Miracle-dz/UniFAR-FTUs huggingface dataset:
Turning heterogeneity into an advantage in overlay routing

Distributed hash table (DHT)-based overlay networks, represented by Pastry, CAN, and Chord, offer an administration-free and fault-tolerant application-level overlay network. While elegant from a theoretical perspective, these systems have some disadvantages. First, they rely on application-level routing, which may be inefficient with respect to network delays and bandwidth consumption. Second, they typically construct a homogeneously structured overlay even though nodes in these networks usually have varying physical connectivity and packet-forwarding capacities. In this paper, we propose two approaches for constructing an auxiliary expressway network to take advantage of the different connectivity, forwarding capacities, and availabilities of the nodes. As a result, we are able to reconcile the conflict of presenting the applications with a homogeneous structured overlay to simplify management, while at the same time taking advantage of the inherent heterogeneity of the underlying physical network to speed up routing. Our simulation results show that our expressway can achieve close to optimal routing performance (on average, 1.07 and 1.41 times optimal routing for an Internet-like topology and a large synthesized transit-stub graph, respectively) in overlay networks.
High Electroporation Efficiency of Corynebacterium glutamicum with Xenogeneic Plasmid DNA

The restriction-modification systems of C. glutamicum impede its uptake of foreign DNA and thus limiting its transformation efficiency. Here we investigated the possibility of improving the transformation efficiency of C. glutamicum by characterizing and circumventing their restriction/modification barrier, as well as by optimizing the conditions of electroporation. We found that, among various conditions tested for electroporation, the most important factor is the source of plasmid DNA. When plasmid DNA isolated from the dam--dcm- E. coli mutant JM110 was used for transformation of C. glutamicum that had been grown in BHIS supplemented with glycine 2.5% (w/v), INH (4 mg/ml) and tween80 0.1% (w/v) at 18°C, and harvested at an OD600 of 0.5, the maximum transformation efficiency of 6.5×106 transformants/µg of plasmid DNA was obtained at a field strength of 20 kV/cm, while plasmid DNA isolated from the other E. coli strains such as DH5&#945; led to a extremely low level of transformation efficiency. Our observations strongly indicate that the use of unmethylated plasmid DNA is critical to achieve high transformation efficiency in C. glutamicum.
The GIVE-2 Corpus of Giving Instructions in Virtual Environments

We present the GIVE-2 Corpus, a new corpus of human instruction giving. The corpus was collected by asking one person in each pair of subjects to guide the other person towards completing a task in a virtual 3D environment with typed instructions. This is the same setting as that of the recent GIVE Challenge, and thus the corpus can serve as a source of data and as a point of comparison for NLG systems that participate in the GIVE Challenge. The instruction-giving data we collect is multilingual (45 German and 63 English dialogues), and can easily be extended to further languages by using our software, which we have made available. We analyze the corpus to study the effects of learning by repeated participation in the task and the effects of the participants' spatial navigation abilities. Finally, we present a novel annotation scheme for situated referring expressions and compare the referring expressions in the German and English data.
Women's interest in GP-initiated pre-conception counselling in The Netherlands.

BACKGROUND Pre-conception counselling has the potential to reduce pregnancy complications and congenital disorders. The timing of counselling, before conception, is crucial to maximize the benefit. As many couples are unaware of their risk status and the fact that the first period of pregnancy is crucial, they do not seek information before pregnancy occurs. To reach couples with timely information, it seems that a health care worker needs to take the initiative. In The Netherlands, the GP is in an ideal position to offer pre-conception counselling. OBJECTIVE The aim of this study was to determine the interest of women aged 18-40 in pre-conception counselling if this is offered to them by their own GP. METHOD A cohort of women (n = 1206) received a personal letter from their own GP with an offer of pre-conception counselling. The women were requested to fill in a reply form, indicating if they were interested, might be interested (if they decided to become pregnant) or were not interested in an invitation for pre-conception counselling. When interested, they were asked to give an indication as to when they were planning a pregnancy. Women who were not interested were requested to give a reason. RESULTS Almost 70% of the women returned the reply form. Up to the age of 29 years, at least 80% of the respondents were interested or might be interested should they decide to have children. Most women, especially the younger women, do not know exactly when they wish to become pregnant. Regardless of age, >70% of the respondents were interested. Only 11% of the respondents indicated specifically that they were not interested in advice. CONCLUSION Women are interested in GP-initiated pre-conception counselling. Further research is needed to assess the effect of programmed and systematic pre-conception counselling, offered by GPs, on pregnancy outcome and the health of the children. A randomized controlled trial to assess these effects currently is being conducted at the Department of General Practice in Leiden.
Techniques to Reduce the Ammonia Emission from a Cowshed with Tied Dairy Cattle

The influence of different techniques to reduce the ammonia emission from a building with 42 tied dairy cows was investigated at the university farm Brogarden in Skara, Sweden. The release of ammonia from the building was measured before and after measures were taken to reduce the emission. The following changes of the building design were made in 2000; improved gutters with a 3% slope towards a urine drainage channel equipped with a rotating auger; cooling of manure by water pipes in the gutters and manure gas ventilation from the urine channels and manure culvert. The air flow through the manure and urine disposal system was adjusted to prevent ammonia from being released to the inside air without increasing the total emission. The concentrations of ammonia in the exhaust air and ventilation rates were monitored continuously using an infrared spectrophotometer and outlet impellers. Before changing the building design the average ammonia emission was 42 g/h corresponding to 24 g/cow and day, which was equivalent to a nitrogen loss of 5.5%. During the same period the average daily ammonia concentration in the cowshed was 8 ppm. The first year after the changes had been made the ammonia emission through the exhaust air was reduced with 38% to 15 g/cow and day. The second year the ammonia emission was 18 g/cow and day. The average nitrogen loss after the changes of the building was 4.0%. The average ammonia concentration inside the building was reduced to 3 ppm.
Electron and Positron Fluxes in Primary Cosmic Rays Measured with the Alpha Magnetic Spectrometer on the International Space Station

Precision measurements by the Alpha Magnetic Spectrometer on the International Space Station of the primary cosmic-ray electron flux in the range 0.5 to 700 GeV and the positron flux in the range 0.5 to 500 GeV are presented. The electron flux and the positron flux each require a description beyond a single power-law spectrum. Both the electron flux and the positron flux change their behavior at ∼30 GeV but the fluxes are significantly different in their magnitude and energy dependence. Between 20 and 200 GeV the positron spectral index is significantly harder than the electron spectral index. The determination of the differing behavior of the spectral indices versus energy is a new observation and provides important information on the origins of cosmic-ray electrons and positrons.
Molecular Characterization of the Diversity and Distribution of a Thermal Spring Microbial Community by Using rRNA and Metabolic Genes

ABSTRACT The diversity and distribution of a bacterial community from Coffee Pots Hot Spring, a thermal spring in Yellowstone National Park with a temperature range of 39.3 to 74.1°C and pH range of 5.75 to 6.91, were investigated by sequencing cloned PCR products and quantitative PCR (qPCR) of 16S rRNA and metabolic genes. The spring was inhabited by three Aquificae genera—Thermocrinis, Hydrogenobaculum, and Sulfurihydrogenibium—and members of the Alpha-, Beta-, and Gammaproteobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, and candidate division OP5. The in situ chemical affinities were calculated for 41 potential metabolic reactions using measured environmental parameters and a range of hydrogen and oxygen concentrations. Reactions that use oxygen, ferric iron, sulfur, and nitrate as electron acceptors were predicted to be the most energetically favorable, while reactions using sulfate were expected to be less favorable. Samples were screened for genes used in ammonia oxidation (amoA, bacterial gene only), the reductive tricarboxylic acid (rTCA) cycle (aclB), the Calvin cycle (cbbM), sulfate reduction (dsrAB), nitrogen fixation (nifH), nitrite reduction (nirK), and sulfide oxidation (soxEF1) by PCR. Genes for carbon fixation by the rTCA cycle and nitrogen fixation were detected. All aclB sequences were phylogenetically related and spatially correlated to Sulfurihydrogenibium 16S rRNA gene sequences using qPCR (R2 = 0.99). This result supports the recent finding of citrate cleavage by enzymes other than ATP citrate lyase in the rTCA cycle of the Aquificaceae family. We briefly consider potential biochemical mechanisms that may allow Sulfurihydrogenibium and Thermocrinis to codominate some hydrothermal environments.
MvirDB—a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications

Knowledge of toxins, virulence factors and antibiotic resistance genes is essential for bio-defense applications aimed at identifying ‘functional’ signatures for characterizing emerging or engineered pathogens. Whereas genetic signatures identify a pathogen, functional signatures identify what a pathogen is capable of. To facilitate rapid identification of sequences and characterization of genes for signature discovery, we have collected all publicly available (as of this writing), organized sequences representing known toxins, virulence factors, and antibiotic resistance genes in one convenient database, which we believe will be of use to the bio-defense research community. MvirDB integrates DNA and protein sequence information from Tox-Prot, SCORPION, the PRINTS virulence factors, VFDB, TVFac, Islander, ARGO and a subset of VIDA. Entries in MvirDB are hyperlinked back to their original sources. A blast tool allows the user to blast against all DNA or protein sequences in MvirDB, and a browser tool allows the user to search the database to retrieve virulence factor descriptions, sequences, and classifications, and to download sequences of interest. MvirDB has an automated weekly update mechanism. Each protein sequence in MvirDB is annotated using our fully automated protein annotation system and is linked to that system's browser tool. MvirDB can be accessed at .
Optimizing Stroke Systems of Care by Enhancing Transitions Across Care Environments

Stroke affects many aspects of the lives of stroke survivors and their family caregivers. Supporting long-term recovery and rehabilitation are necessary to help stroke survivors adapt to living with the effects of stroke and to help family members adapt to the caregiving role. During recovery and rehabilitation, many elements of the health care continuum are utilized, including emergency response, acute care, inpatient and outpatient rehabilitation, and community and long-term care. With the advent of thrombolytic therapy and the benefits of stroke units, stroke survival and outcomes are improving. As a result, the current emphasis of stroke system improvement is to implement stroke units throughout the developed world. To enhance the patient centeredness of stroke care delivery, an important next phase of stroke system improvement will center on the experiences of stroke survivors and their family caregivers as they move through diverse care environments. The objective of this article was to conduct a scoping review of the literature on stroke transitions to identify the current areas of research emphasis. This article highlights stroke survivors’ and family caregivers’ experiences with transitions across care environment and some potential strategies to improve those transitions.
Unified Hanani-Tutte Theorem

We introduce a common generalization of the strong Hanani-Tutte theorem and the weak Hanani-Tutte theorem: if a graph $G$ has a drawing $D$ in the plane where every pair of independent edges crosses an even number of times, then $G$ has a planar drawing preserving the rotation of each vertex that was incident only to even edges in $D$. The theorem is implicit in the proof of the strong Hanani-Tutte theorem by Pelsmajer, Schaefer and \v{S}tefankovi\v{c}. We give a new, somewhat simpler proof.
Service Selection Algorithm Based on Constraint for Cloud Workflow System

It is possible to utilize cloud computing to address the problems of resource extendibility and flexibility for managing large scale workflow applications. Therefore, the investigation of workflow systems based on cloud computing, namely cloud workflow systems is a timely issue and worthwhile for increasing efforts. The technology and application of workflow in cloud computing environment also becomes a research focus. The paper firstly proposes a brief introduction to the cloud workflow system. Next, based on cloud architecture, the paper presents the architecture of cloud workflow system. Then, as the key content of the paper, considering the service selection strategy based on constraint, the paper presents a new service selection algorithm–SSAC. The simulation results show that SSAC algorithm further decreases the total execution cost and total execution time in comparison with other algorithms.
Appearance-based Localization across Seasons in a Metric Map

In this paper we address the problem of appearance-based long-term outdoor localization across seasons. This is a difficult task due to the changing appearance of visual landmarks across seasons and time of day. Our approach operates based on the premise that combining visual landmarks observed at different times of the year into a single metric map will yield better localization results than a map created from a single sequence alone. We integrate stereo imagery collected at two different times of the year into a unified 3D map, and use this as the basis for localization. A landmark visibility prediction framework is utilized to efficiently retrieve a small subset of landmarks and their feature descriptors from a database of millions of landmarks. The proposed approach is experimentally validated on a challenging sequence collected a year earlier.
An ABI3-interactor of conifers responds to multiple hormones

CnAIP2 (Callitropsis nootkatensis ABI3-Interacting Protein 2) was previously identified as a protein that interacts with the yellow-cedar ABI3 protein. CnAIP2 plays important roles during several key transitions of the plant lifecycle and acts as a global regulator with functions opposite to those of ABI3 proteins. Here we report that the CnAIP2 gene promoter is strongly upregulated by all of the major plant hormones. Young Arabidopsis seedlings expressing a chimeric CnAIP2pro-GUS construct were subjected to exogenously applied hormones; the maximum fold-enhancement of GUS activity was as high as 47-fold, and each hormone showed a distinctive cell/tissue-specific pattern of GUS induction. By far the greatest response was elicited by the synthetic auxin 2,4-D (47-fold induction); the other hormones tested stimulated GUS activities by 8- to 21-fold. The CnAIP2 promoter also responded to glucose and salt (NaCl), albeit to a lesser extent (2- to 3-fold induction). As well as acting in an antagonistic way to the global regulator ABI3, CnAIP2 appears to participate in multiple hormonal crosstalk pathways to carry out its functions.
A Study on Pore Diameter Distribution of Saliniferous Dredger Fill Consolidated by Vacuum Preloading

The pore structure of soil plays a decisive role in its engineering properties. In order to investigate the consolidation effect and pore distribution characteristic of saliniferous dredger fill after vacuum preloading, the indoor simulation experiments of vacuum preloading were carried out in two boxes, after vacuum preloading, the dredger fill was tested for its physicochemical and mechanical properties. Simultaneously, the mercury intrusion porosimetry was performed to obtain distribution of pore characteristic parameters, and analyzed its pore diameter distribution of dredger fill after vacuum preloading and the consolidation effect in the perspective of micro and macro. The research showed that the total pore volume and porosity of the No.1 box is lower than the No.2 box, and its bearing capacity and consolidation effect are much higher. When the dredger fill locates at the same distance from drainage plate, the deeper the dredger fill is buried, the smaller the porosity is, the better the bearing capacity and consolidation effect are. The pore of dredger fill in No.1 box is based mainly on meso pore, while the one in No.2 box is based mainly on meso pore and macro pore.
PSI Conscious Write Scheduling: Architectural Support for Reliable Power Delivery in 3-D Die-Stacked PCM

In 3-D-stacked memory chips, the problem of power supply integrity (PSI) is aggravating due to the additional through-silicon-via resistance and the higher current density in 3-D power delivery network. In particular, for the 3-D phase-change memory (PCM) well known for its high-amplitude programming current, IR-drop violation poses a serious threat that enforces a strict guard band of requesting concurrence, and consequently reduces the write throughput. This paper presents the implication of an IR-drop phenomenon in a 3-D PCM cube, and investigates IR-drop's impacts on write management in the PCM. From the obtained SPICE simulation results, we find that the issued writes have to meet the IR-drop constraint to be reliably processed, and then propose a PSI conscious write scheduler to improve the write performance within the constraint of the IR-drops and the power budget in the 3-D PCM cube. First, a Bloom-filter-based method is proposed to avoid the invalid write decisions for the PCM. Second, to support fine-grained write management in the cutting-edge PCM, we develop an inexpensive approach, weighted token assignment (WTA), to filter out PSI-unsafe write decisions by employing a support vector machine-based learning model. Last, a write reordering policy is proposed to cooperate with WTA and optimize the total write throughput for better memory performance. In the simulated hybrid main memory composed of both dynamic random access memory and 3-D PCM, the proposed scheduler significantly improves the write throughput.
Human immunodeficiency virus (HIV) type 1 infection status and in vitro susceptibility to HIV infection among high-risk HIV-1-seronegative hemophiliacs.

Blood samples were obtained from 16 hemophiliacs who had a 50%-94% defined risk of human immunodeficiency virus (HIV) type 1 infection on the basis of treatment history and from 14 controls not at risk for HIV infection. HIV-1 was not detected in any of 12 patient samples by cocultivation nor in 14 patient samples by the polymerase chain reaction. Peripheral blood cells from 7 seronegative hemophiliacs at highest risk of seroconversion (94%) were less susceptible to HIV-1 infection in vitro than were cells from healthy controls (P < .025, one-tailed Wilcoxon rank sum test). In contrast, the susceptibility to HIV-1 infection of lymphocytes from 6 seronegative hemophiliacs at moderate risk (50%-56%) of seroconversion did not differ from that of cells from controls or from high-risk hemophiliacs. Therefore, prolonged periods of seronegative HIV-1 infection are not common in this high-risk population. In addition, among hemophiliacs there may exist heterogeneity in susceptibility to HIV-1 infection in vitro and in vivo.
Transfer-messenger RNA-SmpB Protein Regulates Ribonuclease R Turnover by Promoting Binding of HslUV and Lon Proteases*

Background: RNase R is unstable due to its acetylation and resulting binding of tmRNA-SmpB but is stabilized under stress conditions. Results: tmRNA-SmpB promotes RNase R proteolysis by stimulating binding of Lon and HslUV. Conclusion: Acetylation initiates a series of events ultimately leading to RNase R proteolysis. Significance: This work elucidates a novel regulatory mechanism previously unknown in bacteria. RNase R, an important exoribonuclease involved in degradation of structured RNA, is subject to a novel mechanism of regulation. The enzyme is extremely unstable in rapidly growing cells but becomes stabilized under conditions of stress, such as stationary phase or cold shock. RNase R instability results from acetylation which promotes binding of tmRNA-SmpB, two trans-translation factors, to its C-terminal region. Here, we examine how binding of tmRNA-SmpB leads to proteolysis of RNase R. We show that RNase R degradation is due to two proteases, HslUV and Lon. In their absence, RNase R is stable. We also show, using an in vitro system that accurately replicates the in vivo process, that tmRNA-SmpB is not essential, but it stimulates binding of the protease to the N-terminal region of RNase R and that it does so by a direct interaction between the protease and SmpB which stabilizes protease binding. Thus, a sequence of events, initiated by acetylation of a single Lys residue, results in proteolysis of RNase R in exponential phase cells. RNase R in stationary phase or in cold-shocked cells is not acetylated, and thereby remains stable. Such a regulatory mechanism, dependent on protein acetylation, has not been observed previously in bacterial cells.
Gelatin- and DNA-based ionic conducting membranes for electrochromic devices

Gelatin and DNA are abundant natural products with very good biodegradation properties and can be used to obtain acetic acid or LiClO4-based gel polymer electrolytes (GPEs) with high ionic conductivity and good stability. This article presents the results of the ionic conductivity measurements of GPEs membranes based on crosslinked and plasticized gelatin and on plasticized DNA as well as on inserted/extracted charge density of electrochemical devices (ECDs) obtained with these samples. The membranes were analyzed by impedance spectroscopy, UV-Vis spectroscopy and the ECDs by charge density measurements, respectively. At room temperature the measured ionic conductivity of the membranes is in the range of 10-4-10-5 S/cm. It obeys predominantly an Arrhenius relationship in function of temperature. The ECD with red gelatin changed the color from red to deep red and the ECD with DNA-based electrolyte changes from transparent to blue. The inserted charge density values of these ECDs were of -3.0 mC/cm2 for the device with red gelatin and -6.6 mC/cm2 for the ECD with DNA-based electrolyte. The reverse potential application promoted a charge extraction and, as consequence, bleaching of the devices. Good ionic conductivity results combined with transparency and good adhesion to the electrodes and promising preliminary results of small ECDs have shown that gelatin and DNA-based GPEs are very promising materials to be used as gel polymer electrolytes in electrochromic devices.