Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Host Specificity of Human- and Pig- Associated Staphylococcus aureus Clonal Lineages

Bacterial adhesion is a crucial step in colonization of the skin. In this study, we investigated the differential adherence to human and pig corneocytes of six Staphylococcus aureus strains belonging to three human-associated [ST8 (CC8), ST22 (CC22) and ST36(CC30)] and two pig-associated [ST398 (CC398) and ST433(CC30)] clonal lineages, and their colonization potential in the pig host was assessed by in vivo competition experiments. Corneocytes were collected from 11 humans and 21 pigs using D-squame® adhesive discs, and bacterial adherence to corneocytes was quantified by a standardized light microscopy assay. A previously described porcine colonization model was used to assess the potential of the six strains to colonize the pig host. Three pregnant, S. aureus-free sows were inoculated intravaginally shortly before farrowing with different strain mixes [mix 1) human and porcine ST398; mix 2) human ST36 and porcine ST433; and mix 3) human ST8, ST22, ST36 and porcine ST398] and the ability of individual strains to colonize the nasal cavity of newborn piglets was evaluated for 28 days after birth by strain-specific antibiotic selective culture. In the corneocyte assay, the pig-associated ST433 strain and the human-associated ST22 and ST36 strains showed significantly greater adhesion to porcine and human corneocytes, respectively (p<0.0001). In contrast, ST8 and ST398 did not display preferential host binding patterns. In the in vivo competition experiment, ST8 was a better colonizer compared to ST22, ST36, and ST433 prevailed over ST36 in colonizing the newborn piglets. These results are partly in agreement with previous genetic and epidemiological studies indicating the host specificity of ST22, ST36 and ST433 and the broad-host range of ST398. However, our in vitro and in vivo experiments revealed an unexpected ability of ST8 to adhere to porcine corneocytes and persist in the nasal cavity of pigs.
A Prospective, Single-Center, Nonblinded, Comparative, Postmarket Clinical Evaluation of a Bovine-Derived Collagen With Ionic Silver Dressing versus a Carboxymethylcellulose and Ionic Silver Dressing for the Reduction of Bioburden in Variable-Etiology, Bilateral Lower-Extremity Wounds

OBJECTIVE: There are numerous dressings designed to manage the overabundance of matrix metalloproteinases, while also addressing the excessive bioburden found in chronic wounds. The authors compared the efficacy of 2 such dressings: a sodium carboxymethylcellulose/1.2% ionic silver (CMC), which theoretically reduces bacteria by providing silver ions, versus a bovine native collagen (BDC)/ionic silver dressing, which also delivers silver ions in an aqueous environment. Both dressings theoretically modulate the wound bed; CMC through moist wound care and fibrin ingrowth and BDC through matrix metalloproteinase balancing. METHODS: A prospective protocol was undertaken using patients as their own controls. Ten patients with bilateral venous stasis or diabetic foot ulcers were selected. One limb was randomized to treatment by either CMC or BDC, whereas the contralateral wound was treated with the other dressing. Biopsies for quantitative cultures were taken at weeks 1 and 4. Wound area was assessed at the weekly visits. RESULTS: The BDC wounds started with 1.0 × 105 (±1.2 × 105) bacteria, and the CMC wounds started with 1.4 × 105 (±1.3 × 105) bacteria. Over the 4-week period, the bacteria in the 3-ppm (parts per million) silver-treated wound increased 1.53 × 105, whereas in the 21-ppm silver-treated wound, the bacteria increased 1.42 × 105. The rates of closure for CMC-treated wounds was 0.79 ± 0.735 cm2/wk and for BDC-treated wounds was 1.38 ± 1.44 cm2/wk. Only 1 wound treated with either dressing exhibited a decrease in bacteria. CONCLUSION: Both CMC and BDC silver dressings appeared to have statistically similar efficacy regarding the rate of wound healing and little impact on the actual bioburden in chronic lower-extremity wounds. Interestingly, there was no correlation in the size of the wound and any effect on bioburden. Although the BDC dressing showed a higher absolute rate of wound closure, neither technology demonstrated a statistically significant difference in wound closure rate when corrected for initial wound size.
Dipeptidyl Peptidase 4 Is a Novel Adipokine Potentially Linking Obesity to the Metabolic Syndrome

OBJECTIVE Comprehensive proteomic profiling of the human adipocyte secretome identified dipeptidyl peptidase 4 (DPP4) as a novel adipokine. This study assessed the functional implications of the adipokine DPP4 and its association to the metabolic syndrome. RESEARCH DESIGN AND METHODS Human adipocytes and skeletal and smooth muscle cells were used to monitor DPP4 release and assess the effects of soluble DPP4 on insulin signaling. In lean and obese subjects, depot-specific expression of DPP4 and its release from adipose tissue explants were determined and correlated to parameters of the metabolic syndrome. RESULTS Fully differentiated adipocytes exhibit a substantially higher release of DPP4 compared with preadipocytes or macrophages. Direct addition of DPP4 to fat and skeletal and smooth muscle cells impairs insulin signaling. A fivefold higher level of DPP4 protein expression was seen in visceral compared with subcutaneous fat of obese patients, with no regional difference in lean subjects. DPP4 serum concentrations significantly correlated with adipocyte size. By using adipose tissue explants from lean and obese subjects, we observed a twofold increase in DPP4 release that strongly correlated with adipocyte volume and parameters of the metabolic syndrome and was decreased to the lean level after weight reduction. DPP4 released from adipose tissue correlated positively with an increasing risk score for the metabolic syndrome. CONCLUSIONS DPP4 is a novel adipokine that may impair insulin sensitivity in an autocrine and paracrine fashion. Furthermore, DPP4 release strongly correlates with adipocyte size, potentially representing an important source of DPP4 in obesity. Therefore, we suggest that DPP4 may be involved in linking adipose tissue and the metabolic syndrome.
On the limit-cycle instability in magnetized accretion discs

Observational evidence accumulated over the past decade indicates that accretion discs in X-ray binaries are viscously stable unless they accrete very close to the Eddington limit. This is at odds with the most basic standard accretion disc theory, but could be explained by either having the discs to be much cooler whereby they are not radiation pressure dominated, or a more sophisticated viscosity law. Here we argue that the latter is taking place in practice, on the basis of a stability analysis that assumes that the magnetorotational instability (MRI) responsible for generating the turbulent stresses inside the discs is also the source for a magnetically dominated corona. We show that observations of stable discs in the high/soft states of black hole binaries, on the one hand, and of the strongly variable microquasar GRS 1915+105 on the other, can all be explained if the magnetic turbulent stresses inside the disc scale proportionally to the geometric mean of gas and total pressure with a constant of proportionality (viscosity parameter) having a value of a few times 10 -2 . Implications for bright AGN are also briefly discussed.
Predicting Complications in Critical Care Using Heterogeneous Clinical Data

Patients in hospitals, particularly in critical care, are susceptible to many complications affecting morbidity and mortality. Digitized clinical data in electronic medical records can be effectively used to develop machine learning models to identify patients at risk of complications early and provide prioritized care to prevent complications. However, clinical data from heterogeneous sources within hospitals pose significant modeling challenges. In particular, unstructured clinical notes are a valuable source of information containing regular assessments of the patient's condition but contain inconsistent abbreviations and lack the structure of formal documents. Our contributions in this paper are twofold. First, we present a new preprocessing technique for extracting features from informal clinical notes that can be used in a classification model to identify patients at risk of developing complications. Second, we explore the use of collective matrix factorization, a multi-view learning technique, to model heterogeneous clinical data-text-based features in combination with other measurements, such as clinical investigations, comorbidites, and demographic data. We present a detailed case study on postoperative respiratory failure using more than 700 patient records from the MIMIC II database. Our experiments demonstrate the efficacy of our preprocessing technique in extracting discriminatory features from clinical notes as well as the benefits of multi-view learning to combine clinical measurements with text data for predicting complications.
A Citation Centric Annotation Scheme for Scientific Articles

This paper presents an annotation scheme for modelling citation contexts in scientific articles. We present an argumentation framework based on the Toulmin model for scientific articles and develop an annotation scheme with different context types based on the argumentation model. We present the results of the inter-rater reliability study carried out for studying the reliability of our annotation scheme.
Determining the Polarity of Postings for Discussion Search

When performing discussion search it might be desirable to consider non-topical measures like the number of positive and negative replies to a posting, for instance as one possible indicator for the trustworthiness of a comment. Systems like POLAR are able to integrate such values into the retrieval function. To automatically detect the polarity of postings, they need to be classified into positive and negative ones w.r. t. the comment or document they are annotating. We present a machine learning approach for polarity detection which is based on Support Vector Machines. We discuss and identify appropriate term and context features. Experiments with ZDNet News show that an accuracy of around 79%80% can be achieved for automatically classifying comments according to their polarity.
Differential Post Detection Integration Techniques for Robust Code Acquisition

In this paper, the problem of code acquisition for spread-spectrum systems is investigated in the presence of frequency errors. The classic approach of noncoherent post detection integration (NCPDI) is contrasted with differential post detection integration (DPDI), presented in two different versions, namely DPDI-Real and DPDI-Abs, respectively, suited for fine and large frequency offsets. The differential schemes are characterized thoroughly introducing a novel analytical treatment that is validated by simulations. In order to fairly quantify the potential gains introduced by the differential solutions, specific detector parameter optimization is performed for each scheme. The interesting result is that the DPDI significantly outperforms the classic NCPDI approach for large frequency errors, and behaves close to it for small offsets. DPDI can, thus, be considered as a very robust PDI solution with moderate complexity.
Sentence Compression Beyond Word Deletion

In this paper we generalise the sentence compression task. Rather than simply shorten a sentence by deleting words or constituents, as in previous work, we rewrite it using additional operations such as substitution, reordering, and insertion. We present a new corpus that is suited to our task and a discriminative tree-to-tree transduction model that can naturally account for structural and lexical mismatches. The model incorporates a novel grammar extraction method, uses a language model for coherent output, and can be easily tuned to a wide range of compression specific loss functions.
SC-DCNN: Highly-Scalable Deep Convolutional Neural Network using Stochastic Computing

With the recent advance of wearable devices and Internet of Things (IoTs), it becomes attractive to implement the Deep Convolutional Neural Networks (DCNNs) in embedded and portable systems. Currently, executing the software-based DCNNs requires high-performance servers, restricting the widespread deployment on embedded and mobile IoT devices. To overcome this obstacle, considerable research efforts have been made to develop highly-parallel and specialized DCNN accelerators using GPGPUs, FPGAs or ASICs. Stochastic Computing (SC), which uses a bit-stream to represent a number within [-1, 1] by counting the number of ones in the bit-stream, has high potential for implementing DCNNs with high scalability and ultra-low hardware footprint. Since multiplications and additions can be calculated using AND gates and multiplexers in SC, significant reductions in power (energy) and hardware footprint can be achieved compared to the conventional binary arithmetic implementations. The tremendous savings in power (energy) and hardware resources allow immense design space for enhancing scalability and robustness for hardware DCNNs. This paper presents SC-DCNN, the first comprehensive design and optimization framework of SC-based DCNNs, using a bottom-up approach. We first present the designs of function blocks that perform the basic operations in DCNN, including inner product, pooling, and activation function. Then we propose four designs of feature extraction blocks, which are in charge of extracting features from input feature maps, by connecting different basic function blocks with joint optimization. Moreover, the efficient weight storage methods are proposed to reduce the area and power (energy) consumption. Putting all together, with feature extraction blocks carefully selected, SC-DCNN is holistically optimized to minimize area and power (energy) consumption while maintaining high network accuracy. Experimental results demonstrate that the LeNet5 implemented in SC-DCNN consumes only 17 mm2 area and 1.53 W power, achieves throughput of 781250 images/s, area efficiency of 45946 images/s/mm2, and energy efficiency of 510734 images/J.
All about Eve: Execute-Verify Replication for Multi-Core Servers

This paper presents Eve, a new Execute-Verify architecture that allows state machine replication to scale to multi-core servers. Eve departs from the traditional agree-execute architecture of state machine replication: replicas first execute groups of requests concurrently and then verify that they can reach agreement on a state and output produced by a correct replica; if they can not, they roll back and execute the requests sequentially. Eve minimizes divergence using application-specific criteria to organize requests into groups of requests that are unlikely to interfere. Our evaluation suggests that Eve's unique ability to combine execution independence with nondetermistic interleaving of requests enables high-performance replication for multi-core servers while tolerating a wide range of faults, including elusive concurrency bugs.
Clinical implications of autoantibody screening in patients with autoimmune myositis

Objective: To evaluate the clinical usefulness of serum autoantibody profiling in patients with autoimmune myositis. Methods: We retrospectively studied 74 consecutive patients: 68 had definite or probable myositis according to Bohan–Peter criteria, six suffered from antisynthetase syndrome with subclinical myopathy. Myositis specific antibodies (MSA) (anti-ARS, -SRP, -Mi-2) were determined by RNA immunoprecipitation or immunoblot, myositis associated antibodies (MAA) (anti-RoRNP, -U1RNP, -PM/Scl, -Ku) by immunoblot. Results: Forty-three patients (58%) were positive for MSA: anti-Jo-1 in 15/27 polymyositis (PM) (55%), 4/33 dermatomyositis (DM) (12%), 1/8 overlap (12%) and 2/6 antisynthetase syndrome (33%); anti-ARS non-Jo-1 in 1/27 PM (4%), 2/33 DM (6%) and 4/6 antisynthetase syndrome (67%); anti-Mi-2 in 1/27 PM (4%) and 11/33 DM (33%); anti-SRP in 3/27 PM (11%) and 1/33 DM (3%). One patient was anti-Jo-1/Mi-2 positive, one anti-Jo-1/SRP positive. Moreover, 27 patients (36%) were positive for MAA: anti-Ro/SSA in 8/27 PM (30%), 7/33 DM (21%), 1/8 overlap (12%), and 3/6 antisynthetase syndrome (50%); anti-U1RNP in 1/27 PM (3.7%), 1/33 DM (3%), and 2/8 overlap (25%); anti-PM/Scl in 2/8 overlap (25%), anti-Ku in 2/8 overlap (25%). Anti-Jo-1 was predominantly associated with PM, anti-Mi-2 was almost exclusively found in DM patients. Anti-ARS antibodies were closely associated with interstitial lung disease and polyarthritis; notably, anti-ARS non-Jo-1 was more frequent in patients without overt muscle alterations. Anti-Ro/SSA antibody was not associated with any disease subset, but significantly more frequent in antisynthetase syndrome. Conclusions: Searching for MSA and MAA in patients with autoimmmune myositis is recommended because of its diagnostic and clinical value. Anti-ARS non-Jo-1 antibodies seem to preferentially target patients with pulmonary fibrosis without overt myopathy.
Assessment of Endothelial Dysfunction: The Role of Symmetrical Dimethylarginine and Proinflammatory Markers in Chronic Kidney Disease and Renal Transplant Recipients

Objectives. The study was designed to evaluate associations between symmetric dimethylarginine (SDMA), inflammation, and superoxide anion (O2∙−) with endothelial function and to determine their potential for screening of endothelial dysfunction in patients with chronic kidney disease (CKD) and renal transplant (RT) recipients. Materials and Methods. We included 64 CKD and 52 RT patients. Patients were stratified according to brachial artery flow-mediated dilation (FMD). Results. Logistic regression analysis showed that high SDMA and high sensitive C-reactive protein (hs-CRP) were associated with impaired FMD in CKD and RT patients, after adjustment for glomerular filtration rate. The ability of inflammation, SDMA, and O2∙− to detect impaired FMD was investigated by receiving operative characteristic analysis. Hs-CRP (area under the curves (AUC) = 0.754, P < 0.001), IL-6 (AUC = 0.699, P = 0.002), and SDMA (AUC = 0.689, P = 0.007) had the highest ability to detect impaired FMD. SDMA in combination with inflammatory parameters and/or O2∙− had better screening performance than SDMA alone. Conclusions. Our results indicate a strong predictable association between hs-CRP, SDMA, and endothelial dysfunction in CKD patients and RT recipients. The individual marker that showed the strongest discriminative ability for endothelial dysfunction is hs-CRP, but its usefulness as a discriminatory marker for efficient diagnosis of endothelial dysfunction should be examined in prospective studies.
Factors Associated With Exclusive Breastfeeding in the United States

OBJECTIVES: To estimate the proportions of US infants who were breastfed exclusively for 6 months, according to characteristics of the mother, child, and household environment, and to compare associations between those characteristics and exclusive breastfeeding with associations between those characteristics and breastfeeding initiation. METHODS: Data were obtained from the 2007 National Survey of Children's Health, a nationally representative, cross-sectional survey. Multivariate logistic regression was used to calculate the adjusted odds ratios for breastfeeding among all infants and for breastfeeding exclusively for 6 months among infants who had initiated breastfeeding. All analyses were limited to children aged 6 months through 5 years for whom breastfeeding data were available (N = 25 197). RESULTS: Of the nearly 75% of children in the study who had ever been breastfed, 16.8% had been breastfed exclusively for 6 months. Non-Hispanic black children were significantly less likely to have ever been breastfed compared with their non-Hispanic white counterparts (adjusted odds ratio: 0.54 [95% confidence interval: 0.44–0.66]). However, no significant differences in the odds of exclusive breastfeeding according to race were observed. Children with birth weights of <1500 g were most likely to have ever been breastfed and least likely to have been breastfed exclusively. Maternal age was significantly associated with exclusive breastfeeding; however, maternal age was not associated with breastfeeding initiation. CONCLUSIONS: In the United States, the prevalence of exclusive breastfeeding for 6 months remains low among those who initiate breastfeeding. Factors associated with breastfeeding exclusively for 6 months differ from those associated with breastfeeding initiation.
Efficacy of Topically Delivered Moxifloxacin against Wound Infection by Pseudomonas aeruginosa and Methicillin-Resistant Staphylococcus aureus

ABSTRACT Wound infection is a common risk for patients with chronic nonhealing wounds, causing high morbidity and mortality. Currently, systemic antibiotic treatment is the therapy of choice, despite often leading to several side effects and the risk of an insufficient tissue penetration due to impaired blood supply. If systemically delivered, moxifloxacin penetrates well into inflammatory blister fluid, muscle, and subcutaneous adipose tissues and might therefore be a possible option for the topical treatment of skin and infected skin wounds. In this study, topical application of moxifloxacin was investigated in comparison to mupirocin, linezolid, and gentamicin using a porcine wound infection and a rat burn infection model. Both animal models were performed either by an inoculation with methicillin-resistant Staphylococcus aureus (MRSA) or Pseudomonas aeruginosa. Wound fluid, tissue, and blood samples were taken, and bacterial counts as well as the moxifloxacin concentration were determined for a 14-day follow-up. A histological comparison of the rat burn wound tissues was performed. Both strains were susceptible to moxifloxacin and gentamicin, whereas mupirocin and linezolid were effective only against MRSA. All antibiotics showed efficient reduction of bacterial counts, and except with MRSA, infected burn wounds reached bacterial counts below 105 CFU/g tissue. Additionally, moxifloxacin was observed to promote wound healing as determined by histologic analysis, while no induction of bacterial resistance was observed during the treatment period. The use of topical antibiotics for the treatment of infected wounds confers many benefits. Moxifloxacin is therefore an ideal candidate, due to its broad antibacterial spectrum, its high efficiency, and its potential to promote wound healing.
Endothelial function and hemodynamic responses during mental stress.

OBJECTIVE The hemodynamic basis of blood pressure responses during psychological stress shows striking individual differences that share an interesting similarity with risk for cardiovascular disease. Factors accounting for these individual differences are poorly understood. The present study examined the relationship of vascular endothelial function to stress-induced hemodynamic responses. METHODS Subjects were 40 healthy men and women, aged 25 to 44 years. Hemodynamic responses were assessed during exposure to a battery of four diverse laboratory stressors. Endothelium-dependent arterial dilation (EDAD) was measured by ultrasound imaging of the brachial artery in response to reactive hyperemia. RESULTS High EDAD response was associated with lower resting systolic (p < .01) and diastolic blood pressure (p < .05). EDAD response was unrelated to blood pressure responses during stress. However, systemic vascular resistance responses during laboratory stress were significantly greater (p < .02) for individuals with low EDAD responses. CONCLUSIONS Exaggerated systemic vascular resistance responses during stress may reflect endothelial dysfunction. This association may help explain the growing evidence of a relationship between stress hemodynamics and cardiovascular disease risk. The nature of this association is discussed in terms of a possible interplay between the sympathetic nervous system and the endothelium in regulation of vascular tone.