Miracle-dz/UniFAR-FTUs huggingface dataset:
KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features

Productive herpesvirus infection requires a profound, time-controlled remodeling of the viral transcriptome and proteome. To gain insights into the genomic architecture and gene expression control in Kaposi's sarcoma-associated herpesvirus (KSHV), we performed a systematic genome-wide survey of viral transcriptional and translational activity throughout the lytic cycle. Using mRNA-sequencing and ribosome profiling, we found that transcripts encoding lytic genes are promptly bound by ribosomes upon lytic reactivation, suggesting their regulation is mainly transcriptional. Our approach also uncovered new genomic features such as ribosome occupancy of viral non-coding RNAs, numerous upstream and small open reading frames (ORFs), and unusual strategies to expand the virus coding repertoire that include alternative splicing, dynamic viral mRNA editing, and the use of alternative translation initiation codons. Furthermore, we provide a refined and expanded annotation of transcription start sites, polyadenylation sites, splice junctions, and initiation/termination codons of known and new viral features in the KSHV genomic space which we have termed KSHV 2.0. Our results represent a comprehensive genome-scale image of gene regulation during lytic KSHV infection that substantially expands our understanding of the genomic architecture and coding capacity of the virus.
VoteTrust: Leveraging Friend Invitation Graph to Defend against Social Network Sybils

Online social networks (OSNs) suffer from the creation of fake accounts that introduce fake product reviews, malware and spam. Existing defenses focus on using the social graph structure to isolate fakes. However, our work shows that Sybils could befriend a large number of real users, invalidating the assumption behind social-graph-based detection. In this paper, we present VoteTrust, a scalable defense system that further leverages user-level activities. VoteTrust models the friend invitation interactions among users as a directed, signed graph, and uses two key mechanisms to detect Sybils over the graph: a voting-based Sybil detection to find Sybils that users vote to reject, and a Sybil community detection to find other colluding Sybils around identified Sybils. Through evaluating on Renren social network, we show that VoteTrust is able to prevent Sybils from generating many unsolicited friend requests. We also deploy VoteTrust in Renen, and our real experience demonstrates that VoteTrust can detect large-scale collusion among Sybils.
Lipopolysaccharide (LPS)-Induced Biliary Epithelial Cell NRas Activation Requires Epidermal Growth Factor Receptor (EGFR)

Cholangiocytes (biliary epithelial cells) actively participate in microbe-induced proinflammatory responses in the liver and contribute to inflammatory and infectious cholangiopathies. We previously demonstrated that cholangiocyte TLR-dependent NRas activation contributes to proinflammatory/ proliferative responses. We test the hypothesis that LPS-induced activation of NRas requires the EGFR. SV40-transformed human cholangiocytes (H69 cells), or low passage normal human cholangiocytes (NHC), were treated with LPS in the presence or absence of EGFR or ADAM metallopeptidase domain 17 (TACE) inhibitors. Ras activation assays, quantitative RT-PCR, and proliferation assays were performed in cells cultured with or without inhibitors or an siRNA to Grb2. Immunofluorescence for phospho-EGFR was performed on LPS-treated mouse samples and specimens from patients with primary sclerosing cholangitis, primary biliary cirrhosis, hepatitis C, and normal livers. LPS-treatment induced an association between the TLR/MyD88 and EGFR/Grb2 signaling apparatus, NRas activation, and EGFR phosphorylation. NRas activation was sensitive to EGFR and TACE inhibitors and correlated with EGFR phosphorylation. The TACE inhibitor and Grb2 depletion prevented LPS-induced IL6 expression (p<0.05) and proliferation (p<0.01). Additionally, cholangiocytes from LPS-treated mouse livers and human primary sclerosing cholangitis (PSC) livers exhibited increased phospho-EGFR (p<0.01). Moreover, LPS-induced mouse cholangiocyte proliferation was inhibited by concurrent treatment with the EGFR inhibitor, Erlotinib. Our results suggest that EGFR is essential for LPS-induced, TLR4/MyD88-mediated NRas activation and induction of a robust proinflammatory cholangiocyte response. These findings have implications not only for revealing the signaling potential of TLRs, but also implicate EGFR as an integral component of cholangiocyte TLR-induced proinflammatory processes.
Anticancer effect of eupatilin on glioma cells through inhibition of the Notch-1 signaling pathway

Eupatilin, one of the major flavonoids in Artemisia asiatica Nakai (Asteraceae), has been reported to possess antitumor properties. However, thus far there have been no reports regarding the effects of eupatilin on glioma. Therefore, in the current study the effects of eupatilin on glioma and the underlying molecular mechanism were explored. The effect of eupatilin on cell viability was detected by the MTT assay. Cell invasion and migration were performed with Transwell assays and cell apoptosis was determined by flow cytometric analysis. Notch-1 knockdown cells were established by transfection with Notch-1 small interfering RNA (siRNA). The expression levels of Notch-1 were detected by quantitative reverse transcription-polymerase chain reaction and western blotting. The results of the present study indicated that eupatilin exhibits an anticancer effect on glioma cells. Eupatilin inhibited proliferation, reduced cell invasion and migration, and promoted the apoptosis of glioma cells. Additionally, it suppressed Notch-1 expression. Knockdown of Notch-1 by siRNA contributed to the inhibitory effect of eupatilin on proliferation and invasion of glioma cells. In conclusion, eupatilin had an inhibitory effect on proliferation, invasion and migration, and promoted apoptosis of glioma cells through suppression of the Notch-1 signaling pathway. Therefore, eupatilin may have potential as an effective agent for the treatment of glioma.
Borealis-R: a replication-transparent stream processing system for wide-area monitoring applications

Borealis-R is a replication-based system for both fast and highly-available processing of data streams over wide-area networks. In Borealis-R, multiple operator replicas send outputs to downstream replicas, allowing each replica to use whichever data arrives first. To further reduce latency, replicas run without coordination, possibly processing data in different orders. Despite this flexibility, Borealis-R guarantees that applications always receive the same results as in the non-replicated, failure-free case. In addition, Borealis-R deploys replicas at select network locations to effectively improve performance as well as availability. We demonstrate the strengths of Borealis-R using a live wide-area monitoring application. We show that Borealis-R outperforms previous solutions in terms of latency and that it uses system resources efficiently by carefully deploying and discarding replicas.
Plasmacytoid Dendritic Cells Support Melanoma Progression by Promoting Th2 and Regulatory Immunity through OX40L and ICOSL

Combining the analyses of samples from melanoma patients and from melanoma-bearing humanized mice, the authors delineated the mechanism by which plasmacytoid dendritic cells mediate tumor progression and early relapse and identified potential therapeutic options for patients with metastatic melanoma. Even though melanoma is considered to be one of the most immunogenic solid tumors, handling its development remains a challenge. The basis for such escape from antitumor immune control has not yet been documented. Plasmacytoid dendritic cells (pDC) are emerging as crucial but still enigmatic cells in cancer. In melanoma, the function of tumor-infiltrating pDCs remains poorly explored. We investigated the pathophysiologic role of pDCs in melanoma, both ex vivo from a large cohort of melanoma patients and in vivo in melanoma-bearing humanized mice. pDCs were found in high proportions in cutaneous melanoma and tumor-draining lymph nodes, yet associated with poor clinical outcome. We showed that pDCs migrating to the tumor microenvironment displayed particular features, subsequently promoting proinflammatory Th2 and regulatory immune profiles through OX40L and ICOSL expression. Elevated frequencies of interleukin (IL)-5-, IL-13- and IL-10–producing T cells in patients with melanoma correlated with high proportions of OX40L- and ICOSL-expressing pDCs. Strikingly TARC/CCL17, MDC/CCL22, and MMP-2 found in the melanoma microenvironment were associated with pDC accumulation, OX40L and ICOSL modulation, and/or early relapse. Thus, melanoma actively exploits pDC plasticity to promote its progression. By identifying novel insights into the mechanism of hijacking of immunity by melanoma, our study exposes potential for new therapeutic opportunities. Cancer Immunol Res; 1(6); 402–15. ©2013 AACR.
The formation of urine by the prosobranch gastropod mollusc Viviparus viviparus Linn.

1. The urine of Viviparus is hypotonic to the blood by about 30 mM. /l. NaCl in tap water, and remains hypotonic in concentrations of up to 10% sea water. 2. The rate of production of urine is between 0·25 and 0·91 µl. /g. /min. in tap water at 19° C. The rate decreases in proportion to the decrease in osmotic difference between blood and external medium. Viviparus may be able to detect changes in salt concentration of the external medium and alter its rate of urine production accordingly. 3. Pericardial fluid is similar to blood in composition; the rate of flow of pericardial fluid through the reno-pericardial canal is proportional to the blood pressure; and when inulin is injected into the blood, concentrations in blood and pericardial fluid are approximately the same. For these reasons it is supposed that blood is filtered through the heart into the pericardium. 4. About 20 mM. /l. NaCl, and probably some water, are reabsorbed in the kidney. Liquid is passed through the kidney by rhythmic contractions of the kidney musculature. Pericardial pressure does not influence the overall rate of urine production but blood pressure does have an effect. 5. About 5 mM. / NaCl, and probably a little water, are reabsorbed in the ureter.
1-Deoxynojirimycin Alleviates Insulin Resistance via Activation of Insulin Signaling PI3K/AKT Pathway in Skeletal Muscle of db/db Mice

1-Deoxynojirimycin (DNJ) is widely used for the treatment of diabetes mellitus as an inhibitor of intestinal α-glucosidase. However, there are few reports about its effect on insulin sensitivity improvement. The aim of the present study was to investigate whether DNJ decreased hyperglycemia by improving insulin sensitivity. An economical method was established to prepare large amounts of DNJ. Then, db/db mice were treated with DNJ intravenously (20, 40 and 80 mg·kg−1·day−1) for four weeks. Blood glucose and biochemical analyses were conducted to evaluate the therapeutic effects on hyperglycemia and the related molecular mechanisms in skeletal muscle were explored. DNJ significantly reduced body weight, blood glucose and serum insulin levels. DNJ treatment also improved glucose tolerance and insulin tolerance. Moreover, although expressions of total protein kinase B (AKT), phosphatidylinositol 3 kinase (PI3K), insulin receptor beta (IR-β), insulin receptor substrate-1 (IRS1) and glucose transporter 4 (GLUT4) in skeletal muscle were not affected, GLUT4 translocation and phosphorylation of Ser473-AKT, p85-PI3K, Tyr1361-IR-β and Tyr612-IRS1 were significantly increased by DNJ treatment. These results indicate that DNJ significantly improved insulin sensitivity via activating insulin signaling PI3K/AKT pathway in skeletal muscle of db/db mice.
The Nonverbal Expression of Pride: Evidence for Cross-cultural Recognition

The present research tests whether recognition for the nonverbal expression of pride generalizes across cultures. Study 1 provided the first evidence for cross-cultural recognition of pride, demonstrating that the expression generalizes across Italy and the United States. Study 2 found that the pride expression generalizes beyond Western cultures; individuals from a preliterate, highly isolated tribe in Burkina Faso, West Africa, reliably recognized pride, regardless of whether it was displayed by African or American targets. These Burkinabe participants were unlikely to have learned the pride expression through cross-cultural transmission, so their recognition suggests that pride may be a human universal. Studies 3 and 4 used drawn figures to systematically manipulate the ethnicity and gender of targets showing the expression, and demonstrated that pride recognition generalizes across male and female targets of African, Asian, and Caucasian descent. Discussion focuses on the implications of the findings for the universality of the pride expression. One of the major findings in the behavioral and social sciences is the discovery that a small set of basic emotions—anger, disgust, fear, happiness, sadness, and surprise— have distinct, universally recognized nonverbal expressions research on highly isolated preliterate tribal groups in Papua New Guinea, led many researchers to accept Darwin's (1872) view that emotions and their expressions are a universal, evolved part of human nature. Over the past few decades, several attempts have been made to identify additional universally recognized emotion expressions, but, with a few possible exceptions (contempt, embarrassment, and, these attempts have failed. As a result, the six basic emotions have a special status in the emotion literature. In contrast, emotions assumed to lack universal expressions have received considerably less attention within the field of affective science. In particular, researchers have largely neglected the self-conscious (or social) emotions, such as embarrassment, pride, and shame. These emotions involve complex self-evaluative processes (Tangney & Dearing, 2002; Tracy & Robins, 2004a), emerge later in development than do basic emotions (M. Lewis, Alessandri, & Sullivan, 1992), are thought to be unique to humans and possibly the great apes (Hart & Karmel, 1996), and play a central role in status seeking, dominance, and other fundamental social behaviors (Keltner & Buswell, 1997; Tracy & Robins, 2007c). However, recent research suggests that the self-conscious emotion of pride may have a recognizable nonverbal expression. The pride expression, shown in Figure 1, includes the body (i.e., expanded posture, head tilted back) as well as the face (i.e., …
Bat guilds, a concept to classify the highly diverse foraging and echolocation behaviors of microchiropteran bats

Throughout evolution the foraging and echolocation behaviors as well as the motor systems of bats have been adapted to the tasks they have to perform while searching and acquiring food. When bats exploit the same class of environmental resources in a similar way, they perform comparable tasks and thus share similar adaptations independent of their phylogeny. Species with similar adaptations are assigned to guilds or functional groups. Habitat type and foraging mode mainly determine the foraging tasks and thus the adaptations of bats. Therefore, we use habitat type and foraging mode to define seven guilds. The habitat types open, edge and narrow space are defined according to the bats' echolocation behavior in relation to the distance between bat and background or food item and background. Bats foraging in the aerial, trawling, flutter detecting, or active gleaning mode use only echolocation to acquire their food. When foraging in the passive gleaning mode bats do not use echolocation but rely on sensory cues from the food item to find it. Bat communities often comprise large numbers of species with a high diversity in foraging areas, foraging modes, and diets. The assignment of species living under similar constraints into guilds identifies patterns of community structure and helps to understand the factors that underlie the organization of highly diverse bat communities. Bat species from different guilds do not compete for food as they differ in their foraging behavior and in the environmental resources they use. However, sympatric living species belonging to the same guild often exploit the same class of resources. To avoid competition they should differ in their niche dimensions. The fine grain structure of bat communities below the rather coarse classification into guilds is determined by mechanisms that result in niche partitioning.
Religiosity and fairness perceptions.

We measure the impact of religiosity on preferences over distribution of resources, using two surveys conducted among undergraduate students in Turkey. The subjects were asked to assess the fairness of three hypothetical distributions of resources between two agents. These agents differed in their ability to convert resources into goods that provide utility, and we manipulated the information about the source of these differences across different problems. Even though relative popularity of alternative distributions is similar among religious or non-religious people, some significant differences emerge between these two groups. With minimal information, less religious people are significantly more likely to prefer the Egalitarian distribution and significantly less likely to prefer the Rawlsian distribution. When differences are explained to be due to external factors, higher religiosity implies a higher likelihood of ranking both the Rawlsian and Utilitarian distributions above the Egalitarian distribution. However, when differences are due to voluntary choices of agents, differences between religious and non-religious people disappear inducing subjects to think efficiency as the most fair alternative. These results are robust when we control for other relevant factors. Religious and nonreligious people also disagree on the issues around working towards making everyone equal, and insuring people who make unlucky economic choices.
Characterization of the Cardiac Overexpression of HSPB2 Reveals Mitochondrial and Myogenic Roles Supported by a Cardiac HspB2 Interactome

Small Heat Shock Proteins (sHSPs) are molecular chaperones that transiently interact with other proteins, thereby assisting with quality control of proper protein folding and/or degradation. They are also recruited to protect cells from a variety of stresses in response to extreme heat, heavy metals, and oxidative-reductive stress. Although ten human sHSPs have been identified, their likely diverse biological functions remain an enigma in health and disease, and much less is known about non-redundant roles in selective cells and tissues. Herein, we set out to comprehensively characterize the cardiac-restricted Heat Shock Protein B-2 (HspB2), which exhibited ischemic cardioprotection in transgenic overexpressing mice including reduced infarct size and maintenance of ATP levels. Global yeast two-hybrid analysis using HspB2 (bait) and a human cardiac library (prey) coupled with co-immunoprecipitation studies for mitochondrial target validation revealed the first HspB2 “cardiac interactome” to contain many myofibril and mitochondrial-binding partners consistent with the overexpression phenotype. This interactome has been submitted to the Biological General Repository for Interaction Datasets (BioGRID). A related sHSP chaperone HspB5 had only partially overlapping binding partners, supporting specificity of the interactome as well as non-redundant roles reported for these sHSPs. Evidence that the cardiac yeast two-hybrid HspB2 interactome targets resident mitochondrial client proteins is consistent with the role of HspB2 in maintaining ATP levels and suggests new chaperone-dependent functions for metabolic homeostasis. One of the HspB2 targets, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), has reported roles in HspB2 associated phenotypes including cardiac ATP production, mitochondrial function, and apoptosis, and was validated as a potential client protein of HspB2 through chaperone assays. From the clientele and phenotypes identified herein, it is tempting to speculate that small molecule activators of HspB2 might be deployed to mitigate mitochondrial related diseases such as cardiomyopathy and neurodegenerative disease.
Aligning where to see and what to tell: image caption with region-based attention and scene factorization

Recent progress on automatic generation of image captions has shown that it is possible to describe the most salient information conveyed by images with accurate and meaningful sentences. In this paper, we propose an image caption system that exploits the parallel structures between images and sentences. In our model, the process of generating the next word, given the previously generated ones, is aligned with the visual perception experience where the attention shifting among the visual regions imposes a thread of visual ordering. This alignment characterizes the flow of "abstract meaning", encoding what is semantically shared by both the visual scene and the text description. Our system also makes another novel modeling contribution by introducing scene-specific contexts that capture higher-level semantic information encoded in an image. The contexts adapt language models for word generation to specific scene types. We benchmark our system and contrast to published results on several popular datasets. We show that using either region-based attention or scene-specific contexts improves systems without those components. Furthermore, combining these two modeling ingredients attains the state-of-the-art performance.
Growth hormone therapy improves bone mineral density in children with cerebral palsy: a preliminary pilot study.

CONTEXT Cerebral palsy is associated with osteopenia, increased fracture risk, short stature, and decreased muscle mass, whereas GH therapy is associated with increased bone mineral density (BMD) and linear growth and improvement in body composition. OBJECTIVE We conducted a pilot study to evaluate the effect of 18 months of GH therapy on spinal BMD, linear growth, biochemical markers, and functional measures in children with cerebral palsy. DESIGN AND SETTING The study was a randomized control trial, conducted from 2002-2005 at the University of California, Los Angeles, Orthopedic Hospital's Center for Cerebral Palsy. PATIENTS Patients included 12 males with cerebral palsy, ages 4.5-15.4 yr. INTERVENTION We compared 18 months of GH (50 microg daily) vs. no treatment. PRIMARY OUTCOME MEASURES Spinal BMD (dual-energy x-ray absorptiometry scan), height, growth factors, and bone markers were assessed. RESULTS Ten subjects (five in each group) completed the study. Pre- and post-average height z-scores were -1.47 +/- 0.23 and 0.8 +/- 0.2 (GH-treated group) vs. -1.35 +/- 1.26 and -1.36 +/- 1.27 (control group) (Delta SD score, 0.67 vs. -0.01; P = 0.01). Average change in spinal BMD z-score (Delta SD score corrected for height) was 1.169 +/- 0.614 vs. 0.24 +/- 0.25 in the treated and control groups, respectively (P = 0.03). Osteocalcin, IGF-I, and IGF-binding protein 3 levels increased during GH therapy. There was no change in quality of life scores as measured by the Pediatric Orthopedic Disability Inventory. CONCLUSIONS This small pilot study suggests that 18 months of GH therapy is associated with statistically significant improvement in spinal BMD and linear growth.