Miracle-dz/UniFAR-FTUs huggingface dataset:
Introducing OCTAVE Allegro: Improving the Information Security Risk Assessment Process

Abstract : This technical report introduces the next generation of the Operationally Critical Threat, Asset, and Vulnerability Evaluation (OCTAVE) methodology, OCTAVE Allegro. OCTAVE Allegro is a methodology to streamline and optimize the process of assessing information security risks so that an organization can obtain sufficient results with a small investment in time, people, and other limited resources. It leads the organization to consider people, technology, and facilities in the context of their relationship to information and the business processes and services they support. This report highlights the design considerations and requirements for OCTAVE Allegro based on field experience with existing OCTAVE methods and provides guidance, worksheets, and examples that an organization can use to begin performing OCTAVE Allegro-based risk assessments.
Peptide barcoding for establishment of new types of genotype–phenotype linkages

Measuring binding properties of binders (e.g., antibodies) is essential for developing useful experimental reagents, diagnostics, and pharmaceuticals. Display technologies can evaluate a large number of binders in a high-throughput manner, but the immobilization effect and the avidity effect prohibit the precise evaluation of binding properties. In this paper, we propose a novel methodology, peptide barcoding, to quantitatively measure the binding properties of multiple binders without immobilization. In the experimental scheme, unique peptide barcodes are fused with each binder, and they represent genotype information. These peptide barcodes are designed to have high detectability for mass spectrometry, leading to low identification bias and a high identification rate. A mixture of different peptide-barcoded nanobodies is reacted with antigen-coated magnetic beads in one pot. Peptide barcodes of functional nanobodies are cleaved on beads by a specific protease, and identified by selected reaction monitoring using triple quadrupole mass spectrometry. To demonstrate proof-of-principle for peptide barcoding, we generated peptide-barcoded anti-CD4 nanobody and anti-GFP nanobody, and determined whether we could simultaneously quantify their binding activities. We showed that peptide barcoding did not affect the properties of the nanobodies, and succeeded in measuring the binding activities of these nanobodies in one shot. The results demonstrate the advantages of peptide barcoding, new types of genotype–phenotype linkages.
Dicer regulates activation of the NLRP3 inflammasome

Inflammation plays a critical role in initiation of adaptive immunity, pathogen clearance and tissue repair. Interleukin (IL)-1β is a potent pro-inflammatory cytokine and therefore its production is tightly regulated: its secretion requires the assembly of a macromolecular protein complex, termed the inflammasome. Aberrant activation of the inflammasome has been linked to debilitating human diseases including chronic inflammatory and autoimmune diseases. Thus, there is a great interest in understanding how inflammasomes are regulated. Here we show that Dicer, an enzyme necessary for the production of mature micro-RNAs (miRNAs), is required for optimal activation of NLRP3 inflammasomes in bone marrow macrophages. Our data indicate that miRNAs may play an important role in promoting inflammasome activation.
Neonatal Resuscitation with an Intact Cord: Current and Ongoing Trials

Premature and full-term infants are at high risk of morbidities such as intraventricular hemorrhage or hypoxic-ischemic encephalopathy. The sickest infants at birth are the most likely to die and or develop intraventricular hemorrhage. Delayed cord clamping has been shown to reduce these morbidities, but is currently not provided to those infants that need immediate resuscitation. This review will discuss recently published and ongoing or planned clinical trials involving neonatal resuscitation while the newborn is still attached to the umbilical cord. We will discuss the implications on neonatal management and delivery room care should this method become standard practice. We will review previous and ongoing trials that provided respiratory support compared to no support. Lastly, we will discuss the implications of implementing routine resuscitation support outside of a research setting.
Augmentation of Electrocardiographic QRS R-Amplitude Precedes Radiocontrast-Induced Hypotension during Mobile Computed Tomography Scanning

Although intravenous administration of contrast media may trigger a variety of adverse reactions, sedated patients undergoing computed tomography (CT) scanning usually are not able to report their symptoms, which may delay detection of adverse reactions. Furthermore, changes in vital signs cannot be typically measured during mobile CT scanning, which worsens the situation. We aimed to characterize contrast-related hemodynamic changes that occur during mobile CT scanning and predict sudden hypotension based on subtle but robust changes in the electrocardiogram (ECG). We analyzed the digitized hemodynamic data of 20 consecutive patients who underwent clipping of a cerebral artery aneurysm and contrast-enhanced CT scanning following the surgical procedure. Hemodynamic variables, including ECG findings, invasive blood pressure (BP), pulse oximetry results, capnography findings, cardiac output, and systemic vascular resistance, were monitored simultaneously. We measured morphological changes in ECG-derived parameters, including the R–R interval, ST height, and QRS R-amplitude, on a beat-to-beat basis, and evaluated the correlation between those parameters and hemodynamic changes. After the radiocontrast injection, systolic BP decreased by a median 53 mmHg from baseline and spontaneously recovered after 63 ± 19 s. An increase in QRS R-amplitude (median 0.43 mV) occurred 25 ± 10 s before hypotension developed. The receiver operating characteristic curve showed that a 16% increase in QRS R-amplitude can predict a decrease in systolic BP of >25% (area under the curve 0.852). Increased cardiac output (median delta 2.7 L/min from baseline) and decreased systemic vascular resistance (median delta 857 dyn·s/cm5 from baseline) were also observed during hypotension. During mobile CT scanning, profound but transient hypotension can be observed, associated with decreased vascular resistance. Augmentation of QRS R-amplitude from an ECG represents a sensitive surrogate for onset of a hypotensive episode after contrast injection, thereby serving as a simple and continuous noninvasive hemodynamic monitoring tool.
In Vitro Evaluation of Antifungal Drug Combinations against Multidrug-Resistant Candida auris Isolates from New York Outbreak

Since 2016, New York hospitals and health care facilities have faced an unprecedented outbreak of the pathogenic yeast Candida auris. We tested over 1,000 C. auris isolates from affected facilities and found high resistance to fluconazole (MIC > 256 mg/liter) and variable resistance to other antifungal drugs. Therefore, we tested if two-drug combinations are effective in vitro against multidrug-resistant C. auris. ABSTRACT Since 2016, New York hospitals and health care facilities have faced an unprecedented outbreak of the pathogenic yeast Candida auris. We tested over 1,000 C. auris isolates from affected facilities and found high resistance to fluconazole (MIC > 256 mg/liter) and variable resistance to other antifungal drugs. Therefore, we tested if two-drug combinations are effective in vitro against multidrug-resistant C. auris. Broth microdilution antifungal combination plates were custom manufactured by TREK Diagnostic System. We used 100% inhibition endpoints for the drug combination as reported earlier for the intra- and interlaboratory agreements against Candida species. The results were derived from 12,960 readings, for 15 C. auris isolates tested against 864 two-drug antifungal combinations for nine antifungal drugs. Flucytosine (5FC) at 1.0 mg/liter potentiated the most combinations. For nine C. auris isolates resistant to amphotericin B (AMB; MIC ≥ 2.0 mg/liter), AMB-5FC (0.25/1.0 mg/liter) yielded 100% inhibition. Six C. auris isolates resistant to three echinocandins (anidulafungin [AFG], MIC ≥ 4.0 mg/liter; caspofungin [CAS], MIC ≥ 2.0 mg/liter; and micafungin [MFG], MIC ≥ 4.0 mg/liter) were 100% inhibited by AFG-5FC and CAS-5FC (0.0078/1 mg/liter) and MFG-5FC (0.12/1 mg/liter). None of the combinations were effective for C. auris 18-1 and 18-13 (fluconazole [FLC] > 256 mg/liter, 5FC > 32 mg/liter) except MFG-5FC (0.1/0.06 mg/liter). Thirteen isolates with a high voriconazole (VRC) MIC (>2 mg/liter) were 100% inhibited by the VRC-5FC (0.015/1 mg/liter). The simplified two-drug combination susceptibility test format would permit laboratories to provide clinicians and public health experts with additional data to manage multidrug-resistant C. auris.
Physical and Mental Health and Functioning Among Traumatic Brain Injury Close Relatives: The Role of Posttraumatic Stress Symptoms.

Severe Traumatic brain injury (sTBI) often instigates widespread long-lasting disability and is accompanied by extensive rehabilitation. Unsurprisingly, sTBI also holds malignant consequences for patients' close relatives. The burden caused by the injury and its severity explains some of the ramifications for the relatives. Additionally, some findings demonstrate that patients with sTBI and their relatives develop posttraumatic stress (PTS) symptoms. However, although the link between PTS symptoms and physical and mental health is well-documented in literature, the effect of PTS symptoms on relatives of patients with sTBI has barely been examined. This study examines the influence of PTS symptoms of patients with sTBI and their relatives on the physical and mental health and functioning of the relatives. Patients who sustained a severe sTBI (Abbreviated Injury Scale of the head region > 3) and close relatives were included in a multi-center, prospective cohort study (TRAST-MI). One-hundred patients and their relatives were assessed at 2, 6, and 12 months post injury. Outcome variables included health-related quality of life (SF-12) as well as emotional, cognitive, interpersonal, and total functioning (PCRS). Relatives' physical health was predicted by relatives' PTS symptoms (Slope=-1.76; p = .043), and mental health was predicted by both patients' (Slope=-2.77; p = .034) and relatives' (Slope=-6.59; p < .001) PTS symptoms. Functioning level was only predicted by patients' PTS symptoms (Slope=-.25; p< .001). The findings emphasize that TBI should be considered a comprehensive traumatic experience reaching further than mere physical damage to the brain and its direct consequences, affecting the injured individual and close relatives.
IL-1 Inhibition and Function of the HDL-Containing Fraction of Plasma in Patients with Stages 3 to 5 CKD.

BACKGROUND AND OBJECTIVES Systemic inflammation modulates cardiovascular disease risk and functionality of HDL in the setting of CKD. Whether interventions that modify systemic inflammation can improve HDL function in CKD is unknown. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We conducted a post hoc analysis of two randomized, clinical trials, IL-1 trap in participants with GFR 15-59 ml/min per 1.73 m2 (study A) and IL-1 receptor antagonist in participants on maintenance hemodialysis (study B), to evaluate if IL-1 blockade had improved the anti-inflammatory activity (IL-6, TNF-α, and Nod-like receptor protein 3), antioxidant function (superoxide production), and net cholesterol efflux capacity of HDL. HDL function was measured using LPS-stimulated THP-1 macrophages or peritoneal macrophages of apoE-deficient mice exposed to the apoB-depleted, HDL-containing fraction obtained from the plasma of the study participants, collected before and after the interventions to block IL-1 effects. Analysis of covariance was used for between group comparisons. RESULTS The mean age of the participants was 60±13 years, 72% (n=33) were men, and 39% (n=18) were black. There were 32 CKD (16 IL-1 trap and 16 placebo) and 14 maintenance hemodialysis (7 IL-1 receptor antagonist and 7 placebo) participants. Compared with placebo, IL-1 inhibition, in study A and B reduced cellular expression of TNF-α by 15% (P=0.05) and 64% (P=0.02), IL-6 by 38% (P=0.004) and 56% (P=0.08), and Nod-like receptor protein 3 by 16% (P=0.01) and 25% (P=0.02), respectively. The intervention blunted superoxide production in the treated arm compared with placebo, with the values being higher by 17% in the placebo arm in study A (P<0.001) and 12% in the placebo arm in study B (P=0.004). Net cholesterol efflux capacity was not affected by either intervention. CONCLUSIONS IL-1 blockade improves the anti-inflammatory and antioxidative properties of the HDL-containing fraction of plasma in patients with stages 3-5 CKD, including those on maintenance hemodialysis.
Inverse Occlusion: A Binocularly Motivated Treatment for Amblyopia

Recent laboratory findings suggest that short-term patching of the amblyopic eye (i.e., inverse occlusion) results in a larger and more sustained improvement in the binocular balance compared with normal controls. In this study, we investigate the cumulative effects of the short-term inverse occlusion in adults and old children with amblyopia. This is a prospective cohort study of 18 amblyopes (10-35 years old; 2 with strabismus) who have been subjected to 2 hours/day of inverse occlusion for 2 months. Patients who required refractive correction or whose refractive correction needed updating were given a 2-month period of refractive adaptation. The primary outcome measure was the binocular balance which was measured using a phase combination task; the secondary outcome measures were the best-corrected visual acuity which was measured with a Tumbling E acuity chart and converted to logMAR units and the stereoacuity which was measured with the Random-dot preschool stereogram test. The average binocular gain was 0.11 in terms of the effective contrast ratio (z = −2.344, p = 0.019, 2-tailed related samples Wilcoxon Signed Rank Test). The average acuity gain was 0.13 logMAR equivalent (t(17) = 4.76, p < 0.001, 2-tailed paired samples t-test). The average stereoacuity gain was 339 arc seconds (z = −2.533, p = 0.011). Based on more recent research concerning adult ocular dominance plasticity, we conclude that inverse occlusion in adults and old children with amblyopia does produce long-term gains to binocular balance and that acuity and stereopsis can improve in some subjects.
Spatial distribution of major bacterial species and different volatile fatty acids in a two-phase anaerobic biofilm reactor with PVA gel beads as bio-carrier

Abstract Conventional completely mixed anaerobic treatment systems limit the chances of the different species of bacteria to spatially group together according to their mutual cooperation and as a result, show a lower efficiency and vulnerability towards shock situations. It is interesting to know about the stratification of the different bacterial species participating in the degradation process and the intermediates that they produce. In this study, we established and optimized a two-phase anaerobic packed bed biofilm reactor system (AnPBR) with porous PVA gel beads used as bio-carriers and ran the reactor system in a steady state to observe the VFAs produced along with the microbial diversity of the predominant species at different stages of the reactor system. We observed that acetate and butyrate were the predominant intermediate VFAs while concentrations of other VFAs such that propionic acid were low. Acetobacterium and Clostridium were found to be the most abundant bacterial species in acidogenic reactor while methanogenic reactor was highly enriched with Methanobacterium and Methanosarcina. Apart from the above, syntrophic populations such as Syntrophobactor wolinii were also observed to be dominant in both the reactors – especially towards the end of acidogenic reactor and the initial part of the methanogenic reactor.
An Experimental Study of Flow and Heat Transfer in Wavy Passages

Wavy passages are one of the many devices being considered by manufacturers in the HV ACIR industry to increase the air-side heat transfer coefficient for a variety of heat exchanger applications. The purpose of this research is to obtain a better understanding of the flow instabilities and heat transfer in wavy passages so that design guidelines may be developed. Flow visualization experiments on twelve different geometries revealed the flow patterns and behavior in laminar wavy-channel flow. At low Reynolds numbers, there is evidence of macroscopic mixing between the core flow and the near-wall fluid. The onset location of this macroscopic mixing moves closer to the entrance of the channel with increasing Reynolds number. The instabilities in the cp=180° geometry appear to be fundamentally different from the instabilities in the cp=O° and the cp=90° geometries. A parametric study revealed that for a given Reynolds number, instabilities in the cp=00 and the cp=90° geometries occur at a farther upstream location than in the cp=180° geometries. Relative wavelength did not affect channel performance in the experimental range. An increase in the relative amplitude of the channel delayed the intial onset of instability in the wavy passage, but had little effect as the location of the onset of instabiltiy moved closer to the entrance of the channel. Heat transfer experiments confirmed that the instabilities observed in the flow visualization experiments enhance heat transfer. The results of this research may help in determining wavy channel geometries with high heat transfer rates for a particular application.
Chronic recording and electrochemical performance of amorphous silicon carbide-coated Utah electrode arrays implanted in rat motor cortex

Objective. Clinical applications of implantable microelectrode arrays are currently limited by device failure due to, in part, mechanical and electrochemical failure modes. To overcome this challenge, there is significant research interest in the exploration of novel array architectures and encapsulation materials. Amorphous silicon carbide (a-SiC) is biocompatible and corrosion resistant, and has recently been employed as a coating on biomedical devices including planar microelectrode arrays. However, to date, the three-dimensional Utah electrode array (UEA) is the only array architecture which has been approved by the food and drug administration (FDA) for long-term human trials. Approach. Here, we demonstrate, for the first time, that UEAs can be fabricated with a-SiC encapsulation and sputtered iridium oxide film (SIROF) electrode coatings, and that such arrays are capable of single-unit recordings over a 30 week implantation period in rat motor cortex. Over the same period, we carried out electrochemical measurements, including voltage transients, cyclic voltammetry, and electrochemical impedance spectroscopy (EIS), to evaluate potential failure modes. Furthermore, we evaluated chronic foreign body response via fluorescence immunohistochemistry following device explantation. Main results. During the indwelling period, we observed a reduction in active electrode yield percentage from 94.6 ± 5.4 (week 1) to 16.4 ± 11.5% (week 30). While the average active electrode yield showed a steady reduction, it is noteworthy that 3 out of 8 UEAs recorded greater than 60% active electrode yield at all times through 24 weeks and 1 out of 8 UEAs recorded greater than 60% active electrode yield at all times through the whole implantation period. Significance. In total, these findings further suggest that a-SiC may serve as a mechanically and electrochemically stable device encapsulation alternative to polymeric coatings such as Parylene-C.
The Food Literacy Action Logic Model: A Tertiary Education Sector Innovative Strategy to Support the Charitable Food Sectors Need for Food Literacy Training

Food literacy is seen as a key component in improving the increasing levels of food insecurity. While responsibility for providing training falls on the charitable service organizations, they may not have the capacity to adequately reach those in need. This paper proposes a tertiary education - (university or higher education) led model to support the food literacy training needs of the food charity sector. A cross-sectional study comprised of online surveys and discussions investigated food services offered by Western Australia (WA) and Australian Capital Territory (ACT) agencies, food literacy training needs for staff, volunteers and clients, and challenges to delivering food literacy training programs. Purposive sampling was used, and ACT and WA charitable service originations (survey: ACT n = 23, WA n = 32; interviews: ACT n = 3, WA n = 2) were invited to participate. Findings suggest organizations had limited financial and human resources to address the gap in food literacy training. Nutrition, food budgeting, and food safety education was delivered to paid staff only with limited capacity for knowledge transfer to clients. The Food Literacy Action Logic Model, underpinned by a tertiary education engagement strategy, is proposed to support and build capacity for organizations to address training gaps and extend the reach of food literacy to this under-resourced sector.
The optimization of sintering treatment on bovine-derived bone grafts for bone regeneration: in vitro and in vivo evaluation.

Modifications of sintering temperature and treatment time of bovine-derived bone grafts affect their physicochemical properties and further influence biological activity. Three different temperature sintered bovine-derived bone grafts: group I (300 °C 3 h), group II (300 °C 3 h plus 530 °C 6 h), and group III (300 °C 3 h plus 1000 °C 2 h) and Bio-Oss® were characterized and then compared in vitro for their effects on bone marrow stromal cells (BMSCs) migration, proliferation, and differentiation as estimated by cell migration assay, Alkaline phosphatase (ALP) activity assay, and Alizarin red staining. Further, the four bone grafts were implanted into the calvarial defects of rabbits to evaluate bone regeneration and graft degradation. The four deproteinized bovine-derived bone grafts displayed different surface topography. Group II displayed the highest potential of attracting cells. Both groups I and II markedly promote BMSCs differentiation. After 6 and 12 weeks, defects grafted with groups I and II displayed a significant higher bone fraction than defects grafted with group III and Bio-Oss®. Bone graft remnants remained in all four groups. Taken together, sintering at 300 °C for 3 h and sintering at 300 °C for 3 h with an addition of 530 °C for 6 h of bovine-dervied bone grafts displayed potential use in bone regeneration. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res B Part B, 2019.