Miracle-dz/UniFAR-FTUs huggingface dataset:
Biogas production from raw and oil-spent date palm seeds mixed with wastewater treatment sludge

ABSTRACT The objective of this study was to evaluate biogas production from raw and oil-spent date palm (Phoenix dactylifera) seeds mixed with wastewater treatment sludge. Two types of date seeds were ground to three size ranges (1.18–3.75, 0.6–1.18, and 0.425–0.6 mm) and co-digested with wastewater sludge at seed/sludge total solids (TS) ratios of 0% (sludge alone), 2.5, 5, 7.5, 10, 20 and 40% (i.e. 10% ratio results from adding 0.2 g dry seeds to 100 ml 2% sludge containing 2 g dry solids). After 14 weeks of incubation, biogas production, expressed in terms of the date seed/sludge ratios, was in the following order: 10% > 7.5% ≈ 5% ≈ 2.5% ≈ 0% > 20% > 40%. The size of date seed particles did not significantly affect biogas production. The specific biogas production was in the range of 370–390 ml g–1 volatile solids (VS) for the 0–10% seed/sludge ratios, 245 ml g–1 at 20% and 120 ml g–1 VS at 40%. The relatively low biogas production from the 20 and 40% seed/sludge mixtures indicated inhibition, which was also indicated by the low pH in the mixtures following digestion. Oil extraction from the date seeds reduced, but did not fully overcome, inhibition of biogas production from the 20 and 40% mixtures. The inhibition reduction due to oil-extraction was indicated by observed discrepancy between biogas production and solids digestion. The discrepancy between biogas production and solids digestion suggested inhibition of the acid forming but not the more sensitive methane forming microorganisms.
Dental Pulp Cells Isolated from Teeth with Superficial Caries Retain an Inflammatory Phenotype and Display an Enhanced Matrix Mineralization Potential

We have isolated dental pulp cells (DPCs) from three healthy (hDPCs) and three carious (cDPCs) donors and shown that compared to hDPCs cells isolated from superficial carious lesions show higher clonogenic potential; show an equivalent proportion of cells with putative stem cell surface markers; show enhanced matrix mineralization capability; have enhanced angiogenic marker expression and retain the inflammatory phenotype in vitro characteristic of superficial caries lesions in vivo. Our findings suggest that cDPCs may be used for further investigation of the cross talk between inflammatory, angiogenic and mineralization pathways in repair of carious pulp. In addition cells derived from carious pulps (almost always discarded) may have potential for future applications in mineralized tissue repair and regeneration.
Efficient and precise dynamic impact analysis using execute-after sequences

As software evolves, impact analysis estimates the potential effects of changes, before or after they are made, by identifying which parts of the software may be affected by such changes. Traditional impact-analysis techniques are based on static analysis and, due to their conservative assumptions, tend to identify most of the software as affected by the changes. Researchers have begun to investigate dynamic impact-analysis techniques, which rely on dynamic, rather than static, information about software behavior. Existing dynamic impact-analysis techniques are either very expensive in terms of execution overhead or amount of dynamic information collected - or imprecise. In this paper, we present a new technique for dynamic impact analysis that is almost as efficient as the most efficient existing technique and is as precise as the most precise existing technique. The technique is based on a novel algorithm that collects (and analyzes) only the essential dynamic information required for the analysis. We discuss our technique, prove its correctness, and present a set of empirical studies in which we compare our new technique with two existing techniques, in terms of performance and precision.
Serum miR‐221 serves as a biomarker for Parkinson's disease

Parkinson's disease (PD) is the common age‐related neurodegenerative disorder. Sensitive, noninvasive biomarkers that facilitate PD diagnosis and stage assignment are currently unavailable. This study aims to investigate the potential of 16 previous reported PD‐associated miRNAs as novel biomarkers for PD. The expression of 16 serum miRNAs was measured by quantitative reverse transcriptase polymerase chain reaction in 138 PD patients and 112 control populations. Analyses were undertaken to assess the specificity and sensitivity of miRNAs to predict PD. In addition, the relationship between deregulated miRNAs and Part III of the United Parkinson's Disease Rating Scale (UPDRS‐III) and Part V of the UPDRS (UPDRS‐V; the modified Hoehn and Yahr staging of PD) in PD patients was also assessed. It was found that the serums miR‐29c, miR‐146a, miR‐214, and miR‐221 were significantly decreased in PD patients compared with healthy control populations. In addition, serum miR‐221 was positively correlated with UPDRS‐III (r = .4702) and UPDRS‐V (r = .4788) score in PD patients. Furthermore, the receiver operating characteristic result of serum miR‐221 for prediction of PD was 0.787. Our preliminary findings indicate that downregulated serum miR‐221 might be a potential biomarker for PD evaluation.
Primary production dynamics of dominant hydrophytes in Lake Provala (Serbia)

The objective of this investigation was to analyze the primary production of the dominant hydrophytes by monitoring levels of organic matter and organic carbon and estimating photosynthetic potential via the total chlorophyll content. The survey was conducted in Lake Provala (Serbia) throughout the peak vegetation period of the year 2000. The contents of organic matter and organic carbon for Myriophyllum spicatum L. were 105.11 g m−2 and 73.66 g m−2, Nymphoides peltata (Gmel.) Kunt. were 95.51 g m−2 and 45.26 g m−2 and Ceratophyllum demersum L. were 52.17 g m−2 and 29.75 g m−2. Chlorophyll A (Chl a) and chlorophyll A+B (Chl a+b) pigments ranged from 1.54 mg g−1(Chl a) and 2.1 mg g−1(Chl a+b) in M. spicatum to 5.27 mg g−1(Chl a) and 7.53 mg g−1(Chl a+b) in C. demersum. At full leaf out, the latter aquatic plants exceeded 50% cover of the open water surface. All species achieved maximum growth in June, but significant differences in growth dynamics were observed. At the end of the vegetation period, these plants sink to the bottom and decompose
Association of Dietary Glycemic Index and Glycemic Load with Endometrial Cancer Risk Among Chinese Women

We evaluated the association of dietary glycemic index (GI) and glycemic load (GL) with the risk of endometrial cancer in a population-based, case-control study of 1199 endometrial cancer patients and 1212 age-frequency-matched controls in urban Shanghai, China, where diets are typically high in carbohydrates and have a high GL. Information on dietary habits, physical activity, and other relevant information was collected using a validated questionnaire, and anthropometric measurements were taken. Logistic regression was applied in the analysis. Dietary GI and GL were independently associated with risk for endometrial cancer but carbohydrate intake was unrelated to risk. Multivariable-adjusted odds ratios (ORs) for increasing quartiles of intake were 1.0, 1.3, 1.4, and 2.2 [95% confidence interval (CI): 1.2–4.0] for dietary GL (Ptrend = 0.02) and 1.0, 1.2, 1.4, and 1.4 (95% CI: 1.0–2.0) for dietary GI (Ptrend = 0.02). High intake of staples, especially rice, was positively associated with endometrial cancer. The association with GI was more evident among lean and normal weight women, although the test for interaction was not significant. This study suggests that intake of high GL or GI foods, but not carbohydrates per se, may increase risk for endometrial cancer.
Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation

Diverse point mutations in the enzyme Cu, Zn superoxide dismutase (SOD1) are linked to its aggregation in the familial form of the disease amyotrophic lateral sclerosis. The disease‐associated mutations are known to destabilize the protein, but the structural basis of the aggregation of the destabilized protein and the structure of aggregates are not well understood. Here, we investigate in silico the sequence and structural determinants of SOD1 aggregation: (1) We identify sequence fragments in SOD1 that have a high aggregation propensity, using only the sequence of SOD1, and (2) we perform molecular dynamics simulations of the SOD1 dimer folding and misfolding. In both cases, we identify identical regions of the protein as having high propensity to form intermolecular interactions. These regions correspond to the N‐ and C‐termini, and two crossover loops and two β‐strands in the Greek‐key native fold of SOD1. Our results suggest that the high aggregation propensity of mutant SOD1 may result from a synergy of two factors: the presence of highly amyloidogenic sequence fragments (“hot spots”), and the presence of these fragments in regions of the protein that are structurally most likely to form intermolecular contacts under destabilizing conditions. Therefore, we postulate that the balance between the self‐association of aggregation‐prone sequences and the specific structural context of these sequences in the native state determines the aggregation propensity of proteins. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Routing and Channel Assignment in Multi-Channel Multi-Hop Wireless Networks with Single Network Interface ( Invited Paper )

In this paper, we present a routing and channel assignment protocol for multi-channel multi-hop wireless networks. We view a multi-hop network as an extension to infrastructure networks, where a mobile host may connect to an access point using multi-hop wireless routes, via other mobile hosts or wireless routers. The access points are configured to operate on one of multiple available channels. Mobile hosts and wireless routers can select its operating channel dynamically through channel switching. In this environment, we propose a routing protocol that finds routes and assigns channels to balance load among channels while maintaining connectivity. The protocol works with nodes equipped with a single network interface, which distinguishes our work with other multi-channel routing protocols that require multiple interfaces per node. Supporting nodes with single network interface is beneficial because having multiple interfaces can be costly for small and cheap devices. The protocol discovers multiple routes to multiple access points, possibly operating on different channels. Based on traffic load information, each node selects the “best” route to an access point, and synchronizes its channel with the access point. With this behavior, the channel load is balanced, removing hot spots and improving channel utilization. The channel assignment assures every node has at least one route to an access point, where all intermediate nodes are operating on the same channel. Our simulation results show that the proposed protocol successfully adapts to changing traffic conditions and improves performance over a single-channel protocol and a protocol with random channel assignment. This research is funded in part by Motorola Center for Communication.
Together and apart: inhibition of DNA synthesis by connexin-43 and its relationship to transforming growth factor β

The membrane and channel protein connexin-43 (Cx43), as well as the cytokine transforming growth factor (TGF) β, suppress proliferative growth in cardiomyocytes and other cell types. Previously we showed that the inhibitory effect of Cx43 is canceled when Cx43 becomes phosphorylated at serine (S) 262 in response to mitogen stimulation. We have now asked if the TGFβ-triggered inhibition of DNA synthesis is associated with changes in Cx43 phosphorylation at S262. Conversely, we investigated if inhibition of DNA synthesis by overexpressed Cx43 is dependent on engaging TGFβ signal transduction. We report that TGFβ acutely prevented mitogen-induced Cx43 phosphorylation at S262, while chronic inhibition of TGFβ signal transduction raised baseline levels of endogenous phospho-S262-Cx43 without affecting total Cx43. Inhibition of baseline TGFβ signal transduction through (a) inhibiting TGFβ receptor I (TGFβRI) with SB431542, (b) inhibiting TGFβ receptor II (TGFβRII) by overexpressing dominant-negative (DN) TGFβRII, (c) inhibiting the downstream signaling mediator Smad2 by overexpressing DN Smad2, each separately increased baseline cardiomyocyte DNA synthesis, but could not reverse DNA synthesis inhibition by overexpressed Cx43. It is suggested that inhibition of cardiomyocyte DNA synthesis by TGFβ/TGFβRI/II/phospho-Smad2 signaling is mediated, at least in part, by reducing endogenous phospho-S262-Cx43 levels.
Single Nucleotide Polymorphisms in the FADS Gene Cluster but not the ELOVL2 Gene are Associated with Serum Polyunsaturated Fatty Acid Composition and Development of Allergy (in a Swedish Birth Cohort)

Exposure to polyunsaturated fatty acids (PUFA) influences immune function and may affect the risk of allergy development. Long chain PUFAs are produced from dietary precursors catalyzed by desaturases and elongases encoded by FADS and ELOVL genes. In 211 subjects, we investigated whether polymorphisms in the FADS gene cluster and the ELOVL2 gene were associated with allergy or PUFA composition in serum phospholipids in a Swedish birth-cohort sampled at birth and at 13 years of age; allergy was diagnosed at 13 years of age. Minor allele carriers of rs102275 and rs174448 (FADS gene cluster) had decreased proportions of 20:4 n-6 in cord and adolescent serum and increased proportions of 20:3 n-6 in cord serum as well as a nominally reduced risk of developing atopic eczema, but not respiratory allergy, at 13 years of age. Minor allele carriers of rs17606561 in the ELOVL2 gene had nominally decreased proportions of 20:4 n-6 in cord serum but ELOVL polymorphisms (rs2236212 and rs17606561) were not associated with allergy development. Thus, reduced capacity to desaturase n-6 PUFAs due to FADS polymorphisms was nominally associated with reduced risk for eczema development, which could indicate a pathogenic role for long-chain PUFAs in allergy development.
Visualization of unconstrained negative supercoils of DNA on polytene chromosomes of Drosophila

Bulk DNA within the eukaryotic genome is torsionarily relaxed. However, unconstrained negative supercoils of DNA have been detected in few local domains of the genome through preferential binding of psoralen. To make a genome-wide survey for such domains, we introduced biotinylated psoralen into Drosophila salivary glands and visualized it on polytene chromosomes with fluorescent streptavidin. We observed bright psoralen signals on many transcriptionally active interbands and puffs. Upon heat shock, the signals appeared on heat-shock puffs. The signals were resistant to RNase treatment but disappeared or became faint by previous nicking of DNA or inhibition of transcription with α-amanitin. These data show that transcription-coupled, unconstrained negative supercoils of DNA exist in approximately 150 loci within the interphase genome.
Variations of DNA polymerases-a and -3 during prolonged stimulation of human lymphocytes

Stimulation of human lymphocytes with phytohemagglutinin is known to induce an increase in overall DNA polymerase activity (DNA nucleotidyltransfer- ase; deoxynucleosidetriphosphate:DNA deoxynucleotidyl- transferase, EC 2.7.7.7). Previous work [Pedrali Noy, G. , Dal- pra, L. , Pedrini, A. M. , Ciarrocchi, G. , Giulotto, E. , Nuzzo, F. & Falaschi, A. (1974) Nucleic Acids Res. 1, 1183] has shown that two subsequent waves of induction of DNA polymerase can be observed in this system; a first wave occurs in parallel with the increase in DNA replication rate; a second one occurs when the DNA synthesis rate is returned to minimal lev- els; the second peak is parallel to a maximum in DNA ligase and DNase levels. In the present work we have measured the levels of the DNA polymerases-a and -, in phytohemagglutinin-stimulat- ed lymphocytes during a 12-day period; both enzymes are present at detectable levels at time zero; in correspondence to the peak of DNA synthesis rate (between the fourth and fifth day) a peak of DNA polymerase-a is observed, increas- ing by a factor of approximately 20-fold over the zero time value; subsequently, the level of
Frequency-Dependent Changes in NMDAR-Dependent Synaptic Plasticity

The NMDAR-dependent synaptic plasticity is thought to mediate several forms of learning, and can be induced by spike trains containing a small number of spikes occurring with varying rates and timing, as well as with oscillations. We computed the influence of these variables on the plasticity induced at a single NMDAR containing synapse using a reduced model that was analytically tractable, and these findings were confirmed using detailed, multi-compartment model. In addition to explaining diverse experimental results about the rate and timing dependence of synaptic plasticity, the model made several novel and testable predictions. We found that there was a preferred frequency for inducing long-term potentiation (LTP) such that higher frequency stimuli induced lesser LTP, decreasing as 1/f when the number of spikes in the stimulus was kept fixed. Among other things, the preferred frequency for inducing LTP varied as a function of the distance of the synapse from the soma. In fact, same stimulation frequencies could induce LTP or long-term depression depending on the dendritic location of the synapse. Next, we found that rhythmic stimuli induced greater plasticity then irregular stimuli. Furthermore, brief bursts of spikes significantly expanded the timing dependence of plasticity. Finally, we found that in the ∼5–15-Hz frequency range both rate- and timing-dependent plasticity mechanisms work synergistically to render the synaptic plasticity most sensitive to spike timing. These findings provide computational evidence that oscillations can have a profound influence on the plasticity of an NMDAR-dependent synapse, and show a novel role for the dendritic morphology in this process.
Crucial Role of Perfringolysin O D1 Domain in Orchestrating Structural Transitions Leading to Membrane-perforating Pores

Background: Pore formation by perfringolysin O consists of well defined stages, but the mechanism is not fully understood. Results: We mapped regions in toxin that undergo stabilization and destabilization upon oligomerization. Conclusion: Properly folded D1 orchestrates structural transitions in other domains necessary for pore formation. Significance: Study of structural changes in cytolysin domains upon binding to membrane is crucial for understanding pore formation mechanism. Perfringolysin O (PFO) is a toxic protein that binds to cholesterol-containing membranes, oligomerizes, and forms a β-barrel transmembrane pore, leading to cell lysis. Previous studies have uncovered the sequence of events in this multistage structural transition to a considerable detail, but the underlying molecular mechanisms are not yet fully understood. By measuring hydrogen-deuterium exchange patterns of peptide bond amide protons monitored by mass spectrometry (MS), we have mapped structural changes in PFO and its variant bearing a point mutation during incorporation to the lipid environment. We have defined all regions that undergo structural changes caused by the interaction with the lipid environment both in wild-type PFO, thus providing new experimental constraints for molecular modeling of the pore formation process, and in a point mutant, W165T, for which the pore formation process is known to be inefficient. We have demonstrated that point mutation W165T causes destabilization of protein solution structure, strongest for domain D1, which interrupts the pathway of structural transitions in other domains necessary for proper oligomerization in the membrane. In PFO, the strongest changes accompanying binding to the membrane focus in D1; the C-terminal part of D4; and strands β1, β4, and β5 of D3. These changes were much weaker for PFOW165Tlipo where substantial stabilization was observed only in D4 domain. In this study, the application of hydrogen-deuterium exchange analysis monitored by MS provided new insight into conformational changes of PFO associated with the membrane binding, oligomerization, and lytic pore formation.
Emerging drugs for acute and chronic heart failure: current and future developments

Heart failure continues to be a major public health issue. Although angiotensin-converting enzyme inhibitors and β-adrenergic blockers have been broadly used as evidence-based therapies in heart failure, morbidity and mortality remains high. Furthermore, treatment for acute decompensated heart failure and diastolic heart failure (or ‘heart failure with preserved ejection fraction’) is far from perfect. This review provides a broad overview of some of the novel compounds under investigation for the treatment of heart failure. Novel strategies include drugs that aim to alleviate congestion and improve hemodynamics, drugs that preserve renal function, drugs that reduce arterial and myocardial stiffness, drugs that module myocardial contractility, drugs that affect metabolic and hormonal balance, and drugs that act on existing and novel physiologic targets.
Frequency-domain homogenization for litz-wire bundles in finite element calculations

This work deals with a frequency-domain homogenization method for litz-wire bundles embedded in a finite element (FE) model. The approach consists in adopting a frequency-dependent complex reluctivity in the litz-wire bundles and a frequency-dependent complex impedance in the electrical circuit in terms of dimensionless coefficients. The litz-wire bundles become homogeneous conductors which are easy to integrate into a finite element model. The homogenization methods in previous works are also reviewed. The complex permeability achieved with our model is compared to the most accurate expression found in literature. The agreement is very good despite the different elementary cell and condition setting. Moreover, the homogenization method in this paper is validated for both 2-D and 3-D FE calculations with the translational-symmetry transformer model and the axisymmetric inductor model respectively. The reference solutions of those models are computed by finely discretizing each conductor inside the litz-wire bundle. The results of the computed resistance and inductance agree well with those computed by the reference fine model, resulting in less than 3% and 0.05% maximum errors respectively in 2-D FE model, and 4% and 1.8% respectively in 3-D FE model with several times less computational cost.