Miracle-dz/UniFAR-FTUs huggingface dataset:
Malformation Disease in Tabebuia rosea (Rosy Trumpet) Caused by Fusarium pseudocircinatum in Mexico.

Tabebuia rosea (rosy trumpet) is an economically important Neotropical tree in Mexico that is highly valued for the quality of its wood, which is used for furniture, crafts, and packing, and for its use as an ornamental and shade tree in parks and gardens. During surveys conducted in the lower Balsas River Basin region in the states of Guerrero and Michoacán, symptoms of floral malformation were detected in T. rosea trees. The main objectives of this study were to describe this new disease, to determine its causal agent, and to identify it using DNA sequence data. A second set of objectives was to analyze the phylogenetic relationship of the causal agent to Fusarium associated with Swietenia macrophylla trees with malformation surveyed in the same region, and to compare mycotoxin production and the mating type idiomorphs of fusaria recovered from T. rosea and S. macrophylla. Tabebuia rosea showed malformed inflorescences with multiple, tightly curled shoots, and shortened internodes. A total of 31 Fusarium isolates recovered from symptomatic T. rosea (N = 20) and S. macrophylla (N = 11) trees were identified by molecular analysis as F. pseudocircinatum. Pathogenicity tests showed that isolates of F. pseudocircinatum recovered from T. rosea, induced malformation in inoculated T. rosea seedlings. Eighteen F. pseudocircinatum isolates were tested for their ability to produce mycotoxins and other secondary metabolites. Moniliformin, fusaric acid, bikaverin, beauvericin, aurofusarin and 8-O-methylbostrycoidin were produced by at least 1 strain of the 18 isolates tested. A multiplex PCR assay for mating type idiomorph revealed that 22 F. pseudocircinatum isolates were MAT1-1 and 9 were MAT1-2. Here we report a new disease of T. rosea in Mexico caused by F. pseudocircinatum.
Cost-effectiveness of trifluridine/tipiracil as a third-line treatment of metastatic gastric cancer, including adenocarcinoma of the gastrohesophageal junction, among patients previously treated in Greece

ABSTRACT Objective To evaluate the cost-effectiveness of trifluridine/tipiracil (FTD/TPI) compared with best supportive care (BSC) for the treatment of patients with metastatic gastric cancer(mGC), including gastroesophageal junction adenocarcinoma(GEJ), who have received at least two prior therapies for metastatic disease and are eligible for third-line treatment, in Greece. Methods A partitioned survival model was locally adapted from a public payer perspective over a 10-year time horizon. Clinical, safety and utility data were extracted from literature. Resource consumption data obtained from a panel of local experts using a questionnaire developed for the study was combined with unit costs obtained from official sources. All costs reflect the year 2020 (€). Outcomes of the model were patients’ life years (LYs) and quality-adjusted life years (QALYs), total costs and incremental cost-effectiveness ratio (ICER) per QALY and LY gained. Results The total cost per patient was estimated to be €6,965 for FTD/TPI and €1,906 for BSC, while FTD/TPI was associated with 0.180 and 0.107 increments in LYs and QALYs, respectively, compared with BSC, resulting in an ICER of €47,144 per QALY gained and €28,112 per LY gained. Conclusion FTD/TPI was estimated to be a cost-effective treatment option for eligible third line mGC patients, including GEJ in Greece.
Multimechanistic Monoclonal Antibody Combination Targeting Key Staphylococcus aureus Virulence Determinants in a Rabbit Model of Prosthetic Joint Infection

In a rabbit model of methicillin-resistant Staphylococcus aureus prosthetic joint infection (PJI), prophylaxis with AZD6389*—a combination of three monoclonal antibodies targeting alpha-hemolysin, bicomponent cytotoxins (LukSF/LukED/HlgAB/HlgCB), and clumping factor A—resulted in significant reductions in joint swelling, erythema, intra-articular pus, and bacterial burden in synovial tissues and biofilm-associated prosthetic implants compared with isotype-matched control IgG. ABSTRACT In a rabbit model of methicillin-resistant Staphylococcus aureus prosthetic joint infection (PJI), prophylaxis with AZD6389*—a combination of three monoclonal antibodies targeting alpha-hemolysin, bicomponent cytotoxins (LukSF/LukED/HlgAB/HlgCB), and clumping factor A—resulted in significant reductions in joint swelling, erythema, intra-articular pus, and bacterial burden in synovial tissues and biofilm-associated prosthetic implants compared with isotype-matched control IgG. Targeting specific staphylococcal virulence factors may thus have potential clinical utility for prevention of PJI.
Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity

ABSTRACT Severe Helicobacter pylori-linked gastric disorders are especially prevalent in the East Asia region. The ability of H. pylori to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical H. pylori strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their association with pathogenicity. Population analysis showed that 92.9% of the Shanghai H. pylori isolates were clustered in the East Asia group. Among 2,866 genes detected in all genomes, 1,146 genes formed the core genome, whereas 209 unique genes were detected in individual disease groups. The unique genes of peptic ulcer and gastric cancer groups represented the inorganic ion transport and metabolism function gene clusters. Sixteen virulence genes were detected with statistically different detection rates among the four disease groups. Furthermore, 127 clustered regularly interspaced short palindromic repeats were found with significantly different rates in the four disease groups. A total of 337 putative genomic islands were identified, and three genomic islands were individually found in more than 10% of strains. The genomic islands included several metabolism-associated genes and many genes with unknown function. In total, 88 sequence types were detected among the 112 Shanghai H. pylori isolates. Our study provides an essential milestone in the mapping of specific genomic features and their functions to identify factors needed to induce specific gastric disorders in H. pylori.
The linked lives of young women with metastatic breast cancer

Abstract Purpose/Objectives With a growing number of young women with metastatic breast cancer (MBC) in the United States, it is important to consider how their diagnoses affect their relationships with others. The dual identities of being young and having MBC create unique challenges for women’s relationships. However, there is little extant research on the relationship experiences and needs of young women with MBC. The purpose of this study is to understand how young women describe their lived experiences with social and intimate relationships following their diagnoses of MBC. Design A cross-sectional qualitative study with a life course theoretical framework was employed. Sample/Participants Purposive sampling yielded nine participants who took part in semi-structured interviews. Phenomenology informed understanding of the lived experience of young women with MBC. Findings The findings describe how young women with MBC made meaning out of their relationships to other people following their diagnoses, via themes of feeling alienated from other women with breast cancer, friendship trajectories, managing intimate relationships, how much to share with children, losing the dream of (more) children, and finding a voice in the MBC community. Conclusion MBC links participants’ lives to individuals from their preexisting relationships, new friendships, and the breast cancer community in irrevocable ways. Implications for Psychosocial Providers These findings present new information about the social and relationship needs of young women with MBC. Psychosocial providers and medical team members should not presume MBC patients’ disinterest in fertility preservation.
Novel lab-on-a-disk platforms: a powerful tool for molecular fingerprinting of oral and respiratory tract infections

Respiratory tract infections (RTIs) are communicable, bacteriaor virus-borne diseases [1] which, especially in acute phase, can progress rapidly and lead to hospitalizations, complications or even death, while some of them lead to epidemic outbreaks. In any case, they require urgent handling. Oral infections, in particular referring to the bacteria-borne caries and periodontitis, are non-communicable diseases. Caries affects the hard tissue of the teeth causing tooth decay, while periodontitis affects the tissues that surround and support the teeth (gums), leading to tooth loss [2]. Both caries and periodontitis are treatable, though not life-threatening to the degree of RTIs. However, especially periodontitis has been shown to be related to systemic disorders such as diabetes and cardiovascular diseases [3].
Meditation Monologue can Reduce Clinical Injection-Related Anxiety: Randomized Controlled Trial

Background. Strategies to reduce anxiety prior to injection procedures are not well understood. The purpose is to determine the effect of a meditation monologue intervention delivered via phone/mobile application on pre-injection anxiety levels among patients undergoing a clinical injection. The following hypothesis was tested: patients who listened to a meditation monologue via phone/mobile application prior to clinical injection would experience less anxiety compared to those who did not. Methods. A prospective, randomized controlled trial was performed at an orthopedics and sports medicine clinic of a tertiary level medical center in the New England region, USA. Thirty patients scheduled for intra- or peri-articular injections were randomly allocated to intervention (meditation monologue) or placebo (nature sounds) group. Main outcome variables were state and trait anxiety inventory (STAI) scores and blood pressure (BP), heart rate, and respiratory rate. Results. There were 16 participants who were allocated to intervention (meditation monologue) while 14 participants were assigned to placebo (nature sounds). There was no interaction effect. However, a main time effect was found. Both state anxiety (STAI-S) and trait anxiety (STAI-T) scores were significantly reduced post-intervention compared to pre-intervention (STAI-S: p = 0.04, STAI-T: p = 0.04). Also, a statistically significant main group effect was detected. The pre- and post- STAI-S score reduction was greater in the intervention group (p = 0.028). Also, a significant diastolic BP increase between pre- and post-intervention was recorded in the intervention group (p = 0.028), but not in the placebo group (p = 0.999). Conclusion. Listening to a meditation monologue via phone/mobile application prior to clinical injection can reduce anxiety in adult patients receiving intra- and peri-articular injections. Registration: ClinicalTrials.gov NCT02690194
Controlling the magnetic properties of polymer–iron oxide nanoparticle composite thin films via spatial particle orientation

We investigated the effect of Fe3O4 nanoparticle orientation on the magnetic properties of hybrid polymer nanocomposite thin films. A multilayer thin film consisting of alternating layers of polymers and assembled iron oxide nanoparticles was prepared by spin coating and Langmuir–Blodgett techniques. Transmission electron microscopy and neutron reflectivity measurements were employed to determine structural information related to the lateral orientation of the Fe3O4 nanoparticle monolayer and the layered architecture along the depth of the multilayer, respectively. The magnetic properties of the hybrid multilayer were characterized by SQUID magnetometry and compared with the properties of a spin-coated polymer nanocomposite thin film containing homogenously dispersed Fe3O4 nanoparticles. We found that the closely-packed monolayer structure of the Fe3O4 nanoparticles changed the magnetic properties on account of the dipolar interactions between particles, whereas the homogeneously-dispersed nanoparticles embedded in the polymer matrix exhibited zero remanent magnetization and coercivity due to isolation of the nanoparticles and lack of dipolar interactions.
Annual Research Review: Achieving universal health coverage for young children with autism spectrum disorder in low- and middle-income countries: a review of reviews.

BACKGROUND Autism presents with similar prevalence and core impairments in diverse populations. We conducted a scoping review of reviews to determine key barriers and innovative strategies which can contribute to attaining universal health coverage (UHC), from early detection to effective interventions for autism in low- and middle-income countries (LAMIC). METHODS A systematic literature search of review articles was conducted. Reviews relevant to the study research question were included if they incorporated papers from LAMIC and focused on children (<eight years old) with autism or their caregivers. The database search was supplemented with bibliographic search of included articles and key informant suggestions. Data were extracted and mapped onto a Theory of Change model toward achieving UHC for autism in LAMIC. RESULTS We identified 31 articles which reviewed data from over fifty countries across Africa, Latin America, Middle East, and Asia and addressed barriers across one or more of four inter-related domains: (a) the social context and family experience for a child with autism; (b) barriers to detection and diagnosis; (c) access to appropriate evidence-based intervention; and (d) social policy and legislation. Key barriers identified included: lack of appropriate tools for detection and diagnosis; low awareness and experienced stigma impacting demand for autism care; and the prevalence of specialist models for diagnosis and treatment which are not scalable in LAMIC. CONCLUSIONS We present a Theory of Change model which describe the strategies and resources needed to realize UHC for children with autism in LAMIC. We highlight the importance of harnessing existing evidence to best effect, using task sharing and adapted intervention strategies, community participation, and technology innovation. Scaling up these innovations will require open access to appropriate detection and intervention tools, systematic approaches to building and sustaining skills in frontline providers to support detection and deliver interventions embedded within a stepped care architecture, and community awareness of child development milestones.
The experience of D/deaf healthcare professionals during the coronavirus pandemic

Abstract Background The coronavirus pandemic, in particular the introduction of masks, presented a huge challenge for the UK’s D/deaf community, many of whom rely on visual cues in lipreading and sign language. This particularly affected D/deaf healthcare professionals (HCPs), who faced significant communication challenges at work due to the lack of transparent masks or other reasonable adjustments. Aims To determine the impact that a lack of transparent masks and reasonable adjustments had on communication, confidence at work and well-being among D/deaf HCPs during the coronavirus pandemic. Methods A survey was sent to all members of the ‘UK Deaf Healthcare Professionals Group’ on Facebook, the ‘Healthcare Professionals with Hearing Loss’ listserver and promoted on Social Media. Results Eighty-three responses were received. Nine (11%) individuals had access to transparent masks. Over three-quarters of respondents reported feeling anxious and fearful of making a mistake due to communication difficulties. Fourteen (17%) were removed from clinical roles due to a lack of reasonable adjustments. One-third felt they would need to consider an alternative career if improvements were not made. Seventy-eight per cent felt the communication needs of D/deaf HCPs had not been met during the pandemic. Conclusions D/deaf HCPs felt left behind, isolated and frustrated by a lack of transparent masks and reasonable adjustments to meet their communication needs. Loss of experienced, qualified HCPs has a significant economic and workforce impact, particularly during a pandemic. Urgent action is needed to ensure D/deaf HCPs are provided with the workplace support required under the Equality Act (2010).
Local and CNS-Wide Astrocyte Intracellular Calcium Signaling Attenuation In Vivo with CalExflox Mice

Astrocytes exist throughout the CNS and affect neural circuits and behavior through intracellular Ca2+ signaling. Studying the function(s) of astrocyte Ca2+ signaling has proven difficult because of the paucity of tools to achieve selective attenuation. Based on recent studies, we generated and used male and female knock-in mice for Cre-dependent expression of mCherry-tagged hPMCA2w/b to attenuate astrocyte Ca2+ signaling in genetically defined cells in vivo (CalExflox mice for Calcium Extrusion). We characterized CalExflox mice following local AAV-Cre microinjections into the striatum and found reduced astrocyte Ca2+ signaling (∼90%) accompanied with repetitive self-grooming behavior. We also crossed CalExflox mice to astrocyte-specific Aldh1l1-Cre/ERT2 mice to achieve inducible global CNS-wide Ca2+ signaling attenuation. Within 6 d of induction in the bigenic mice, we observed significantly altered ambulation in the open field, disrupted motor coordination and gait, and premature lethality. Furthermore, with histologic, imaging, and transcriptomic analyses, we identified cellular and molecular alterations in the cerebellum following mCherry-tagged hPMCA2w/b expression. Our data show that expression of mCherry-tagged hPMCA2w/b with CalExflox mice throughout the CNS resulted in substantial attenuation of astrocyte Ca2+ signaling and significant behavioral alterations in adult mice. We interpreted these findings candidly in relation to the ability of CalEx to attenuate astrocyte Ca2+ signaling, with regards to additional mechanistic interpretations of the data, and their relation to past studies that reduced astrocyte Ca2+ signaling throughout the CNS. The data and resources provide complementary ways to interrogate the function(s) of astrocytes in multiple experimental scenarios. SIGNIFICANCE STATEMENT Astrocytes represent a significant fraction of all brain cells and tile the entire central nervous system. Unlike neurons, astrocytes lack propagated electrical signals. Instead, astrocytes are proposed to use diverse and dynamic intracellular Ca2+ signals to communicate with other cells. An open question concerns if and how astrocyte Ca2+ signaling regulates behavior in adult mice. We approached this problem by generating a new transgenic mouse line to achieve inducible astrocyte Ca2+ signaling attenuation in vivo. We report our data with this mouse line and we interpret the findings candidly in relation to past studies and within the framework of different mechanistic interpretations.
Functional redundancy and specific taxa modulate the contribution of prokaryotic diversity and composition to multifunctionality

Observational and experimental evidence has revealed the functional importance of microbial diversity. However, the effects of microbial diversity loss on ecosystem functions are not consistent across studies, which are probably tempered by microbial functional redundancy, specific taxa and functions evaluated. Here we conducted diversity manipulation experiments in two independent soils with distinct prokaryotic communities, and investigated how the initial community traits (e.g., distinct functional redundancy and taxonomic composition) modulate the contribution of prokaryotic diversity loss and composition shift to eight ecosystem functions related to soil nutrient cycling. We found that diversity loss impaired three functions (potential nitrification rate, N2‐fixation activity and phosphatase) and multifunctionality only in the communities with low functional redundancy, but all examined functions were unaffected in the communities with high functional redundancy. All significantly affected functions belonged to specialized functions, while the broad function (soil basal respiration) was unaffected. Moreover, prokaryotic composition explained more functional variation than diversity, which was ascribed to the crucial role of specific taxa that influence particular functions. Taken together, this study provides empirical evidence for identifying the mechanism underlying the ecosystem response to changes in microbial community, with implications for improving the prediction of ecosystem process models and managing microbial communities to promote ecosystem services.
Design and validation of a recognition instrument—the stroke aid for emergency scale—to predict large vessel occlusion stroke

Background and purpose: Rapidly recognizing patients with large-vessel occlusion stroke (LVOS) and transferring them to a center offering recanalization therapy is crucial of maximizing the benefits of early treatment. We therefore aimed to design an easy-to-use recognition instrument for identifying LVOS. Methods: Prospective data were collected from emergency departments of 12 stroke-center hospitals in China during a 17-month study period. The Stroke Aid for Emergency (SAFE) scale is based on consciousness commands, facial palsy, gaze, and arm motor ability. Receiver operating characteristic analysis was used to obtain the area under the curve for the SAFE scale and previously established scales to predict LVOS. Results: The SAFE scale could accurately predict LVOS at an accuracy rate comparable to that of the National Institutes of Health Stroke Scale (c-statistics: 0.823 versus 0.831, p = 0.4798). The sensitivity, specificity, positive predictive value, and negative predictive value for the SAFE scale were 0.6875, 0.8577, 0.6937, and 0.8542, respectively, with a cutoff point of 4. The SAFE scale also performed well in a subgroup analysis based on the patients’ ages, occluded vessel locations, and the onset-to-door times. Conclusions: The SAFE scale can accurately recognize LVOS at a rate comparable to those of other, similar scales.
tSFM 1.0: tRNA Structure-Function Mapper

MOTIVATION Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their evolutionary divergences. Although permutation p-values can quantify the significance of CIF divergences between two taxa, their naive Monte Carlo approximation is slow and inaccurate. The Peaks-over-Threshold approach of Knijnenburg et al. (2009) promises improvements to both speed and accuracy of permutation p-values, but has no publicly available API. AVAILABILITY AND IMPLEMENTATION We present tRNA Structure-Function Mapper (tSFM) v1.0, an open-source, multi-threaded application that efficiently computes, visualizes, and assesses significance of single- and paired-site CIFs and their evolutionary divergences for any RNA, protein, gene or genomic element sequence family. multiple estimators of permutation p-values for CIF evolutionary divergences are provided along with condidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI. SUPPLEMENTARY INFORMATION Supplementary materials are available at Bioinformatics online.