bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of core genes associated with the anti-atherosclerotic effects of Salvianolic acid B and immune cell infiltration characteristics using bioinformatics analysis
Authors: Jin Zheng , Zhao Huanyi , Luo Yuan , Li Xiushen , Cui Jiayan , Yan Jing , Yang Pingzhen 
Published: July 2022

Abstract
Background
Atherosclerosis (AS) is the greatest contributor to pathogenesis of atherosclerotic cardiovascular disease (ASCVD), which is associated with increased mortality and reduced quality of life. Early intervention to mitigate AS is key to prevention of ASCVD. Salvianolic acid B (Sal B) is mainly extracted from root and rhizome of Salvia Miltiorrhiza Bunge, and exerts anti-atherosclerotic effect. The purpose of this study was to screen for anti-AS targets of Sal B and to characterize immune cell infiltration in AS.

Methods
We identified targets of Sal B using SEA (http://sea.bkslab.org/) and SIB (https://www.sib.swiss/) databases. GSE28829 and GSE43292 datasets were obtained from Gene Expression Omnibus database. We identified differentially expressed genes (DEGs) and performed enrichment analysis. Weighted gene co-expression network analysis (WGCNA) was used to determine the most relevant module associated with atherosclerotic plaque stability. Intersecting candidate genes were evaluated by generating receiver operating characteristic (ROC) curves and molecular docking. Then, immune cell types were identified using CIBERSOFT and single-sample gene set enrichment analysis (ssGSEA), the relationship between candidate genes and immune cell infiltration was evaluated. Finally, a network-based approach to explore the candidate genes relationship with microRNAs (miRNAs) and Transcription factors (TFs).

Results
MMP9 and MMP12 were been selected as candidate genes from 64 Sal B-related genes, 81 DEGs and turquoise module with 220 genes. ROC curve results showed that MMP9 (AUC = 0.815, P<0.001) and MMP12 (AUC = 0.763, P<0.001) were positively associated with advanced atherosclerotic plaques. The results of immune infiltration showed that B cells naive, B cells memory, Plasma cells, T cells CD8, T cells CD4 memory resting, T cells CD4 memory activated, T cells regulatory (Tregs), T cells gamma delta, NK cells activated, Monocytes, and Macrophages M0 may be involved in development of AS, and the candidate genes MMP9 and MMP12 were associated with these immune cells to different degrees. What’ s more, miR-34a-5p and FOXC1, JUN maybe the most important miRNA and TFs.

Conclusion
The anti-AS effects of Sal B may be related to MMP9 and MMP12 and associated with immune cell infiltration, which is expected to be used in the early intervention of AS.
Development and implementation of a formative instructional coaching program using the Teaching Practices Inventory within a health professions program
Authors: Olsen Amanda A. , Morbitzer Kathryn A. , Zambrano Skye , Zeeman Jacqueline M. , Persky Adam M. , Bush Antonio , McLaughlin Jacqueline E. 
Published: July 2022

Abstract
Background
A growing body of literature describes teaching practices that are positively associated with student achievement. Observing, characterizing, and providing feedback on these teaching practices is a necessary, yet significant challenge to improving teaching quality. This study describes the design, implementation, and evaluation of an instructional coaching program created to provide formative feedback to instructors based on their use of evidence-based teaching practices.

Methods
The program was designed for formative purposes utilizing an instrument adapted from the Teaching Practices Inventory. All faculty were invited to participate in the program on a voluntary basis when the program launched in Fall 2019. Program coaches included any School personnel who completed required training. Two rounds of instrument development were conducted with multiple observers and assessed using Krippendorff’s Alpha. The program was evaluated using an anonymous post-session survey.

Results
Interrater reliability of the form improved over two rounds of piloting and no differences were found in scoring between trainees and education professionals. Seventeen observations were completed by nine coaches. Instructors indicated that feedback was practical, timely, specific, and collegial, suggesting that including student perspectives (e.g., focus groups, student course evaluations) in the coaching program might be helpful.

Conclusions
Creating programs that emphasize and foster the use of evidence-based teaching are critical for health professions education. Additional research is needed to further develop coaching programs that ensure teaching practices in the health professions are optimizing student learning.
Perceptions on the current content and pedagogical approaches used in end-of-life care education among undergraduate nursing students: a qualitative, descriptive study
Authors: Cao Wenjing , Li Chunyan , Zhang Qianqian , Tong Huiru 
Published: July 2022

Abstract
Background
With the aging of the population, high rates of cancer and comorbidity complexity, the end-of-life care for patients will be ever more important. Nurses have always played an essential role in end-of-life care. Insufficient education and training in end-of-life care has been regarded as a major reason of inadequate symptom recognition, symptom management, and communication which results in mental trauma for both the patient’s family and attending health care providers. Undergraduate nurses do end-of-life care as part of their clinical learning. However, undergraduate nurses’ perceptions of the education they received about end-of-life care are not documented.

Objective
This study aimed to critically explore the current state of education regarding end-of-life care from the perspectives of undergraduate nurses.

Methods
We used a descriptive qualitative design. Face-to-face semi-structured interviews were conducted from May to August 2020, with a purposive sample of 15 fourth-year undergraduate nurses who finished the internship. Data were transcribed verbatim and analyzed using content analysis.

Findings
Three main themes relating to undergraduate nurses’ experiences of end-of-life care education emerged from the thematic analysis: 1) Universities provide foundational knowledge about end-of-life care, but it still needs improvement; 2) Clinical practice consolidates and drives undergraduate nurses’ knowledge, skills and confidence about end-of-life care; and 3) cultural attitudes of patients’ family toward disease and death sometimes impedes learning and knowledge translation about end-of-life care.

Conclusion
Undergraduate nursing students benefit from not only theoretical content delivered in the university setting but also practice happened on clinical placement. The current undergraduate curriculum, related to end-of-life care, is disjointed. Meanwhile, undergraduate nurses’ learning and knowledge translation of end-of-life care are impeded by cultural attitudes toward disease and death.
Identification of Mycobacterium avium subspecies paratuberculosis in sheep farms in Bayannaoer, Inner Mongolia, China (short communication)
Authors: Yu Yuandi , Zhang Suhui , Xu Guoyang , Xu Dengfeng , Zheng Hua , Li Bo , Shen Kefei , Fu Lizhi 
Published: July 2022

Abstract
Background
Paratuberculosis is a widespread chronic infection of Mycobacterium avium subspecies paratuberculosis (MAP) that causes significant economic losses to the sheep industry. The current study investigated this disease, which causes diarrhea in sheep, particularly, in Bayannaoer, Inner Mongolia, China. Diagnosis was based on clinical symptoms, pathological autopsy, histopathological inspection, and serological and molecular methods.

Results
MAP was confirmed using polymerase chain reaction using DNA extracted from tissue and fecal samples. Serum samples from 472 individual sheep were obtained to detect antibodies against MAP using an enzyme-linked immunosorbent assay. MAP antibodies were separately detected in 17.86% (35/196) and 18.48% (51/276) of sheep herds at approximately 6 months and ≥ 1 year of age, respectively. The tissue lesion and pathological section results were consistent with paratuberculosis infection.

Conclusions
To our knowledge, this is the first report of Mycobacterium avium subspecies paratuberculosis seroprevalence in Bayannaoer sheep in Inner Mongolia. Our findings show that MAP is not only prevalent, but also a potential threat to this region. Further investigations, including long-term epidemiological surveillance and isolation are needed for the awareness and effective treatment of paratuberculosis in sheep of Inner Mongolia.
Identification of six novel variants from nine Chinese families with hypophosphatemic rickets
Authors: Cao Yixuan , You Yi , Wang Qiong , Ren Xiuzhi , Li Shan , Li Lulu , Xia Weibo , Guan Xin , Yang Tao , Ikegawa Shiro , Wang Zheng , Zhao Xiuli 
Published: July 2022

Abstract
Background
Hypophosphatemic rickets (HR) is a rare genetic disorder associated with renal phosphate wasting and characterized by bone defects. Inactivating mutations in the phosphate regulating endopeptidase homolog X‑linked gene (PHEX) account for most cases of HR. The aim of this study was to identify causative variants in nine unrelated Chinese families associated with HR, and to determine potential pathogenicity of the identified variants.

Methods
Genomic DNA was isolated from the peripheral blood of HR patients and their healthy relatives, followed by next-generation sequencing and/or Sanger sequencing. In silico prediction combined with conservation analysis was performed to assess the effects of the variants, and 3D protein modeling was conducted to predict the functional effects on the encoded protein.

Results
All HR patients recruited in this study displayed bone deformities and tooth agenesis, as well as reduced serum phosphate levels and elevated urine phosphate levels. Nine PHEX variants were identified in eight families, including four novel variants (c.1661_1726del, c.980A > G, c.1078A > T, and c.1017_1051dup). Of the nine identified PHEX variants, five caused a truncated protein, two caused an altered amino acid, and the other two were the canonical splicing variants. Novel variants c.1336G > A and c.1364 T > C in SLC34A3 were also found in one family. Conservation analysis showed that all the amino acids corresponding to the missense variants were highly conserved. In silico analysis and 3D protein structure modeling confirmed the pathogenicity of these variants.

Conclusions
This study identified four novel variants in PHEX and two novel variants in SLC34A3 in a Chinese cohort with HR. Our findings highlight the dominant role of PHEX in HR, and expand the genotypic and phenotypic spectra of this disorder.
Efficient and scalable synthesis of 1,5-diamino-2-hydroxy-pentane from l-lysine via cascade catalysis using engineered Escherichia coli
Authors: Li Yangyang , Zhang Alei , Hu Shewei , Chen Kequan , Ouyang Pingkai 
Published: July 2022

Abstract
Background
1,5-Diamino-2-hydroxy-pentane (2-OH-PDA), as a new type of aliphatic amino alcohol, has potential applications in the pharmaceutical, chemical, and materials industries. Currently, 2-OH-PDA production has only been realized via pure enzyme catalysis from lysine hydroxylation and decarboxylation, which faces great challenges for scale-up production. However, the use of a cell factory is very promising for the production of 2-OH-PDA for industrial applications, but the substrate transport rate, appropriate catalytic environment (pH, temperature, ions) and separation method restrict its efficient synthesis. Here, a strategy was developed to produce 2-OH-PDA via an efficient, green and sustainable biosynthetic method on an industrial scale.

Results
In this study, an approach was created for efficient 2-OH-PDA production from l-lysine using engineered E. coli BL21 (DE3) cell catalysis by a two-stage hydroxylation and decarboxylation process. In the hydroxylation stage, strain B14 coexpressing l-lysine 3-hydroxylase K3H and the lysine transporter CadB-argT enhanced the biosynthesis of (2S,3S)-3-hydroxylysine (hydroxylysine) compared with strain B1 overexpressing K3H. The titre of hydroxylysine synthesized by B14 was 2.1 times higher than that synthesized by B1. Then, in the decarboxylation stage, CadA showed the highest hydroxylysine activity among the four decarboxylases investigated. Based on the results from three feeding strategies, l-lysine was employed to produce 110.5 g/L hydroxylysine, which was subsequently decarboxylated to generate a 2-OH-PDA titre of 80.5 g/L with 62.6% molar yield in a 5-L fermenter. In addition, 2-OH-PDA with 95.6% purity was obtained by solid-phase extraction. Thus, the proposed two-stage whole-cell biocatalysis approach is a green and effective method for producing 2-OH-PDA on an industrial scale.

Conclusions
The whole-cell catalytic system showed a sufficiently high capability to convert lysine into 2-OH-PDA. Furthermore, the high titre of 2-OH-PDA is conducive to separation and possesses the prospect of industrial scale production by whole-cell catalysis.
Bioprocess development as a sustainable platform for eco-friendly alkaline phosphatase production: an approach towards crab shells waste management
Authors: Abdelgalil Soad A. , Abo-Zaid Gaber A. 
Published: July 2022

AbstractBackgroundThere are substantial environmental and health risks associated with the seafood industry's waste of crab shells. In light of these facts, shellfish waste management is critical for environmental protection against hazardous waste produced from the processing industries. Undoubtedly, improved green production strategies, which are based on the notion of "Green Chemistry," are receiving a lot of attention. Therefore, this investigation shed light on green remediation of the potential hazardous crab shell waste for eco-friendly production of bacterial alkaline phosphatase (ALP) through bioprocessing development strategies.ResultsIt was discovered that by utilizing sequential statistical experimental designs, commencing with Plackett–Burman design and ending with spherical central composite design, and then followed by pH-uncontrolled cultivation conditions in a 7 L bench-top bioreactor, an innovative medium formulation could be developed that boosted ALP production fromBacillus licheniformisstrain ALP3 to 212 U L−1. The highest yield of ALP was obtained after 22 h of incubation time with yield coefficientYp/sof 795 U g−1, which was 4.35-fold higher than those obtained in the shake-flask system. ALP activity has a substantial impact on the volatilization of crab shell particles, as shown by the results of several analytical techniques such as atomic absorption spectrometry, TGA, DSC, EDS, FTIR, and XRD.ConclusionsWe highlighted in the current study that the biovalorization of crab shell waste and the production of cost-effective ALP were being combined and that this was accomplished via the use of a new and innovative medium formulation design for seafood waste management as well as scaling up production of ALP on the bench-top scale.
Exploring the multi-level regulation of lignocellulases in the filamentous fungus Trichoderma guizhouense NJAU4742 from an omics perspective
Authors: Xia Yanwei , Wang Jingfan , Guo Chuanxu , Xu Huanhuan , Wang Wei , Yang Mingzhu , Shen Qirong , Zhang Ruifu , Miao Youzhi 
Published: July 2022

Abstract
Background
Filamentous fungi are highly efficient at deconstructing plant biomass by secreting a variety of enzymes, but the complex enzymatic regulation underlying this process is not conserved and remains unclear.

Results
In this study, cellulases and xylanases could specifically respond to Avicel- and xylan-induction, respectively, in lignocellulose-degrading strain Trichoderma guizhouense NJAU4742, however, the differentially regulated cellulases and xylanases were both under the absolute control of the same TgXyr1-mediated pathway. Further analysis showed that Avicel could specifically induce cellulase expression, which supported the existence of an unknown specific regulator of cellulases in strain NJAU4742. The xylanase secretion is very complex, GH10 endoxylanases could only be induced by Avicel, while, other major xylanases were significantly induced by both Avicel and xylan. For GH10 xylanases, an unknown specific regulator was also deduced to exist. Meanwhile, the post-transcriptional inhibition was subsequently suggested to stop the Avicel-induced xylanases secretion, which explained the specifically high xylanase activities when induced by xylan in strain NJAU4742. Additionally, an economical strategy used by strain NJAU4742 was proposed to sense the environmental lignocellulose under the carbon starvation condition, that only slightly activating 4 lignocellulose-degrading genes before largely secreting all 33 TgXyr1-controlled lignocellulases if confirming the existence of lignocellulose components.

Conclusions
This study, aiming to explore the unknown mechanisms of plant biomass-degrading enzymes regulation through the combined omics analysis, will open directions for in-depth understanding the complex carbon utilization in filamentous fungi.
Advancing behavioral interventions for African American/Black and Latino persons living with HIV using a new conceptual model that integrates critical race theory, harm reduction, and self-determination theory: a qualitative exploratory study
Authors: Gwadz Marya , Cluesman Sabrina R. , Freeman Robert , Collins Linda M. , Dorsen Caroline , Hawkins Robert L. , Cleland Charles M. , Wilton Leo , Ritchie Amanda S. , Torbjornsen Karen , Leonard Noelle R. , Martinez Belkis Y. , Silverman Elizabeth , Israel Khadija , Kutnick Alexandra 
Published: July 2022

Abstract
Background
Rates of participation in HIV care, medication uptake, and viral suppression are improving among persons living with HIV (PLWH) in the United States. Yet, disparities among African American/Black and Latino PLWH are persistent, signaling the need for new conceptual approaches. To address gaps in services and research (e.g., insufficient attention to structural/systemic factors, inadequate harm reduction services and autonomy support) and improve behavioral interventions, we integrated critical race theory, harm reduction, and self-determination theory into a new conceptual model, then used the model to develop a set of six intervention components which were tested in a larger study. The present qualitative study explores participants’ perspectives on the study’s acceptability, feasibility, and impact, and the conceptual model’s contribution to these experiences.

Methods
Participants in the larger study were African American/Black and Latino PLWH poorly engaged in HIV care and with non-suppressed HIV viral load in New York City (N = 512). We randomly selected N = 46 for in-depth semi-structured interviews on their experiences with and perspectives on the study. Interviews were audio-recorded and professionally transcribed verbatim, and data were analyzed using directed qualitative content analysis.

Results
On average, participants were 49 years old (SD = 9) and had lived with HIV for 19 years (SD = 7). Most were male (78%) and African American/Black (76%). All had taken HIV medication previously. Challenging life contexts were the norm, including poverty, poor quality/unstable housing, trauma histories exacerbated by current trauma, health comorbidities, and substance use. Participants found the study highly acceptable. We organized results into four themes focused on participants’ experiences of: 1) being understood as a whole person and in their structural/systemic context; 2) trustworthiness and trust; 3) opportunities for self-reflection; and 4) support of personal autonomy. The salience of nonjudgment was prominent in each theme. Themes reflected grounding in the conceptual model. Participants reported these characteristics were lacking in HIV care settings.

Conclusions
The new conceptual model emphasizes the salience of systemic/structural and social factors that drive health behavior and the resultant interventions foster trust, self-reflection, engagement, and behavior change. The model has potential to enhance intervention acceptability, feasibility, and effectiveness with African American/Black and Latino PLWH.
Blood speckle imaging compared with conventional Doppler ultrasound for transvalvular pressure drop estimation in an aortic flow phantom
Authors: Dockerill Cameron , Gill Harminder , Fernandes Joao Filipe , Nio Amanda Q. X. , Rajani Ronak , Lamata Pablo 
Published: July 2022

Abstract
Background
Transvalvular pressure drops are assessed using Doppler echocardiography for the diagnosis of heart valve disease. However, this method is highly user-dependent and may overestimate transvalvular pressure drops by up to 54%. This work aimed to assess transvalvular pressure drops using velocity fields derived from blood speckle imaging (BSI), as a potential alternative to Doppler.

Methods
A silicone 3D-printed aortic valve model, segmented from a healthy CT scan, was placed within a silicone tube. A CardioFlow 5000MR flow pump was used to circulate blood mimicking fluid to create eight different stenotic conditions. Eight PendoTech pressure sensors were embedded along the tube wall to record ground-truth pressures (10 kHz). The simplified Bernoulli equation with measured probe angle correction was used to estimate pressure drop from maximum velocity values acquired across the valve using Doppler and BSI with a GE Vivid E95 ultrasound machine and 6S-D cardiac phased array transducer.

Results
There were no significant differences between pressure drops estimated by Doppler, BSI and ground-truth at the lowest stenotic condition (10.4 ± 1.76, 10.3 ± 1.63 vs. 10.5 ± 1.00 mmHg, respectively; p > 0.05). Significant differences were observed between the pressure drops estimated by the three methods at the greatest stenotic condition (26.4 ± 1.52, 14.5 ± 2.14 vs. 20.9 ± 1.92 mmHg for Doppler, BSI and ground-truth, respectively; p < 0.05). Across all conditions, Doppler overestimated pressure drop (Bias = 3.92 mmHg), while BSI underestimated pressure drop (Bias = -3.31 mmHg).

Conclusions
BSI accurately estimated pressure drops only up to 10.5 mmHg in controlled phantom conditions of low stenotic burden. Doppler overestimated pressure drops of 20.9 mmHg. Although BSI offers a number of theoretical advantages to conventional Doppler echocardiography, further refinements and clinical studies are required with BSI before it can be used to improve transvalvular pressure drop estimation in the clinical evaluation of aortic stenosis.