Miracle-dz/UniFAR-FTUs huggingface dataset:
Species Diversity of Environmental GIM-1-Producing Bacteria Collected during a Long-Term Outbreak

ABSTRACT Reports of outbreaks concerning carbapenemase-producing Gram-negative bacteria in which the main source of transmission is the hospital environment are increasing. This study describes the results of environmental sampling in a protracted polyspecies metallo-beta-lactamase GIM-1 outbreak driven by plasmids and bacterial clones of Enterobacter cloacae and Pseudomonas aeruginosa in a tertiary care center. Environmental sampling targeting wet locations (especially sinks) was carried out on a surgical intensive care unit and on a medical ward on several occasions in 2012 and 2013. We were able to demonstrate 43 bla GIM-1-carrying bacteria (mainly nonfermenters but also Enterobacteriaceae) that were either related or unrelated to clinical strains in 30 sinks and one hair washbasin. GIM-1 was found in 12 different species, some of which are described here as carriers of GIM-1. Forty out of 43 bacteria displayed resistance to carbapenems and, in addition, to various non-beta-lactam antibiotics. Colistin resistance was observed in two E. cloacae isolates with MICs above 256 mg/liter. The bla GIM-1 gene was harbored in 12 different class 1 integrons, some without the typical 3′ end. The bla GIM-1 gene was localized on plasmids in five isolates. In vitro plasmid transfer by conjugation was successful in one isolate. The environment, with putatively multispecies biofilms, seems to be an important biological niche for multidrug-resistant bacteria and resistance genes. Biofilms may serve as a “melting pot” for horizontal gene transfer, for dissemination into new species, and as a reservoir to propagate future hospital outbreaks. IMPORTANCE In Gram-negative bacteria, resistance to the clinically relevant broad-spectrum carbapenem antibiotics is a major public health concern. Major reservoirs for these resistant organisms are not only the gastrointestinal tracts of animals and humans but also the (hospital) environment. Due to the difficulty in eradicating biofilm formation in the latter, a sustained dissemination of multidrug-resistant bacteria from the environment can occur. In addition, horizontal transfer of resistance genes on mobile genetic elements within biofilms adds to the total “resistance gene pool” in the environment. To gain insight into the transmission pathways of a rare and locally restricted carbapenemases resistance gene (bla GIM-1), we analyzed the genetic background of the bla GIM-1 gene in environmental bacteria during a long-term polyspecies outbreak in a German hospital.
Fortification of Pan Bread With Healthy Flaxseed

Flaxseed (Linum Usitatissimum) is being used extensively for the development of functional foods. The components of flaxseed, identified to exhibit the health benefits are fiber, proteins, lignans and linolenic acid. Moreover flaxseed is a good source of high quality protein, soluble fibers and phenolic compounds. The research work was carried out to evaluate the acceptability of flaxseed utilization in the bread. Flaxseed flours (partially defatted and full fat) supplemented wheat flour significantly improved the chemical composition (crude fat, crude fiber and crude protein). The scores assigned to all the sensory parameters of breads affected significantly with the variation in levels of flaxseed supplementation in wheat flours. The 12% replacements of both flaxseed flours resulted in acceptable product.
Long-Term and Short-Term Antidepressant Use in General Practice: Data from a Large Cohort in the Netherlands

Background: Antidepressant use is highly prevalent. Research has mainly focused on efficacy during short periods of use for depression and anxiety. There is a relative paucity of data regarding the frequency of long-term use. Methods: To determine the prevalence and possible increase of long-term use of antidepressants over recent years, we analyzed routine general practice care data in a large cohort of patients (n = 156,620) in and around Amsterdam, The Netherlands. Additionally, predictors of long-term use were studied. Results: Prevalence of long-term use of antidepressants is substantial, and such use appears to be increasing: 30.3% of use was long-term over the period 1995-2005 compared to 43.7% for the period 2005-2015. Higher age, a registered diagnosis of anxiety or depression, and the use of SSRIs or SNRIs were associated with long-term use in multivariate analysis. In addition, specific antidepressants were differentially associated with long-term use. Conclusions: Long-term antidepressant use is substantial and appears to be on the rise. Awareness of this phenomenon should be increased, such use should be prevented when possible, and reasons for long-term use need to be examined.
Cognitive behavioural therapy in multiple sclerosis: a randomized controlled pilot study of acceptance and commitment therapy.

OBJECTIVE The aim of this study was to design a trial that could evaluate the effect of acceptance and commitment therapy as a group-intervention for multiple sclerosis patients with psychological distress. DESIGN Randomized controlled trial with assessment at pretreatment, end of treatment, and at 3-month follow-up. SUBJECTS Multiple sclerosis outpatients with elevated symptoms of anxiety and/or depression (n = 21). METHODS Patients were randomly assigned to acceptance and commitment therapy or relaxation training. Both treatments consisted of 5 sessions over 15 weeks containing didactic sessions, group discussions, and exercises. Outcome was assessed by self-rated symptoms of anxiety, depression, and a measure of acceptance. RESULTS At 3-month follow-up, the relaxation training group had a significant decline in anxiety symptoms whereas the acceptance and commitment therapy group showed a maintained improvement in rated acceptance at follow-up. CONCLUSION The results reflect the different emphases of the therapies. Acceptance and commitment therapy is aimed at living an active, valued life and increasing acceptance, while relaxation training focuses directly on coping strategies to handle emotional symptoms. The results are preliminary, but supportive of further study of brief group interventions for reducing psychological distress in patients with multiple sclerosis.
Spatio-Temporal Compressive Sensing-Based Data Gathering in Wireless Sensor Networks

Sensory data in many wireless sensor networks feature spatio-temporal correlations, and compressive sensing (CS) plays an important role in energy-efficient data gathering. In this letter, we design a new CS-based data gathering algorithm, utilizing random sampling and random walks to select sensory data in temporal and spatial domains, respectively. Each measurement is obtained by summing the selected data. A novel sensing matrix is also designed based on the adjacency matrix of an unbalanced expander graph. Simulation shows that our proposed algorithm reduces energy consumption by up to 50.0% compared to the existing algorithms in a daily sea surface temperature measurement scenario.
Diagnostic Criteria and Clinical Outcomes in Sarcopenia Research: A Literature Review

By the sixth decade of life, nearly one quarter of the population has substantial muscle atrophy, or sarcopenia. Despite the creation of a standardized definition of sarcopenia by the European Working Group on Sarcopenia in Older People, variability may exist in the diagnostic criteria utilized for clinical sarcopenia research. The primary objectives of this review were to characterize diagnostic criteria used for measurement of sarcopenia in original studies, and to describe associations between sarcopenia and important clinical outcomes. We performed a literature review of the term “sarcopenia” in PubMed. Inclusion criteria were English language, original data, a clear and specific definition for diagnosing sarcopenia, and the analysis of sarcopenia’s effect on a clinical outcome. A total of 283 studies met inclusion criteria. More than half of the included sarcopenia investigations were level IV studies (54.1%), while 43.1% provided level II evidence. Under one third (27.6%) of studies examined sarcopenia with regard to surgical outcomes. In terms of diagnostic criteria for sarcopenia, 264 (93.3%) studies used measures of skeletal muscle mass, with dual energy X-ray absorptiometry (DEXA) being the most common modality (43.6%). Sarcopenia was found to be a consistent predictor of chronic disease progression, all-cause mortality, poorer functional outcomes, and postoperative complications. In conclusion, there is substantial evidence that sarcopenia impacts both medical and surgical outcomes. However, current research has utilized heterogeneous diagnostic criteria for sarcopenia. Further efforts to standardize the modalities used to diagnose sarcopenia in clinical research and practice will help strengthen our ability to study this important phenomenon.
The Equilibrium Consequences of Indexing

We develop a benchmark model to study the equilibrium consequences of indexing in a standard rational expectations setting. Individuals incur costs to participate in financial markets, and these costs are lower for individuals who restrict themselves to indexing. A decline in indexing costs directly increases the prevalence of indexing, thereby reducing the price efficiency of the index and augmenting relative price efficiency. In equilibrium, these changes in price efficiency in turn further increase indexing, and raise the welfare of uninformed traders. For well-informed traders, the share of trading gains stemming from market timing increases relative to stock selection trades.
“Music & Memory” and improved swallowing in advanced dementia

Background Dysphagia and difficulty with eating affects a significant portion of individuals with advanced dementia. Such problems with oral intake can have serious health consequences including mealtime distress, dehydration and malnutrition, aspiration, reduced quality of life, and increased mortality risk. Design We present the first data indicating that “Music & Memory” interventions improve swallowing in individuals with advanced dementia, thereby making oral feeding easier and potentially diminishing reliance on PEG. Setting Columbia Health Care Center, Wyocena, WI (with Music&Memory.org, Mineola, NY and Stony Brook University). Participants Residents with advanced dementia (N = 5). Measurements: Observation by eight professional caregivers. Results (1) Enhanced swallowing mechanism with Music & Memory prior to dining; (2) decreased incidents of choking during mealtime; (3) improved nutritional status; (4) reduced weight loss; (5) reduced need for speech interventions; (6) enhanced quality of life. Conclusions The preliminary results call for additional research.
Antibiotic susceptibility of Helicobacter pylori isolates in Dakar, Senegal.

BACKGROUND Helicobacter pylori is the primary cause of peptic ulcer disease and an etiologic agent in the development of gastric cancer. A high frequency of H. pylori infection has been reported from resource-poor regions. H. pylori infection is curable with regimens of multiple antimicrobial agents. However, antibiotic resistance is a leading cause of treatment failure. In Africa, there are very little data concerning the susceptibility of H. pylori isolates to antibiotics. METHODOLOGY H. pylori isolates from gastric biopsies from outpatients > or = 18 years old affected by a gastro-duodenal ulcer were used in this study. Susceptibility testing was performed for amoxicillin, ciprofloxacin and metronidazole by using the Epsilometer test (E-test) method. RESULTS H. pylori strains were isolated from 40 patients of whom 36 were diagnosed as having duodenal ulcer, two with gastric ulcer, and two with gastro-duodenal ulcer. Thirty-six (90%) of the isolates were resistant to metronidazole (MICs > or = 8 microg/l), whereas all isolates were susceptible to amoxicillin (MICs < or = 0.5 microg/ml) and ciprofloxacin (MICs < or = 1 microg/ml). CONCLUSION These data suggest that metronidazole should not be used therapeutically among Senegalese patients in first-line therapy, while ciprofloxacin could be recommended in association with amoxicillin and a proton pump inhibitor in Senegal.
Mitigating sampling error when measuring internet client IPv6 capabilities

Despite the predicted exhaustion of unallocated IPv4 addresses between 2012 and 2014, it remains unclear how many current clients can use its successor, IPv6, to access the Internet. We propose a refinement of previous measurement studies that mitigates intrinsic measurement biases, and demonstrate a novel web-based technique using Google ads to perform IPv6 capability testing on a wider range of clients. After applying our sampling error reduction, we find that 6% of world-wide connections are from IPv6-capable clients, but only 1--2% of connections preferred IPv6 in dual-stack (dual-stack failure rates less than 1%). Except for an uptick around IPv6-day 2011 these proportions were relatively constant, while the percentage of connections with IPv6-capable DNS resolvers has increased to nearly 60%. The percentage of connections from clients with native IPv6 using happy eyeballs has risen to over 20%.
The Impact of Education and R&D Investment on Regional Economic Growth

The purpose of this paper is to examine the impact of education and R&D investment on regional economic growth in South Korea. We develop a simultaneous model of production, human capital accumulation, migration, population and physical capital investment of two regions: the Seoul Metropolitan Area and the rest of Korea. We decompose the regional growth path into a quality path and a quantity path to identify how regional economies grow and run simulations to evaluate alternative policies in terms of effectiveness and adaptability. The impact of education and R&D investment on regional growth in the rest of Korea is only 22.3% of that in the Seoul Metropolitan Area due to lower elasticity values of young in-migrants with respect to the investment in the rest of Korea. An enhanced efficiency of regional human capital accumulation is effective and adaptable to alleviate regional economic disparity.
Complications and Disease Recurrence After Primary Ileocecal Resection in Pediatric Crohn's Disease: A Multicenter Cohort Analysis

Background: Studies on the outcome of ileocecal resection in pediatric Crohn's disease (CD) have a limited follow-up and fail to assign predictors of adverse outcomes. Therefore, we aimed to investigate (I) the complication and disease recurrence rates and (II) identify risk factors for these adverse outcomes after ileocecal resection for pediatric CD. Methods: This is a retrospective cohort analysis of all children (<18 years) that underwent ileocecal resection as first intestinal resection for CD derived from 7 tertiary hospitals in the Netherlands (1990–2015). Risk factors were identified using multivariable analysis. Results: In total, 122 children were included (52% male; median age 15.5 years [interquartile range 14.0–16.0]). Severe postoperative complications rate was 10%. Colonic disease (odds ratio: 5.6 [95% confidence interval {CI}: 1.3–26.3], P = 0.024), microscopically positive resection margins (odds ratio: 10.4 [95% CI: 1.1–100.8] P = 0.043), and emergency surgery (odds ratio: 6.8 [95% CI: 1.1–42.2], P = 0.038) were risk factors for severe complications. Clinical and surgical recurrence rates after 1, 5 and 10 years were 19%, 49%, 71% and 2%, 12%, 22%, respectively. Female sex (hazard ratio [HR]: 2.1 [95% CI: 1.1–3.8], P = 0.023) was a risk factor for clinical recurrence, whereas ileocecal disease (HR: 3.9 [95% CI: 1.2–12.5], P = 0.024) and microscopically positive resection margins (HR: 9.6 [95% CI: 1.2–74.5], P = 0.031) were risk factors for surgical recurrence. Immediate postoperative therapy reduced the risk of both clinical (HR: 0.3 [95% CI: 0.1–0.6], P = 0.001) and surgical (HR: 0.5 [95% CI: 0.1–0.9], P = 0.035) recurrence. Conclusions: Ileocecal resection is an effective and durable treatment of pediatric CD, although postoperative complications occur frequently. Postoperative therapy may be started immediately to prevent disease recurrence.
Type I interferon pathway in CNS homeostasis and neurological disorders

Type I interferons (IFNs), IFN‐α and IFN‐β, represent the major effector cytokines of the host immune response against viruses and other intracellular pathogens. These cytokines are produced via activation of numerous pattern recognition receptors, including the Toll‐like receptor signaling network, retinoic acid‐inducible gene‐1 (RIG‐1), melanoma differentiation‐associated protein‐5 (MDA‐5) and interferon gamma‐inducible protein‐16 (IFI‐16). Whilst the contribution of type I IFNs to peripheral immunity is well documented, they can also be produced by almost every cell in the central nervous system (CNS). Furthermore, IFNs can reach the CNS from the periphery to modulate the function of not only microglia and astrocytes, but also neurons and oligodendrocytes, with major consequences for cognition and behavior. Given the pleiotropic nature of type I IFNs, it is critical to determine their exact cellular impact. Inappropriate upregulation of type I IFN signaling and interferon‐stimulated gene expression have been linked to several CNS diseases termed “interferonopathies” including Aicardi–Goutieres syndrome and ubiquitin specific peptidase 18 (USP18)‐deficiency. In contrast, in the CNS of mice with virus‐induced neuroinflammation, type I IFNs can limit production of other cytokines to prevent potential damage associated with chronic cytokine expression. This capacity of type I IFNs could also explain the therapeutic benefits of exogenous type I IFN in chronic CNS autoimmune diseases such as multiple sclerosis. In this review we will highlight the importance of a well‐balanced level of type I IFNs for healthy brain physiology, and to what extent dysregulation of this cytokine system can result in brain ‘interferonopathies’.
Preparation and Characterization of Nanostructured CuO Thin Films using Sol-gel Dip Coating

Nanostructured CuO thin films were deposited onto quartz substrates by sol-gel dip coating technique. The precursor solution was prepared by dissolving copper acetate powder into isopropanol with molarity of 0.25M. Preheating and annealing temperature were fixed at 250°C and 600°C respectively. This study focused on various film thicknesses by varying the frequent number of deposited layers. The effect of thickness on electrical, surface morphology and optical properties of CuO thin film were studied. The surface morphology was examined using field emission scanning electron microscopy (FE-SEM), surface profiler for thickness measurement, optical properties of CuO thin film were characterized by using ultraviolet- visible spectroscopy (UV-VIS) for transmittance and absorbance, and the electrical property was examined by using two point probes method. The films were found to be denser at higher film thickness due to lesser porous observed on the surface. The thickness of these CuO thin films varied from 87.14 – 253.58 nm and the direct band gap energy was observed in between 1.9 to 2.35 eV. Lowest resistivity was found for sample with a thickness of 253.58 nm.
Differential Scavenging Among Pig, Rabbit, and Human Subjects ,

Different animal species have been used as proxies for human remains in decomposition studies for decades, although few studies have sought to validate their use in research aimed at estimating the postmortem interval. This study examines 45 pig, rabbit, and human subjects placed in three seasonal trials at the Anthropology Research Facility. In an earlier paper, we found that overall decomposition trends did vary between species that could be due to differential insect and scavenger behavior. This study specifically examines if scavenger behavior differs by carrion species. Daily photographs, game camera photographs, written observations, and Total Body Score (TBS) documented scavenging and decomposition changes. Results show that raccoons were the most commonly observed vertebrate scavenger, that scavenging was most extensive in winter, and that certain human subjects were preferred over other humans and all non‐human subjects. Finally, scavenging activity greatly reduces the accuracy of postmortem interval estimates based on TBS.
Cost-comparison of two trabecular micro-bypass stents versus selective laser trabeculoplasty or medications only for intraocular pressure control for patients with open-angle glaucoma

Abstract Aim: Patients with open-angle glaucoma (OAG) whose intraocular pressure is not adequately controlled by one medication have several treatment options in the US. This analysis evaluated direct costs of unilateral eye treatment with two trabecular micro-bypass stents (two iStents) compared to selective laser trabeculoplasty (SLT) or medications only. Materials and methods: A population-based, annual state-transition, probabilistic, cost-of-care model was used to assess OAG-related costs over 5 years. Patients were modeled to initiate treatment in year zero with two iStents, SLT, or medications only. In years 1–5, patients could remain on initial treatment or move to another treatment option(s), or filtration surgery. Treatment strategy change probabilities were identified by a clinician panel. Direct costs were included for drugs, procedures, and complications. Results: The projected average cumulative cost at 5 years was lower in the two-stent treatment arm ($4,420) compared to the SLT arm ($4,730) or medications-only arm ($6,217). Initial year-zero costs were higher with two iStents ($2,810) than with SLT ($842) or medications only ($996). Average marginal annual costs in years 1–5 were $322 for two iStents, $777 for SLT, and $1,044 for medications only. The cumulative cost differences between two iStents vs SLT or medications only decreased over time, with breakeven by 5 or 3 years post-initiation, respectively. By year 5, cumulative savings with two iStents over SLT or medications only was $309 or $1,797, respectively. Limitations: This analysis relies on clinical expert panel opinion and would benefit from real-world evidence on use of multiple procedures and treatment switching after two-stent treatment, SLT, or polypharmaceutical initial approaches. Conclusions: Despite higher costs in year zero, annual costs thereafter were lowest in the two-stent treatment arm. Two-stent treatment may reduce OAG-related health resource use, leading to direct savings, especially over medications only or at longer time horizons.