Miracle-dz/UniFAR-FTUs huggingface dataset:
Chrysene : a carcinogen and its microbial degradation

Corresponding Author: Arif, A. , () Gene Expression Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi-110025 Email: ali.arifali@gmail.com P a te l e t a l. 2 0 1 4 J o u rn a l o f In n o v a ti v e B io lo g y hrysene is a colorless to white, crystalline solid. It is also known as benzo(a)phenanthrene. It is most often found as the gaseous by-product from the incomplete combustion of fossil fuel, wood, Coal Tar and Creosote. High environmental concerns due to its carcinogenic and mutagenic nature (Smith et al. 1989; Nwanna et al. 2006) compel us to look for innovative methodologies for its biodegradation. Chrysene oxidation occurs by incorporation of an oxygen molecule in an aromatic ring catalyzed by dioxygenases to a cis-dihydrodiol intermediate, which undergoes further catabolism results in complete mineralization (Hinchee et al. 1994). Dioxygeneses is thus a group of enzymes which play a key role in metabolism of PAHs i.e. catalysed the first ring opening step of aromatic hydrocarbon (including chrysene) and presence of catabolic genes encoding this enzyme in microbes is indicative of their role in biodegradation. The ubiquitous distribution of polycyclic aromatic hydrocarbons (PAHs) in aquatic environments has long been of great concern for their potential hazards to human health via tropic transfer in aquatic food chains. PAHs tend to be bio-accumulated and biomagnified due to their lipophilicity and chemical stability. A broad spectrum of microorganisms had been found capable of degrading PAHs, and bioremediation based on microbial processes has been considered as a promising alternative to conventional technologies to remove PAHs from contaminated soils and waters (Dean-Ross et al. 2002). However, PAHs can be photochemically decomposed under strong ultraviolet light or sunlight, and thus a fraction of PAHs is oxidized during atmospheric sampling. PAHs can also react with ozone, hydroxyl radicals, nitrogen and sulfur oxides, and nitric and sulfuric acids, which affect the environmental fate or conditions of PAHs. While physicochemical processes means to eliminate PAHs from the contaminated site but they degrade the quality of soil. The biological treatment of soil contaminated with PAHs is more environmental friendly, financially affordable and adaptable choice. It has the potential advantages such as the complete degradation of the pollutants, lower treatment cost, and greater safety and less soil disturbance (Habe and Omori, 2003).
ILP platform optimization of a YAPI parallel H.264/AVC encoder

The H.264/AVC (Advanced Video Codec) new video coding standard provides higher coding efficiency relative to former standards at the expense of higher computational requirements. Given the potential applications of this technology, we are developing an application environment able to decode an MPEG2 stream, convert it into an H.264 stream, and stream it over a network. This paper focuses on the H.264 video encoder implementation. The absolute complexity of the obtained cost-efficient configuration outlined the potential of using a multiple processors platform for executing a parallel code version of the H.264 reference software. For this, a starting YAPI parallel Kahn Process Network (KPN) model is proposed. This model has been implemented and validated at a high system-level using the YAPI multi-threading programming interface. To identify the potential bottlenecks of the starting parallel model, communication and computation workload analysis are considered. Based on this analysis, an optimized parallel YAPI/KPN model with maximum workload balance is provided. For cost-effective realization, mapping the validated parallel model on the STMicroelectronics mb392 multiprocessor platform is motivated. For this purpose, a static code parser for the ST220 Very Large Instruction Word (VLIW) processor is developed to analyze, for each process of the model, the instruction level parallelism (ILP) effectively used by the ST220 cross compiler. Using this tool, the binary code of each process, cross-compiled for an ST220, is statically analyzed and the processes demanding further low level optimization are identified. To maximize the ILP for the ST220 VLIW architecture, a low-level algorithmic optimization of the motion estimation and compensation process is performed.
PSI1 is responsible for the stearic acid enrichment that is characteristic of phosphatidylinositol in yeast

In yeast, both phosphatidylinositol and phosphatidylserine are synthesized from cytidine diphosphate‐diacylglycerol. Because, as in other eukaryotes, phosphatidylinositol contains more saturated fatty acids than phosphatidylserine (and other phospholipids), it has been hypothesized that either phosphatidylinositol is synthesized from distinct cytidine diphosphate‐diacylglycerol molecules, or that, after its synthesis, it is modified by a hypothetical acyltransferase that incorporates saturated fatty acid into neo‐synthesized molecules of phosphatidylinositol. We used database search methods to identify an acyltransferase that could catalyze such an activity. Among the various proteins that we studied, we found that Psi1p (phosphatidylinositol stearoyl incorporating 1 protein) is required for the incorporation of stearate into phosphatidylinositol because GC and MS analyses of psi1Δ lipids revealed an almost complete disappearance of stearic (but not of palmitic acid) at the sn‐1 position of this phospholipid. Moreover, it was found that, whereas glycerol 3‐phosphate, lysophosphatidic acid and 1‐acyl lysophosphatidylinositol acyltransferase activities were similar in microsomal membranes isolated from wild‐type and psi1Δ cells, microsomal membranes isolated from psi1Δ cells are devoid of the sn‐2‐acyl‐1‐lysolysophosphatidylinositol acyltransferase activity that is present in microsomal membranes isolated from wild‐type cells. Moreover, after the expression of PSI1 in transgenic psi1Δ cells, the sn‐2‐acyl‐1‐lysolysophosphatidylinositol acyltransferase activity was recovered, and was accompanied by a strong increase in the stearic acid content of lysophosphatidylinositol. As previously suggested for phosphatidylinositol from animal cells (which contains almost exclusively stearic acid as the saturated fatty acid), the results obtained in the present study demonstrate that the existence of phosphatidylinositol species containing stearic acid in yeast results from a remodeling of neo‐synthesized molecules of phosphatidylinositol.
Procyclic acidic repetitive protein (PARP) genes located in an unusually small alpha-amanitin-resistant transcription unit: PARP promoter activity assayed by transient DNA transfection of Trypanosoma brucei

At least one of the procyclic acidic repetitive protein (PARP or procyclin) loci of Trypanosoma brucei is a small (5- to 6-kilobase) polycistronic transcription unit which is transcribed in an alpha-amanitin-resistant manner. Its single promoter, as mapped by run-on transcription analysis and UV inactivation of transcription, is located immediately upstream of the first alpha-PARP gene. Transcription termination occurs in a region approximately 3 kilobases downstream of the beta-PARP gene. The location of the promoter was confirmed by its ability to direct transcription of the bacterial chloramphenicol acetyltransferase gene in insect-form (procyclic) T. brucei. The putative PARP promoter is located in the region between the 3' splice acceptor site (nucleotide position 0) and nucleotide position -196 upstream of the alpha-PARP genes. Regulatory regions influencing the levels of PARP expression may be located further upstream. We conclude that a single promoter, which is located very close to the 3' splice acceptor site of the alpha-PARP genes, directs the transcription of a small, polycistronic, and alpha-amanitin-resistant transcription unit.
Characterizing N-port packages and interconnections with a 2-port network analyzer

In this paper a technique is described for the measurement of the correct S-parameters of an N-port package or interconnection using a 2-port network analyzer with 50 /spl Omega/ system impedance and N imperfect terminations. The technique is fully general and can be applied using arbitrary terminations. Broadband 50 n loads are not required. The method is illustrated on a coupled microstrip line structure.
Harrington instrumentation without fusion plus external orthotic support for the treatment of difficult curvature problems in young children.

In selected patients a method of rod insertion without fusion combined with use of a full-time external orthotic support, e.g., the Milwaukee brace, is effective. The orthopedic surgeon confronted with young children who have curves that do not respond to conservative treatment alone or in which bracing is contraindicated should find this procedure particularly suitable. The method allows for the expression of full growth potential while maintaining curve correction.
Barcoding of Plants and Fungi

DNA barcoding enables rapid and accurate identification of species in many groups of organisms, but cannot always distinguish between closely related species of land plants or fungi. Rapid identification of biological specimens or fragments of biological origin has always been desirable, but has rarely been possible owing to a shortage of natural history specialists. Very often, for a particular group of organisms there is only one expert worldwide, and no one person can be expected to identify every organism that is relevant to ecological studies. Also, environmental samples (for example, from water or soil) that contain mixtures of minute organisms with few morphological traits pose great identification challenges. Short, standardized DNA regions—or “barcodes”—have been used to identify biological material from many groups of animals (1–3). The barcoding approach also has great potential for identifying plants (4, 5) and fungi (6), but faces different challenges when applied to these groups.
Proteomics analysis of growth hormone isoforms in the human pituitary

In order to elucidate the roles of human growth hormone (hGH) in the normal (control) pituitary and in adenomas, the hGH isoforms in the human pituitary were analyzed with two‐dimensional gel electrophoresis, immobilized metal affinity column (Ga+3) chromatography, mass spectrometry (MS), and bioinformatics. Twenty‐four hGH‐containing proteins, with significantly different expression proportions of their isoforms were found. The proportions of isoforms were as follows: isoform 1 (87.5%) > isoform 2 (8.1%) > isoform 3 (3.3%) > isoform 4 (1.1%). Deamidation of asparagine to aspartate was identified with matrix‐assisted laser desorption/ionization‐time of flight MS. Tandem mass spectrometry data demonstrated that hGH is a phosphoprotein (spot 6); phosphorylation was found at Ser‐77 in the tryptic peptide 68YSFLQNPQTSLCFSESIPTPSNR90, at Ser‐176 in the tryptic peptide 172FDTNSHNDDALLK184, and at Ser‐132 in the peptide 126SLVYGASDSNVYDLLK141. The phosphorylation sites at Ser‐77 and Ser‐176 were consistent with computer‐program predictions (NetPhos). These results provide novel clues for further studies of the functions, and mechanisms of action, of hGH in the human pituitary and in growth hormone‐related diseases.
Patient‐reported signs of dampness at home may be a risk factor for chronic rhinosinusitis: A cross‐sectional study

An association between dampness at home and respiratory conditions has been convincingly demonstrated in children. Fewer studies have been performed in adults, and data are lacking for chronic rhinosinusitis (CRS). With a prevalence of 10.9% in Europe, CRS imposes a significant burden on quality of life, as well as economy.
Encouraging pulmonary outcome for surviving, neurologically intact, extremely premature infants in the postsurfactant era.

OBJECTIVE The aim of this study was to determine the long-term pulmonary outcome of extreme prematurity at a single tertiary-care center from 1997 to 2001 in the postsurfactant era. METHODS We assessed symptoms, exhaled nitric oxide, spirometry, methacholine challenge (provocative concentration of methacholine required to decrease FEV₁ by 20% [PC(20)]), lung volumes, diffusion, and cardiopulmonary exercise tolerance. RESULTS Of 279 infants born, 192 survived to discharge, and 79 of these developed bronchopulmonary dysplasia (BPD) (65 mild, 12 moderate, two severe). We studied a subgroup of 53 neurologically intact preterm subjects aged 10 ± 1.5 years (28 with BPD [born, 26.2 ± 1.4 weeks; birth weight, 821 ± 164 g] and 25 without BPD [born, 27.2 ± 1 weeks; birth weight, 1,050 ± 181 g]) and compared them with 23 term control subjects. Of the BPD cases, 21 were mild, seven were moderate, and none was severe; 77.4% of subjects received antenatal steroids, and 83% received postnatal surfactant. Sixty percent of the preterm subjects wheezed at age < 2 years compared with 13% of the control subjects (P < .001), but only 13% wheezed in the past year compared with 0% of control subjects (not significant). For preterm and control subjects, respectively (mean ± SD), FEV₁ % predicted was 85% ± 10% and 94% ± 10% (P < .001), with limited reversibility; residual volume/total lung capacity was 29.3% ± 5.5% and 25% ± 8% (P < .05); diffusing capacity/alveolar volume was 89.6% ± 9.2% and 97% ± 10% (P < .005); and PC(20) was 6.5 ± 5.8 mg/mL and 11.7 ± 5.5 mg/mL (P < .001). PC(20) was < 4 mg/mL in 49% of preterm subjects despite normal exhaled nitric oxide. Most measurements were similar in premature subjects with and without BPD. Peak oxygen consumption and breathing reserve were normal, but % predicted maximal load (measured in Watts) was 69% ± 15% for subjects with BPD compared with 88% ± 23% for subjects without and 86% ± 20% for control subjects (P < .01). CONCLUSIONS Pulmonary outcome was encouraging at mid-childhood for neurologically intact survivors in the postsurfactant era. Despite mechanical ventilation and oxygen therapy, most had no or mild BPD. Changes found probably reflect the hypoplastic lungs of prematurity.
What if Multiusers Wish to Reconcile Their Data?

Reconciliation is the process of providing a consistent view of the data imported from different sources. Despite some efforts reported in the literature for providing data reconciliation solutions with asynchronous collaboration, the challenge of reconciling data when multiple users work asynchronously over local copies of the same imported data has received less attention. In this paper, we propose AcCORD, an asynchronous collaborative data reconciliation model based on data provenance. AcCORD is innovative because it supports applications in which all users are required to agree on the data integration in order to provide a single consistent view to all of them, as well as applications that allow users to disagree on the correct data value, but promote collaboration by sharing updates. We also introduce different policies based on provenance for solving conflicts among multiusersâ updates. An experimental study investigates the main characteristics of the policies, showing the efficacy of AcCORD.
Sensory modulation disorder: a risk factor for participation in daily life activities

Participation in childhood daily functional performance was examined in 78 children: 44 with sensory modulation disorder (SMD); (33 males, 11 females; mean age 7y 6mo [SD 1.20]) and 34 without SMD (18 males, 16 females; mean age 7y 8mo [SD 1.33]). Group classification was determined using two measures: the Short Sensory Profile (SSP) and the Full‐form Sensory Profile. Parents completed a battery of caregiver questionnaires. Children with SMD scored significantly lower on all three participation scales than the control group. A high correlation was observed between level of activity performance of the Participation in Childhood Occupations Questionnaire (PICO‐Q) and the SSP, and a moderate correlation was observed between the Enjoyment of Performance of the PICO‐Q and the SSP. A low correlation was observed between Frequency of Performance of the PICO‐Q and the SSP. Logistic regression indicated that all three participation scales (level of activity performance, level of enjoyment of the activity, and frequency of performance of the activity) are significantly associated with group classification, with odds ratios of 3.13, 2.05, and 1.73 respectively. These findings are the first, to our knowledge, to confirm claims of limited participation in daily activities among children with SMD. Our results have significant clinical implications and provide support for the need for practitioners and caregivers of children with SMD to facilitate participation.
The penetration of antibiotics into peritoneal fluid.

S ELECTION of an antibiotic for treatment of peritonitis or intra-ab-dominal abscess should reflect both the drug's spectrum of antibacterial activity and its ability to penetrate the peritoneum. Should the penetration of the peritoneum by the antibiotic be inadequate, administration directly into the peritoneum may be indicated. We have recently investigated the penetration of two groups of antibiotics into peritoneal fluid obtained experimentally through chambers implanted in rabbits.
Flavonoid Intake in Relation to Lung Cancer Risk: Case-Control Study Among Women in Greece

Abstract: We have examined the role of three classes of flavonoids that are relatively common in the Greek diet (flavanones, flavan-3-ols, and flavonols) in the etiology of lung cancer using data from a case-control study among women, which was undertaken in Athens, Greece, in the late 1980s. Study subjects were 154 women with lung cancer and 145 control women with orthopedic conditions. Women reported their life-long smoking histories and average frequency of consumption, before onset of present disease, of 47 food items or beverages that collectively covered >80% of the intake of each of the energy-providing nutrients. Intakes of flavonoids were calculated using the recently published U.S. Department of Agriculture database. The data were modeled through logistic regression, controlling for energy intake and smoking. There was no indication that intake of any of the studied flavonoid categories reduces the risk of lung cancer; indeed, for flavonols there was an unexpected positive association. Thus, our study does not indicate a protective effect of flavanones, flavan-3-ols, or flavonols on lung cancer risk and indicates that the factors responsible for the protective effect of vegetables and fruits against the risk of this cancer are unlikely to belong to these flavonoid categories.
Acetaldehyde, Microbes, and Cancer of the Digestive Tract

Excessive alcohol consumption and heavy smoking are the main risk factors of upper digestive tract cancer in industrialized countries. The association between heavy drinking and cancer appears to be particularly prominent in Asian individuals who have an inherited deficient ability to detoxify the first metabolite of ethanol oxidation, acetaldehyde. Alcohol itself is not carcinogenic. However, according to cell culture and animal experiments acetaldehyde is highly toxic, mutagenic, and carcinogenic. In addition to somatic cells, microbes representing normal human gut flora are also able to produce acetaldehyde from ethanol. After the ingestion of alcoholic beverages, this results in high local acetaldehyde concentrations in the saliva, gastric juice, and the contents of the large intestine. In addition, microbes may produce acetaldehyde endogenously without alcohol administration. This review summarizes the epidemiological, genetic, and biochemical evidence supporting the role of locally produced acetaldehyde in the pathogenesis of digestive tract cancer. Special emphasis is given to those factors that regulate local acetaldehyde concentration in the contents of the gastrointestinal tract. The new evidence presented in this review may open a microbiological approach to the pathogenesis of digestive tract cancer and may have an influence on future preventive strategies. Referee: Dr. Esteban Mezey, The Johns Hopkins University, School of Medicine, 921 Ross, 720 Rutland Ave., Baltimore, MD 21205-2195 USA
Elimination of the vitamin B12 uptake or synthesis pathway does not diminish the virulence of Escherichia coli K1 or Salmonella typhimurium in three model systems

The role of iron in infection is of great importance and is well understood. During infection, both the host and the pathogen go through many complicated changes to regulate iron levels. Iron and vitamin B12 share certain features. For example, Escherichia coli has similar transport systems for both nutrients, and binding proteins for both are located in gastric juice, liver, saliva, granulocytes, and milk. It is because of such parallels between iron and B12 that we have explored the role of B12 in virulence. A btuB::Tn10 insertion which disrupts the gene encoding the vitamin B12 receptor from E. coli K-12 was P1 transduced into a virulent E. coli K1 strain. In both an infant-rat model and a chicken embryo model, no difference in virulence between the wild-type and the mutant strains was found. Strains of Salmonella typhimurium with mutations in the cobalamin synthesis pathway (Cob) and in btuB were used in a mouse model of virulence. Mutation of the Cob locus or of btuB does not decrease virulence. Interestingly, the inability to synthesize vitamin B12 actually increases virulence compared with the wild type in the S. typhimurium model. This effect is independent of the B12 intake of the mice.
A Implementing Curve 25519 for Side-Channel-Protected Elliptic Curve Cryptography

For security-critical embedded applications Elliptic Curve Cryptography (ECC) has become the predominant cryptographic system for efficient key agreement and digital signatures. However, ECC still involves complex modular arithmetic that is a particular burden for small processors. In this context, Bernstein proposed the highly efficient ECC instance Curve25519 that particularly enables efficient software implementations at a security level comparable to AES-128 with inherent resistance to simple power analysis (SPA) and timing attacks. In this work we show that Curve25519 is likewise competitive on FPGAs even when countermeasures to thwart side-channel power analysis are included. Our basic multi-core DSP-based architectures achieves a maximal performance of more than 32,000 point multiplications per second on a Xilinx Zynq 7020 FPGA. Including a mix of side-channel countermeasures to impede simple and differential power analysis we still achieve more than 27,500 point multiplications per second with a moderate increase in logic resources.
Tube wave signatures in cylindrically layered poroelastic media computed with spectral method

SUMMARY This paper describes a new algorithm based on the spectral method for the computation of Stoneley wave dispersion and attenuation propagating in cylindrical structures composed of fluid, elastic and poroelastic layers. The spectral method is a numerical method which requires discretizationofthestructurealongtheradialaxisusingChebyshevpoints.Toapproximatethe differential operators of the underlying differential equations, we use spectral differentiation matrices. After discretizing equations of motion along the radial direction, we can solve the problem as a generalized algebraic eigenvalue problem. For a given frequency, calculated eigenvaluescorrespondtothewavenumbersofdifferentmodes.Theadvantageofthisapproach is that it can very efficiently analyse structures with complicated radial layering composed of different fluid, solid and poroelastic layers. This work summarizes the fundamental equations, followed by an outline of how they are implemented in the numerical spectral schema. The interface boundary conditions are then explained for fluid/porous, elastic/porous and porous interfaces. Finally, we discuss three examples from borehole acoustics. The first model is a fluid-filledboreholesurroundedbyaporoelasticformation.Thesecondconsidersanadditional elastic layer sandwiched between the borehole and the formation, and finally a model with radially increasing permeability is considered.