Miracle-dz/UniFAR-FTUs huggingface dataset:
The Cellular Antiviral Protein APOBEC3G Interacts with HIV-1 Reverse Transcriptase and Inhibits Its Function during Viral Replication

ABSTRACT The cytidine deaminase APOBEC3G (A3G) exerts a multifaceted antiviral effect against HIV-1 infection. First, A3G was shown to be able to terminate HIV infection by deaminating the cytosine residues to uracil in the minus strand of the viral DNA during reverse transcription. Also, a number of studies have indicated that A3G inhibits HIV-1 reverse transcription by a non-editing-mediated mechanism. However, the mechanism by which A3G directly disrupts HIV-1 reverse transcription is not fully understood. In the present study, by using a cell-based coimmunoprecipitation (Co-IP) assay, we detected the direct interaction between A3G and HIV-1 reverse transcriptase (RT) in produced viruses and in the cotransfected cells. The data also suggested that their interaction did not require viral genomic RNA bridging or other viral proteins. Additionally, a deletion analysis showed that the RT-binding region in A3G was located between amino acids 65 and 132. Overexpression of the RT-binding polypeptide A3G65-132 was able to disrupt the interaction between wild-type A3G and RT, which consequently attenuated the anti-HIV effect of A3G on reverse transcription. Overall, this paper provides evidence for the physical and functional interaction between A3G and HIV-1 RT and demonstrates that this interaction plays an important role in the action of A3G against HIV-1 reverse transcription.
Discovering Semantic Patterns of a Word from Texts

This paper describes a methodology for identifying semantic patterns of a word from texts by creating a sequence of coexisting triples that consistently carries the semantics of the word and developing an algorithm that finds the most important information among these triples in order to make a decision. This method is evaluated by words having different categories such as nouns, adjectives, or verbs. The results show that our method is effective and surpass the state-of-art accuracy level.
Exact BCS stochastic schemes for a time-dependent many-body fermionic system

A common approximate way to study the time evolution of a superfluid Fermi gas is to consider the mean-field time-dependent BCS equations. We show that, by inclusion of an appropriate fluctuating term in these mean-field equations, the exact quantum evolution of the Fermi gas is recovered, after an average over all possible realizations of the noise term: this leads to an exact quantum Monte Carlo technique for the real-time evolution of an interacting fermionic system. In practice, we derive the general conditions on the noise term, ensuring that the exact dynamics is reproduced, and we explore several explicit realizations of this noise term, trying to minimize the statistical spreading of the quantum Monte Carlo simulations. The convergence issue is discussed in detail, with upper bounds obtained on the statistical spreading, and the relation between the stochastic and the mean-field equations is analyzed. Finally, we apply the method to a simple two-site model, to exemplify that the simulations can display effects out of reach of the mean-field approximation.
Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome

A prominent feature of transcription in Giardia lamblia is the abundant production of sterile antisense transcripts (Elmendorf et al. The abundance of sterile transcripts in Giardia lamblia. Nucleic Acids., 29, 4674–4683). Here, we use a computational biology analysis of SAGE data to assess the abundance and distribution of sense and antisense messages in the parasite genome. Sterile antisense transcripts are produced at ∼50% of loci with detectable transcription, yet their abundance at a given locus does not correlate to the abundance of the complementary sense transcripts at that locus or to transcription levels at neighboring loci. These data suggest that sterile antisense transcripts are not simply a local effect of open chromatin structure. Using 5′RACE, we demonstrate that Giardia promoters are a source of antisense transcripts through bidirectional transcription, producing both downstream coding sense and upstream sterile antisense transcripts. We use a dual reporter system to explore roles of specific promoter elements in this bidirectional initiation of transcription and suggest that the degenerate AT-rich nature of TATA and Inr elements in Giardia permits them to function interchangeably. The phenomenon of bidirectional transcription in G. lamblia gives us insight into the interaction between transcriptional machinery and promoter elements, and may be the prominent source of the abundant antisense transcription in this parasite.
Maternal anthropometric changes during pregnancy and lactation in a rural Taiwanese population.

Changes in maternal weight, triceps, and subscapular skinfold thickness during 2 consecutive pregnancies (n=125) and lactation periods (n=225) are described for a sample of rural Taiwanese women studied during a longitudinal nutrition intervention study. Mean pregnancy weight gain was 7.63 kg, with a maximum weight velocity of 1.46 kg/month in 2nd trimester. Skinfold thicknesses increased slightly early in pregnancy, then declined during the last trimester, reaching a minimum just after birth. After an initial increase from birth to 1 postpartum month, mean weight and skinfold thicknesses declined throughout lactation. Closer examination revealed that 1/3 of the mothers gained weight and a greater proportion gained skinfold thickness during 12-15 months of lactation. Mothers who lost weight tended to have been fatter at the beginning of lactation compared with those who gained weight. Individual weight change patterns of the 1st lactation period studied (L1) were replicated by 87% of the women during the 2nd (L2). Due in part to a secular trend, mothers weighed more and tended to have thicker skinfolds during L2 compared with L1. Birth intervals (mean=758 days) were related to anthropometric maternal variables: fatter mothers had longer birth intervals. Anthropometric data interpreted in the context of energy balance demonstrate that the Taiwanese population, although it could be considered malnourished based on caloric intake estimates by and comparison with US weight for height standards, shows no evidence of longterm energy dificits. Rather, as judged by moderate weight and skinfold increases with time and by reproductive success, the population is well adapted.
KRAS oncogene in lung cancer: focus on molecularly driven clinical trials

KRAS mutations are the most frequent molecular abnormalities found in one out of four nonsmall cell lung cancers (NSCLC). Their incidence increases in cases of adenocarcinoma, smokers and Caucasian patients. Their negative value in terms of prognosis and responsiveness to both standard chemotherapy and targeted therapies remains under debate. Many drugs have been developed specifically for KRAS-mutated NSCLC patients. Direct inhibition of RAS activation failed to show any clinical efficacy. Inhibition of downstream targets of the mitogen-activated protein kinase (MEK) pathway is a promising strategy: phase II combinations of MEK 1/2 kinase inhibitors with chemotherapy doubled patients’ clinical outcomes. One phase III trial in such a setting is ongoing. Double inhibition of MEK and epidermal growth factor receptor proteins is currently being assessed in early-phase trials. The association with mammalian target of rapamycin pathway inhibition leads to non-manageable toxicity. Other strategies, such as inhibition of molecular heat-shock proteins 90 or focal adhesion kinase are currently assessed. Abemaciclib, a cyclin-dependent kinase 4/6 inhibitor, showed promising results in a phase I trial, with a 54% disease control rate. Results of an ongoing phase III trial are warranted. Immunotherapy might be the next relevant step in KRAS-mutated NSCLC management due to the high burden of associated mutations and neo-antigens. MEK inhibition and immunotherapy are very promising therapeutic advances in KRAS-mutated nonsmall cell lung cancer http://ow.ly/U2ohp
Salvage treatment of relapsed/refractory LCH

The Langerhan's cell histiocytosis (LCH) is a rare hematologic disorder of all age group, and the classification of LCH as a neoplasm of myeloid origin was introduced with the current observation of recurrent BRAFV600E mutation in LCH patients. LCH shows broad spectrum of clinical manifestations from single system involvement to wide spread multi-system (MS) disease, and this clinical variety is assumed to be determined by the differentiation stage of myeloid dendritic cells in which the mitogen-activated protein kinase (MAPK) pathway is aberrantly activated. The lesions of LCH typically show clonal proliferation of CD1a+/CD207+ cells with significant infiltration of inflammatory cells, and the documentation of this CD1a+ or CD207+ cell in biopsy specimen is required for the diagnosis of LCH. The survival of relapsed/refractory (R/R) high risk LCH patients was significantly improved with intensification of therapy, and the disease reactivation rate was somewhat reduced overtime due to prolongation of therapy during last two decades. Despite this improvements in survival and reactivation rate, the risk of permanent consequences of LCH was only marginally reduced [1]. Although most of the relapsed patients without risk organ involvement (RO−) can be salvaged successfully with less intensive chemotherapies, they are more likely to develop permanent consequences. The poor survival rate of MS LCH patients with RO involvement (RO+) who are refractory to or relapsing after standard chemotherapy was much improved with the introduction of salvage chemotherapy using 2CdA and Ara-C [2], but still there are patients not responding and dying with R/R disease. Therefore, the intensity and duration of second line treatment for these R/R MS LCH patients should be decided according to the status of RO involvement. LCH-IV protocols of the Histiocyte Society also employ the strategies of salvage therapy for patients with R/R LCH according to the status of RO involvement. The second line treatment for R/R RO− LCH patient needs to achieve disease resolution, prevent further reactivations and permanent consequences. Moreover, the goal of second line treatment for R/R RO+ LCH patient needs to include further reduction of mortality due to disease progression as well.
Localization of actin and microfilament-associated proteins in the microvilli and terminal web of the intestinal brush border by immunofluorescence microscopy

Indirect immunofluorescence microscopy was used to localize microfilament-associated proteins in the brush border of mouse intestinal epithelial cells. As expected, antibodies to actin decorated the microfilaments of the microvilli, giving rise to a very intense fluorescence. By contrast, antibodies to myosin, tropomyosin, filamin, and alpha-actinin did not decorate the microvilli. All these antibodies, however, decorated the terminal web region of the brush border. Myosin, tropomyosin, and alpha-actinin, although present throughout the terminal web, were found to be preferentially located around the periphery of the organelle. Therefore, two classes of microfilamentous structures can be documented in the brush border. First, the highly ordered microfilaments which make up the cores of the microvilli apparently lack the associated proteins. Second, seemingly less-ordered microfilaments are found in the terminal web, in which region the myosin, tropomyosin, filamin and alpha-actinin are located.
Validating diffusion spectrum imaging-based fiber tractography for cognitive neuroscience research

White matter fiber tractography based on diffusion-weighted magnetic resonance imaging is a promising method for non-invasive investigation of anatomical connectivity in the human brain. Knowledge of the white matter connections linking functional brain areas can inform interpretation of functional imaging results and allow the construction of biologically informed computational and statistical models. However, relatively little attention has been paid to the reproducibility and external validity of tractography results, even as the user base of this technology continues to grow, and as tractography research is applied to cognitive neuroscience research in novel ways. In this investigation, we addressed the reliability and validity of deterministic tractography results based on diffusion spectrum imaging (DSI). Reliability was evaluated both in terms of the presence/absence of fiber connections across sessions and the correlation of fiber density values. Validity was assessed by comparing tractography results to findings from invasive studies of the macaque monkey: we focused on the cortical and subcortical connections of the frontal eye fields (FEF). Results indicated significant variability in tractography: on average, intercortical connections present in one session had only a 75% likelihood of being detected in a second session from the same individual. However, the fiber density of repeatedly-detected connections was highly reliable, with an average between-session correlation coefficient of 0.94. Next, we investigated how global vs. targeted tractography approaches affected reliability and detection power. We found that a targeted approach, involving the use of region-of interest (ROI) constraints, yielded a large advantage in detection power and modest improvements in reliability. Finally, fiber connections of the human FEF were broadly consistent with hypotheses derived from a meta-analysis of macaque findings: we found reliable projections to the supplementary eye fields (SEF), striatum, thalamus, and parietal cortex. In contrast, we found lesser connectivity to a set of foil regions. The combined results of this study validate the use of DSI-based fiber tractography to address hypotheses relating to human brain connectivity. However, widespread noise in tractography results highlights the need for conservative approaches to fiber tracking research. We especially emphasize the benefits of collecting multiple data samples per participant and of addressing targeted hypotheses.
Modeling of Surface Roughness for Flow Over a Complex Vegetated Surface

Turbulence modeling of large-scale flow over a vegetated surface is complex. Such problems involve large scale computational domains, while the characteristics of flow near the surface are also involved. In modeling large scale flow, surface roughness including vegetation is generally taken into account by mean of roughness parameters in the modified law of the wall. However, the turbulence structure within the canopy region cannot be captured with this method, another method which applies source/sink terms to model plant drag can be used. These models have been developed and tested intensively but with a simple surface geometry. This paper aims to compare the use of roughness parameter, and additional source/sink terms in modeling the effect of plant drag on wind flow over a complex vegetated surface. The RNG k-e turbulence model with the non-equilibrium wall function was tested with both cases. In addition, the k-ω turbulence model, which is claimed to be computationally stable, was also investigated with the source/sink terms. All numerical results were compared to the experimental results obtained at the study site Mason Bay, Stewart Island, New Zealand. In the near-surface region, it is found that the results obtained by using the source/sink term are more accurate than those using roughness parameters. The k-ω turbulence model with source/sink term is more appropriate as it is more accurate and more computationally stable than the RNG k-e turbulence model. At higher region, there is no significant difference amongst the results obtained from all simulations. Keywords—CFD, canopy flow, surface roughness, turbulence models.
Super-Samples from Kernel Herding

We extend the herding algorithm to continuous spaces by using the kernel trick. The resulting "kernel herding" algorithm is an infinite memory deterministic process that learns to approximate a PDF with a collection of samples. We show that kernel herding decreases the error of expectations of functions in the Hilbert space at a rate O(1/T) which is much faster than the usual O(1/pT) for iid random samples. We illustrate kernel herding by approximating Bayesian predictive distributions.
Thermal Sensor-Based Multiple Object Tracking for Intelligent Livestock Breeding

Visual object tracking is an essential technique for constructing intelligent livestock management systems. Behavior patterns estimated from the trajectories of animals provide substantial useful information related to estrus cycle, disease prognosis and so on. However, similar colors and shapes between animals often lead to the failure of tracking multiple objects, and the background clutter of the breeding space further makes the problem intractable. In this paper, we propose a novel method for tracking animals using a single thermal sensor. The key idea of the proposed method is to represent the foreground (i.e., animals) easily obtained by a simple thresholding in a thermal frame as a topographic surface, which is very helpful for finding the boundary of each object even in cases with overlapping. Based on the segmentation results derived from morphological operations on the topographic surface, the center positions of all the animals are consistently updated with an efficient refinement scheme that is robust to the abrupt motions of animals. Experimental results using various thermal video sequences demonstrate the efficiency and robustness of our method for tracking animals in a breeding space compared to previous approaches proposed in the literature.
Hopfing and puffing warped anti-de Sitter space

Three dimensional spacelike warped anti-de Sitter space is studied in the context of Einstein theories of gravity and string theory, where there is no gravitational Chern-Simons term in the action. We propose that it is holographically dual to a two-dimensional conformal field theory with equal left and right moving central charges. Various checks of the central charges are offered, based on the Bekenstein-Hawking entropy of the stretched warped black holes and warped self-dual solutions. The proposed central charges are applied to compute the Bekenstein-Hawking entropy of the Hopf T-dual of six-dimensional dyonic black strings which have a near horizon consisting of three dimensional warped anti-de Sitter space times a three-sphere. We find that the Hopf T-duality is a map between thermal states with equal entropy of the CFTs dual to the dyonic black string and the Hopf T-dualized black string.
A Study of Edge-On Galaxies with the Hubble Space Telescope Advanced Camera for Surveys. I. Initial Results

We present the initial results of a Hubble Space Telescope/Advanced Camera for Surveys snapshot survey of 16 nearby, edge-on, late-type galaxies covering a range in distance from 2 to 19 Mpc. The images of these galaxies show significant resolved stellar populations. We derive F606W and F814W photometry for more than 1.2 million stars and present color-magnitude diagrams that show a mixture of young, intermediate, and old stars in each galaxy. In one of the fields we serendipitously detect stars from the Large Magellanic Cloud. We also identify a candidate young dwarf galaxy lying ∼2 kpc above the plane of NGC 4631. For the nearest six galaxies, we derive tip of the red giant branch distances and demonstrate that these galaxies fall on the K-band Tully-Fisher relation established in clusters. From the color of the red giant branch, we also find evidence that these galaxies possess a metal-poor thick-disk or halo population.
Defective Phagocytic Corpse Processing Results in Neurodegeneration and Can Be Rescued by TORC1 Activation

The removal of apoptotic cell corpses is important for maintaining homeostasis. Previously, defects in apoptotic cell clearance have been linked to neurodegeneration. However, the mechanisms underlying this are still poorly understood. In this study, we report that the absence of the phagocytic receptor Draper in glia leads to a pronounced accumulation of apoptotic neurons in the brain of Drosophila melanogaster. These dead cells persist in the brain throughout the lifespan of the organism and are associated with age-dependent neurodegeneration. Our data indicate that corpses persist because of defective phagosome maturation, rather than recognition defects. TORC1 activation, or inhibition of Atg1, in glia is sufficient to rescue corpse accumulation as well as neurodegeneration. These results suggest that phagocytosis of apoptotic neurons by glia during development is essential for brain homeostasis in adult flies. Furthermore, it suggests that TORC1 regulates Draper-mediated phagosome maturation. SIGNIFICANCE STATEMENT Previously, defects in dead cell clearance were linked to neurodegeneration, but the exact mechanisms are not well understood. In this study, we report that the absence of an engulfment receptor leads to a pronounced accumulation of dead neurons in the brain of the fruit fly Drosophila melanogaster. These dead cells persist in the brain throughout the lifespan of the organism and are associated with age-dependent neurodegeneration. Our data indicate that corpses persist because of defective degradation of cells rather than recognition of dead cells.
Block-Structured Adaptive Grids on the Sphere: Advection Experiments

Abstract A spherical 2D adaptive mesh refinement (AMR) technique is applied to the so-called Lin–Rood advection algorithm, which is built upon a conservative and oscillation-free finite-volume discretization in flux form. The AMR design is based on two modules: a block-structured data layout and a spherical AMR grid library for parallel computer architectures. The latter defines and manages the adaptive blocks in spherical geometry, provides user interfaces for interpolation routines, and supports the communication and load-balancing aspects for parallel applications. The adaptive grid simulations are guided by user-defined adaptation criteria. Both statically and dynamically adaptive setups that start from a regular block-structured latitude–longitude grid are supported. All blocks are logically rectangular, self-similar, and independent data units that are split into four in the event of refinement requests, thereby doubling the horizontal resolution. Grid coarsenings reverse this refinement principle.
The MUG facial expression database

This paper presents a new extended collection of posed and induced facial expression image sequences. All sequences were captured in a controlled laboratory environment with high resolution and no occlusions. The collection consists of two parts: The first part depicts eighty six subjects performing the six basic expressions according to the “emotion prototypes” as defined in the Investigator's Guide in the FACS manual. The second part contains the same subjects recorded while they were watching an emotion inducing video. Most of the database recordings are available to the scientific community. Beyond the emotion related annotation the database contains also manual and automatic annotation of 80 facial landmark points for a significant number of frames. The database contains sufficient material for the development and the statistical evaluation of facial expression recognition systems using posed and induced expressions.