Miracle-dz/UniFAR-FTUs huggingface dataset:
TE-TSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS)

Abstract Transposable elements (TEs) are abundant in the genome and serve as crucial regulatory elements. Some TEs function as epigenetically regulated promoters, and these TE-derived transcription start sites (TSSs) play a crucial role in regulating genes associated with specific functions, such as cancer and embryogenesis. However, the lack of an accessible database that systematically gathers TE-derived TSS data is a current research gap. To address this, we established TE-TSS, an integrated data resource of human and mouse TE-derived TSSs (http://xozhanglab.com/TETSS). TE-TSS has compiled 2681 RNA sequencing datasets, spanning various tissues, cell lines and developmental stages. From these, we identified 5768 human TE-derived TSSs and 2797 mouse TE-derived TSSs, with 47% and 38% being experimentally validated, respectively. TE-TSS enables comprehensive exploration of TSS usage in diverse samples, providing insights into tissue-specific gene expression patterns and transcriptional regulatory elements. Furthermore, TE-TSS compares TE-derived TSS regions across 15 mammalian species, enhancing our understanding of their evolutionary and functional aspects. The establishment of TE-TSS facilitates further investigations into the roles of TEs in shaping the transcriptomic landscape and offers valuable resources for comprehending their involvement in diverse biological processes.
Comparison of baseline drifts using three reflector blocks versus using a single reflector block for the calibration of wall‐mounted Respiratory Gating for Scanner (RGSC) camera integrated with a CT

Abstract Background The calibration of the Respiratory Gating for SCanner (RGSC) system is critical to achieve better and more stable accuracy. The current procedure for a wall‐mounted RGSC system has a relatively large residual error. Purpose To compare the baseline drifts in the image acquisition of DIBH using three reflector blocks versus using a single reflector block in the calibration of a wall‐mounted RGSC camera system. Materials and methods Varian provides a calibration plate with three rows of calibration points: each row is separated by 15 cm longitudinally and by 10 cm laterally. In Varian's single‐block calibration method, the reflector block was first placed on the center point of the calibration plate and aligned with the scanner isocenter. The calibration took a picture of the block, then placed the block on the other eight points sequentially. In the proposed three‐block method, we placed three reflector blocks on the center row, with the center block aligned with the isocenter, and we took a picture of the center block by manually blocking the other two blocks in calibration. By moving the couch longitudinally in or out 15 cm, the calibration goes through all nine points. Monte Carlo simulation was done using Matlab to analyze the calibration matrix eigenvalue characteristics. Results For a typical scan length of 40 cm of DIBH, the residual baseline drift in simulated DIBH is 0.02 ± 0.03 versus 0.30 ± 0.12 cm for three‐block calibration and single‐block calibration, respectively. To achieve 0.5 mm tolerance for the eigenvalue, the laser and reflector box should be within ±3 mm uncertainties based on the eigenvalue simulation. Conclusion Three‐block calibration method effectively removes baseline drift caused by couch movement in DIBH/4D CT scan for the wall‐mounted camera while the single‐block calibration method still has significant residual baseline drift.
KnockTF 2.0: a comprehensive gene expression profile database with knockdown/knockout of transcription (co-)factors in multiple species

Abstract Transcription factors (TFs), transcription co-factors (TcoFs) and their target genes perform essential functions in diseases and biological processes. KnockTF 2.0 (http://www.licpathway.net/KnockTF/index.html) aims to provide comprehensive gene expression profile datasets before/after T(co)F knockdown/knockout across multiple tissue/cell types of different species. Compared with KnockTF 1.0, KnockTF 2.0 has the following improvements: (i) Newly added T(co)F knockdown/knockout datasets in mice, Arabidopsis thaliana and Zea mays and also an expanded scale of datasets in humans. Currently, KnockTF 2.0 stores 1468 manually curated RNA-seq and microarray datasets associated with 612 TFs and 172 TcoFs disrupted by different knockdown/knockout techniques, which are 2.5 times larger than those of KnockTF 1.0. (ii) Newly added (epi)genetic annotations for T(co)F target genes in humans and mice, such as super-enhancers, common SNPs, methylation sites and chromatin interactions. (iii) Newly embedded and updated search and analysis tools, including T(co)F Enrichment (GSEA), Pathway Downstream Analysis and Search by Target Gene (BLAST). KnockTF 2.0 is a comprehensive update of KnockTF 1.0, which provides more T(co)F knockdown/knockout datasets and (epi)genetic annotations across multiple species than KnockTF 1.0. KnockTF 2.0 facilitates not only the identification of functional T(co)Fs and target genes but also the investigation of their roles in the physiological and pathological processes.
Filipino Americans’ Social and Cultural Experiences of Type 2 Diabetes Management: Cultural Paradox, Ownership, and Success Definition

Background: Although type 2 diabetes mellitus (T2DM) disproportionately affects Filipino Americans, they have not received much attention in the literature. Focusing on how Filipino Americans’ social and cultural contextual experiences affect their self-management is critical. This study examined T2DM self-management among Filipino Americans by describing their sociocultural experiences, strategies, and significance of self-management. Method: An interpretive descriptive qualitative design was used. Data were analyzed using thematic analysis. The study followed the Consolidated Criteria for Reporting Qualitative Research (COREQ) checklist. Results: Filipino Americans (n = 19) with T2DM were interviewed. Three themes emerged: (a) cultural paradox of being Filipino American, (b) movement from invisibility to ownership of T2DM, and (c) definition of successful management of T2DM. Conclusion: Results contribute to a greater understanding of Filipino Americans’ T2DM self-management experiences. Implications include the provision of culturally congruent health care, being aware of Filipino Americans’ sociocultural experiences, and involvement of family/community.
A cavernous sinus dural arteriovenous fistula treated by direct puncture of the superior ophthalmic vein with craniotomy: illustrative case

BACKGROUND The authors report a case of symptomatic cavernous sinus (CS) dural arteriovenous fistula (dAVF) that was successfully treated using direct puncture of the superior ophthalmic vein (SOV) with craniotomy. CS dAVF is commonly treated using transvenous embolization (TVE), with the most common access route via the inferior petrosal sinus (IPS). However, this route is sometimes unavailable because of an occluded, hypoplastic, aplastic, or tortuous IPS. The SOV is an alternative, albeit tortuous and long, route to the CS; therefore, direct SOV puncture is occasionally performed. Direct SOV puncture is mostly percutaneous; however, in this case, it was difficult because of subcutaneous SOV narrowing. OBSERVATIONS As the patient experienced increased intraocular pressure, decreased vision, and eye movement disorders, CS embolization was performed via direct puncture with a craniotomy because of other access difficulties. LESSONS Several reports have described CS dAVF in patients receiving endovascular treatment via direct SOV puncture using a transorbital approach. However, to the best of the authors’ knowledge, this is the first reported case of a CS dAVF treated using TVE with craniotomy. This approach is useful when the SOV cannot be reached intravenously and its distance from the epidermis is long.
A narrative review of nontuberculous mycobacterial pulmonary disease: microbiology, epidemiology, diagnosis, and management challenges

ABSTRACT Introduction Nontuberculous mycobacteria (NTM) are a diverse group of mycobacterial species that are ubiquitous in the environment. They are opportunistic pathogens that can cause a range of diseases, especially in individuals with underlying structural lung disease or compromised immune systems. Areas covered This paper provides an in-depth analysis of NTM infections, including microbiology, environmental sources and transmission pathways, risk factors for disease, epidemiology, clinical manifestations and diagnostic approaches, guideline-based treatment recommendations, drugs under development, and management challenges. Expert opinion Future approaches to the management of NTM pulmonary disease will require therapies that are well tolerated, can be taken for a shorter time period and perhaps less frequently, have few drug–drug interactions, and are active against the various strains of pathogens. As the numbers of infections increase, such therapies will be welcomed by clinicians and patients.
Chloroplast phosphate transporter CrPHT4-7 regulates phosphate homeostasis and photosynthesis in Chlamydomonas

Abstract In eukaryotic cells, phosphorus is assimilated and utilized primarily as phosphate (Pi). Pi homeostasis is mediated by transporters that have not yet been adequately characterized in green algae. This study reports on PHOSPHATE TRANSPORTER 4-7 (CrPHT4-7) from Chlamydomonas reinhardtii, a member of the PHT4 transporter family, which exhibits remarkable similarity to AtPHT4;4 from Arabidopsis (Arabidopsis thaliana), a chloroplastic ascorbate transporter. Using fluorescent protein tagging, we show that CrPHT4-7 resides in the chloroplast envelope membrane. Crpht4-7 mutants, generated by the CRISPR/Cas12a-mediated single-strand templated repair, show retarded growth, especially in high light, reduced ATP level, strong ascorbate accumulation, and diminished non-photochemical quenching in high light. On the other hand, total cellular phosphorous content was unaffected, and the phenotype of the Crpht4-7 mutants could not be alleviated by ample Pi supply. CrPHT4-7-overexpressing lines exhibit enhanced biomass accumulation under high light conditions in comparison with the wild-type strain. Expressing CrPHT4-7 in a yeast (Saccharomyces cerevisiae) strain lacking Pi transporters substantially recovered its slow growth phenotype, demonstrating that CrPHT4-7 transports Pi. Even though CrPHT4-7 shows a high degree of similarity to AtPHT4;4, it does not display any substantial ascorbate transport activity in yeast or intact algal cells. Thus, the results demonstrate that CrPHT4-7 functions as a chloroplastic Pi transporter essential for maintaining Pi homeostasis and photosynthesis in C. reinhardtii.
Providing a scaffold for considering theoretical frameworks in evidence implementation projects: the JBI approach to evidence implementation

ABSTRACT There are many theories, models, and frameworks that have been proposed in the field of implementation science. Despite this, many evidence implementation or practice improvement projects do not consider these theories, models, or frameworks in their improvement efforts. The JBI approach is one example of an implementation theory, model, or framework. This approach has been developed particularly with health care professionals in mind and is designed to clearly guide pragmatic evidence implementation efforts based on the best available evidence. In this paper, we discuss how the JBI approach to evidence implementation can interact with and support theory-informed, pragmatic evidence implementation projects.
Optimizing process for biogas fermentation of some agricultural wastes.

In optimizing biogas fermentation process of agricultural wastes,the orthogonal tests were conducted in a lab scale fermentation unit equipped with a temperature controller.Materials such as pig dung,dry straw,green grass and pumpkin leaves were used with controlled ratios of C/N,temperature and total solid.It was found that some trace nutrition elements assisted in biogas yielding,such as cobalt(Co).
The phage-encoded PIT4 protein affects multiple two-component systems of Pseudomonas aeruginosa

ABSTRACT Two-component systems (TCSs) control a large proportion of virulence factors in Pseudomonas aeruginosa. Yet, investigations on inhibitors of regulatory pathways of TCSs remain scarce, despite their potential in anti-virulence strategies. This work elucidates the molecular mechanism of PIT4, a protein encoded by the lytic P. aeruginosa phage LSL4. Single-copy expression of this early phage gene inhibits bacterial motility, in particular twitching motility, and reduces the virulence of P. aeruginosa in HeLa cells. Differential gene expression and a yeast two-hybrid screen showed that PIT4 interacts with components of different two-component systems. In one-on-one interaction assays, it was confirmed that PIT4 specifically interacts with the histidine kinase domains of FleS, PilS, and PA2882. This identified phage mechanism therefore demonstrates the ability of phage proteins to simultaneously target and impact multiple pathways and hints toward a biological function as an infection-exclusion mechanism. This work highlights the potential of previously unknown phage proteins in virulence regulation of multidrug resistant pathogens that could in future be exploited for anti-virulence strategies and biotechnological applications. IMPORTANCE More and more Pseudomonas aeruginosa isolates have become resistant to antibiotics like carbapenem. As a consequence, P. aeruginosa ranks in the top three of pathogens for which the development of novel antibiotics is the most crucial. The pathogen causes both acute and chronic infections, especially in patients who are the most vulnerable. Therefore, efforts are urgently needed to develop alternative therapies. One path explored in this article is the use of bacteriophages and, more specifically, phage-derived proteins. In this study, a phage-derived protein was studied that impacts key virulence factors of the pathogen via interaction with multiple histidine kinases of TCSs. The fundamental insights gained for this protein can therefore serve as inspiration for the development of an anti-virulence compound that targets the bacterial TCS. More and more Pseudomonas aeruginosa isolates have become resistant to antibiotics like carbapenem. As a consequence, P. aeruginosa ranks in the top three of pathogens for which the development of novel antibiotics is the most crucial. The pathogen causes both acute and chronic infections, especially in patients who are the most vulnerable. Therefore, efforts are urgently needed to develop alternative therapies. One path explored in this article is the use of bacteriophages and, more specifically, phage-derived proteins. In this study, a phage-derived protein was studied that impacts key virulence factors of the pathogen via interaction with multiple histidine kinases of TCSs. The fundamental insights gained for this protein can therefore serve as inspiration for the development of an anti-virulence compound that targets the bacterial TCS.
Mixing of event and pre‐event water in a shallow Entisol in sloping farmland based on isotopic and hydrometric measurements, SW China

Water percolation and flow processes in subsurface geologic media play an important role in determining the water source for plants and the transport of contaminants or nutrients, which is essential for water resource management and the development of measures for pollution mitigation. During June 2013, the dynamics of the rainwater, soil water, subsurface flows and groundwater in a shallow Entisol on sloping farmland were monitored using a hydrometric and isotopic approach. The results showed that effective mixing of rainwater and soil water occurred in hours. The rebound phenomenon of δD profiles in soils showed that most isotope‐depleted rainwater largely bypassed the soil matrix when the water saturation in the soil was high. Preferential‐flow, which was the dominant water movement pattern in the vadose zone, occurred through the whole soil profile, and infrequent piston‐flow was mainly found at 20–40 cm in depth. The interflow in the soil layer, composed of 75.2% rainwater, was only generated when the soil profile had been saturated. Underflow in the fractured mudrock was the dominant flow type in this hillslope, and outflow was dominated by base flow (groundwater flow) with a mean contribution of 76.7%. The generation mechanism of underflow was groundwater ridging, which was superimposed upon preferential‐flow composed mainly of rainwater. The quick mixing process of rainwater and soil water and the rapid movement of the mixture through preferential channels in the study soil, which shows a typical bimodal pore size distribution, can explain the prompt release of pre‐event water in subsurface flow. Water sources of subsurface flows at peak discharge could be affected by the antecedent soil water content, rain characteristics and antecedent groundwater levels. Copyright © 2016 John Wiley & Sons, Ltd.
Privacy Concerns Related to Data Sharing for European Diabetes Devices.

BACKGROUND Individuals with diabetes rely on medical equipment (eg, continuous glucose monitoring (CGM), hybrid closed-loop systems) and mobile applications to manage their condition, providing valuable data to health care providers. Data sharing from this equipment is regulated via Terms of Service (ToS) and Privacy Policy documents. The introduction of the Medical Devices Regulation (MDR) and In Vitro Diagnostic Medical Devices Regulation (IVDR) in the European Union has established updated rules for medical devices, including software. OBJECTIVE This study examines how data sharing is regulated by the ToS and Privacy Policy documents of approved diabetes medical equipment and associated software. It focuses on the equipment approved by the Norwegian Regional Health Authorities. METHODS A document analysis was conducted on the ToS and Privacy Policy documents of diabetes medical equipment and software applications approved in Norway. RESULTS The analysis identified 11 medical equipment and 12 software applications used for diabetes data transfer and analysis in Norway. Only 3 medical equipment (OmniPod Dash, Accu-Chek Insight, and Accu-Chek Solo) were registered in the European Database on Medical Devices (EUDAMED) database, whereas none of their respective software applications were registered. Compliance with General Data Protection Regulation (GDPR) security requirements varied, with some software relying on adequacy decisions (8/12), whereas others did not (4/12). CONCLUSIONS The study highlights the dominance of non-European Economic Area (EEA) companies in medical device technology development. It also identifies the lack of registration for medical equipment and software in the EUDAMED database, which is currently not mandatory. These findings underscore the need for further attention to ensure regulatory compliance and improve data-sharing practices in the context of diabetes management.
Functional divergence of Arabidopsis REPRESSOR OF UV-B PHOTOMORPHOGENESIS 1 and 2 in repression of flowering

Abstract Photoperiodic plants coordinate the timing of flowering with seasonal light cues, thereby optimizing their sexual reproductive success. The WD40-repeat protein REPRESSOR OF UV-B PHOTOMORPHOGENESIS 2 (RUP2) functions as a potent repressor of UV RESISTANCE LOCUS 8 (UVR8) photoreceptor-mediated UV-B induction of flowering under noninductive, short-day conditions in Arabidopsis (Arabidopsis thaliana); however, in contrast, the closely related RUP1 seems to play no major role. Here, analysis of chimeric ProRUP1:RUP2 and ProRUP2:RUP1 expression lines suggested that the distinct functions of RUP1 and RUP2 in repressing flowering are due to differences in both their coding and regulatory DNA sequences. Artificial altered expression using tissue-specific promoters indicated that RUP2 functions in repressing flowering when expressed in mesophyll and phloem companion cells, whereas RUP1 functions only when expressed in phloem companion cells. Endogenous RUP1 expression in vascular tissue was quantified as lower than that of RUP2, likely underlying the functional difference between RUP1 and RUP2 in repressing flowering. Taken together, our findings highlight the importance of phloem vasculature expression of RUP2 in repressing flowering under short days and identify a basis for the functional divergence of Arabidopsis RUP1 and RUP2 in regulating flowering time.
Assessing the scientific quality and reliability of YouTube videos about chemotherapy

No studies have evaluated the interaction, quality, and reliability of chemotherapy-related videos published on YouTube. The aim was to evaluate the content of YouTube videos about chemotherapy using 5 different scoring tools. In this cross-sectional register-based study, popular videos on YouTube about the following keywords were examined; “chemotherapy,” “what is chemotherapy,” “types of chemotherapy,” “chemotherapy side effects” and “chemotherapy treatments. ” Quality and reliability of video content were measured using the modified DISCERN (mDISCERN), the Journal of the American Medical Association (JAMA), the Global Quality Score (GQS), the Video Information Quality Index (VIQI), and Health on the Net code (HONcode) scores. A total of 108 videos were analyzed in the study. The median duration was 200 (30-2020) seconds and the median total number of views was 17500 (61-8615000). Among the video publishers, private hospitals were the most (n = 36, 33%). The most (n = 71, 66%) populer category of videos were patient education videos. Half (n = 55, 51%) of the narrators in the videos were only oncology professionals. Mean DISCERN, JAMA, GQS, VIQI, and HONcode scores were 2.73 ± 1.18, 1.97 ± 1.05, 2.94 ± 1.08, 14.03 ± 3.73, and 4.68 ± 2.46, respectively. A positive correlation was found between the 5 scoring points (P < .001 for all pairwise comparisons). There was a significant difference between video quality scores according to video categories and video publishers (P < .001 for both). Although most YouTube videos about chemotherapy were helpful to patients, content quality and reliability were moderate-low. Cancer patients looking for information on chemotherapy may find YouTube videos beneficial, but clinicians must be cautious to clear up any misunderstandings.
Investigational non‐antibiotic therapeutics for infections in hematopoietic cell transplant recipients and patients with hematologic malignancies receiving cellular therapies

In the age of progressive antimicrobial resistance and increased difficulty combating infections in immunocompromised hosts, there has been renewed interest in the use of nontraditional therapeutics for infections. Herein, we review the use of investigational non‐pharmaceutical anti‐infective agents targeting fungal, bacterial, and viral infections in patients with hematologic malignancies, focusing on those receiving hematopoietic cell transplantation or cellular therapies. We discuss immune checkpoint inhibitors, granulocyte transfusions, bone marrow colony‐stimulating factors, bacteriophages, fecal microbiota transplantation, and virus specific T‐cell therapy. Although there is promising early experience with many of these treatments, further studies will be required to define their optimal role in the therapeutic armamentarium against infections in immunocompromised hosts.