Miracle-dz/UniFAR-FTUs huggingface dataset:
Site-specific Protein Photochemical Covalent Attachment to Carbon Nanotube Side Walls and its Electronic Impact on Single Molecule Function.

Functional integration of proteins with carbon-based nanomaterials such as nanotubes holds great promise in emerging electronic and optoelectronic applications. Control over protein attachment poses a major challenge for consistent and useful device fabrication, especially when utilizing single/few molecule properties. Here, we exploit genetically encoded phenyl azide photochemistry to define the direct covalent attachment of four different proteins, including the fluorescent protein GFP and a -lactamase binding protein (BBP), to carbon nanotube side walls. AFM showed that on attachment BBP could still recognize and bind additional protein components. Single molecule fluorescence revealed that on attachment to SWCNTs function was retained and there was feedback to GFP in terms of fluorescence intensity and improved resistance to photobleaching; GFP is fluorescent for much longer on attachment. The site of attachment proved important in terms of electronic impact on GFP function, with the attachment site furthest from the chromophore having the larger effect on fluorescence. Our approach provides a versatile and general method for generating intimate protein-CNT hybrid bioconjugates. It can be potentially applied easily to any protein of choice; attachment position and thus interface characteristics with the CNT can easily be changed by simply placing the phenyl azide chemistry at different residues by gene mutagenesis. Thus, our approach will allow consistent construction and modulate functional coupling through changing the protein attachment position.
The Staphylococcus aureus Transcriptome during Cystic Fibrosis Lung Infection

Although bacteria have been studied in infection for over 100 years, the majority of these studies have utilized laboratory and animal models that often have unknown relevance to the human infections they are meant to represent. A primary challenge has been to assess bacterial physiology in the human host. To address this challenge, we performed transcriptomics of S. aureus during human cystic fibrosis (CF) lung infection. Using a machine learning framework, we defined a “human CF lung transcriptome signature” that primarily included genes involved in metabolism and virulence. In addition, we were able to apply our findings to improve an in vitro model of CF infection. Understanding bacterial gene expression within human infection is a critical step toward the development of improved laboratory models and new therapeutics. ABSTRACT Laboratory models have been invaluable for the field of microbiology for over 100 years and have provided key insights into core aspects of bacterial physiology such as regulation and metabolism. However, it is important to identify the extent to which these models recapitulate bacterial physiology within a human infection environment. Here, we performed transcriptomics (RNA-seq), focusing on the physiology of the prominent pathogen Staphylococcus aureus in situ in human cystic fibrosis (CF) infection. Through principal-component and hierarchal clustering analyses, we found remarkable conservation in S. aureus gene expression in the CF lung despite differences in the patient clinic, clinical status, age, and therapeutic regimen. We used a machine learning approach to identify an S. aureus transcriptomic signature of 32 genes that can reliably distinguish between S. aureus transcriptomes in the CF lung and in vitro. The majority of these genes were involved in virulence and metabolism and were used to improve a common CF infection model. Collectively, these results advance our knowledge of S. aureus physiology during human CF lung infection and demonstrate how in vitro models can be improved to better capture bacterial physiology in infection. IMPORTANCE Although bacteria have been studied in infection for over 100 years, the majority of these studies have utilized laboratory and animal models that often have unknown relevance to the human infections they are meant to represent. A primary challenge has been to assess bacterial physiology in the human host. To address this challenge, we performed transcriptomics of S. aureus during human cystic fibrosis (CF) lung infection. Using a machine learning framework, we defined a “human CF lung transcriptome signature” that primarily included genes involved in metabolism and virulence. In addition, we were able to apply our findings to improve an in vitro model of CF infection. Understanding bacterial gene expression within human infection is a critical step toward the development of improved laboratory models and new therapeutics.
Current Statistical Challenges in Oncology Clinical Trials in the Era of Targeted Therapy

The mapping of the human genome has led to rapid advances in our understanding of diseases at the molecular level. This new knowledge is shifting the drug development paradigm in cancer trials. For example, traditional Phase 1 to 3 trials of dose finding, evaluating activity, and confirming efficacy are becoming less common with all the three objectives accomplished within one protocol. Molecular marker-based clinical trials are also on the rise in place of the traditional disease-based clinical trials. In addition, patients receiving control treatment are routinely switched to the experimental treatment after disease progression, complicating the final comparison of survival rates between treatment groups. In this article, we describe these and other challenges in the regulatory review of cancer therapies as a result of this paradigm shift and also describe some innovative ideas that have the potential to improve evaluation of new agents to treat cancer in clinical trials.
PROMIS Computer Adaptive Tests and Their Correlation With Disease Activity in Juvenile Idiopathic Arthritis.

BACKGROUND/OBJECTIVE The importance of patient-reported outcomes, like the Patient-Reported Outcomes Measurement Information System (PROMIS) measures, is increasingly recognized both in clinical care and in research. While "short forms" have been studied in juvenile idiopathic arthritis (JIA), study of PROMIS computer adaptive tests (CATs) in JIA is limited. This cross-sectional study evaluates whether PROMIS CATs correlate with disease activity in patients with JIA. METHODS A convenience sample of patients with JIA (N = 44) was recruited from a single center. Patients and parents completed pediatric and parent proxy PROMIS CATs. Disease activity was evaluated using the Juvenile Arthritis Disease Activity Score in 71 joints (JADAS-71) and the Childhood Health Assessment Questionnaire (CHAQ). Correlation of the CAT T scores with disease activity was assessed using Spearman correlation coefficients. RESULTS Forty-four of 80 eligible subjects (29 patients and 15 parents) completed all or some PROMIS CATs. Pain interference and mobility CATs correlated moderately with JADAS-71. Nearly all correlations with the JADAS-71 were weakened when the patient global was removed. Pain interference, mobility, and fatigue were strongly correlated with the CHAQ. Among parent proxy CATs, only mobility and depressive symptoms correlated strongly with the CHAQ. CONCLUSIONS Only pain interference and mobility PROMIS CATs showed strong correlation with standard disease activity measures in JIA, and nearly all correlations were weakened when the patient global was removed. Correlations of the CATs with the CHAQ were stronger than correlations with the JADAS-71, indicating that although the CHAQ is no longer routinely used it may be a better measure of health-related quality of life in routine clinical care.
Using natural experimental studies to guide public health action: turning the evidence-based medicine paradigm on its head

Despite smaller effect sizes, interventions delivered at population level to prevent non-communicable diseases generally have greater reach, impact and equity than those delivered to high-risk groups. Nevertheless, how to shift population behaviour patterns in this way remains one of the greatest uncertainties for research and policy. Evidence about behaviour change interventions that are easier to evaluate tends to overshadow that for population-wide and system-wide approaches that generate and sustain healthier behaviours. Population health interventions are often implemented as natural experiments, which makes their evaluation more complex and unpredictable than a typical randomised controlled trial (RCT). We discuss the growing importance of evaluating natural experiments and their distinctive contribution to the evidence for public health policy. We contrast the established evidence-based practice pathway, in which RCTs generate ‘definitive’ evidence for particular interventions, with a practice-based evidence pathway in which evaluation can help adjust the compass bearing of existing policy. We propose that intervention studies should focus on reducing critical uncertainties, that non-randomised study designs should be embraced rather than tolerated and that a more nuanced approach to appraising the utility of diverse types of evidence is required. The complex evidence needed to guide public health action is not necessarily the same as that which is needed to provide an unbiased effect size estimate. The practice-based evidence pathway is neither inferior nor merely the best available when all else fails. It is often the only way to generate meaningful evidence to address critical questions about investing in population health interventions.
Copper-Mediated Nitrosation: 2-Nitrosophenolato Complexes and Their Use in the Synthesis of Heterocycles

A simple protocol yielding ortho-substituted nitrosophenols from phenols is demonstrated, in the form of copper(II) bis(nitrosophenolato) complexes. The developed methodology was applied to a range of substrates, confirming the role of the copper in both the formation and protection of the challenging 1, 2-substitution pattern. Using polymer supported thiourea, the Cu could be stripped from the complexes and thus enabled the isolation or identification of the uncoordinated ligands and their decomposition products, in yields generally low in line with the intrinsic high reactivity of 2-nitrosophenols. The product complexes are useful intermediates as demonstrated in revisiting a formal [4 + 2] cycloaddition with dimethylacetylene dicarboxylate to synthesise bicyclic products in variable yields, revealing the product has a novel structure different from those previously reported in the literature.
Supersonic Cold Spraying for Energy and Environmental Applications: One‐Step Scalable Coating Technology for Advanced Micro‐ and Nanotextured Materials

Supersonic cold spraying is an emerging technique for rapid deposition of films of materials including micrometer‐size and sub‐micrometer metal particles, nanoscale ceramic particles, clays, polymers, hybrid materials composed of polymers and particulates, reduced graphene oxide (rGO), and metal–organic frameworks. In this method, particles are accelerated to a high velocity and then impact a substrate at near ambient temperature, where dissipation of their kinetic energy produces strong adhesion. Here, recent progress in fundamentals and applications of cold spraying is reviewed. High‐velocity impact with the substrate results in significant deformation, which not only produces adhesion, but can change the particles' internal structure. Cold‐sprayed coatings can also exhibit micro‐ and nanotextured morphologies not achievable by other means. Suspending micro‐ or nanoparticles in a liquid and cold‐spraying the suspension produces fine atomization and even deposition of materials that could not otherwise be processed. The scalability and low cost of this method and its compatibility with roll‐to‐roll processing make it promising for many applications, including ultrathin flexible materials, solar cells, touch‐screen panels, nanotextured surfaces for enhanced heat transfer, thermal and electrical insulation films, transparent conductive films, materials for energy storage (e.g., Li‐ion battery electrodes), heaters, sensors, photoelectrodes for water splitting, water purification membranes, and self‐cleaning films.
Alexithymia and anhedonia in early Richardson's syndrome and progressive supranuclear palsy with predominant parkinsonism

Phenotypic variants of progressive supranuclear palsy (PSP) are all characterized by the combination of motor symptoms of parkinsonism with a number of neuropsychiatric and cognitive disorders. Despite the strong effort in characterizing these features in PSP, alexithymia and anhedonia have not been investigated at present. Here, we aimed at investigating the qualitative and quantitative differences of alexithymia and anhedonia in the two more frequent variants of PSP, Richardson's syndrome (PSP‐RS) and PSP with predominant parkinsonism (PSP‐P) compared to Parkinson's disease (PD) patients recruited within 24 months after the onset of motor symptoms.
Processive DNA synthesis is associated with localized decompaction of constitutive heterochromatin at the sites of DNA replication and repair

ABSTRACT Constitutive heterochromatin is considered as a functionally inert genome compartment, important for its architecture and stability. How such stable structure is maintained is not well understood. Here, we apply four different visualization schemes to label it and investigate its dynamics during DNA replication and repair. We show that replisomes assemble over the heterochromatin in a temporally ordered manner. Furthermore, heterochromatin undergoes transient decompaction locally at the active sites of DNA synthesis. Using selective laser microirradiation conditions that lead to damage repaired via processive DNA synthesis, we measured similarly local decompaction of heterochromatin. In both cases, we could not observe large-scale movement of heterochromatin to the domain surface. Instead, the processive DNA synthesis machinery assembled at the replication/repair sites. Altogether, our data are compatible with a progression of DNA replication/repair along the chromatin in a dynamic mode with localized and transient decompaction that does not globally remodels the whole heterochromatin compartment.
Seizures Do Not Affect Disability and Mortality Outcomes of Stroke: A Population-Based Study

Although seizures are frequently seen after cerebrovascular accidents, their effects on long-term outcome in stroke patients are still unknown. Therefore, the aim of this study was to investigate the relationship between post-stroke seizures and the risk of long-term disability and mortality in stroke patients. This study is part of a larger population-based study. All patients were prospectively followed up by a face-to-face interview or a structured telephone interview. We enrolled 635 patients with first-ever stroke and without a history of seizures. Prevalence of ischemic stroke (IS) was 85.2%, while the remaining 14.8% of patients were affected by intracerebral hemorrhage (ICH). During the study period, 51 subjects (8%) developed post-stroke seizures. Patients with post-stroke seizures were younger, had a higher prevalence of ICH, had a more severe stroke at admission, were more likely to have an IS involving the total anterior circulation, and were more likely to have a lobar ICH than patients without seizures. Moreover, subjects with seizures had more frequently hemorrhagic transformation after IS and cortical strokes. At 24 months, the risk of disability in patients with seizures was almost twice than in those without seizures. However, the negative effect of seizures disappeared in multivariate analysis. Kaplan-Meier survival curves at 12 years were not significantly different between patients with and without post-stroke seizures. Using the Cox multivariate analysis, age, NIHSS at admission, and pre-stroke mRS were independently associated with all-cause long-term mortality. In our sample, seizures did not impair long-term outcome in patients affected by cerebrovascular accidents. The not significant, slight difference in favor of a better survival for patients with seizures may be attributed to the slight age difference between the two groups.
Nanoparticles for antiparasitic drug delivery

Abstract As an emerging novel drug carrier, nanoparticles provide a promising way for effective treatment of parasitic diseases by overcoming the shortcomings of low bioavailability, poor cellular permeability, nonspecific distribution and rapid elimination of antiparasitic drugs from the body. In recent years, some kinds of ideal nanocarriers have been developed for antiparasitic drug delivery. In this review, the progress of the enhanced antiparasitic effects of different nanoparticles payload and their influencing factors were firstly summarized. Secondly, the transport and disposition process in the body were reviewed. Finally, the challenges and prospects of nanoparticles for antiparasitic drug delivery were proposed. This review will help scholars to understand the development trend of nanoparticles in the treatment of parasitic diseases and explore strategies in the development of more efficient nanocarriers to overcome the difficulty in the treatment of parasite infections in the future.
Comparison of the Stanford ECG Left Atrial Criteria With the International ECG Criteria for Sports Screening

Objective: Because the International left atrial enlargement electrocardiographic (ECG) screening criteria (ECG-LAE) for athletes are rarely fulfilled in young athletes, we compared it with evidence-based criteria from a recent clinical outcome study of ECG left atrial abnormality (ECG-LAA). Design: Retrospective analyses. Setting: Routine preparticipation ECG screening in California. Participants: Four thousand four hundred thirty-eight young individuals (18.5 ± 5.4 years, 40% women). Assessment of Risk Factors: The International criteria for ECG-LAE were applied: prolonged P wave duration of ≥120 ms in leads I or II AND negative portion of ≥1 mm in depth in lead V1. This was compared with Stanford criteria for ECG-LAA: prolonged P wave duration of ≥140 ms odds ratio (OR) negative portion in V1 and V2 greater than 1 mm. Main Outcome Measures: Differences in the classification of abnormal ECGs between the 2 criteria applied to the same population of young athletes. Results: Only 33 (0.7%) of our subjects fulfilled the International criteria for ECG-LAE while 110 (2.5%) fulfilled the ECG-LAA criteria. Adding our new ECG-LAA criterion and considering it a major criterion raised the abnormal ECG prevalence and athletes referred for further evaluation from 2.9% to 4.4%. Conclusions: The Stanford evidence-based criterion for ECG-LAA incorporating V2 and replacing “or” for “and” regarding P wave duration increased the yield of abnormal classification for P waves. Future follow-up studies are needed to confirm that this new criterion should be included in future ECG screening consensus documents.
scafSLICR: A MATLAB-based slicing algorithm to enable 3D-printing of tissue engineering scaffolds with heterogeneous porous microarchitecture

3D-printing is a powerful manufacturing tool that can create precise microscale architectures across macroscale geometries. Within biomedical research, 3D-printing of various materials has been used to fabricate rigid scaffolds for cell and tissue engineering constructs with precise microarchitecture to direct cell behavior and macroscale geometry provides patient specificity. While 3D-printing hardware has become low-cost due to modeling and rapid prototyping applications, there is no common paradigm or platform for the controlled design and manufacture of 3D-printed constructs for tissue engineering. Specifically, controlling the tissue engineering features of pore size, porosity, and pore arrangement is difficult using currently available software. We have developed a MATLAB approach termed scafSLICR to design and manufacture tissue-engineered scaffolds with precise microarchitecture and with simple options to enable spatially patterned pore properties. Using scafSLICR, we designed, manufactured, and characterized porous scaffolds in acrylonitrile butadiene styrene with a variety of pore sizes, porosities, and gradients. We found that transitions between different porous regions maintained an open, connected porous network without compromising mechanical integrity. Further, we demonstrated the usefulness of scafSLICR in patterning different porous designs throughout large anatomic shapes and in preparing craniofacial tissue engineering bone scaffolds. Finally, scafSLICR is distributed as open-source MATLAB scripts and as a stand-alone graphical interface.
Early epigenomic and transcriptional changes reveal Elk-1 transcription factor as a therapeutic target in Huntington’s disease

Significance Improved therapeutic intervention for neurodegenerative diseases, particularly early in progression of the disease course, is a critical need. Huntington’s disease (HD) is a paradigmatic disorder in this search in which vulnerable individuals can be identified early. This study focuses on the earliest stages of disease in a well-characterized animal model system. We identify early aberrant transcription and chromatin changes in affected brain regions of HD mice. The study identifies the Elk-1 transcription factor as a significant regulator of early transcriptional changes in HD. Enhanced Elk-1 levels exerted beneficial effects in an in vitro model and resulted in extensive restoration of transcriptional dysregulation in vivo. These results suggest a target for alleviating pathology in HD and other neuropsychiatric conditions. Huntington’s disease (HD) is a chronic neurodegenerative disorder characterized by a late clinical onset despite ubiquitous expression of the mutant Huntingtin gene (HTT) from birth. Transcriptional dysregulation is a pivotal feature of HD. Yet, the genes that are altered in the prodromal period and their regulators, which present opportunities for therapeutic intervention, remain to be elucidated. Using transcriptional and chromatin profiling, we found aberrant transcription and changes in histone H3K27acetylation in the striatum of R6/1 mice during the presymptomatic disease stages. Integrating these data, we identified the Elk-1 transcription factor as a candidate regulator of prodromal changes in HD. Exogenous expression of Elk-1 exerted beneficial effects in a primary striatal cell culture model of HD, and adeno-associated virus-mediated Elk-1 overexpression alleviated transcriptional dysregulation in R6/1 mice. Collectively, our work demonstrates that aberrant gene expression precedes overt disease onset in HD, identifies the Elk-1 transcription factor as a key regulator linked to early epigenetic and transcriptional changes in HD, and presents evidence for Elk-1 as a target for alleviating molecular pathology in HD.