Miracle-dz/UniFAR-FTUs huggingface dataset:
Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome

The archaeal exosome is a phosphorolytic 3′–5′ exoribonuclease complex. In a reverse reaction it synthesizes A-rich RNA tails. Its RNA-binding cap comprises the eukaryotic orthologs Rrp4 and Csl4, and an archaea-specific subunit annotated as DnaG. In Sulfolobus solfataricus DnaG and Rrp4 but not Csl4 show preference for poly(rA). Archaeal DnaG contains N- and C-terminal domains (NTD and CTD) of unknown function flanking a TOPRIM domain. We found that the NT and TOPRIM domains have comparable, high conservation in all archaea, while the CTD conservation correlates with the presence of exosome. We show that the NTD is a novel RNA-binding domain with poly(rA)-preference cooperating with the TOPRIM domain in binding of RNA. Consistently, a fusion protein containing full-length Csl4 and NTD of DnaG led to enhanced degradation of A-rich RNA by the exosome. We also found that DnaG strongly binds native and in vitro transcribed rRNA and enables its polynucleotidylation by the exosome. Furthermore, rRNA-derived transcripts with heteropolymeric tails were degraded faster by the exosome than their non-tailed variants. Based on our data, we propose that archaeal DnaG is an RNA-binding protein, which, in the context of the exosome, is involved in targeting of stable RNA for degradation.
This Paper Is Included in the Proceedings of the 12th Usenix Symposium on Operating Systems Design and Implementation (osdi '16). Shuffler: Fast and Deployable Continuous Code Re-randomization Shuffler: Fast and Deployable Continuous Code Re-randomization

While code injection attacks have been virtually eliminated on modern systems, programs today remain vulnerable to code reuse attacks. Particularly pernicious are Just-In-Time ROP (JIT-ROP) techniques, where an attacker uses a memory disclosure vulnerability to discover code gadgets at runtime. We designed a code-reuse defense , called Shuffler, which continuously re-randomizes code locations on the order of milliseconds, introducing a real-time deadline on the attacker. This deadline makes it extremely difficult to form a complete exploit, particularly against server programs that often sit tens of milliseconds away from attacker machines. Shuffler focuses on being fast, self-hosting, and non-intrusive to the end user. Specifically, for speed, Shuffler randomizes code asynchronously in a separate thread and atomically switches from one code copy to the next. For security, Shuffler adopts an " egalitarian " principle and randomizes itself the same way it does the target. Lastly, to deploy Shuffler, no source, kernel, compiler, or hardware modifications are necessary. Evaluation shows that Shuffler defends against all known forms of code reuse, including ROP, direct JIT-ROP, indirect JIT-ROP, and Blind ROP. We observed 14.9% overhead on SPEC CPU when shuffling every 50 ms, and ran Shuffler on real-world applications such as Nginx. We showed that the shuffled Nginx scales up to 24 worker processes on 12 cores.
Carer related research and knowledge: findings from a scoping review

The review discussed in this paper provides a unique synthesis of evidence and knowledge about carers. The authors adopted a scoping review methodology drawing on a wide range of material from many different sources published between 2000-16. It offers key insights into what we know and how we know it; reinforces and expands evidence about carers’ profile; shows knowledge is uneven e.g. much is known about working carers, young carers, and carers of people with dementia but far less i about older carers or caring for someone with multiple needs. A striking feature of much research is a focus on caring as a set of tasks, rather than a dimension of an, often dyadic, relationship. Whilst there is substantive evidence about the negative impact of caring, the review suggests that links between caring and carer outcomes are neither linear nor inevitable and vary in depth and nature. A reliance on cross-sectional studies using standardised measures is a major weakness of existing research: this approach fails to capture the multi-dimensionality of the caring role, and the lived experience of the carer. Although research relating to formal support suggests that specific interventions for particular groups of carers may be effective, overall the evidence base is weak. There is a tension between cost effectiveness and what is valued by carers. Developing robust evaluative models that accommodate this tension, and take account of the dyadic context of caring is a critical challenge. A fundamental deficit of carer related research is its location in one of two, largely separate, paradigmatic frameworks: the ‘Gatherers and Evaluators’ and the ‘Conceptualisers and Theorisers’. The authors suggest that developing an integrated paradigm, that draws on the strengths and methods of existing paradigms, has considerable potential to generate new knowledge and new evidence and extend understanding of care and caring.
Thin layer compared to direct smear in thyroid fine needle aspiration

The efficacy of preparing thyroid fine needle aspirations (FNAs) by the thin layer as opposed to the direct smear method has not been evaluated sufficiently in a regional laboratory setting. At the Foothills Hospital (Calgary, Canada), the method of processing thyroid FNAs was changed from direct smear to thin layer in January 1996. The results of 327 patients who had direct smear from 1994 to 1995 were compared to 401 who had thin layer between 1996 and 1997. While there were no significant differences across a broad range of quality indicators, thin layer showed a trend towards a higher proportion of true benign diagnoses (31%vs 24%), a lower proportion of inadequate specimens (41%vs 50%) and, most importantly, a lower false negative rate (3%vs 9%). In conclusion, the changeover to thin layer did not compromise the interpretation of thyroid FNAs.
Efficacy and safety of ustekinumab in psoriatic arthritis patients with peripheral arthritis and physician-reported spondylitis: post-hoc analyses from two phase III, multicentre, double-blind, placebo-controlled studies (PSUMMIT-1/PSUMMIT-2)

Objective To evaluate ustekinumab efficacy and safety in psoriatic arthritis (PsA) patients with peripheral arthritis and physician-reported spondylitis (termed the ‘spondylitis subset’). Methods Adults with active PsA (PSUMMIT-1/PSUMMIT-2, n=615/312) were randomised to ustekinumab 45 mg, 90 mg or placebo at week 0/week 4/q12 week. At week 16, patients with <5% improvement in tender and swollen joints entered blinded early escape. A subset of patients with physician-identified spondylitis was evaluated with spondylitis-specific assessments, including Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) and Ankylosing Spondylitis Disease Activity Score employing C reactive protein (ASDAS-CRP), through week 24. Results 256/927 (27.6%) PSUMMIT-1/PSUMMIT-2 patients (placebo/ustekinumab, n=92/164) comprised the evaluable spondylitis subset. At week 24, in this analysis subset, significantly more patients achieved BASDAI20/50/70 responses (54.8%/29.3%/15.3% vs 32.9%/11.4%/0%; p≤0.002), improvement in BASDAI question 2 concerning axial pain (1.85 vs 0.24; p<0.001) and mean per cent ASDAS-CRP improvements (27.8% vs 3.9%; p<0.001) for ustekinumab versus placebo recipients, respectively. Comparable to the overall study population, significant improvements were also achieved in psoriasis, peripheral arthritis, enthesitis, dactylitis, physical function and peripheral joint radiographs in the spondylitis subset. Conclusions In this post-hoc analysis of PsA patients with baseline peripheral arthritis and physician-reported spondylitis, ustekinumab-treated patients demonstrated significant improvements in axial signs and symptoms through week 24. Trial registration number PSUMMIT-1 (NCT01009086, EudraCT 2009-012264-14) and PSUMMIT-2 (NCT01077362, EudraCT 2009-012265-60); post-study results.
Mental health: a report of the Surgeon General.

America is home to a boundless array of cultures, races, and ethnicities. With this diversity comes incalculable energy and optimism. Diversity has enriched our Nation by bringing global ideas, perspectives, and productive contributions to all areas of contemporary life. The enduring contributions of minorities, like those of all Americans, rest on a foundation of mental health. Mental health is fundamental to overall health and productivity. It is the basis for successful contributions to family, community, and society. Throughout the lifespan, mental health is the wellspring of thinking and communication skills, learning, resilience, and selfesteem. It is all too easy to dismiss the value of mental health until problems appear. Mental health problems and illnesses are real and disabling conditions that are experienced by one in five Americans. Left untreated, mental illnesses can result in disability and despair for families, schools, communities, and the workplace. This toll is more than any society can afford.
Natural succession on abandoned cropland effectively decreases the soil erodibility and improves the fungal diversity.

Changes in plants and soils during natural succession have been evaluated, but little is known about the effects of succession on the activities of soil microbes and their interactions with soil erodibility. We conducted a field study on the Chinese Loess Plateau, typical of this semiarid area, to determine the effect of secondary succession on the stability of soil structure against erosion and on the composition of soil fungal communities. Characteristics of plant, soil, and fungal communities were assessed across a 30-yr chronosequence of grassland developed from abandoned cropland. The diversity and composition of the fungal communities were determined using high-throughput sequencing of the internal transcribed spacer. Six grasslands were selected to represent different successional age classes: 0 (cropland), 5, 10, 15, 20, and 30 yr. Short-term decreases (initial 5 yr) in the amounts of soil organic carbon, total nitrogen, available phosphorus, and fungal biomass and in fungal diversity had returned to original levels (i.e., cropland) within 15 yr and were much higher after continued succession. Abandoning cropland for succession caused the soil erodibility (K) decrease and the aboveground coverage, soil nutrient levels, content of larger (>5 mm) water-stable aggregate, mean aggregate weight diameter, and diversity of the fungal communities improvement including arbuscular mycorrhizas (AMF), ectomycorrhizas (EMF), and saprotrophs. The fungal communities were dominated by Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota during the succession. The successional patterns of the plant and fungal communities were similar, although distinct fungal communities were not observed in the two initial stages, suggesting that fungal succession may develop more slowly than plant succession. Plant root biomass, EMF, and soil organic carbon content accounted for most of the variation of soil erodibility (28.6%, 19.5%, and 11.8%, respectively), indicating their importance in shaping soil structure to prevent erosion. Our results demonstrated that abandoning cropland for natural succession could decrease soil erodibility and increase fungal diversity. EMF plays an important role in soil stability against erosion in the Loess Plateau. Abandoning cropland for natural succession should be recommended for alleviating soil erosion and improving the degraded soils in this area.
Abundance and survival of common benthic biota in a river affected by water diversion during an historic drought

Hydrologic changes, such as drought or managed flow, can influence the abundance and survival of aquatic biota. The purpose of this research is to understand the effects of naturally low streamflows coupled with water withdrawals on an abundant net-spinning caddisfly (Hydropsychidae) and a common benthic darter (Percidae). Results show that caddisfly production was lower than in a previous study and that larvae preferred habitats vulnerable to periodic exposure from water withdrawals, likely leading to the observed decline in abundance and production. Using capture-recapture methods, fish were estimated to be abundant with considerable site fidelity; estimated survival rates were lower for young-of-year fish compared to adult fish. Results from this study allow for future comparisons of fish population responses to interannual changes in streamflow. The coupling of natural drought and human-induced flow alterations provided a unique opportunity to study flow-ecology linkages in a sixth-order flowaltered stream. INDEX WORDS: Middle Oconee River, sixth-order stream, drought, water withdrawal, low streamflow, environmental flows, shoal, caddisfly, Hydropsychidae, secondary production, darter, Etheostoma inscriptum, survival, abundance, capture-recapture, tag loss ABUNDANCE AND SURVIVAL OF COMMON BENTHIC BIOTA IN A RIVER AFFECTED BY WATER DIVERSION DURING AN HISTORIC DROUGHT
Distributed Control of Wind Farm

The growing use of wind energy as major energy source, has led to the construction of large wind farms. The control of such wind farms is typically separated into control at wind turbine level and at wind farm level. The wind farm controller assures that the wind farm produces the demanded amount of power, by providing set-points for the turbines in the farm. The local turbine control assures that the local set-point is tracked. Current wind farm controllers conduct the power distribution in a static manner. In this work it is explored, how fatigue reduction in the wind farm can be achieved, by letting the controller distribute the power demand dynamically. In the first part of this work, the problem of reducing the fatigue on the turbines by dynamic power distribution is presented. A controller is designed based on this problem formulation, taking both tower and shaft fatigue into account. The controller is designed, such that it is both modular and scalable. This has the advantage of the controller being identical on all turbines in the wind farm. Also, the modularity allows turbines to be added or removed from the wind farm, without changing the controllers on the remaining turbines. Evaluation of the controller in a realistic simulation environment verifies the functionality of the controller, and shows that fatigue reductions of the tower and shaft in the magnitude of 10 % and 50 % respectively, can be expected. The final part of this work examines how the concept of fatigue reduction through dynamic wind farm control can be implemented on the offshore wind farm Thanet. Simulations indicate that the limitations of the server system at Thanet does not render this type of control possible. (Less)
Neighbor-cell assisted error correction for MLC NAND flash memories

Continued scaling of NAND flash memory to smaller process technology nodes decreases its reliability, necessitating more sophisticated mechanisms to correctly read stored data values. To distinguish between different potential stored values, conventional techniques to read data from flash memory employ a single set of reference voltage values, which are determined based on the overall threshold voltage distribution of flash cells. Unfortunately, the phenomenon of program interference, in which a cell's threshold voltage unintentionally changes when a neighboring cell is programmed, makes this conventional approach increasingly inaccurate in determining the values of cells. This paper makes the new empirical observation that identifying the value stored in the immediate-neighbor cell makes it easier to determine the data value stored in the cell that is being read. We provide a detailed statistical and experimental characterization of threshold voltage distribution of flash memory cells conditional upon the immediate-neighbor cell values, and show that such conditional distributions can be used to determine a set of read reference voltages that lead to error rates much lower than when a single set of reference voltage values based on the overall distribution are used. Based on our analyses, we propose a new method for correcting errors in a flash memory page, neighbor-cell assisted correction (NAC). The key idea is to re-read a flash memory page that fails error correction codes (ECC) with the set of read reference voltage values corresponding to the conditional threshold voltage distribution assuming a neighbor cell value and use the re-read values to correct the cells that have neighbors with that value. Our simulations show that NAC effectively improves flash memory lifetime by 33% while having no (at nominal lifetime) or very modest (less than 5% at extended lifetime) performance overhead.
Vaccination with autologous tumor-loaded dendritic cells induces clinical and immunologic responses in indolent B-cell lymphoma patients with relapsed and measurable disease: a pilot study.

Eighteen relapsed patients with measurable indolent non-Hodgkin lymphoma (NHL) were vaccinated with dendritic cells (DCs) loaded with killed autologous tumor cells. Six patients had objective clinical responses including 3 continuous complete responses (CRs) and 3 partial responses (PRs), with a median follow up of 50.5 months. Eight patients had stable disease, whereas 4 had progressive disease. Clinical responses were significantly associated with a reduction in CD4(+)CD25(+)FOXP3(+) regulatory T cells, an increase in CD3(-)CD56(dim)CD16(+) natural killer (NK) cells, and maturation of lymphocytes to the effector memory stage in either postvaccination peripheral blood or tumor specimen samples. In partial responding patients, vaccination significantly boosted the IFN-gamma-producing T-cell response to autologous tumor challenge. In one HLA-A*0201(+) patient who achieved CR, IL-4 release by circulating T cells in response to tumor-specific IgH-encoded peptides was also documented. Immunohistochemical analysis of tumor biopsies using biotin-conjugated autologous serum samples revealed a tumor-restricted humoral response only in the postvaccination serum from responding patients. Collectively these results demonstrate that vaccination with tumor-loaded DCs may induce both T- and B-cell responses and produces clinical benefits in indolent NHL patients with measurable disease. This study is registered with the Istituto Superiore di Sanità: http://www.iss. it with protocol number 7578-PRE 21-801.
On the importance of wave‐like structures in the occurrence of equatorial plasma bubbles: A case study

[1] Coordinated observations of equatorial plasma bubbles (EPBs) have been made with an all-sky airglow imager, narrow bandwidth photometer, VHF radar, and ionosonde over the Indian sector on the night of 23 March 2009. The prereversal enhancement (PRE) in the vertical plasma drift during the postsunset hours on this day was moderate. Range type spread F was found to occur immediately after the satellite traces were noted in the ionograms. This was well recorded in measurements made by all-sky imager, narrow band photometer, and VHF radar. The airglow emission intensities also revealed the presence of a large-scale wave-like structure (LSWS) together with the plasma bubbles that coincided with plume structures observed in the VHF radar echoes. The periodicity of the occurrence of bubbles (and plumes) and their interdepletion distances suggest the presence of small-scale wave-like structures (SSWS) on this night. The results are compared with the ionosonde observations made on the night of 21 February 2008. The PRE and the maximum height attained by the F layer were very similar to that of 23 March 2009. In addition, the ionograms showed the presence of satellite traces. However, no subsequent evolution of spread F was noticed. Considering the satellite traces to have their origin in LSWS, these observations imply that though the presence of LSWS is important for the triggering of EPBs, they alone are not sufficient. However, the coexistence of both LSWS and SSWS may have the potential to trigger EPBs.
Learning decreases heterospecific courtship and mating in fruit flies

Recent theory and data suggest that adaptive use of learning in the context of sexual behaviour could contribute to assortative mating. Experiments examining this issue indicated that male Drosophila persimilis that experienced courtship and rejection by heterospecific females exhibited significantly lower levels of heterospecific courtship and mating compared with those of inexperienced males. These results indicate that experience in the context of sexual behaviour in fruit flies could reduce gene flow between diverging populations, which may contribute to incipient speciation.
Effect of polyatomic ion structure on thin-film growth: Experiments and molecular dynamics simulations

The experiments described here examine 25–100 eV CF3+ and C3F5+ ion modification of a polystyrene (PS) surface, as analyzed by x-ray photoelectron spectroscopy. The molecular dynamics computer simulations probe the structurally and chemically similar reactions of 20–100 eV CH3+ and C3H5+ with PS. CF3+ and C3F5+ each form a distribution of different fluorocarbon (FC) functional groups on PS in amounts dependent upon the incident ion energy, structure, and fluence. Both ions deposit mostly intact upon the surface at 25 eV, although they also undergo some crosslinking upon deposition. Fragmentation of the two ions increases as the ion energies are increased to 50 eV. Both ions show increases in total fluorine and fluorinated carbon content when changing the ion energy from 25 to 50 eV. The simulations predict that CH3+ and C3H5+ behave in a similar fashion to their FC analogs, remaining mostly intact and either embedding or scattering from the surface without reacting at 20 eV. At 50 and 100 eV, the simulati.
Hierarchy of Neural Organization in the Embryonic Spinal Cord: Granger-Causality Graph Analysis of In Vivo Calcium Imaging Data

The recent development of genetically encoded calcium indicators enables monitoring in vivo the activity of neuronal populations. Most analysis of these calcium transients relies on linear regression analysis based on the sensory stimulus applied or the behavior observed. To estimate the basic properties of the functional neural circuitry, we propose a network approach to calcium imaging recorded at single cell resolution. Differently from previous analysis based on cross-correlation, we used Granger-causality estimates to infer information propagation between the activities of different neurons. The resulting functional network was then modeled as a directed graph and characterized in terms of connectivity and node centralities. We applied our approach to calcium transients recorded at low frequency (4 Hz) in ventral neurons of the zebrafish spinal cord at the embryonic stage when spontaneous coiling of the tail occurs. Our analysis on population calcium imaging data revealed a strong ipsilateral connectivity and a characteristic hierarchical organization of the network hubs that supported established propagation of activity from rostral to caudal spinal cord. Our method could be used for detecting functional defects in neuronal circuitry during development and pathological conditions.