Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiplex Touchdown PCR for Rapid Typing of the Opportunistic Pathogen Propionibacterium acnes

ABSTRACT The opportunistic human pathogen Propionibacterium acnes is composed of a number of distinct phylogroups, designated types IA1, IA2, IB, IC, II, and III, which vary in their production of putative virulence factors, their inflammatory potential, and their biochemical, aggregative, and morphological characteristics. Although multilocus sequence typing (MLST) currently represents the gold standard for unambiguous phylogroup classification and individual strain identification, it is a labor-intensive and time-consuming technique. As a consequence, we developed a multiplex touchdown PCR assay that in a single reaction can confirm the species identity and phylogeny of an isolate based on its pattern of reaction with six primer sets that target the 16S rRNA gene (all isolates), ATPase (types IA1, IA2, and IC), sodA (types IA2 and IB), atpD (type II), and recA (type III) housekeeping genes, as well as a Fic family toxin gene (type IC). When applied to 312 P. acnes isolates previously characterized by MLST and representing types IA1 (n = 145), IA2 (n = 20), IB (n = 65), IC (n = 7), II (n = 45), and III (n = 30), the multiplex displayed 100% sensitivity and 100% specificity for detecting isolates within each targeted phylogroup. No cross-reactivity with isolates from other bacterial species was observed. This multiplex assay will provide researchers with a rapid, high-throughput, and technically undemanding typing method for epidemiological and phylogenetic investigations. It will facilitate studies investigating the association of lineages with various infections and clinical conditions, and it will serve as a prescreening tool to maximize the number of genetically diverse isolates selected for downstream higher-resolution sequence-based analyses.
Influence of sulfate reduction rates on the Phanerozoic sulfur isotope record

Phanerozoic levels of atmospheric oxygen relate to the burial histories of organic carbon and pyrite sulfur. The sulfur cycle remains poorly constrained, however, leading to concomitant uncertainties in O2 budgets. Here we present experiments linking the magnitude of fractionations of the multiple sulfur isotopes to the rate of microbial sulfate reduction. The data demonstrate that such fractionations are controlled by the availability of electron donor (organic matter), rather than by the concentration of electron acceptor (sulfate), an environmental constraint that varies among sedimentary burial environments. By coupling these results with a sediment biogeochemical model of pyrite burial, we find a strong relationship between observed sulfur isotope fractionations over the last 200 Ma and the areal extent of shallow seafloor environments. We interpret this as a global dependency of the rate of microbial sulfate reduction on the availability of organic-rich sea-floor settings. However, fractionation during the early/mid-Paleozoic fails to correlate with shelf area. We suggest that this decoupling reflects a shallower paleoredox boundary, primarily confined to the water column in the early Phanerozoic. The transition between these two states begins during the Carboniferous and concludes approximately around the Triassic–Jurassic boundary, indicating a prolonged response to a Carboniferous rise in O2. Together, these results lay the foundation for decoupling changes in sulfate reduction rates from the global average record of pyrite burial, highlighting how the local nature of sedimentary processes affects global records. This distinction greatly refines our understanding of the S cycle and its relationship to the history of atmospheric oxygen.
Hybrid wireless-optical broadband access network(woban) : prototype development and research challenges

The hybrid wireless-optical broadband access network is emerging as a promising technology to provide economical and scalable broadband Internet access. In this cross-domain network architecture, end users receive broadband services through a wireless, mesh front end that is connected to the optical backhaul through gateway nodes. In this article, we present the architecture and functional characteristics of a WOBAN prototype built in the Networks Lab at UC Davis. We discuss research challenges for hybrid networks based on our experimental observations.
Counting networks

Many fundamental multi-processor coordination problems can be expressed as <italic>counting problems</italic>: Processes must cooperate to assign successive values from a given range, such as addresses in memory or destinations on an interconnection network. Conventional solutions to these problems perform poorly because of synchronization bottlenecks and high memory contention. Motivated by observations on the behavior of sorting networks, we offer a new approach to solving such problems, by introducing <italic>counting networks</italic>, a new class of networks that can be used to count. We give two counting network constructions, one of depth log <italic>n</italic>(1 + log <italic>n</italic>)/2 using <italic>n</italic> log <italic></italic>(1 + log <italic>n</italic>)/4 “gates,” and a second of depth log<supscrpt>2</supscrpt> <italic>n</italic> using <italic>n</italic> log<supscrpt>2</supscrpt> <italic>n</italic>/2 gates. These networks avoid the sequential bottlenecks inherent to earlier solutions and substantially lower the memory contention. Finally, to show that counting networks are not merely mathematical creatures, we provide experimental evidence that they outperform conventional synchronization techniques under a variety of circumstances.
A Novel Maneuver Used to Rule Out Intraarterial Placement of the Introducer Sheath in a Patient with an Ipsilateral Mature Forearm Hemodialysis Fistula

To the Editor:—We read with interest the case report by Cladis and Litman regarding the intravascular injection of 3% 2-chlorprocaine. The authors are to be congratulated on their ability to postoperatively radiologically document the intravascular placement of the epidural catheter. However, we have concerns with the total dose of 2-chloroprocaine used. The authors state that they injected 4 ml 2-chlorprocaine, 3%, over approximately 30 s. When this dose is calculated on a per-kilogram basis for the 2-month-old, 4-kg child described in the case report, the dose is 30 mg/kg for a total dose of 120 mg. Neonates and infants up to 6 months of age have approximately half the plasma cholinesterase of older children. Singler suggests a maximum of 7 mg/kg 2-chlorprocaine in infants. Although the rapidity of the cardiac toxicity after administration of the local anesthetic suggests an intravascular injection, the 4 ml 2-chloroprocaine, 3%, seems large enough that it was rapidly absorbed from the epidural space, producing a transient peak blood level and causing the transient cardiovascular effects. Rapidity of development of peak serum concentrations of local anesthetics is known to be related to the site of injection, with intercostal being the fastest, followed by caudal and then epidural. Because no blood was aspirated from the epidural catheter on two occasions does not mean that the catheter was not in an epidural vein. It is possible that the catheter migrated into the vein during the case and was found postoperatively. However, regardless of the catheter placement, we believe that the total dose was too large for the patient.
Eddies in the Western Mediterranean seen in thermal infrared imagery and SLA fields

ABSTRACT In this article, daily fields of sea surface temperature (SST) and sea level anomaly (SLA) of the Western Mediterranean Sea obtained in 2011–2013 are being co-analysed. The study is aimed at assessing potentials of the fields of SLA for manifestation of mesoscale eddies in the region of interest. First, the SST imagery was inspected visually and locations of mesoscale eddies noticed in the images were detected. After that, closed contours were extracted in the fields of SLA and their locations were compared with locations of eddies directly seen in the SST images. Such a comparison showed that among anticyclonic eddies found in SST, about 56.3% had corresponding closed contours of SLA; the percentage was increasing with increasing eddy diameter. For cyclonic eddies, supposedly due to their smaller spatial and time scales, such percentage was only about 20.2%. During the warm season, when the mixed layer is particularly shallow and the turbulence is closer to the two-dimensional model, the correspondence between eddies seen in SST and closed contours of SLA was higher than during the cold period.
A Compact Low-Power 320-Gb/s WDM Transmitter Based on Silicon Microrings

We demonstrate a compact and low-power wavelength-division multiplexing transmitter near a 1550-nm wavelength using silicon microrings. The transmitter is implemented on a silicon-on-insulator photonics platform with a compact footprint of 0.5 mm2. The transmitter incorporates 8 wavelength channels with 200-GHz spacing. Each channel achieved error-free operation at 40 Gb/s, resulting in an aggregated data transmission capability of 320 Gb/s. To our knowledge, this is the highest aggregated data rate demonstrated in silicon wavelength-division multiplexing transmitters. Owing to the small device capacitance and the efficient pn-junction modulator design, the transmitter achieves low energy-per-bit values of 36 fJ/bit under 2.4 Vpp drive and 144 fJ/bit under 4.8 Vpp drive. Comparisons are made to a commercial lithium niobate modulator in terms of bit-error-rate versus optical signal-to-noise ratio.
Phase I-II trial of bortezomib plus oral cyclophosphamide and prednisone in relapsed and refractory multiple myeloma.

PURPOSE The combination of oral weekly cyclophosphamide and alternate day prednisone is a convenient regimen for relapsed/refractory multiple myeloma (MM), and we sought to improve its efficacy by adding bortezomib, a proteasome inhibitor with proven antimyeloma activity. PATIENTS AND METHODS We conducted a phase I-II trial evaluating six dose levels to define the maximum tolerated dose (MTD) of this combination in relapsed/refractory MM. An additional 10 patients were evaluated at the highest dose level reached. RESULTS Thirty-seven patients were treated on this study. The MTD was not defined. Both of the highest dose levels of bortezomib tested (1.3 mg/m(2) on days 1, 4, 8, and 11 and 1.5 mg/m(2) on days 1, 8, and 15, each on a 28-day cycle) could be safely given with cyclophosphamide 300 mg/m(2) per week and prednisone. At these dose levels, the overall response rate was 95% (complete responses [CR] plus partial response plus minimal response), with CR observed in more than 50% of patients. The weekly bortezomib regimen resulted in fewer instances of grade 3 thrombocytopenia and grade 1 to 2 peripheral neuropathy; the 1-year progression-free and overall survival probabilities with this dose level were 83% (95% CI, 73% to 96%) and 100%, respectively. CONCLUSION Weekly bortezomib 1.5 mg/m(2) plus oral cyclophosphamide and prednisone produces an unprecedented response rate and encouraging 1-year survival in relapsed/refractory patients with MM. Further evaluation of this promising regimen is warranted both in relapsed and newly diagnosed disease.
Federated Access to Cyber Observables for Detection of Targeted Attacks

Current DoD enterprise networks routinely face targeted cyber attacks, and even though attack-related information is recorded in various places, this information is often left unexamined until after attacker objectives have been achieved. This is especially true for large networks consisting of continuously changing networked devices, including laptops, servers, printers, IP phones, and more. This paper describes the design of Gestalt, a next-generation cyber information management platform that simplifies access to cyber event data stored in the nooks and crannies of a distributed enterprise. The ready and secure access to cyber information provided by Gestalt is a key enabler for a new set of techniques that can detect and mitigate targeted cyber attacks within hours instead of months. Current state-of-the-art approaches to automated and operator assisted cyber defense are ill-suited to counter targeted cyber attacks because these technol-ogies (1) focus only on aggregated one-dimensional features across multiple devices, (2) do not provide the required coverage over all networked devices and observables accessible on those devices, and (3) lack the expressiveness and deeper semantic backing required to detect targeted attacks across a sea of low-level observables. Gestalt provides innovations in (1) automati-cally discovering devices and useful data sources in the enterprise (beyond simple IP connectivity), (2) maintaining a metadata in-dex of devices and observable information (even of devices with-out schemas and connectors), and (3) transparently decomposing and federating semantic graph queries to devices (rather than extracting and aggregating information in a central store), and integrating the results back into a well-defined ontology.
Tendencies in current climate change and atmospheric circulation variability in the Arctic region of West Siberia

The main goal of this study is to carry out the investigation of the climatic parameters variability and the role of global atmospheric circulation in their trends over the Arctic region of West Siberia (60-70°N, 60-90°E) using reanalysis data. The characteristics of spatial and temporal variability of meteorological parameters (surface air temperature and soil temperature, atmospheric pressure, snow depth and surface albedo) were calculated using ERA-Interim reanalysis data over the period of 1979−2015. It was established that in the beginning of XXI century, there is an air and soil temperature decrease in winter and autumn and its statistically significant increase in spring and summer. The tendency to permafrost area degradation is observed for the Arctic region. The maximal changes are observed in low-temperature permafrost soils than in soils with higher temperature. This trend is accompanied by the decrease in snow cover depth and surface albedo. Global circulation indices variability, its relationships with meteorological parameters in West Siberia and with sea ice cover extent in the Arctic Seas indicate that atmospheric blocking processes, which are responsible for anticyclonic type of weather, were developed in the region during last decades.
Differential Cardiovascular Effects of Centrally Administered Vasopressin in Conscious Long Evans and Brattleboro Rats

The cardiovascular effects of arginine vasopressin (AVP) administered into a lateral cerebral ventricle or into the cisterna magna were investigated in conscious Long Evans (control) rats and AVP-deficient Brattleboro rats. The effects of subpressor intracerebroventricular and intracisternal doses of AVP on cardiac baroreflex sensitivities were also determined. Intracerebroventricular and intracisternal AVP increased blood pressure of both strains of rat in a dose-dependent manner. The maximum pressor response produced by intracerebroventricular AVP in Long Evans rats was 13 ± 2/13 ± 1 mm Hg (systolic/diastolic, n =6) after 100 ng AVP. The pressor response to the highest intracerebroventricular dose of AVP tested in Brattleboro rats (30 ng) was 46 ± 13/21 ± 6 mm Hg (n =6). Intracerebroventricular AVP caused a tachycardia in Brattleboro rats but had no effect on heart rate of Long Evans rats. At doses greater than 1 ng, the increases in blood pressure produced by intracisternal AVP in both groups of rats were significantly greater than the increases produced by the same doses given intracerebroventricularly. Heart rate fell in a dose-dependent manner after intracisternal AVP in Long Evans rats but not in Brattleboro rats. Cardiac baroreflex sensitivities of Brattleboro rats were not significantly different from those of Long Evans rats and were not modified by intracerebroventricular (0.3 ng) or intracisternal (0.1 ng) AVP. In Long Evans rats, intracisternal AVP (0.3 ng) increased cardiac baroreflex responses to both increases and decreases in pressure. Intracerebroventricular AVP (0.3 ng) increased the sensitivity of the reflex in response to an elevation but not to a reduction in blood pressure. These results suggest that Brattleboro rats are more sensitive than Long Evans rats to the central pressor action of AVP and indicate that AVP can modify the baroreflex of Long Evans rats at a site(s) within the brain. Brattleboro rats may maintain normal baroreflex function through mechanisms that do not use, and are not modified by, central AVP.
Gene Cloning and Nucleotide Sequencing and Properties of a Cocaine Esterase from Rhodococcus sp . Strain MB 1

A strain of Rhodococcus designated MB1, which was capable of utilizing cocaine as a sole source of carbon and nitrogen for growth, was isolated from rhizosphere soil of the tropane alkaloid-producing plant Erythroxylum coca. A cocaine esterase was found to initiate degradation of cocaine, which was hydrolyzed to ecgonine methyl ester and benzoate; both of these esterolytic products were further metabolized by Rhodococcus sp. strain MB1. The structural gene encoding a cocaine esterase, designated cocE, was cloned from Rhodococcus sp. strain MB1 genomic libraries by screening recombinant strains of Rhodococcus erythropolis CW25 for growth on cocaine. The nucleotide sequence of cocE corresponded to an open reading frame of 1,724 bp that codes for a protein of 574 amino acids. The amino acid sequence of cocaine esterase has a region of similarity with the active serine consensus of X-prolyl dipeptidyl aminopeptidases, suggesting that the cocaine esterase is a serine esterase. The cocE coding sequence was subcloned into the pCFX1 expression plasmid and expressed in Escherichia coli. The recombinant cocaine esterase was purified to apparent homogeneity and was found to be monomeric, with an Mr of approximately 65,000. The apparent Km of the enzyme (mean 6 standard deviation) for cocaine was measured as 1.33 6 0.085 mM. These findings are of potential use in the development of a linked assay for the detection of illicit cocaine.
Replication Section Introduction

Replication, widely acknowledged as the cornerstone of science, brings many benefits to the discipline that embraces it. First among them, successful replication ensures that a particular contribution to the cumulated body of knowledge is correct. Second, unsuccessful replication purges incorrect results from the cumulated body of knowledge. Other benefits are enumerated in the article by King [7]. The economic “science” has denied itself these benefits and perhaps even jeopardized its standing as a science, due its longstanding refusal to embrace replication. This is particularly noteworthy because all available evidence strongly suggests that the economic literature is filled with incorrect results. Dewald et al. ([3], hereafter “DTA”) were able to replicate only 2 of 54 articles, while McCullough et al. [9] were able to replicate only 14 of 62. It appears that the cumulated body of economic knowledge may be filled with incorrect results. Of course, nobody knows which results are correct and which are incorrect. The only prospsect for purging these incorrect results is for the principle of replication to be embraced actively by all parts of the economics profession: journals, researchers, professors and students. The philospher C.S. Peirce [12] identified the “unlimited community” of investigators as the sole guarantor of the integrity of the scientic method. In order for the scientific method to succeed at uncovering truth, the members of the community must not be selfish – to the contrary, they must identify their own inerests with those of the unlimited community. In this way, they can correct each other’s errors and build effectively on each other’s work, and in so doing ultimately arrive at the truth. Regrettably, many researchers prefer to put their own interests ahead of those of the scientific community, and do not make their research available for inspection by others. While this is “rational” behavior by a utility-maximizing economist (see, e.g., Mirowski and Sklivas [11]), one would hope that institutional constructs would provide incentives to counteract this behavior. Yet too many journals refuse to ensure that the “research” they publish can be checked for accuracy by independent third parties. Some journals have paid lip service to the scientific method. For example, in response to DTA, the American Economic Review adopted a “replication policy” [1] whereby authors would agree to make available their data and code for purposes of
Privacy and Integrity Preserving in Cloud Storage Devices

Cloud computing is an internet based model which allows the user all the “services on demand”. The services provided by cloud are infrastructure, software and platform. Cloud Computing has great potential of providing robust computational power to the society at reduced cost. Despite the tremendous benefits, security is the primary obstacle that prevents the wide adoption of this promising computing model, especially for customers when their confidential data are consumed and produced during the computation. Wang proposed enabling public audit ability and data dynamics for storage security in cloud computing which provides data integrity and dynamic operation but cannot assure confidentiality. Here in this scheme we are providing a new method which provide confidentiality and also manage the storage space in cloud server. In this we are providing confidentiality by using cryptographic algorithm and storage space is managed by using complete binary tree by arranging all the files by their size and checking the integrity using TPA(third party auditor). Thus providing integrity, memory management as well as confidentiality in cloud computing.
TLM METHOD AND SGI INDEX AS AN INDICATOR OF GROUNDWATER DROUGHT

Previous studies of drought in Poland practically neglected the aspect of groundwater shortage, focusing on atmospheric, agricultural and hydrological drought. Therefore, the aim of this work was groundwater drought analysis in selected sites of South-Western Poland, based on the analytical methods used in other European countries. The intermediate objective was to assess the possibility of using the TLM method and the SGI for monitoring groundwater drought based on data from the National Geological Institute – National Research Institute. Investigations demonstrated that both methods gave results that complemented existing information on droughts in Poland in the last 30 years. Studies show that in the 1990s there was groundwater drought, not only atmospheric and agricultural drought described by Bąk and Łabędzki (2002), Bobiński, Meyer (1992, 1992), Bartczak (2014).