Miracle-dz/UniFAR-FTUs huggingface dataset:
ALEVIN - A Framework to Develop, Compare, and Analyze Virtual Network Embedding Algorithms

Network virtualization is recognized as an enabling technology for the Future Internet. Applying virtualization of network resources leads to the problem of mapping virtual resources to physical resources, known as “Virtual Network Embedding” (VNE). Several algorithms attempting to solve this problem have been discussed in the literature, so far. However, comparison of VNE algorithms is hard, as each algorithm focuses on different criteria. To that end, we introduce a framework to compare different algorithms according to a set of metrics, which allow to evaluate the algorithms and compute their results on a given scenario for arbitrary parameters.
Application and Analysis of Biological Electrospray in Tissue Engineering

Nan-fiber scaffolds are suitable tools for tissue engineering. Electro spinning materials together with cells presents not adequate to obtain a high cellular zing tissue constructs as the shear force, tensile force, and other physical effects excited in the electro spinning process, which are harmful to cellular differentiation, development and function. However, this limitation has been overcome by a micro integration system of simultaneously bio-electro spraying human adipose stem cells (ASCs) and electro spinning Polyvinyl alcohol (PVA). Then it was compared to the single electro spinning nan-fiber scaffolds in relation to cell viability, which showed that the scaffolds by micro integration approach has a larger number of surviving cells and more suitable for cell growth and proliferation. In addition, the relationship between different parameters of biological electrospray (voltage, flow rate and distance of the needle from the collecting board) and droplet size of cell suspension was elucidated and the droplets with a near-mono distribution (<50um) could be generated to deposit a single living cell within a droplet. The association of bio-electro spraying with electro spinning (a scaffold preparation technique) has been demonstrated to be a promising and suitable tissue engineering approach in producing nan-fiber based three-dimensional (3-D) cell seeded scaffolds.
A novel effect of zinc on the lobster muscle GABA receptor

The effect of zinc (and copper) was investigated on the lobster muscle γ-aminobutyric acid (GABA) receptor. Zinc (10 μm-1 mM) depressed the GABA-evoked conductance increase in a fully reversible manner by possibly binding to an imidazole group, suggested from pH titration studies on the evoked-chloride conductance. Other transition metal (period 4) divalent cations (up to 500 μM) were inactive in antagonizing GABA responses. Variation of external chloride or anion substitution did not perturb the zinc antagonism ; however, decreasing the pH markedly decreased the potency of zinc. A possible explanation for these results is discussed. Although the zinc antagonism resembled that produced by picrotoxinin, combination of these two agents depressed the GABA dose-conductance curve in a manner expected for two antagonists acting on independent sites. The zinc binding site was also discrete from the GABA recognition site; the results are interpreted in terms of a distinct binding site for zinc and H+. The distortion of an agonist dose-response curve by formation of an inactive agonist-divalent cation complex is discussed; however, complexation of GABA did not explain the observed antagonism by zinc. By comparison, zinc had no effect on the GABA responses of rat ganglionic neurons. It is concluded that the zinc binding site, on lobster muscle, may be an important modulatory site for the GABA-evoked chloride conductance.
Oral Contraceptive Use, Micronutrient Deficiency, and Obesity among Premenopausal Females in Korea: The Necessity of Dietary Supplements and Food Intake Improvement

This study addressed the associations between oral contraceptive (OC) use and obesity as measured by recording the body mass index (BMI) of premenopausal females, and possible interactions with micronutrient intake were considered. A group of 39,189 premenopausal females aged 35–59 were included in the analysis; they were in the Health Examinee cohort. Participant BMIs were calculated from anthropometric measurements, and females with a BMI≥25kg/m2 were considered obese. Individual OC use, age at first OC use, duration of OC use, nutrient intake, and other covariates were measured with a structured questionnaire. A multivariate logistic regression with an interaction term was applied to identify the odds ratio (OR) and 95% confidence intervals (CI) between OC use and obesity along with consideration of micronutrient intake interactions. OC use is associated with an increased risk of obesity (OR = 1.12, 95% CI = 1.04–1.20), and females who used OCs for more than 6 months over their lifetimes were more likely to be obese (OR = 1.15, 95% CI = 1.01–1.32) compared with those who used OCs for <6 months. There were interaction effects between phosphorus, potassium, vitamin A, vitamin B1, vitamin B2, niacin, vitamin C intake and total duration of OC use on being obesity (P-value<0.05). When stratified by micronutrient intake, the associations between total OC use duration and obesity were present only among those with calcium, phosphorus, potassium, vitamin A, B1, B2, C, niacin, and folate intakes below the recommended levels. Efforts to estimate nutrient intake and prevent micronutrient depletion with supplements or food should be considered by clinicians for females who take OC for a long period.
Fourier Analysis of the Envelope of the Ophthalmic Artery Blood Flow Velocity: Age- and Blood Pressure–Related Impact

The harmonic content of the envelope waveform of the blood flow velocity in the ophthalmic artery was analyzed in aging and arterial hypertension. The case-control study enrolled 98 healthy men (age: 44.0±15.6 years), 100 healthy women (age: 44.5±19.1 years), which is group 1, and overall 199 hypertensive patients with increased systolic and diastolic blood pressure (in millimeters of mercury) before registration of the blood flow velocity using pulsed Doppler sonography. Group 2 was sufficiently treated (≤140/≤90), group 3 (>140/≤90) and group 5 (>140/>90) were insufficiently treated, and group 4 (>140/≤90) and group 6 (>140/>90) were untreated. Cronbach-&agr; reliability of the calculated spectral coefficient and SI (SI) was 0.88 and 0.93, respectively. In control subjects, the SI was influenced by age (men: 45.1%; women: 50.2%; P<0.001 each) and in women additionally by mean arterial pressure (13.1%; P<0.001). The SI differed in subjects >43 years of age (men: 0.37±0.11; women: 0.26±0.08; P<0.001 each) as compared with subjects ≤43 years of age (men: 0.60±0.18; women: 0.48±0.13). All of these changes were lacking for the resistance index. In both men and women with hypertension, the SI decreases, whereas the mean arterial pressure increases, but the resistance index did not change. The SI of the ophthalmic artery allows an assessment of the ocular circulation in consideration of age and arterial blood pressure in contrast to the resistance index.
QUANTITATIVE STUDIES ON THE MIXED LYMPHOCYTE INTERACTION IN RATS

These studies were designed to determine what influence prior immunization with homologous H isoantigens might have on the subsequent proliferative activity of lymphocytes from these animals in the mixed lymphocyte interaction. The results demonstrate the following: (a) Subcutaneous immunization with splenic cells from donors differing at the major H locus accelerates the tempo of the proliferative response to F1 cells bearing these same antigens in the MLI, whereas antigen given systemically reduces the proliferative response. (b) The altered proliferative behavior is specific for the immunizing antigens. (c) The period after immunization during which the MLI displays an altered tempo is a short one, lasting not longer than 3 wk. (d) Whether they are derived from previously immunized or from normal donors, the proportion of lymphocytes responsive in the MLI is the same, even though the response profiles are different. These results suggest that in comparison to immune responses to other types of antigens, immunologic reactivity to the major H isoantigens already involves a large number of antigen-reactive cells in normal animals and that the proportion of these cells is not increased as a result of immunization. Rather, lymphocytes from immunized animals respond more rapidly to the presence of these antigens.
Implementing Centers of Excellence: A Case Study

This paper explores the implementation of shared services, and in particular centers of excellence, in Swedish government agencies. It investigates how context shapes the translation of general guidelines on how to implement this type of backoffices. The study shows that the homogeneous picture drawn up in the management literature is not met in reality. Instead, different translations take place based on how context influences the implementation. This clearly shows that it does not exist one common approach as suggested in the literature. It proves that general guidelines cannot simply be applied by organizations, but that they rather need to be translated to fit an organization’s specific preconditions and demands. It also proves that the literature takes a too simple view on implementing shared services centers.
Laparoscopic management of cholecystoenteric fistulas.

BACKGROUND Cholecystoenteric fistulas are a rare complication of gallstone disease and affect 3-5% of patients with cholelithiasis. Most fistulas are diagnosed intraoperatively. MATERIALS AND METHODS Between January 1997 and June 2003, 12428 patients underwent laparoscopic cholecystectomy at our department. Cholecystoenteric fistula was diagnosed intraoperatively and treated in 63 patients: 45 patients (71.4%) had cholecystoduodenal fistulas, while cholecystogastric and cholecystocolic fistulas were found in 9 patients (14.3%) and 4 patients (6.3%), respectively; and 5 patients (7.9%) were found to have Mirizzi syndrome type I along with a cholecytoenteric fistula. The operation could be completed laparoscopically in 59 patients. An endostapler was used in 47 patients to transect the fistula and in 12 patients the defect in the bowel was repaired with intracorporeal sutures. RESULTS Major morbidity occurred in 3 patients (4.76%). One patient developed a loculated subdiaphragmatic collection which was treated by ultrasound guided aspiration and antibiotic therapy. Prolonged biliary drainage occurred in 2 patients. In addition, 7 patients (11.11%) had minor postoperative complications. The mean postoperative hospital stay was 5.2 days. All the patients are asymptomatic at a mean follow-up of 2.4 years. CONCLUSION Cholecystoenteric fistula is a difficult problem usually diagnosed intraoperatively. A high degree of suspicion at operation is mandatory. A stapled cholecystofistulectomy may be the procedure of choice since it avoids contamination of the peritoneal cavity. Complete laparoscopic management of cholecystoenteric fistulas is possible in well-equipped high-volume centers.
Relative effectiveness of additive pain interventions during vaccination in infants

BACKGROUND: Vaccine injections can cause acute pain and distress in infants, which can contribute to dissatisfaction with the vaccination experience and vaccine hesitancy. We sought to compare the effectiveness of additive pain interventions administered consistently during vaccine injections in the first year of life. METHODS: We conducted a multicentre, longitudinal, double-blind, add-on, randomized controlled trial. Healthy infants were randomly assigned to 1 of 4 levels of pain management for all vaccine injections at 2, 4, 6 and 12 months: (i) placebo control; (ii) parent-directed video education about infant soothing; (iii) the video plus sucrose administered orally or (iv) the video plus sucrose plus liposomal lidocaine applied topically. All infants benefit from injection techniques that minimize pain. We used a double-dummy design; hence all parents watched a video (active psychological intervention or placebo) and all infants received oral solution (sucrose or placebo) and topical cream (lidocaine or placebo). We assessed infant distress during 3 phases — preinjection (baseline), vaccine injection (needle), and 1 minute postinjection (recovery) — using the Modified Behavioural Pain Scale (range 0–10). We compared scores between groups and across infant ages using a mixed-model repeated-measures analysis. RESULTS: A total of 352 infants participated in the study, from Jan. 17, 2012, to Feb. 2, 2016. Demographics did not differ among intervention groups (p > 0.05). Baseline pain scores did not differ among intervention groups (p = 0.4), but did differ across ages (p < 0.001). Needle pain scores differed among groups (p = 0.003) and across ages (p < 0.001). The mean (± standard deviation) needle score was 6.3 (± 0.8) in the video–sucrose–lidocaine group compared with 6.7 (± 0.8) in each of the other groups. There were no other between-group differences. Recovery scores did not differ among groups (p = 0.98), but did differ across ages (p < 0.001). INTERPRETATION: Only liposomal lidocaine provided consistent analgesia within an additive pain intervention regimen during vaccinations in infants. Trial registration: ClinicalTrials.gov, no. NCT01503060
Biomedical Text Mining for Research Rigor and Integrity: Tasks, Challenges, Directions

An estimated quarter of a trillion US dollars is invested in the biomedical research enterprise annually. There is growing alarm that a significant portion of this investment is wasted, due to problems in reproducibility of research findings and in the rigor and integrity of research conduct and reporting. Recent years have seen a flurry of activities focusing on standardization and guideline development to enhance the reproducibility and rigor of biomedical research. Research activity is primarily communicated via textual artifacts, ranging from grant applications to journal publications. These artifacts can be both the source and the end result of practices leading to research waste. For example, an article may describe a poorly designed experiment, or the authors may reach conclusions not supported by the evidence presented. In this article, we pose the question of whether biomedical text mining techniques can assist the stakeholders in the biomedical research enterprise in doing their part towards enhancing research integrity and rigor. In particular, we identify four key areas in which text mining techniques can make a significant contribution: plagiarism/fraud detection, ensuring adherence to reporting guidelines, managing information overload, and accurate citation/enhanced bibliometrics. We review the existing methods and tools for specific tasks, if they exist, or discuss relevant research that can provide guidance for future work. With the exponential increase in biomedical research output and the ability of text mining approaches to perform automatic tasks at large scale, we propose that such approaches can add checks and balances that promote responsible research practices and can provide significant benefits for the biomedical research enterprise. Supplementary information Supplementary material is available at BioRxiv.
An Emerging Infectious Disease Triggering Large-Scale Hyperpredation

Hyperpredation refers to an enhanced predation pressure on a secondary prey due to either an increase in the abundance of a predator population or a sudden drop in the abundance of the main prey. This scarcely documented mechanism has been previously studied in scenarios in which the introduction of a feral prey caused overexploitation of native prey. Here we provide evidence of a previously unreported link between Emergent Infectious Diseases (EIDs) and hyperpredation on a predator-prey community. We show how a viral outbreak caused the population collapse of a host prey at a large spatial scale, which subsequently promoted higher-than-normal predation intensity on a second prey from shared predators. Thus, the disease left a population dynamic fingerprint both in the primary host prey, through direct mortality from the disease, and indirectly in the secondary prey, through hyperpredation. This resulted in synchronized prey population dynamics at a large spatio-temporal scale. We therefore provide evidence for a novel mechanism by which EIDs can disrupt a predator-prey interaction from the individual behavior to the population dynamics. This mechanism can pose a further threat to biodiversity through the human-aided disruption of ecological interactions at large spatial and temporal scales.
Atoms of recognition in human and computer vision

Significance Discovering the visual features and representations used by the brain to recognize objects is a central problem in the study of vision. Recent successes in computational models of visual recognition naturally raise the question: Do computer systems and the human brain use similar or different computations? We show by combining a novel method (minimal images) and simulations that the human recognition system uses features and learning processes, which are critical for recognition, but are not used by current models. The study uses a “phase transition” phenomenon in minimal images, in which minor changes to the image have a drastic effect on its recognition. The results show fundamental limitations of current approaches and suggest directions to produce more realistic and better-performing models. Discovering the visual features and representations used by the brain to recognize objects is a central problem in the study of vision. Recently, neural network models of visual object recognition, including biological and deep network models, have shown remarkable progress and have begun to rival human performance in some challenging tasks. These models are trained on image examples and learn to extract features and representations and to use them for categorization. It remains unclear, however, whether the representations and learning processes discovered by current models are similar to those used by the human visual system. Here we show, by introducing and using minimal recognizable images, that the human visual system uses features and processes that are not used by current models and that are critical for recognition. We found by psychophysical studies that at the level of minimal recognizable images a minute change in the image can have a drastic effect on recognition, thus identifying features that are critical for the task. Simulations then showed that current models cannot explain this sensitivity to precise feature configurations and, more generally, do not learn to recognize minimal images at a human level. The role of the features shown here is revealed uniquely at the minimal level, where the contribution of each feature is essential. A full understanding of the learning and use of such features will extend our understanding of visual recognition and its cortical mechanisms and will enhance the capacity of computational models to learn from visual experience and to deal with recognition and detailed image interpretation.
Trigger Factor Forms a Protective Shield for Nascent Polypeptides at the Ribosome*

In prokaryotes, the ribosome-associated Trigger Factor is the first chaperone newly synthesized polypeptides encounter when they emerge from the ribosomal exit tunnel. The effects that Trigger Factor exerts on nascent polypeptides, however, remain unclear. Here we analyzed the potential of the Trigger Factor to shield nascent polypeptides at the ribosome. A set of arrested nascent polypeptides differing in origin, size, and folding status were synthesized in an Escherichia coli-based in vitro transcription/translation system and tested for sensitivity to degradation by the unspecific protease proteinase K. In the absence of Trigger Factor, nascent polypeptides exposed outside the ribosomal exit tunnel were rapidly degraded unless they were folded into a compact domain. The presence of Trigger Factor, as well as a Trigger Factor fragment lacking its peptidyl-prolyl isomerase domain, counteracted degradation of all unfolded nascent polypeptides tested. This protective function was specific for ribosome-tethered Trigger Factor, since neither non-ribosomal Trigger Factor nor the DnaK system, which cooperates with Trigger Factor in the folding process in vivo, revealed a comparable efficiency in protection. Furthermore, shielding by Trigger Factor was not restricted to short stretches of nascent chains but was evident for large, non-native nascent polypeptides exposing up to 41 kDa outside the ribosome. We suggest that Trigger Factor supports productive de novo folding by shielding nascent polypeptides on the ribosome thereby preventing untimely degradation or aggregation processes. This protected environment provided by Trigger Factor might be particularly important for large multidomain proteins to fold productively into their native states.
Simple centromere, complex kinetochore

Although the budding yeast centromere is extremely short (125 bp) compared to those of other eukaryotes, the kinetochore that assembles on this DNA displays a rich molecular complexity. Here, we describe recent advances in our understanding of kinetochore function in budding yeast and present a model describing the attachment that is formed between spindle microtubules and centromeric DNA. This analysis may provide general principles for kinetochore function and regulation.
Femoral deep vein thrombosis associated with central venous catheterization: results from a prospective, randomized trial.

OBJECTIVE To determine the frequency of central venous catheter-induced deep vein thrombosis of the femoral vein. DESIGN Prospective, randomized, controlled trial. SETTING Tertiary care center. PATIENTS Forty-five patients in a medical-surgical intensive care unit who required central venous catheterization. INTERVENTIONS Patients were randomized to receive central venous catheterization in either upper (subclavian or internal jugular veins) or lower (femoral vein) catheterization sites. Lower extremity duplex ultrasound examinations were performed before central venous catheter placement, after removal of the catheter, and 7 days after catheter removal. Ultrasound examinations were reported as positive, nondiagnostic, or negative for deep vein thrombosis. MEASUREMENTS AND MAIN RESULTS Of the 21 patients randomized to upper access sites, none developed positive or nondiagnostic duplex ultrasound examinations. Six (25%) of 24 patients randomized to the femoral access site developed lower extremity deep vein thrombosis (p = .02). In addition, seven (29%) patients randomized to the lower access site sustained non-diagnostic ultrasound examinations. A total of 13 (54%) of 24 patients from the lower access group developed abnormal ultrasound examinations (p < .001). Age, duration of catheterization, coagulation profile, deep vein thrombosis prophylaxis, and Acute Physiology and Chronic Health Evaluation II scores were similar between the upper and lower access groups. CONCLUSIONS Based on the data from this study, we concluded that femoral vein catheterization is associated with a 25% frequency of lower extremity deep vein thrombosis compared with similar patients receiving subclavian or internal jugular vein catheters. The femoral vein remains an important emergency venous access route. Physicians inserting femoral vein catheters should be aware of the risk of lower extremity deep vein thrombosis and should consider performing lower extremity duplex ultrasound examinations on removal of femoral vein catheters.