Miracle-dz/UniFAR-FTUs huggingface dataset:
Search for point sources of gamma radiation above 15 TeV with the HEGRA AIROBICC array

A search for potential point sources of very high energy gamma rays has been carried out on the data taken simul- taneously by the HEGRA AIROBICC and Scintillator arrays from August 1994 to March 2000. The list of sought sources includes supernova remnants, pulsars, AGNs and binary systems. The energy threshold is around 15 TeV. For the Crab Nebula, a modest excess of 2.5 standard deviations above the cosmic ray background has been observed. Flux upper limits (at 90% c.l.) of around 1.3 times the flux of the Crab Nebula are obtained, in average, for the candidate sources. A dierent search procedure has been used for an all-sky search which yields absolute flux upper limits between 4 and 9crabs depending on declination, in the band from= 0t o= 60.
Replication bands and nucleoli in the macronucleus of Euplotes eurystomus: An ultrastructural and cytochemical study

The principal structural compartments of the macronucleus of Euplotes eurystomus were examined by ultrastructural and cytochemical procedures. Interphase chromatin is condensed in highly compact granules that stain intensely with the DNA‐specific osmium‐amine procedure. Nucleoli react strongly with silver and with thiol‐specific reagents, but are almost completely unstained by osmium‐amine. The organelle of DNA synthesis, the replication band, is composed of 2 zones. The forward zone consists of highly ordered chromatin fibers, stains strongly with osmium‐amine, with silver, and with thiol‐specific reagents. The rear zone, which is the site of DNA synthesis, is impoverished in DNA, and is very sensitive to collapse induced by in vivo heat shock, or during nuclear isolation.
Real-Time Depth Refinement for Specular Objects

The introduction of consumer RGB-D scanners set off a major boost in 3D computer vision research. Yet, the precision of existing depth scanners is not accurate enough to recover fine details of a scanned object. While modern shading based depth refinement methods have been proven to work well with Lambertian objects, they break down in the presence of specularities. We present a novel shape from shading framework that addresses this issue and enhances both diffuse and specular objects' depth profiles. We take advantage of the built-in monochromatic IR projector and IR images of the RGB-D scanners and present a lighting model that accounts for the specular regions in the input image. Using this model, we reconstruct the depth map in real-time. Both quantitative tests and visual evaluations prove that the proposed method produces state of the art depth reconstruction results.
Autologous bone marrow transplantation in the therapy of small cell carcinoma of the lung.

Ten patients with small cell carcinoma of the lung were entered into a chemotherapeutic treatment program consisting of cyclophosphamide, vincristine, Adriamycin, and 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea. Two courses of combination chemotherapy were administered to each patient followed by a third course with the same doses of drugs used on Course 2 but with autologous bone marrow transplantation given 24 to 48 hr after drug infusion. No differences could be detected between Courses 2 and 3 in terms of the magnitude, timing, or degree of myelosuppression. Serial bone marrow biopsies documented a progressive decline in granulocyte-macrophage colony-forming units in culture per mg bone marrow medullary core from 138 +/- 179 (S.D.) prior to chemotherapy to 7 +/- 11 after the marrow transplant recovery (p = 0.05). These data suggest that autologous bone marrow transplantation does not reduce the myelosuppression seen following the drugs used in this study at the dosages used. Autologous bone marrow transplantation may be useful only in the setting of marrow lethal therapy. Its usefulness in shortening recovery time from nonlethal therapy appears questionable.
An ent-kaurene-derived diterpenoid virulence factor from Xanthomonas oryzae pv. oryzicola.

Both plants and fungi produce ent-kaurene as a precursor to the gibberellin plant hormones. A number of rhizobia contain functionally conserved, sequentially acting ent-copalyl diphosphate and ent-kaurene synthases (CPS and KS, respectively), which are found within a well-conserved operon that may lead to the production of gibberellins. Intriguingly, the rice bacterial leaf streak pathogen Xanthomonas oryzae pv. oryzicola (Xoc) contains a homologous operon. Here, we report biochemical characterization of the encoded CPS and KS, and the impact of insertional mutagenesis on virulence and the plant defense response for these genes, as well as that for one of the cytochromes P450 (CYP112) found in the operon. Activity of the CPS and KS found in this phytopathogen was verified - that is, Xoc is capable of producing ent-kaurene. Moreover, knocking out CPS, KS or CYP112 led to mutant Xoc that exhibited reduced virulence. Investigation of the effect on marker gene transcript levels suggests that the Xoc diterpenoid affects the plant defense response, most directly that mediated by jasmonic acid (JA). Xoc produces an ent-kaurene-derived diterpenoid as a virulence factor, potentially a gibberellin phytohormone, which is antagonistic to JA, consistent with the recent recognition of opposing effects for these phytohormones on the microbial defense response.
Subcutaneous Panniculitis-Like T-cell Lymphoma: A Clinical and Pathologic Study of 14 Korean Patients

Background Subcutaneous panniculitis-like T-cell lymphoma (SPTL) is a distinctive skin lymphoma characterized by neoplastic T-cell infiltration of the subcutaneous tissue, mimicking panniculitis. Objective To describe the clinical and pathologic features of SPTL in Korean patients. Methods Fourteen SPTL patients evaluated over 15 years were retrospectively reviewed. Results The mean patient age was 35 years (range: 7~73 years), with male predominance (2.5:1). Most patients presented with either nodules or plaques, occurring most commonly on the trunk, with two patients (14%) having hemophagocytic syndrome. Histopathologically, all patients showed infiltrates of small-to-medium pleomorphic cells mimicking panniculitis, with some also showing rimming, bean-bag cells, and fat necrosis. Most patients were positive for CD3 (14/14), CD8 (12/13), TIA-1 (9/9) and βf1 (5/5), but were negative for CD4 (11/12), CD20 (8/8), CD56 (14/14) and Epstein-Barr virus (8/8). Ten patients (71%) received chemotherapy and 2 (14%) died due to the disease, with an average survival time of 4 months. Survival analysis did not reveal any significant prognostic factors. Conclusion This is the first series of patients with SPTL in Korea. Due to its indolent clinical course and relatively high survival rate, SPTL should be differentiated from cutaneous γδ T-cell lymphoma.
Design, Validation and Annotation of Transcriptome-Wide Oligonucleotide Probes for the Oligochaete Annelid Eisenia fetida

High density oligonucleotide probe arrays have increasingly become an important tool in genomics studies. In organisms with incomplete genome sequence, one strategy for oligo probe design is to reduce the number of unique probes that target every non-redundant transcript through bioinformatic analysis and experimental testing. Here we adopted this strategy in making oligo probes for the earthworm Eisenia fetida, a species for which we have sequenced transcriptome-scale expressed sequence tags (ESTs). Our objectives were to identify unique transcripts as targets, to select an optimal and non-redundant oligo probe for each of these target ESTs, and to annotate the selected target sequences. We developed a streamlined and easy-to-follow approach to the design, validation and annotation of species-specific array probes. Four 244K-formatted oligo arrays were designed using eArray and were hybridized to a pooled E. fetida cRNA sample. We identified 63,541 probes with unsaturated signal intensities consistently above the background level. Target transcripts of these probes were annotated using several sequence alignment algorithms. Significant hits were obtained for 37,439 (59%) probed targets. We validated and made publicly available 63.5K oligo probes so the earthworm research community can use them to pursue ecological, toxicological, and other functional genomics questions. Our approach is efficient, cost-effective and robust because it (1) does not require a major genomics core facility; (2) allows new probes to be easily added and old probes modified or eliminated when new sequence information becomes available, (3) is not bioinformatics-intensive upfront but does provide opportunities for more in-depth annotation of biological functions for target genes; and (4) if desired, EST orthologs to the UniGene clusters of a reference genome can be identified and selected in order to improve the target gene specificity of designed probes. This approach is particularly applicable to organisms with a wealth of EST sequences but unfinished genome.
Livin‐α promotes cell proliferation by regulating G1‐S cell cycle transition in prostate cancer

Prostate cancer is the third most common cancer and the second leading cause of cancer death for males in US. Livin has recently been described as a cancer‐associated member of inhibitor of apoptosis proteins family, highly expressed in prostate cancer. Livin gene encodes two splicing variants, termed Livin‐α and Livin‐β. We hypothesized that deregulation of proliferation could be due in part to Livin expression.
Thr729 in human topoisomerase I modulates anti-cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations

The role of Thr729 in modulating the enzymatic function of human topoisomerase I has been characterized by molecular dynamics (MD) simulation. In detail, the structural–dynamical behaviour of the Thr729Lys and the Thr729Pro mutants have been characterized because of their in vivo and in vitro functional properties evidenced in the accompanying paper. Both mutants can bind to the DNA substrate and are enzymatically active, but while Thr729Lys is resistant even at high concentration of the camptothecin (CPT) anti-cancer drug, Thr729Pro shows only a mild reduction in drug sensitivity and in DNA binding. MD simulations show that the Thr729Lys mutation provokes a structural perturbation of the CPT-binding pocket. On the other hand, the Thr729Pro mutant maintains the wild-type structural scaffold, only increasing its rigidity. The simulations also show the complete abolishment, in the Thr729Lys mutant, of the protein communications between the C-terminal domain (where the active Tyr723 is located) and the linker domain, that plays an essential role in the control of the DNA rotation, thus explaining the distributive mode of action displayed by this mutant.
INTRODUCTION Age-related osteoporosis is associated with an increase in adipocytes and a reciprocal decrease in osteoblast numbers within bone

INTRODUCTION Age-related osteoporosis is associated with an increase in adipocytes and a reciprocal decrease in osteoblast numbers within bone marrow (Beresford et al., 1992; Burkhardt et al., 1987; Kajkenova et al., 1997; Koo et al., 1998; Meunier et al., 1971; Nuttall and Gimble, 2000; Verma et al., 2002). Both of these cell types differentiate from a bone marrow-derived multipotent precursor called a mesenchymal stem cell (MSC) (Phinney and Prockop, 2007). Differentiation of MSCs into adipocytes and osteoblasts is driven by Peroxisome proliferator-activated receptor gamma (Pparg) and Runt-related transcription factor 2 (Runx2; also known as Core binding factor a1), respectively (Komori et al., 1997; Otto et al., 1997; Tontonoz et al., 1994). Intriguingly, mice that lack one copy of Pparg have increased bone mass and elevated osteoblast differentiation (Kawaguchi et al., 2005). Furthermore, pharmaceutical activation of PPARG as a treatment for diabetes in humans leads to a decrease in bone mass and has been shown to reduce osteoblast differentiation in mice (Akune et al., 2004; Ali et al., 2005; Grey, 2008). Several other pathways have been shown to regulate adipocyte and osteoblast differentiation from MSCs (Zhao et al., 2008). Whereas Leptin, Estrogen, Wnt and TGFb promote osteoblast differentiation while inhibiting adipogenesis, Pparg has the opposite effect. In addition, the transcription factor Tafazzin is known to act in MSCs to promote osteoblastogenesis by activating Runx2 and inhibiting Pparg (Hong et al., 2005). Although the mutually exclusive relationship of these two lineages suggests the existence of a bipotent adipo/osteoprogenitor, there is no strong evidence to support this hypothesis. Recent studies in zebrafish have highlighted its potential as a tool for the analysis of obesity (Flynn et al., 2009; Liu et al., 2007; Schlegel and Stainier, 2006; Song and Cone, 2007; Yang et al., 2008). In addition, several mutant zebrafish lines have been shown to accurately model human skeletal diseases (Clement et al., 2008; Fisher et al., 2003; Lang et al., 2006). Here we analyse the role that the retinoic acid (RA) and Pparg pathways play in specifying osteoblast and adipocyte cell fate choices in the cephalic neural crest (CNC). Our findings shed light on how neural crest cells diversify in vivo and might increase our understanding of human diseases such as osteoporosis, diabetes and obesity. These results might also aid in the advancement of new technologies based upon neural crest stem cells (Delfino-Machin et al., 2007; Dupin et al., 2007).
SOCIAL SUPPORT RECEIVED ONLINE AND OFFLINE BY INDIVIDUALS DIAGNOSED WITH CANCER

SOCIAL SUPPORT RECEIVED ONLINE AND OFFLINE BY INDIVIDUALS DIAGNOSED WITH CANCER By Jessye Cohen, M.S. A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. Virginia Commonwealth University, 2011 Major Director: Kathleen M. Ingram, J.D. , Ph.D. Associate Professor, Department of Psychology Life after treatment for cancer has become a primary focus for health service provider communities as the number of individuals living longer grows. The medical and psychosocial needs of cancer survivors have been prominent in the popular and scientific literature. A major focus for psychologists has been the relationships and social support networks of individuals diagnosed with cancer. The current study explored a recent phenomenon within this realm, the use of Internet resources for online support. The purpose of this study was to compare social support received online and social support received offline among people diagnosed with cancer who use the Internet for cancerrelated support. Specifically, the study first compared types of support received online and offline. Based on the existing literature, the study then explored relationships between offline and online social support and other psychological variables, including positive affect, health-related quality of life, and coping. The research design was crosssectional, and self-report data were collected from 102 participants who had been diagnosed with cancer. Participants reported a variety of reasons for using cancer-related websites and online communities and provided information regarding types, frequency, and intensity of online activities. Most hypotheses were supported for traditional social support but were not supported for online support. Consistent with hypotheses, total social support received offline was higher than support received online. Emotional support and informational support were significantly higher offline than online. As predicted, participants experienced fewer unsupportive interactions online than offline. Also consistent with the hypotheses, emotional support received from the main support person was positively associated with positive affect and health related quality of life, whereas online emotional support was only positively associated with Focus on the Positive coping. Contrary to the hypotheses, hierarchical regression equations indicated that received informational support was positively associated with avoidant coping. This study contributes to the literature as one of the first studies to explore social support received online in a systematic manner. The results have important research and clinical implications for understanding the distinct and overlapping elements of social support received online and offline by individuals with cancer. Future research directions are also discussed.
Umbrella Branding and the Provision of Quality

Consider a two-product firm that decides on the quality of each product. Product quality is unknown to consumers. If the firm sells both products under the same brand name, consumers adjust their beliefs about quality subject to the performance of both products. We show that if the probability that low quality will be detected is in an intermediate range, the firm produces high quality under umbrella branding whereas it would sell low quality in the absence of umbrella branding. Hence, umbrella branding mitigates the moral hazard problem. We also find that umbrella branding survives in asymmetric markets and that even unprofitable products may be used to stabilize the umbrella brand. However, umbrella branding does not necessarily imply high quality; the firm may choose low-quality products with positive probability.
Active Queue Management for Fair Bandwidth Allocation of Mixed Responsive and Non-Responsive Traffic Using a Closed-Loop Congestion Control Scheme

Today’s known and widely used active queue management (AQM) schemes do not differentiate between packets from responsive (e.g., TCP sessions) and non-responsive traffic (e.g., UDP). This results in further widening the gap of unfair advantage already inherent to non-responsive traffic, as the responsive sender will significantly reduce its future transmit rate as a result of the congestion signals. As a simple work-around, responsive and non-responsive traffic are often assigned distinct AQM parameters. This approach however requires tuning for each traffic class that potentially depends on the current or expected offered load. In other words, responsiveness and TCPfriendliness cannot be estimated easily—not at last due to shortlived TCP sessions. In this paper we propose a closed-loop congestion control (CLCC) scheme on top of an existing AQM scheme to achieve fair bandwidth distribution among concurrent responsive and non-responsive traffic. The new scheme has the advantage that it does not need to estimate the level of responsiveness of traffic. We analyze our scheme on top of an existing rate-based AQM scheme known to approximate max-min fairness, and by means of simulations show that our extension significantly improves fair bandwidth allocation for responsive and non-responsive traffic.
Incidence and predictors of silent cerebral embolism during pulmonary vein catheter ablation for atrial fibrillation.

AIMS Left atrial catheter ablation of the pulmonary veins (PV) has evolved as an important therapeutic option for the treatment of atrial fibrillation (AF). We aimed to investigate the incidence and predictors of silent cerebral embolism associated with PV catheter ablation, detected by diffusion-weighted magnetic resonance imaging (DW-MRI). METHODS AND RESULTS We performed a prospective analysis of 53 consecutive patients with persistent or paroxysmal AF that underwent PV ablation and post-procedural cerebral MRI 1 day after lasso catheter-guided ostial PV ablation. Patients were analysed for possible demographical, medical, echocardiographical, and procedural predictors of embolic events. A mean of 3.5 +/- 0.5 PVs were ablated per patient. In six patients, DW-MRI depicted new clinically silent microembolism after PV ablation (11%). The number of ineffective medical antiarrhythmic agents prior to ablation procedure was significantly higher in the embolism group (3.3 +/- 0.5 vs. 2.2 +/- 1.4, P = 0.014). Coronary heart disease (CAD) was more frequent in patients with cerebral embolisms (33 vs. 2%, P = 0.031); left ventricular volume (130 +/- 12 vs. 103 +/- 26 mL, P = 0.002), and septal wall thickness (13.0 +/- 1.4 vs. 7.9 +/- 4.8 mm, P = 0.025) were significantly increased. CONCLUSION This study shows a high incidence of silent micro-embolic events after PV ablation. CAD, left ventricular dilatation, and hypertrophy were potential predictors of this complication.
Predation in the presence of decoys: an inhibitory factor on pathogen control by bacteriophages or bdellovibrios in dense and diverse ecosystems.

Several attempts have been made at the removal of specific pathogens from the intestinal microflora using either bacteriophages or "predatory" bacteria such as Bdellovibrio spp. To date these attempts have had mixed success. A mechanism explaining these findings based on competitive hindrance by non-prey, or decoy species is put forward. It is shown that this hindrance tends to damp out predator-prey oscillations, and therefore reduces the probability of prey extinction. Possible experiments to verify this theory are discussed. The decoy effect may play a role in any system with high densities of bacteria or other particulate matter, such as activated sludge or biofilms.
Discovery of Enzyme Modulators via High-Throughput Time-Resolved FRET in Living Cells

We have used a “two-color” SERCA (sarco/endoplasmic reticulum calcium ATPase) biosensor and a unique high-throughput fluorescence lifetime plate reader (FLT-PR) to develop a high-precision live-cell assay designed to screen for small molecules that perturb SERCA structure. A SERCA construct, in which red fluorescent protein (RFP) was fused to the N terminus and green fluorescent protein (GFP) to an interior loop, was stably expressed in an HEK cell line that grows in monolayer or suspension. Fluorescence resonance energy transfer (FRET) from GFP to RFP was measured in the FLT-PR, which increases precision 30-fold over intensity-based plate readers without sacrificing throughput. FRET was highly sensitive to known SERCA modulators. We screened a small chemical library and identified 10 compounds that significantly affected two-color SERCA FLT. Three of these compounds reproducibly lowered FRET and inhibited SERCA in a dose-dependent manner. This assay is ready for large-scale HTS campaigns and is adaptable to many other targets.
Human Brain-Derived Aβ Oligomers Bind to Synapses and Disrupt Synaptic Activity in a Manner That Requires APP

Compelling genetic evidence links the amyloid precursor protein (APP) to Alzheimer's disease (AD) and several theories have been advanced to explain the relationship. A leading hypothesis proposes that a small amphipathic fragment of APP, the amyloid β-protein (Aβ), self-associates to form soluble aggregates that impair synaptic and network activity. Here, we used the most disease-relevant form of Aβ, protein isolated from AD brain. Using this material, we show that the synaptotoxic effects of Aβ depend on expression of APP and that the Aβ-mediated impairment of synaptic plasticity is accompanied by presynaptic effects that disrupt the excitatory/inhibitory (E/I) balance. The net increase in the E/I ratio and inhibition of plasticity are associated with Aβ localizing to synapses and binding of soluble Aβ aggregates to synapses requires the expression of APP. Our findings indicate a role for APP in AD pathogenesis beyond the generation of Aβ and suggest modulation of APP expression as a therapy for AD. SIGNIFICANCE STATEMENT Here, we report on the plasticity-disrupting effects of amyloid β-protein (Aβ) isolated from Alzheimer's disease (AD) brain and the requirement of amyloid precursor protein (APP) for these effects. We show that Aβ-containing AD brain extracts block hippocampal LTP, augment glutamate release probability, and disrupt the excitatory/inhibitory balance. These effects are associated with Aβ localizing to synapses and genetic ablation of APP prevents both Aβ binding and Aβ-mediated synaptic dysfunctions. Our results emphasize the importance of APP in AD and should stimulate new studies to elucidate APP-related targets suitable for pharmacological manipulation.