Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems

Synthetic biology integrates diverse engineering disciplines to create novel biological systems for biomedical and technological applications. The substantial growth of the synthetic biology field in the past decade is poised to transform biotechnology and medicine. To streamline design processes and facilitate debugging of complex synthetic circuits, cell-free synthetic biology approaches has reached broad research communities both in academia and industry. By recapitulating gene expression systems in vitro, cell-free expression systems offer flexibility to explore beyond the confines of living cells and allow networking of synthetic and natural systems. Here, we review the capabilities of the current cell-free platforms, focusing on nucleic acid-based molecular programs and circuit construction. We survey the recent developments including cell-free transcription–translation platforms, DNA nanostructures and circuits, and novel classes of riboregulators. The links to mathematical models and the prospects of cell-free synthetic biology platforms will also be discussed.
Complete Genome Sequence of Hospital-Acquired Methicillin-Resistant Staphylococcus aureus Strain WCUH29

The hospital-acquired methicillin-resistant Staphylococcus aureus (HA-MRSA) strain WCUH29 has been intensively and widely used as a model system for identification and evaluation of novel antibacterial targets and pathogenicity. In this announcement, we report the complete genome sequence of HA-MRSA WCUH29 (NCIMB 40771). ABSTRACT The hospital-acquired methicillin-resistant Staphylococcus aureus (HA-MRSA) strain WCUH29 has been intensively and widely used as a model system for identification and evaluation of novel antibacterial targets and pathogenicity. In this announcement, we report the complete genome sequence of HA-MRSA WCUH29 (NCIMB 40771).
Fighting multidrug resistance with a fruit extract: anti-cancer and anti-biofilm activities of Acca sellowiana

Abstract In this study, the efficacy of Acca sellowiana fruit acetonic extract on human MDR cancer cells was tested for the first time, and it was demonstrated that the fruit extract is effective on both sensitive and resistant tumor cells. The effects of A. sellowiana extract on bacterial biofilm were also examined for the first time. By crystal violet assays and confocal microscopy analyses, it was demonstrated that the plant extract is able to strongly inhibit biofilm formation of both sensitive and resistant bacterial strains. Furthermore, antimicrobial activity assays and TEM analyses clearly demonstrated the effectiveness of plant extract on planktonic bacterial cells in both sensitive and resistant strains. Altogether, these findings intriguingly expand the panel of activities of A. sellowiana fruit extract with respect to previous reports, and open interesting perspectives to its therapeutic applications. Graphical Abstract
Aspiration and complaint system: From literature survey to implementation

The culture in an organization influence the intention of employees to give useful information or report any unethical and illegal behaviors performed by their colleagues or leaders in the organization. This limits the freedom of the employees in expressing their opinions which can further affect the performance of the organization. It is required to have a whistleblower system where the employees can express their opinions efficiently, effectively, and anonymously. In this paper, we study existing whistleblower systems that are already used in several organizations. We further identify which system is most suited to our organization in School of Electrical Engineering and Informatics (SEEI), Institut Teknologi Bandung (ITB). We develop the standard operating procedure (SOP) for accomodating aspiration and complaint from the SEEI civitas. Based on this SOP, we adopt the Globaleaks whistleblower system as the Aspiration and Complaint System (ACS) in SEEI ITB.
506: DEVELOPMENT OF A PREDICTION MODEL FOR LONG-TERM QUALITY OF LIFE IN CRITICALLY ILL PATIENTS

Crit Care Med 2016 • Volume 44 • Number 12 (Suppl.) had no missingness. The mean UI1y in the LM depended significantly on: UIb (P<0.001); activity of daily living (P<0.001); hematological patients (P=0.001); long.do-not-resuscitate (DNR)-order (P=0.003); age (P=0.004); patients ≥80 years (P=0.007); long.organ failure assessment (SOFA) score (P=0.007); previous hospitalization < 6 months (P=0.013); imaging D1 (P=0.026); tracheotomy D1 (P=0.028). Time had a weak effect on UI1y (P=0.172). A higher UIb and no previous hospitalization were associated with a better UI1y. Conclusions: Prediction of QOL at 1 year in ICU patients improved when D1 characteristics were combined with longitudinal data in a longitudinal prediction model.
A Novel Bristle-Shaped Semi-Dry Electrode With Low Contact Impedance and Ease of Use Features for EEG Signal Measurements

Objective: In this paper, we present a novel soft bristle-shaped semi-dry electrode for electroencephalography (EEG) recording. Because the bristle-shaped structure with electric conductivity could overcome the obstacle of hair and enable direct connection to scalp, the semi-dry electrode could work with drinking water instead of saline water that was widely used in previous semi-dry or water electrodes to improve its convenience. The electrode consisted of conductive bristles and a 3D-printed casing. Carbon-coated nylon conductive bristles could achieve low impedance and soft properties of the semi-dry electrode. The bristles could spread on skin and realize a larger contact area. The carbon-coated conductive bristles could also continuously penetrate water into the corneum of skin to reduce contact impedance. The contact impedance of the bristle-shaped semi-dry electrode was similar to the traditional wet electrode, but much lower than dry electrode. Although the saline water had much lower impedance than drinking water, our electrode still achieved even lower skin-electrode contact impedance than previous semi-dry or water electrode with saline water. The alpha rhythms, P300 visual evoked potential, and steady-state visual evoked potential were, respectively, measured to evaluate the electrode performance for EEG recording.
Interdependent self-construal modulates the adrenocortical stress response in the socially evaluated cold-pressor test

Abstract Previous studies suggested that the Trier social stress test (TSST) induced a higher cortisol stress response in individuals with high interdependent self-construal (InterSC) as compared to those with low InterSC, and that participants’ perception of social evaluative threat mediated the association between InterSC and cortisol stress response. To further examine if individuals with high InterSC exhibit a strong psychological stress response independent of the stress paradigm, the current study investigated the stress response of individuals with high InterSC in a socially evaluated cold-pressor test (SECPT) paradigm, which has also been shown to reliably increase hypothalamus–pituitary–adrenal (HPA) activity with a social evaluative element. Fifty-five healthy participants (29 females; mean age = 20.55 years) completed the Self-Construal Scale and their salivary cortisol samples were collected at 0, 30, 45, and 60 minutes after waking up on a weekday morning. Participants’ cardiovascular and adrenocortical stress responses in the SECPT were also measured while they immersed their hand in ice water, and they were observed by the experimenter and videotaped during this task. Our results indicated that participants with high InterSC showed a higher level of cortisol awakening response (CAR). Additionally, they perceived higher levels of social evaluative threat and exhibited higher saliva cortisol response to the SECPT. Taken together, the present findings and those obtained from previous studies suggest a significant and reliable role of InterSC in regulating biological and psychological stress responses.
Contribution of microRNAs to CLL Biology and Their Potential as New Biomarkers

After the complete description of the human genome (approximately 3x109 bases) the best estimates of protein-coding genes account for about 30,000 to 40,000 genes representing approximately 1% of the genome. A significantly remainder fraction of the genome is transcribed into RNAs that do not code for proteins which are classified as non-coding RNAs (ncRNAs) (Wright et al., 2001). These ncRNAs were unnoticed in the genome until recent improvements in high-throughput technology for gene expression assays led to the discovery that most human transcriptional units are ncRNAs. These ncRNAs have been segregated into two main classes; long and small non-coding RNAs. Over the last almost two decades, the family of small ncRNAs (i.e. microRNAs, siRNAs and piRNAs) has grown in number and relevance and emerged as new key regulators of gene expression. These small ncRNAs, which are ~19–32 nucleotides (nt) in length, act as sequence-specific triggers for mRNA degradation, translation repression, heterochromatin formation and genome stability affecting biological functions either by posttranscriptional silencing or stimulating transcript degradation. The most well known small ncRNAs are the microRNAs (miRNAs). To date, more than 1500 human miRNAs genes have been annotated. They are organized as monoor policystronic transcriptional units in the genome located either in intergenic regions or within introns and exons of non-coding as well as coding transcription units (miRBase, release 18: November 2011).
A Human Embryonic Stem Cell Reporter Line for Monitoring Chemical-induced Cardiotoxicity.

AIMS Human embryonic stem cells (hESCs) can be used to generate scalable numbers of cardiomyocytes for studying cardiac biology, disease modeling, drug screens, and potentially for regenerative therapies. A fluorescence-based reporter line will significantly enhance our capacities to visualize the derivation, survival and function of hESC-derived cardiomyocytes. Our goal was to develop a reporter cell line for real-time monitoring of live hESC-derived cardiomyocytes. METHODS AND RESULTS We used CRISPR/Cas9 to knock an mCherry reporter gene into the MYH6 locus of hESC lines, H1 and H9, enabling real-time monitoring of the generation of cardiomyocytes. MYH6:mCherry+ cells express atrial or ventricular markers and display a range of cardiomyocyte action potential morphologies. At 20 days of differentiation, MYH6:mCherry+ cells show features characteristic of human cardiomyocytes and can be used successfully to monitor drug-induced cardiotoxicity and oleic acid-induced cardiac arrhythmia. CONCLUSION We created two MYH6:mCherry hESC reporter lines, and documented the application of these lines for disease modeling relevant to cardiomyocyte biology. TRANSLATIONAL PERSPECTIVE Cardiovascular disease is a leading cause of death in the world. Moreover, 90% of pharmaceutical compounds eventually fail and are withdrawn from the market primarily due to drug-induced cardiovascular toxicity. Thus, it is compelling needed to establish a platform to overcome this hurdle. We here report to generate a fluorescence-based cardiomyocyte reporter, the benefit of studying underlying mechanism of heart disease as well as providing a platform for cardiotoxicity screening.
Improving the Accuracy of Fetal Foot Length to Confirm Gestational Duration

OBJECTIVE: To establish normative fetal foot length ranges using last menstrual period (LMP) and ultrasound dating by biparietal diameter and to examine variations in these ranges by ethnicity. METHODS: A consecutive series of 1,099 eligible subjects receiving abortions had fetal foot lengths measured directly. Models of fetal foot length were developed by using assessment of gestational duration by LMP alone, ultrasonography alone, and “best estimate” (LMP confirmed by ultrasonography). RESULTS: The full sample model using ultrasound dating (n = 1,099) yielded the following equation: foot length = −30.3 + days of gestation × 0.458 (R2 of 0.92). Regression by LMP-determined gestational duration by using the “best estimate” sample (n = 491) provided an almost identical equation (foot length = −29.8 + days of gestation × 0.45) and a similar R2 value of 0.87, although the standard errors were larger. Gestational duration by ultrasonography alone produced a better model fit than duration by LMP alone. Regressions by ethnicity were not significantly different compared with the simple regression, regardless of method used to determine gestational duration. CONCLUSION: A reconsideration of fetal foot length measurements to confirm gestational duration is important. More accurate tables of these measurements allow for greater precision in correlating gestational duration and foot length. Fetal foot length tables using ultrasonographically confirmed gestational duration and current statistical standards should replace tables currently used. Biparietal diameter as a single measurement provides adequate estimation of gestational duration in the second trimester for pregnancy termination, proving more reliable than LMP dating. LEVEL OF EVIDENCE: II-2
Disposable Multi-Walled Carbon Nanotubes-Based Plasticizer-Free Solid-Contact Pb2+-Selective Electrodes with a Sub-PPB Detection Limit †

Potentiometric plasticizer-free solid-contact Pb2+-selective electrodes based on copolymer methyl methacrylate-n-butyl acrylate (MMA-BA) as membrane matrix and multi-walled carbon nanotubes (MWCNTs) as intermediate ion-to-electron transducing layer have been developed. The disposable electrodes were prepared by drop-casting the copolymer membrane onto a layer of MWCNTs, which deposited on golden disk electrodes. The obtained electrodes exhibited a sub-ppb level detection limit of 10−10 mol·L−1. The proposed electrodes demonstrated a Nernstian slope of 29.1 ± 0.5 mV/decade in the linear range from 2.0 × 10−10 to 1.5 × 10−3 mol·L−1. No interference from gases (O2 and CO2) or water films was observed. The electrochemical impedance spectroscopy of the fabricated electrodes was compared to that of plasticizer-free Pb2+-selective electrodes without MWCNTs as intermediated layers. The plasticizer-free MWCNTs-based Pb2+-selective electrodes can provide a promising platform for Pb(II) detection in environmental and clinical application.
e-Therapies in England for stress, anxiety or depression: how are apps developed? A survey of NHS e-therapy developers

Objective To document the quality of web and smartphone apps used and recommended for stress, anxiety or depression by examining the manner in which they were developed. Design The study was conducted using a survey sent to developers of National Health Service (NHS) e-therapies. Data sources Data were collected via a survey sent out to NHS e-therapy developers during October 2015 and review of development company websites during October 2015. Data collection/extraction methods Data were compiled from responses to the survey and development company websites of the NHS e-therapies developers. Results A total of 36 (76.6%) out of the 48 app developers responded. One app was excluded due to its contact details and developer website being unidentifiable. Data from the missing 10 was determined from the app developer’s website. The results were that 12 out of 13 web apps and 20 out of 34 smartphone apps had clinical involvement in their development. Nine out of 13 web apps and nine out of 34 smartphone apps indicated academic involvement in their development. Twelve out of 13 web apps and nine out of 34 smartphone apps indicated published research evidence relating to their app. Ten out of 13 web apps and 10 out of 34 smartphone apps indicated having other evidence relating to their app. Nine out of 13 web apps and 19 out of 34 smartphone apps indicated having a psychological approach or theory behind their app. Conclusions As an increasing number of developers are looking to produce e-therapies for the NHS it is essential they apply clinical and academic best practices to ensure the creation of safe and effective apps.
The Patient–Provider Relationship: Predictors of black/African American Cancer Patients’ Perceived Quality of Care and Health Outcomes

ABSTRACT We examined whether the patient–provider relationship (PPR) is associated with Black survivors’ health outcomes and whether this association was mediated by the quality of care. The outcome variables were survivors’ quality of care and health outcome, and the predictor variable was PPR (communication, emotional support, time spent, and survivors’ shared-decision making). A sample of 223 Black cancer survivors (age 63.0 ± 14.0 years) provided evaluable data. The most common cancer types reported by the participants were: gynecologic (32.7%), genitourinary (21.5%), and gastrointestinal cancers (11.2%). After controlling for covariates. A Structural Equation Model (SEM) showed that PPR was significantly associated with both health outcome (p = .015) and quality of care (p = .002). When PPR and quality of care were tested in the mediation model, the direct association between PPR and health outcome was attenuated, and it was no longer significant (b = −0.05, SE = 0.11, p = .65). However, indirectly, there was a strong association between PPR and health outcome through the quality of care (b = 0.22, SE = 0.08, p = .003), indicating full mediation. Providers’ interpersonal relationships had a significant influence on the health of Black survivors, and this influence may be due to the increased positive perception of the quality of care. The implications of these findings for further research are discussed.
Natural Killer Cells as Allogeneic Effectors in Adoptive Cancer Immunotherapy

Natural killer (NK) cells are attractive within adoptive transfer settings in cancer immunotherapy due to their potential for allogeneic use; their alloreactivity is enhanced under conditions of killer immunoglobulin-like receptor (KIR) mismatch with human leukocyte antigen (HLA) ligands on cancer cells. In addition to this, NK cells are platforms for genetic modification, and proliferate in vivo for a shorter time relative to T cells, limiting off-target activation. Current clinical studies have demonstrated the safety and efficacy of allogeneic NK cell adoptive transfer therapies as a means for treatment of hematologic malignancies and, to a lesser extent, solid tumors. However, challenges associated with sourcing allogeneic NK cells have given rise to controversy over the contribution of NK cells to graft-versus-host disease (GvHD). Specifically, blood-derived NK cell infusions contain contaminating T cells, whose activation with NK-stimulating cytokines has been known to lead to heightened release of proinflammatory cytokines and trigger the onset of GvHD in vivo. NK cells sourced from cell lines and stem cells lack contaminating T cells, but can also lack many phenotypic characteristics of mature NK cells. Here, we discuss the available published evidence for the varying roles of NK cells in GvHD and, more broadly, their use in allogeneic adoptive transfer settings to treat various cancers.
Prosody and comprehension of ambiguous dative NPs in Korean

The current study reports the results from a cross-modal naming experiment investigating the effects of a prosodic boundary location on the comprehension of ambiguous dative NPs in Korean (Yeongmi-ka Ceonghi-eykey norae-rul pwulecwu-n pwuin-ul …). The underlined dative NP, Ceonghi-eykey, can temporarily be attached to the embedded rel-marked verb, pwulecwu-n (‘sing-rel’) or to the matrix verb to appear later. Participants heard sentence fragments manipulated for the location of Intonation Phrase boundary (the biggest prosodic boundary in the model of Seoul Korean) and right after that, had to name visually presented naming targets, which resolve the ambiguity of dative NPs. The prosodic manipulation did not result in difference in naming time, suggesting that the location of a prosodic boundary failed to influence the way Korean listeners interpreted ambiguous dative NPs. Possible reasons for the null effect were discussed.
Changes in antibiotic use following implementation of a telehealth stewardship pilot program

Abstract Starting in 2016, we initiated a pilot tele-antibiotic stewardship program at 2 rural Veterans Affairs medical centers (VAMCs). Antibiotic days of therapy decreased significantly (P < .05) in the acute and long-term care units at both intervention sites, suggesting that tele-stewardship can effectively support antibiotic stewardship practices in rural VAMCs.
Three-dimensional pseudocontinuous arterial spin labeling and susceptibility-weighted imaging associated with clinical progression in amnestic mild cognitive impairment and Alzheimer's disease

Abstract Background: This study aimed to evaluate the value of 3-dimensional pseudocontinuous arterial spin labeling (3D-pcASL) and susceptibility-weighted imaging (SWI) for the early disease-sensitive markers of conversion from amnestic MCI (aMCI) to Alzheimer disease (AD) in this process. Methods: Forty patients with aMCI and AD respectively were recruited in the study, and 40 healthy subjects were taken as controls. Data were recorded using 3T MR scanner. We assessed the cerebral blood flow (CBF) in 11 different regions of interest, and counted number of microhemorrhages (MB) in 3 regions of brain lobes, bilateral basal ganglia/thalamus, and brain stem/cerebellum, and then investigated correlations between Montreal Cognitive Assessment (MoCA) scores, CBF, and susceptibility-weighted imaging (SWI) features in these 3 groups. Results: The results revealed that for AD patients, the MoCA scores and CBF values in frontal gray matter (FGM), occipital gray matter (OGM), temporal gray matter (TGM), parietal gray matter (PGM), hippocampus, anterior cingulate cortex (ACC), precuneus, posterior cingulate cortex (PCC), precuneus, basal ganglia and thalamus decreased compared with aMCI patients and control group, and significant difference was revealed among the 3 groups. While in cerebellum, statistical significance was only found between AD patients and control group. On SWI, the average numbers of hemorrhage in regions of lobes for AD patients were significantly higher than aMCI patients and control group. The same results occurred in the bilateral basal ganglia/thalamus. We further found the MoCA score was positively correlated with CBF, but negatively correlated with hypointense signal on SWI. Conclusion: 3D-pCASL and SWI have promising potential to be biomarkers for conversion from aMCI to AD in this process.