Miracle-dz/UniFAR-FTUs huggingface dataset:
Telomere‐led bouquet formation facilitates homologous chromosome pairing and restricts ectopic interaction in fission yeast meiosis

A polarized chromosomal arrangement with clustered telomeres in a meiotic prophase nucleus is often called bouquet and is thought to be important for the pairing of homologous chromosomes. Fluorescence in situ hybridization in fission yeast indicated that chromosomal loci are positioned in an ordered manner as anticipated from the bouquet arrangement. Blocking the formation of the telomere cluster with the kms1 mutation created a disorganized chromosomal arrangement, not only for the regions proximal to the telomere but also for interstitial regions. The kms1 mutation also affected the positioning of a linear minichromosome. Consistent with this cytological observation, the frequency of ectopic homologous recombination between a linear minichromosome and a normal chromosome increased in the kms1 background. Intragenic recombination between allelic loci is reduced in the kms1 mutant, but those between non‐allelic loci are unaffected or slightly increased. Thus, telomere‐led chromosome organization facilitates homologous pairing and also restricts irregular chromosome pairing during meiosis.
Discrete stochastic simulation of cell signaling: comparison of computational tools

Several stochastic simulation tools have been developed recently for cell signaling. A comparative evaluation of the stochastic simulation tools is needed to highlight the current state of the development. In our study, we have chosen to evaluate three stochastic simulation tools: Dizzy, Systems Biology Toolbox, and Copasi, using our own MATLABreg implementation as a benchmark. The Gillespie stochastic simulation algorithm is used in all tests. With all the tools, we are able to simulate stochastically the behavior of the selected test case and to produce similar results as our own MATLABreg implementation. However, it is not possible to use time-dependent inputs in stochastic simulations in Systems Biology Toolbox and Copasi. The present study is one of the first evaluations of stochastic simulation tools for realistic signal transduction pathways
Effects of Climatic Change on Temperature and Thermal Structure of a Mountain Reservoir

A 35‐year monitoring record for the water column of Lake Dillon, a reservoir of the southern Rocky Mountains, shows near‐surface warming of 0.76 °C/decade and warming at all greater depths (55 m); warming was progressively smaller with depth. Annual heat budget of the lake increased (67 cal·cm−2·year−1; 0.089 W/m2) as did Schmidt stability (41%). The mixed layer was affected by climatic conditions at the high elevation of the lake (2,750 m above mean sea level); heat fluxes were high during both the seasonal warming and cooling. Density gradients below the mixed layer were weak because of low water temperatures associated with high elevation. Annual cooling of the mixed layer was rapid following a brief initial stabilization and showed high interannual variability across years for a given month, which obscured any trend in mixed layer thickness that might have been caused by heat accumulation. The hypolimnion was warmed by advective heat exchange from tributary inflow and deep water withdrawal, not by carryover of fall or spring warming; advective warming by tributaries can be expected in many reservoirs.
Paternal Mitochondrial DNA Transmission During Nonhuman Primate Nuclear Transfer

Offspring produced by nuclear transfer (NT) have identical nuclear DNA (nDNA). However, mitochondrial DNA (mtDNA) inheritance could vary considerably. In sheep, homoplasmy is maintained since mtDNA is transmitted from the oocyte (recipient) only. In contrast, cattle are heteroplasmic, harboring a predominance of recipient mtDNA along with varying levels of donor mtDNA. We show that the two nonhuman primate Macaca mulatta offspring born by NT have mtDNA from three sources: (1) maternal mtDNA from the recipient egg, (2) maternal mtDNA from the egg contributing to the donor blastomere, and (3) paternal mtDNA from the sperm that fertilized the egg from which the donor blastomere was isolated. The introduction of foreign mtDNA into reconstructed recipient eggs has also been demonstrated in mice through pronuclear injection and in humans through cytoplasmic transfer. The mitochondrial triplasmy following M. mulatta NT reported here forces concerns regarding the parental origins of mtDNA in clinically reconstructed eggs. In addition, mtDNA heteroplasmy might result in the embryonic stem cell lines generated for experimental and therapeutic purposes (“therapeutic cloning”).
Forms and vertical distributions of soil phosphorus in newly formed coastal wetlands in the Yellow River Delta estuary

To study the forms and vertical distributions of soil phosphorus (P) in a newly formed coastal wetland in the Yellow River Delta estuary, China, two transects from the Yellow River bank to the bare beach that encompassed a variety of vegetation covers were selected for soil sampling and field monitoring. A modified sequential fractionation method was used to partition the soil P, and the related properties were measured. The soils in this newly formed estuarine coastal wetland, only covered by salt‐tolerant plant communities, are strongly alkaline (pH 8.4–9.2) with high soil salinity (mean, 6.23‰). The content of total P (Pt) ranged from 548.3 to 728.5 mg kg−1 in these soils. Dil.HCl‐Pi (extracted with 1 M HCl) was the highest P fraction (mean, 58.1–72.8%), whereas NaHCO3‐Pi was the lowest fraction (mean, 0.4–1.7%) of all the P forms. Vertical distributions showed a surface accumulation of Resin‐P. Resin‐P, NaHCO3‐Pi, NaOH‐Pi, and Conc.HCl‐Pi (extracted with 11.3 M HCl) were positively or negatively correlated with some properties. Attributed to the spatial deposition and hydrology, Dil.HCl‐Pi presented a poor correlation with Ca. The results also showed some clear differences in the P forms and P availability among vegetation covers. The vegetation cover could modify the soil quality, and Suaeda heteroptera, as the pioneer plant community species, significantly enhanced the freely exchangeable Pi and increased P availability, providing important ideas for salt‐soil sustainable use.
Sirt3 Protects Cortical Neurons against Oxidative Stress via Regulating Mitochondrial Ca2+ and Mitochondrial Biogenesis

Oxidative stress is a well-established event in the pathology of several neurobiological diseases. Sirt3 is a nicotinamide adenine nucleotide (NAD+)-dependent protein deacetylase that regulates mitochondrial function and metabolism in response to caloric restriction and stress. This study aims to investigate the role of Sirt3 in H2O2 induced oxidative neuronal injury in primary cultured rat cortical neurons. We found that H2O2 treatment significantly increased the expression of Sirt3 in a time-dependent manner at both mRNA and protein levels. Knockdown of Sirt3 with a specific small interfering RNA (siRNA) exacerbated H2O2-induced neuronal injury, whereas overexpression of Sirt3 by lentivirus transfection inhibited H2O2-induced neuronal damage reduced the generation of reactive oxygen species (ROS), and increased the activities of endogenous antioxidant enzymes. In addition, the intra-mitochondrial Ca2+ overload, but not cytosolic Ca2+ increase after H2O2 treatment, was strongly attenuated after Sirt3 overexpression. Overexpression of Sirt3 also increased the content of mitochondrial DNA (mtDNA) and the expression of mitochondrial biogenesis related transcription factors. All these results suggest that Sirt3 acts as a prosurvival factor playing an essential role to protect cortical neurons under H2O2 induced oxidative stress, possibly through regulating mitochondrial Ca2+ homeostasis and mitochondrial biogenesis.
Overexpression and clinical significance of MYC-associated zinc finger protein in pancreatic carcinoma

This study aimed to investigate the expression and clinical significance of MYC-associated zinc finger protein (MAZ) in pancreatic carcinoma (PC), and the biological functions of MAZ in PC cells. MAZ expression was detected in 57 PC tissues and 41 paired adjacent nontumor tissues by immunohistochemistry. Compared to the expression in adjacent nontumor tissues, MAZ was significantly higher expressed in PC tissues (P<0.0001). In addition, MAZ expression had a significant correlation with certain clinical characteristics of PC patients, such as age, tumor diameter, tumor number, and the serum level of CA199 (P<0.05). The survival analysis showed that the survival time of PC patients with high expression of MAZ was significantly lower than patients with low expression of MAZ (P=0.0365). After MAZ was knocked down in PANC-1 cells by RNA interference, the cells’ ability to proliferate, invade, and migrate was decreased significantly (P<0.01). Moreover, MAZ expression was found to be associated with Ki-67, a cell proliferation marker, in PC tissues, further supporting the idea that MAZ promotes PC cell proliferation. Our study clarifies an oncogenic role of MAZ in pathogenesis of PC and provides MAZ as a biomarker in the treatment and prognosis of PC.
Characterizing the Community Structure of Complex Networks

Background Community structure is one of the key properties of complex networks and plays a crucial role in their topology and function. While an impressive amount of work has been done on the issue of community detection, very little attention has been so far devoted to the investigation of communities in real networks. Methodology/Principal Findings We present a systematic empirical analysis of the statistical properties of communities in large information, communication, technological, biological, and social networks. We find that the mesoscopic organization of networks of the same category is remarkably similar. This is reflected in several characteristics of community structure, which can be used as “fingerprints” of specific network categories. While community size distributions are always broad, certain categories of networks consist mainly of tree-like communities, while others have denser modules. Average path lengths within communities initially grow logarithmically with community size, but the growth saturates or slows down for communities larger than a characteristic size. This behaviour is related to the presence of hubs within communities, whose roles differ across categories. Also the community embeddedness of nodes, measured in terms of the fraction of links within their communities, has a characteristic distribution for each category. Conclusions/Significance Our findings, verified by the use of two fundamentally different community detection methods, allow for a classification of real networks and pave the way to a realistic modelling of networks' evolution.
Legalization algorithm for multiple-row height standard cell design

Typical standard cell placement algorithms assume that all cells are of the same height such that cells can be aligned along the placement rows. However, modern standard cell designs are getting more complicated and multiple-row height cell becomes more common. With multiple-row height cells, placement of cells are not independent among different rows. It turns out that most of the commonly used detailed placement and legalization techniques cannot be extended easily to handle the problem. We propose a novel algorithm in handling legalization of placement involving multiple-row height cells. The algorithm can efficiently legalize a local region of cells with various heights, which is especially useful for local cell movement, cell sizing, and buffer insertion. Experiments on the application of the technique in detailed placement show that our approach can effectively and efficiently legalize global placement results and obtain significant improvement in the objective function.
Idiopathic pulmonary fibrosis: lessons from clinical trials over the past 25 years

Idiopathic pulmonary fibrosis (IPF) is a progressive and ultimately fatal disease. A major breakthrough in treatment came when, after decades of clinical trials which failed to identify an efficacious treatment regimen, two therapies were successful in Phase-III trials. The advent of these therapies, nintedanib and pirfenidone, meant that for the first time IPF patients had two treatment options that could reduce disease progression. This review summarises the key lessons to be obtained from the clinical trials that led to the current international clinical practice guidelines for the treatment of IPF and provides insights for the design of future clinical trials that are needed if we are to improve outcomes that are clinically meaningful to IPF patients. Clinical trials in IPF have transformed our understanding of how this devastating disease should be treated http://ow.ly/47lM30eX5Pr
Effect of cow dung and variety on the growth and yield of Okra (Abelmoschus esculentus (L.)

A trial to investigate the effect of cow dung and inorganic fertilizer on the growth and yield of Okra (Abelmoschus esculentus) was conducted in the Teaching and Research Farm of Ibrahim Badamsi Babangida University during the 2011 and 2012 cropping seasons. The trial was a factorial experiment consisting of two varieties of Okra (NHe47-4 and LD88-1) and four levels of cow dung (0, 5 10 and 15 tha-1). The inorganic fertilizer was applied at rate of 200kg ha-1. The experiment was fitted into randomized complete block design (RCBD). Cow dung applied at 20 t ha-1 and inorganic fertilizer significantly produced taller plants, more leaves and more fruits. Non application of fertilizer significantly delayed flowering. In 2011, cow dung at 20 t ha-1 and inorganic fertilizer statistically gave similar fruit weight which was significantly higher than other treatments. The highest fruit weight in 2012 was obtained with cow dung at 20 t ha-1. The varietal difference was not significant in most of the parameters measured
Pregnancy spacing and maternal morbidity in Matlab, Bangladesh.

OBJECTIVE The study examines the relationship between pregnancy spacing and seven measures of maternal morbidity in Matlab, Bangladesh. METHOD The study analyzes maternal morbidity data on 11,122 women who visited a health center during their third trimester of pregnancy between 1996 and 2002. Adjusted odds ratios were obtained through logistic regression analysis to assess the effects of pregnancy intervals of differing lengths while holding constant other influences (six variables) on maternal morbidity. RESULTS After controlling these variables, pre-eclampsia and high blood pressure are significantly more likely for women with preceding inter-pregnancy intervals of less than 6 months or 75 months or more compared to those with intervals of 27-50 months. Premature rupture of membranes is significantly more likely following inter-pregnancy intervals of 6-14 months, and edema is significantly more likely following inter-pregnancy intervals over 50 months. CONCLUSION Short and long inter-pregnancy intervals are associated with increased incidence of some maternal morbidities.
Energy expenditure and substrate oxidation in patients with cirrhosis: The impact of cause, clinical staging and nutritional state

Many clinicians subjectively feel that cirrhotic patients frequently have clinical signs of hypermetabolism. However, it is unknown whether hypermetabolism is a constant feature of chronic liver disease, corresponds to liver destruction and repair or is of prognostic value. This article is about resting energy expenditure and substrate oxidation rates in 123 patients with biopsy‐proven cirrhosis differing with respect to cause, duration of the disease, biochemical parameters of parenchymal cell damage, cholestasis, liver function, number of complications, clinical staging and nutritional state.
Predicting students' final exam scores from their course activities

A common approach to the problem of predicting students' exam scores has been to base this prediction on the previous educational history of students. In this paper, we present a model that bases this prediction on students' performance on several tasks assigned throughout the duration of the course. In order to build our prediction model, we use data from a semi-automated peer-assessment system implemented in two undergraduate-level computer science courses, where students ask questions about topics discussed in class, answer questions from their peers, and rate answers provided by their peers. We then construct features that are used to build several multiple linear regression models. We use the Root Mean Squared Error (RMSE) of the prediction models to evaluate their performance. Our final model, which has recorded an RMSE of 2.93 for one course and 3.44 for another on predicting grades on a scale of 18 to 30, is built using 14 features that capture various activities of students. Our work has possible implications in the MOOC arena and in similar online course administration systems.
The Neurotropic Parasite Toxoplasma Gondii Increases Dopamine Metabolism

The highly prevalent parasite Toxoplasma gondii manipulates its host's behavior. In infected rodents, the behavioral changes increase the likelihood that the parasite will be transmitted back to its definitive cat host, an essential step in completion of the parasite's life cycle. The mechanism(s) responsible for behavioral changes in the host is unknown but two lines of published evidence suggest that the parasite alters neurotransmitter signal transduction: the disruption of the parasite-induced behavioral changes with medications used to treat psychiatric disease (specifically dopamine antagonists) and identification of a tyrosine hydroxylase encoded in the parasite genome. In this study, infection of mammalian dopaminergic cells with T. gondii enhanced the levels of K+-induced release of dopamine several-fold, with a direct correlation between the number of infected cells and the quantity of dopamine released. Immunostaining brain sections of infected mice with dopamine antibody showed intense staining of encysted parasites. Based on these analyses, T. gondii orchestrates a significant increase in dopamine metabolism in neural cells. Tyrosine hydroxylase, the rate-limiting enzyme for dopamine synthesis, was also found in intracellular tissue cysts in brain tissue with antibodies specific for the parasite-encoded tyrosine hydroxylase. These observations provide a mechanism for parasite-induced behavioral changes. The observed effects on dopamine metabolism could also be relevant in interpreting reports of psychobehavioral changes in toxoplasmosis-infected humans.
ISDL: An Instruction Set Description Language For Retargetability

We present the Instruction Set Description Language,ISDL, a machine description language used to describetarget architectures to a retargetable compiler. The featuresand flexibility of ISDL enable the description of vastly differentarchitectures, in particular VLIW architectures. ISDL explicitlysupports constraints that define valid operation groupingswithin an instruction, increasing the range of specifiable architectures.We have written a tool that, given an ISDL descriptionof a processor, automatically generates an assembler forit. Ongoing work includes the development of an automaticcode-generator generator.
Warped Higgsless Models with IR--Brane Kinetic Terms

We examine a warped Higgsless $SU(2)_L\times SU(2)_R\times U(1)_{B-L}$ model in 5--$d$ with IR(TeV)--brane kinetic terms. It is shown that adding a brane term for the $U(1)_{B-L}$ gauge field does not affect the scale ($\sim 2-3$ TeV) where perturbative unitarity in $W_L^+ W_L^- \to W_L^+ W_L^-$ is violated. This term could, however, enhance the agreement of the model with the precision electroweak data. In contrast, the inclusion of a kinetic term corresponding to the $SU(2)_D$ custodial symmetry of the theory delays the unitarity violation in $W_L^\pm$ scattering to energy scales of $\sim 6-7$ TeV for a significant fraction of the parameter space. This is about a factor of 4 improvement compared to the corresponding scale of unitarity violation in the Standard Model without a Higgs. We also show that null searches for extra gauge bosons at the Tevatron and for contact interactions at LEP II place non-trivial bounds on the size of the IR-brane terms.
Improvement in Stroke Mortality in Canada and the United States, 1990 to 2002

Background— In the United States and Canada, folic acid fortification of enriched grain products was fully implemented by 1998. The resulting population-wide reduction in blood homocysteine concentrations might be expected to reduce stroke mortality if high homocysteine levels are an independent risk factor for stroke. Methods and Results— In this population-based cohort study with quasi-experimental intervention, we used segmented log-linear regression to evaluate trends in stroke-related mortality before and after folic acid fortification in the United States and Canada and, as a comparison, during the same period in England and Wales, where fortification is not required. Average blood folate concentrations increased and homocysteine concentrations decreased in the United States after fortification. The ongoing decline in stroke mortality observed in the United States between 1990 and 1997 accelerated in 1998 to 2002 in nearly all population strata, with an overall change from −0.3% (95% CI, −0.7 to 0.08) to −2.9 (95% CI, −3.5 to −2.3) per year (P=0.0005). Sensitivity analyses indicate that changes in other major recognized risk factors are unlikely to account for the reduced number of stroke-related deaths in the United States. The fall in stroke mortality in Canada averaged −1.0% (95% CI, −1.4 to −0.6) per year from 1990 to 1997 and accelerated to −5.4% (95% CI, −6.0 to −4.7) per year in 1998 to 2002 (P≤0.0001). In contrast, the decline in stroke mortality in England and Wales did not change significantly between 1990 and 2002. Conclusions— The improvement in stroke mortality observed after folic acid fortification in the United States and Canada but not in England and Wales is consistent with the hypothesis that folic acid fortification helps to reduce deaths from stroke.
Noncanonical Notch Signaling Modulates Cytokine Responses of Dendritic Cells to Inflammatory Stimuli

Dendritic cell (DC)-derived cytokines play a key role in specifying adaptive immune responses tailored to the type of pathogen encountered and the local tissue environment. However, little is known about how DCs perceive the local environment. We investigated whether endogenous Notch signaling could affect DC responses to pathogenic stimuli. We demonstrate that concurrent Notch and TLR stimulation results in a unique cytokine profile in mouse bone-marrow derived DCs characterized by enhanced IL-10 and IL-2, and reduced IL-12 expression compared with TLR ligation alone. Unexpectedly, modulation of cytokine production occurred through a noncanonical Notch signaling pathway, independent of γ-secretase activity. Modulation required de novo protein synthesis, and PI3K, JNK, and ERK activity were necessary for enhanced IL-2 expression, whereas modulation of IL-10 required only PI3K activity. Further, we show that this γ-secretase–independent Notch pathway can induce PI3K activity. In contrast, expression of the canonical Notch target gene Hes1 was suppressed in DCs stimulated with Notch and TLR ligands simultaneously. Thus, our data suggest that Notch acts as an endogenous signal that modulates cytokine expression of DCs through a noncanonical pathway and therefore has the potential to tailor the subsequent adaptive immune response in a tissue- and/or stage-dependent manner.