bluuebunny/crossref_metadata_2025 huggingface dataset:
Mathematical modelling of oxygenation under veno-venous ECMO configuration using either a femoral or a bicaval drainage
Authors: Charbit Jonathan , Courvalin Elie , Dagod Geoffrey , Deras Pauline , Laumon Thomas , Girard Mehdi , Maury Camille , Weber Hugues , Capdevila Xavier
Published: March 2022

Background

The bicaval drainage under veno-venous extracorporeal membrane oxygenation (VV ECMO) was compared in present experimental study to the inferior caval drainage in terms of systemic oxygenation.

Method

Two mathematical models were built to simulate the inferior vena cava-to-right atrium (IVC → RA) route and the bicaval drainage-to-right atrium return (IVC + SVC → RA) route using the following parameters: cardiac output (QC), IVC flow/QC ratio, venous oxygen saturation, extracorporeal pump flow (QEC), and pulmonary shunt (PULM-Shunt) to obtain pulmonary artery oxygen saturation (SPAO2) and systemic blood oxygen saturation (SaO2).

Results

With the IVC → RA route, SPAO2 and SaO2 increased linearly with QEC/QC until the threshold of the IVC flow/QC ratio, beyond which the increase in SPAO2 reached a plateau. With the IVC + SVC → RA route, SPAO2 and SaO2 increased linearly with QEC/QC until 100% with QEC/QC = 1. The difference in required QEC/QC between the two routes was all the higher as SaO2 target or PULM-Shunt were high, and occurred all the earlier as PULM-Shunt were high. The required QEC between the two routes could differ from 1.0 L/min (QC = 5 L/min) to 1.5 L/min (QC = 8 L/min) for SaO2 target = 90%. Corresponding differences of QEC for SaO2 target = 94% were 4.7 L/min and 7.9 L/min, respectively.

Conclusion

Bicaval drainage under ECMO via the IVC + SVC → RA route gave a superior systemic oxygenation performance when both QEC/QC and pulmonary shunt were high. The VV-V ECMO configuration (IVC + SVC → RA route) might be an attractive rescue strategy in case of refractory hypoxaemia under VV ECMO.
High coenzyme affinity chimeric amine dehydrogenase based on domain engineering
Authors: Li Jialin , Mu Xiaoqing , Wu Tao , Xu Yan
Published: March 2022

NADH-dependent phenylalanine amine dehydrogenase (F-AmDH) engineered from phenylalanine dehydrogenase (PheDH) catalyzes the synthesis of aromatic chiral amines from prochiral ketone substrates. However, its low coenzyme affinity and catalytic efficiency limit its industrial application. Here, we developed a chimeric amine dehydrogenase, cFLF-AmDH, based on the relative independence of the structure at the domain level, combined with a substrate-binding domain from F-AmDH and a high-affinity cofactor-binding domain from leucine amine dehydrogenase (L-AmDH). The kinetic parameters indicated that cFLF-AmDH showed a twofold improvement in affinity for NADH and a 4.4-fold increase in catalytic efficiency (kcat/Km) compared with the parent F-AmDH. Meanwhile, cFLF-AmDH also showed higher thermal stability, with the half-life increased by 60% at 55 °C and a broader substrate spectrum, than the parent F-AmDH. Molecular dynamics simulations suggested that the constructed cFLF-AmDH had a more stable structure than the parent F-AmDH, thereby improving the affinity of the coenzyme. The reaction rate increased by 150% in the reductive amination reaction catalyzed by cFLF-AmDH. When the NAD+ concentration was 0.05 mM, the conversion rate was increased by 150%. These results suggest that the chimeric protein by domain shuffling from different domain donors not only increased the cofactor affinity and catalytic efficiency, but also changed the specificity and thermal stability. Our study highlights that domain engineering is another effective method for creating biodiversity with different catalytic properties.

Graphical Abstract
An unusual presentation of intestinal duplication mimicking torsion of Meckel’s diverticulum: a rare report of a pediatric case
Authors: Matsukubo Makoto , Muto Mitsuru , Kedoin Chihiro , Matsui Mayu , Murakami Masakazu , Sugita Koshiro , Yano Keisuke , Onishi Shun , Harumatsu Toshio , Yamada Koji , Yamada Waka , Kaji Tatsuru , Ieiri Satoshi
Published: March 2022

Background

Enteric duplication is a congenital disease that occurs throughout the entire gastrointestinal tract. Although it may sometimes cause intestinal volvulus, a few reports have described cases of enteric duplication twisted on itself. We experienced a rare pediatric case of long-segment tubular ileal duplication showing torsion. Torsion of enteric duplication is extremely rare. We herein report a pediatric case showing unusual torsion of ileal duplication requiring emergency surgery.

Case presentation

A 3-year-old boy presented with abdominal pain and vomiting. Contrast-enhanced computed tomography (CT) revealed a cystic luminal structure with a blind end and fluid collection in the pelvic cavity. CT also showed no findings of ileus or intestinal dilatation except for a cystic luminal structure. The preoperative diagnosis was torsion of Meckel’s diverticulum. The patient underwent emergent explorative diagnostic laparoscopy. As a result, a necrotic luminal structure and bloody ascites were recognized, and small-scale laparotomy was performed. Long-segment ileal duplication was recognized. The long-segment tubular ileal duplication shared the anti-mesenteric side of the intestinal wall along one-third of its length. The residual two-thirds of its length was free from the ileum and its blind end was twisted in a manner that looked similar to Meckel’s diverticulum. Normal ileum and the duplication, including the twisted necrotic portion, were resected, and ileal anastomosis was performed. The postoperative course was uneventful. A pathological examination confirmed the definitive diagnosis of enteric duplication.

Conclusions

We reported the unusual presentation of intestinal duplication mimicking torsion of Meckel’s diverticulum. Enteric duplication shows various clinical symptoms and presentations. We must understand that the classification of digestive enteric duplication is diverse with a variety of associated clinical symptoms.
Bacterial communities in surface and basal ice of a glacier terminus in the headwaters of Yangtze River on the Qinghai–Tibet Plateau
Authors: Ren Ze , Gao Hongkai , Luo Wei , Elser James J.
Published: March 2022

Background

On the front lines of climate change, glacier termini play crucial roles in linking glaciers and downstream ecosystems during glacier retreat. However, we lack a clear understanding of biological processes that occur in surface and basal ice at glacier termini.

Methods

Here, we studied the bacterial communities in surface ice and basal ice (the bottom layer) of a glacier terminus in the Yangtze River Source, Qinghai–Tibet Plateau.

Results

Surface and basal ice harbored distinct bacterial communities but shared some core taxa. Surface ice communities had a higher α-diversity than those in basal ice and were dominated by Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Cyanobacteria while basal ice was dominated by Firmicutes and Proteobacteria. The bacterial communities were also substantially different in functional potential. Genes associated with functional categories of cellular processes and metabolism were significantly enriched in surface ice, while genes connected to environmental information processing were enriched in basal ice. In terms of biogeochemical cycles of carbon, nitrogen, phosphorus, and sulfur, bacterial communities in surface ice were enriched for genes connected to aerobic carbon fixation, aerobic respiration, denitrification, nitrogen assimilation, nitrogen mineralization, sulfur mineralization, alkaline phosphatase, and polyphosphate kinase. In contrast, bacterial communities in basal ice were enriched for genes involved in anaerobic carbon fixation, fermentation, nitrate reduction, 2-aminoethylphosphonic acid pathway, G3P transporter, glycerophosphodiester phosphodiesterase, and exopolyphosphatase. Structural equation modeling showed that total nitrogen and environmental carbon:phosphorus were positively while environmental nitrogen:phosphorus was negatively associated with taxonomic β-diversity which itself was strongly associated with functional β-diversity of bacterial communities.

Conclusions

This study furthers our understanding of biogeochemical cycling of the mountain cryosphere by revealing the genetic potential of the bacterial communities in surface and basal ice at the glacier terminus, providing new insights into glacial ecology as well as the influences of glacier retreat on downstream systems.
Recent strategies of collagen-based biomaterials for cartilage repair: from structure cognition to function endowment
Authors: Yu Xiaoyue , Zhang Haiping , Miao Yiliang , Xiong Shanbai , Hu Yang
Published: March 2022

Collagen, characteristic in biomimetic composition and hierarchical structure, boasts a huge potential in repairing cartilage defect due to its extraordinary bioactivities and regulated physicochemical properties, such as low immunogenicity, biocompatibility and controllable degradation, which promotes the cell adhesion, migration and proliferation. Therefore, collagen-based biomaterial has been explored as porous scaffolds or functional coatings in cell-free scaffold and tissue engineering strategy for cartilage repairing. Among those forming technologies, freeze-dry is frequently used with special modifications while 3D-printing and electrospinning serve as the structure-controller in a more precise way. Besides, appropriate cross-linking treatment and incorporation with bioactive substance generally help the collagen-based biomaterials to meet the physicochemical requirement in the defect site and strengthen the repairing performance. Furthermore, comprehensive evaluations on the repair effects of biomaterials are sorted out in terms of in vitro, in vivo and clinical assessments, focusing on the morphology observation, characteristic production and critical gene expression. Finally, the challenge of biomaterial-based therapy for cartilage defect repairing was summarized, which is, the adaption to the highly complex structure and functional difference of cartilage.

Graphical abstract
Facile synthesis of reduced graphene oxide by Tecoma stans extracts for efficient removal of Ni (II) from water: batch experiments and response surface methodology
Authors: Mahmoud Alaa El Din , Hosny Mohamed , El-Maghrabi Nourhan , Fawzy Manal
Published: March 2022

A facile approach to synthesize reduced graphene oxide (rGO) was investigated using three different extract concentrations of Tecoma stans leaves as reducing/capping agents. The surface morphology of the rGOs was examined by scanning electron microscopy with energy dispersive X-ray. The optimum prepared rGOs were confirmed with characteristic peaks at ~ 280 nm using UV–Vis Spectroscopy. Fourier-transform infrared spectroscopy results indicated the capacity of plant extracts to reduce the oxygen functional groups on graphite oxides’ surfaces. Furthermore, the organic constituents of the plant extract were determined to highlight the reduction mechanism of graphene oxide to rGO. The optimized rGO was subsequently utilized as an adsorbent for the removal of Ni (II) from simulated wastewater. Adsorption experiments were conducted using methods of one factor at a time as well as Box Behnken Design. The Ni (II) adsorption is fitted well to the non-linear isotherm models and the calculated maximum uptake capacity was 69 mg g− 1. The optimum removal of Ni (II) was found 93% with pH of 6, initial Ni (II) concentration of 2 mg L− 1, and rGO dose of 0.2 g L− 1. The reliability of the developed model was 99.4% between experimental and predicted values. In addition, the average desorption efficiency of Ni (II) was 94%, which highlight the applicability of rGO reusability.
Assessment of surface water quality and monitoring in southern Vietnam using multicriteria statistical approaches
Authors: Nguyen Thanh Giao , Huynh Thi Hong Nhien
Published: March 2022

The study was conducted to analyze surface water quality fluctuations in the the southern region of Vietnam using monitoring data at 58 locations. Seventeen water quality indicators were analyzed including pH, temperature, electrical conductivity (EC), dissolved oxygen (DO), total dissolved solids (TDS), total suspended solids (TSS), chemical oxygen demand (COD), biological oxygen demand (BOD), ammoniacal nitrogen (NH4+- N), nitrite nitrogen (NO2−-N), nitrate nitrogen, iron (Fe), lead (Pb), cadmium (Cd), mercury (Hg), arsenic (As), and chloride (Cl− ions). The study used water quality index (WQI), cluster analysis (CA), principal component analysis (PCA), and Entropy weighted methods to analyze surface water quality. The results showed that the surface water was contaminated with organics (low DO and high TSS, BOD, COD), nutrients (high NH4+-N) and Fe. While Pb at some locations exceeded the allowable limit of the national technical regulation, other indicators (Cd, Hg and As) were within this standard. Moreover, DO, TSS, BOD, COD, NH4+-N, Fe, EC, TDS, and Cl− were seasonally fluctuated. WQI classified water quality from bad to very good (WQI = 42–100) due to the impact of hydrological conditions, navigation, wastewater from industrial zones, and fishing ports. The results of CA suggested that it is possible to reduce the 11 sampling locations (from 33 to 22 locations) in clusters 1–6 and the frequency of monitoring from 8 to 5 times per year, which still ensures representativeness of water quality over time. This reduction allows lowering the monitoring costs by 56.5%. The PCA identified five major potential sources explaining 87.3% and 8 minor sources explaining only 12.7% of water quality variation. Temperature, pH, EC, DO, BOD, COD, NH4+-N, NO2−-N, Fe, Cl−, Pb are important indicators need to periodically be monitored. Furthermore, orthophosphate, total phosphate, total nitrogen, coliforms should be considered to add into the next monitoring program. Locations with medium and bad water quality are concentrated in Dong Nai, Ho Chi Minh City and Long An, which requires finding effective solutions to improve the water quality. The current results can assist in decision-making related to environmental quality monitoring in the southern region of Vietnam.
Comparison Between Subparaneural Upper Trunk and Conventional Interscalene Blocks for Arthroscopic Shoulder Surgery: A Randomized Noninferiority Trial
Authors: Zhang Hongye , Qu Zongyang , Miao Yongsheng , Jia Ruifang , Li Feng , Hua Zhen
Published: March 2022

BACKGROUND:

Although interscalene nerve block is the standard for shoulder analgesia, the risk of hemidiaphragmatic paralysis restricts its use in patients with compromised pulmonary function. We hypothesized that a novel subparaneural upper trunk block would provide noninferior postoperative analgesia but superior diaphragmatic sparing effect compared to interscalene block.

METHODS:

This randomized controlled trial comprised 96 patients who underwent arthroscopic shoulder surgery under either subparaneural upper trunk block (5 mL of 0.5% ropivacaine) or interscalene block (15 mL of 0.5% ropivacaine), followed by supraclavicular nerve block (5 mL of 0.5% ropivacaine). General anesthesia was standardized. The coprimary outcomes were (1) recovery room resting pain score at 30 minutes, measured on an 11-point numerical rating scale, with a prespecified noninferiority margin of 1 point and (2) the incidence of hemidiaphragmatic paralysis, diagnosed using ultrasound. Among secondary outcomes, resting pain scores were assessed with numerical rating scale at 4, 8, and 24 hours postoperatively.

RESULTS:

Recovery room resting pain scores at 30 minutes were 0 (0–1) in the subparaneural upper trunk group versus 0 (0–0) in the interscalene group, with a median difference of 0 (95% CI, 0–0); the upper 95% CI limit was lower than the prespecified noninferiority margin (noninferiority P < .001). Hemidiaphragmatic paralysis was observed in 16.7% of patients in the subparaneural upper trunk group versus 100% of those in the interscalene group (RR, 0.17; 95% CI, 0.09–0.31; P < .001), with complete paralysis occurring in 6.3% and 93.7% of patients, respectively. In this study, any reported differences in pain scores at 4, 8, and 24 hours postoperatively were not clinically important.

CONCLUSIONS:

The subparaneural upper trunk block compared to interscalene block provided noninferior analgesia at 30 minutes in the recovery room after arthroscopic shoulder surgery but resulted in less hemidiaphragmatic paralysis.
The yeast LYST homolog Bph1 is a Rab5 effector and prevents Atg8 lipidation at endosomes
Authors: Vargas Duarte Prado , Hardenberg Ralph , Mari Muriel , Walter Stefan , Reggiori Fulvio , Fröhlich Florian , González Montoro Ayelén , Ungermann Christian
Published: March 2022

Lysosomes mediate degradation of macromolecules to their precursors for cellular recycling. Additionally, lysosome-related organelles mediate cell type-specific functions. Chédiak–Higashi syndrome is an autosomal, recessive disease, in which loss of the protein LYST causes defects in lysosomes and lysosome-related organelles. The molecular function of LYST, however, is largely unknown. Here, we dissected the function of the yeast LYST homolog, Bph1. We show that Bph1 is an endosomal protein and an effector of the minor Rab5 isoform Ypt52. Strikingly, bph1Δ mutant cells have lipidated Atg8 on their endosomes, which is sorted via late endosomes into the vacuole lumen under non-autophagy-inducing conditions. In agreement with this, proteomic analysis of bph1Δ vacuoles reveals an accumulation of Atg8, reduced flux via selective autophagy, and defective endocytosis. Additionally, bph1Δ cells have reduced autophagic flux under starvation conditions. Our observations suggest that Bph1 is a novel Rab5 effector that maintains endosomal functioning. When Bph1 is lost, Atg8 is lipidated at endosomes even during normal growth and ends up in the vacuole lumen. Thus, our results contribute to the understanding of the role of LYST-related proteins and associated diseases.
Differential diagnosis of hip pain in children referred to a specialist bone tumour service
Authors: Choraria Anika , O’Donnell Paul , Saifuddin Asif
Published: March 2022

Objective:

To determine the differential diagnosis of bone lesions causing hip pain in children and the association between radiographic features of aggression and MRI appearances with final diagnosis.

Methods:

Retrospective review of children with hip pain referred to a specialist musculoskeletal oncology service between September 2018 and December 2020. Patient demographics, lesion location, the radiographic and MRI features, and the final diagnosis, which was made either by image-guided biopsy, surgical curettage or based on typical imaging features were recorded. Statistical analysis examined the association between the Lodwick-Madewell score (determined from available radiographs) and MRI findings with final diagnosis.

Results:

Fifty-nine patients were included, 40 males and 19 females with mean age 10.9 years, (range 3–16 years). Final diagnoses were based on histology in 24 (40.7%) cases and imaging in 35 (59.3%) cases. Eighteen lesions (30.5%) were classed as non-neoplastic, 31 (52.5%) as benign and 10 (16.9%) as malignant, of which four were primary bone sarcomas. There was a significant association between the Lodwick-Madewell score and final diagnosis (p < 0.001). On MRI, bone marrow oedema, presence of a focal lesion, bone expansion and the presence of an extraosseous mass were all significantly associated with final diagnostic classification.

Conclusion:

The differential diagnosis of hip pain in children presenting to a bone tumour service is wide. Most cases are due to benign or non-neoplastic conditions, with only 10 out of 59 children having a malignant lesion. Radiography complemented by MRI plays a major role in differentiating non-neoplastic, benign neoplastic and malignant lesions and in determining the requirement for needle biopsy.

Advances in knowledge:

This is the first study to consider how imaging features relate to diagnosis in suspected paediatric hip tumours. Use of this information can help in determining which cases should undergo needle biopsy.
Integration of HIV prevention and sexual and reproductive health in the era of anti-retroviral-based prevention: findings from assessments in Kenya, Malawi and Zimbabwe
Authors: Kachale Fannie , Mahaka Imelda , Mhuriro Fatima , Mugambi Mary , Murungu Joseph , Ncube Barbra , Ncube Getrude , Ndwiga Albert , Nyirenda Rose , Otindo Violet , Carter Anna , Dunbar Megan , Fleischman Janet , Rodrigues Jessica , Segal Kate
Published: March 2022

Background: Though substantial progress has helped curb the HIV epidemic, high rates of new HIV infections persist among adolescent girls and young women (AGYW) in sub-Saharan Africa, reflecting critical gaps in reaching them with integrated HIV prevention and sexual and reproductive health (SRH) services. The scale-up of oral pre-exposure prophylaxis (PrEP) and multiple novel HIV prevention products on the horizon offer countries a unique opportunity to expand innovative approaches to deliver comprehensive, integrated HIV prevention/SRH services.

Methods: This article comparatively analyzes findings from rapid assessments in Kenya, Malawi and Zimbabwe across key themes to highlight cross-country trends and contextual realities around HIV prevention/SRH integration, with a focus on oral PrEP and contraception. In Kenya and Zimbabwe, assessments were completed by Ministries of Health (MOH) and the HIV Prevention Market Manager and include 20 health facility assessments, 73 key informant interviews (KIIs) and six community dialogues. In Malawi, the assessment was completed by the MOH and Georgetown University Center for Innovation in Global Health and includes 70 KIIs and a review of national policies and program implementation in Blantyre. Findings were contextualized through a review of literature and policies in each country.

Results: Across countries, the policy environment is conducive to HIV prevention/SRH integration, though operationalization presents ongoing challenges, with most policies preceding and not accounting for oral PrEP rollout. National coordination mechanisms, youth-friendly health services and prevention of mother-to-child transmission programs are promising practices, while siloed and resource-constrained health systems, limited provider capacity, underfunded demand generation and structural factors exacerbate barriers to achieving integration.

Conclusions: As new HIV prevention products are introduced, demand for integrated HIV prevention/SRH services is likely to grow. Investing in HIV prevention/SRH integration can help to ensure a sustainable response to the HIV epidemic, streamline service delivery and improve the health outcomes and lives of AGYW.
Methodology of Natsal-COVID Wave 1: a large, quasi-representative survey with qualitative follow-up measuring the impact of COVID-19 on sexual and reproductive health in Britain
Authors: Dema Emily , Copas Andrew J , Clifton Soazig , Conolly Anne , Blake Margaret , Riddell Julie , Boso Perez Raquel , Tanton Clare , Bonell Chris , Sonnenberg Pam , Mercer Catherine H , Mitchell Kirstin R , Field Nigel
Published: March 2022

Background: Britain’s National Surveys of Sexual Attitudes and Lifestyles (Natsal) have been undertaken decennially since 1990 and provide a key data source underpinning sexual and reproductive health (SRH) policy. The COVID-19 pandemic disrupted many aspects of sexual lifestyles, triggering an urgent need for population-level data on sexual behaviour, relationships, and service use at a time when gold-standard in-person, household-based surveys with probability sampling were not feasible. We designed the Natsal-COVID study to understand the impact of COVID-19 on the nation’s SRH and assessed the sample representativeness.

Methods: Natsal-COVID Wave 1 data collection was conducted four months (29/7-10/8/2020) after the announcement of Britain’s first national lockdown (23/03/2020). This was an online web-panel survey administered by survey research company, Ipsos MORI. Eligible participants were resident in Britain, aged 18-59 years, and the sample included a boost of those aged 18-29. Questions covered participants’ sexual behaviour, relationships, and SRH service use. Quotas and weighting were used to achieve a quasi-representative sample of the British general population. Participants meeting criteria of interest and agreeing to recontact were selected for qualitative follow-up interviews. Comparisons were made with contemporaneous national probability surveys and Natsal-3 (2010-12) to understand bias.

Results: 6,654 participants completed the survey and 45 completed follow-up interviews. The weighted Natsal-COVID sample was similar to the general population in terms of gender, age, ethnicity, rurality, and, among sexually-active participants, numbers of sexual partners in the past year. However, the sample was more educated, contained more sexually-inexperienced people, and included more people in poorer health.

Conclusions: Natsal-COVID Wave 1 rapidly collected quasi-representative population data to enable evaluation of the early population-level impact of COVID-19 and lockdown measures on SRH in Britain. Although sampling was less representative than the decennial Natsals, Natsal-COVID will complement national surveillance data and Natsal-4 (planned for 2022).
The genome sequence of the tree wasp, Dolichovespula sylvestris Scopoli, 1763
Authors: Falk Steven ,   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, Broad Gavin R. ,   Darwin Tree of Life Consortium
Published: March 2022

We present a genome assembly from an individual male Dolichovespula sylvestris (the tree wasp; Arthropoda; Insecta; Hymenoptera; Vespidae). The genome sequence is 233 megabases in span. The majority of the assembly (95.56%) is scaffolded into 26 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 21.3 kilobases in length.
Getting Personal: A Deep Learning Artifact for Text-Based Measurement of Personality
Authors: Yang Kai , Lau Raymond Y. K. , Abbasi Ahmed
Published: March 2022

Analysts, managers, and policymakers are interested in predictive analytics capable of offering better foresight. It is generally accepted that in forecasting scenarios involving organizational policies or consumer decision making, personal characteristics, including personality, may be an important predictor of downstream outcomes. The inclusion of personality features in forecasting models has been hindered by the fact that traditional measurement mechanisms are often infeasible. Text-based personality detection has garnered attention due to the public availability of digital textual traces, however state-of-the-art models proposed by IBM, Google, Facebook, and academic research are not accurate enough to be used for downstream real-world forecasting tasks. We propose a novel text-based personality measurement approach that improves detection of personality dimensions by 10–20 percentage points relative to the best existing methods developed in industry and academia. Using case studies in the finance and health domains, we show that more accurate text-based personality detection can translate into significant improvements in downstream applications such as forecasting future firm performance or predicting pandemic infection rates. Our findings have important implications for managers focused on enabling, producing, or consuming predictive analytics for enhanced agility in decision making.
Influence of drift correction precision on super-resolution localization microscopy
Authors: Shang Mingtao , Huang Zhen-li , Wang Yujie
Published: March 2022

Super-resolution localization microscopy (SRLM) breaks the diffraction limit successfully and improves the resolution of optical imaging systems by nearly an order of magnitude. However, SRLM typically takes several minutes or longer to collect a sufficient number of image frames that are required for reconstructing a final super-resolution image. During this long image acquisition period, system drift should be tightly controlled to ensure the imaging quality; thus, several drift correction methods have been developed. However, it is still unclear whether the performance of these methods is able to ensure sufficient image quality in SRLM. Without a clear answer to this question, it is hard to choose a suitable drift correction method for a specific SRLM experiment. In this paper, we use both theoretical analysis and simulation to investigate the relationship among drift correction precision, localization precision, and position estimation precision. We propose a concept of relative localization precision for evaluating the effect of drift correction on imaging resolution, which would help to select an appropriate drift correction method for a specific experiment.
Super-resolution reconstruction of terahertz images based on a deep-learning network with a residual channel attention mechanism
Authors: Yang Xiuwei , Zhang Dehai , Wang Zhongmin , Zhang Yanbo , Wu Jun , Wu Biyuan , Wu Xiaohu
Published: March 2022

To date, the existing terahertz super-resolution reconstruction methods based on deep-learning networks have achieved noteworthy success. However, the terahertz image degradation process needs to fully consider the blur and noise of the high-frequency part of the image during the network training process, and cannot be replaced simply by interpolation, which has high complexity. The terahertz degradation model is systematically investigated, and effectively solves the above problems by introducing the remaining channel mechanism into the deep-learning network. On the one hand, an image degradation model suitable for the terahertz imaging process is adopted for the images in the training dataset, which improves the accuracy of network training. On the other hand, the residual channel attention mechanism is introduced to realize the adaptive adjustment of the dependence between network channels, which results in the network being more focused on the restoration of high-frequency information, thereby supporting the extraction of high-frequency edge details in the image. In addition, experimental results demonstrate that this method successfully improves the peak signal-to-noise ratios, and offers clearer edge details and a better overall reconstruction effect. We believe that this work may provide a new possibility to improve the resolution of terahertz images.
In vivo assessment of corneal biomechanics under a localized cross-linking treatment using confocal air-coupled optical coherence elastography
Authors: Zvietcovich Fernando , Nair Achuth , Singh Manmohan , Aglyamov Salavat R. , Twa Michael D. , Larin Kirill V.
Published: March 2022

The localized application of the riboflavin/UV-A collagen cross-linking (UV-CXL) corneal treatment has been proposed to concentrate the stiffening process only in the compromised regions of the cornea by limiting the epithelium removal and irradiation area. However, current clinical screening devices dedicated to measuring corneal biomechanics cannot provide maps nor spatial-dependent changes of elasticity in corneas when treated locally with UV-CXL. In this study, we leverage our previously reported confocal air-coupled ultrasonic optical coherence elastography (ACUS-OCE) probe to study local changes of corneal elasticity in three cases: untreated, half-CXL-treated, and full-CXL-treated in vivo rabbit corneas (n = 8). We found a significant increase of the shear modulus in the half-treated (>450%) and full-treated (>650%) corneal regions when compared to the non-treated cases. Therefore, the ACUS-OCE technology possesses a great potential in detecting spatially-dependent mechanical properties of the cornea at multiple meridians and generating elastography maps that are clinically relevant for patient-specific treatment planning and monitoring of UV-CXL procedures.
Performance optimization of a metasurface incorporating non-volatile phase change material
Authors: Sakda Natsima , Ghosh Souvik , Chitaree Ratchapak , Rahman B. M. Azizur
Published: March 2022

Optical metasurface is a combination of manufactured periodic patterns of many artificial nanostructured unit cells, which can provide unique and attractive optical and electrical properties. Additionally, the function of the metasurface can be altered by adjusting the metasurface's size and configuration to satisfy a particular required property. However, once it is fabricated, such specific property is fixed and cannot be changed. Here, phase change material (PCM) can play an important role due to its two distinct states during the phase transition, referred to as amorphous and crystalline states, which exhibit significantly different refractive indices, particularly in the infrared wavelength. Therefore, a combination of metasurface with a phase change material may be attractive for achieving agile and tunable functions. In this paper, we numerically investigate an array of silicon cylinders with a thin PCM layer at their centers. The GST and GSST are the most well-known PCMs and were chosen for this study due to their non-volatile properties. This structure produces two resonant modes, magnetic dipole and electric dipole, at two different resonating wavelengths. We have numerically simulated the effect of cylinder's height and diameter on the reflecting profile, including the effect of thickness of the phase change material. Additionally, it is shown here that a superior performance can be achieved towards reduced insertion loss, enhanced extinction ratio, and increased figure of merit when a GST layer is replaced by a GSST layer.
Biological action at a distance: Correlated pattern formation in adjacent tessellation domains without communication
Authors: Brooke John M. , James Sebastian S. , Jimenez-Rodriguez Alejandro , Wilson Stuart P.
Published: March 2022

Tessellations emerge in many natural systems, and the constituent domains often contain regular patterns, raising the intriguing possibility that pattern formation within adjacent domains might be correlated by the geometry, without the direct exchange of information between parts comprising either domain. We confirm this paradoxical effect, by simulating pattern formation via reaction-diffusion in domains whose boundary shapes tessellate, and showing that correlations between adjacent patterns are strong compared to controls that self-organize in domains with equivalent sizes but unrelated shapes. The effect holds in systems with linear and non-linear diffusive terms, and for boundary shapes derived from regular and irregular tessellations. Based on the prediction that correlations between adjacent patterns should be bimodally distributed, we develop methods for testing whether a given set of domain boundaries constrained pattern formation within those domains. We then confirm such a prediction by analysing the development of ‘subbarrel’ patterns, which are thought to emerge via reaction-diffusion, and whose enclosing borders form a Voronoi tessellation on the surface of the rodent somatosensory cortex. In more general terms, this result demonstrates how causal links can be established between the dynamical processes through which biological patterns emerge and the constraints that shape them.
Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials
Authors: Dyson Zoe Anne , Malau Elisheba , Horwood Paul F. , Ford Rebecca , Siba Valentine , Yoannes Mition , Pomat William , Passey Megan , Judd Louise M. , Ingle Danielle J. , Williamson Deborah A. , Dougan Gordon , Greenhill Andrew R. , Holt Kathryn E.
Published: March 2022

Background

Typhoid fever, a systemic infection caused by Salmonella enterica serovar Typhi, remains a considerable public health threat in impoverished regions within many low- and middle-income settings. However, we still lack a detailed understanding of the emergence, population structure, molecular mechanisms of antimicrobial resistance (AMR), and transmission dynamics of S. Typhi across many settings, particularly throughout the Asia-Pacific islands. Here we present a comprehensive whole genome sequence (WGS) based overview of S. Typhi populations circulating in Papua New Guinea (PNG) over 30 years.

Principle findings

Bioinformatic analysis of 86 S. Typhi isolates collected between 1980–2010 demonstrated that the population structure of PNG is dominated by a single genotype (2.1.7) that appears to have emerged in the Indonesian archipelago in the mid-twentieth century with minimal evidence of inter-country transmission. Genotypic and phenotypic data demonstrated that the PNG S. Typhi population appears to be susceptible to former first line drugs for treating typhoid fever (chloramphenicol, ampicillin and co-trimoxazole), as well as fluoroquinolones, third generation cephalosporins, and macrolides. PNG genotype 2.1.7 was genetically conserved, with very few deletions, and no evidence of plasmid or prophage acquisition. Genetic variation among this population was attributed to either single point mutations, or homologous recombination adjacent to repetitive ribosomal RNA operons.

Significance

Antimicrobials remain an effective option for the treatment of typhoid fever in PNG, along with other intervention strategies including improvements to water, sanitation and hygiene (WaSH) related infrastructure and potentially the introduction of Vi-conjugate vaccines. However, continued genomic surveillance is warranted to monitor for the emergence of AMR within local populations, or the introduction of AMR associated genotypes of S. Typhi in this setting.
No-reference panoramic image quality assessment based on multi-region adjacent pixels correlation
Authors: Huang Xinpeng , Liu Xin , Ding Wenxin , Meng Chunli , An Ping
Published: March 2022

The distortion measurement plays an important role in panoramic image processing. Most measurement algorithms judge the panoramic image quality by means of weighting the quality of the local areas. However, such a calculation fails to globally reflect the quality of the panoramic image. Therefore, the multi-region adjacent pixels correlation (MRAPC) is proposed as the efficient feature for no-reference panoramic images quality assessment in this paper. Specifically, from the perspective of the statistical characteristics, the differences of the adjacent pixels in panoramic image are proved to be highly related to the degree of distortion and independent of image content. Besides, the difference map has limited pixel value range, which can improve the efficiency of quality assessment. Based on these advantages, the proposed MRAPC feature collaborates with the support vector regression to globally predict the quality of panoramic images. Extensive experimental results show that the proposed no-reference panoramic image quality assessment algorithm achieves higher evaluation performance than the existing algorithms.
A novel CSP C-terminal epitope targeted by an antibody with protective activity against Plasmodium falciparum
Authors: Beutler Nathan , Pholcharee Tossapol , Oyen David , Flores-Garcia Yevel , MacGill Randall S. , Garcia Elijah , Calla Jaeson , Parren Mara , Yang Linlin , Volkmuth Wayne , Locke Emily , Regules Jason A. , Dutta Sheetij , Emerling Daniel , Early Angela M. , Neafsey Daniel E. , Winzeler Elizabeth A. , King C. Richter , Zavala Fidel , Burton Dennis R. , Wilson Ian A. , Rogers Thomas F.
Published: March 2022

Potent and durable vaccine responses will be required for control of malaria caused by Plasmodium falciparum (Pf). RTS,S/AS01 is the first, and to date, the only vaccine that has demonstrated significant reduction of clinical and severe malaria in endemic cohorts in Phase 3 trials. Although the vaccine is protective, efficacy declines over time with kinetics paralleling the decline in antibody responses to the Pf circumsporozoite protein (PfCSP). Although most attention has focused on antibodies to repeat motifs on PfCSP, antibodies to other regions may play a role in protection. Here, we expressed and characterized seven monoclonal antibodies to the C-terminal domain of CSP (ctCSP) from volunteers immunized with RTS,S/AS01. Competition and crystal structure studies indicated that the antibodies target two different sites on opposite faces of ctCSP. One site contains a polymorphic region (denoted α-ctCSP) and has been previously characterized, whereas the second is a previously undescribed site on the conserved β-sheet face of the ctCSP (denoted β-ctCSP). Antibodies to the β-ctCSP site exhibited broad reactivity with a diverse panel of ctCSP peptides whose sequences were derived from field isolates of P. falciparum whereas antibodies to the α-ctCSP site showed very limited cross reactivity. Importantly, an antibody to the β-site demonstrated inhibition activity against malaria infection in a murine model. This study identifies a previously unidentified conserved epitope on CSP that could be targeted by prophylactic antibodies and exploited in structure-based vaccine design.
Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting
Authors: Knödlseder Nastassia , Nevot Guillermo , Fábrega Maria-José , Mir-Pedrol Julia , Sanvicente-García Marta , Campamà-Sanz Nil , Paetzold Bernhard , Lood Rolf , Güell Marc
Published: March 2022

Cutibacterium acnes (C. acnes) is a gram-positive bacterium and a member of the human skin microbiome. Despite being the most abundant skin commensal, certain members have been associated with common inflammatory disorders such as acne vulgaris. The availability of the complete genome sequences from various C. acnes clades have enabled the identification of putative methyltransferases, some of them potentially belonging to restriction-modification (R-M) systems which protect the host of invading DNA. However, little is known on whether these systems are functional in the different C. acnes strains. To investigate the activity of these putative R-M and their relevance in host protective mechanisms, we analyzed the methylome of six representative C. acnes strains by Oxford Nanopore Technologies (ONT) sequencing. We detected the presence of a 6-methyladenine modification at a defined DNA consensus sequence in strain KPA171202 and recombinant expression of this R-M system confirmed its methylation activity. Additionally, a R-M knockout mutant verified the loss of methylation properties of the strain. We studied the potential of one C. acnes bacteriophage (PAD20) in killing various C. acnes strains and linked an increase in its specificity to phage DNA methylation acquired upon infection of a methylation competent strain. We demonstrate a therapeutic application of this mechanism where phages propagated in R-M deficient strains selectively kill R-M deficient acne-prone clades while probiotic ones remain resistant to phage infection.
From blended to online
Authors: Szabó Éva
Published: March 2022

The paper describes the process of designing a pre-service teacher training course on the use of information and communication technologies in ELT and shows how the transition to online education caused by the Covid-19 pandemic affected it. The course was originally designed as a blended one with a focus on exploiting ICT for effective skills development in face-to-face lessons and online home assignments. Due to the pandemic in 2020, it moved online, which created an unexpected opportunity for experimenting with ICT inclusion in fully online ELT and modifying the course accordingly. While the original focus on skills development was kept, new content areas, such as online assessment, gamification and interactions in online environments were added. The process described as well as the participating students’ post-course reflections refined our understanding of online course design and ICT use and is hoped to provide guidelines for similar experiments in other teacher education contexts.
Los jóvenes escolares: una mirada desde las representaciones sociales de los maestros
Authors: Hernández Cano Edilberto
Published: March 2022

maestros de educación básica secundaria y media de Bogotá sobre los jóvenes en su condición escolar. El objetivo del estudio fue develar y comprender las representaciones sociales de los jóvenes escolares que han construido los maestros de tres colegios de la ciudad de Bogotá. La investigación fue cualitativa, asumió un paradigma interpretativo y, dentro de los enfoques de los estudios en representaciones sociales, retomó el enfoque procesual. El análisis permitió develar los sentidos que orientan las acciones de los maestros, así como sus significados y concepciones sobre los jóvenes escolares. Los resultados muestran cómo los profesores han construido representaciones sociales polisémicas y contradictorias sobre los jóvenes; se los representa en una doble condición, como sujeto joven y como alumno, representaciones que no se integran ni se relacionan, es decir, se ven de manera excluyente.
Comparative analysis of the results of surgical correction of idiopathic thoracic scoliosis in patients with active bone growth
Authors: Chernyadjeva M. A. , Vasyura A. S. , Lukinov V. L. , Novikov V. V.
Published: March 2022

Objective. To conduct a comparative analysis of surgical treatment results for idiopathic thoracic scoliosis in patients during active bone growth and to identify the most effective methods of scoliosis correction for the considered age group.

Material and Methods. The results of surgical treatment of 343 patients aged 10–14 years with continued active growth and progressive idiopathic thoracic scoliosis were analyzed. The patients were operated on in 1998–2018 using five surgical techniques: hybrid fixation with and without anterior stage, transpedicular fixation, and laminar fixation with and without anterior stage.

Results. Statistically significant deformity progression was observed in patients operated on using laminar (Group IV) and hybrid (Group I) fixation. An additional anterior stage (discectomy and interbody fusion) in combination with laminar fixation (Group V) does not prevent deformity progression after surgery. In patients who underwent hybrid fixation in combination with the anterior stage (Group II) or total transpedicular fixation (Group III), no statistically significant progression of scoliotic deformity was observed in the postoperative period. Patients operated on with total transpedicular fixation (Group III) show improvement in all domains of the SRS-24 questionnaire: no increase in pain throughout the entire follow-up period, higher assessment of appearance after surgery and satisfaction with the treatment result. In groups II and III, there was no negative dynamics of topographic parameters in the long-term period after treatment; the initial correction of the deformity was maintained throughout the entire postoperative follow-up.

Conclusion. Total transpedicular fixation provides the best correction of scoliosis in the absence of progression in the long-term postoperative follow-up in children during the period of active bone growth (age 10–14 years). According to the survey data, patients operated on with total transpedicular fixation demonstrate improvement in the following domains: the absence of pain syndrome throughout the entire postoperative follow-up period, the highest assessment of appearance after surgery and satisfaction with the result of surgical treatment. Hybrid fixation in combination with the anterior stage and total transpedicular fixation ensure the absence of negative dynamics of topographic parameters in the long term after surgery with maintenance of the initial surgical correction of spinal deformity.