Miracle-dz/UniFAR-FTUs huggingface dataset:
Interdisciplinary Mobile Health Model to Improve Clinical Care After Heart Transplantation: Implementation Strategy Study

Background Solid organ transplantation could be the only life-saving treatment for end-stage heart failure. Nevertheless, multimorbidity and polypharmacy remain major problems after heart transplant. A technology-based behavioral intervention model was established to improve clinical practice in a heart transplant outpatient setting. To support the new strategy, the mHeart app, a mobile health (mHealth) tool, was developed for use by patients and providers. Objective The primary objective of this study was to describe the implementation of the mHeart model and to outline the main facilitators identified when conceiving an mHealth approach. The secondary objectives were to evaluate the barriers, benefits, and willingness to use mHealth services reported by heart transplant recipients and cardiology providers. Methods This was an implementation strategy study directed by a multidisciplinary cardiology team conducted in four stages: design of the model and the software, development of the mHeart tool, interoperability among systems, and quality and security requirements. A mixed methods study design was applied combining a literature review, several surveys, interviews, and focus groups. The approach involved merging engineering and behavioral theory science. Participants were chronic-stage heart transplant recipients, patient associations, health providers, stakeholders, and diverse experts from the legal, data protection, and interoperability fields. Results An interdisciplinary and patient-centered process was applied to obtain a comprehensive care model. The heart transplant recipients (N=135) included in the study confirmed they had access to smartphones (132/135, 97.7%) and were willing to use the mHeart system (132/135, 97.7%). Based on stakeholder agreement (>75%, N=26), the major priorities identified of the mHealth approach were to improve therapy management, patient empowerment, and patient-provider interactions. Stakeholder agreement on the barriers to implementing the system was weak (<75%). Establishing the new model posed several challenges to the multidisciplinary team in charge. The main factors that needed to be overcome were ensuring data confidentiality, reducing workload, minimizing the digital divide, and increasing interoperability. Experts from various fields, scientific societies, and patient associations were essential to meet the quality requirements and the model scalability. Conclusions The mHeart model will be applicable in distinct clinical and research contexts, and may inspire other cardiology health providers to create innovative ways to deal with therapeutic complexity and multimorbidity through health care systems. Professionals and patients are willing to use such innovative mHealth programs. The facilitators and key strategies described were needed for success in the implementation of the new holistic theory–based mHealth strategy.
Increased Institutional Surgical Experience in Robot-Assisted Radical Hysterectomy for Early Stage Cervical Cancer Reduces Recurrence Rate: Results from a Nationwide Study

The aim of this study was to evaluate the impact of institutional surgical experience on recurrence following robotic radical hysterectomy (RRH) for early stage cervical cancer. All women in Sweden who underwent an RRH for stage IA2-IB1 cervical cancer at tertiary referral centers from its implementation in December 2005 until June 2017 were identified using a Swedish nationwide register and local hospital registers. Registry data were controlled by a chart review of all women. Recurrence rates and patterns of recurrence were compared between early and late (≤50 vs. >50 procedures) institutional series. Six hundred and thirty-five women were included. Regression analysis identified a lower risk of recurrence with increased experience but without a clear cut off level. Among the 489 women who did not receive adjuvant radio chemotherapy (RC-T), the rate of recurrence was 3.6% in the experienced cohort (>50 procedures) compared to 9.3% in the introductory cohort (p < 0.05). This was also seen in tumors < 2 cm regardless of RC-T (p < 0.05), whereas no difference in recurrence was seen when analyzing all women receiving RC-T. In conclusion, the rate of recurrence following RRH for early stage cervical cancer decreased with increased institutional surgical experience, in tumors < 2 cm and in women who did not receive adjuvant RC-T.
Role of iRhoms 1 and 2 in Endochondral Ossification

Growth of the axial and appendicular skeleton depends on endochondral ossification, which is controlled by tightly regulated cell–cell interactions in the developing growth plates. Previous studies have uncovered an important role of a disintegrin and metalloprotease 17 (ADAM17) in the normal development of the mineralized zone of hypertrophic chondrocytes during endochondral ossification. ADAM17 regulates EGF-receptor signaling by cleaving EGFR-ligands such as TGFα from their membrane-anchored precursor. The activity of ADAM17 is controlled by two regulatory binding partners, the inactive Rhomboids 1 and 2 (iRhom1, 2), raising questions about their role in endochondral ossification. To address this question, we generated mice lacking iRhom2 (iR2−/−) with floxed alleles of iRhom1 that were specifically deleted in chondrocytes by Col2a1-Cre (iR1∆Ch). The resulting iR2−/−iR1∆Ch mice had retarded bone growth compared to iR2−/− mice, caused by a significantly expanded zone of hypertrophic mineralizing chondrocytes in the growth plate. Primary iR2−/−iR1∆Ch chondrocytes had strongly reduced shedding of TGFα and other ADAM17-dependent EGFR-ligands. The enlarged zone of mineralized hypertrophic chondrocytes in iR2−/−iR1∆Ch mice closely resembled the abnormal growth plate in A17∆Ch mice and was similar to growth plates in Tgfα−/− mice or mice with EGFR mutations. These data support a model in which iRhom1 and 2 regulate bone growth by controlling the ADAM17/TGFα/EGFR signaling axis during endochondral ossification.
A general model of hippocampal and dorsal striatal learning and decision making

Significance A central question in neuroscience concerns how humans and animals trade off multiple decision-making strategies. Another question pertains to the use of egocentric and allocentric strategies during navigation. We introduce reinforcement-learning models based on learning to predict future reward directly from states and actions or via learning to predict future “successor” states, choosing actions from either system based on the reliability of its predictions. We show that this model explains behavior on both spatial and nonspatial decision tasks, and we map the two model components onto the function of the dorsal hippocampus and the dorsolateral striatum, thereby unifying findings from the spatial-navigation and decision-making fields. Humans and other animals use multiple strategies for making decisions. Reinforcement-learning theory distinguishes between stimulus–response (model-free; MF) learning and deliberative (model-based; MB) planning. The spatial-navigation literature presents a parallel dichotomy between navigation strategies. In “response learning,” associated with the dorsolateral striatum (DLS), decisions are anchored to an egocentric reference frame. In “place learning,” associated with the hippocampus, decisions are anchored to an allocentric reference frame. Emerging evidence suggests that the contribution of hippocampus to place learning may also underlie its contribution to MB learning by representing relational structure in a cognitive map. Here, we introduce a computational model in which hippocampus subserves place and MB learning by learning a “successor representation” of relational structure between states; DLS implements model-free response learning by learning associations between actions and egocentric representations of landmarks; and action values from either system are weighted by the reliability of its predictions. We show that this model reproduces a range of seemingly disparate behavioral findings in spatial and nonspatial decision tasks and explains the effects of lesions to DLS and hippocampus on these tasks. Furthermore, modeling place cells as driven by boundaries explains the observation that, unlike navigation guided by landmarks, navigation guided by boundaries is robust to “blocking” by prior state–reward associations due to learned associations between place cells. Our model, originally shaped by detailed constraints in the spatial literature, successfully characterizes the hippocampal–striatal system as a general system for decision making via adaptive combination of stimulus–response learning and the use of a cognitive map.
The SERCA residue Glu340 mediates interdomain communication that guides Ca2+ transport

Significance We present a crystal structure, functional data, and molecular dynamics (MD) simulations of the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) mutant E340A. The mutation slows Ca2+-binding kinetics, and the structural differences between wild type and E340A indicate that the mutation disrupts a central interdomain “communication hub” governing Ca2+ binding/dissociation. MD simulations reveal altered dynamics in regions mediating Ca2+ occlusion, a critical step in SERCA’s alternating access mechanism. The mutation stabilizes a more occluded state of the Ca2+ sites. The strict conservation of Glu340 among P-type ATPases is the result of its critical role in interdomain communication between the cytosolic headpiece and the transmembrane domain, ensuring a delicate balance between dynamics of ion binding, occlusion, and release—key steps in the transport process. The sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) is a P-type ATPase that transports Ca2+ from the cytosol into the sarco(endo)plasmic reticulum (SR/ER) lumen, driven by ATP. This primary transport activity depends on tight coupling between movements of the transmembrane helices forming the two Ca2+-binding sites and the cytosolic headpiece mediating ATP hydrolysis. We have addressed the molecular basis for this intramolecular communication by analyzing the structure and functional properties of the SERCA mutant E340A. The mutated Glu340 residue is strictly conserved among the P-type ATPase family of membrane transporters and is located at a seemingly strategic position at the interface between the phosphorylation domain and the cytosolic ends of 5 of SERCA’s 10 transmembrane helices. The mutant displays a marked slowing of the Ca2+-binding kinetics, and its crystal structure in the presence of Ca2+ and ATP analog reveals a rotated headpiece, altered connectivity between the cytosolic domains, and an altered hydrogen bonding pattern around residue 340. Supported by molecular dynamics simulations, we conclude that the E340A mutation causes a stabilization of the Ca2+ sites in a more occluded state, hence displaying slowed dynamics. This finding underpins a crucial role of Glu340 in interdomain communication between the headpiece and the Ca2+-binding transmembrane region.
Suppression of Malachite Green-Induced Toxicity to Human Liver Cells Utilizing Host-Guest Chemistry of Cucurbit[7]uril

We investigated a host-guest complex between cucurbit[7]uril and malachite green, and its effect on the toxicity to human liver cells. The host-guest complexation was evaluated by a UV/vis titration and electrospray-ionization mass spectrometry. Interestingly, the host-guest complex resulted in remarkable suppression of the toxicity of malachite green in its practical concentration range ( ca . ~6 µM). This study is one step forward to the active control of the biological effects of potent toxicants utilizing host-guest chemistry.
tRNA import across the mitochondrial inner membrane in T. brucei requires TIM subunits but is independent of protein import

Abstract Mitochondrial tRNA import is widespread, but mechanistic insights of how tRNAs are translocated across mitochondrial membranes remain scarce. The parasitic protozoan T. brucei lacks mitochondrial tRNA genes. Consequently, it imports all organellar tRNAs from the cytosol. Here we investigated the connection between tRNA and protein translocation across the mitochondrial inner membrane. Trypanosomes have a single inner membrane protein translocase that consists of three heterooligomeric submodules, which all are required for import of matrix proteins. In vivo depletion of individual submodules shows that surprisingly only the integral membrane core module, including the protein import pore, but not the presequence-associated import motor are required for mitochondrial tRNA import. Thus we could uncouple import of matrix proteins from import of tRNAs even though both substrates are imported into the same mitochondrial subcompartment. This is reminiscent to the outer membrane where the main protein translocase but not on-going protein translocation is required for tRNA import. We also show that import of tRNAs across the outer and inner membranes are coupled to each other. Taken together, these data support the ‘alternate import model’, which states that tRNA and protein import while mechanistically independent use the same translocation pores but not at the same time.
Intrinsically disordered protein PID‐2 modulates Z granules and is required for heritable piRNA‐induced silencing in the Caenorhabditis elegans embryo

In Caenorhabditis elegans, the piRNA (21U RNA) pathway is required to establish proper gene regulation and an immortal germline. To achieve this, PRG‐1‐bound 21U RNAs trigger silencing mechanisms mediated by RNA‐dependent RNA polymerase (RdRP)‐synthetized 22G RNAs. This silencing can become PRG‐1‐independent and heritable over many generations, a state termed RNA‐induced epigenetic gene silencing (RNAe). How and when RNAe is established, and how it is maintained, is not known. We show that maternally provided 21U RNAs can be sufficient for triggering RNAe in embryos. Additionally, we identify PID‐2, a protein containing intrinsically disordered regions (IDRs), as a factor required for establishing and maintaining RNAe. PID‐2 interacts with two newly identified and partially redundant eTudor domain‐containing proteins, PID‐4 and PID‐5. PID‐5 has an additional domain related to the X‐prolyl aminopeptidase APP‐1, and binds APP‐1, implicating potential N‐terminal proteolysis in RNAe. All three proteins are required for germline immortality, localize to perinuclear foci, affect size and appearance of RNA inheritance‐linked Z granules, and are required for balancing of 22G RNA populations. Overall, our study identifies three new proteins with crucial functions in C. elegans small RNA silencing.
Characterization and complete genome sequences of two novel variants of the family Closteroviridae from Chinese kiwifruit

Two distinct closterovirus-like genome sequences (termed AdV-1 v1 and v2) were identified in Actinidia chinensis var. deliciosa ‘Miliang-1’ that had no disease symptoms using high-throughput sequencing. Using overlapping reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends, the genomic sequences of AdV-1 v1 and v2 were confirmed as 17,646 and 18,578 nucleotides in length, respectively. The two complete genomes contained 9 and 15 open reading frames, respectively, coding for proteins having domains typical of Closteroviridae, such as RNA-dependent RNA polymerase (RdRp), heat shock protein 70 homolog (HSP70h) and coat protein (CP). Sequence analysis showed that the amino acid sequences of RdRp, HSP70h, and CP of the two variants exhibited high similarity (> 80%), while their genomic organization was somewhat different. This suggested that the two viral genomes identified here are variants of the family Closteroviridae in a single kiwifruit host. Furthermore, phylogenetic relationship analysis revealed that the two variants had a closer relationship with the unclassified virus Persimmon virus B (PeVB) and Actinidia virus 1 (AcV-1) than with other members of the family Closteroviridae, as did their genomic organization. It is speculated that the two variants, together with PeVB and AcV-1 belong to a new subfamily of Closteroviridae.
Chromosomal Evolution in Aspredinidae (Teleostei, Siluriformes): Insights on Intra- and Interspecific Relationships with Related Groups

The family Aspredinidae comprises a clade of complex systematic relationships, both from molecular and morphological approaches. In this study, conventional and molecular cytogenetic studies coupled with nucleotide sequencing were performed in 6 Aspredininae species (Amaralia hypsiura, Bunocephalus cf. aloikae, Bunocephalus amaurus, Bunocephalus aff. coracoideus, Bunocephalus verrucosus, and Platystacus cotylephorus) from different locations of the Amazon hydrographic basin. Our results showed highly divergent diploid numbers (2n) among the species, ranging from 49 to 74, including the occurrence of an XX/X0 sex chromosome system. A neighbor-joining phylogram based on the cytochrome c oxidase I (COI) showed that Bunocephalus coracoideus is not a monophyletic clade, but closely related to B. verrucosus. The karyotypic data associated with COI suggest an ancestral karyotype for Aspredinidae with a reduced 2n, composed of bi-armed chromosomes and a trend toward chromosomal fissions resulting in higher diploid number karyotypes, mainly composed of acrocentric chromosomes. Evolutionary relationships were discussed under a phylogenetic context with related species from different Siluriformes families. The karyotype features and chromosomal diversity of Aspredinidae show an amazing differentiation, making this family a remarkable model for investigating the evolutionary dynamics in siluriforms as well as in fish as a whole.
Novel insights into the role of N6-methyladenosine (m6A) RNA modification in bone Pathophysiology.

Thus far, there are more than known 150 modifications to RNA，in which common internal modifications of mRNA include N6-Methyladenosine(m6A), N1-methyladenosine(m1A) and 5-methylcytosine (5-mC). Among them, m6A RNA modification is one of the highest abundance modifications in eukaryotes, regulating mechanisms controlling gene expression at the molecular level. As an invertible and dynamic epigenetic marker, m6A base modification influences almost all vital biological processes, cellular components, and molecular functions. Once the m6A modification process is abnormal, a series of diseases -including cancer, neurological diseases, and growth disorders -will be caused. Besides, several base modification activities also have been existed by non-coding RNAs, for instance, microRNAs (miRNAs), and circular RNAs (circRNAs) ，long non-coding RNAs (lncRNAs), which dynamically regulated during Bone and cartilage Pathophysiology processes. Therefore，it has now been clear that dynamic modification on coding RNAs and non-coding RNAs represents a completely new way to modulate genetic information. In this review, we highlight up-to-date progress and applications of N6-methyladenosine (m6A) RNA modification in bone and cartilage pathophysiology, and discuss the pathological roles and underlying molecular mechanism of m6A modifications in osteoarthritis and osteoporosis pathogenesis.
Choroidal Thickening in Patients with Coronavirus Disease – 2019

Objective: To evaluate choroidal thickness in the macular region of patients with coronavirus disease 2019 (COVID-19). Methods: Patients recovered from COVID-19 were included in this cross-sectional study. Macular imaging with an SD-OCT device was performed at least 2 weeks after recovery from systemic COVID-19 and choroidal thickness was measured as the main outcome measure.Results: Thirty-four subjects were included in this study. One patient was monocular and high-quality SD-OCT images were available for the remaining 67 eyes. Dilated choroidal vessels were observed in 55 eyes (82%) and retinal pigment epitheliopathy was noticeable in 4 eyes (6%); these findings resemble those of the pachychoroid spectrum. The mean subfoveal choroidal thickness (SFCT) in our patients was 380.3±12.40 µm, which was significantly thicker than the previously reported SFCT in the normal population (310.7 ± 57.5 µm) (p<0.001). Conclusion: Patients with COVID-19 demonstrate remarkable changes in the choroid of the macular region.
Genomic and Transcriptomic Analysis of Biofilm Formation in Persistent and Transient Listeria monocytogenes Isolates from the Retail Deli Environment Does Not Yield Insight into Persistence Mechanisms.

Persistence of Listeria monocytogenes in retail deli environments is a serious food safety issue, potentially leading to cross-contamination of ready-to-eat foods such as deli meats, salads, and cheeses. We previously discovered strong evidence of L. monocytogenes persistence in delis across multiple states. We hypothesized that this was correlated with isolates' innate characteristics, such as biofilm-forming capacity or gene differences. To test this hypothesis, we sequenced the genomes of 21 L. monocytogenes isolates previously collected longitudinally from the retail deli environment. Isolates were chosen to represent varying attachment capacity and sanitizer tolerance as well as persistence or transience. We used single-nucleotide polymorphism analysis to characterize the isolates' genetic relationships and used BLAST to search the isolates' genomes for antibiotic resistance elements, quaternary ammonium tolerance genes, and stress survival islets. We further chose four isolates for RNA-sequencing analysis and compared their global biofilm transcriptome with their global planktonic transcriptome. We did not find genetic content that explained persistence. The presence of stress survival islet-1 correlated to increased attachment capacity (p < 0.05), but not persistence. Further, the presence of sanitizer tolerance elements was not significantly correlated with phenotypic sanitizer tolerance. Analysis of biofilm versus planktonic gene expression did not show the expected differences in gene expression patterns. Overall, L. monocytogenes persistence in the deli environment is likely a matter of poor sanitation and/or facility design, rather than isolates' biofilm-forming capacity, sanitizer tolerance, or genomic content.
Two-photon fluorescence imaging of subsurface tissue structures with volume holographic microscopy

Abstract. Significance: Two-photon (2P) fluorescence imaging can provide background-free high-contrast images from the scattering tissues. However, obtaining a multiplane image is not straightforward. We present a two-photon volume holographic imaging (2P-VHI) system for multiplane imaging. Aim: Our goal was to design and implement a 2P-VHI system that can provide the high-contrast optically sectioned images at multiple planes. Approach: A 2P-VHI system is presented that incorporates angularly multiplexed volume holographic gratings and a femtosecond laser source for fluorescence excitation for multiplane imaging. A volume hologram with multiplexed gratings provides multifocal observation, whereas nonlinear excitation using a femtosecond laser helps in significantly enhancing both depth resolution and contrast of images. Results: Standard fluorescent beads are used to demonstrate the imaging performance of the 2P-VHI system. Two-depth resolved optical-sectioning images of fluorescently labeled thick mice intestine samples were obtained. In addition, the optical sectioning capability of our system is measured and compared with that of a conventional VHI system. Conclusions: Results demonstrated that 2P excitation in VHI systems provided the optical sectioning ability that helps in reducing background noise in the images. Integration of nonlinear fluorescence excitation in the VHI provides some unique advantages to the system and has potential to design multidepth optical sectioned spatial–spectral imaging systems.