Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural analysis of the adenovirus type 5 E1B 55-kilodalton-E4orf6 protein complex

The adenovirus type 5 (Ad5) early 1B (E1B) 55-kDa (E1B-55kDa)-E4orf6 protein complex has been implicated in the selective modulation of nucleocytoplasmic mRNA transport at late times after infection. Using a combined immunoprecipitation-immunoblotting assay, we mapped the domains in E1B-55kDa required for the interaction with the E4orf6 protein in lytically infected A549 cells. Several domains in the 496-residue 55-kDa polypeptide contributed to a stable association with the E4orf6 protein in E1B mutant virus-infected cells. Linker insertion mutations at amino acids 180 and 224 caused reduced binding of the E4orf6 protein, whereas linker insertion mutations at amino acid 143 and in the central domain of E1B-55kDa eliminated the binding of the E4orf6 protein. Earlier work showing that the central domain of E1B-55kDa is required for binding to p53 and the recent observation that the E4orf6 protein also interacts with the tumor suppressor protein led us to suspect that p53 might play a role in the E1B-E4 protein interaction. However, coimmunoprecipitation assays with extracts prepared from infected p53-negative H1299 cells established that p53 is not needed for the E1B-E4 protein interaction in adenovirus-infected cells. Using two different protein-protein interaction assays, we also mapped the region in the E4orf6 protein required for E1B-55kDa interaction to the amino-terminal 55 amino acid residues. Interestingly, both binding assays established that the same region in the E4orf6/7 protein can potentially interact with E1B-55kDa. Our results demonstrate that two distinct segments in the 55-kDa protein encoding the transformation and late lytic functions independently interact with p53 and the E4orf6 protein in vivo and provide further insight by which the multifunctional 55-kDa EIB protein can exert its multiple activities in lytically infected cells and in adenovirus transformation.
Targeting the Renin Angiotensin System in Dialysis Patients

Patients on chronic dialysis therapy have a dramatic excess cardiovascular risk compared to any other population, including those with overt diabetic nephropathy. Despite this, patients on dialysis are almost invariably excluded from trials evaluating the cardioprotective effect of novel treatments. Consistent evidence is available that inhibitors of the renin–angiotensin system, such as angiotensin‐converting enzyme (ACE) inhibitors or angiotensin II receptor blockers (ARBs), are more cardioprotective than other antihypertensive agents in patients with chronic renal disease or diabetes (with or without renal involvement), but whether this applies also to patients on dialysis is unknown. However, clear evidence is available that ACE inhibitors and ARBs reduce morbidity and mortality in patients on dialysis with heart failure (HF) or atrial fibrillation (AF). Moreover, these drugs may preserve residual renal function in those with preterminal kidney failure as well as vascular access and peritoneal membrane function in those on extracorporeal or peritoneal dialysis, respectively. These drugs also show an excellent tolerability profile in this population. Thus, ACE inhibitors and ARBs are indicated in patients on dialysis with HF or AF. Available evidence suggests that they should be first‐choice therapy in patients on dialysis with hypertension, though trials are still needed to formally demonstrate their superior cardioprotective effect over other antihypertensives in this population.
CandlestiCK Charting in European stock markets

The purpose of this study is to investigate whether an old Japanese trading technique can function in a Western context. This paper employs a 1 4 vector to categorise two-day candlestick patterns systematically, and then examines their profitability for the FTSE 100, DAX 30 and CAC 40 component stocks. After conducting statistical tests and the bootstrap methodology, we find that three patterns can produce profits after considering transaction costs in the major European stock markets. We also investigate the effects of the global financial crisis on the efficacy of the candlestick method.
Splenectomy Protects against Sepsis Lethality and Reduces Serum HMGB1 Levels1

High mobility group box 1 (HMGB1) is a critical mediator of lethal sepsis. Previously, we showed that apoptotic cells can activate macrophages to release HMGB1. During sepsis, apoptosis occurs primarily in lymphoid organs, including the spleen and thymus. Currently, it is unclear whether this accelerated lymphoid organ apoptosis contributes to systemic release of HMGB1 in sepsis. In this study, we report that splenectomy significantly reduces systemic HMGB1 release and improves survival in mice with polymicrobial sepsis. Treatment with a broad-spectrum caspase inhibitor reduces systemic lymphocyte apoptosis, suppresses circulating HMGB1 concentrations, and improves survival during polymicrobial sepsis, but fails to protect septic mice following splenectomy. These findings indicate that apoptosis in the spleen is essential to the pathogenesis of HMGB1-mediated sepsis lethality.
Fresh Analysis of Streaming Media Stored on the Web

With the steady increase in the bandwidth available to end users and Web sites hosting user generated content, there appears to be more multimedia content on the Web than ever before. Studies to quantify media stored on the Web done in 1997 and 2003 are now dated since the nature, size and number of streaming media objects on the Web have changed considerably. Although there have been more recent studies characterizing specific streaming media sites like YouTube, there are only a few studies that focus on characterizing the media stored on the Web as a whole. We build customized tools to crawl the Web, identify streaming media content and extract the characteristics of the streaming media found. We choose 16 different starting points and crawled 1.25 million Web pages from each starting point. Using the custom built tools, the media objects are identified and analyzed to determine attributes including media type, media length, codecs used for encoding, encoded bitrate, resolution, and aspect ratio. A little over half the media clips we encountered are video. MP3 and AAC are the most prevalent audio codecs whereas H.264 and FLV are the most common video codecs. The median size and encoded bitrates of stored media have increased since the last study. Information on the characteristics of stored multimedia and their trends over time can help system designers. The results can also be useful for empirical Internet measurements studies that attempt to mimic the behavior of streaming media traffic over the Internet.
S-adenosylhomocysteine hydrolase deficiency in a human: A genetic disorder of methionine metabolism

We report studies of a Croatian boy, a proven case of human S-adenosylhomocysteine (AdoHcy) hydrolase deficiency. Psychomotor development was slow until his fifth month; thereafter, virtually absent until treatment was started. He had marked hypotonia with elevated serum creatine kinase and transaminases, prolonged prothrombin time and low albumin. Electron microscopy of muscle showed numerous abnormal myelin figures; liver biopsy showed mild hepatitis with sparse rough endoplasmic reticulum. Brain MRI at 12.7 months revealed white matter atrophy and abnormally slow myelination. Hypermethioninemia was present in the initial metabolic study at age 8 months, and persisted (up to 784 μM) without tyrosine elevation. Plasma total homocysteine was very slightly elevated for an infant to 14.5–15.9 μM. In plasma, S-adenosylmethionine was 30-fold and AdoHcy 150-fold elevated. Activity of AdoHcy hydrolase was ≈3% of control in liver and was 5–10% of the control values in red blood cells and cultured fibroblasts. We found no evidence of a soluble inhibitor of the enzyme in extracts of the patient's cultured fibroblasts. Additional pretreatment abnormalities in plasma included low concentrations of phosphatidylcholine and choline, with elevations of guanidinoacetate, betaine, dimethylglycine, and cystathionine. Leukocyte DNA was hypermethylated. Gene analysis revealed two mutations in exon 4: a maternally derived stop codon, and a paternally derived missense mutation. We discuss reasons for biochemical abnormalities and pathophysiological aspects of AdoHcy hydrolase deficiency.
Opioid–Volatile Anesthetic Synergy: A Response Surface Model with Remifentanil and Sevoflurane as Prototypes

Background:Combining a hypnotic and an analgesic to produce sedation, analgesia, and surgical immobility required for clinical anesthesia is more common than administration of a volatile anesthetic alone. The aim of this study was to apply response surface methods to characterize the interactions between remifentanil and sevoflurane. Methods:Sixteen adult volunteers received a target-controlled infusion of remifentanil (0–15 ng/ml) and inhaled sevoflurane (0–6 vol%) at various target concentration pairs. After reaching pseudo–steady state drug levels, the Observer's Assessment of Alertness/Sedation score and response to a series of randomly applied experimental pain stimuli (pressure algometry, electrical tetany, and thermal stimulation) were observed for each target concentration pair. Response surface pharmacodynamic interaction models were built using the pooled data for sedation and analgesic endpoints. Using computer simulation, the pharmacodynamic interaction models were combined with previously reported pharmacokinetic models to identify the combination of remifentanil and sevoflurane that yielded the fastest recovery (Observer's Assessment of Alertness/Sedation score ≥ 4) for anesthetics lasting 30–900 min. Results:Remifentanil synergistically decreased the amount of sevoflurane necessary to produce sedation and analgesia. Simulations revealed that as the duration of the procedure increased, faster recovery was produced by concentration target pairs containing higher amounts of remifentanil. This trend plateaued at a combination of 0.75 vol% sevoflurane and 6.2 ng/ml remifentanil. Conclusion:Response surface analyses demonstrate a synergistic interaction between remifentanil and sevoflurane for sedation and all analgesic endpoints.
A Latent Contingency Table Approach to Dose Finding for Combinations of Two Agents

Summary Two‐agent combination trials have recently attracted enormous attention in oncology research. There are several strong motivations for combining different agents in a treatment: to induce the synergistic treatment effect, to increase the dose intensity with nonoverlapping toxicities, and to target different tumor cell susceptibilities. To accommodate this growing trend in clinical trials, we propose a Bayesian adaptive design for dose finding based on latent 2 × 2 tables. In the search for the maximum tolerated dose combination, we continuously update the posterior estimates for the unknown parameters associated with marginal probabilities and the correlation parameter based on the data from successive patients. By reordering the dose toxicity probabilities in the two‐dimensional space, we assign each coming cohort of patients to the most appropriate dose combination. We conduct extensive simulation studies to examine the operating characteristics of the proposed method under various practical scenarios. Finally, we illustrate our dose‐finding procedure with a clinical trial of agent combinations at M. D. Anderson Cancer Center.
Do changes in spring phenology affect earlywood vessels? Perspective from the xylogenesis monitoring of two sympatric ring-porous oaks.

This study addresses relationships between leaf phenology, xylogenesis, and functional xylem anatomy in two ring-porous oak species, the temperate Quercus robur and the sub-Mediterranean Q. pyrenaica. Earlywood vessel (EV) formation and leaf phenology were monitored in 2012 and 2013. Ten individuals per species were sampled at each of three sites located in NW Iberian Peninsula. EV areas measured on microcore sections were used to calculate the hydraulic tree diameter (Dh ), in order to model relationships to phenology. Thermal requirements were evaluated using growing degree days (GDD). A species-specific timing of growth resumption was found. The onset of EV formation and budburst were associated to a particular GDD in each species. The onset and duration of EV enlargement affected Dh (and EV size) in Q. robur, but hardly in Q. pyrenaica. The relationship between the timings of EV formation and xylem structure appears to be stronger for the temperate oak, whose larger vessels may result from thermal-induced earlier resumption. In contrast, the sub-Mediterranean oak would maintain a more conservative hydraulic architecture under warming conditions.
Trinucleotide microsatellite loci in a swarm‐founding neotropical wasp, Parachartergus colobopterus and their usefulness in other social wasps

'The neotropical swarm-founding wasps have societies in which genetic conflicts of interest among females may be great. Not only do many queens lay eggs, which can considerably reduce average relatedness within colonies, but workers have been found to control production of males and females in ways which favour their (and not the queens') interests (Queller et al. 1993a). Teasing out winners and losers in conflicts for reproductive rights among close relatives can be very difficult, especially when neither mothers nor fathers of specific young can be identified. The short DNA repeat regions known as microsatellites provide highly polymorphic, codominant, Mendelian markers which can be genotyped from degraded DNA, or samples as minute as the sperm in a female's spermatheca (Evans 1993; Queller et al. 1993b; Peters ef a! . 1995). Application of microsatellites to wasp societies will enhance our understanding of their genetic structure, allow us to assign parentage of young and explore genetic conflicts of interest and their resolution. Here we describe 15 microsatellite loci derived from Parachartergus coloboptms that are likely to be usefuI in this and many other species of the subfamily Polistinae. Trinucleotide microsatelli te loci have considerable advantages over dinucleotides. They produce easily distinguishable alleles even when a method of visualization other than labelling one primer is used. Ambiguous cases are much less likely since alleles differ by three bases. The presence of trinucleotide repeats within coding regions (Edwards et al. 1991) may mean that primer sites for these loci are more conserved than are those for other repeat types. Though trinucleotide repeats may be less common than dinucleotide repeats (Rassman et al. 1991), it is not difficult to find enough polymorphic loci for studies of parentage and genetic relatedness. To obtain these loci, we constructed a partial genomic library in a plasmid with inserts averaging 700 bp (Hughes
Structural variation of the human genome: mechanisms, assays, and role in male infertility

Genomic disorders are defined as diseases caused by rearrangements of the genome incited by a genomic architecture that conveys instability. Y-chromosome related dysfunctions such as male infertility are frequently associated with gross DNA rearrangements resulting from its peculiar genomic architecture. The Y-chromosome has evolved into a highly specialized chromosome to perform male functions, mainly spermatogenesis. Direct and inverted repeats, some of them palindromes with highly identical nucleotide sequences that can form DNA cruciform structures, characterize the genomic structure of the Y-chromosome long arm. Some particular Y chromosome genomic deletions can cause spermatogenic failure likely because of removal of one or more transcriptional units with a potential role in spermatogenesis. We describe mechanisms underlying the formation of human genomic rearrangements on autosomes and review Y-chromosome deletions associated with male infertility.
FoldingNet: Interpretable Unsupervised Learning on 3D Point Clouds

Recent deep networks that directly handle points in a point set, e.g., PointNet, have been state-of-the-art for supervised semantic learning tasks on point clouds such as classification and segmentation. In this work, a novel end-to-end deep auto-encoder is proposed to address unsupervised learning challenges on point clouds. On the encoder side, a graph-based enhancement is enforced to promote local structures on top of PointNet. Then, a novel folding-based approach is proposed in the decoder, which folds a 2D grid onto the underlying 3D object surface of a point cloud. The proposed decoder only uses about 7\% parameters of a decoder with fully-connected neural networks, yet leads to a more discriminative representation that achieves higher linear SVM classification accuracy than the benchmark. In addition, the proposed decoder structure is shown, in theory, to be a generic architecture that is able to reconstruct an arbitrary point cloud from a 2D grid. Finally, this folding-based decoder is interpretable since the reconstruction could be viewed as a fine granular warping from the 2D grid to the point cloud surface.
Ecological factors influencing the beneficial endosymbionts of the hemlock woolly adelgid (Hemiptera: Adelgidae)

Bacterial endosymbionts of sap‐sucking insects provide their host with a number of beneficial qualities, including the supply of nutrition, defense against parasitoids, and protection from heat stress. Damage to these bacterial associates can therefore have a negative impact on the fitness of their insect host. We evaluated observational and experimental factors regarding the nonnative hemlock woolly adelgid (Adelges tsugae Annand) (Hemiptera: Adelgidae) to help understand the roles of its three recently identified symbionts, including under heat stress conditions. The prevalence of A. tsugae’s facultative symbiont (Serratia symbiotica) was examined at different spatial scales to determine how variable infection rates are for this symbiont. There was no significant difference found in infection rates between adelgids on a tree, within a plot, or within a state. However, significantly more adelgids in Georgia (95%) had S. symbiotica compared to those in New York (68%). Microsatellite genotyping of the adelgids found that this difference was most likely not the result of a second introduction of A. tsugae into eastern North America. Comparison of S. symbiotica proportions between first and fourth instars showed that symbiont absence did not affect the ability of A. tsugae to survive aestivation. Evaluations of symbiont densities within each adelgid found that when S. symbiotica was absent, the density of obligate symbionts was significantly higher. Exposure to heat stress (32.5 °C) was not consistently correlated with changes in symbiont densities over a 4‐d period. Overall, we have shown that symbiont prevalence and densities vary within the broad population of A. tsugae in eastern North America, with potentially significant effects upon the ecology of this important pest.
Listado ictiofaunístico de las bahías del Parque Nacional Huatulco, Oaxaca, México

espanolSe determino la composicion ictica de las bahias del Parque Nacional Huatulco con la tecnica de censos visuales mediante 351 transectos de una longitud de 10 m efectuados entre enero de 2009 y diciembre de 2010. Se identificaron 89 especies pertenecientes a 69 generos y 42 familias. Las familias Labridae, Pomacentridae y Carangidae integraron el mayor numero de especies y los generos mejor representados fueron Haemulon, Halichoeres y Scarus. Las especies Acanthurus triostegus, Bothus constellathus, Chaetodipterus zonatus, Hemicaranx leucurus, Microlepidotus brevipinnis y Xenichthys xanti representan nuevos registros para las bahias de Huatulco y se confirma la presencia de Chaenomugil proboscideus, Narcine entemedor y Pseudobatos leucorhynchus en las mismas. La comunidad ictica de dichas bahias presenta mayor similitud con las comunidades icticas de Panama y Costa Rica. catalaEs va determinar la composicio ictica de les badies del Parc Nacional Huatulco amb la tecnica de censos visuals mitjancant 351 transsectes d’una llargada de 10 m portats a terme entre gener de 2009 i desembre de 2010. Es van identificar 89 especies pertanyents 69 generes i 42 families. Les families Labridae, Pomacentridae i Carangidae van integrar el nombre mes gran d’especies i els generes mes ben representats van ser Haemulon, Halichoeres i Scarus. Les especies Acanthurus triostegus, Bothus constellathus, Chaetodipterus zonatus, Hemicaranx leucurus, Microlepidotus brevipinnis i Xenichthys xanti representen nous registres per a les badies de Huatulco i s’hi confirma la presencia de Chaenomugil proboscideus, Narcine entemedor i Pseudobatos leucorhynchus. La comunitat ictica d’aquestes badies presenta mes similituds amb les comunitats ictiques de Panama i Costa Rica. EnglishWe determined the composition of ichthyofauna of the bays of Huatulco National Park using the the visual census technique for 351 ten-meter-long transects between January 2009 and December 2010. Eighty-nine species belonging to 69 genera and 42 families were identified. The most frequently represented families, according to numbers of species, were Pomacentridae, Labridae and Carangidae, and the most numerous genera were Haemulon, Halichoeres and Scarus. Acanthurus triostegus, Bothus constellathus, Chaetodipterus zonatus, Hemicaranx leucurus, Microlepidotus brevipinnis and Xenichthys xanti were recently recorded for the first time in the study area. The presence of Chaenomugil proboscideus, Narcine entemedor and Pseudobatos leucorhynchus in the Huatulco Bays is confirmed. The fish community in the Huatulco Bays was most similar to those in Panama and Costa Rica.
A prospective single centre study comparing computed tomography pneumocolon against colonoscopy in the detection of colorectal neoplasms

BACKGROUND AND AIMS To determine the sensitivity and specificity of computed tomography (CT) pneumocolon in the detection of colorectal neoplasms. METHODS A total of 201 consecutive patients with colorectal symptoms or requiring surveillance for colorectal neoplasms underwent both conventional colonoscopy and CT pneumocolon. RESULTS On conventional colonoscopy 13 invasive colorectal carcinomas were detected in 13 patients, and 118 polyps in 63 patients (14 polyps were ⩾1 cm in diameter, 25 were 6–9 mm, and 79 were ⩽5 mm). CT pneumocolon detected all 13 cancers, two false positive cancers, but only 20 polyps (seven were ⩾1 cm). This resulted in a sensitivity of 100% (95% confidence interval (CI) 87–100%) and specificity of 99% (95% CI 97–100%) for detection of invasive carcinoma, and a sensitivity of 73% (95% CI 56–90%) and specificity of 94% (95% CI 91–98%) for detection of invasive carcinoma and/or ⩾1 cm polyps. CT pneumocolon also identified invasive carcinoma not seen at colonoscopy because of incomplete examination in three patients, and detected metastases in six colorectal carcinoma patients and extracolonic carcinoma in a further seven patients. CONCLUSIONS CT pneumocolon had a high sensitivity and specificity for detection of invasive colorectal carcinoma but not colorectal polyps. CT pneumocolon may be suitable for initial investigation of patients with symptoms of colorectal malignancy.
Time variation in Okun’s law in Sweden

ABSTRACT In this article we estimate an Okun’s law relationship for Sweden using a model with time-varying parameters. Employing quarterly data from 1982 to 2014, results indicate that the GDP growth needed to keep the unemployment rate unchanged in the long rung has fallen considerably over the last 10 years.