Miracle-dz/UniFAR-FTUs huggingface dataset:
The Chromatin Structure of the Long Control Region of Human Papillomavirus Type 16 Represses Viral Oncoprotein Expression

ABSTRACT The long control region (LCR) of human papillomavirus type 16 (HPV-16) has a size of 850 bp (about 12% of the viral genome) and regulates transcription and replication of the viral DNA. The 5′ segment of the LCR contains transcription termination signals and a nuclear matrix attachment region, the central segment contains an epithelial cell-specific enhancer, and the 3′ segment contains the replication origin and the E6 promoter. Here we report observations on the chromatin organization of this part of the HPV-16 genome. Treatment of the nuclei of CaSki cells, a cell line with 500 intrachromosomal copies of HPV-16, with methidiumpropyl-EDTA-Fe(II) reveals nucleosomes in specific positions on the LCR and the E6 and E7 genes. One of these nucleosomes, which we termed Ne, overlaps with the center of the viral enhancer, while a second nucleosome, Np16, overlaps with the replication origin and the E6 promoter. The two nucleosomes become positioned on exactly the same segments after in vitro assembly of chromatin on the cloned HPV-16 LCR. Primer extension mapping of DNase I-cleaved chromatin revealed Np16 to be positioned centrally over E6 promoter elements, extending into the replication origin. Ne covers the center of the enhancer but leaves an AP-1 site, one of the strongestcis-responsive elements of the enhancer, unprotected. Np16, or a combination of Np16 and Ne, represses the activity of the E6 promoter during in vitro transcription of HPV-16 chromatin. Repression is relieved by addition of Sp1 and AP-1 transcription factors. Sp1 alters the structure of Np16 in vitro, while no changes can be observed during the binding of AP-1. HPV-18, which has a similar arrangement ofcis-responsive elements despite its evolutionary divergence from HPV-16, shows specific assembly in vitro of a nucleosome, Np18, over the E1 binding site and E6 promoter elements but positioned about 90 bp 5′ of the position of Np16 on the homologous HPV-16 sequences. The chromatin organization of the HPV-16 and HPV-18 genomes suggests important regulatory roles of nucleosomes during the viral life cycle.
Multi image retrieval for kernel-based automated intruder detection

This paper focuses on a novel approach for handling radical overhaul of anomalous behavior in a visual surveillance network. The initial objective is online detection of anomalies using a Kernel-based online anomaly detection algorithm. The algorithm will operate onimages collected from a moving camera over a span of space and time. The proposed algorithm established based upon machine learning principles. The eventual target is to connect our proposed system with face detection algorithm. Our proposed system is tested on real data and compared with benchmark existing methods based on the technique of Principal Component Analysis (PCA.) We show that our proposed system achieves high detection accuracy with low computational complexity, while also providing the added benefits of being adaptive, portable, and involving low infrastructural costs.
Holistic Representation of Negative Numbers is Formed When Needed for the Task

Past research suggested that negative numbers are represented in terms of their components—the polarity marker and the number (e.g., Fischer & Rottmann, 2005; Ganor-Stern & Tzelgov, 2008). The present study shows that a holistic representation is formed when needed for the task requirement. Specifically, performing the numerical comparison task on positive and negative numbers presented sequentially required participants to hold both the polarity and the number magnitude in memory. Such a condition resulted in a holistic representation of negative numbers, as indicated by the distance and semantic congruity effects. This holistic representation was added to the initial components representation, thus producing a hybrid holistic-components representation.
A Hybrid ABC-DE Algorithm and Its Application for Time-Modulated Arrays Pattern Synthesis

In this paper, a novel hybrid algorithm based on artificial bee colony (ABC) algorithm and differential evolution (DE) algorithm called ABC-DE is proposed to inherit their advantages and overcome their drawbacks. In ABC-DE algorithm, employed bees employ the mutation and crossover strategies of DE to enforce their exploration ability while onlooker bees keep their original updating strategy to retain the exploitation ability. Classical test functions have been provided to testify the ABC-DE algorithm. Furthermore, ABC-DE is applied to different types of time-modulated arrays (TMAs) pattern synthesis problems, including the syntheses of low equal-ripple sidelobe level (SLL) pattern, deep null level pattern, multiple-beams patterns and satellite footprint pattern. Experiment results reveal that ABC-DE has a promising performance in the convergence rate and the exploration ability when compared with other improved evolutionary algorithms, which indicates that the proposed algorithm can be an effective approach for TMAs synthesis problems.
Unsupervised Multiclass Region Cosegmentation via Ensemble Clustering and Energy Minimization

The problem of unsupervised segmentation of multi-class regions can be significantly boosted when they irregularly recur in multiple images. The existing segmentation methods are either weakly supervised, such as tagging images with object classes, or are limited by the assumption that each image contains all the object instances. In this paper, we propose a new method to cosegment multiclass regions from a group of images without the assumption about object configurations. The key idea is to discover the unknown object-like proposals via a robust ensemble clustering scheme. The proposals are then used to derive unary and pairwise energy potentials across all the images, which can be minimized with the α-expansion. Experimental evaluation on a number of image groups demonstrates the good performance of the proposed method on the multiclass region cosegmentation.
Noninvasive assessment of hepatobiliary and renal elimination of cysteinyl leukotrienes by positron emission tomography

N‐Acetyl‐leukotriene E4 has been identified as an endogenous, biologically less active cysteinyl leukotriene metabolite in rodents and humans. To evaluate the ratio of hepatobiliary to renal elimination of leukotrienes noninvasively by positron emission tomography (PET), we synthesized N‐[11C]acetyl‐leukotriene E4 by chemical N‐acetylation of leukotriene E4. After the intravenous injection of N‐[11C]acetyl‐leukotriene E4 in normal rats and monkey, uptake by the liver and subsequent excretion into bile were largely responsible for its rapid elimination from blood. In the Cynomolgus monkey, renal excretion of the leukotriene into urine was of additional quantitative importance. Kinetic modeling indicated a mean transit time through the liver of 17 minutes and 34 minutes in rat and monkey, respectively; the corresponding hepatic excretion half‐times amounted to 8.5 minutes and 16 minutes. In a mutant rat strain deficient in the hepatobiliary excretion of cysteinyl leukotrienes across the canalicular membrane, the apparent mean liver transit time was 54 minutes, and the hepatic excretion half‐time was 29 minutes, indicating prolonged organ storage and metabolism. After transport from the liver back into the circulating blood of ω‐oxidized and β‐oxidized metabolites of N‐[11C]acetyl‐leukotriene E4, renal excretion compensated for the impairment of hepatobiliary elimination in the transport mutant. Metabolite analyses in urine after intravenous injection of N‐[3H]acetyl‐leukotriene E4 indicáted the extensive inactivation of N‐acetyl‐leukotriene E4 by β‐oxidation from the ω‐end in the mutants. A similar shift from hepatobiliary to renal cysteinyl leukotriene elimination was monitored in rats with cholestasis due to bile duct obstruction. N‐[11C]Acetyl‐leukotriene E4 enables the assessment of hepatobiliary function by PET as well as the quantitative and noninvasive evaluation of the contribution of liver and kidney to leukotriene elimination under normal and various pathophysiological conditions.
A Two-component Signal Transduction Pathway Regulates Manganese Homeostasis in Synechocystis 6803, a Photosynthetic Organism*

Elemental manganese is essential for the production of molecular oxygen by cyanobacteria, plants, and algae. In the cyanobacterium Synechocystis sp. PCC 6803, transcription of the mntCAB operon, encoding a high affinity Mn transporter, occurs under Mn starvation (nm Mn) conditions but not in Mn-sufficient (μm Mn) growth medium. Using a strain in which the promoter of this operon directs the transcription of the luxAB reporter genes, we determined that inactivation of the slr0640 gene, which encodes a histidine kinase sensor protein component of a two-component signal transduction system, resulted in constitutive high levels oflux luminescence. Systematic targeted inactivation mutagenesis also identified slr1837 as the gene encoding the corresponding response regulator protein. We have named these two genes manS (manganese-sensor) andmanR (manganese-regulator), respectively. A polyhistidine-tagged form of the ManS protein was localized in the Synechocystis 6803 cell membrane. Directed replacement of the conserved catalytic His-205 residue of this protein by Leu abolished its activity, although the mutated protein was present in cyanobacterial membrane. This mutant also showed suboptimal rates of Mn uptake under either Mn-starved or Mn-sufficient growth condition. These data suggest that the ManS/ManR two-component system plays a central role in the homeostasis of manganese inSynechocystis 6803 cells.
ERG expression is an independent prognostic factor and allows refined risk stratification in cytogenetically normal acute myeloid leukemia: a comprehensive analysis of ERG, MN1, and BAALC transcript levels using oligonucleotide microarrays.

PURPOSE Recently, several novel molecular prognostic markers were identified in cytogenetically normal acute myeloid leukemia (CN-AML). In addition to the well-known influence of FLT3, NPM1, and CEBPA mutations, high transcript levels of the ERG, BAALC, and MN1 genes have been associated with inferior outcomes, but the relative importance of these risk markers remains to be defined. PATIENTS AND METHODS We analyzed ERG, BAALC, and MN1 expression levels in a cohort of 210 patients with CN-AML who received intensive chemotherapy. Expression levels of ERG, BAALC, and MN1 were determined in bone marrow samples by using oligonucleotide microarrays. RESULTS High transcript levels of ERG, BAALC, and MN1 were predictors for inferior overall survival (OS) and a lower rate of complete remissions (CRs). There were significant positive correlations between the expression levels of all three genes. ERG expression levels predicted OS in elderly patients (ie, age 60 years or older) with CN-AML (P = .006) as well as in younger patients (P = .013). In multivariate analyses, high ERG expression was independently associated with a lower CR rate (P = .013), shorter event-free survival (P = .008), and shorter OS (P = .005). Patients who had low ERG levels and absent FLT3 internal tandem duplication (ITD) had a 5-year OS of 44%, and patients who had high ERG expression and FLT3 ITD had a 5-year OS of only 5%. CONCLUSION We analyzed a comprehensive set of molecular risk factors in a large, homogeneous CN-AML patient cohort. In this study, high ERG expression levels emerged as a strong negative prognostic factor and provided prognostic information in addition to established molecular markers.
Data analysis, visualization, and hidden factor discovery by unsupervised learning

With the continuous increase in computing power, it has become possible to process and classify masses of natural data, such as statistical information, images, speech, as well as other kinds of signals and measurements coming from very different sources. Many problems occur in industry, finance, remote sensing, medicine, and natural sciences, to mention only a few main fields, in which one needs efficient tools for visualization, prediction, clustering, and profiling. Often the explicit modelling of the processes underlying the measurements is very hard and so inferences from the measurement data must be made by learning methods. A widely used class of learning algorithms are the neural learning paradigms. In this paper, emphasis is on unsupervised neural learning. Especially the techniques of self-organizing maps and independent component analysis are reviewed and shown to be useful in this context. Some examples are shown on applications of these techniques on financial data analysis.
Compact Mach–Zehnder Interferometer Based on Tapered Hollow Optical Fiber

A compact fiber Mach-Zehnder interferometer based on tapered hollow optical fiber (THOF) has been demonstrated. The THOF is sandwiched between two single mode fibers (SMFs), forming a SMF-THOF-SMF (STS) structure. The discharging during the splicing and tapering processes induces the collapsed regions in the hollow fiber, which form the modal coupling/re-coupling areas of the interferometer. The THOF has a length of about 2 mm and the taper waist diameter is about 66.5 μm. The refractive index (RI), stress, and temperature response properties of the STS interferometer have been investigated, which show a high RI sensitivity and low temperature cross-sensitivity. The STS interferometer holds the merits of compact structure, low cost and easy fabrication, making it a suitable candidate in the biochemical and physical sensing fields.
Anti-dyslipidemic and Antioxidant Potentials of Methanol Extract of Kalanchoe crenata Whole Plant in Streptozotocin-induced Diabetic Nephropathy in Rats

Purpose : The activity of the methanol extract of the whole plant of Kalanchoe crenata (MEKC) was studied for the treatment of diabetes-induced nephropathy in rats. Methods : Five-day old Wistar rats received a single intraperitoneal streptozotocin injection (90 ig/kg body weight) to induce diabetes. Kidney disease onset in the rats was observed six weeks after diabetes induction. The rats were orally administered MEKC (0, 50 and 68 mg/kg) or glibenclamide (5 mg/kg), once daily for 6 weeks. Blood and urine glucose, proteins, lipids, creatinine, malondialdehyde (MDA), superoxide dismutase (SOD) and catalase (CAT) were then evaluated. Results : After 6 weeks of treatment, 50 and 68 mg/kg MEKC, and glibenclamide significantly (p < 0.01) decreased glycaemia (-35, -44 and -39 %), glycosuria (-38, -47 and -61 %) and proteinuria (-82, -80 and -72 %) in diabetes-nephropathic rats. The extract (68 mg/kg) decreased MDA by up to -44 % (blood), -35 % (liver) and -34 % (kidney); increased SOD up to 257 % (blood), 116 % (liver) and 118 % (kidney); and CAT by up to 176 % (blood), 78 % (liver) and 96 % (kidney) in the rats, compared with nephropathic control. The extract (50 and 68 mg/kg, respectively) lowered (p < 0.01) total cholesterolemia (-24 and - 27 %), blood triglycerides (-55 and -54 %), blood LDL cholesterol (-48 and -59 %), but increased blood HDL cholesterol (71 and 58 %). Overall, atherogenic index was decreased by 31 %. Conclusion : The results indicate that MEKC holds promise for the development of a standardized phytomedicine for diabetes mellitus and kidney disease treatment. Keywords : Diabetes, Dyslipidemia, Antioxidant, Kalanchoe crenata extract, Nephropathy.
Extractives from Eusideroxylon Zwageri and Potoxylon Melagangai Against white-Rot Fungi

Pusat Asasi, Universiti Teknologi MARA, 42300 Bandar Puncak Alam, Malaysia; Department of Plant Science and Environmental Ecology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Malaysia; Department of Chemistry, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Malaysia; E-mail: faiezah2892@puncakalam.uitm. edu.my
Multifactorial analysis of the outcome of 6430 cadaver kidney grafts

A total of 6430 cadaver kidney grafts performed within the network of France-Transplant between 1 January 1978 and 1 January 1989 were analyzed. Each case was examined comprehensively in regard to 12 variables. A multifactorial analysis (Cox regression) was used to determine the degree of association between each covariate and the outcome of the graft. The results were evaluated by calculating relative risks of graft failure for each variable. A total of seven covariates appeared to influence graft survival significantly: the period of transplantation (P=10-8), retransplantations (P=0.003), age and sex of the donor (P=0.003 and 0.009 respectively), duration of pretransplant dialysis (P=0.03), pretransplant sensitization to HLA antigens (P=0.05), and matching for HLA-A,-B, and-DR loci (P=0.03). This last parameter has previously been reported as influencing the outcome of the graft in seven out of eight international studies carried out using similar methodology.
The Effect of Press Fit on Osseointegration of Acetabular Cup

The primary cause of Total Hip Replacement (THR) failure for younger patients is aseptic loosening. This complication is twice more likely to happen in acetabular cup than in femoral stem. Excessive micromotion between bone and implant will cause loosening and it depends in patient activities, age and bone. In this project, the effects of different metal back design of press fit on osseointegration of the acetabular cup are carried out. Commercial acetabular cup designs, namely Spiked, Superfix and Quadrafix are modelled and analyzed using commercial finite element software. The diameter of acetabular cup is based on the diameter of acetabular rim to make sure the component fit to the acetabular cavity. A new design of acetabular cup are proposed and analyzed to get better osseointegration between the bones and implant interface. Results shows that the proposed acetabular cup designs are more stable compared to other designs with respect to stress and displacement aspects.
Small pelagic fish, trawling discards and breeding performance of the critically endangered Balearic shearwater : improving conservation diagnosis

Conservation diagnosis should identify which demographic parameters (or vital rates) are having a negative effect on the population growth rate of a threatened organism. Diagnosis can analyse how the environment is influencing the vital rates of this organism. In the present study, we tried to improve the diagnosis of a critically endangered seabird, the Balearic shearwater Puffinus mauretanicus, through analysis of the spatio-temporal variability of breeding performance, using long-term data sets covering most of its breeding range. We also analysed the potential influence of 2 food resources, namely small pelagic fish and trawling discards, as measured by purse-seine and trawling landings, respectively. We found inter-annual variability in breeding performance, which could be related to the changes in the availability of both small pelagic fish and trawling discards. Results showed that these variations affected all study colonies in a similar way, thus supporting pre- vious investigations that identified a major foraging area for the whole breeding population. A fitness landscape suggested that current values of breeding success are not responsible for the sharp decline of the species, although incoming fisheries policies could affect its breeding performance in the long term. Factors affecting adult survival, both at sea and in colonies, remain the most important threat, and conservation efforts should concentrate on these issues to prevent the extinction of this endemic species of the Mediterranean region.
Abdominal Compartment Syndrome Is Common in Medical Intensive Care Unit Patients Receiving Large-Volume Resuscitation

Intra-abdominal hypertension (IAH) and abdominal compartment syndrome (ACS) have been well described in surgical patients. Large-volume resuscitation is thought to be a risk factor for IAH/ACS in this group. However, little is known of the incidence of IAH/ACS in critically ill medical patients. The authors aim to ascertain the incidence of ACS in critically ill medical patients receiving large-volume resuscitation. Over an 8-month study period, the authors performed a prospective cohort study of medical intensive care unit (ICU) patients with a minimum net positive fluid balance of 5 L within the preceding 24 hours. The primary outcome of interest is the development of ACS, defined as an intra-abdominal pressure (IAP) ≥20 mm Hg associated with new organ dysfunction. IAP was measured by transducing bladder pressure and was recorded along with fluid balance at enrollment and every 12 hours thereafter up to 96 hours. The setting is a medical ICU at a major university hospital. Of the 468 medical ICU admissions screened, 40 (8.5%) were identified who met the 24-hour fluid balance inclusion criterion. Upon enrollment, this cohort had a mean Acute Physiology And Chronic Health Evaluation II score of 23 and a median positive fluid balance of 6.9 L. Thirty-four of the 40 study patients (85%) had intra-abdominal hypertension (IAP ≥12 mm Hg). During the study period, 13 of the 40 (33%) patients developed IAP ≥20 mm Hg and 10 (25%) met the criteria for ACS. None underwent laparotomy. ACS is frequently found in critically ill medical patients receiving large-volume resuscitation. The clinical significance of this finding remains unclear. However, routine monitoring of IAP should be considered in medical patients with a 5-L net positive fluid balance in 24 hours. Future studies are warranted to evaluate clinical outcomes of medical patients with ACS and risk factors for its development.
DNA-damaging agents greatly increase the transduction of nondividing cells by adeno-associated virus vectors

None of the vector systems currently available for gene therapy applications have been shown to be capable of both efficient gene transfer into nondividing cells and long-term expression through stable integration into host cell DNA. While integrating vectors based on adeno-associated virus are capable of mediating gene transfer into nondividing cells, this process is 200-fold less efficient than transduction of dividing cells. We demonstrate that the transduction efficiency of adeno-associated virus vectors can be increased by treatment with DNA-damaging agents. Nondividing cells are especially responsive, with increases in transduction efficiency of up to 750-fold. This finding has the potential to facilitate gene therapy applications requiring gene transfer to nondividing cells.