Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of O157:H7 and non-O157 E. coli in Iranian domestic sheep.

The aim of the present study was the isolation of both E. coli O157 and non-O157 in sheep. Verotoxins (VT) 1, 2 and eae genes were tested for this propose. Sheep faces are an important source of Shiga toxin-producing Escherichia coli (STEC). Escherichia coli O157:H7 is a highly virulent food-borne pathogen and threat to public health. Rectal swab samples from sheep were collected during 2009-2010. Conventional plating and Polymerase Chain Reaction (PCR) were carried out according to virulence factors (Stx1, Stx2 and eaeA). There significant differences between prevalence of STEC and session were observed. It was at highest in spring and late summer. Six (3.92%) sheep carcasses were contaminated by E. coli O157:H7.Only six samples were positive by PCR specific for the VT2 gene and produced verocytotoxin VT2, whereas all isolates were negative for the presence of VT1 and eae virulence genes considered. Geographical variations and season may be influenced in the prevalence rate. The composition of the gastrointestinal flora may be changed by different diet and, therefore O157 STEC rate in sheep and lamb was different. Iranian sheep indicated as a natural host of E. coli O157 strains therefore, may be potentially pathogenic for humans. This is the first report of E. coli O157 detection from sheep in Iran.
KYOTO Project

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Mobile technology to empower people with Diabetes Mellitus: Design and development of a mobile application

Recent advances in information and communication technologies permitted the design and development of new patient-centric models for the provision of better health care services and enhancement of patient's self-management. This paper presents a prototype mobile phone application which is being designed to improve the self-management of individuals with Type 1 Diabetes Mellitus (T1DM). The developed application using the Microsoft . Net framework runs on 3G mobile phones. The application consists of five major interfaces for the management of: blood glucose measurements, blood pressure measurements, insulin dosage, food/drink intake and physical activity. Furthermore, the user has the following capabilities i) to keep notes, and ii) in case of an emergency to press a button, in order to transmit immediately his/her position to both an emergency call center, and the attendant physician. It has to be noted, that the above mentioned data are stored locally to the mobile phone, and regularly transmitted via the mobile network to a dedicated hospital web-server. Technical evaluation of the prototype indicates that the use of the mobile network makes feasible the self-management of T1DM.
Homogenization of evolutionary Stokes-Cahn-Hilliard equations for two-phase porous media flow

We consider homogenization of a phase-field model for two-phase immiscible, incompressible porous media flow with surface tension effects. The pore-scale model consists of a strongly coupled system of time-dependent Stokes-Cahn-Hilliard equations. In the considered model the fluids are separated by an evolving diffuse interface of a finite width, which is assumed to be independent of the scale parameter ε. We obtain upscaled equations for the considered model by a rigorous two-scale convergence approach.
Convergence rate of structural risk minimization principle on quasi-probability space

In this paper, the concepts of annealed entropy, growth function and VC dimension are proposed on quasi-probability space; the rate of uniform convergence of structural risk minimization principle based on VC dimension on quasi-probability space are given and proven. These lay the theoretical basis to systematically establish statistical learning theory and construe support vector machine on quasi-probability.
Guest Editors' Introduction: Speeding Up Analog Integration and Test for Mixed-Signal SoCs

The seven articles in this special section initiatives to standardize methods, measurements, and tools that support mixed-signal design. The papers are organized along the lines of the overall design-to-test flow, covering verification, selection of test content, defect level estimation, silicon validation, and data-driven test optimization and yield recovery. Presents examples on how to perform comprehensive verification, how to measure and ensure adequate analog test coverage, and how to create and track a specification compliance matrix across the entire design-to-manufacturing flow.
Mismatch Repair Proteins MSH2, MLH1, and EXO1 Are Important for Class-Switch Recombination Events Occurring in B Cells That Lack Nonhomologous End Joining

In the absence of core nonhomologous end-joining (NHEJ) factors, Ab gene class-switch recombination (CSR) uses an alternative end-joining (A-EJ) pathway to recombine switch (S) region DNA breaks. Previous reports showing decreased S-junction microhomologies in MSH2-deficient mice and an exonuclease 1 (EXO1) role in yeast microhomology-mediated end joining suggest that mismatch repair (MMR) proteins might influence A-EJ–mediated CSR. We have directly investigated whether MMR proteins collectively or differentially influence the A-EJ mechanism of CSR by analyzing CSR in mice deficient in both XRCC4 and individual MMR proteins. We find CSR is reduced and that Igh locus chromosome breaks are reduced in the MMR/XRCC4 double-deficient B cells compared with B cells deficient in XRCC4 alone, suggesting MMR proteins function upstream of double-strand break formation to influence CSR efficiency in these cells. Our results show that MLH1, EXO1, and MSH2 are all important for efficient A-EJ–mediated CSR, and we propose that MMR proteins convert DNA nicks and point mutations into dsDNA breaks for both C-NHEJ and A-EJ pathways of CSR. We also find Mlh1-XRCC4− B cells have an increased frequency of direct S junctions, suggesting that MLH1 proteins may have additional functions that influence A-EJ–mediated CSR.
Construction of delta aroA his delta pur strains of Salmonella typhi

Salmonella typhi strains with two deletion mutations, each causing an attenuating auxotrophy, have been constructed from strains Ty2 and CDC 10-80 for possible use as oral-route live vaccines. An aroA(serC)::Tn10 transposon insertion was first transduced from a Salmonella typhimurium donor into each wild-type S. typhi strain. Transductants of the Aro- SerC- phenotype were treated with transducing phage grown on an S. typhimurium strain with an extensive deletion at aroA; selection for SerC+ yielded transductants, some of which were delta aroA. A his mutation was next inserted into a delta aroA strain in each line by two steps of transduction. Two deletions affecting de novo purine biosynthesis were used as second attenuating mutations: delta purHD343, causing a requirement for hypoxanthine (or any other purine) and thiamine, and delta purA155, causing an adenine requirement. The purHD343 deletion was introduced into the delta aroA his derivatives of each strain by cotransduction with purH::Tn10, and the purA155 deletion was introduced into the CDC 10-80 delta aroA his derivative by cotransduction with an adjacent silent Tn10 insertion by selection for tetracycline resistance. Tetracycline-sensitive mutants of each of the three delta aroA his delta pur strains were isolated by selection for resistance to fusaric acid. The tetracycline-sensitive derivative of the CDC 10-80 delta aroA his delta purA155 strain, designated 541Ty, and its Vi-negative mutant, 543Ty, constitute the candidate oral-route live-vaccine strains used in a recent volunteer trail (M. M. Levine, D. Herrington, J. R. Murphy, J. G. Morris, G. Losonsky, B. Tall, A. A. Lindberg, S. Stevenson, S. Baqar, M. F. Edwards, and B. A. D. Stocker, J. Clin. Invest. 79:885-902, 1987). Tetracycline-sensitive mutants of the delta aroA his delta purHD derivative of strains Ty2 and CDC 10-80 may also be appropriate as live vaccines but have not been tested as such.
Medline Abstracts Classification - Average-based Discrimination for Noun Phrases Selection and Weighting Applied to Categorization of Medline Abstracts

In a parallel processing array wherein each processor therein issues a ready signal to signify that it is ready to begin a parallel processing task and initiates the task upon receipt of an initiate signal the parallel processing array is rendered partitionable into parallel processing subarrays by a control node tree having a plurality of control nodes connected to the plurality of processors and in decreasing levels to each other in a tree-like fashion down to a single root node. Each node is controlled to function as a non-root wherein it receives a ready signal from its processor side and passes it along toward the single root node or as a root node whereupon receiving a ready signal it issues back an initiate signal toward the plurality of processors.
Synthesizing Extraction Rules from User Examples with SEER

Our demonstration showcases SEER's end-to-end Information Extraction (IE) workflow where users highlight texts they wish to extract. Given a small set of user-specified example extractions, SEER synthesizes easy-to-understand IE rules and suggests them to the user. In addition to rule suggestions, users can quickly pick the desired rule by filtering the rule suggestion by accepting or rejecting proposed extractions. SEER's workflow allows users to jump start the IE rule development cycle; it is a less time-consuming alternative to machine learning methods that require large labeled datasets or rule-based approaches that are labor-intensive. SEER's design principles and learning algorithm are motivated by how rule developers naturally construct data extraction rules.
A novel form of oxytocin in New World monkeys

Oxytocin is widely believed to be present and structurally identical in all placental mammals. Here, we report that multiple species of New World monkeys possess a novel form of oxytocin, [P8] oxytocin. This mutation arises from a substitution of a leucine to a proline in amino acid position 8. Further analysis of this mutation in Saimiri sciureus (squirrel monkey) indicates that [P8] oxytocin is transcribed and translated properly. This mutation is specific to oxytocin, as the peptide sequence for arginine vasopressin, a structurally related nonapeptide, is unaltered. These findings dispel the notion that all placental mammals possess a ‘universal’ oxytocin sequence, and highlight the need for research on the functional significance of this novel nonapeptide in New World monkeys.
Experimental study on transparency induced by metamaterials

With the deformation theory of continuum mechanics, we extend the coordinate transformation method to design arbitrary transformation metamaterials, which are inherently transparent for electromagnetic waves. In the experiment, the metamaterial capable of bending waves is verified. The transparency phenomenon based on the field cancellation effect is also discussed. The composites fabricated with Carbon nanotubes and rubbers are demonstrated experimentally to have the cloaking effect for metal cylinders.
Detailed Analysis of Random Pyramid Surfaces With Ray Tracing and Image Processing

For the optimization of alkaline texturing in industrial monocrystalline silicon solar cells, it is of paramount importance to understand the correlation between surface reflectance and surface morphology. In this study, the reflectance is related to the surface geometry using image processing and ray tracing. Surfaces with a variation of random pyramid texturing were scanned with laser scanning microscopy. The resulting height maps were either directly used as input for the ray tracing or used as a template for a synthetic height map. A procedure was developed to extract an effective pyramid base angle from the images. It takes on values from 47.9° to 54.3°, which are below the {111} pyramid base angle of 54.74°. The reflectance decreases linearly with the effective base angle and the pyramid height. Ray tracing of as-measured and reconstructed height maps with ideal pyramid base angle shows that both are a poor representation of the pyramid landscape. The best fit between measured and simulated reflectance is obtained when the effective base angle is used to reconstruct the surface. The surface with lowest reflectance is characterized by pyramids with high base angle and large size.
Stimulatory effect of trehalose on formation and activity of Escherichia coli RNA polymerase E sigma38 holoenzyme

The intracellular concentration of trehalose increases in the stationary-phase cells of Escherichia coli. The effects of trehalose on transcription in vitro by E. coli RNA polymerase were compared for two holoenzymes, E sigma70 and E sigma38, which were reconstituted from purified core enzyme and either sigma70 (the major sigma at the exponential growth phase) or sigma38 (the essential sigma at the stationary growth phase), respectively. The optimum trehalose concentration giving maximum transcription by E sigma38 was higher than that by E sigma70. Transcription activation by trehalose was attributed to both increased formation of E sigma38 holoenzyme and increased transcription initiation by E sigma38 from sigma38-dependent promoters. The activation of E sigma38 by trehalose was additive with the transcription enhancement by decreased superhelicity of template DNA prepared from stationary-phase cells. We thus propose that the selective activation of transcription by E sigma38 holoenzyme takes place in the presence of specific conditions and factors present under stress conditions.
Quantitative Ultrasound Techniques for the Assessment of Osteoporosis: Expert Agreement on Current Status

Quantitative ultrasound (QUS) methods have been introduced in recent years for the assessment of skeletal status in osteoporosis. The performance of QUS techniques has been evaluated in a large number of studies. Reviewing existing knowledge, an international expert panel formulated the following consensus regarding the current status of this technology. To date, evidence supports the use of QUS techniques for the assessment of fracture risk in elderly women. This has been best established for water‐based calcaneal QUS systems. Future studies should include the predictive validity of other QUS systems. Additional clinical applications of QUS, specifically the assessment of rates of change for monitoring disease progression or response to treatment, require further investigation. Its low cost and portability make QUS an attractive technology for assessing risk of fractures in larger populations than may be suitable or feasible for bone densitometry. Additional investigations that assess innovative QUS techniques in well defined research settings are important to determine and utilize the full potential of this technology for the benefit of early detection and monitoring of osteoporosis.
Patterns and characteristics of hepatitis C transmission clusters among HIV-positive and HIV-negative individuals in the Australian trial in acute hepatitis C.

BACKGROUND Injecting drug users remain the population at greatest risk of acquiring hepatitis C virus (HCV) infection, although a recent increase in cases of sexually transmitted HCV infection has been observed among human immunodeficiency virus (HIV)-infected individuals. The extent to which these separate epidemics overlap is unknown. METHODS The Australian Trial in Acute Hepatitis C (ATAHC) enrolled 163 individuals (29% of whom were HIV infected) with recent HCV infection. E1/HVR1 sequences were used to construct phylogenetic trees demonstrating monophyletic clusters or pairs, and viral epidemic history and phylogeography were assessed using molecular clock analysis. Individual clusters were characterized by clinical and demographic characteristics. RESULTS Transmission through injection drug use occurred for 73% of subjects, with sexual transmission occurring for 18% (92% of whom were HIV infected). Among 112 individuals with available E1/HVR1 sequences, 23 (20%) were infected with a strain of HCV identical to that of another subject, comprising 4 homologous clusters and 3 monophyletic pairs, the majority of which (78%) were HIV infected. Clusters contained individuals with both injection drug use-related and sex-related acquisition, and in all clusters (except for 1 female HIV-uninfected pair), individuals identified as men who have sex with men, irrespective of HIV status. CONCLUSIONS This large unique study of HIV-infected and HIV-uninfected individuals with recently acquired HCV infection demonstrates that clustering is common in the HIV-infected population and that it occurred almost invariably among men who have sex with men, irrespective of the actual mode of acquisition. These findings suggest the coexistence of both injection drug use and sexual risk behaviors for individuals in the same social networks and have implications for the development of public health messages. Clinical trial registration. NCT00192569.
Effect of postharvest storage and processing on the antioxidant constituents (flavonoids and vitamin C) of fresh-cut spinach.

The effect of modified atmosphere packaging (MAP) and cooking on the flavonoids and vitamin C content (ascorbic + dehydroascorbic acid; AA + DHAA) of fresh-cut spinach was evaluated. The total flavonoid content (approximately 1000 mg kg(-)(1) f.w. ) remained quite constant during storage in both air and MAP atmospheres, while vitamin C (750 mg kg(-)(1)f.w. ) was better preserved in MAP-stored spinach. AA was transformed to DHAA during storage, and its concentration was higher in MAP-stored tissues. The free-radical scavenging activity of the isolated flavonoids was tested, and only those flavonoids with either a dihydroxyl grouping or acylated with ferulic acid showed significant activity. A decrease in the total antioxidant activity was observed during storage, particularly important in MAP-stored spinach. The higher content of DHAA and lower content of both AA and antioxidant flavonoids in the MAP-stored samples could explain this antioxidant activity decrease. Boiling extracted 50% of total flavonoids and 60% vitamin C in the cooking water. However, flavonoid glucuronides were extracted more in the cooking water than the other glycosides. The vitamin C content of the cooked tissue was higher in those samples stored in MAP.
Novel estimation method of EVM with channel correction for linear impairments in multi-standard RF transceivers

Since recent wireless communication devices support multiple communication standards on a single chip, Error Vector Magnitudes (EVMs) for multiple standards are measured to evaluate the devices. The EVM is defined by the particular calculation methods of the communication standards, especially channel correction methods. Therefore the EVM value is different between standards, even if the modulation methods are identical. This paper describes an EVM evaluation method for multi-standard devices, performing channel correction particular to each standard. The EVM for the various standards can be calculated by a unique algorithm, which uses the values of the frequency-dependent I/Q imbalances and the Signal-to-Noise Ratio (SNR) calculated from a single measurement data. The validity of this technique is confirmed using an actual WiMAX transceiver on an ATE.
Resolving The Placement Problem in a Load-balanced Environment Using a Heuristic Approach

In recent years, cloud computing technology has become one of the most significant IT infrastructures. Cloud users are increasing every day; thus, cloud must be able to handle the huge number of requests received at any given moment, causing concerns for resourced load balancing. The load balancing problem occurs when some cloud resources are overloaded with user tasks while other resources are idle. The solution to this problem is manifold, requiring a number of techniques, such as live migration and placement strategies, to balance the load on cloud resources. In this research, a heuristic algorithm called “activity selection problem” is implemented in order to select the destination of the migrated virtual machine.
Prevention of rheumatic fever by treatment of previous streptococcic infections; effect of sulfadiazine.

• Patients receiving sulfadiazine for acute streptococcic pharyngitis were compared with patients receiving other therapy for the same condition. The sulfadiazine reduced the incidence of complications during the acute phase. After the first week, however, the incidence of suppurative complications was about the same in both groups. The streptococci were not eradicated. The subsequent incidence of recurrent pharyngitis in the sulfadiazine group was three times that in the contratest group, and the sulfadiazine did not prevent rheumatic fever.
Prediction of axillary lymph node involvement of women with invasive breast carcinoma

The concept of Tenju-gann proposed by Kitagawa et al. and discussed in the accompanying editorial by Kennedy deserves broader application than these authors suggest. Although cancer is increasingly an illness of the elderly, there remains a significant burden of disease among the young and middleaged, particularly in terms of years of potential life lost. There is also evidence that some solid tumors occurring in those younger than 40 years behave more aggressively and result in poorer outcomes than the same disease diagnosed at a more advanced age. Being cheated of health and forced to pay the cancer “tax” before enjoying the fruits of a long life is a devastating situation that leads patients, families, and physicians to pursue every reasonable attempt at therapy. The vast majority of advanced solid cancers become refractory to therapy over time or never demonstrate initial sensitivity to systemic treatment. In many cases, symptomatic and supportive care become the best and most appropriate therapeutic options. In these situations, the concept of Tenju-gann or “natural-end cancer,” as presented by Kitagawa et al. could be applied to patients of all ages, including children, in an effort to help them and their families cope with the shattering consequences of terminal disease. The increasing focus on quality of life issues in clinical trial design as well as the development of hospice organizations are practical attempts at understanding and relieving the suffering of advanced malignancy. The concept of Tenjugann may further aid in our care of individuals with terminal disease, regardless of age. It could help avoid the application of medically futile therapeutic procedures that interfere with the ability of our patients to experience the “peaceful death with minimal suffering” that is central to the diagnosis of a Tenju-gann cancer. This does not imply therapeutic nihilism, but rather the admission that, for most patients diagnosed with advanced cancer, succumbing to their disease is inevitable and leads to a “natural-end” despite aggressive therapeutic efforts. Dying of advanced cancer at age 40 years is no less “natural” than dying of the same illness at age 90 years. Oncologists can play a critical role in helping patients of any age accept their disease and experience a peaceful death. Perhaps there is a derivative of Tenju that could encompass those dying after having enjoyed shorter-than-expected lives. We should not let reverse ageism deprive our younger patients of the potential comfort that is the ultimate result of the application of the philosophy of Tenju-gann.