Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genomics in Salt Tolerance between Arabidopsis and Arabidopsis-Related Halophyte Salt Cress Using Arabidopsis Microarray1

Salt cress (Thellungiella halophila), a halophyte, is a genetic model system with a small plant size, short life cycle, copious seed production, small genome size, and an efficient transformation. Its genes have a high sequence identity (90%–95% at cDNA level) to genes of its close relative, Arabidopsis. These qualities are advantageous not only in genetics but also in genomics, such as gene expression profiling using Arabidopsis cDNA microarrays. Although salt cress plants are salt tolerant and can grow in 500 mm NaCl medium, they do not have salt glands or other morphological alterations either before or after salt adaptation. This suggests that the salt tolerance in salt cress results from mechanisms that are similar to those operating in glycophytes. To elucidate the differences in the regulation of salt tolerance between salt cress and Arabidopsis, we analyzed the gene expression profiles in salt cress by using a full-length Arabidopsis cDNA microarray. In salt cress, only a few genes were induced by 250 mm NaCl stress in contrast to Arabidopsis. Notably a large number of known abiotic- and biotic-stress inducible genes, including Fe-SOD, P5CS, PDF1.2, AtNCED, P-protein, β-glucosidase, and SOS1, were expressed in salt cress at high levels even in the absence of stress. Under normal growing conditions, salt cress accumulated Pro at much higher levels than did Arabidopsis, and this corresponded to a higher expression of AtP5CS in salt cress, a key enzyme of Pro biosynthesis. Furthermore, salt cress was more tolerant to oxidative stress than Arabidopsis. Stress tolerance of salt cress may be due to constitutive overexpression of many genes that function in stress tolerance and that are stress inducible in Arabidopsis.
Cefazolin concentration in surgically created wounds treated with negative pressure wound therapy compared to surgically created wounds treated with nonadherent wound dressings.

OBJECTIVE To compare cefazolin concentrations in biopsied tissue samples collected from surgically created wounds treated with negative pressure wound therapy to those collected from surgically created wounds treated with nonadherent dressings. STUDY DESIGN Prospective, controlled, experimental study. ANIMALS Adult female spayed Beagles (n = 12). METHODS Full thickness cutaneous wounds were created on each antebrachium (n = 24). Immediately after surgery, cefazolin (22 mg/kg intravenously [IV]) was administered to each dog and continued every 8 hours during the study. The right wound was randomly assigned to group I or group II whereas the wound on the contralateral antebrachium was assigned to the other group. Group I wounds were treated with negative pressure wound therapy (NPWT) and group II wounds were treated with nonadherent dressings for 3 days. Dressings were changed and tissue biopsies obtained from wound beds at 24 hours intervals for both groups. Cefazolin wound tissue and plasma concentrations were measured by liquid chromatography mass spectrometry (LC-MS/MS). Blood samples for measuring plasma cefazolin concentrations were collected before biopsy sampling. At the time of surgery and at each subsequent bandage change, wound beds were swabbed and submitted for aerobic and anaerobic culture. RESULTS After initiating cefazolin treatment, wound tissue antibiotic concentrations between treatment groups were not significantly different at any sampling time. Similarly, after initiating cefazolin treatment, plasma cefazolin concentrations were not significantly different at any sampling time for individual dogs. CONCLUSIONS Using a canine experimental model, NPWT treatment of surgically created wounds does not statistically impact cefazolin tissue concentrations when compared with conventional nonadherent bandage therapy.
People, process and the poverty-pew: a functional analysis of mundane buildings in the Nottinghamshire framework-knitting industry

Industrial archaeology has traditionally concentrated on the recording and study of technological and engineering survivals — hence the name ‘industrial’ as, often, a near-synonym for ‘post-medieval’ in naming the archaeology of early modern capitalism. This study of three mundane industrial buildings draws upon building and documentary evidence as aids to understanding working structures not distinguished by technological or engineering innovation.
House Prices, Credit and Willingness to Lend

This paper establishes a Tobin's q model in which house prices fluctuate around their long run equilibrium due to fluctuations in credit availability and income. It is shown that house prices are positively related to credit in the short run, however, negatively related to the availability of credit in the long run. Using survey data on banks' willingness to lend and data on disintermediation for the U.S. over a long period and for nine OECD countries over a short period it is shown that the availability of credit is the principal variable driving house prices around their long run equilibrium. Shocks to interest rates and income have only secondary effects on house price fluctuations.
An optimal tracking neuro-controller for nonlinear dynamic systems

Multilayer neural networks are used to design an optimal tracking neuro-controller (OTNC) for discrete-time nonlinear dynamic systems with quadratic cost function. The OTNC is made of two controllers: feedforward neuro-controller (FFNC) and feedback neuro-controller (FBNC). The FFNC controls the steady-state output of the plant, while the FBNC controls the transient-state output of the plant. The FFNC is designed using a novel inverse mapping concept by using a neuro-identifier. A generalized backpropagation-through-time (GBTT) algorithm is developed to minimize the general quadratic cost function for the FBNC training. The proposed methodology is useful as an off-line control method where the plant is first identified and then a controller is designed for it. A case study for a typical plant with nonlinear dynamics shows good performance of the proposed OTNC.
Immune Modulation in the Treatment of Amyotrophic Lateral Sclerosis: A Review of Clinical Trials

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by the degeneration of motor neurons. Though many molecular and genetic causes are thought to serve as predisposing or disease propagating factors, the underlying pathogenesis of the disease is not known. Recent discoveries have demonstrated the presence of inflammation propagating substrates in the central nervous system of patients afflicted with ALS. Over the past decade, this hypothesis has incited an effort to better understand the role of the immune system in ALS and has led to the trial of several potential immune-modulating therapies. Here, we briefly review advances in the role of such therapies. The clinical trials discussed here are currently ongoing or have been concluded at the time of writing.
Novel Antimalarial Compounds Isolated in a Survey of Self-Medicative Behavior of Wild Chimpanzees in Uganda

ABSTRACT Following a veterinary and behavioral survey of chimpanzees from a natural population in Uganda, leaf samples of Trichilia rubescens were collected because of the unusual method of ingestion observed. The methanolic crude extract of T. rubescens leaves exhibited significant antimalarial activity in vitro. Bioassay-directed fractionation provided two new limonoids, trichirubines A and B. A greater understanding of the role of secondary compounds in the primate diet may be helpful in recovering naturally occurring compounds of medicinal significance for human medicine.
Modeling Spatial Relationships within a Fuzzy Framework

In this article, we present a model for defining and representing binary topological and directional relationships between 2‐dimensional objects that is used to provide a basis for fuzzy querying capabilities. The definition of the relationships is based on an extension of Allen's temporal relations (Allen, 1983) to the spatial domain. This is done by allowing each of Allen's 13 relations to represent the interaction of 2‐dimensional objects in terms of an x and y relationship component. The resulting set of relationships is then used for defining topological and directional relationship terminology. A data structure called an abstract spatial graph (ASG) is defined for the binary relationships that maintains all necessary information regarding topology and direction. Abstract spatial graphs provide the basis for processing of fuzzy topological and directional queries. © 1998 John Wiley & Sons, Inc.
Protection of Human Tumor Cells of Differing Radiosensitivity by WR-1065

Abstract Murray, D. , Rosenberg, E. and Allalunis-Turner, M. J. Protection of Human Tumor Cells of Differing Radiosensitivity by WR-1065. We examined the ability of WR-1065, the biologically active aminothiol form of the clinically used drug amifostine (WR-2721, Ethyol®), to protect cultures of two human glioblastoma cell lines of greatly differing radiosensitivity from the cytotoxic effects of γ radiation. M059J cells are extremely radiosensitive compared to M059K cells (which were derived from the same tumor) and are defective in the DNA-dependent protein kinase (DNAPK)-mediated pathway for the repair of DSBs. In spite of their marked phenotypic differences, the two glioblastoma lines were protected equivalently (∼1.8-fold) after a 30-min preirradiation treatment with 4 mM WR-1065. These findings are in agreement with earlier studies that showed no relationship between the ability of another aminothiol, cysteamine, to protect human tumor cells with differing abilities to repair DSBs and/or radiosensitivity. Thus it appears that differences in intrinsic radiosensitivity and ability to repair DSBs are not important general factors in the modulation of the radiosensitivity of human cells by aminothiols. Because of a previous report that the radiosensitive mutant rodent xrs5 cell line (which, like M059J, is defective in the DNAPK-mediated pathway for repairing DSBs) is unusually refractory to the radioprotective effects of WR-1065, we re-examined the ability of WR-1065 to protect these cells. In contrast to the earlier studies, both the wild-type and mutant rodent lines were protected extensively by WR-1065. This discrepancy might be related to some unknown factor, such as differences in chromatin organization among xrs5 subclones that arise during their karyotypic evolution, possibly leading to altered DNA–drug associations.
Racing performance after combined prosthetic laryngoplasty and ipsilateral ventriculocordectomy or partial arytenoidectomy: 135 Thoroughbred racehorses competing at less than 2400 m (1997-2007).

REASONS FOR PERFORMING STUDY The success of combined prosthetic laryngoplasty with ipsilateral ventriculocordectomy (LPVC) has not been compared to that of partial arytenoidectomy (PA) in a clinical population. HYPOTHESES In Thoroughbred (TB) racehorses: (1) earnings after LPVC are unaffected by the severity of recurrent laryngeal neuropathy (RLN) (laryngeal grade III vs. grade IV); (2) LPVC and PA yield similar results in the treatment of grade III RLN; (3) performance outcome following PA is independent of diagnosis (RLN vs. unilateral arytenoid chondritis [UAC]); and (4) neither LPVC nor PA returns horses to the level of performance of controls. METHODS Medical and racing records of 135 TB racehorses undergoing LPVC or PA for the treatment of grade III or IV RLN or UAC were reviewed. Racing records of age and sex matched controls were also reviewed. RESULTS After LPVC, horses with grade III RLN performed better compared to those with grade IV RLN. Furthermore, horses treated for grade III RLN by LPVC showed post operative earnings comparable to controls. Rate of return to racing were similar for PA and LPVC, although LPVC resulted in higher post operative earnings. Performance after PA was similar regardless of diagnosis (UAC or RLN). Finally, neither LPVC when performed for grade IV RLN, nor PA performed for either diagnosis restored post operative earnings to control levels. CONCLUSIONS Thoroughbred racehorses treated by LPVC for grade III RLN show significantly better post operative earnings compared to horses treated for grade IV disease. In grade III RLN, LPVC returns earning potential to control levels. PA and LPVC lead to similar success in terms of rate of return to racing, but PA leads to inferior earnings after surgery. POTENTIAL RELEVANCE Laryngoplasty should be recommended for all TB racehorses with grade III RLN to maximise return to racing at a high level. This contradicts the common approach of waiting for complete paralysis.
Context Aware On-line Diagramming Recognition

This paper presents a context aware, online immediate-mode diagramming recognition and beautification software for hand-sketched diagrams. The system is independent of stroke-order, -number, -direction and is invariant to scaling, translation and rotation. In our stroke-based recognition model, we propose convexity features along with spatial and temporal proximity features to prune the combinatorial search space of possible stroke configurations to form shapes. This reduces the problem of exponential complexity to polynomial one while reducing the error by 24% compared to temporal proximity based criterion. The strokes are then recognized using geometric polygonal features against a neural-net based classifier for 17 classes. The diagramming system is based on stroke-based classifier combination model where an arbitrator makes context aware decisions using suggestions from shape, connector and writing-drawing experts. We achieved an accuracy of 92.7%, 81.4% and 91.5% on the respective experts for a collection of 700,000 online shapes.
Inhibition of DNA binding of purified p55v‐myc in vitro by antibodies against bacterially expressed myc protein and a synthetic peptide.

To identify viral myc proteins, we have prepared myc‐specific antibodies: (i) against a synthetic peptide corresponding to the nine carboxy‐terminal amino acids of the viral myc (C9); (ii) against a bacterially expressed viral myc protein obtained by inserting the SalI‐BamHI fragment of the viral MC29 DNA clone in the expression vector pPLc24. Both antisera recognize a protein of 55 000 mol. wt. , p55v‐myc, in MH2‐ and OK10‐transformed fibroblasts. The protein is located in the nucleus, as shown by indirect immunofluorescence and cell fractionation. Antibodies against the C9 peptide were used to purify the p55v‐myc by immunoaffinity column purification (3000‐fold) from OK10‐ and MH2‐transformed fibroblasts. p55v‐myc binds to double‐stranded DNA in vitro as does p110gag‐myc. DNA binding in vitro is inhibited by the immunoglobulin fraction of antibodies against the bacterially expressed myc protein. Furthermore, a synthetic peptide consisting of 16 amino acids (C16) was used to isolate specific immunoglobulins which also inhibit DNA binding in vitro. OK10 codes, in addition to p55v‐myc, for a p200gag‐pol‐myc polyprotein. The majority of this protein is located in the cytoplasm (79%). The purified protein binds to single‐stranded RNA in vitro, unlike other gag‐myc or myc proteins.
Emerging Leaders: An Annotated Bibliography

Intuitively, a set, function, or relation is computable if there is an algorithm for computing membership, output, or truth-values, respectively. A set of natural numbers A is Turing reducible to another set B, written A ≤T B, if it is possible to write an algorithm that uses information from B to determine membership in A. This pre-ordering of sets induces an equivalence relation on the power set of the natural numbers, and the equivalence classes are the Turing degrees. Sets having the same Turing degree (for example, a set and its complement) are said to be Turing equivalent, written A ≡T B. If a set is enumerable via an algorithm, it is computably enumerable (c.e.) and so is its Turing degree.
Anti-miRNA-221 sensitizes human colorectal carcinoma cells to radiation by upregulating PTEN.

AIM To investigate the regulative effect of miRNA (miR)-221 on colorectal carcinoma (CRC) cell radiosensitivity and the underlying mechanisms. METHODS A human CRC-derived cell line was cultured conventionally and exposed to different doses of X-rays (0, 2, 4, 6 and 8 Gy). The total RNA and protein of the cells were extracted 24 h after irradiation, and the alteration of miR-221 and phosphatase and tensin homolog deleted on chromosome 10 (PTEN) gene mRNA expression was detected by real-time reverse transcriptase polymerase chain reaction (PCR). The protein alteration of PTEN in the cells was detected by Western blotting. Caco2 cells were pretreated with or without anti-PTEN-siRNA prior to the addition of pre-miR-221 or anti-miR-221 using Lipofectamine 2000. Colony formation assay and flow cytometry analysis were used to measure the surviving cell fraction and the sensitizing enhancement ratio after irradiation. Additionally, PTEN 3'-untranslated region fragment was PCR amplified and inserted into a luciferase reporter plasmid. The luciferase reporter plasmid construct was then transfected into CRC cells together with pre-miR-221 or anti-miR-221, and the luciferase activity in the transfected cells was detected. RESULTS The X-ray radiation dose had a significant effect on the expression of miR-221 and PTEN protein in human Caco2 cells in a dose-dependent manner. The miR-221 expression level improved gradually with the increase in irradiation dose, while the PTEN protein expression level reduced gradually. miR-221 expression was significantly reduced in the anti-miR-221 group compared with the pre-miR-221 and negative control groups (P < 0.01). Anti-miR-221 upregulated expression of PTEN protein and enhanced the radiosensitivity of Caco2 cells (P < 0.01). Moreover, the inhibitory effect was dramatically abolished by pretreatment with anti-PTEN-siRNA, suggesting that the enhancement of radiosensitivity was indeed mediated by PTEN. A significant increase of luciferase activity was detected in CRC cells that were cotransfected with the luciferase reporter plasmid construct and anti-miR-221 (P < 0.01). CONCLUSION Anti-miR-221 can enhance the radiosensitivity of CRC cells by upregulating PTEN.
Systolic Pattern Matching Hardware With Out-of-Plane Nanomagnet Logic Devices

We present the design and simulation of systolic information processing hardware that is comprised of single domain, Co/Pt magnets (i.e., out-of-plane nanomagnet logic or oNML). The designed circuit can identify instances of a preprogrammed bit sequence in streaming data. The systolic architecture 1) exploits unique benefits of the oNML device architecture such as nonvolatility and inherently pipelined logic with no memory overhead for holding the bits in the pipeline and 2) mitigates less desirable features of oNML such as nearest neighbor dataflow and longer device switching times when compared to a CMOS transistor. The designed layout is verified and analyzed by micromagnetic simulations. We quantify how the performance and energy of oNML information processing hardware compares to CMOS equivalents and conclude that the initial oNML design (including the overhead of magnetic field generation) is about an order of magnitude more power efficient at essentially iso-performance.
Face to face with emotion: Holistic face processing is modulated by emotional state

Negative emotions are linked with a local, rather than global, visual processing style, which may preferentially facilitate feature-based, relative to holistic, processing mechanisms. Because faces are typically processed holistically, and because social contexts are prime elicitors of emotions, we examined whether negative emotions decrease holistic processing of faces. We induced positive, negative, or neutral emotions via film clips and measured holistic processing before and after the induction: participants made judgements about cued parts of chimeric faces, and holistic processing was indexed by the interference caused by task-irrelevant face parts. Emotional state significantly modulated face-processing style, with the negative emotion induction leading to decreased holistic processing. Furthermore, self-reported change in emotional state correlated with changes in holistic processing. These results contrast with general assumptions that holistic processing of faces is automatic and immune to outside influences, and they illustrate emotion's power to modulate socially relevant aspects of visual perception.
Reported multivitamin consumption and the occurrence of multiple congenital anomalies

The purpose of this case‐control study was to determine whether multivitamin use is associated with the occurrence of multiple congenital anomalies (MCA). MCA case‐infants were infants with two or more major birth defects affecting at least two different organ systems, with no recognized chromosome abnormality or single gene disorder. Control‐infants were a random sample of live births with no major birth defects from the same population (metropolitan Atlanta) and time period (1993–1997) as the case‐infants. Exposure to multivitamins, cereals, and supplements was ascertained from a maternal telephone interview and classified based on folic acid content. We compared women who used multivitamins three or more times per week with women who were not exposed to vitamins/cereals/supplements during the periconceptional period (3 months before pregnancy through the first trimester), adjusting for maternal age, education, race/ethnicity, first degree family history of a major birth defect, pre‐pregnancy maternal body mass index, gravidity, and first trimester alcohol use and cigarette smoking. Periconceptional multivitamin use was associated with MCA among all infants (adjusted odds ratio [aOR] = 2.4, 95% confidence interval [CI] 0.9–6.7), and especially when analysis was limited to those with no family history of major defects (aOR = 4.0, 95% CI 1.3–12.8). MCA‐infants with urinary obstructive defects were more common among multivitamin‐exposed infants than among unexposed infants, but this defect did not occur within a consistent pattern of defects. While these findings provide some support for one previous study, the interpretation remains unclear given the proven protective effect of multivitamins containing folic acid on isolated neural tube defects and possibly other types of defects. Published 2005 Wiley‐Liss, Inc.
22 Pharmacogenetics for T 2 DM and Anti-Diabetic Drugs

The potassium inwardly rectifying channel subfamily J member 11 (KCNJ11) gene encodes Kir6.2 protein, the inwardly rectifying potassium channel, which is a complex of two subunits [2]. ATP-sensitive K+ (KATP) channels critically control insulin secretion by coupling metabolism to electrical activity [3]. The ┚-cell channels are assembled, with tetradimeric stoichiometry, from two structurally distinct subunits: inwardly rectifying K-channel subunit (KIR6.2) and the regulatory sulfonylurea receptor subunit-1 (SUR1). Some studies showed that the KCNJ11 E23K (Lys23Glu, 67 G>A, rs5219) polymorphism could affect insulin secretion and T2DM susceptibility by influencing the sensitivity of the KATP channel to ATP [4-6]. E23K promotes development of T2DM by increasing the threshold ATP concentration, thus inducing over activity of pancreatic ┚-cell KATP channels and inhibiting insulin secretion [7]. E23K markedly affected channel gating, significantly reduced the time spent in long inter burst closed states. Meta-analysis of all case-control data showed that the E23K allele was associated with T2DM [8]. The E23K variant was associated with a reduction in estimates of glucose-induced serum insulin levels in middle-aged glucosetolerant subjects. This result is in accordance with the recent in vitro finding that the E23K variant is associated with a reduced ATP sensitivity of the Kir6.2/SUR1channel complex [4, 7]. T2DM patients with one A allele of the KCNJ11 E23K polymorphism seem to be more sensitive to repaglinide as compared with individuals with the GG genotype [9].