Miracle-dz/UniFAR-FTUs huggingface dataset:
The paradox of the "ancient" bacterium which contains "modern" protein-coding genes.

The isolation of microorganisms from ancient materials and the verification that they are as old as the materials from which they were isolated continue to be areas of controversy. Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels. This fact has historically been used by critics to argue that these isolates are not ancient but are modern contaminants introduced either naturally after formation of the surrounding material (for further details, see Hazen and Roeder 2001 and the reply by Powers, Vreeland, and Rosenzweig 2001) or because of flaws in the methodology of sample isolation (reviewed recently in Vreeland and Rosenzweig 2002). Such criticism has been addressed experimentally by the development of highly rigorous protocols for sample selection, surface sterilization, and contamination detection and control procedures. Using the most scrupulous and well-documented sampling procedures and contamination-protection techniques reported to date, Vreeland, Rosenzweig, and Powers (2000) reported the isolation of a sporeforming bacterium, Bacillus strain 2-9-3, from a brine inclusion within a halite crystal recovered from the 250-Myr-old Permian Salado Formation in Carlsbad, NM. As had been noted in earlier studies, a striking observation by Vreeland, Rosenzweig, and Powers (2000) was that the 16S rDNA of isolate 2-9-3 is 99% identical to that of Salibacillus marismortui, a bacterium isolated from the Dead Sea in 1936 (Arahal et al. 1999). In fact, Arahal et al. (1999) identified as S. marismortui three strains with 16S rDNA sequences differing by 0.01%, suggesting that isolate 2-9-3 might also be classified as S. marismortui. Two groups have since used phylogenetic analyses of 16S rDNA sequences to argue that isolate 2-9-3 is unlikely to be 250 Myr old. Graur and Pupko (2001) used a relative rate test to compare evolutionary rates of 16S rDNA on the branches leading to isolate 2-9-3 and S. marismortui and found no differences between the evolutionary rates. Considering the possibility that S. marismortui may also be ancient (Arahal et al. 1999; Vreeland, Rosenzweig, and Powers 2000), they also
Overview of Clostridium difficile Infection in Cancer Patients

Clostridium difficile Associated Diarrhoea (CDAD) is the leading cause of nosocomial diarrhoea. Clostridium difficile Infections (CDIs) may be induced by medication or medical procedures that disrupt normal bowel flora or interfere with bowel motility. The emergence of hyper-virulent strains of CDI, reports of severe or recurrent CDI in immunocompetent populations, advent of various infection control challenges, and diagnostic and therapeutic dilemmas have contributed to a shift in the disease paradigm. However, there is insufficient data on the risk of CDI in vulnerable cancer patients receiving chemotherapy or who are admitted to health care settings for long periods of time. This review describes the epidemiology, risk factors, pathophysiology, and management of CDIs in cancer patients receiving chemotherapeutic agents.
Effective Domain Mixing for Neural Machine Translation

Neural Machine Translation (NMT) models are often trained on heterogeneous mixtures of domains, from news to parliamentary proceedings, each with unique distributions and language. In this work we show that training NMT systems on naively mixed data can degrade performance versus models fit to each constituent domain. We demonstrate that this problem can be circumvented, and propose three models that do so by jointly learning domain discrimination and translation. We demonstrate the efficacy of these techniques by merging pairs of domains in three languages: Chinese, French, and Japanese. After training on composite data, each approach out-performs its domain-specific counter-parts, with a model based on a discriminator network doing so most reliably. We obtain consistent performance improvements and an average increase of 1.1 BLEU.
Factors influencing the occurence of nosocomial bloodstream infections observed in thoracic and cardiosurgical postoperative care units.

BACKGROUND The aim of this study was to analyse the epidemiology and aetiology of laboratoryconfirmed bloodstream infections (LC-BSI) and central line-associated bloodstream infections (CLABSI) after pulmonary and coronary surgery, in postoperative intensive care units in 2009. METHODS Sources of infections were identified by the hospital Infection Control Team in cooperation with ITU personnel using the CDC definitions. RESULTS A total of 37 LC-BSI and 21 CLA-BSI cases in 3.096 patients were detected. Central line device utilization ratio was 0.50. The total cumulative LC-BSI incidence rate was 1.2% and CLA-BSI rate 8.7 per 1,000 central line days. The most common causes of LC-BSI were Gram-positive cocci (Staphylococcus aureus - 5.9%, CNS - 50.0%, Enterococcus faecium - 5.9%). CONCLUSIONS We found that in those units in which surveillance of CLA-BSI had been conducted since 2002, BSI incidence rates were higher than those reported in the NHSN programme.
Development of Iodimetric Redox Method for Routine Estimation of Ascorbic Acid from Fresh Fruit and Vegetables

Summary: The iodimetric method (Im) is developed for rapid estimation of ascorbic acid from fresh fruit and vegetables. The efficiency of Im was compared with standard dye method (Dm) utilizing a variety of model solutions and aqueous extracts from fresh fruit and vegetables of different colors. The Im presented consistently accurate and precise results from colorless to colored model solutions and from fruit/vegetable extracts with standard deviation (Stdev) in the range of ±0.013 - ±0.405 and ±0.019 - ±0.428 respectively with no significant difference between the replicates. The Dm worked also satisfactorily for colorless model solutions and extracts (Stdev range ±0.235 - ±0.309) while producing unsatisfactory results (±0.464 - ±3.281) for colored counterparts. Severe discrepancies/ overestimates continued to pileup (52% to 197%) estimating the nutrient from high (3.0 mg/10mL) to low (0.5 mg/10mL) concentration levels, respectively. On the basis of precision and reliability, the Im technique is suggested for adoption in general laboratories for routine estimation of ascorbic acid from fruit and vegetables possessing any shade.
Troubleshooting in platelet storage temperature and new perspectives through proteomics.

Platelets represent a key cellular blood component under physiological conditions, due to their implications in the maintenance of vascular integrity and prevention of haemorrhagic phenomena1. Dysfunctions associated with thrombocytopenia constitute a significant threat to patients’ health. So far, administration of platelet concentrates (PCs) from healthy donors is the only known strategy for medical care of patients with active bleeding, thrombocytopenia caused by bone marrow dysfunctions or due to chemotherapy for treatments of malignancies, or upon preliminary treatments prior to stem cell transplantation. Qualitative and quantitative changes in platelets could also occur following coronary artery bypass surgery and trauma, and may represent a key indicator of likely thrombotic complications2. Platelets are basically collected from donors in two ways: extraction from whole blood throughout centrifugation (buffy-coat) or through apheresis. Both methods are currently employed and have bright sides and disadvantages. Analogously to other blood components, techniques to improve the shelf life of platelets (currently, only five days), while maintaining their safety and effectiveness, are under constant investigation worldwide. Indeed, blood transfusion services are always in shortage of PCs, because of the impossibility to prolong their storage in like fashion to hypothermic storage of erythrocyte concentrates or frozen storage of fresh frozen plasma. In order to improve storage of PCs, lowering temperature has been attempted as well, although results were not as positive as expected, since platelets do not tolerate refrigeration. Hypothermic (4°C) storage conditions cause deep modifications in platelet shape and functionality. These are relevant issues which compromise viability of cold stored platelets, as they exert their physiological role through their ability to change shape and activate under various conditions. Low temperature appears to be a triggering factor for activation as well, thus yielding yet activated platelets as unviable blood product at the end of the storage. This review focuses on platelet storage temperatures and the main issues which affect both current (22 °C) and alternative (4 °C) storage protocols for PCs. In particular, we herein discuss the initial events which trigger morphological and physiological changes upon cold activation, partially distinguishable from physiological activation. Moreover, a glance will be given at recent proteomic approaches, which promise to improve current knowledge on blood components of transfusion interest, mainly addressing current technical hurdles (such as the analysis of membrane proteins and their reciprocal interaction).
Molecular characterization of vancomycin-resistant enterococci in Hangzhou, China.

State Key Laboratory for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79, Qing Chun Road, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial People’s Hospital, No. 158, Shang Tang Road, Hangzhou, Zhejiang 310014, China; Hangzhou First People’s Hospital, No. 261, Wan Sha Road, Hangzhou, Zhejiang 310006, China; Zhejiang Hospital, No. 12, Ling Ying Road, Hangzhou, Zhejiang 310013, China; Hangzhou Third People’s Hospital, No. 38, Western Lake Road, Hangzhou, Zhejiang 310009, China
Quorum Sensing in Staphylococcus aureus Biofilms

ABSTRACT Several serious diseases are caused by biofilm-associated Staphylococcus aureus, infections in which the accessory gene regulator (agr) quorum-sensing system is thought to play an important role. We studied the contribution of agr to biofilm development, and we examined agr-dependent transcription in biofilms. Under some conditions, disruption of agr expression had no discernible influence on biofilm formation, while under others it either inhibited or enhanced biofilm formation. Under those conditions where agr expression enhanced biofilm formation, biofilms of an agr signaling mutant were particularly sensitive to rifampin but not to oxacillin. Time lapse confocal scanning laser microscopy showed that, similar to the expression of an agr-independent fluorescent reporter, biofilm expression of an agr-dependent reporter was in patches within cell clusters and oscillated with time. In some cases, loss of fluorescence appeared to coincide with detachment of cells from the biofilm. Our studies indicate that the role of agr expression in biofilm development and behavior depends on environmental conditions. We also suggest that detachment of cells expressing agr from biofilms may have important clinical implications.
Numerical investigation into the performance of two reconfigurable gaseous plasma antennas

Plasma antennas constitute a promising alternative to conventional metallic antennas for applications in which reconfigurability with respect to some property is desired. The latter feature can be achieved by tuning the plasma discharge parameters. We use a full-wave numerical tool, ADAMANT (Advanced coDe for Anisotropic Media and ANTennas), based on integral equations, to assess the role played by plasma discharge parameters in shaping the radiation pattern, which is mainly determined by the plasma current distribution. Numerical results for different discharge parameters show that the antenna radiation efficiency can be controlled by adjusting plasma density and magneto-static field.
Diploposthe laevis (Bloch) Jacobi (Eucestoda, Hymenolepididae) from Netta peposaca (Vieillot) (Aves: Anatidae): first record for the Neotropical Region and a new host

One hundred eight rosy-billed pochards, Netta peposaca (Vieillot, 1816), collected in Brazil and Argentina were examined for endoparasites. Collection sites included the municipalities of Santa Vitoria do Palmar and Jaguarao, Rio Grande do Sul State, Brazil (wintering site) and Alvear, Corrientes Province, northern Argentina (nesting site). Birds were frozen in dry ice after collection. During necropsy they were categorized according to sex and maturation, either adult or juvenile. The cestode Diploposthe laevis (Bloch) Jacobi, 1896 was found (prevalence 68.5%, mean infection was 2). The mean prevalence of D. laevis in Alvear (25.9%) was higher than found in Jaguarao and Santa Vitoria do Palmar, Rio Grande do Sul (19%), and could be related to the nesting site and to the period when the birds may ingest a higher amount of food. This is the first record of a species of the genus Diploposthe in anatideans from South America, and the first record of the species in N. peposaca. Details of the cirrus pouch and vagina were described based on histological sections.
A Generative Model for Deep Convolutional Learning

A generative model is developed for deep (multi-layered) convolutional dictionary learning. A novel probabilistic pooling operation is integrated into the deep model, yielding efficient bottom-up (pretraining) and top-down (refinement) probabilistic learning. Experimental results demonstrate powerful capabilities of the model to learn multi-layer features from images, and excellent classification results are obtained on the MNIST and Caltech 101 datasets.
An Analog Technique for Distributed MPPT PV Applications

TEODI is the acronym of a maximum power point tracking (MPPT) technique which has been recently presented in the literature. Such a technique is particularly suitable in distributed MPPT photovoltaic (PV) applications, and it is based on the equalization of the output operating points, of the dc/dc converters dedicated to each subsection of the PV array, in correspondence of the forced displacement of their input operating points. The main advantages of TEODI, its performances in terms of MPPT efficiency and speed of tracking, and the intrinsic capability to attenuate the effect, on the voltages of the PV modules, of the 100/120 Hz disturbances coming from the grid are shown by means of simulation results and experimental findings obtained by using a laboratory prototype developed by means of analog circuitry only.
SC-FDMA with iterative multiuser detection: improvements on power/spectral efficiency

This article outlines the basic principles of single-carrier frequency division multiple access with iterative multiuser detection, called grouped frequency division multiple access. GFDMA allows multiple users to share a common set of subcarriers and separates the signals of users by employing distinct interleavers and frequency-domain multiuser detection. Some attractive features of GFDMA are explained, including low-cost iterative multiuser detection, multiuser and frequency diversity gains, and flexibility in resource allocation. We also discuss the applications of GFDMA to spatial diversity schemes and to intercell interference mitigation in the cell edge. It is shown that GFDMA offers advantages over SC-FDMA with respect to power/spectral efficiency. Such power/spectral efficiency can provide considerable performance improvements in future wireless communication networks.
Real Indications for Adrenalectomy in Renal Cell Carcinoma

Objectives: We determined the incidence and characteristics of adrenal involvement in localized and advanced renal cell carcinoma, and evaluated the role of adrenalectomy as part of radical nephrectomy. Patients and Methods: From 1993 to 1999, 210 patients with renal cell carcinoma (RCC) (139 men and 71 women, mean age 60.8 years, range 12-96 years) underwent radical nephrectomy with associated adrenalectomy. Patients were divided into two subgroups of 106 with localized (stage T1-2 tumor, group 1) and 104 with advanced (stage T3-4N01M01, group 2) renal cell carcinoma. A retrospective review of preoperative computerized tomography (CT) of the abdomen was performed. Radiographic findings were subsequently compared with postoperative histopathological results to assess the predictive value of tumor characteristics and imaging in determining adrenal metastasis. Results: Of the 210 patients, 15 (7.1%) had adrenal involvement. Tumor stage correlated with probability of adrenal spread, with T3-4 and T1-2 accounting for 13.4% and 0.9% of cases, respectively ( p < 0.001). Upper pole intrarenal RCC most likely to spread was local extension to the adrenal gland, representing 53.3% of adrenal involvement. In contrast, multifocal, lower pole and mid region RCC tumors metastasized hematogenously, representing 21.4%, 7%, and 14% of adrenal metastasis, respectively. The relationship between intrarenal tumor size (mean 7.8 cm, range 4-21) and adrenal involvement was not statistically significant. Preoperative CT demonstrated 97.7% specificity, 98.4% negative predictive value, 87% sensitivity and 80% positive value for adrenal involvement by RCC. Conclusions: Ipsilateral adrenalectomy should only be performed if a lesion is seen preoperatively on CT scan or if gross disease is seen at the time of nephrectomy. The prognosis is poor for RCC with ipsilateral involvement even with complete removal. Because of this poor prognosis we believe that adrenal involvement should constitute a separate stage category.
Power Density-Aware Resource Management for Heterogeneous Tiled Multicores

Increasing power densities have led to the dark silicon era, for which heterogeneous multicores with different power and performance characteristics are promising architectures. This paper focuses on maximizing the overall system performance under a critical temperature constraint for heterogeneous tiled multicores, where all cores or accelerators inside a tile share the same voltage and frequency levels. For such architectures, we present a resource management technique that introduces power density as a novel system level constraint, in order to avoid thermal violations. The proposed technique then assigns applications to tiles by choosing their degree of parallelism and the voltage/frequency levels of each tile, such that the power density constraint is satisfied. Moreover, our technique provides runtime adaptation of the power density constraint according to the characteristics of the executed applications, and reacting to workload changes at runtime. Thus, the available thermal headroom is exploited to maximize the overall system performance.
Channel Estimation for FDD Multi-User Massive MIMO: A Variational Bayesian Inference-Based Approach

This paper addresses downlink channel estimation for frequency division duplex multi-user massive multiple-input multiple-output systems. Suppose that a base station communicates with <inline-formula> <tex-math notation="LaTeX">$K$ </tex-math></inline-formula> mobile users, then the task is to estimate <inline-formula> <tex-math notation="LaTeX">$K$ </tex-math></inline-formula> channel matrices, each corresponding to one user. Due to the limited scattering in physical propagation, each channel matrix is sparse in the virtual angular domain. Besides, different user links tend to share some common scatterers. As such, different channel matrices may have a partially common sparsity pattern. These observations motivate us to take a variational Bayesian inference based approach for channel estimation. Specifically, we design a Gaussian mixture prior model, which can efficiently capture the individual sparsity in each channel matrix and the partially joint sparsity shared by different channel matrices. Furthermore, we develop a variational expectation maximization strategy to estimate the hyperparameters associated with the prior model and the channel matrices. Compared with the existing counterparts, the proposed approach achieves much better performance in terms of the channel estimation accuracy, while maintaining a low computational complexity.
AdSelector: A Privacy-Preserving Advertisement Selection Mechanism for Mobile Devices

Targeted mobile advertising (TMA) enables organisations to tailor advertisements to speciﬁc consumers by analysing the personal information collected from consumers’ mobile devices. Although TMA oﬀers great beneﬁts to advertisers, the privacy concerns associated with it may reduce the advertising eﬀectiveness. It follows that there is a need for an advertisement selection mechanism that can support the existing TMA business model in a manner that takes into account consumers’ privacy concerns. We present such an ad selection mechanism that has the potential to provide beneﬁts to both consumers and advertisers. The mechanism is novel in its combination of a user subscription mechanism, a two-stage ad selection process, and the application of a trustworthy billing system. In particular: (1) the user subscription mechanism helps users to identify their interests and subscribe to desirable categories of ads; (2) the two-stage ad selection process ensures that ad servers can only obtain coarse-grained user proﬁles, with ﬁne-grained user proﬁles stored and used only on the mobile devices; and (3) the trustworthy billing system helps to report ad-clicks without revealing users’ identities and assists in detecting click-fraud attacks. The performance of the mechanism is evaluated in the context of a prototype privacy-preserving targeted mobile advertising framework.
Informed Detour Selection Using iPlane Helps Reliability

In this report we propose to use the daily traceroute data generated by iPlane [9] to improve the reliability of the Internet paths. Previous work put forth a simple idea of using an overlay network of intermediary detour nodes that can be used to route around failures on direct Internet paths [1]. We provide the mechanism for choosing these intermediary nodes. The underlying idea of our work is that knowledge of the point-of-presence (PoP) path between the source and destination as well as the PoP paths between potential detour nodes and destination can be used to pick the intermediary for routing around failures on the direct path. We leverage the existing iPlane infrastructure and perform an experiment using PlanetLab [3]. We obtain a substantial improvement in path availability over the state-of-the-art using the data from iPlane.
sloWCrowd: A crowdsourcing tool for lexicographic tasks

The paper presents sloWCrowd, a simple tool developed to facilitate crowdsourcing lexicographic tasks, such as error correction in automatically generated wordnets and semantic annotation of corpora. The tool is open-source, language-independent and can be adapted to a broad range of crowdsourcing tasks. Since volunteers who participate in our crowdsourcing tasks are not trained lexicographers, the tool has been designed to obtain multiple answers to the same question and compute the majority vote, making sure individual unreliable answers are discarded. We also make sure unreliable volunteers, who systematically provide unreliable answers, are not taken into account. This is achieved by measuring their accuracy against a gold standard, the questions from which are posed to the annotators on a regular basis in between the real question. We tested the tool in an extensive crowdsourcing task, i.e. error correction of the Slovene wordnet, the results of which are encouraging, motivating us to use the tool in other annotation tasks in the future as well.