Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative phosphoproteome analysis of embryonic stem cell differentiation toward blood

Murine embryonic stem (ES) cells can differentiate in vitro into three germ layers (endodermic, mesodermic, ectodermic). Studies on the differentiation of these cells to specific early differentiation stages has been aided by an ES cell line carrying the Green Fluorescent Protein (GFP) targeted to the Brachyury (Bry) locus which marks mesoderm commitment. Furthermore, expression of the Vascular Endothelial Growth Factor receptor 2 (Flk1) along with Bry defines hemangioblast commitment. Isobaric-tag for relative and absolute quantification (iTRAQTM) and phosphopeptide enrichment coupled to liquid chromatography separation and mass spectrometry allow the study of phosphorylation changes occurring at different stages of ES cell development using Bry and Flk1 expression respectively. We identified and relatively quantified 37 phosphoentities which are modulated during mesoderm-induced ES cells differentiation, comparing epiblast-like, early mesoderm and hemangioblast-enriched cells. Among the proteins differentially phosphorylated toward mesoderm differentiation were: the epigenetic regulator Dnmt3b, the protein kinase GSK3b, the chromatin remodeling factor Smarcc1, the transcription factor Utf1; as well as protein specifically related to stem cell differentiation, as Eomes, Hmga2, Ints1 and Rif1. As most key factors regulating early hematopoietic development have also been implicated in various types of leukemia, understanding the post-translational modifications driving their regulation during normal development could result in a better comprehension of their roles during abnormal hematopoiesis in leukemia.
Mortality prediction in the elderly by an easily measured metabolic index

Objective: Hyperglycaemia enhances the risk of cardiovascular events and death, while high-density lipoprotein cholesterol (HDLc) is protective. Information on these associations among the elderly population is scanty. We applied a cardiometabolic risk index (CMRI) based on HDLc and fasting plasma glucose (FPG) in an elderly Swedish population. Methods: In total, 432 75-year-olds were followed for 10-year mortality. The impact of risk factors on survival was analysed using Cox regression. Results: HDLc (mmol/l; median and interquartile range) was 1.6 (1.3–2.0) in women and 1.4 (1.2–1.5) in men, while FPG was 5.9 (5.5–6.6) and 5.9 (5.5–6.5). Some 89 persons were at high risk according to CMRI, and 163 persons died. FPG was related to mortality in women (HR; 95% CI: 1.23; 1.10–1.37) and there was a similar trend in men (1.08; 1.00–1.17; p = 0.061). Increasing HDLc was protective in men (0.38; 0.19–0.77) but not in women (0.77; 0.45–1.29). CMRI was related to mortality in both genders even after adjustment for established risk factors (1.79; 1.14–2.79; p = 0.011). Conclusions: The CMRI helps identify elderly subjects at risk and may serve as a cost-effective risk prediction tool.
Impact of Mandated Case Review Policy on Opioid Discontinuation and Mortality Among High-Risk Long-Term Opioid Therapy Patients: The STORM Stepped-Wedge Cluster Randomized Controlled Trial

Background: Although long-term opioid therapy (LTOT) has its own risks, opioid discontinuation could pose harm for high-risk Veterans Health Administration (VHA) patients receiving LTOT. There is limited information on the impact of a mandate requiring providers to perform case reviews on high-risk patients with an active opioid prescription (ie, mandated case review policy) on opioid discontinuation and mortality. Methods: Our study is a secondary data analysis of a 23-month stepped-wedge cluster randomized controlled trial between April 2018 and March 2020. The study included 10 685 LTOT patients with a predicted risk of a serious adverse event between the top 1% to 5% nationally who entered the risk range between 4/18/2018 and 11/9/2019. We examined whether the mandated case review policy had an impact on opioid discontinuation and mortality for the patients. Results: Among 10 685 LTOT patients (88.2% male; mean [SD] age, 61.1 [11.7] years), 29.1% experienced discontinuation and the mortality rate was 9.5%. Patients under mandated case review had a decreased risk of opioid discontinuation (average marginal effect [AME], −11.16 [95% CI, −15.30 to −7.01] percentage points) and all-cause mortality (AME, −3.31 [95% CI, −5.63 to −1.00] percentage points), relative to patients who were not under the mandate. Conclusions: The VHA mandated case review policy was associated with lower probability of discontinuation and all-cause mortality for high-risk patients receiving LTOT. Interventions that maintain care engagement while optimizing pain management for high-risk patients may be beneficial for minimizing mortality and other risks associated with discontinuation.
Public participation and satisfaction in urban regeneration projects in Tanzania: The case of Kariakoo, Dar es Salaam

Based on predictions, almost 60% of the world population will be living in cities by 2030. Tanzania is urbanizing at a rapid rate of 4.7%, and 30% of the total population lives in urban areas. Urban regeneration projects in developing countries are facing various challenges. Moreover, the issue of challenges of community participation and satisfaction in regeneration projects is less documented. In recent decades, a bottom-up planning approach has been advocated as an approach for sustainable development planning whereby local actors participate in decision-making. But how top-down planning meets bottom-up planning is less documented, as well as the correlation between participation and satisfaction. This is due to the fact that zoning system has been dominating in urban planning, where experts zone areas according to land uses with an input from the community. In this research community participation, public satisfaction in urban regeneration projects was investigated. The research was based on Kariakoo, Dar es Salaam, Tanzania. The research explored public perceptions on satisfaction and the relationship between community participation and community satisfaction in urban regeneration projects. 292 respondents were interviewed on their perceptions on the redevelopment satisfaction. The results were analyzed using SPSS and tabulated in a form of tables, figures, and charts. The results revealed that it is not necessary that the more the participation the more the satisfaction, hence the more the quality of the service/plan. This means that several factors have an influence on satisfaction of urban redevelopment such as gender, level of education, age, time lived or stayed in the area, as well as the level of participation.
Spatial Modeling of Sediment Transport over the Upper Citarum Catchment

This paper discusses set up of a spatial model applied in Geographic Information System (GIS) environment for predicting annual erosion rate and sediment yield of a watershed. The study area is situated in the Upper Citarum Catchment of West Java. Annual sediment yield is considered as product of erosion rate and sediment delivery ratio to be modelled under similar modeling tool. Sediment delivery ratio is estimated on the basis of sediment resident time. The modeling concept is based on the calculation of water flow velocity through sub-catchment surface, which is controlled by topography, rainfall, soil characteristics and various types of land use. Relating velocity to known distance across digital elevation model, sediment resident time can be estimated. Data from relevance authorities are used. Bearing in mind limited knowledge of some governing factors due to lack of observation, the result has shown the potential of GIS for spatially modeling regional sediment transport. Validation of model result is carried out by evaluating measured and computed total sediment yield at the main outlet. Computed total sediment yields for 1994 and 2001 are found to be 1.96×10 6 and 2.10×10 6 tons/year. They deviate roughly 54 and 8% with respect to those measured in the field. Model response due to land use change observed in 2001 and 1994 is also recognised. Under presumably constant rainfall depth, an increase of overall average annual erosion rate of 11% resulted in an increase of overall average sediment yield of 7%.
Palonosetron in the management of chemotherapy-induced nausea and vomiting in patients receiving multiple-day chemotherapy

: Prevention of chemotherapy-induced nausea and vomiting (CINV) is a key component of treatment for patients with cancer. Guidelines are available to assist prescribers in the management of CINV associated with single-day chemotherapy regimens. However, currently there are no clear guidelines for management of CINV in patients receiving multiple-day chemotherapy regimens. Serotonin (5-HT 3 ) receptor antagonists are a mainstay in preventing CINV, and palonosetron, given its longer half-life and duration of action relative to other 5-HT 3 receptor antagonists, may be a useful option for managing CINV in multiple-day chemotherapy. Here we provide an overview of CINV and CINV treatment options, with a focus on palonosetron. We describe existing challenges in managing CINV, and discuss two patients receiving multiple-day chemotherapy, in whom CINV was managed successfully with palonosetron.
Understanding Values in a Large Health Care Organization through Work-Life Narratives of High-Performing Employees

Objective— To understand high-performing frontline employees’ values as reflected in their narratives of day-to-day interactions in a large health care organization. Methods— A total of 150 employees representing various roles within the organization were interviewed and asked to share work-life narratives (WLNs) about value-affirming situations (i.e. situations in which they believed their actions to be fully aligned with their values) and value-challenging situations (i.e. when their actions or the actions of others were not consistent with their values), using methods based on appreciative inquiry. Results— The analysis revealed 10 broad values. Most of the value-affirming WLNs were about the story-teller and team providing care for the patient/family. Half of the value-challenging WLNs were about the story-teller or a patient and barriers created by the organization, supervisor, or physician. Almost half of these focused on “treating others with disrespect/respect”. Only 15% of the value-challenging WLNs contained a resolution reached by the participants, often leaving them describing unresolved and frequently negative feelings. Conclusions— Appreciative inquiry and thematic analysis methods were found to be an effective tool for understanding the important and sometimes competing role personal and institutional values play in day-to-day work. There is remarkable potential in using WLNs as a way to surface and reinforce shared values and, perhaps more importantly, respectfully to identify and discuss conflicting personal and professional values.
Whole-genome sequences of two Drosophila melanogaster microbiome symbionts

ABSTRACT Lactiplantibacillus plantarum and Acetobacter tropicalis are bacterial symbionts commonly isolated from decaying fruits and from the microbiome of Drosophila melanogaster. Studies have shown that these organisms interact synergistically, imparting beneficial effects on the host. Here, we report whole-genome sequences of these microbes obtained from long and short reads.
School Nurses’ Experiences and Roles in Promoting and Administering the HPV Vaccine: A Systematic Review Using the Socioecological Framework

Understanding the school nurse's experience in human papillomavirus (HPV) vaccine promotion can reduce vaccine disparities. HPV vaccination is critical to cancer prevention. Despite the importance of the school nurse in vaccine promotion, there is a lack of understanding. This article aims to examine the knowledge, attitude, experience, and role of school nurses related to HPV vaccination and promotion in school settings. A systematic search for school nurses and their experiences related to HPV vaccination was conducted. A thematic synthesis was undertaken using the socioecological model. This review highlights the complexity of HPV vaccine promotion in schools over time. Multilevel factors impact nursing practice. Nurses have good vaccine knowledge and positive attitudes. Poor workflow processes, competing demands, and vaccine communication challenge school nurses. The themes that were synthesized informed the LEADS model. With the support of school nurses, reaching the goal of eliminating cervical cancer as a public health problem is possible.
Measurement of Trogocytosis: Quantitative Analyses Validated with Rigorous Controls

Trogocytosis is a process in which receptors on acceptor cells remove and internalize cognate ligands from donor cells. Trogocytosis has a profound and negative impact on mAb‐based cancer immunotherapy, as seen in the treatment of chronic lymphocytic leukemia (CLL) with CD20 mAbs, such as rituximab (RTX) and ofatumumab (OFA). Our clinical observations of RTX/OFA‐mediated loss of the CD20 target from circulating CLL cells have been replicated in our in vitro studies. Here we describe flow cytometry and fluorescence microscopy experiments, which demonstrate that acceptor cells, such as monocytes/macrophages that express FcγR, remove and internalize both antigen and donor cell‐bound cognate IgG mAbs for several different mAb‐donor cell pairs. Fluorescent mAbs and portions of the plasma cell membrane are transferred from donor cells to acceptor cells, which include the THP‐1 monocytic cell line as well as freshly isolated monocytes. We describe rigorous controls to validate the reactions and eliminate dissociation or internalization as alternative mechanisms. Trogocytosis is likely to contribute to neutropenia, thrombocytopenia, and liver damage associated with use of antibody‐drug conjugates. The methods we have described should allow for examination of strategies focused on blocking trogocytosis and its adverse effects. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
Cement‐Augmented Screw Fixation with PHILOS Plating for Osteoporotic Proximal Humeral Fractures: An Observation of Mid‐ and Long‐Term Curative Efficacy

The mid‐ and long‐term clinical outcomes of cement‐augmented screws in the treatment of osteoporotic proximal humeral fractures have rarely been reported. The aim of this study was to observe the mid‐ and long‐term efficacy of combined cement‐augmented screw fixation and PHILOS plating in the treatment of osteoporotic fractures of the proximal humerus.
Collaborative Retrieval Practice Reduces Mind-Wandering During Learning

Abstract: Research has shown engaging in retrieval practice can reduce the frequency of mind-wandering. However, no prior research has examined how engaging in collaborative (as compared to individual) retrieval practice impacts mind-wandering during learning. In the current experiment, participants were asked to study a list of words, followed by retrieval practice that either occurred collaboratively (as a dyad) or individually. During retrieval practice, participants provided self-reports as to whether they were on task or off task. Following retrieval practice, all participants completed an individual final test. Of greatest interest, the results showed that engaging in collaborative retrieval practice decreased the frequency of mind-wandering during learning. In addition, and consistent with prior collaborative learning research, collaborative inhibition during practice and postcollaborative benefits on the final test were observed. The current results provide the first demonstration of an additional benefit to using collaborative retrieval practice: This technique reduces the frequency of mind-wandering.
Reconsidering emissions of ammonia from chemical fertilizer usage in Midwest USA

We present alternative methods for estimating spatial surrogates and temporal factors for ammonia (NH3) emissions from chemical fertilizer usage (CFU), in the USA, at spatial and temporal scales used to simulate regional air quality and deposition of reactive nitrogen to ecosystems. The newly developed Improved Spatial Surrogate (ISS) method incorporates year‐specific fertilizer sales data, high resolution and year‐specific crop maps, and local crop nitrogen demands to allocate NH3 emissions at 4 km × 4 km grid cells. Results are compared with the commonly used gridded emission estimates by the Sparse Matrix Operator Kernel Emissions (SMOKE) preprocessor. NH3 emissions over Central Illinois in the USA, estimated at the 4 km × 4 km grid level in SMOKE and ISS methods, exhibit differences between −10% and 120%, with 58% of the grid cells exhibiting more than ±10% difference. Application of the ISS method for a larger domain over the Midwest USA, at 4 km × 4 km, reflected similar differences. We also employed the Denitrification Decomposition (DNDC) model to develop daily temporal factors of NH3 emissions from CFU using multi‐site and multi‐year analyses. Ratio of temporal factors estimated by SMOKE and DNDC methods is 0.54 ± 2.35, with DNDC identifying daily emission peaks 2.5–8 times greater than SMOKE. Identified emission peaks will be useful for future air quality modeling efforts to understand particulate matter episodes, as well as trends in regional particulate matter formation and nitrogen deposition for Midwest USA, using the proposed NH3 emissions inventory.
Crystal Structures of the SpoIID Lytic Transglycosylases Essential for Bacterial Sporulation*

Bacterial spores are the most resistant form of life known on Earth and represent a serious problem for (i) bioterrorism attack, (ii) horizontal transmission of microbial pathogens in the community, and (iii) persistence in patients and in a nosocomial environment. Stage II sporulation protein D (SpoIID) is a lytic transglycosylase (LT) essential for sporulation. The LT superfamily is a potential drug target because it is active in essential bacterial processes involving the peptidoglycan, which is unique to bacteria. However, the absence of structural information for the sporulation-specific LT enzymes has hindered mechanistic understanding of SpoIID. Here, we report the first crystal structures with and without ligands of the SpoIID family from two community relevant spore-forming pathogens, Bacillus anthracis and Clostridium difficile. The structures allow us to visualize the overall architecture, characterize the substrate recognition model, identify critical residues, and provide the structural basis for catalysis by this new family of enzymes.
Coarse Mask Guided Interactive Object Segmentation

Interactive object segmentation aims to produce object masks with user interactions, such as clicks, bounding boxes, and scribbles. Click point is the most popular interactive cue for its efficiency, and related deep learning methods have attracted lots of interest in recent years. Most works encode click points as gaussian maps and concatenate them with images as the model’s input. However, the spatial and semantic information of gaussian maps would be noised through multiple convolution layers and won’t be fully exploited by top layers for mask prediction. To pass click information to top layers exactly and efficiently, we propose a coarse mask guided model (CMG) which predicts coarse masks with a coarse module to guide the object mask prediction. Specifically, the coarse module encodes user clicks as query features and enriches their semantic information with backbone features through transformer layers, coarse masks are generated based on the enriched query feature and fed into CMG’s decoder. Benefiting from the efficiency of transformer, CMG’s coarse module and decoder module are lightweight and computationally efficient, making the interaction process more smooth. Experiments on several segmentation benchmarks demonstrate the effectiveness of our method, and we get new state-of-the-art results compared with previous works.
Ultrastructural Characteristics and Synaptic Connectivity of Photoreceptors in the Simplex Retina of Little Skate (Leucoraja erinacea)

Abstract The retinas of the vast majority of vertebrate species are termed “duplex,” that is, they contain both rod and cone photoreceptor neurons in different ratios. The retina of little skate (Leucoraja erinacea) is a rarity among vertebrates because it contains only a single photoreceptor cell type and is thus “simplex. ” This unique retina provides us with an important comparative model and an exciting opportunity to study retinal circuitry within the context of a visual system with a single photoreceptor cell type. What is perhaps even more intriguing is the fact that the Leucoraja retina is able use that single photoreceptor cell type to function under both scotopic and photopic ranges of illumination. Although some ultrastructural characteristics of skate photoreceptors have been examined previously, leading to a general description of them as “rods” largely based on outer segment (OS) morphology and rhodopsin expression, a detailed study of the fine anatomy of the entire cell and its synaptic connectivity is still lacking. To address this gap in knowledge, we performed serial block-face electron microscopy imaging and examined the structure of skate photoreceptors and their postsynaptic partners. We find that skate photoreceptors exhibit unusual ultrastructural characteristics that are either common to rods or cones in other vertebrates (e.g., outer segment architecture, synaptic ribbon number, terminal extensions), or are somewhere in between those of a typical vertebrate rod or cone (e.g., number of invaginating contacts, clustering of multiple ribbons over a single synaptic invagination). We suggest that some of the ultrastructural characteristics we observe may play a role in the ability of the skate retina to function across scotopic and photopic ranges of illumination. Our findings have the potential to reveal as yet undescribed principles of vertebrate retinal design.