Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction and In Vitro Properties of a Series of Attenuated Simian Immunodeficiency Viruses with All Accessory Genes Deleted

ABSTRACT We have generated simplified simian immunodeficiency virus (SIV) constructs lacking the nef, vpr,vpx, vif, tat, and revgenes (Δ6 viruses). To accomplish this, we began with an infectious molecular clone of SIV, i.e. SIVmac239, and replaced the deleted segments with three alternate elements: (i) a constitutive transport element (CTE) derived from simian retrovirus type 1 to replace the Rev/Rev-responsive element (RRE) posttranscriptional regulation system, (ii) a chimeric SIV long terminal repeat (LTR) containing a cytomegalovirus (CMV) promoter to augment transcription and virus production, and (iii) an internal ribosome entry site (IRES) upstream of the env gene to ensure expression of envelope proteins. This simplified construct (Δ6CCI) efficiently produced all viral structural proteins, and mature virions possessed morphology typical of wild-type virus. It was also observed that deletion of the six accessory genes dramatically affected both the specificity and efficiency of packaging of SIV genomic RNA into virions. However, the presence of both the CTE and the chimeric CMV promoter increased the specificity of viral genomic RNA packaging, while the presence of the IRES augmented packaging efficiency. The Δ6CCI virus was extremely attenuated in replication capacity yet retained infectiousness for CEMx174 and MT4 cells. We also generated constructs that retained either the rev gene or both the rev andvif genes and showed that these viruses, when complemented by the CMV promoter, i.e., Δ5-CMV and Δ4-CMV, were able to replicate in MT4 cells with moderate and high-level efficiency, respectively. Long-term culture of each of these constructs over 6 months revealed no potential for reversion. We hope to shortly evaluate these simplified constructs in rhesus macaques to determine their long-term safety as well as ability to induce protective immune responsiveness as proviral DNA vaccines.
New Surgical Technique for Management of Recurrent Macular Hole

Recurrence of macular hole (MH) following the standard approach of pars plana vitrectomy, posterior hyaloids removal, internal limiting membrane peeling, gas tamponade, and postoperative positioning is a common postoperative complication following MH surgery. We present a new surgical technique which involves induction of serous macular detachment around the MH, parafoveal retinal massage to bring its edges closer, gas tamponade, and face down positioning. The recurrent MHs had closed in all four consecutive patients with a parallel gain in visual acuity following this technique. All patients had Type 1 closure of the MH indicating its closure without any defect of the neurosensory retina. The MHs remained closed during the follow-up without any late reopening.
Mineralisation of soil organic nitrogen and microbial respiration after simulated summer rainfall events in an agricultural soil

Simulated rainfall events were applied during the summer fallow period to a Western Australian agricultural soil, a loamy sand, under continuous wheat and after the second pasture phase of a 2 pasture : 1 wheat (2P : 1W) rotation. The aims of this study were to determine the change in microbial activity, amount of net and gross nitrogen (N) mineralised, and inorganic N produced after dry soil was re-wet during summer rainfall. Three irrigation treatments were applied: (i) control soils received no water, (ii) the single wet treatment received 45 mm of water on day 0 and was allowed to dry, and (iii) the multiple wet treatment received 45 mm of water on day 0 plus further applications of 5 mm on days 3 and 8. The CO2 production and N mineralisation were measured in the surface 10 cm of soil for a period of 14 days after initial irrigation. Net N mineralisation was measured from in situ incubation of soil cores and gross N mineralisation by 15N isotopic dilution. The CO2 production was measured by infrared gas analysis of air samples taken from a closed headspace above the soil. A large flush in CO2 production and gross N mineralisation occurred immediately after rewetting the dry soil. This response was short-lived and rates of CO2 production and gross N mineralisation declined rapidly after 2 days. After irrigation on day 0, CO2 production was twice as large and gross N mineralisation was slightly larger in the 2P : 1W soil than continuous wheat. Gross N mineralisation and CO2 production were not significantly different in the multiple and single wet treatments after the re-wet on day 3, but an additional flush in activity occurred in the multiple wet treatment after the re-wet on day 8. The patterns of gross N mineralisation and CO2 production corresponded to changes in the soil water content, especially in the surface 2·5 cm of soil. Net and gross N mineralised and gross N immobilised over the 14-day period after the initial re-wet were greater in the multiple wet compared with the single wet treatments under both wheat and 2P : 1W. However, gross N mineralisation was approximately 4-fold greater than net N mineralisation under wheat and 15-fold greater under 2P : 1W. The majority of gross N mineralised after simulated summer rainfall was immobilised which resulted in an increase in inorganic N within the soil profile (0-50 cm) during opening winter rains.
Multidimensional Human Dynamics in Mobile Phone Communications

In today's technology-assisted society, social interactions may be expressed through a variety of techno-communication channels, including online social networks, email and mobile phones (calls, text messages). Consequently, a clear grasp of human behavior through the diverse communication media is considered a key factor in understanding the formation of the today's information society. So far, all previous research on user communication behavior has focused on a sole communication activity. In this paper we move forward another step on this research path by performing a multidimensional study of human sociality as an expression of the use of mobile phones. The paper focuses on user temporal communication behavior in the interplay between the two complementary communication media, text messages and phone calls, that represent the bi-dimensional scenario of analysis. Our study provides a theoretical framework for analyzing multidimensional bursts as the most general burst category, that includes one-dimensional bursts as the simplest case, and offers empirical evidence of their nature by following the combined phone call/text message communication patterns of approximately one million people over three-month period. This quantitative approach enables the design of a generative model rooted in the three most significant features of the multidimensional burst - the number of dimensions, prevalence and interleaving degree - able to reproduce the main media usage attitude. The other findings of the paper include a novel multidimensional burst detection algorithm and an insight analysis of the human media selection process.
Truncated Pyramid Peer-to-Peer Architecture with Vertical Tunneling Model

Peer-to-Peer (P2P) technologies have many advantages over traditional client/server technologies, including cost-effectiveness, scalability and robustness, due to their decentralized network structure. However, the performance has traditionally been an issue in P2P systems. Especially the higher lookup latencies, when compared with the traditional client/server systems, have been the bottleneck in many P2P systems. In this paper, we propose a truncated pyramid P2P architecture together with an enhanced model, Vertical Tunneling Model (VTM) for improving the lookup performance. The proposed architecture is built on Peer-to-Peer SIP (P2PSIP) network. VTM builds up vertical tunnels between the upper and lower sub-overlays to speed up the service lookup and decrease the session setup delay. Based on the performance analysis and results, it is shown that VTM has better performance compared with the existing systems in average lookup hops, which is about 1/3 of that of the existing systems, the predominance is more evident as the network scale increases.
Mass flow deposits on a mid-Tertiary carbonate shelf, southern New Zealand

Summary Sheet-like and channel-filling conglomerates and pebbly biomicrudites occur within a sequence of cross-stratified shallow-water bioclastic limestones, the Forest Hill Formation of Late Oligocene to Early Miocene age. The largest channel, 50 m wide, 9 m deep, and at least 1.2 km long, is infilled with four separate conglomerate units of pebble- to boulder-sized limestone lithoclasts in a sparse muddy matrix (biomicrudite). Both the conglomerates and associated pebbly biomicrudites possess features characteristic of high concentration mass flows - both of laminar flow (preferred clast orientation, inverse grading or massive bedding) and of turbulent flow (normal coarse-tail or distribution grading and stratification). Clast imbrication (a- or b-axes) is suggestive of gradual deposition. Some flows travelled far enough to allow both vertical and horizontal differentiation of the coarse sediment. Facies models which have been proposed for conglomerates of deep water (turbidite) association can also be applied to the small-scale neritic conglomerates. Formation and remobilisation of such coarse grained facies in a shelf setting is attributed to eustatic sea-level changes and/or to local tectonism.
Absolute Proteome and Phosphoproteome Dynamics during the Cell Cycle of Schizosaccharomyces pombe (Fission Yeast)*

To quantify cell cycle-dependent fluctuations on a proteome-wide scale, we performed integrative analysis of the proteome and phosphoproteome during the four major phases of the cell cycle in Schizosaccharomyces pombe. In highly synchronized cells, we identified 3753 proteins and 3682 phosphorylation events and relatively quantified 65% of the data across all phases. Quantitative changes during the cell cycle were infrequent and weak in the proteome but prominent in the phosphoproteome. Protein phosphorylation peaked in mitosis, where the median phosphorylation site occupancy was 44%, about 2-fold higher than in other phases. We measured copy numbers of 3178 proteins, which together with phosphorylation site stoichiometry enabled us to estimate the absolute amount of protein-bound phosphate, as well as its change across the cell cycle. Our results indicate that 23% of the average intracellular ATP is utilized by protein kinases to phosphorylate their substrates to drive regulatory processes during cell division. Accordingly, we observe that phosphate transporters and phosphate-metabolizing enzymes are phosphorylated and therefore likely to be regulated in mitosis.
Identifying Software Project Risks: An International Delphi Study

Advocates of software risk management claim that by identifying and analyzing threats to success (i.e., risks) action can be taken to reduce the chance of failure of a project. The first step in the risk management process is to identify the risk itself, so that appropriate countermeasures can be taken. One problem in this task, however, is that no validated lists are available to help the project manager understand the nature and types of risks typically faced in a software project. This paper represents a first step toward alleviating this problem by developing an authoritative list of common risk factors. We deploy a rigorous data collection method called a "ranking-type" Delphi survey to produce a rank-order list of risk factors. This data collection method is designed to elicit and organize opinions of a panel of experts through iterative, controlled feedback. Three simultaneous surveys were conducted in three different settings: Hong Kong, Finland, and the United States. This was done to broaden our view of the types of risks, rather than relying on the view of a single culture-an aspect that has been ignored in past risk management research. In forming the three panels, we recruited experienced project managers in each country. The paper presents the obtained risk factor list, compares it with other published risk factor lists for completeness and variation, and analyzes common features and differences in risk factor rankings in the three countries. We conclude by discussing implications of our findings for both research and improving risk management practice.
Japanese Morphological Analyzer using Word Co-occurrence - JTAG

We developed a Japanese morphological analyzer that uses the co-occurrence of words to select the correct sequence of words in an unsegmented Japanese sentence. The co-occurrence information can be obtained from cases where the system incorrectly analyzes sentences. As the amount of information increases, the accuracy of the system increases with a small risk of degradation. Experimental results show that the proposed system assigns the correct phonological representations to unsegmented Japanese sentences more precisely than do other popular systems.
Trends in snag populations in Northern Arizona mixed-conifer and ponderosa pine forests, 1997-2012

Snags (standing dead trees) are important components of forests that contribute to ecological processes and provide habitat for many life forms. We monitored dynamics of snag populations on 1-ha plots in southwestern mixed-conifer (n = 53 plots) and ponderosa pine (Pinus ponderosa, n = 60 plots) forests in north-central Arizona from 1997 to 2002. Of 2,240 snags marked in 1997, at least 76% remained standing in 2002, 17% had fallen and were relocated as logs, 0.5% were cut down, and the remainder (6%) were unaccounted for. Snag density increased significantly in mixed-conifer forest but not in ponderosa pine forest. Snag density increased mainly in the smaller size classes in both forest types. Density of large snags (≥46 cm in diameter and 9 m in height) increased slightly but nonsignificantly from 1997 levels in both forest types, and fell below current targets for retention. Species composition of snags differed between 1997 and 2002 in ponderosa pine forest, but not in mixed-conifer forest, and decay-class distributions differed among years in both forest types. A classification-tree analysis indicated that a ratio of height to diameter, species, and diameter were key variables in predicting whether a snag survived from 1997 to 2002. These results provide empirical data on snag populations and dynamics in this area and establish a basis for longer-term monitoring of snag populations and dynamics.
PATIENTS LONGING FOR AUTHENTIC PERSONAL CARE: A PHENOMENOLOGICAL STUDY OF VIOLENT ENCOUNTERS IN PSYCHIATRIC SETTINGS

This article focuses on patients' violence against caregivers. Several studies show that violence and threats within the health care setting are an increasing problem. Encounters that become violent have been the issue of many debates but the phenomenon is still not fully understood. It is important to understand the course of events in violent encounters, both for the sake of the patients and the caregivers' well-being. The aim of this study was to describe the essence of violent encounters, as experienced by nine patients within psychiatric care. Guided by a phenomenological method, data were analyzed within a reflective lifeworld approach. The findings explicate violent encounters characterized by a tension between “authentic personal” and “detached impersonal” caring. “Authentic personal” patients are encountered in an undisguised, straightforward, and open way, and they sense unrestricted respect that caregivers would show another human being. In these encounters violence does not develop well. However, in caring that is “detached impersonal,” the encounters are experienced by the patients as uncontrolled and insecure. These encounters are full of risks and potential violence.
Novel Acid Phosphatase in Candida glabrata Suggests Selective Pressure and Niche Specialization in the Phosphate Signal Transduction Pathway

Evolution through natural selection suggests unnecessary genes are lost. We observed that the yeast Candida glabrata lost the gene encoding a phosphate-repressible acid phosphatase (PHO5) present in many yeasts including Saccharomyces cerevisiae. However, C. glabrata still had phosphate starvation-inducible phosphatase activity. Screening a C. glabrata genomic library, we identified CgPMU2, a member of a three-gene family that contains a phosphomutase-like domain. This small-scale gene duplication event could allow for sub- or neofunctionalization. On the basis of phylogenetic and biochemical characterizations, CgPMU2 has neofunctionalized to become a broad range, phosphate starvation-regulated acid phosphatase, which functionally replaces PHO5 in this pathogenic yeast. We determined that CgPmu2, unlike ScPho5, is not able to hydrolyze phytic acid (inositol hexakisphosphate). Phytic acid is present in fruits and seeds where S. cerevisiae grows, but is not abundant in mammalian tissues where C. glabrata grows. We demonstrated that C. glabrata is limited from an environment where phytic acid is the only source of phosphate. Our work suggests that during evolutionary time, the selection for the ancestral PHO5 was lost and that C. glabrata neofunctionalized a weak phosphatase to replace PHO5. Convergent evolution of a phosphate starvation-inducible acid phosphatase in C. glabrata relative to most yeast species provides an example of how small changes in signal transduction pathways can mediate genetic isolation and uncovers a potential speciation gene.
Study of magnitudes, seismicity, and earthquake detectability using a global network

Abstract Based on 10 yr of observations reported in the International Seismological Centre bulletins (1971-1980), m b magnitudes for about 70,000 earthquakes have been recomputed using a maximum-likelihood estimation technique. Reportings from a network of 115 globally distributed stations were used in these calculations. Comparison to conventional m b estimates show that the network magnitude bias problem is quite significant at low and intermediate magnitudes. Recurrence statistics based on the revised m b estimates give b values consistent with those obtained from LASA and NORSAR data, and indicate that the number of earthquakes worldwide of m b ≧ 4.0 averages about 7,500 annually. This number is much lower than previous estimates. The teleseismic detection capability of the network (requiring at least four detecting stations) has been evaluated based on recurrence statistics. The estimated 90 per cent incremental m b threshold ranges from 3.9 to 4.5 in the northern hemisphere and from 4.2 to 4.8 in the southern hemisphere. This is consistent with results obtained by the “Networth” approach.
Bag-of-Tasks Self-Scheduling over Range-Queriable Search Overlays

The opportunistic computing paradigm is extremely valuable to modern technical and scientific endeavors, as it can support the demand for large and steady amounts of computing capacity. The applications of opportunistic computing environments often require independent and intensive processing over different data sets, characterizing themselves as BoT applications. Opportunistic computing systems, however, usually employ centralized approaches to do task allocation, a problematic situation on sizable settings. This paper proposes and evaluates a peer-to-peer technique that allows the self-scheduling of tasks without any central controller whatsoever, aiming at opportunistic computing scenarios running BoT applications. Its key is to employ range query capabilities of search overlays like Skip Graphs as an infrastructure for fully distributed allocation decisions. Experimental results obtained in a message-passing simulator consisting of 5,000 nodes and 75,000 tasks show that central points of failure were eliminated and communication bottlenecks were highly alleviated, subject to some congestion characteristics of the search overlay.
Exercise training prevents ventricular tachycardia in CPVT1 due to reduced CaMKII-dependent arrhythmogenic Ca2+ release.

AIMS Catecholaminergic polymorphic ventricular tachycardia type 1 (CPVT1) is caused by mutations in the cardiac ryanodine receptor (RyR2) that lead to disrupted Ca(2+) handling in cardiomyocytes and ventricular tachycardia. The aim of this study was to test whether exercise training could reduce the propensity for arrhythmias in mice with the CPVT1-causative missense mutation Ryr2-R2474S by restoring normal Ca(2+) handling. METHODS AND RESULTS Ryr2-R2474S mice (RyR-RS) performed a 2 week interval treadmill exercise training protocol. Each exercise session comprised five 8 min intervals at 80-90% of the running speed at maximal oxygen uptake (VO2max) and 2 min active rest periods at 60%. VO2max increased by 10 ± 2% in exercise trained RyR-RS (ET), while no changes were found in sedentary controls (SED). RyR-RS ET showed fewer episodes of ventricular tachycardia compared with RyR-RS SED, coinciding with fewer Ca(2+) sparks and waves, less diastolic Ca(2+) leak from the sarcoplasmic reticulum, and lower phosphorylation levels at RyR2 sites associated with Ca(2) (+)-calmodulin-dependent kinase type II (CaMKII) compared with RyR-RS SED. The CaMKII inhibitor autocamtide-2-related inhibitory peptide and also the antioxidant N-acetyl-l-cysteine reduced Ca(2+) wave frequency in RyR-RS equally to exercise training. Protein analysis as well as functional data indicated a mechanism depending on reduced levels of oxidized CaMKII after exercise training. Two weeks of detraining reversed the beneficial effects of the interval treadmill exercise training protocol in RyR-RS ET. CONCLUSION Long-term effects of interval treadmill exercise training reduce ventricular tachycardia episodes in mice with a CPVT1-causative Ryr2 mutation through lower CaMKII-dependent phosphorylation of RyR2.
The last deglacial sea level rise in the South Pacific: offshore drilling in Tahiti (French Polynesia)

Integrated Ocean Drilling Program (IODP) Expedition 310 to the reef terraces around Tahiti, French Polynesia, was the second expedition to utilize a mission-specific platform and was conducted by the European Consortium for Ocean Research Drilling (ECORD) Science Operator (ESO). The objectives of Expedition 310 are to establish the course of last deglacial sea level rise at Tahiti, to define sea-surface temperature variations for the region over the period 20,000–10,000 cal. y BP, and to analyze the impact of sea level changes on reef growth and geometry. To meet these objectives, the last deglacial reef sequence, which consists of successive reef terraces seaward of the living barrier reef, was cored from a dynamically positioned vessel during October and November 2005. A total of 37 boreholes at 22 sites were cored in water depths ranging from 41.65 to 117.54 m. Borehole logging operations in ten boreholes at seven sites provided continuous geophysical information about the drilled strata. Cores were described during the Onshore Science Party at the IODP Bremen Core Repository during February and March 2006, where minimum and some standard measurements were made. Further postcruise research on samples taken during the Onshore Science Party is expected to fulfill the objectives of the expedition.
An exploration of pen rolling for pen-based interaction

Current pen input mainly utilizes the position of the pen tip, and occasionally, a button press. Other possible device parameters, such as rolling the pen around its longitudinal axis, are rarely used. We explore pen rolling as a supporting input modality for pen-based interaction. Through two studies, we are able to determine 1) the parameters that separate intentional pen rolling for the purpose of interaction from incidental pen rolling caused by regular writing and drawing, and 2) the parameter range within which accurate and timely intentional pen rolling interactions can occur. Building on our experimental results, we present an exploration of the design space of rolling-based interaction techniques, which showcase three scenarios where pen rolling interactions can be useful: enhanced stimulus-response compatibility in rotation tasks [7], multi-parameter input, and simplified mode selection.