Miracle-dz/UniFAR-FTUs huggingface dataset:
H-NS Silences Gene Expression of LeuO, the Master Regulator of the Cyclic(Phe-Pro)-dependent Signal Pathway, in Vibrio vulnificus

The histone-like nucleoid structuring protein (H-NS) is an abundant global regulator of environmentally controlled gene expression. Herein, we demonstrate that H-NS represses the expression of LeuO, the master regulator of the cyclic(Phe-Pro)-dependent signaling pathway, by directly binding to the upstream region of the gene. H-NS binds to a long stretched region (more than 160-bp long), which overlaps with binding sites for ToxR and LeuO. A high quantity of H-NS outcompetes ToxR for binding to the cis-acting element of leuO. However, our footprinting analyses suggests that the binding of H-NS is relatively weaker than LeuO or ToxR at the same molarity. Considering that the DNA nucleotide sequences of the upstream regions of leuO genes are highly conserved among various Vibrio, such patterns as those found in V. vulnificus would be a common feature in the regulation of leuO gene expression in Vibrionaceae. Taken together, these results suggest that, in species belonging to Vibrionaceae, H-NS regulates the expression of leuO as a basal stopper when cFP-ToxR mediated signaling is absent.
Targeted chemotherapy overcomes drug resistance in melanoma

In this study, Yue et al. describe a therapeutic strategy termed “targeted chemotherapy” that involves depleting PP2A or inhibiting it using a small molecule inhibitor, phendione, in drug-resistant melanoma. The authors show phendione induces DNA damage response without causing DNA breaks or inducing cellular dormancy, therefore blocking tumor growth of BRAF mutant and NRAS mutant melanomas.
Acute respiratory illness among a prospective cohort of pediatric patients using emergency medical services in India: Demographic and prehospital clinical predictors of mortality

Background In India, acute respiratory illnesses, including pneumonia, are the leading cause of early childhood death. Emergency medical services are a critical component of India’s public health infrastructure; however, literature on the prehospital care of pediatric patients in low- and middle-income countries is minimal. The aim of this study is to describe the demographic and clinical characteristics associated with 30-day mortality among a cohort of pediatric patients transported via ambulance in India with an acute respiratory complaint. Methods Pediatric patients less than 18 years of age using ambulance services in one of seven states in India, with a chief complaint of “shortness of breath”, or a “fever” with associated “difficulty breathing” or “cough”, were enrolled prospectively. Patients were excluded if evidence of choking, trauma or fire-related injury, patient was absent on ambulance arrival, or refused transport. Primary exposures included demographic, environmental, and clinical indicators, including hypoxemia and respiratory distress. The primary outcome was 7 and 30-day mortality. Multivariable logistic regression, stratified by transport type, was constructed to estimate associations between demographic and clinical predictors of mortality. Results A total of 1443 patients were enrolled during the study period: 981 (68.5%) were transported from the field, and 452 (31.5%) were interfacility transports. Thirty-day response was 83.4% (N = 1222). The median age of all patients was 2 years (IQR: 0.17–10); 93.9% (N = 1347) of patients lived on family incomes below the poverty level; and 54.1% (N = 706) were male. Cumulative mortality at 2, 7, and 30-days was 5.2%, 7.1%, and 7.7%, respectively; with 94 deaths by 30 days. Thirty-day mortality was greatest among those 0–28 days (N = 38,17%); under-5 mortality was 9.8%. In multivariable modeling prehospital oxygen saturation <95% (OR: 3.18 CI: 1.77–5.71) and respiratory distress (OR: 3.72 CI: 2.17–6.36) were the strongest predictors of mortality at 30 days. Conclusions This is the first study to detail prehospital predictors of death among pediatric patients with shortness of breath in LMICs. The risk of death is particularly high among neonates and those with documented mild hypoxemia, or respiratory distress. Early recognition of critically ill children, targeted prehospital interventions, and diversion to higher level of care may help to mitigate the mortality burden in this population.
Using Deep Learning to Identify Molecular Junction Characteristics.

The scanning tunneling microscope-based break junction (STM-BJ) is used widely to create and characterize single metal-molecule-metal junctions. In this technique, conductance is continuously recorded as a metal point-contact is broken in a solution of molecules. Conductance plateaus are seen when stable molecular junctions are formed. Typically, thousands of junctions are created and measured, yielding thousands of distinct conductance versus extension traces. However, such traces are rarely analyzed individually to recognize the types of junctions formed. Here, we present a deep learning-based method to identify molecular junctions and show that it performs better than several commonly used and recently reported techniques. We demonstrate molecular junction identification from mixed solution measurements with accuracies as high as 97%. We also apply this model to an in situ electric-field driven isomerization reaction of a [3]cumulene to follow the reaction over time. Furthermore, we demonstrate that our model can remain accurate even when a key parameter, the average junction conductance, is eliminated from the analysis, showing that our model goes beyond conventional analysis in existing methods.
Treat and Trick: Common Regulation and Manipulation of Sugar Transporters During Sink Establishment by the Plant and the Invader.

Sugar transport proteins are crucial for coordinated allocation of sugars. In this review we summarize recent key findings of roles and regulations of sugar transporters in inter- and intracellular transport by focusing on applied approaches, demonstrating how sucrose transporter activity may alter source and sink dynamics and their identities. The plant itself alters its sugar transport activity in a developmental-dependent manner to either establish or load endogenous sinks, e.g. during tuber formation and filling. Pathogens represent aberrant sinks, triggering the plant to induce the same processes resulting in loss of carbon assimilates. We explore common mechanisms of intrinsic, developmental-dependent processes and such aberrant, pathogen-induced manipulation of sugar transport. Transporter activity may also be targeted by breeding or GMO approaches in crop plants to alter source and sink metabolism upon over- or heterologous expression of these proteins. In addition, we highlight recent progress in the use of sugar analogs to study these processes in vivo.
Fragment-Based Design of Mycobacterium tuberculosis InhA Inhibitors

Tuberculosis (TB) remains a leading cause of mortality among infectious diseases worldwide. InhA has been the focus of numerous drug discovery efforts as this is the target of the first line pro-drug isoniazid. However, with resistance to this drug becoming more common, the aim has been to find new clinical candidates that directly inhibit this enzyme and that do not require activation by the catalase peroxidase KatG, thus circumventing the majority of the resistance mechanisms. In this work, the screening and validation of a fragment library are described, and the development of the fragment hits using a fragment growing strategy was employed, which led to the development of InhA inhibitors with affinities of up to 250 nM.
Effects of psychosocial interventions and caregiving stress on cardiovascular biomarkers in family dementia caregivers: The UCSD Pleasant Events Program (PEP) randomized controlled trial.

BACKGROUND This study examined whether biological mechanisms linking dementia caregiving with an increased risk of coronary heart disease can be modified by psychosocial interventions and which caregivers might benefit the most from an intervention. METHODS Spousal dementia caregivers were randomized to 12-week treatment with either a behavioral activation intervention (i.e., Pleasant Events Program PEP; n=60), or an active control Information and Support (IS; n=63) condition. Indicators of caregiving stress were assessed pre-treatment and circulating cardiovascular biomarkers were measured pre- and post-treatment. RESULTS There were no significant changes in biomarker levels from pre- to post-treatment both by treatment condition and across all caregivers. Regardless of the treatment condition, exploratory regression analysis revealed that caregivers were more likely to show significant decreases in C-reactive protein (CRP) and D-dimer when their spouse had severe functional impairment; in interleukin (IL)-6 and CRP when they had greater distress due to care recipient's problem behaviors; in tumor necrosis factor (TNF)-α when they had higher levels of negative affect; and in IL-6, CRP, TNF-α and D-dimer when they had higher personal mastery. Within the PEP group, caregivers with higher negative affect and those with higher positive affect were more likely to show a reduction in von Willebrand factor and D-dimer, respectively. Within the IS group, caregivers whose spouse had severe functional impairment were more likely to show a decrease in IL-6. CONCLUSIONS Unlike the average caregiver, caregivers high in burden/distress and resources might benefit from psychosocial interventions to improve cardiovascular risk, although these observations need confirmation. ClinicalTrials.gov #NCT02317523.
A scoping review of the moral experiences of children with medical complexity in Brazil.

OBJECTIVES The aim of this review was to identify and summarize how the moral experiences of children with medical complexity are being expressed within the Brazilian health-related literature and discuss research gaps and directions for future research. METHODS A scoping review was performed using the methodological framework of Arksey and O'Malley and the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). Systematic searches were conducted on Medline, CINAHL, Scopus, and Embase databases. Articles were included if using qualitative methodologies, having children as participants, and published in Brazil. RESULTS In total, 6,360 articles were retrieved from databases. Sixteen studies were selected for the analysis. FINAL CONSIDERATIONS The studies were not primarily focused on children's moral experiences. Yet, the studies demonstrate morally relevant accounts concerning children's capacity to reason and interpret their lived experiences, expressing deep concerns about isolation, suffering, future aspirations, and feelings of normality.
Molecular basis of impaired extraocular muscle function in a mouse model of congenital myopathy due to compound heterozygous Ryr1 mutations.

Mutations in the RYR1 gene are the most common cause of human congenital myopathies and patients with recessive mutations are severely affected and often display ptosis and/or ophthalmoplegia. In order to gain insight into the mechanism leading to extraocular muscle involvement, we investigated the biochemical, structural and physiological properties of eye muscles from mouse models we created knocked-in for Ryr1 mutations. Ex vivo force production in extraocular muscles from compound heterozygous RyR1p.Q1970fsX16 + p.A4329D mutant mice was significantly reduced compared to that observed in wild type, single heterozygous mutant carriers or homozygous RyR1p.A4329D mice. The decrease in muscle force was also accompanied by approximately a 40% reduction in RyR1 protein content, a decrease in electrically evoked calcium transients, disorganization of the muscle ultrastructure and a decrease in the number of calcium release units. Unexpectedly, the superfast and ocular-muscle specific myosin heavy chain-EO isoform was almost undetectable in RyR1p.Q1970fsX16 + p.A4329D mutant mice. The results of this study show for the first time that the extraocular muscle phenotype caused by the RyR1p.Q1970fsX16 + p.A4329D compound heterozygous Ryr1 mutations is complex and due to a combination of modifications including a direct effect on the macromolecular complex involved in calcium release and indirect effects on the expression of myosin heavy chain isoforms.
Skeletal muscle mass as a prognostic indicator of outcomes in ovarian cancer: a systematic review and meta-analysis

Background Muscle mass plays a key role in predicting clinical outcomes in cancer. This systematic review and meta-analysis aimed to evaluate whether computed tomography (CT) scan indexes of muscle mass quantity and quality could be used as prognostic factors in ovarian cancer. Methods Three electronic bibliographic databases (MEDLINE, Web of Science, and Cochrane Central Register of Controlled Trials) were used to conduct a systematic literature search from inception to January 2020. The primary outcome was overall survival. Pooled analyses of hazard ratios (HRs) and 95% confidence intervals (CIs) were performed with Review Manager 5.3. Heterogeneity was assessed by measuring inconsistency (I2 based on the χ2 test). Secondary outcomes included progression free survival, disease free survival, postoperative complications, and chemotoxicity. Study quality and quality of evidence were assessed. Results A total of 15 studies were included in the systematic review, of which six studies (1226 patients) were included in the meta-analysis. Summary unadjusted HRs (HR 1.11, 95% CI 0.84 to 1.46, p=0.47) and adjusted HRs (HR 1.10, 95% CI 0.84 to 1.43, p=0.49) did not show a significant association between low skeletal muscle index and overall survival (p>0.05) in ovarian cancer. Instead, although the quality of evidence was low, pooled data of three studies, comprising 679 patients, showed a significant association between low skeletal muscle radiodensity and poor overall survival (HR 1.63, 95% CI 1.28 to 2.07, p<0.0001). Moreover, the heterogeneity between studies precluded the possibility of performing a meta-analysis and reaching conclusions for progression free survival, disease free survival, surgical complications, and chemotoxicity. Conclusions This work suggested that the measurement of skeletal muscle radiodensity by routine CT scan at diagnosis, with standardization of diagnostic criteria, could be a reliable tool to select at risk patients and to individualize effective nutritional strategies. However, prospective homogeneous studies with a larger number of patients are required to confirm these results.
Proteinase-Activated Receptor 4 Activation Triggers Cell Membrane Blebbing through RhoA and β-Arrestin

Proteinase-activated receptors (PARs) are a four-member family of G-protein–coupled receptors that are activated via proteolysis. PAR4 is a member of this family that is cleaved and activated by serine proteinases such as thrombin, trypsin, and cathepsin-G. PAR4 is expressed in a variety of tissues and cell types, including platelets, vascular smooth muscle cells, and neuronal cells. In studying PAR4 signaling and trafficking, we observed dynamic changes in the cell membrane, with spherical membrane protrusions that resemble plasma membrane blebbing. Since nonapoptotic membrane blebbing is now recognized as an important regulator of cell migration, cancer cell invasion, and vesicular content release, we sought to elucidate the signaling pathway downstream of PAR4 activation that leads to such events. Using a combination of pharmacological inhibition and CRISPR/CRISPR-associated protein 9 (Cas9)–mediated gene editing approaches, we establish that PAR4-dependent membrane blebbing occurs independently of the Gαq/11- and Gαi-signaling pathways and is dependent on signaling via the β-arrestin-1/2 and Ras homolog family member A (RhoA) signaling pathways. Together these studies provide further mechanistic insight into PAR4 regulation of cellular function. SIGNIFICANCE STATEMENT We find that the thrombin receptor PAR4 triggers cell membrane blebbing in a RhoA–and β-arrestin–dependent manner. In addition to identifying novel cellular responses mediated by PAR4, these data provide further evidence for biased signaling in PAR4 since membrane blebbing was dependent on some, but not all, signaling pathways activated by PAR4.
The Paralogous Krüppel-like Factors 9 and 13 Regulate the Mammalian Cellular Circadian Clock Output Gene Dbp

An intricate transcription-translation feedback loop (TTFL) governs cellular circadian rhythms in mammals. Here, we report that the zinc finger transcription factor Krüppel-like factor 9 (KLF9) is regulated by this TTFL, it associates in chromatin at the core circadian clock and clock-output genes, and it acts to modulate transcription of the clock-output gene Dbp. Our earlier genome-wide analysis of the mouse hippocampus-derived cell line HT22 showed that KLF9 associates in chromatin with Per1, Per3, Dbp, Tef, Bhlhe40, Bhlhe41, Nr1d1, and Nr1d2. Of the 3514 KLF9 peaks identified in HT22 cells, 1028 contain E-box sequences to which the transcriptional activators CLOCK and BMAL1 may bind, a frequency significantly greater than expected by chance. Klf9 mRNA showed circadian oscillation in synchronized HT22 cells, mouse hippocampus, and liver. At the clock-output gene Dbp, KLF9 exhibited circadian rhythmicity in its association in chromatin in HT22 cells and hippocampus. Forced expression of KLF9 in HT22 cells repressed basal Dbp transcription and strongly inhibited CLOCK+BMAL1-dependent transcriptional activation of a transfected Dbp reporter. Mutational analysis showed that this action of KLF9 depended on 2 intact KLF9-binding motifs within the Dbp locus that are in close proximity to E-boxes. Knockout of Klf9 or the paralogous gene Klf13 using CRISPR/Cas9 genome editing in HT22 cells had no effect on Dbp expression, but combined knockout of both genes strongly impaired circadian Dbp mRNA oscillation. Like KLF9, KLF13 also showed association in chromatin with clock- and clock-output genes, and forced expression of KLF13 inhibited the actions of CLOCK+BMAL1 on Dbp transcription. Our results suggest novel and partly overlapping roles for KLF9 and KLF13 in modulating cellular circadian clock output by a mechanism involving direct interaction with the core TTFL.
Norhierridin B, a New Hierridin B-Based Hydroquinone with Improved Antiproliferative Activity

Hierridin B (6), a methylated hydroquinone isolated from the marine picocyanobacterium Cyanobium sp. LEGE 06113, moderately inhibited the growth of colon adenocarcinoma HT-29 cells. Aiming to improve the potential antitumor activity of this natural product, the demethylated analogue, norhierridin B (10), as well as its structurally-related quinone (9), were synthesized and evaluated for their growth inhibitory effect on a panel of human tumor cell lines, including the triple-negative breast cancer (TNBC) cells MDA-MB-231, SKBR3, and MDA-MB-468. Norhierridin B (10) showed a potent growth inhibitory effect on all cancer cell lines. Moreover, the growth inhibitory effect of compound 10 on MDA-MB-231 cells was associated with cell cycle arrest and apoptosis. Norhierridin B (10) interfered with several p53 transcriptional targets, increasing p21, Bax, and MDM2, while decreasing Bcl-2 protein levels, which suggested the potential activation of a p53 pathway. Altogether, these results evidenced a great improvement of the antitumor activity of hydroquinone 10 when compared to 6 and its structurally-related quinone (9). Notably, hydroquinone 10 displayed a prominent growth inhibitory activity against TNBC cells, which are characterized by high therapeutic resistance.
Novel team-based approach to quality improvement effectively engages staff and reduces adverse events in healthcare settings

Background Despite significant attention to safety and quality in healthcare over two decades, patient harm in hospitals remains a challenge. There is now growing emphasis on continuous quality improvement, with approaches that engage front-line staff. Our objective was to determine whether a novel approach to reviewing routine clinical practice through structured conversations—map-enabled experiential review—could improve engagement of front-line staff in quality improvement activities and drive improvements in indicators of patient harm. Methods Once a week over a 10-month period, front-line staff were engaged in 35 min team-based conversations about routine practices relating to five national safety standards. Structure for the conversations was provided by interactive graphical logic maps representing each standard. Staff awareness of—and attitudes to—quality improvement, as well as their perceptions of the intervention and its impact, were canvassed through surveys. The impact of the intervention on measures of patient safety was determined through analysis of selected incident data reported in the hospital’s risk management system. Results The map-enabled experiential review approach was well received by staff, who reported increased awareness and understanding of national standards and related hospital policies and protocols, as well as increased interest in quality issues and improvement. The data also indicate an improvement in quality and safety in the two participating units, with a 34% statistically significant decrease in the recorded incident rates of the participating units relative to the rest of the hospital for a set of independently recorded incidents relating to patient identification. Discussion This exploratory study provided promising initial results on the feasibility and effectiveness of map-enabled experiential review as a quality improvement approach in an acute clinical setting.
Identification of MLKL membrane translocation as a checkpoint in necroptotic cell death using Monobodies

Significance Dysregulation of cell death by necroptosis has been implicated in human inflammatory diseases. Phosphorylation of the MLKL pseudokinase, the terminal effector in the pathway, by RIPK3 is a hallmark of pathway activation, but additional checkpoints downstream in the pathway remain incompletely understood. Here, we generated synthetic protein ligands, monobodies, against MLKL to dissect key checkpoints in the pathway. We identified monobodies that inhibit necroptotic signaling by binding to an indispensable site on the α4 helix of human MLKL’s N-terminal four-helix bundle “killer” domain, which we propose blocks recruitment of essential adaptor(s). These data distinguish assembly of MLKL into higher-order complexes from membrane translocation as separate key checkpoints, and underscore the utility of monobodies as reagents to dissect signal transduction mechanisms. The necroptosis cell death pathway has been implicated in host defense and in the pathology of inflammatory diseases. While phosphorylation of the necroptotic effector pseudokinase Mixed Lineage Kinase Domain-Like (MLKL) by the upstream protein kinase RIPK3 is a hallmark of pathway activation, the precise checkpoints in necroptosis signaling are still unclear. Here we have developed monobodies, synthetic binding proteins, that bind the N-terminal four-helix bundle (4HB) “killer” domain and neighboring first brace helix of human MLKL with nanomolar affinity. When expressed as genetically encoded reagents in cells, these monobodies potently block necroptotic cell death. However, they did not prevent MLKL recruitment to the “necrosome” and phosphorylation by RIPK3, nor the assembly of MLKL into oligomers, but did block MLKL translocation to membranes where activated MLKL normally disrupts membranes to kill cells. An X-ray crystal structure revealed a monobody-binding site centered on the α4 helix of the MLKL 4HB domain, which mutational analyses showed was crucial for reconstitution of necroptosis signaling. These data implicate the α4 helix of its 4HB domain as a crucial site for recruitment of adaptor proteins that mediate membrane translocation, distinct from known phospholipid binding sites.