Miracle-dz/UniFAR-FTUs huggingface dataset:
Hypoxia-inducible factor 1 upregulation of both VEGF and ANGPTL4 is required to promote the angiogenic phenotype in uveal melanoma

Purpose Expression of the hypoxia-inducible factor (HIF)-1-regulated gene product, vascular endothelial growth factor (VEGF), correlates with tumor vascularity in patients with uveal melanoma (UM). While the relationship between HIF-1 and VEGF in cancer is well-studied, their relative contribution to the angiogenic phenotype in UM has not previously been interrogated. Here we evaluate the contribution of HIF-1, VEGF, and a second HIF-1-regulated gene product, angiopoietin-like 4 (ANGPTL4), to angiogenesis in UM. Experimental Design UM cells were examined for expression of HIF-1α, VEGF, and ANGPTL4. Their contribution to the angiogenic potential of UM cells was assessed using the endothelial cell tubule formation and directed in vivo angiogenesis assays. These results were corroborated in tissue from UM animal models and in tissue from patients with UM. Results Inhibition of VEGF partially reduced tubule formation promoted by conditioned medium from UM cells. Inhibition of ANGPTL4, which was highly expressed in hypoxic UM cells, a UM orthotopic transplant model, a UM tumor array, and vitreous samples from UM patients, inhibited the angiogenic potential of UM cells in vitro and in vivo; this effect was additive to VEGF inhibition. Conclusions Targeting both ANGPTL4 and VEGF may be required for the effective inhibition of angiogenesis in UM.
Inference of the Activity Timeline of Cattle Foraging on a Mediterranean Woodland Using GPS and Pedometry

The advent of the Global Positioning System (GPS) has transformed our ability to track livestock on rangelands. However, GPS data use would be greatly enhanced if we could also infer the activity timeline of an animal. We tested how well animal activity could be inferred from data provided by Lotek GPS collars, alone or in conjunction with IceRobotics IceTag pedometers. The collars provide motion and head position data, as well as location. The pedometers count steps, measure activity levels, and differentiate between standing and lying positions. We gathered synchronized data at 5-min resolution, from GPS collars, pedometers, and human observers, for free-grazing cattle (n = 9) at the Hatal Research Station in northern Israel. Equations for inferring activity during 5-min intervals (n = 1,475), classified as Graze, Rest (or Lie and Stand separately), and Travel were derived by discriminant and partition (classification tree) analysis of data from each device separately and from both together. When activity was classified as Graze, Rest and Travel, the lowest overall misclassification rate (10%) was obtained when data from both devices together were subjected to partition analysis; separate misclassification rates were 8, 12, and 3% for Graze, Rest and Travel, respectively. When Rest was subdivided into Lie and Stand, the lowest overall misclassification rate (10%) was again obtained when data from both devices together were subjected to partition analysis; misclassification rates were 6, 1, 26, and 17% for Graze, Lie, Stand, and Travel, respectively. The primary problem was confusion between Rest (or Stand) and Graze. Overall, the combination of Lotek GPS collars with IceRobotics IceTag pedometers was found superior to either device alone in inferring animal activity.
WEGO: a web tool for plotting GO annotations

Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many tools have been created for use with the GO ontologies. WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO annotation results. Different from other commercial software for creating chart, WEGO is designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of GO annotation results. WEGO has been used widely in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. WEGO, along with the two other tools, namely External to GO Query and GO Archive Query, are freely available for all users at . There are two available mirror sites at and . Any suggestions are welcome at wego@genomics.org. cn.
Evaluation of advanced TCP stacks in the iSCSI environment using simulation model

Enterprise storage demands have overwhelmed traditional storage mechanisms and have led to the development of storage area networks (SANs). This has resulted in the design of SCSI transport protocols that encapsulate SCSI commands and data for transfer over the network. Fiber channel protocol was the first such protocol that used gigabit per second speed links to carry SCSI commands and data over long distances. However, with the emergence of gigabit Ethernet and the iSCSI (Internet SCSI) protocol that maps the SCSI block oriented storage data over TCP/IP and enables storage devices to be accessed over standard Ethernet based TCP/IP networks, reduction in costs and a unified network infrastructure can be achieved. The iSCSI data flow is regulated by the TCP congestion control algorithm. The standard TCP Reno congestion control algorithm substantially under utilizes the network bandwidth over high speed connections for most applications. To address this limitation of TCP, variants of the TCP congestion control algorithm, designed for high bandwidth networks, such as FAST TCP, BIC-TCP, H-TCP, and Scalable TCP have been proposed. We use simulations and experiments to compare the performance of these TCP variants in an iSCSI environment. Our results indicate that H-TCP outperforms the other TCP variants in an iSCSI environment. However H-TCP results in unfair sharing of network bandwidth when simultaneous multiple flows exist. Performance obtained using BIC-TCP is only second to that using H-TCP and it is relatively fairer as compared to H-TCP.
5-Keto-d-Gluconate Production Is Catalyzed by a Quinoprotein Glycerol Dehydrogenase, Major Polyol Dehydrogenase, in Gluconobacter Species

ABSTRACT Acetic acid bacteria, especially Gluconobacter species, have been known to catalyze the extensive oxidation of sugar alcohols (polyols) such as d-mannitol, glycerol, d-sorbitol, and so on. Gluconobacter species also oxidize sugars and sugar acids and uniquely accumulate two different keto-d-gluconates, 2-keto-d-gluconate and 5-keto-d-gluconate, in the culture medium by the oxidation of d-gluconate. However, there are still many controversies regarding their enzyme systems, especially on d-sorbitol and also d-gluconate oxidations. Recently, pyrroloquinoline quinone-dependent quinoprotein d-arabitol dehydrogenase and d-sorbitol dehydrogenase have been purified from G. suboxydans, both of which have similar and broad substrate specificity towards several different polyols. In this study, both quinoproteins were shown to be identical based on their immuno-cross-reactivity and also on gene disruption and were suggested to be the same as the previously isolated glycerol dehydrogenase (EC 1.1.99.22). Thus, glycerol dehydrogenase is the major polyol dehydrogenase involved in the oxidation of almost all sugar alcohols in Gluconobacter sp. In addition, the so-called quinoprotein glycerol dehydrogenase was also uniquely shown to oxidize d-gluconate, which was completely different from flavoprotein d-gluconate dehydrogenase (EC 1.1.99.3), which is involved in the production of 2-keto-d-gluconate. The gene disruption experiment and the reconstitution system of the purified enzyme in this study clearly showed that the production of 5-keto-d-gluconate in G. suboxydans is solely dependent on the quinoprotein glycerol dehydrogenase.
Rapid and sensitive detection of Feline immunodeficiency virus using an insulated isothermal PCR-based assay with a point-of-need PCR detection platform

Feline immunodeficiency virus (FIV) is an important infectious agent of cats. Clinical syndromes resulting from FIV infection include immunodeficiency, opportunistic infections, and neoplasia. In our study, a 5′ long terminal repeat/gag region–based reverse transcription insulated isothermal polymerase chain reaction (RT-iiPCR) was developed to amplify all known FIV strains to facilitate point-of-need FIV diagnosis. The RT-iiPCR method was applied in a point-of-need PCR detection platform—a field-deployable device capable of generating automatically interpreted RT-iiPCR results from nucleic acids within 1 hr. Limit of detection 95% of FIV RT-iiPCR was calculated to be 95 copies standard in vitro transcription RNA per reaction. Endpoint dilution studies with serial dilutions of an ATCC FIV type strain showed that the sensitivity of lyophilized FIV RT-iiPCR reagent was comparable to that of a reference nested PCR. The established reaction did not amplify any nontargeted feline pathogens, including Felid herpesvirus 1, feline coronavirus, Feline calicivirus, Feline leukemia virus, Mycoplasma haemofelis, and Chlamydophila felis. Based on analysis of 76 clinical samples (including blood and bone marrow) with the FIV RT-iiPCR, test sensitivity was 97.78% (44/45), specificity was 100.00% (31/31), and agreement was 98.65% (75/76), determined against a reference nested-PCR assay. A kappa value of 0.97 indicated excellent correlation between these 2 methods. The lyophilized FIV RT-iiPCR reagent, deployed on a user-friendly portable device, has potential utility for rapid and easy point-of-need detection of FIV in cats.
Constrained ATPG for functional RTL circuits using F-Scan

In this paper, we present an approach to constrained automatic test pattern generation (ATPG) for functional circuits at register-transfer level (RTL) with the help of a design-for-testability (DFT) technique called F-scan. The DFT method optimally utilizes existing functional elements and paths for test, thus it effectively reduces the hardware overhead due to test. This is done by arranging all registers in the circuit into F-scan-paths and augmenting necessary circuitry at RTL. After DFT, we create the constraint test generation model of the circuit based on the test environment obtained from the information of F-scan-paths. With this approach, only the applicable test vectors to the F-scan-paths can be generated and test application time is kept at the minimum. The comparison of F-scan with the performance of gate-level full scan design is shown through the experimental results.
Rapid Genome Divergence at Orthologous Low Molecular Weight Glutenin Loci of the A and Am Genomes of Wheat Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.011023.

To study genome evolution in wheat, we have sequenced and compared two large physical contigs of 285 and 142 kb covering orthologous low molecular weight (LMW) glutenin loci on chromosome 1AS of a diploid wheat species (Triticum monococcum subsp monococcum) and a tetraploid wheat species (Triticum turgidum subsp durum). Sequence conservation between the two species was restricted to small regions containing the orthologous LMW glutenin genes, whereas >90% of the compared sequences were not conserved. Dramatic sequence rearrangements occurred in the regions rich in repetitive elements. Dating of long terminal repeat retrotransposon insertions revealed different insertion events occurring during the last 5.5 million years in both species. These insertions are partially responsible for the lack of homology between the intergenic regions. In addition, the gene space was conserved only partially, because different predicted genes were identified on both contigs. Duplications and deletions of large fragments that might be attributable to illegitimate recombination also have contributed to the differentiation of this region in both species. The striking differences in the intergenic landscape between the A and Am genomes that diverged 1 to 3 million years ago provide evidence for a dynamic and rapid genome evolution in wheat species.
Effect of laparoscopy on the risk of small-bowel obstruction: a population-based register study.

OBJECTIVE To investigate the incidence and risk factors for small-bowel obstruction (SBO) after certain surgical procedures. DESIGN A population-based retrospective register study. SETTING Small-bowel obstruction causes considerable patient suffering. Risk factors for SBO have been identified, but the effect of surgical technique (open vs laparoscopic) on the incidence of SBO has not been fully elucidated. PATIENTS The Inpatient Register held by the Swedish National Board of Health and Welfare was used. The hospital discharge diagnoses and registered performed surgical procedures identified data for cholecystectomy, hysterectomy, salpingo-oophorectomy, bowel resection, anterior resection, abdominoperineal resection, rectopexy, appendectomy, and bariatric surgery performed from January 1, 2002, through December 31, 2004. Data on demographic characteristics, comorbidity, previous abdominal surgery, and death were collected. MAIN OUTCOME MEASURES Episodes of hospital stay and surgery for SBO within 5 years after the index surgery. RESULTS A total of 108,141 patients were included. The incidence of SBO ranged from 0.4% to 13.9%. Multivariate analysis revealed age, previous surgery, comorbidity, and surgical technique to be risk factors for SBO. Laparoscopy exceeded other risk factors in reduction of the risk of SBO for most of the surgical procedures. CONCLUSIONS Open surgery seems to increase the risk of SBO at least 4 times compared with laparoscopy for most of the abdominal surgical procedures studied. Other factors such as age, previous abdominal surgery, and comorbidity are also of importance.
Validation of a blind transpyloric feeding tube placement technique in pediatric intensive care: Rapid, simple, and highly successful

Objective Nasogastric feeding in intensive care is poorly tolerated as a result of gastroparesis. Transpyloric (TP) feeding has been limited by difficulty in tube placement. This study was to independently validate the success rate of a previously published bedside TP feeding tube (FT) placement technique. Design Prospective interventional study. Setting Tertiary pediatric intensive care unit (PICU) in a university hospital. Patients Children whose intensivist requested TP feeding, and who were without known fundoplication, pharyngeal trauma, or gastric ulceration. Interventions After informed consent, an unweighted polyurethane feeding tube with a flexible wire stylet was inserted using a standard technique with metoclopramide, right lateral position, and air insufflation during advancement until <2 mL air could be aspirated after insufflation of 5–10 mL air. The tubes were inserted by one of the authors, whose training was only to observe one insertion, then perform one insertion with supervision. Measurements and Main Results Patient demographics, procedural data, and success rate based on radiography were prospectively recorded. There were 71 insertions on 38 patients from February 1999 to October 1999. Patients were aged 56 ± 69.8 months, weighed 17.8 ± 18 kg, 69% were ventilated, and 56% received procedural sedation. Success rate for TP-FT placement was 63/71 insertions (88.7%) in an average of 7.43 ± 6.85 mins (median, 5 mins; range, <1–45 mins); of 38 patients, 36 had a successful TP- FT (95%). Insertion was well tolerated. Of the successful TP-FTs, on day 1 (n = 63) the FT was in distal duodenum or jejunum in 51% and by days 3–5 (n = 51), this increased to 75%. Conclusions Bedside placement of a TP-FT with this technique is simple, rapid, well tolerated, and highly successful with little training. Immediate radiograph to confirm TP placement may not always be necessary. In our experience, this technique has obviated the need to search for another method to achieve a transpyloric feeding tube.
Adult neurogenesis in the crayfish brain: Proliferation, migration, and possible origin of precursor cells

The birth of new neurons and their incorporation into functional circuits in the adult brain is a characteristic of many vertebrate and invertebrate organisms, including decapod crustaceans. Precursor cells maintaining life‐long proliferation in the brains of crayfish (Procambarus clarkii, Cherax destructor) and clawed lobsters (Homarus americanus) reside within a specialized niche on the ventral surface of the brain; their daughters migrate to two proliferation zones along a stream formed by processes of the niche precursors. Here they divide again, finally producing interneurons in the olfactory pathway. The present studies in P. clarkii explore (1) differential proliferative activity among the niche precursor cells with growth and aging, (2) morphological characteristics of cells in the niche and migratory streams, and (3) aspects of the cell cycle in this lineage. Morphologically symmetrical divisions of neuronal precursor cells were observed in the niche near where the migratory streams emerge, as well as in the streams and proliferation zones. The nuclei of migrating cells elongate and undergo shape changes consistent with nucleokinetic movement. LIS1, a highly conserved dynein‐binding protein, is expressed in cells in the migratory stream and neurogenic niche, implicating this protein in the translocation of crustacean brain neuronal precursor cells. Symmetrical divisions of the niche precursors and migration of both daughters raised the question of how the niche precursor pool is replenished. We present here preliminary evidence for an association between vascular cells and the niche precursors, which may relate to the life‐long growth and maintenance of the crustacean neurogenic niche. © 2009 Wiley Periodicals, Inc. Develop Neurobiol, 2009
Schrödinger's token

A common problem when writing compilers for programming languages or little, domain‐specific languages is that an input token may have several interpretations, depending on context. Solutions to this problem demand programmer intervention, obfuscate the language's grammar, and may introduce subtle bugs. We present a technique which is simple and without the above drawbacks—allowing a token to simultaneously have different types—and show how it can be applied to areas such as little language processing and fuzzy parsing. We also describe ways that compiler tools can support this technique. Copyright © 2001 John Wiley & Sons, Ltd.
Inhibition of MDM 2 homodimerization by XIAP IRES stabilizes MDM 2 , influencing cancer cell survival

Background: It is known that the MDM2 protein is stabilized when it forms a heterodimer with its partner MDM4, but MDM2 protein stability in its homodimer form is not known. The MDM2 protein contains a C-terminal RING domain that not only functions as an E3 ligase to regulate ubiquitination of p53 and MDM2 itself, but also is characterized to be able to bind several specific cellular mRNAs to regulate gene expression. In this study, we evaluate whether the MDM2 protein stability is regulated by the binding of a specific small RNA (XIAP IRES mRNA). Methods: We performed chemical cross-linking and bimolecular fluorescence complementation (BiFC) assay to measure the human MDM2 protein stability in its homodimer form and the effect of XIAP IRES on MDM2 homodimerization and protein stabilization. Ubiquitination and pulse-chase assays were used to detect MDM2 self-ubiquitination and protein turn-over. Fluorescent titration and ITC were used to examine the binding between MDM2 RING protein and XIAP IRES. Western blot assay was used for determining protein expression. Clonogenic assay, WST and flow cytometry were used to test the effects of XIAP IRES, siXIAP and IR on cancer cell growth and apoptosis. Results: We found that self-association (homodimerization) of MDM2 occurs through the C-terminal RING domain of MDM2 and that the MDM2 protein becomes unstable when it is homodimerized. MDM2 homodimerization resulted in an increased function of the RING domain for MDM2 self-ubiquitination. Binding of XIAP IRES to the RING domain inhibited MDM2 homodimerization and self-ubiquitination, which resulted in stabilization of MDM2, as well as increased XIAP expression. Upregulation of XIAP and MDM2 that led to inhibition of p53 by the XIAP IRES resulted in cell growth and survival in both p53-normal and -deficient cancer cells. Conclusions: Our study identified a new IRES RNA that interacts with MDM2 protein and regulates its stabilization, which suggested that targeting of MDM2 through disruption of MDM2 protein-RNA interaction might be a useful strategy for developing novel anti-cancer therapeutics.
Inhibitory control of the excitatory/inhibitory balance in psychiatric disorders

Neuronal networks consist of different types of neurons that all play their own role in order to maintain proper network function. The two main types of neurons segregate in excitatory and inhibitory neurons, which together regulate the flow of information through the network. It has been proposed that changes in the relative strength in these two opposing forces underlie the symptoms observed in psychiatric disorders, including autism and schizophrenia. Here, we review the role of alterations to the function of the inhibitory system as a cause of psychiatric disorders. First, we explore both patient and post-mortem evidence of inhibitory deficiency. We then discuss the function of different interneuron subtypes in the network and focus on the central role of a specific class of inhibitory neurons, parvalbumin-positive interneurons. Finally, we discuss genes known to be affected in different disorders and the effects that mutations in these genes have on the inhibitory system in cortex and hippocampus. We conclude that alterations to the inhibitory system are consistently identified in animal models of psychiatric disorders and, more specifically, that mutations affecting the function of parvalbumin-positive interneurons seem to play a central role in the symptoms observed in these disorders.
Fast algorithms for mutual information based independent component analysis

This paper provides fast algorithms to perform independent component analysis based on the mutual information criterion. The main ingredient is the binning technique and the use of cardinal splines, which allows the fast computation of the density estimator over a regular grid. Using a discretized form of the entropy, the criterion can be evaluated quickly together with its gradient, which can be expressed in terms of the score functions. Both offline and online separation algorithms have been developed. Our density, entropy, and score estimators also have their own interest.
Evidence for Monophyly and Arthropod Affinity of Cambrian Giant Predators

The Chinese Early Cambrian Chengjiang fauna includes three different anomalocaridids, a globally spread, extinct marine group including the largest known Cambrian animals. Anomalocaridids were active predators, and their presence implies that a complex ecosystem appeared abruptly in the earliest Phanerozoic. Complete specimens display several sets of characters shared only with some other exclusively Cambrian forms. This evidence indicates that anomalocaridids, Opabinia, and Kerygmachela form a monophyletic clade. Certain features indicate arthropod affinities of the lade, and for this group an unnamed (sub)phylum-level taxon within an arthropod (super)phylum is proposed.