Miracle-dz/UniFAR-FTUs huggingface dataset:
Massive Parallel Sequencing Provides New Perspectives on Bacterial Brain Abscesses

ABSTRACT Rapid development within the field of massive parallel sequencing (MPS) is about to bring this technology within reach for diagnostic microbiology laboratories. We wanted to explore its potential for improving diagnosis and understanding of polymicrobial infections, using bacterial brain abscesses as an example. We conducted a prospective nationwide study on bacterial brain abscesses. Fifty-two surgical samples were included over a 2-year period. The samples were categorized as either spontaneous intracerebral, spontaneous subdural, or postoperative. Bacterial 16S rRNA genes were amplified directly from the specimens and sequenced using Ion Torrent technology, with an average of 500,000 reads per sample. The results were compared to those from culture- and Sanger sequencing-based diagnostics. Compared to culture, MPS allowed for triple the number of bacterial identifications. Aggregatibacter aphrophilus, Fusobacterium nucleatum, and Streptococcus intermedius or combinations of them were found in all spontaneous polymicrobial abscesses. F. nucleatum was systematically detected in samples with anaerobic flora. The increased detection rate for Actinomyces spp. and facultative Gram-negative rods further revealed several species associations. We suggest that A. aphrophilus, F. nucleatum, and S. intermedius are key pathogens for the establishment of spontaneous polymicrobial brain abscesses. In addition, F. nucleatum seems to be important for the development of anaerobic flora. MPS can accurately describe polymicrobial specimens when a sufficient number of reads is used to compensate for unequal species concentrations and principles are defined to discard contaminant bacterial DNA in the subsequent data analysis. This will contribute to our understanding of how different types of polymicrobial infections develop.
Mitochondrial DNA Targets Increase Sensitivity of Malaria Detection Using Loop-Mediated Isothermal Amplification

ABSTRACT Loop-mediated isothermal amplification (LAMP) of DNA offers the ability to detect very small quantities of pathogen DNA following minimal tissue sample processing and is thus an attractive methodology for point-of-care diagnostics. Previous attempts to diagnose malaria by the use of blood samples and LAMP have targeted the parasite small-subunit rRNA gene, with a resultant sensitivity for Plasmodium falciparum of around 100 parasites per μl. Here we describe the use of mitochondrial targets for LAMP-based detection of any Plasmodium genus parasite and of P. falciparum specifically. These new targets allow routine amplification from samples containing as few as five parasites per μl of blood. Amplification is complete within 30 to 40 min and is assessed by real-time turbidimetry, thereby offering rapid diagnosis with greater sensitivity than is achieved by the most skilled microscopist or antigen detection using lateral flow immunoassays.
Transparent quantization of speech LSP parameters based on KLT and 2-D-prediction

Abstruct- In this correspondence, a two-stage approach based on Karhunen-Loeve transform and 2-D prediction is proposed for efficient quantization of line spectrum pair (LSP) parameters of speech. Besides, a switched classifier is incorporated with this approach to reduce the outlier frames (spectral distortion greater than 2 dB) down to about 0.27% and to eliminate frames with spectral distortion greater than 4 dB at an average bit-rate below 19 b/frame.
The effectiveness of Colourful Semantics on narrative skills in children with intellectual disabilities in Sri Lanka

Background: Children diagnosed with intellectual difficulties experience difficulties with narrative skills, due to limited syntactic knowledge. The Colourful Semantics approach with thematic roles and a colour coding system may encourage syntactic development in children experiencing intellectual disabilities. Aim: To evaluate the effectiveness of using the Colourful Semantics approach to develop narrative skills in Sri Lankan Tamil-speaking children diagnosed with intellectual difficulties. Methods: Thirty Sri Lankan Tamil-speaking children identified with intellectual difficulties were included. The Colourful Semantics approach was offered twice a week for 6 weeks, facilitated by the class teachers. Pre- and post-intervention narrative skill assessments were undertaken and analysed for content and syntactic structures. Results: The results indicate positive changes post-intervention on the qualitative and quantitative narrative skills measures undertaken on content and syntactic structures. Conclusions and Implications: The Colourful Semantics approach is an effective therapy approach to support development of narrative skills in children with intellectual difficulties.
Relaxation therapy and anxiety, self-esteem, and emotional regulation among adults with intellectual disabilities

This pilot study is a randomized controlled trial on the effects of relaxation on anxiety, self-esteem, and emotional regulation in adults with intellectual disabilities (ID) working in a center of supported employment in France. We studied 30 adults with mild or moderate ID who were split at random into a relaxation group (RG, 15 subjects), who completed 10 sessions of relaxation therapy, and a control group (CG, 15 subjects), who were on a waiting list. The method used is the pretest and posttest. Variables were assessed by the State-Trait Anxiety Inventory form Y scale, the Rosenberg Self-Esteem scale, and the Emotion Regulation Questionnaire. We found that in the RG, relaxation significantly reduced state anxiety, t(14, 15) = 17.8***, d = −0.72, and improved self-esteem, t(14, 15) = −7.7***, d = 1.03, and cognitive reappraisal, t(14, 15) = −6.3***, d = 1.3, while the CG showed no change for these variables. We conclude that relaxation seems to be an interesting therapeutic option for reducing anxiety in people with ID in a supported employment setting.
A review of research on direct-care staff data collection regarding the severity and function of challenging behavior in individuals with intellectual and developmental disabilities

In working with individuals with intellectual and developmental disabilities (IDDs), it is direct care staff who are often required to collect data on individuals’ behavior which is used as the basis for implementation of empirically based approaches for intervention and treatment. Due to limited resources, indirect and descriptive measures of challenging behaviors are employed to analyze the function of individuals’ behaviors in place of the preferred method of multimodal assessment, which includes experimental functional analysis. To ensure the most effective services and support to individuals with IDDs, accurate and consistent data collection is critical. In this article, we highlight the importance of accurate data collection practices, conduct a comparison of data collection methods, and discuss limitations . … and barriers for staff. The article concludes with recommendations for best practices and future research.
ICDAR 2013 Competitions on Signature Verification and Writer Identification for On- and Offline Skilled Forgeries (SigWiComp 2013)

This paper presents the results of the ICDAR2013 competitions on signature verification and writer identification for on- and offline skilled forgeries jointly organized by PR researchers and Forensic Handwriting Examiners (FHEs). The aim is to bridge the gap between recent technological developments and forensic casework. Two modalities (signatures, and handwritten text) are considered where training and evaluation data (in Dutch and Japanese) were collected and provided by FHEs and PR-researchers. Four tasks were defined where the systems had to perform Dutch offline signature verification, Japanese offline signature verification, Japanese online signature verification, and Dutch writer identification. The participants of the signatures modality were motivated to report their results in Likelihood Ratios (LR). This has made the systems even more interesting for application in forensic casework. For evaluation of signatures modality, we used both the traditional Equal Error Rate (EER) and forensically substantial Cost of Log Likelihood Ratios (Ĉllr). The system having the smallest value of the Minimum Cost of Log Likelihood Ratio (Ĉllrmin) is declared winner. For evaluation of the handwritten text modality, we used the precision and accuracy measures and winners are announced on the basis of best F-measure value.
Evaluation of the Aptima HIV-1 Quant Dx Assay for HIV-1 RNA Quantitation in Different Biological Specimen Types

ABSTRACT The search for a cure for HIV infection has highlighted the need for increasingly sensitive and precise assays to measure viral burden in various tissues and body fluids. We describe the application of a standardized assay for HIV-1 RNA in multiple specimen types. The fully automated Aptima HIV-1 Quant Dx assay (Aptima assay) is FDA cleared for blood plasma HIV-1 RNA quantitation. In this study, the Aptima assay was applied for the quantitation of HIV RNA in peripheral blood mononuclear cells (PBMCs; n = 72), seminal plasma (n = 20), cerebrospinal fluid (CSF; n = 36), dried blood spots (DBS; n = 104), and dried plasma spots (DPS; n = 104). The Aptima assay was equivalent to or better than commercial assays or validated in-house assays for the quantitation of HIV RNA in CSF and seminal plasma. For PBMC specimens, the sensitivity of the Aptima assay in the detection of HIV RNA decayed as background uninfected PBMC counts increased; proteinase K treatment demonstrated some benefit in restoring signal at higher levels of background PBMCs. Finally, the Aptima assay yielded 100% detection rates of DBS in participants with plasma HIV RNA levels of ≥35 copies/ml and 100% detection rates of DPS in participants with plasma HIV RNA levels of ≥394 copies/ml. The Aptima assay can be applied to a variety of specimens from HIV-infected subjects to measure HIV RNA for studies of viral persistence and cure strategies. It can also detect HIV in dried blood and plasma specimens, which may be of benefit in resource-limited settings.
ICDAR 2013 Table Competition

Table understanding is a well studied problem in document analysis, and many academic and commercial approaches have been developed to recognize tables in several document formats, including plain text, scanned page images and born-digital, object-based formats such as PDF. Despite the abundance of these techniques, an objective comparison of their performance is still missing. The Table Competition held in the context of ICDAR 2013 is our first attempt at objectively evaluating these techniques against each other in a standardized way, across several input formats. The competition independently addresses three problems: (i) table location, (ii) table structure recognition, and (iii) these two tasks combined. We received results from seven academic systems, which we have also compared against four commercial products. This paper presents our findings.
Speech balloon and speaker association for comics and manga understanding

Comics and manga are one of the most important forms of publication and play a major role in spreading culture all over the world. In this paper we focus on balloons and their association to comic characters or more generally text and graphic links retrieval. This information is not directly encoded in the image, whether scanned or digital-born, it has to be understood according to other information present in the image. Such high level information allows new browsing experience and story understanding (e.g. dialog analysis, situation retrieval). We propose a speech balloon and comic character association method able to retrieve which character is emitting which speech balloon. The proposed method is based on geometric graph analysis and anchor point selection. This work has been evaluated over various comic book styles from the eBDtheque dataset and also a volume of the Kingdom manga series.
Cost Optimization of Elasticity Cloud Resource Subscription Policy

In cloud computing, resource subscription is an important procedure which enables customers to elastically subscribe to IT resources based on their service requirements. Resource subscription can be divided into two categories, namely long-term reservation and on-demand subscription. Although customers need to pay the upfront fee for a long-term reservation contract, the usage charge of reserved resources is generally much cheaper than that of the on-demand subscription. To provide a better Internet service by using cloud resource, service operators will expect to make a trade-off between the amount of long-term reserved resources and that of on-demand subscribed resources. Therefore, how to properly make resource provision plans is a challenging issue. In this paper, we present a two-phase algorithm for service operators to minimize their service provision cost. In the first phase, we propose a mathematical formulae to compute the optimal amount of long-term reserved resources. In the second phase, we use the Kalman filter to predict resource demand and adaptively change the subscribed on-demand resources such that provision cost could be minimized. We evaluated our solution by using real-world data. Our numerical results indicated that the proposed mechanisms are able to significantly reduce the provision cost.
Table Detection Using Deep Learning

Table detection is a crucial step in many document analysis applications as tables are used for presenting essential information to the reader in a structured manner. It is a hard problem due to varying layouts and encodings of the tables. Researchers have proposed numerous techniques for table detection based on layout analysis of documents. Most of these techniques fail to generalize because they rely on hand engineered features which are not robust to layout variations. In this paper, we have presented a deep learning based method for table detection. In the proposed method, document images are first pre-processed. These images are then fed to a Region Proposal Network followed by a fully connected neural network for table detection. The proposed method works with high precision on document images with varying layouts that include documents, research papers, and magazines. We have done our evaluations on publicly available UNLV dataset where it beats Tesseract's state of the art table detection system by a significant margin.
Molecular Epidemiology of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Isolates from Global Clinical Trials

ABSTRACT Determining the genetic characteristics of Staphylococcus aureus is important for better understanding of the global and dynamic epidemiology of this organism as we witness the emergence and spread of virulent and antibiotic-resistant clones. We genotyped 292 S. aureus isolates (105 methicillin resistant and 187 methicillin susceptible) using a combination of pulsed-field gel electrophoresis, multilocus sequence typing, and SCCmec typing. In addition, S. aureus isolates were tested for the presence of the Panton-Valentine leukocidin (PVL) genes. Isolates were recovered from patients with uncomplicated skin infections in 10 different countries during five phase III global clinical trials of retapamulin, a new topical antibiotic agent. The most common methicillin-resistant clone had multilocus sequence type 8, pulsed-field type USA300, and SCCmec type IV and possessed the PVL genes. This clone was isolated exclusively in the United States. The most common PVL-positive, methicillin-susceptible clone had multilocus sequence type 121 and pulsed-field type USA1200. This clone was found primarily in South Africa and the Russian Federation. Other clones were found at lower frequencies and were limited in their geographic distribution. Overall, considerable genetic diversity was observed within multilocus sequence type clonal complexes and pulsed-field types.
Epidural volume extension with saline in combined spinal epidural anesthesia for dynamic hip screw surgeries using low dose of intrathecal hyperbaric bupivacaine

Background Combined spinal epidural (CSE) anesthesia is the preferred and widely used method for lower limb orthopedic surgeries. The epidural volume extension (EVE) technique is a modification of CSE in which the level of sensory analgesia obtained by subarachnoid block is increased by a small volume of saline administered through the epidural catheter. Patients and methods Fifty patients of both sexes, aged between 50 and 70 years scheduled for dynamic hip screw surgery were enrolled in the study. Patients were divided into two groups: group I (the CSE-EVE group) included 25 patients who were anesthetized using CSE with EVE and group II (the CSE group) included patients who were anesthetized using CSE without EVE, using the same technique and the same dose of intrathecal hyperbaric bupivacaine and fentanyl. Results Regarding all demographic data (age, height, weight, sex, and duration of operation), there were no statistically significant differences between the studied groups (P = 0.248, 0.901, 0.064, 0.564, and 0.967, respectively). Regarding the block profile, there was a statistically significant difference between the two groups regarding the level of maximal sensory block (P < 0.02), as five patients (20%) of group I showed sensory block level extended to T1-T2 and 20 patients (80%) showed sensory block below T2, whereas in group II, the sensory block level in all patients was limited below T2. The time required for reaching the maximal sensory block level was faster in group I, ranging from 8 to 15 min (mean ± SD: 10.7 ± 1.7), whereas in group II the time ranged from 9 to 16 min (mean ± SD: 13.4 ± 2.4; P < 0.001). Two-segment regression was faster in group II, ranging from 60 to 80 min (mean ± SD: 67.9 ± 5.1), whereas in group I it ranged from 70 to 95 min (mean ± SD: 81.0 ± 7.3; P < 0.001). The time required to reach the maximum motor block was faster in group I, ranging from 3 to 5 min (mean ± SD: 3.8 ± 0.5), whereas in group II the time ranged from 4.5 to 7.5 min (mean ± SD: 6.1 ± 0.8; P < 0.001). A volume of 10 ml bupivacaine 0.5% was injected by epidural catheter in 16 patients (64%) in group II, whereas only four patients (16%) in group I required activation of epidural anesthesia (P < 0.001). The systolic blood pressure and heart rate showed no significant changes between the two groups. Conclusion It can be concluded that low dose of intrathecal hyperbaric bupivacaine with EVE (10 ml saline) is associated with early onset of motor and sensory block, high level of sensory block, and shorter time of two-segment regression while maintaining hemodynamic stability.
The Interrogator: Protocol Secuity Analysis

The Interrogator is a Prolog program that searches for security vulnerabilities in network protocols for automatic cryptographic key distribution. Given a formal specification of the protocol, it looks for message modification attacks that defeat the protocol objective. It is still under developement, but is has been able to rediscover a known vulnerability in a published protocol. It is implemented in LM-Prolog on a Lisp Machine, with a graphical user interface.
Molecular Types of Methicillin-Resistant Staphylococcus aureus and Methicillin-Sensitive S. aureus Strains Causing Skin and Soft Tissue Infections and Nasal Colonization, Identified in Community Health Centers in New York City

ABSTRACT In November 2011, The Rockefeller University Center for Clinical and Translational Science (CCTS), the Laboratory of Microbiology and Infectious Diseases, and Clinical Directors Network (CDN) launched a research and learning collaborative project with six community health centers in the New York City metropolitan area to determine the nature (clonal type) of community-acquired Staphylococcus aureus strains causing skin and soft tissue infections (SSTIs). Between November 2011 and March 2013, wound and nasal samples from 129 patients with active SSTIs suspicious for S. aureus were collected and characterized by molecular typing techniques. In 63 of 129 patients, the skin wounds were infected by S. aureus: methicillin-resistant S. aureus (MRSA) was recovered from 39 wounds and methicillin-sensitive S. aureus (MSSA) was recovered from 24. Most—46 of the 63–wound isolates belonged to the CC8/Panton-Valentine leukocidin-positive (PVL+) group of S. aureus clone USA300: 34 of these strains were MRSA and 12 were MSSA. Of the 63 patients with S. aureus infections, 30 were also colonized by S. aureus in the nares: 16 of the colonizing isolates were MRSA, and 14 were MSSA, and the majority of the colonizing isolates belonged to the USA300 clonal group. In most cases (70%), the colonizing isolate belonged to the same clonal type as the strain involved with the infection. In three of the patients, the identity of invasive and colonizing MRSA isolates was further documented by whole-genome sequencing.
The Psychology of Competition

Social comparison—the tendency to self-evaluate by comparing ourselves to others—is an important source of competitive behavior. We propose a new model that distinguishes between individual and situational factors that increase social comparison and thus lead to a range of competitive attitudes and behavior. Individual factors are those that vary from person to person: the relevance of the performance dimension, the similarity of rivals, and their relationship closeness to the individual, as well as the various individual differences variables relating to social comparison more generally. Situational factors, conversely, are those factors on the social comparison landscape that affect similarly situated individuals: proximity to a standard (i.e., near the number 1 ranking vs. far away), the number of competitors (i.e., few vs. many), social category fault lines (i.e., disputes across vs. within social categories), and more. The distinction between individual and situational factors also helps chart future directions for social comparison research and generates new vistas across psychology and related disciplines.
Group communication in the Amoeba distributed operating system

Primitives for broadcast communication that have been integrated with the Amoeba distributed operating system are introduced. The semantics of the broadcast primitives are simple and easy to understand, but are still powerful. The proposed primitives, for example, guarantee global ordering of broadcast messages. The proposed primitives are also efficient: a reliable broadcast can be done in just slightly more than two messages, so the performance is comparable to a remote procedure call. In addition, the primitives are flexible; user applications can, for example, trade performance against fault-tolerance. <<ETX>>
Crash recovery with little overhead

Recovering from processor failures in distributed systems is an important problem in the design and development of reliable systems. Two solutions to this problem which involve very little overhead are presented. Without appending any information to the messages of the application program, it is shown that it is possible to recover from failures using O( mod V mod mod E mod ) messages where mod V mod is the number of processors and mod E mod is the number of communication links in the system. The second algorithm can be used to recover from processor failures without forcing nonfaulty processors to roll back under certain conditions. <<ETX>>