Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular and Phenotypic Characterization of Staphylococcus epidermidis Isolates from Healthy Conjunctiva and a Comparative Analysis with Isolates from Ocular Infection

Staphylococcus epidermidis is a common commensal of healthy conjunctiva and it can cause endophthalmitis, however its presence in conjunctivitis, keratitis and blepharitis is unknown. Molecular genotyping of S. epidermidis from healthy conjunctiva could provide information about the origin of the strains that infect the eye. In this paper two collections of S. epidermidis were used: one from ocular infection (n = 62), and another from healthy conjunctiva (n = 45). All isolates were genotyped by pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec), detection of the genes icaA, icaD, IS256 and polymorphism type of agr locus. The phenotypic data included biofilm production and antibiotic resistance. The results displayed 61 PFGE types from 107 isolates and they were highly discriminatory. MLST analysis generated a total of 25 STs, of which 11 STs were distributed among the ocular infection isolates and lineage ST2 was the most frequent (48.4%), while 14 STs were present in the healthy conjunctiva isolates and lineage ST5 was the most abundant (24.4%). By means of a principal coordinates analysis (PCoA) and a discriminant analysis (DA) it was found that ocular infection isolates had as discriminant markers agr III or agr II, SCCmec V or SCCmec I, mecA gene, resistance to tobramycin, positive biofilm, and IS256+. In contrast to the healthy conjunctiva isolates, the discriminating markers were agr I, and resistance to chloramphenicol, ciprofloxacin, gatifloxacin and oxacillin. The discriminant biomarkers of ocular infection were examined in healthy conjunctiva isolates, and it was found that 3 healthy conjunctiva isolates [two with ST2 and another with ST9] (3/45, 6.66%) had similar genotypic and phenotypic characteristics to ocular infection isolates, therefore a small population from healthy conjunctiva could cause an ocular infection. These data suggest that the healthy conjunctiva isolates do not, in almost all cases, infect the eye due to their large genotypic and phenotypic difference with the ocular infection isolates.
High Risk of Cognitive and Functional Decline after Postoperative Delirium

Background/Aims: The aim of the study was to investigate the association of postoperative delirium with the outcomes of cognitive impairment, functional disability and death. Methods: Hip surgery patients aged 60 years or over (n = 200) underwent preoperative and daily postoperative assessment of their cognitive status during hospital stay. Outcome variables were determined at an average of 8 and 38 months after discharge from hospital. Results: Fourty-one patients developed postoperative delirium. Delirium was a strong independent predictor of cognitive impairment and the occurrence of severe dependency in activities of daily living. The associations were more marked for the long- than for the short-term outcome. Thirty-eight months after discharge from hospital, 53.8% of the surviving patients with postoperative delirium suffered from cognitive impairment, as compared to only 4.4% of the nondelirious participants. Logistic regression analysis adjusted for age, sex, medical comorbidity and preoperative cognitive performance revealed highly significant associations between delirium and cognitive impairment (OR = 41.2; 95% CI = 4.3–396.2), subjective memory decline (OR = 6.2; 95% CI = 1.5–25.8) and incident need for long-term care (OR = 5.6; 95% CI = 1.6–19.7). Conclusion: The present study confirms a poor prognosis after delirium in elderly patients. The findings suggest that delirium does not simply persist for a certain time but also predicts a future cognitive decline with an increased risk of dementia.
Hydroclimate variability of the northwestern Amazon Basin near the Andean foothills of Peru related to the South American Monsoon System during the last 1600 years

In this paper we explore a speleothem δ 18 O record from Palestina cave, northwestern Peru, at a site on the eastern side of the Andes cordillera, in the upper Amazon Basin. The δ 18 O record is interpreted as a proxy for South American Summer Monsoon (SASM) intensity and allows the reconstruction of its variability during the last 1600 years. Two periods of anomalous changes in the climate mean state corresponding to the Medieval Climate Anomaly (MCA) and the Little Ice Age (LIA) periods identified in the Northern Hemisphere are recognized in the record, in which decreased and increased SASM activity, respectively, have been documented. Variations in SASM activity between the MCA and the LIA seem to be larger over the northern part of the continent, suggesting a latitudinal dependence of the MCA footprint. Our results, based on time series, composite and wavelet analyses, suggest that the Atlantic Multidecadal Oscillation (AMO) plays an relevant role for SASM modulation on multidecadal scales (∼65 years), especially during dry periods such as the MCA. Composite analyses, applied to evaluate the influence of the AMO on the Palestina cave δ 18 O and other δ 18 O-derived SASM reconstructions, allow insight into the spatial footprints of the AMO over tropical South America and highlight differences between records during key studied periods. This work also reveals that replicating regional climate signals from different sites, and using different proxies is absolutely essential for a comprehensive understanding of past changes in SASM activity.
Multidrug Resistance Proteins 2 and 3 Provide Alternative Routes for Hepatic Excretion of Morphine-Glucuronides

Glucuronidation is a major hepatic detoxification pathway for endogenous and exogenous compounds, resulting in the intracellular formation of polar metabolites that require specialized transporters for elimination. Multidrug resistance proteins (MRPs) are expressed in the liver and can transport glucuronosyl-conjugates. Using morphine as a model aglycone, we demonstrate that morphine-3-glucuronide (M3G), the predominant metabolite, is transported in vitro by human MRP2 (ABCC2), a protein present in the apical membrane of hepatocytes. Loss of biliary M3G secretion in Mrp2(-/-) mice results in its increased sinusoidal transport that can be attributed to Mrp3. Combined loss of Mrp2 and Mrp3 leads to a substantial accumulation of M3G in the liver, from which it is transported across the sinusoidal membrane at a low rate, resulting in the prolonged presence of M3G in plasma. Our results show that murine Mrp2 and Mrp3 provide alternative routes for the excretion of a glucuronidated substrate from the liver in vivo.
Vaccination with M2e-Based Multiple Antigenic Peptides: Characterization of the B Cell Response and Protection Efficacy in Inbred and Outbred Mice

Background The extracellular domain of the influenza A virus protein matrix protein 2 (M2e) is remarkably conserved between various human isolates and thus is a viable target antigen for a universal influenza vaccine. With the goal of inducing protection in multiple mouse haplotypes, M2e-based multiple antigenic peptides (M2e-MAP) were synthesized to contain promiscuous T helper determinants from the Plasmodium falciparum circumsporozoite protein, the hepatitis B virus antigen and the influenza virus hemagglutinin. Here, we investigated the nature of the M2e-MAP-induced B cell response in terms of the distribution of antibody (Ab) secreting cells (ASCs) and Ab isotypes, and tested the protective efficacy in various mouse strains. Methodology/Principal Findings Immunization of BALB/c mice with M2e-MAPs together with potent adjuvants, CpG 1826 oligonucleotides (ODN) and cholera toxin (CT) elicited high M2e-specific serum Ab titers that protected mice against viral challenge. Subcutaneous (s.c.) and intranasal (i.n.) delivery of M2e-MAPs resulted in the induction of IgG in serum and airway secretions, however only i.n. immunization induced anti-M2e IgA ASCs locally in the lungs, correlating with M2-specific IgA in the bronchio-alveolar lavage (BAL). Interestingly, both routes of vaccination resulted in equal protection against viral challenge. Moreover, M2e-MAPs induced cross-reactive and protective responses to diverse M2e peptides and variant influenza viruses. However, in contrast to BALB/c mice, immunization of other inbred and outbred mouse strains did not induce protective Abs. This correlated with a defect in T cell but not B cell responsiveness to the M2e-MAPs. Conclusion/Significance Anti-M2e Abs induced by M2e-MAPs are highly cross-reactive and can mediate protection to variant viruses. Although synthetic MAPs are promising designs for vaccines, future constructs will need to be optimized for use in the genetically heterogeneous human population.
A computational approach for push recovery in case of multiple noncoplanar contacts

This paper presents a new computational approach for humanoid push recovery in a generalized noncoplanar multicontact context. Our approach is based on a simplified model and consists of two main steps. The first one predicts whether the perturbed system can be stopped in a final static state while maintaining fixed contacts with the environment. This prediction can be seen as a dynamic stability indicator. The second one consists of a strategy that stabilizes the system, when stability cannot be reached, through a contact change chosen as the best one among a set of a priori possible contact changes.
Microgeometry capture and RGB albedo estimation by photometric stereo without demosaicing

We present a photometric stereo-based system for retrieving the RGB albedo and the fine-scale details of an opaque surface. In order to limit specularities, the system uses a controllable diffuse illumination, which is calibrated using a dedicated procedure. In addition, we rather handle RAW, non-demosaiced RGB images, which both avoids uncontrolled operations on the sensor data and simplifies the estimation of the albedo in each color channel and of the normals. We finally show on real-world examples the potential of photometric stereo for the 3D-reconstruction of very thin structures from a wide variety of surfaces.
PCR-based cystic fibrosis (CF) carrier screening in a first-year medical student biochemistry laboratory.

nome Initiative, lead to the identification of ever more disease-related genes, we are beginning to appreciate that virtually all disorders have an important genetic component. Even some of the major "somatic" disorders such as cardiovascular disease and cancer are coming to be thought of as genetic diseases that are diagnosable, and perhaps someday treatable, at the DNA level. Many feel that medical school curricula have been slow to adapt to these changes and that at most institutions genetics is still given short shrift. Yet there is no question that today's medical students, who will be practicing in the 21st century, will have to be conversant with molecular genetic methods of diagnosis and, eventually, treatment. The few courses that are now offered do not seem to result in adequate knowledge retention even into the immediate postgraduate years. At our own institution, for example, we are often frustrated by clinical staff who order a complex Southern blot test (for example, a clonal gene rearrangement
The Telefonica Research Spoken Web Search System for MediaEval 2013

In this paper we describe the system proposed by Telefonica research for the Spoken Web Search (SWS) task [3] within the Mediaeval 2013 evaluation. This is the third year we participate in the evaluation and this time we have submitted a system based on the recently proposed Information Retrieval-based Dynamic Time Warping (IR-DTW) Algorithm. This algorithm performs a pattern matching search at frame level similar to the DTW algorithm, but with advantages in memory usage and the possibility to with preindex the search corpora and use fast retrieval techniques. Results obtained this year have been poorer than expected, most probably due to the use of a global voice activity detector that was not adequate to the varying nature of the dierent acoustic conditions in this year’s search corpora.
Effects of centrally acting ACE inhibitors on the rate of cognitive decline in dementia

Objectives There is growing evidence that antihypertensive agents, particularly centrally acting ACE inhibitors (CACE-Is), which cross the blood–brain barrier, are associated with a reduced rate of cognitive decline. Given this, we compared the rates of cognitive decline in clinic patients with dementia receiving CACE-Is (CACE-I) with those not currently treated with CACE-Is (NoCACE-I), and with those who started CACE-Is, during their first 6 months of treatment (NewCACE-I). Design Observational case–control study. Setting 2 university hospital memory clinics. Participants 817 patients diagnosed with Alzheimer's disease, vascular or mixed dementia. Of these, 361 with valid cognitive scores were included for analysis, 85 CACE-I and 276 NoCACE-I. Measurements Patients were included if the baseline and end-point (standardised at 6 months apart) Standardised Mini-Mental State Examination (SMMSE) or Quick Mild Cognitive Impairment (Qmci) scores were available. Patients with comorbid depression or other dementia subtypes were excluded. The average 6-month rates of change in scores were compared between CACE-I, NoCACE-I and NewCACE-I patients. Results When the rate of decline was compared between groups, there was a significant difference in the median, 6-month rate of decline in Qmci scores between CACE-I (1.8 points) and NoCACE-I (2.1 points) patients (p=0.049), with similar, non-significant changes in SMMSE. Median SMMSE scores improved by 1.2 points in the first 6 months of CACE treatment (NewCACE-I), compared to a 0.8 point decline for the CACE-I (p=0.003) group and a 1 point decline for the NoCACE-I (p=0.001) group over the same period. Multivariate analysis, controlling for baseline characteristics, showed significant differences in the rates of decline, in SMMSE, between the three groups, p=0.002. Conclusions Cognitive scores may improve in the first 6 months after CACE-I treatment and use of CACE-Is is associated with a reduced rate of cognitive decline in patients with dementia.
Development, optimization, and validation of novel anti-TEM1/CD248 affinity agent for optical imaging in cancer

Tumor Endothelial Marker-1 (TEM1/CD248) is a tumor vascular marker with high therapeutic and diagnostic potentials. Immuno-imaging with TEM1-specific antibodies can help to detect cancerous lesions, monitor tumor responses, and select patients that are most likely to benefit from TEM1-targeted therapies. In particular, near infrared(NIR) optical imaging with biomarker-specific antibodies can provide real-time, tomographic information without exposing the subjects to radioactivity. To maximize the theranostic potential of TEM1, we developed a panel of all human, multivalent Fc-fusion proteins based on a previously identified single chain antibody (scFv78) that recognizes both human and mouse TEM1. By characterizing avidity, stability, and pharmacokinectics, we identified one fusion protein, 78Fc, with desirable characteristics for immuno-imaging applications. The biodistribution of radiolabeled 78Fc showed that this antibody had minimal binding to normal organs, which have low expression of TEM1. Next, we developed a 78Fc-based tracer and tested its performance in different TEM1-expressing mouse models. The NIR imaging and tomography results suggest that the 78Fc-NIR tracer performs well in distinguishing mouse- or human-TEM1 expressing tumor grafts from normal organs and control grafts in vivo. From these results we conclude that further development and optimization of 78Fc as a TEM1-targeted imaging agent for use in clinical settings is warranted.
Theoretical Fashions in Crowdsourcing: A Snapshot of IS Research

When new information technologies emerge, they stimulate the curiosity of Information System (IS) research and practice. Research and practices regarding emerging technologies can be characterized as IS fashions, which can lead to IS innovations. Yet, researchers and practitioners often wonder if these fashions are the next big thing or just a passing fad. One way to determine the contribution of a scientific fashion is to understand its theoretical state and maturity as reported in the literature. We performed a theoretical assessment of one specific IS fashion: crowdsourcing. The main objective of our research is to understand the characteristics of theories in crowdsourcing research and to determine the origins of these theories. Using Gregor’s (2006) taxonomy, we performed a systematic literature review to identify and categorize the type of theories developed and used in crowdsourcing research. Close to forty percent of the surveyed articles are explanatory in nature, focusing on cause and effects relationships. Most articles use established theories to motivate research questions or hypotheses. Least common is theoretical research to motivate the design of crowdsourcing related artifacts.
Users' brands preference based on SVD++ in recommender systems

Recommender systems provide users with personalized suggestions about products or services. General task of recommender systems is to improve recommendation accuracy, but this paper mostly focuses on improving the degree of surprise, using SVD++ (singular value decomposition) model. First, logistic regression method is used to process raw data including different sorts of user actions on brands, such as click, shopping cart and buy, so that user-brand ratings are obtained. Then SVD++ model is used to analyze the processed data. A better RMSE(root mean square error) is achieved through adjusting parameters, so the system recommend new brands which users have no actions before to improve users' the degree of surprise. Model presented here is applied to analyze Tmall data, and the result proves its efficiency.
Formant shifting for speech intelligibility improvement in car noise environment

In this paper, we propose a novel approach aiming at improving the intelligibility of speech in the context of in-car applications. Speech produced in noisy environments is subject to the Lombard effect which gathers a number of voice transformation effects compared to the speech produced in calm environments. To improve intelligibility of in car speech (radio, message alerts, .), we propose to modify the original speech signal by incorporating one of the important Lombard effect, namely the shift of the lower formant center frequencies away from the competing noise regions. The proposed approach exploits traditional Linear Prediction analysis and overlap and add synthesis. We explore several modification strategies and the merit of each modification is evaluated using both objective and subjective tests. It is in particular shown that the improvement of speech intelligibility in car noise is significantly improved for a majority of listeners.
Under Consideration for Publication in Formal Aspects of Computing Validating a Web Service Security Abstraction by Typing

An XML web service is, to a first approximation, an RPC service in which requests and responses are encoded in XML as SOAP envelopes, and transported over HTTP. We consider the problem of authenticating requests and responses at the SOAP-level, rather than relying on transport-level security. We propose a security abstraction, inspired by earlier work on secure RPC, in which the methods exported by a web service are annotated with one of three security levels: none, authenticated, or both authenticated and encrypted. We model our abstraction as an object calculus with primitives for defining and calling web services. We describe the semantics of our object calculus by translating to a lower-level language with primitives for message passing and cryptography. To validate our semantics, we embed correspondence assertions that specify the correct authentication of requests and responses. By appeal to the type theory for cryptographic protocols of Gordon and Jeffrey's Cryptyc, we verify the correspondence assertions simply by typing. Finally, we describe an implementation of our semantics via custom SOAP headers.
Lab report special section: the University of Massachusetts Center for Intelligent Information Retrieval

The Center for Intelligent Information Retrieval in the Computer Science Department is an NSFsponsored center that is supported by the State of Massachusetts, the Federal government, and industrial members. More than 50 students, professionals, and faculty are involved in a broad range of basic research and technology transfer programs. The faculty involved are Jamie Callan, Wendy Lehnert, Victor Lesser, Kathryn McKinley, Elliot Moss, and Edwina Rissland.
Functional burst imaging

A quiet magnetic resonance (MR) imaging technique for detecting changes in cerebral activity functions is presented. This single‐shot method, functional Burst imaging (FBI), combines elements of Burst imaging with an offset technique known as asymmetric spin echo (ASE). The FBI sequence has the unique feature of being nearly silent, because of the low number of gradient switching steps involved. Furthermore, this approach has the key advantage that it can be implemented on conventional MR systems. Established auditory and visual paradigms were used to evaluate whether FBI can detect changes in cerebral activity using a 1.5 Tesla MR system. In a second set of experiments, the FBI technique was used to evaluate cerebral activity changes during different sleep stages in humans. The results obtained demonstrate that the FBI sequence provides an alternative approach for functional imaging of brain activity in primary and secondary sensory areas of the human brain. Furthermore, in using this quiet MR technique, it was possible to scan continuously during different stages of human sleep without acoustic noise perturbation.
An Alternative Logic Approach to Implement High-Speed Low-Power Full Adder Cells

This paper presents a high-speed low-power 1-bit full adder cell designed upon an alternative logic structure to derive the SUM and CARRY outputs. Hspice and Nanosim simulations show that this full adder cell designed using a 0.35¿m CMOS technology and supplied with 3.3V, exhibits delay and power dissipation around 720ps and 840¿W, respectively. These features reflect an overall improvement of 30% in the power-delay metric, when compared with the performance of other realizations recently published as well featured cells for low-power applications.
Partial Completeness of Abstract Fixpoint Checking (Invited paper)

Abstract interpretation is used in program static analysis and model checking to cope with infinite state spaces and/or with com­ puter resource limitations. One common problem is to check abstract fixpoints for specifications. The abstraction is partially complete when the checking algorithm is exact in that, if the algorithm ever terminates, its answer is always affirmative for correct specifications. We character­ ize partially complete abstractions for various abstract fixpoint checking algorithms, including new ones, and show that the computation of com­ plete abstract domains is essentially equivalent to invariance proofs that is to concrete fixpoint checking.