bluuebunny/crossref_metadata_2025 huggingface dataset:
Arterial spin labeling signal ratio between the lesion and contralateral sides for evaluation of acute middle cerebral artery infarct
Authors: Lee Junyoung , Park Dong Woo , Kim Young Seo , Kim Hyun Young , Lee Young-Jun
Published: January 2022

The purpose of our study was to differentiate arterial transit artifact from post-recanalization luxury perfusion on arterial spin labeling (ASL) image, and obtain the relationship between ASL signal intensity and clinical outcomes in patients with acute ischemic stroke.

Thirty-five subjects with an acute middle cerebral artery (MCA) infarct were enrolled (18 with recanalized and 17 with non-recanalized MCAs). ASL images were obtained using pseudo-continuous ASL technique with 1600 ms (millisecond) of post-label delay within 3 days from symptom onset. Signal intensities on color ASL images were classified as high, intermediate, and poor grade visually. The ratio of maximum ASL signal between the ischemic area and contralateral side was calculated and compared between patients with and without MCA recanalization. Among patients with non-recanalized MCA, ASL signal ratios were compared between patients with and without hyperintense vessel sign on fluid attenuated inversion recovery (FLAIR). Also, correlation between the ASL signal ratio and National Institutes of Health Stroke Scale (NIHSS) score was evaluated.

High or intermediate grade on color ASL images were more frequently found in patients with recanalized MCA (P < .01). Patients with non-recanalized MCA had higher ASL signal ratio in overall ASL signal grade (P = .010) and intermediate grade (P = .011). Among patients with non-recanalized MCA, those with hyperintense vessel sign on FLAIR had higher ASL signal ratios (P = .049). ASL signal ratio was negatively correlated with both initial (P = .023) and final (P = .003) NIHSS scores.

The ASL signal ratio could help to differentiate between the pial collaterals and post-recanalization luxury perfusion. A higher ASL ratio was related with the hyperintense vessel sign on FLAIR and lower NIHSS score.
Immersive virtual reality (VR) training increases the self-efficacy of in-hospital healthcare providers and patient families regarding tracheostomy-related knowledge and care skills
Authors: Chiang Dung-Hung , Huang Chia-Chang , Cheng Shu-Chuan , Cheng Jui-Chun , Wu Cheng-Hsien , Huang Shiau-Shian , Yang Ying-Ying , Yang Ling-Yu , Kao Shou-Yen , Chen Chen-Huan , Shulruf Boaz , Lee Fa-Yauh
Published: January 2022

Background:

Virtual reality (VR)-based simulation in hospital settings facilitates the acquisition of skills without compromising patient safety. Despite regular text-based training, a baseline survey of randomly selected healthcare providers revealed deficiencies in their knowledge, confidence, comfort, and care skills regarding tracheostomy. This prospective pre–post study compared the effectiveness of regular text- and VR-based intervention modules in training healthcare providers’ self-efficacy in tracheostomy care skills.

Methods:

Between January 2018 and January 2020, 60 healthcare providers, including physicians, nurses, and respiratory therapists, were enrolled. For the intervention, a newly developed head-mounted display (HMD) and web VR materials were implemented in training and clinical services. Subsequently, in-hospital healthcare providers were trained using either text or head-mounted display virtual reality (HMD-VR) materials in the regular and intervention modules, respectively. For tracheostomy care skills, preceptors directly audited the performance of trainees and provided feedback.

Results:

At baseline, the degree of trainees’ agreement with the self-efficacy-related statements, including the aspects of familiarity, confidence, and anxiety about tracheostomy-related knowledge and care skills, were not different between the control and intervention groups. At follow-up stage, compared with the regular group, a higher percentage of intervention group’ trainees reported that they are “strongly agree” or “somewhat agree” that the HMD-VR simulation increases their self-efficacy, including the aspects of familiarity and confidence, and reduced their anxiety about tracheostomy-related knowledge and care skills. After implementation, a higher degree of trainees’ average satisfaction with VR-based training and VR materials was observed in the intervention group than in the regular group. Most reported that VR materials enabled accurate messaging and decreased anxiety. The increasing trend of the average written test and hands-on tracheostomy care skills scores among the intervention group trainees was significant compared to those in the regular group. The benefits of HMD-VR simulations and web-VR material-based clinical services for in-hospital healthcare providers and patient families persisted until 3 to 4 weeks later.

Conclusion:

The current study suggests that VR materials significantly enhance trainees’ self-efficacy (increased familiarity, increased confidence, and reduced anxiety) and their satisfaction with the training, while motivating them to use acquired knowledge and skills in clinical practice.
Efficacy and safety of nitrate supplementation on exercise tolerance in chronic obstructive pulmonary disease
Authors: Yang Hongkuan , He Shuifeng , Chen Fang , Liang Linbao , Pan Junjie
Published: January 2022

Background:

Exercise intolerance was prevalent in people with chronic obstructive pulmonary disease (COPD) and had a detrimental effect on the quality of life. We aimed to evaluate the efficacy and safety of nitrate supplementation in exercise tolerance of people with COPD.

Methods:

We searched medical databases including Cochrane Library, EMBASE, and PubMed from inception to October 2020 for randomized control trials in treating COPD with nitrate supplementation.

Results:

Nine trials were identified. Compared with placebo, nitrate supplementation has no significant effect on the following variables: exercise endurance time (standard mean difference [SMD]: 0.06; 95% confidence interval [CI]: –0.39 to 0.52; P = .79), exercise capacity (SMD: 0.30; 95% CI: –0.21 to 0.80; P = .25), oxygen consumption (SMD: –0.04; 95% CI: –0.33 to 0.25; P = .80), resting systolic blood pressure (MD: –2.84; 95% CI: –8.46 to 2.78; P = .32), systolic blood pressure after exercise (MD: –4.66; 95% CI –15.66 to 6.34; P = .41), resting diastolic blood pressure (MD: 0.89; 95% CI: –4.41 to 6.19; P = .74), diastolic blood pressure after exercise (MD: –0.21; 95% CI: –5.51 to 5.10; P = .94), heart rate (MD: –2.52; 95% CI: –7.76 to 2.73; P = .35), and arterial oxygen saturation (MD: –0.44; 95% CI: –2.38 to 1.49; P = .65). No severe adverse effects from nitrate supplementation were reported in the included trails.

Conclusion:

Current evidence suggests that nitrate supplementation may be safe but ineffective for improving exercise tolerance in people with COPD.
Congenital soft tissue Ewing's sarcoma
Authors: Yang Chaoxiang , Chen Wenjun , Han Penghui
Published: January 2022

Rationale:

Most congenital soft tissue masses are benign. Ewing's sarcoma (ES) is a highly malignant tumor that commonly occurs in children and adolescents and rarely occurs during the fetal period. Cases of congenital soft tissue ES with magnetic resonance imaging (MRI) findings are scarce. To the best of our knowledge, no previous reports have described the pre- and postnatal MRI findings of ES.

Patient concerns:

We present a case of congenital soft tissue ES arising in the body wall, which was examined using MRI during the prenatal and neonatal periods.

Diagnoses:

Malignancy was suspected by diffusion-weighted imaging, which demonstrated restricted diffusion within the mass even during the fetal period. ES was confirmed via histopathological examination after birth.

Interventions:

The patient initially underwent conservative treatment for suspected hemangioma. Tumorrectomy was undergone after three weeks based on previously dissatisfied therapeutic effects.

Outcomes:

The patient died of multiple distant metastases despite undergoing postoperative chemotherapy and metastasectomies.

Lessons:

Fetal or neonatal soft tissue ES may be clinically misdiagnosed as a hemangioma. It is important to suspect this through an imaging approach such as diffusion-weighted imaging.
Vitamin D deficiency osteomalacia triggered by long-term social withdrawal and unbalanced diet in a Japanese middle-aged subject
Authors: Iwamoto Yuichiro , Tatsumi Fuminori , Dan Kazunori , Katakura Yukino , Shimoda Masashi , Kimura Tomohiko , Nakanishi Shuhei , Mune Tomoatsu , Kaku Kohei , Kaneto Hideaki
Published: January 2022

Introduction:

Osteomalacia is caused by an increase in the number of osteoids owing to mineralization failure. There are various causes of osteomalacia, such as hypophosphatemia due to excess production of fibroblast growth factor 23, vitamin D deficiency, insufficient vitamin D action, and renal tubular disorders.

Patient concerns:

A 53-year-old man with bone pain and gait disturbance was referred to our institution. At the age of 35, he developed atopic dermatitis. He had eyesight deterioration due to atopic cataracts when he was 37 years old. Subsequently, he stayed home all the time, and his eating habits were unbalanced for a long period of time. Although he had atopic dermatitis, he did not take allergen-free diets, and he did not use sunscreen. Furthermore, when he was 43 years old, he failed to flex his legs and suffered gait disturbance.

Diagnosis:

Hypocalcemia and hypophosphatemia were observed as follow: calcium, 5.5 mg/dL; adjusted calcium, 6.9 mg/dL; inorganic phosphorous, 1.9 mg/dL. In addition, intact parathyroid hormone levels were as high as 277.4 pg/mL, and 1, 25-(OH)2 vitamin D and 25-(OH) vitamin D levels were markedly reduced: 1, 25-(OH)2 vitamin D, ≤4 pg/mL; 25-(OH) vitamin D, 11.0 ng/mL. Fibroblast growth factor 23 levels did not increase. Alkaline phosphatase (ALP) and bone-type ALP (BAP) levels were high: ALP, 784 U/L; BAP, 159.2 μg/L (reference range: 3.7–20.9 μg/L). Based on these findings, we diagnosed this patient with vitamin D-deficient osteomalacia triggered by long-term social withdrawal and an unbalanced diet.

Interventions and outcomes:

After hospitalization, to treat vitamin D-deficient osteomalacia, we started to administer 1 μg/day of alfacalcidol and 3 g/day of calcium lactate. Approximately one month later, 1,25-(OH)2 vitamin D levels increased to 214 pg/mL. Consequently, calcium and inorganic phosphorus were also increased up to 7.8 mg/dL and 3.9 mg/dL, respectively, and intact parathyroid hormone was decreased to 132.0 pg/mL.

Conclusions:

We should bear in mind the possibility of osteomalacia triggered by social withdrawal and vitamin D deficiency even in middle-aged subjects.
Acupuncture for nasal congestion in COVID-19
Authors: Dong Zhibin , Guo Jinyun , Deng Tingting , Zhang Jingwen , Lv Xinwei , Zhang Kaixin , Ma Yuxia , Ma Yuning
Published: January 2022

Background:

From the end of 2019 to now, coronavirus disease 2019 (COVID-19) has put enormous strain on the world's health systems, causing significant deaths and economic losses worldwide. Nasal congestion, one of the symptoms of COVID-19, poses considerable problems for patients. In China, acupuncture has been widely used to treat nasal congestion caused by COVID-19, but there is still a lack of evidence-based medical evaluation.

Methods:

According to the retrieval strategies, randomized controlled trials on the acupuncture for COVID-19 nasal congestion were obtained from China National Knowledge Infrastructure, WanFang, VIP, PubMed, Embase, and Cochrane Library, regardless of publication date, or language. Studies were screened based on inclusion and exclusion criteria, and the Cochrane risk bias assessment tool was used to evaluate the quality of the studies. The meta-analysis was performed using Review Manager (RevMan 5.3) and STATA 14.2 software. Ultimately, the evidentiary grade for the results will be evaluated.

Results:

The study will provide a high-quality and convincing assessment of the efficacy and safety of acupuncture in the treatment of COVID-19's nasal congestion and will be published in peer-reviewed journals.

Conclusion:

Our findings will provide references for future clinical decision and guidance development.

PROSPERO registration number:

NO.CRD42021299482.
Dramatic recovery without steroid therapy and withdrawal from insulin therapy in a subject with hyperglycemic and hyperosmolar syndrome and depletion of insulin secretory capacity induced by type 2 autoimmune pancreatitis
Authors: Iwamoto Yuichiro , Tatsumi Fuminori , Kohara Kenji , Shimoda Masashi , Nakanishi Shuhei , Mune Tomoatsu , Kaku Kohei , Kaneto Hideaki
Published: January 2022

Introduction:

Autoimmune pancreatitis (AIP) is characterized by the involvement of autoimmune mechanisms and is classified as type 1, together with infiltration of IgG4-positive cells, and type 2 with poor serological abnormal findings. In clinical practice, AIP is often treated with steroid therapy.

Patient concerns:

An 81-year-old Japanese woman had thirst and appetite loss in the previous 5 days; thus, she visited a local doctor. The patient had no abdominal or back pain. She had no history of diabetes mellitus, but at that time blood glucose level and HbA1c were as high as 633 mg/dL and 9.7%, respectively, and she was referred to our institution.

Diagnosis:

Based on various clinical findings in this patient, we diagnosed her with hyperglycemic and hyperosmolar syndrome and depletion of insulin secretory capacity induced by type 2 AIP.

Interventions and outcomes:

The patient completely recovered without steroid therapy and was withdrawn from insulin therapy.

Conclusions:

We should bear in mind the possibility of AIP when the sudden onset of hyperglycemia together with enlargement of the pancreas are observed in subjects without a history of diabetes mellitus.
Machine Learning–Based Mortality Prediction of Patients at Risk During Hospital Admission
Authors: Trentino Kevin M. , Schwarzbauer Karin , Mitterecker Andreas , Hofmann Axel , Lloyd Adam , Leahy Michael F. , Tschoellitsch Thomas , Böck Carl , Hochreiter Sepp , Meier Jens
Published: January 2022

Objectives

The ability to predict in-hospital mortality from data available at hospital admission would identify patients at risk and thereby assist hospital-wide patient safety initiatives. Our aim was to use modern machine learning tools to predict in-hospital mortality from standardized data sets available at hospital admission.

Methods

This was a retrospective, observational study in 3 adult tertiary care hospitals in Western Australia between January 2008 and June 2017. Primary outcome measures were the area under the curve for the receiver operating characteristics curve, the F
1 score, and the average precision of the 4 machine learning algorithms used: logistic regression, neural networks, random forests, and gradient boosting trees.

Results

Using our 4 predictive models, in-hospital mortality could be predicted satisfactorily (areas under the curve for neural networks, logistic regression, random forests, and gradient boosting trees: 0.932, 0.936, 0.935, and 0.935, respectively), with moderate F
1 scores: 0.378, 0.367, 0.380, and 0.380, respectively. Average precision values were 0.312, 0.321, 0.334, and 0.323, respectively. It remains unknown whether additional features might improve our models; however, this would result in additional efforts for data acquisition in daily clinical practice.

Conclusions

This study demonstrates that using only a limited, standardized data set in-hospital mortality can be predicted satisfactorily at the time point of hospital admission. More parameters describing patient’s health are likely needed to improve our model.
Increased 68Ga-FAPI Uptake in Facet Joint Osteoarthritis in a Patient With Esophageal Cancer
Authors: Yang Xiao , You Zhouxiang , Gong Weidong , Chen Yue , Liu Huipan
Published: January 2022

A 69-year-old man presented with newly diagnosed esophageal cancer was enrolled in our clinical trial of 68Ga-FAPI PET/CT study in tumors. Increased tracer uptake was noted in esophageal cancer. In addition, the facet joint osteoarthritis of T7/8 vertebrae also revealed elevated 68Ga-FAPI uptake.
Progressive Multifocal Leukoencephalopathy Mimicking Malignancy on 68Ga-FAPI PET/CT
Authors: Gong Weidong , Fu Meng , Zhang Yaling , Yang Xiao , Zhang Chunyin
Published: January 2022

A 43-year-old man presented with weakness in his right upper limb for 2 months. Head MRI showed intracranial multiple abnormal signal foci. Malignancy was suspected. The patient was subsequently enrolled in the clinical trial of 68Ga-FAPI PET/CT. 68Ga-FAPI PET/CT showed intracranial multiple FAPI-avid foci. It was also highly suggestive of malignancy. However, the combination of clinical manifestations, imaging findings, cerebral spinal fluid examinations, and effective immunotherapy confirmed the diagnosis of progressive multifocal leukoencephalopathy. 68Ga-FAPI may have potential advantages in the diagnosis of progressive multifocal leukoencephalopathy.
Quality and Safety in Healthcare, Part XCIII
Authors: Harolds Jay A.
Published: January 2022

Design for Six Sigma (DFSS) is used to design new outputs such as manufactured products or to design new processes. The steps in DFSS are define, measure, analyze, design, and verify. Many sophisticated statistical tools are often used. There are advantages and disadvantages of both Lean and Six Sigma, and often a blending of the 2 methodologies are used in the Lean Six Sigma methodology.
Lymphogranuloma Venereum Mimicking Lymphoma on FDG PET/CT
Authors: Georgopoulou Angeliki N. , Skoura Evangelia , Lakiotaki Eleftheria , Sipsas Nikolaos V. , Vassilakopoulos Theodoros P.
Published: January 2022

A 42-year-old man presented with painless, left inguinal lymphadenopathy, which was suspicious of malignant lymphoma. Multiple left-sided foci of markedly increased metabolic activity were observed on PET/CT (SUVmax up to 22.3), located at the inguinal, iliac, and para-aortic lymph nodes along with small-sized right inguinal lymphadenopathy. Laboratory tests revealed increased inflammation markers and neutrophilic leukocytosis. Pathological examination from dissected inguinal lymph node was consistent with granulomatous disease. Infection by chlamydia trachomatis was made serologically establishing the diagnosis of lymphogranuloma venereum.
Increased 68Ga-FAPI Uptake in Avascular Necrosis of Femoral Head in a Patient With Nasopharyngeal Carcinoma
Authors: Liu Huipan , Fu Wenhui , Yang Xiao , Chen Yue
Published: January 2022

A 73-year-old man with newly diagnosed nasopharyngeal carcinoma included in a clinical trial of 68Ga-FAPI PET/CT study in tumors (ChiCTR2100044131). Increased tracer uptake was noted in nasopharyngeal carcinoma and cervical lymph nodes metastases. In addition, avascular necrosis of right femoral head also revealed increased FAPI activity.
Similar Findings on 18F-MFBG PET/CT and 68Ga-DOTATATE PET/CT in a Patient With Widespread Metastatic Pheochromocytoma
Authors: Wang Peipei , Hou Guozhu , Jing Hongli , Zhuang Hongming , Li Fang
Published: January 2022

A 27-year-old woman with known malignant pheochromocytoma was enrolled in a clinical trial to compare efficacy of 68Ga-DOTATATE PET/CT and 18F-MFBG PET/CT. Images from both studies detected similar number of the metastatic lesions. In addition, both studies detected more lesions than 131I-MIBG imaging.
Colonoscopy Screening and Polyp Detection in the Southeastern United States
Authors: Oden Kristy , Nelson Michelle , Williams Laura
Published: January 2022

Screening colonoscopy is recommended for polyp detection and colorectal cancer prevention for those aged 50–75 years. The aim of this study was to determine colon polyp incidence rates detected through screening colonoscopies in the Southeast United States. A retrospective chart review was conducted to determine polyp rates. Charts with a diagnostic code of “screening” colonoscopy were reviewed for age, gender, number of polyps, and type of polyps. The number of charts reviewed was 534, with a total of 239 found to have polyps. Polyp type was defined as hyperplastic and adenomatous, with all adenomatous types grouped together. Descriptive statistics were used for data analysis. The median age of participants was 62 years with 58% being male. The combined rate of colon polyp detection was 44.6%. Seventy percent of the overall sample was found to have at least one polyp. From 16% to 20% of the study population had mixed (adenomatous and hyperplastic) polyps. This study supports the need for continued screening colonoscopies for polyp detection and removal. Education is key and nurses are often the ones who have the greatest educational opportunity. This study indicates the need for further research that may support colorectal cancer screening beginning at an earlier age.
Jack of all trades, master of each: the diversity of fibroblast growth factor signalling in eye development
Authors: Makrides Neoklis , Wang Qian , Tao Chenqi , Schwartz Samuel , Zhang Xin
Published: January 2022

A central question in development biology is how a limited set of signalling pathways can instruct unlimited diversity of multicellular organisms. In this review, we use three ocular tissues as models of increasing complexity to present the astounding versatility of fibroblast growth factor (FGF) signalling. In the lacrimal gland, we highlight the specificity of FGF signalling in a one-dimensional model of budding morphogenesis. In the lens, we showcase the dynamics of FGF signalling in altering functional outcomes in a two-dimensional space. In the retina, we present the prolific utilization of FGF signalling from three-dimensional development to homeostasis. These examples not only shed light on the cellular basis for the perfection and complexity of ocular development, but also serve as paradigms for the diversity of FGF signalling.
Antibacterial properties of poly (N,N-dimethylaminoethyl methacrylate) obtained at different initiator concentrations in solution polymerization
Authors: Stawski Dawid , Rolińska Karolina , Zielińska Dorota , Sahariah Priyanka , Hjálmarsdóttir Martha Á. , Másson Már
Published: January 2022

The samples of poly(N,N-dimethylaminoethyl methacrylate) were synthesized by radical polymerization. The amount of monomer and solvent was constant as opposed to an amount of initiator which was changing. No clear relationship between polymerization conditions and the molecular weight of the polymer was found, probably due to the branched configuration of produced polymer. Bactericidal interactions in all samples against Gram-positive and Gram-negative bacteria have been demonstrated. However, the observed effect has various intensities, depending on the type of bacteria and the type of sample.
Substantial variability in morphological scaling among bumblebee colonies
Authors: Perl C. D. , Johansen Z. B. , Jie V. W. , Moradinour Z. , Guiraud M. , Restrepo C. E. , Miettinen A. , Baird E.
Published: January 2022

Differences in organ scaling among individuals may play an important role in determining behavioural variation. In social insects, there are well-documented intraspecific differences in colony behaviour, but the extent that organ scaling differs within and between colonies remains unclear. Using 12 different colonies of the bumblebeeBombus terrestris, we aim to address this knowledge gap by measuring the scaling relationships between three different organs (compound eyes, wings and antennae) and body size in workers.Though colonies were exposed to different rearing temperatures, this environmental variability did not explain the differences of the scaling relationships. Two colonies had differences in wing versus antenna slopes, three colonies showed differences in wing versus eye slopes and a single colony has differences between eye versus antenna slopes. There are also differences in antennae scaling slopes between three different colonies, and we present evidence for putative trade-offs in morphological investment. We discuss the utility of having variable scaling among colonies and the implication for understanding variability in colony fitness and behaviour.
A modern baseline for the paired isotopic analysis of skin and bone in terrestrial mammals
Authors: Doherty Sean P. , Collins Matthew J. , Harris Alison J. T. , Sistiaga Ainara , Newton Jason , Alexander Michelle M.
Published: January 2022

We present the isotopic discrimination between paired skin and bone collagen from animals of known life history, providing a modern baseline for the interpretation of archaeological isotopic data. At present, the interpretation of inter-tissue variation (Δ
(skin–bone)
) in mummified remains is based on comparisons with other archaeological material, which have attributed divergence to their contrasting turnover rates, with rapidly remodelling skin collagen incorporating alterations in environmental, cultural and physiological conditions in the months prior to death. While plausible, the lack of baseline data from individuals with known life histories has hindered evaluation of the explanations presented. Our analysis of a range of animals raised under a variety of management practices showed a population-wide trend for skin collagen to be depleted in
13
C by –0.7‰ and enriched in
15
N by +1.0‰ relative to bone collagen, even in stillborn animals. These results are intriguing and difficult to explain using current knowledge; however, on the basis of the findings reported here, we caution any results which interpret simply on differing turnover rates. We hypothesize that there may be a consistent difference in the routing of dietary protein and lipids between skin and bone, with potentially on-site synthesis of non-essential amino acids using carbon and nitrogen that have been sourced via different biochemical pathways.
Porosity of the porous carbonate rocks in the Jingfengqiao–Baidiao area based on finite automata
Authors: Kuang Honghai , Ye Xi , Qing Zhiyi
Published: January 2022

This study is based on the processing of computed microtomography images of rock samples. In this study, a finite automation is constructed using the grey value, red-green-blue (RGB) value and Euler number of polarized images of carbonate rocks from the Jingfengqiao–Baidiao area. The finite automaton is used to perform black and white binary processing of the polarized images of the carbonate rocks. The porosity of the carbonate rock is calculated based on the black and white binarization processing results of the polarized images of the carbonate rocks. The obtained porosity is compared with the carbonate porosity obtained by use of the traditional carbonate research method. When the two porosities are close, the image processing threshold of the finite automata is considered to be credible. Based on the finite automata established using the image processing threshold, the black and white binary images of the polarized images of the carbonate rocks are used to establish a rock pore image using I
mage
J2X. The polarized images of the carbonate rocks are classified according to their RGB values using the finite automata for the porosity classification, and the obtained images are used as textures to paste onto a cube to construct a three-dimensional data model of the carbonate rocks. This study also uses 16S rDNA analysis to verify the formation mechanism of the carbonate pores in the Jingfengqiao–Baidiao area. The results of the 16S rDNA analysis show that the pores in the carbonate rocks in the Jingfengqiao–Baidiao area are closely related to microorganisms, represented by denitrifying bacteria.
Trophic guilds of suction-feeding fishes are distinguished by their characteristic hydrodynamics of swimming and feeding
Authors: Olsson Karin H. , Gurka Roi , Holzman Roi
Published: January 2022

Suction-feeding in fishes is a ubiquitous form of prey capture whose outcome depends both on the movements of the predator and the prey, and on the dynamics of the surrounding fluid, which exerts forces on the two organisms. The inherent complexity of suction-feeding has challenged previous efforts to understand how the feeding strikes are modified when species evolve to feed on different prey types. Here, we use the concept of dynamic similarity, commonly applied to understanding the mechanisms of swimming, flying, walking and aquatic feeding. We characterize the hydrodynamic regimes pertaining to (i) the forward movement of the fish (ram), and (ii) the suction flows for feeding strikes of 71 species of acanthomorph fishes. A discriminant function analysis revealed that feeding strikes of zooplanktivores, generalists and piscivores could be distinguished based on their hydrodynamic regimes. Furthermore, a phylogenetic comparative analysis revealed that there are distinctive hydrodynamic adaptive peaks associated with zooplanktivores, generalists and piscivores. The scaling of dynamic similarity across species, body sizes and feeding guilds in fishes indicates that elementary hydrodynamic principles govern the trophic evolution of suction-feeding in fishes.
The pitfalls of inferring virus–virus interactions from co-detection prevalence data: application to influenza and SARS-CoV-2
Authors: Domenech de Cellès Matthieu , Goult Elizabeth , Casalegno Jean-Sebastien , Kramer Sarah C.
Published: January 2022

There is growing experimental evidence that many respiratory viruses—including influenza and SARS-CoV-2—can interact, such that their epidemiological dynamics may not be independent. To assess these interactions, standard statistical tests of independence suggest that the prevalence ratio—defined as the ratio of co-infection prevalence to the product of single-infection prevalences—should equal unity for non-interacting pathogens. As a result, earlier epidemiological studies aimed to estimate the prevalence ratio from co-detection prevalence data, under the assumption that deviations from unity implied interaction. To examine the validity of this assumption, we designed a simulation study that built on a broadly applicable epidemiological model of co-circulation of two emerging or seasonal respiratory viruses. By focusing on the pair influenza–SARS-CoV-2, we first demonstrate that the prevalence ratio systematically underestimates the strength of interaction, and can even misclassify antagonistic or synergistic interactions that persist after clearance of infection. In a global sensitivity analysis, we further identify properties of viral infection—such as a high reproduction number or a short infectious period—that blur the interaction inferred from the prevalence ratio. Altogether, our results suggest that ecological or epidemiological studies based on co-detection prevalence data provide a poor guide to assess interactions among respiratory viruses.
Deep Proteome Profiling Enabled Functional Annotation and Data-Independent Quantification of Proline Hydroxylation Targets
Authors: Gong Yao , Behera Gaurav , Erber Luke , Luo Ang , Chen Yue
Published: January 2022

Proline hydroxylation (Hyp) regulates protein structure, stability and protein-protein interaction and is widely involved in diverse metabolic and physiological pathways in cells and diseases. To reveal functional features of the proline hydroxylation proteome, we integrated various data sources for deep proteome profiling of proline hydroxylation proteome in human and developed HypDB (https://www.HypDB.site), an annotated database and web server for proline hydroxylation proteome. HypDB provides site-specific evidence of modification based on extensive LC-MS analysis and literature mining with 15319 non-redundant Hyp sites and 8226 sites with high confidence on human proteins. Annotation analysis revealed significant enrichment of proline hydroxylation on key functional domains and tissue-specific distribution of Hyp abundance across 26 types of human organs and fluids and 6 cell lines. The network connectivity analysis further revealed a critical role of proline hydroxylation in mediating protein-protein interactions. Moreover, the spectral library generated by HypDB enabled data-independent analysis (DIA) of clinical tissues and the identification of novel Hyp biomarkers in lung cancer and kidney cancer. Taken together, our integrated analysis of human proteome with publicly accessible HypDB revealed functional diversity of Hyp substrates and provides a quantitative data source to characterize proline hydroxylation in pathways and diseases.
Hypercapnia limits β-catenin-mediated alveolar type 2 cell progenitor function by altering Wnt production from adjacent fibroblasts
Authors: Dada Laura A. , Welch Lynn C. , Magnani Natalia D. , Ren Ziyou , Brazee Patricia L. , Celli Diego , Flozak Annette S. , Weng Anthea , Maciel-Herrerias Mariana , Kryvenko Vitalii , Vadász István , Runyan Constance E , Abdala-Valencia Hiam , Shigemura Masahiko , Casalino-Matsuda S. Marina , Misharin Alexander V. , Budinger G.R. Scott , Gottardi Cara J. , Sznajder Jacob I.
Published: January 2022

Persistent symptoms and radiographic abnormalities suggestive of failed lung repair are among the most common symptoms in patients with COVID-19 after hospital discharge. In mechanically ventilated patients with ARDS secondary to SARS-CoV-2 pneumonia, low tidal volumes to reduce ventilator-induced lung injury necessarily elevate blood CO2 levels, often leading to hypercapnia. The role of hypercapnia on lung repair after injury is not completely understood. Here, we show that hypercapnia limits β-catenin signaling in alveolar type 2 (AT2) cells, leading to reduced proliferative capacity. Hypercapnia alters expression of major Wnts in PDGFRa+-fibroblasts from those maintaining AT2 progenitor activity and towards those that antagonize β-catenin signaling and limit progenitor function. Activation of β-catenin signaling in AT2 cells, rescues the inhibition AT2 proliferation induced by hypercapnia. Inhibition of AT2 proliferation in hypercapnic patients may contribute to impaired lung repair after injury, preventing sealing of the epithelial barrier, increasing lung flooding, ventilator dependency and mortality.
Persistence of parental age effect on somatic mutation rates across generations in Arabidopsis
Authors: Bhushan Shashi , Singh Amit Kumar , Thakur Yogendra , Baskar Ramamurthy
Published: January 2022

In the model plant Arabidopsis thaliana, parental age is known to affect somatic mutation rates in their immediate progeny and here we show that this age dependent effect persists across successive generations. Using a set of detector lines carrying the mutated uidA gene, we examined if a particular parental age maintained across five consecutive generations affected the rates of base substitution (BSR), intrachromosomal recombination (ICR), frameshift mutation (FS), and transposition. The frequency of functional GUS reversions were assessed in seedlings as a function of identical/different parental ages across generations. In the context of a fixed parental age, BCR/ICR rates were unaffected in the first three generations, then dropped significantly in the 4th and increased in most instances in the 5th generation. On the other hand, with advancing parental ages, BSR/ICR rates remained high in the first two/three generations, with a striking resemblance in the pattern of mutation rates. We adopted a novel approach of identifying and tagging flowers pollinated on a particular day, thereby avoiding biases due to potential emasculation induced stress responses. Our results suggest a time component in counting the number of generations a plant has passed through self-fertilization at a particular age in determining the somatic mutation rates.
Impaired spatial memory in adult vitamin D deficient BALB/c mice is associated with reductions in spine density, nitric oxide, and neural nitric oxide synthase in the hippocampus
Authors: Al-Amin Md. Mamun , Sullivan Robert K. P. , Alexander Suzy. , Carter David A. , Bradford DanaKai. , Burne Thomas H. J.
Published: January 2022

Vitamin D deficiency is prevalent in adults and is associated with cognitive impairment. However, the mechanism by which adult vitamin D (AVD) deficiency affects cognitive function remains unclear. We examined spatial memory impairment in AVD-deficient BALB/c mice and its underlying mechanism by measuring spine density, long term potentiation (LTP), nitric oxide (NO), neuronal nitric oxide synthase (nNOS) and endothelial NOS (eNOS) in the hippocampus. Adult male BALB/c mice were fed a control or vitamin D deficient diet for 20 weeks. Spatial memory performance was measured using an active place avoidance (APA) task, where AVD-deficient mice had reduced latency entering the shock zone compared to controls. We characterised hippocampal spine morphology in the CA1 and dentate gyrus (DG) and made electrophysiological recordings in the hippocampus of behaviourally naïve mice to measure LTP. We next measured NO, as well as glutathione, lipid peroxidation and oxidation of protein products and quantified hippocampal immunoreactivity for nNOS and eNOS. Spine morphology analysis revealed a significant reduction in the number of mushroom spines in the CA1 dendrites but not in the DG. There was no effect of diet on LTP. However, hippocampal NO levels were depleted whereas other oxidation markers were unaltered by AVD deficiency. We also showed a reduced nNOS, but not eNOS, immunoreactivity. Finally, vitamin D supplementation for 10 weeks to AVD-deficient mice restored nNOS immunoreactivity to that seen in in control mice. Our results suggest that lower levels of NO, reduced nNOS immunostaining contribute to hippocampal-dependent spatial learning deficits in AVD-deficient mice.
m6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues
Authors: Song Bowen , Huang Daiyun , Zhang Yuxin , Wei Zhen , Su Jionglong , de Magalhães João Pedro , Rigden Daniel J. , Meng Jia , Chen Kunqi
Published: January 2022

As the most pervasive epigenetic marker present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies revealed the distinct patterns of m6A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m6A methylation. We present here a comprehensive online platform m6A-TSHub for unveiling the context-specific m6A methylation and genetic mutations that potentially regulate m6A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB: a comprehensive database of 184,554 functionally annotated m6A sites derived from 23 human tissues and 499,369 m6A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder: a web server for high-accuracy prediction of m6A methylation sites within a specific tissue from RNA sequences, which was constructed using multi-instance deep neural networks with gated attention; (3) m6A-TSVar: a web server for assessing the impact of genetic variants on tissue-specific m6A RNA modification; and (4) m6A-CAVar: a database of 587,983 TCGA cancer mutations (derived from 27 cancer types) that were predicted to affect m6A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m6A methylome and genetic factor of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at: www.xjtlu.edu.cn/biologicalsciences/m6ats.
An antibody targeting the N-terminal domain of SARS-CoV-2 disrupts the spike trimer
Authors: Suryadevara Naveenchandra , Shiakolas Andrea R. , VanBlargan Laura A. , Binshtein Elad , Chen Rita E. , Case James Brett , Kramer Kevin J. , Armstrong Erica , Myers Luke , Trivette Andrew , Gainza Christopher , Nargi Rachel S. , Selverian Christopher N. , Davidson Edgar , Doranz Benjamin J. , Diaz Summer M. , Handal Laura S. , Carnahan Robert H. , Diamond Michael S. , Georgiev Ivelin S. , Crowe James E.
Published: January 2022

The protective human antibody response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus focuses on the spike (S) protein which decorates the virion surface and mediates cell binding and entry. Most SARS-CoV-2 protective antibodies target the receptor- binding domain or a single dominant epitope (‘supersite’) on the N terminal domain (NTD). Here, using the single B cell technology LIBRA-seq, we isolated a large panel of NTD-reactive and SARS-CoV-2 neutralizing antibodies from an individual who had recovered from COVID-19. We found that neutralizing antibodies to the NTD supersite commonly are encoded by the IGHV1-24 gene, forming a genetic cluster that represents a public B cell clonotype. However, we also discovered a rare human antibody, COV2-3434, that recognizes a site of vulnerability on the SARS-CoV-2 S protein in the trimer interface and possesses a distinct class of functional activity. COV2-3434 disrupted the integrity of S protein trimers, inhibited cell-to-cell spread of virus in culture, and conferred protection in human ACE2 transgenic mice against SARS-CoV-2 challenge. This study provides insight about antibody targeting of the S protein trimer interface region, suggesting this region may be a site of virus vulnerability.
COVID-19 infection and vaccination rates in healthcare workers in British Columbia, Canada: A Longitudinal Urban versus Rural Analysis of the Impact of the Vaccine Mandate
Authors: Yassi Annalee , Barker Stephen , Lockhart Karen , Taylor Deanne , Harris Devin , Hundal Harsh , Grant Jennifer M. , Okpani Arnold Ikedichi , Pollock Sue , Sprague Stacy , Sing Chad Kim
Published: January 2022

Purpose

Healthcare workers (HCWs) play a critical role in responding to the COVID-19 pandemic. Early in the pandemic, urban centres were hit hardest globally; rural areas gradually became more impacted. We compared COVID-19 infection and vaccine uptake in HCWs living in urban versus rural locations within, and between, two health authorities in British Columbia (BC), Canada. We also analyzed the impact of a vaccine mandate for HCWs.

Methods

We tracked laboratory-confirmed SARS-CoV-2 infections, positivity rates, and vaccine uptake in 29,021 HCWs in Interior Health (IH) and 24,634 HCWs in Vancouver Coastal Health (VCH), by occupation, age, and home location, comparing to the general population in that region. We then evaluated the impact of infection rates as well as the mandate on vaccination uptake.

Results

By October 27, 2021, the date that unvaccinated HCWs were prohibited from providing healthcare, only 1.6% in VCH yet 6.5% in IH remained unvaccinated. Rural workers in both areas had significantly higher unvaccinated rates compared with urban dwellers. Over 1,800 workers, comprising 6.4% of rural HCWs and 3.3% of urban HCWs, remained unvaccinated and set to be terminated from their employment. While the mandate prompted a significant increase in second doses, the impact on the unvaccinated was less clear.

Conclusions

As rural areas often suffer from under-staffing, loss of HCWs could have serious impacts on healthcare provision as well as on the livelihoods of unvaccinated HCWs. Greater efforts are needed to understand how to better address the drivers of rural-related vaccine hesitancy as the pandemic continues.
Genetic overlap between Parkinson disease and inflammatory bowel disease
Authors: Kang Xiaoying , Ploner Alexander , Wang Yunzhang , Ludvigsson Jonas F , Williams Dylan M , Pedersen Nancy , Wirdefeldt Karin
Published: January 2022

Importance Parkinson disease (PD) and inflammatory bowel disease (IBD) have been associated, implying shared pathophysiology. Characterizing genetic pleiotropy between the two conditions aids the exploration of common etiology.
Objective To estimate the genetic correlation between PD and IBD and to identify specific loci influencing both conditions.
Design Genetic study with applications of high definition likelihood and conditional false discovery rate (FDR) framework.
Setting The study was based on summary statistics of genome-wide association studies (GWAS).
Participants The PD GWAS comprised 37,688 cases and 981,372 controls, and the IBD GWAS included 25,042 cases and 34,915 controls. Participants were of mixed ethnicity.
Exposures None.
Main Outcomes and Measures The main outcomes were a set of single nucleotide polymorphisms (SNPs) identified by conditional FDR analysis as jointly associated with PD and IBD.
Results Weak but statistically significant genetic correlations were detected for PD with both Crohn's disease (CD) and ulcerative colitis (UC), the two main subtypes of IBD. A total of 1333 SNPs in 28 genomic loci and 1915 SNPs in 22 loci were jointly associated with PD-CD and PD-UC, respectively, at conjunctional FDR under 0.01. The pleiotropic loci appeared distinctive for PD-CD and PD-UC, are mostly novel and comprise loci with either same or opposing genetic effects on the two phenotypes. Positional and eQTL mapping prioritized 316 PD-CD and 303 PD-UC genes, among which only <10% are differentially expressed in both colon and substantia nigra. The KEGG pathways enriched by all prioritized genes were highly concordant between PD-CD and PD-UC, with the majority being related to immune and/or autoimmune dysfunction.
Conclusions and Relevance Overall, we found robust evidence for a genetic link between PD and each subtype of IBD. The identified genetic overlap is complex at the locus and gene levels, indicating the presence of both common etiology and antagonistic pleiotropy. At the functional level, our results highlighted a central role of host immunity and/or autoimmunity in the PD-IBD relationship.
Bifidobacterium longum attenuates ovariectomy-induced bone loss via modulating the Immunoporotic “Breg-Treg-Th17” cell axis
Authors: Sapra Leena , Shokeen Niti , Gupta Konica , Saini Chaman , Bhardwaj Asha , Mathew Mary , Mishra Pradyumna K. , Chattopadhyay Naibedya , Verma Bhupendra , Srivastava Rupesh K.
Published: January 2022

Discoveries in the last few years have emphasized the existence of an enormous breadth of communication between osteo-immune system. These discoveries fuel novel approaches for the treatment of several bone-pathologies including osteoporosis, an inflammatory bone anomaly affecting more than 500 million people globally. Bifidobacterium longum (BL) is preferred probiotic of choice due to its varied immunomodulatory potential in alleviating various inflammatory diseases. Here, we evaluate the effect of BL in ovariectomy (ovx)-induced post-menopausal osteoporotic mice model. Our in vitro findings reveal that BL suppresses the differentiation and functional activity of RANKL-induced osteoclastogenesis in both mouse bone marrow cells and human PBMCs. Our in vivo data clearly establish that BL exhibits osteoprotective potential via modulating the “immunoporotic” Breg-Treg-Th17 cell-axis. Furthermore, µCT and bone mechanical strength data support that BL supplementation significantly enhanced bone mass and strength, and improved microarchitecture in ovx mice. Remarkably, alteration in frequencies of CD19+CD1dhiCD5+ Bregs, CD4+Foxp3+IL-10+ Tregs, and CD4+Rorγt+IL-17+ Th17 immune cells in distinct lymphoid organs along with serum-cytokine data (enhanced anti-osteoclastogenic cytokines IFN-γ and IL-10 and reduced osteoclastogenic-cytokines IL-6, IL-17, and TNF-α) strongly support the immunomodulatory potential of BL. Altogether our findings establish a novel osteo-protective and immunoporotic potential of BL in augmenting bone health under osteoporotic conditions.