xu-Lin , Cui Tong , Wang Lei , Liu Tian-Yu , Han Yu-Xiao , Luo Yang , Yue Yuan-Yuan , Song Mu-Sen , Sun Hong-Bo 
Published: February 2022

AbstractStrong light-matter interactions in two-dimensional transition metal dichalcogenides (TMDCs) with robust spin-valley degrees of freedom open up the prospect of valleytronic devices. A thorough understanding on the dynamics of the valley polarizations in the strong coupling regime is urgently required. Here, multiple polarized TMDCs-SPPs hybrid systems were constructed by combining monolayer WS2 flakes to linear, circular, and spiral Ag gratings, resulting in linear and circular polarized modulation on the coherent hybrid states, respectively. Particularly, valley polaritons can be tailored asymmetrically by chiral strong coupling regime. Furthermore, the dynamics of the polarized polaritons were directly analyzed by transient absorption (TA) measurement. Both of the linear and circular polarization difference in the TA spectra can be retained for a remarkable long time, leading to a polarized PL even at room temperature. More importantly, in the chiral strong coupled WS2-spiral Ag grating devices, the mechanism of the asymmetrical valley-polarized PL (p σ+ = 14.9% and p σ- = 10.8%) is proved by the opposite valley polarization dynamics in the circularly polarized TA spectra. The multiple polarization modulation in monolayer TMDCs-SPPs strong coupling devices could provide a viable route toward multiple polarization polaritonic devices.