Miracle-dz/UniFAR-FTUs huggingface dataset:
Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer*

Mass spectrometry-based proteomics has greatly benefitted from enormous advances in high resolution instrumentation in recent years. In particular, the combination of a linear ion trap with the Orbitrap analyzer has proven to be a popular instrument configuration. Complementing this hybrid trap-trap instrument, as well as the standalone Orbitrap analyzer termed Exactive, we here present coupling of a quadrupole mass filter to an Orbitrap analyzer. This “Q Exactive” instrument features high ion currents because of an S-lens, and fast high-energy collision-induced dissociation peptide fragmentation because of parallel filling and detection modes. The image current from the detector is processed by an “enhanced Fourier Transformation” algorithm, doubling mass spectrometric resolution. Together with almost instantaneous isolation and fragmentation, the instrument achieves overall cycle times of 1 s for a top10 higher energy collisional dissociation method. More than 2500 proteins can be identified in standard 90-min gradients of tryptic digests of mammalian cell lysate— a significant improvement over previous Orbitrap mass spectrometers. Furthermore, the quadrupole Orbitrap analyzer combination enables multiplexed operation at the MS and tandem MS levels. This is demonstrated in a multiplexed single ion monitoring mode, in which the quadrupole rapidly switches among different narrow mass ranges that are analyzed in a single composite MS spectrum. Similarly, the quadrupole allows fragmentation of different precursor masses in rapid succession, followed by joint analysis of the higher energy collisional dissociation fragment ions in the Orbitrap analyzer. High performance in a robust benchtop format together with the ability to perform complex multiplexed scan modes make the Q Exactive an exciting new instrument for the proteomics and general analytical communities.
The role of deadenylation in the degradation of unstable mRNAs in trypanosomes

Removal of the poly(A) tail is the first step in the degradation of many eukaryotic mRNAs. In metazoans and yeast, the Ccr4/Caf1/Not complex has the predominant deadenylase activity, while the Pan2/Pan3 complex may trim poly(A) tails to the correct size, or initiate deadenylation. In trypanosomes, turnover of several constitutively-expressed or long-lived mRNAs is not affected by depletion of the 5′–3′ exoribonuclease XRNA, but is almost completely inhibited by depletion of the deadenylase CAF1. In contrast, two highly unstable mRNAs, encoding EP procyclin and a phosphoglycerate kinase, PGKB, accumulate when XRNA levels are reduced. We here show that degradation of EP mRNA was partially inhibited after CAF1 depletion. RNAi-targeting trypanosome PAN2 had a mild effect on global deadenylation, and on degradation of a few mRNAs including EP. By amplifying and sequencing degradation intermediates, we demonstrated that a reduction in XRNA had no effect on degradation of a stable mRNA encoding a ribosomal protein, but caused accumulation of EP mRNA fragments that had lost substantial portions of the 5′ and 3′ ends. The results support a model in which trypanosome mRNAs can be degraded by at least two different, partially independent, cytoplasmic degradation pathways attacking both ends of the mRNA.
IaDEA: A Development Environment Architecture for Building Generic Intelligent User Interface Agents

The need exists in the work force for generic intelligent user interface agents to address the problem of increasing taskload that is overwhelming the human user. Interface agents could help alleviate user taskload by providing abstractions and intelligent assistance in a self-contained software agent that communicates with the user through the existing user interface and also adapts to user needs and behaviors. The benefits of a generic intelligent user interface agent environment is it can be applied to any highly interactive and information intensive software system from freight and parcel management systems to Wall Street financial investment and analysis. We desire to address the two following difficulties with developing interface agents: (1) The extensive number of existing computer systems makes it impractical to build these agents by hand for each system; (2) Any such agent must be compliant with existing user interface standards and business practices (e.g., the United States Air Force’s Common Operating Environment (COE) standards as defined by the Defcnse Information Infrastructure (DII)). Thus, an environment constructing intelligent interface agents that facilitates standards compliance is necessary. We investigate the feasibility of developing an integrated environment for constructing generic intelligent user interface agents. We base our proposed design on three components: (1) a knowledge acquisition tool for support of specification and design of interface agents taking in to account compliance with existing computer-based systems and user interface standards; (2) a utility theory-based methodology for interface agent requirements, assistance, and adaptivity; and (3) a correction model for user adaptivity based on user metrics evaluation.
Performance-based financing in the context of selective free health-care: an evaluation of its effects on the use of primary health-care services in Burundi using routine data.

BACKGROUND Performance-based financing (PBF) is an increasingly adopted strategy in low- and middle-income countries. PBF pilot projects started in Burundi in 2006, at the same time when a national policy removed user fees for pregnant women and children below 5 years old. METHODS PBF was gradually extended to the 17 provinces of the country. This roll-out and data from the national health information system are exploited to assess the impact of PBF on the use of health-care services. RESULTS PBF is associated with an increase in the number of anti-tetanus vaccination of pregnant women (around +20 percentage points in target population, P < 0.10). Non-robust positive effects are also found on institutional deliveries and prenatal consultations. Changes in outpatient visits, postnatal visits and children vaccinations are not significantly correlated with PBF. It is also found that more qualified nurses headed to PBF-supported provinces. The limited quality of the data and the restricted size of the sample have to be taken into account when interpreting these results. Health facility-level figures from PBF-supported provinces show that most indicators but those relative to preventive care are growing through time. DISCUSSION The dataset does not include indicators of the quality of care and does not allow to assess whether changes associated with PBF are resource-driven or due to the incentive mechanism itself. The results are largely consistent with other impact evaluations conducted in Burundi and Rwanda. The fact that PBF is mostly associated with positive changes in the use of services that became free suggests an important interaction effect between the two strategies. A possible explanation is that the removal of user fees increases accessibility to health care and acts on the demand side while PBF gives medical staffs incentives for improving the provision of services. More empirical research is needed to understand the sustainability of (the incentive mechanism of) PBF and the interaction between PBF and other health policies.
The Great Observatories Origins Deep Survey VLT/FORS2 Spectroscopy in the GOODS-South Field: Part II

We present the second campaign of the ESO/GOODS program of spectroscopy of faint galaxies in the GOODS-South field. Objects were selected as candidates for VLT/FORS2 observations primarily based on the expectation that the detection and measurement of their spectral features would benefit from the high throughput and spectral resolution of FORS2. The reliability of the redshift estimates is assessed using the redshift-magnitude and color-redshift diagrams and comparing the results with public data. 807 spectra of 652 individua targets have been obtained in service mode with the FORS2 spectrograph at the ESO/VLT, providing 501 redshift determinations. The typical redshift uncertainty is estimated to be sigma_z ~ 0.001. Galaxies have been selected adopting three different color criteria and using the photometric redshifts.The resulting redshift distribution typically spans two redshift domains: from z=0.5 to 2 and z=3.5 to 6.2. In particular, 94 B435-,V606-,i775"dropout"Lyman break galaxies have been observed, yielding redshifts for 65 objects in the interval 3.4<z<6.2. Three sources have been serendipitously discovered in the redshift interval 4.8<z<5.5. Together with the previous release, 930 sources have now been observed and 724 redshift determinations have been carried out. The reduced spectra and the derived redshifts are released to the community through the ESO web page http://www.eso. org/science/goods/. Large scale structures are clearly detected at z=0.666, 0.734, 1.096, 1.221, 1.300, and 1.614. A sample of 34 sources with tilted [OII]3727 emission has been identified, 32 of them in the redshift range 0.9<z<1.5.
Targeted Deletion of Multiple CTCF-Binding Elements in the Human C-MYC Gene Reveals a Requirement for CTCF in C-MYC Expression

Background Insulators and domain boundaries both shield genes from adjacent enhancers and inhibit intrusion of heterochromatin into transgenes. Previous studies examined the functional mechanism of the MYC insulator element MINE and its CTCF binding sites in the context of transgenes that were randomly inserted into the genome by transfection. However, the contribution of CTCF binding sites to both gene regulation and maintenance of chromatin has not been tested at the endogenous MYC gene. Methodology/Principal Findings To determine the impact of CTCF binding on MYC expression, a series of mutant human chromosomal alleles was prepared in homologous recombination-efficient DT40 cells and individually transferred by microcell fusion into murine cells. Functional tests reported here reveal that deletion of CTCF binding elements within the MINE does not impact the capacity of this locus to correctly organize an ‘accessible’ open chromatin domain, suggesting that these sites are not essential for the formation of a competent, transcriptionally active locus. Moreover, deletion of the CTCF site at the MYC P2 promoter reduces transcription but does not affect promoter acetylation or serum-inducible transcription. Importantly, removal of either CTCF site leads to DNA methylation of flanking sequences, thereby contributing to progressive loss of transcriptional activity. Conclusions These findings collectively demonstrate that CTCF-binding at the human MYC locus does not repress transcriptional activity but is required for protection from DNA methylation.
Content hunting for in-network cache: Design and performance analysis

In-network caching is a core technology for saving network resources and improving the response time in Information-/Content-Centric Networking (ICN/CCN). In an ordinary ICN/CCN, content name based routing is used to find cached content in the network. Although there have been several studies on effective and efficient cache retrieval from in-network caches, we propose a novel content hunting scheme, named Local Tree Hunting (LTH) from the point of view to approach the ideal performance. LTH hunts for the closest node to the request node among the nodes with disseminated cache content. It autonomously adjusts the hunting area by changing the size of the hunting tree depending on the degree to which the content has been disseminated through the network. The proposed scheme was verified in a performance analysis; it was shown to have almost the same level of performance as the case of finding the true closest node. System architecture and operations based on the proposed scheme are also described.
Maximally stable curvature regions for 3D hand tracking

Fast and robust hand detections and tracking is in increasing demand from areas such as natural Human Robot interaction(HRI) and surveillance systems. Previous works always use skin color or contour model to detection hand. However, they always fail for hands always exhibits drastic appearance change due to illumination change, non-rigid nature and hands are hard to discriminate from clutter background. Actually, the hand region has a specific nature that its curvature is relatively higher than other body parts and keeps stable whatever its poses and locations are, but none of pervious works exploit this nature for hand detection. In this work, a novel algorithm MSCR (Maximally Stable Curvature Regions) based on curvature nature to detect hands. It does not require manually initialization in the first frame, the hands are located by MSCR and skin color detector in the global image. 3D optical flow integrated Kalman Filter works to estimate the next location for local detector. Extensive experiments demonstrate that robust 3D tracking of hand articulations can be achieved in real-time with accurate results.
An Endogenous Serine/Threonine Protein Phosphatase Inhibitor, G-Substrate, Reduces Vulnerability in Models of Parkinson's Disease

Relative neuronal vulnerability is a universal yet poorly understood feature of neurodegenerative diseases. In Parkinson's disease, dopaminergic (DA) neurons in the substantia nigra (SN) (A9) are particularly vulnerable, whereas adjacent DA neurons within the ventral tegmental area (A10) are essentially spared. Our previous laser capture microdissection and microarray study (Chung et al., 2005) demonstrated that molecular differences between these DA neurons may underlie their differential vulnerability. Here we show that G-substrate, an endogenous inhibitor of Ser/Thr protein phosphatases, exhibits higher expression in A10 compared with A9 DA neurons in both rodent and human midbrain. Overexpression of G-substrate protected dopaminergic BE(2)-M17 cells against toxins, including 6-OHDA and MG-132 (carbobenzoxy-l-leucyl- l-leucyl-l-leucinal), whereas RNA interference (RNAi)-mediated knockdown of endogenous G-substrate increased their vulnerability to these toxins. G-substrate reduced 6-OHDA-mediated protein phosphatase 2A (PP2A) activation in vitro and increased phosphorylated levels of PP2A targets including Akt, glycogen synthase kinase 3β, and extracellular signal-regulated kinase 2 but not p38. RNAi to Akt diminished the protective effect of G-substrate against 6-OHDA. In vivo, lentiviral delivery of G-substrate to the rat SN increased baseline levels of phosphorylated Akt and protected A9 DA neurons from 6-OHDA-induced toxicity. These results suggest that inherent differences in the levels of G-substrate contribute to the differential vulnerability of DA neurons and that enhancing G-substrate levels may be a neuroprotective strategy for the vulnerable A9 (SN) DA neurons in Parkinson's disease.
Comparative assessment of H.265/MPEG-HEVC, VP9, and H.264/MPEG-AVC encoders for low-delay video applications

The popularity of low-delay video applications dramatically increased over the last years due to a rising demand for realtime video content (such as video conferencing or video surveillance), and also due to the increasing availability of relatively inexpensive heterogeneous devices (such as smartphones and tablets). To this end, this work presents a comparative assessment of the two latest video coding standards: H.265/MPEG-HEVC (High-Efficiency Video Coding), H.264/MPEG-AVC (Advanced Video Coding), and also of the VP9 proprietary video coding scheme. For evaluating H.264/MPEG-AVC, an open-source x264 encoder was selected, which has a multi-pass encoding mode, similarly to VP9. According to experimental results, which were obtained by using similar low-delay configurations for all three examined representative encoders, it was observed that H.265/MPEG-HEVC provides significant average bit-rate savings of 32.5%, and 40.8%, relative to VP9 and x264 for the 1-pass encoding, and average bit-rate savings of 32.6%, and 42.2% for the 2-pass encoding, respectively. On the other hand, compared to the x264 encoder, typical low-delay encoding times of the VP9 encoder, are about 2,000 times higher for the 1-pass encoding, and are about 400 times higher for the 2-pass encoding.
Long-Term Stimulation with Electroacupuncture at DU20 and ST36 Rescues Hippocampal Neuron through Attenuating Cerebral Blood Flow in Spontaneously Hypertensive Rats

This study was designed to investigate the effect of long-term electroacupuncture at Baihui (DU20) and Zusanli (ST36) on cerebral microvessels and neurons in CA1 region of hippocampus in spontaneously hypertensive rats (SHR). A total of 45 male Wistar rats and 45 SHR were randomly grouped, with or without electroacupuncture (EA) at DU20 and ST36, once every other day for a period of 8 weeks. The mean arterial pressure (MAP) was measured once every 2 weeks. Cerebral blood flow (CBF) and the number of open microvessels in hippocampal CA1 region were detected by Laser Doppler and immunohistochemistry, respectively. Nissl staining and Western blotting were performed, respectively, to determine hippocampus morphology and proteins that were implicated in the concerning signaling pathways. The results showed that the MAP in SHR increased linearly over the observation period and was significantly reduced following electroacupuncture as compared with sham control SHR rats, while no difference was observed in Wistar rats between EA and sham control. The CBF, learning and memory capacity, and capillary rarefaction of SHR were improved by EA. The upregulation of angiotensin II type I receptor (AT1R), endothelin receptor (ETAR), and endothelin-1 (ET-1) in SHR rats was attenuated by electroacupuncture, suggesting an implication of AT1R, ETAR, and ET-1 pathway in the effect of EA.
ALTERNATIVE POWER STANDARD REALIZATION AT RADIO FREQUENCY

Modern ac-dc transfer equipments can operate up to 1 GHz at least. These equipments and the related ac-voltage measurements may be attractive for calibrating high frequency power sensors in term of ac-dc transfer difference instead of effective efficiency. Furthermore, below 30 MHz, the ac-voltage standard can be also used as powerful alternative and complement to the microcalorimeter technique for the realization of the RF power standard. In the paper experimental measurements and data analysis are presented that prove the previous assertions.
Three‐dimensional reconstruction of oceanic mesoscale currents from surface information

The ability to reconstruct the three-dimensional (3D) dynamics of the ocean by an effective version of Surface Quasi-Geostrophy (eSQG) is examined. Using the fact that surface density plays an analogous role as interior potential vorticity (PV), the eSQG method consists in inverting the QG PV generated by sea-surface density only. We also make the extra assumption that sea-surface temperature (SST) anomalies fully represent surface density anomalies. This approach requires a single snapshot of SST and the setup of two parameters: the mean Brunt-Vaisala frequency and a parameter that determines the energy level at the ocean surface. The validity of this approach is tested using an Ocean General Circulation Model simulation representing the North Atlantic in winter. It is shown that the method is quite successful in reconstructing the velocity field at the ocean surface for mesoscales (between 30 and 300 km). The eSQG framework can also be applied to reconstruct subsurface fields using surface information. Results show that the reconstruction of velocities and vorticity from surface fields is reasonably good for the upper 500 m and that the success of the method mainly depends on the quality of the SST as a proxy of the density anomaly at the base of the mixed layer. This situation happens after a mixed-layer deepening period. Therefore the ideal situation for the application of this method would be after strong wind events.
Nested clade analysis

In a very influential paper Avise et al. [1] introduced the term “phylogeography” to refer to evolutionary studies lying at the interface of population genetics and systematics. An important property of molecular sequences is that the degree of difference among them contains information about their relatedness. Avise et al. proposed combining information derived from the phylogenetic relationship of molecular sequences with information about where the sequences were collected from to infer something about the biogeography of relationships among populations within species. Figure 1 provides an early and straightforward example. The data are from bowfins, Amia calva, and consist of mtDNA haplotypes detected by restriction site mapping. There are two highly divergent groups of haplotypes separated from one another by a minimum of four restriction site differences. Moreover, the two sets of haplotypes are found in areas that are geographically disjunct. Haplotypes 1-9 are found exclusively in the eastern portion of the range, while haplotypes 10-13 are found exclusively in the western part of the range. This pattern suggests that the populations of bowfin in the two geographical regions have had independent evolutionary histories for a relatively long period of time. Interestingly, this disjunction between populations west and east of the Appalachicola River is shared by a number of other species, as are disjunctions between the Atlantic and Gulf coasts, the west and east sides of the Tombigbee River, the west and east sides of the Appalachian mountains, and the west and east sides of the Mississippi River [2]. Early analyses often provided very clear patterns, like the one in bowfins. As data accumulated, however, it became clear that in some species it was necessary to account for differences in frequency, not just presence versus absence of particular haplotypes. We saw this in the application of AMOVA to mtDNA haplotype variation in humans. These approaches have two critical things in common:
Mosquito and Drosophila entomobirnaviruses suppress dsRNA- and siRNA-induced RNAi

RNA interference (RNAi) is a crucial antiviral defense mechanism in insects, including the major mosquito species that transmit important human viruses. To counteract the potent antiviral RNAi pathway, insect viruses encode RNAi suppressors. However, whether mosquito-specific viruses suppress RNAi remains unclear. We therefore set out to study RNAi suppression by Culex Y virus (CYV), a mosquito-specific virus of the Birnaviridae family that was recently isolated from Culex pipiens mosquitoes. We found that the Culex RNAi machinery processes CYV double-stranded RNA (dsRNA) into viral small interfering RNAs (vsiRNAs). Furthermore, we show that RNAi is suppressed in CYV-infected cells and that the viral VP3 protein is responsible for RNAi antagonism. We demonstrate that VP3 can functionally replace B2, the well-characterized RNAi suppressor of Flock House virus. VP3 was found to bind long dsRNA as well as siRNAs and interfered with Dicer-2-mediated cleavage of long dsRNA into siRNAs. Slicing of target RNAs by pre-assembled RNA-induced silencing complexes was not affected by VP3. Finally, we show that the RNAi-suppressive activity of VP3 is conserved in Drosophila X virus, a birnavirus that persistently infects Drosophila cell cultures. Together, our data indicate that mosquito-specific viruses may encode RNAi antagonists to suppress antiviral RNAi.