Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Sensitive CO2 Pathways and Genes Related to Carbon Uptake and Accumulation in Chlamydomonas reinhardtii through Genomic Scale Modeling and Experimental Validation

The development of microalgae sustainable applications needs better understanding of microalgae biology. Moreover, how cells coordinate their metabolism toward biomass accumulation is not fully understood. In this present study, flux balance analysis (FBA) was performed to identify sensitive metabolic pathways of Chlamydomonas reinhardtii under varied CO2 inputs. The metabolic network model of Chlamydomonas was updated based on the genome annotation data and sensitivity analysis revealed CO2 sensitive reactions. Biological experiments were performed with cells cultivated at 0.04% (air), 2.5, 5, 8, and 10% CO2 concentration under controlled conditions and cell growth profiles and biomass content were measured. Pigments, lipids, proteins, and starch were further quantified for the reference low (0.04%) and high (10%) CO2 conditions. The expression level of candidate genes of sensitive reactions was measured and validated by quantitative real time PCR. The sensitive analysis revealed mitochondrial compartment as the major affected by changes on the CO2 concentrations and glycolysis/gluconeogenesis, glyoxylate, and dicarboxylate metabolism among the affected metabolic pathways. Genes coding for glycerate kinase (GLYK), glycine cleavage system, H-protein (GCSH), NAD-dependent malate dehydrogenase (MDH3), low-CO2 inducible protein A (LCIA), carbonic anhydrase 5 (CAH5), E1 component, alpha subunit (PDC3), dual function alcohol dehydrogenase/acetaldehyde dehydrogenase (ADH1), and phosphoglucomutase (GPM2), were defined, among other genes, as sensitive nodes in the metabolic network simulations. These genes were experimentally responsive to the changes in the carbon fluxes in the system. We performed metabolomics analysis using mass spectrometry validating the modulation of carbon dioxide responsive pathways and metabolites. The changes on CO2 levels mostly affected the metabolism of amino acids found in the photorespiration pathway. Our updated metabolic network was compared to previous model and it showed more consistent results once considering the experimental data. Possible roles of the sensitive pathways in the biomass metabolism are discussed.
Master's Thesis Nr. 90 Real-time Analytics in a High Volume Event Processing System

In recent years the need to process large volumes of data in real-time was fueled by advances in the field of memory and database technologies. Increases in memory capacity and reduced latency make it possible to keep entire databases in main memory. Modern networking technologies allow to distribute in-memory databases across hundreds or even thousands of nodes and process vast amounts of data in parallel. The objective of this thesis is to design and implement a system, which can handle real-time analytical queries while being subject to updates at a high rate. Particular attention is given to address scalability, low latency and high throughput. We evaluate different architectural options and devise two variants built upon RAMCloud and the dense hash map library. Based on a detailed analysis of these approaches, we propose a columnoriented in-memory data structure and implement efficient query processing algorithms that allow the system to answer analytical queries in realtime. In order to achieve higher query throughput, we adopt the concept of shared scan and employ several query performance improvements. We further present an experimental analysis of the proposed system and show that our approach is well-suited for processing large volumes of data.
Seeking Categories in the Brain

Categorizing the objects that we see is a fundamental property of our brain and the brains of other mammals. In their enlightening Perspective, Thorpe and Fabre-Thorpe discuss exciting new findings in monkeys ( Freedman et al.) that identify neurons in the prefrontal cortex that are primarily responsible for categorizing objects.
Overexpression of tumor necrosis factor receptor-associated protein 1 (TRAP1), leads to mitochondrial aberrations in mouse fibroblast NIH/3T3 cells

Cancer cells undergo uncontrolled proliferation, and aberrant mitochondrial alterations. Tumor necrosis factor receptorassociated protein 1 (TRAP1) is a mitochondrial heat shock protein. TRAP1 mRNA is highly expressed in some cancer cell lines and tumor tissues. However, the effects of its overexpression on mitochondria are unclear. In this study, we assessed mitochondrial changes accompanying TRAP1 overexpression, in a mouse cell line, NIH/3T3. We found that overexpression of TRAP1 leads to a series of mitochondrial aberrations, including increase in basal ROS levels, and decrease in mitochondrial biogenesis, together with a decrease in peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α) mRNA levels. We also observed increased extracellular signal-regulated kinase (ERK) phosphorylation, and enhanced proliferation of TRAP1 overexpressing cells. This study suggests that overexpression of TRAP1 might be a critical link between mitochondrial disturbances and carcinogenesis. [BMB Reports 2014; 47(5): 280-285]
Palmitoleate Is a Mitogen, Formed upon Stimulation with Growth Factors, and Converted to Palmitoleoyl-phosphatidylinositol*

Background: Conflicting reports about the function of palmitoleate might depend on the formation of bioactive metabolites. Results: Palmitoleate induces cell proliferation and is formed during stimulation with growth factors and specifically incorporated into palmitoleoyl-phosphatidylinositol during de novo phosphatidylinositol biosynthesis. Conclusion: Palmitoleate or palmitoleoyl-phosphatidylinositol is proposed as mediator during cell proliferation. Significance: The study combines the mitogenic effect of palmitoleate with insights into its metabolism. Controversial correlations between biological activity and concentration of the novel lipokine palmitoleate (9Z-hexadecenoate, 16:1) might depend on the formation of an active 16:1 metabolite. For its identification, we analyzed the glycerophospholipid composition of mouse Swiss 3T3 fibroblasts in response to 16:1 using LC-MS/MS. 16:1 was either supplemented to the cell culture medium or endogenously formed when cells were stimulated with insulin or growth factors as suggested by the enhanced mRNA expression of 16:1-biosynthetic enzymes. The proportion of 1-acyl-2–16:1-sn-phosphatidylinositol (16:1-PI) was time-dependently and specifically increased relative to other glycerophospholipids under both conditions and correlated with the proliferation of fatty acid (16:1, palmitate, oleate, or arachidonate)-supplemented cells. Accordingly, cell proliferation was impaired by blocking 16:1 biosynthesis using the selective stearoyl-CoA desaturase-1 inhibitor CAY10566 and restored by supplementation of 16:1. The accumulation of 16:1-PI occurred throughout cellular compartments and within diverse mouse cell lines (Swiss 3T3, NIH-3T3, and 3T3-L1 cells). To elucidate further whether 16:1-PI is formed through the de novo or remodeling pathway of PI biosynthesis, phosphatidate levels and lyso-PI-acyltransferase activities were analyzed as respective markers. The proportion of 16:1-phosphatidate was significantly increased by insulin and growth factors, whereas lyso-PI-acyltransferases showed negligible activity for 16:1-coenzyme A. The relevance of the de novo pathway for 16:1-PI biosynthesis is supported further by the comparable incorporation rate of deuterium-labeled 16:1 and tritium-labeled inositol into PI for growth factor-stimulated cells. In conclusion, we identified 16:1 or 16:1-PI as mitogen whose biosynthesis is induced by growth factors.
Colorectal serrated adenocarcinoma

Colorectal cancer (CRC) ranks among the three most common cancers in terms of both cancer incidence and cancer‐related deaths in most Western countries. Serrated adenocarcinoma is a recently described, distinct variant of CRC, accounting for about 7.5% of all CRCs and up to 17.5% of most proximal CRCs. It has been postulated that about 10–15% of sporadic CRCs would have their origin in serrated polyps that harbour a significant malignant potential. These lesions include hyperplastic‐type aberrant crypt foci, hyperplastic polyps, sessile serrated adenomas, admixed polyps and serrated adenomas, and constitute the so‐called ‘serrated pathway’, which is distinct from both the conventional adenoma–carcinoma pathway and the mutator pathway of hereditary non‐polyposis CRC and is characterized by early involvement of oncogenic BRAF mutations, excess CpG island methylation (CIM) and subsequent low‐ or high‐level DNA microsatellite instability (MSI). Methylation of hMLH1 is likely to explain the increased frequency of high‐level MSI (16%) and methylation of MGMT is postulated to explain the low‐level MSI (29%) in serrated adenocarcinomas. Reproducible histopathological criteria for serrated adenocarcinoma have recently been established and they have been qualified by DNA expression analysis for 7928 genes, showing clustering of serrated adenocarcinomas into a molecular entity apart from conventional adenocarcinoma, and representing with distinct down‐regulation of EPHB2, PTCH and up‐regulation of HIF1α.
Computing variance for interval data is NP-hard

When we have only interval ranges [<i>x<inf>i</inf>,</i> <i>x<inf>i</inf></i>] of sample values <i>x</i><inf>1</inf>,…, <i>x<inf>n</inf>,</i> what is the interval [<i>V, V</i>] of possible values for the variance <i>V</i> of these values? We prove that the problem of computing the upper bound <i>V</i> is NP-hard. We provide a feasible (quadratic time) algorithm for computing the lower bound <i>V</i> on the variance of interval data. We also provide a feasible algorithm that computes <i>V</i> under reasonable easily verifiable conditions.
Analysis of Antibiotic Resistance Genes in Multidrug-Resistant Acinetobacter sp. Isolates from Military and Civilian Patients Treated at the Walter Reed Army Medical Center

ABSTRACT Military medical facilities treating patients injured in Iraq and Afghanistan have identified a large number of multidrug-resistant (MDR) Acinetobacter baumannii isolates. In order to anticipate the impact of these pathogens on patient care, we analyzed the antibiotic resistance genes responsible for the MDR phenotype in Acinetobacter sp. isolates collected from patients at the Walter Reed Army Medical Center (WRAMC). Susceptibility testing, PCR amplification of the genetic determinants of resistance, and clonality were determined. Seventy-five unique patient isolates were included in this study: 53% were from bloodstream infections, 89% were resistant to at least three classes of antibiotics, and 15% were resistant to all nine antibiotics tested. Thirty-seven percent of the isolates were recovered from patients nosocomially infected or colonized at the WRAMC. Sixteen unique resistance genes or gene families and four mobile genetic elements were detected. In addition, this is the first report of blaOXA-58-like and blaPER-like genes in the U.S. MDR A. baumannii isolates with at least eight identified resistance determinants were recovered from 49 of the 75 patients. Molecular typing revealed multiple clones, with eight major clonal types being nosocomially acquired and with more than 60% of the isolates being related to three pan-European types. This report gives a “snapshot” of the complex genetic background responsible for antimicrobial resistance in Acinetobacter spp. from the WRAMC. Identifying genes associated with the MDR phenotype and defining patterns of transmission serve as a starting point for devising strategies to limit the clinical impact of these serious infections.
Planum temporale asymmetry in developmental dyslexia: Revisiting an old question

Among the various asymmetrical structures of the human brain, the planum temporale, an anatomical region associated with a variety of auditory and language‐related processes, has received particular attention. While its surface area has been shown to be greater in the left hemisphere compared to the right in about two‐thirds of the general population, altered patterns of asymmetry were revealed by post mortem analyses in individuals with developmental dyslexia. These findings have been inconsistently replicated in magnetic resonance imaging studies of this disorder. In this report, we attempt to resolve past inconsistencies by analyzing the T1‐weighted MR images of 81 children (mean age: 11 years, sd: 17 months), including 46 control (25 boys) and 35 dyslexic children (20 boys). We manually outlined Heschl's gyri, the planum temporale and the posterior rami of the Sylvian fissure on participants' brain images, using the same anatomical criteria as in post mortem studies. Results revealed an altered pattern of asymmetry of the planum temporale surface area in dyslexic boys only, with a greater proportion of rightward asymmetrical cases among dyslexic boys compared to control boys. Additionally, analyses of cortical thickness showed no asymmetry differences between groups for any of the regions of interest. Finally, a greater number of Heschl's gyrus full duplications emerged for the right hemisphere of dyslexic boys compared to controls. The present findings confirm and extend early post mortem observations. They also stress the importance of taking gender into account in studies of developmental dyslexia. Hum Brain Mapp 35:5717–5735, 2014. © 2014 Wiley Periodicals, Inc.
Cytochrome oxidase 1 gene sequence analysis in six flatfish species (Teleostei, Pleuronectidae) of Far East Russia with inferences in phylogeny and taxonomy

Mitochondrial DNA at the cytochrome oxidase 1 (Co-1) gene region was sequenced for six flatfish species (in total, 11 sequences of at least 539 base pairs) from the Far East of Russia and compared with other sequences of Pleuronectiformes, comprising altogether 26 flatfish sequences and two outgroup sequences (Perciformes). An analysis of the protein-coding Co-1 gene revealed a statistically substantiated bias in (T+C):(A+G) content, supporting earlier findings. Average scores of the p-distances for different scales of the evolutionary history at the Co-1 gene revealed a clear pattern of increased nucleotide diversity at four different levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intra-order. Scores of average p-distances of the four categories of comparison in flatfishes were (1) 0.17 ± 0.09%, (2) 10.60 ± 1.57%, (3) 12.40 ± 0.27%, and (4) 19.93 ± 0.05%, respectively (mean ± standard error). These data jointly with current knowledge support the concept that speciation in the order Pleuronectiformes mostly follows a geographic mode through accumulation of numerous small genetic changes over a long period of time. A phylogenetic tree for 26 sequences of flatfishes and two other fishes belonging to ray-finned fishes (Actinopterigii) was developed using the Co-1 gene and four different analytical approaches: neighbour-joining, Bayesian (BA), maximum parsimony (MP), and maximum likelihood. The analysis revealed a monophyletic origin for the representatives of Pleuronectidae, which is the principal flatfish family investigated (73–100% support level in our MP and BA analyses). According to the current and literary data, the monophyletic origin for the six compared flatfish families was well supported. Species identification on a per-individual basis (barcoding tagging) was high.
Towards Trustworthy Collaborative Editing

Real-time collaborative editing applications are drastically different from typical client–server applications in that every participant has a copy of the shared document. In this type of environment, each participant acts as both a client and a server replica. In this article, we elaborate on how to adapt Byzantine fault tolerance (BFT) mechanisms to enhance the trustworthiness of such applications. It is apparent that traditional BFT algorithms cannot be used directly because it would dictate that all updates submitted by participants be applied sequentially, which would defeat the purpose of collaborative editing. The goal of this study is to design and implement an efficient BFT solution by exploiting the application semantics and by doing a threat analysis of these types of applications. Our solution can be considered as a form of optimistic BFT in that local states maintained by each participant may diverge temporarily. The states of the participants are made consistent with each other by a periodic synchronization mechanism.
Dip Pen Nanolithography Stamp Tip

A simple and novel method for fabricating poly(dimethylsiloxane) (PDMS)-coated dip pen nanolithography (DPN) stamp tips was developed. These kinds of tips absorb chemicals (“inks”) easily and allow one to generate molecule-based patterns in a conventional DPN experiment. The generated patterns also can be imaged with the same DPN stamp tips. This method is a type of scanning probe contact printing but provides the ability to generate higher resolution structures than one can obtain with the conventional technique, which thus far has only enabled micron scale patterning. Sub-100 nm resolution patterning with 16-mercaptohexadecanoic acid (MHA) as an ink is demonstrated with these novel tips and is comparable to what one can obtain with a conventional ink-coated Si3N4 probe tip. Proof-of-concept is also demonstrated with 1-octadecanethiol (ODT), dendrimers and cystamine as inks.
Niche Segregation between Wild and Domestic Herbivores in Chilean Patagonia

Competition arises when two co-occuring species share a limiting resource. Potential for competition is higher when species have coexisted for a short time, as it is the case for herbivores and livestock introduced in natural systems. Sheep, introduced in the late 19th century in Patagonia, bear a great resemblance in size and diet to the guanaco, the main native herbivore in Patagonia. In such circumstances, it could be expected that the two species compete and one of them could be displaced. We investigated spatial overlap and habitat selection by coexisting sheep and guanaco in winter and in summer. Additionally, we studied habitat selection of the guanaco in a control situation free from sheep, both in summer and winter. We also determined overlap between species in areas with different intensity of use (named preferred and marginal areas) in order to further detect the potential level of competition in the case of overlapping. Guanaco and sheep showed significantly different habitat preferences through all seasons, in spite of their spatial overlap at landscape scale. Additionally, the habitat used by guanaco was similar regardless of the presence or absence of livestock, which further indicates that sheep is not displacing guanaco where they coexist. These results suggest that habitat segregation between guanaco and sheep is due to a differential habitat selection and not to a competitive displacement process. Therefore, the potential for competition is considered low, contrary to what has been previously observed, although this could be a density-dependent result.
Counting Independent Sets in Hypergraphs

Let G be a triangle-free graph with n vertices and average degree t. We show that G contains at least ${\exp\biggl({1-n^{-1/12})\frac{1}{2}\frac{n}{t}\ln t} \biggl(\frac{1}{2}\ln t-1\biggr)\biggr)}$ independent sets. This improves a recent result of the first and third authors [8]. In particular, it implies that as n → ∞, every triangle-free graph on n vertices has at least ${e^{(c_1-o(1)) \sqrt{n} \ln n}}$ independent sets, where $c_1 = \sqrt{\ln 2}/4 = 0.208138 \ldots$. Further, we show that for all n, there exists a triangle-free graph with n vertices which has at most ${e^{(c_2+o(1))\sqrt{n}\ln n}}$ independent sets, where $c_2 = 2\sqrt{\ln 2} = 1.665109 \ldots$. This disproves a conjecture from [8]. Let H be a (k+1)-uniform linear hypergraph with n vertices and average degree t. We also show that there exists a constant ck such that the number of independent sets in H is at least ${\exp\biggl({c_{k} \frac{n}{t^{1/k}}\ln^{1+1/k}{t}\biggr})}. $ This is tight apart from the constant ck and generalizes a result of Duke, Lefmann and Rödl [9], which guarantees the existence of an independent set of size $\Omega\biggl(\frac{n}{t^{1/k}} \ln^{1/k}t\biggr). $ Both of our lower bounds follow from a more general statement, which applies to hereditary properties of hypergraphs.
CarSafe app: alerting drowsy and distracted drivers using dual cameras on smartphones

We present CarSafe, the first driver safety application that uses dual cameras on smartphones to detect and alert drivers to dangerous driving conditions. CarSafe fuses events detected from cameras and readings from embedded sensors on the phone -- such as the GPS, accelerometer and gyroscope -- to detect and alert the driver of dangerous driving behavior in and outside of the car. Results from a 12-driver field trial show CarSafe can infer five of the most commonly occurring dangerous driving conditions with an overall precision and recall of 83% and 75%, respectively.
Increase in the concentration of carbon 18 monounsaturated fatty acids in the liver with hepatitis C: analysis in transgenic mice and humans.

Steatosis is one of the histologic characteristics of chronic hepatitis C and is well reproduced in a transgenic mouse model for hepatocellular carcinoma (HCC) in which the core protein of hepatitis C virus (HCV) plays a pivotal role in inducing steatosis and HCC. In the present study, the lipid composition in the liver of the HCV core gene transgenic mice as well as in those of chronic hepatitis C patients was determined. The concentration of carbon 18 monounsaturated (C18:1) fatty acids, such as oleic and vaccenic acids, which are known to increase membrane fluidity leading to higher cell division rates, significantly increased in the livers of transgenic mice compared to nontransgenic control mice. The concentration of C18:1 fatty acids also significantly increased in the livers of chronic hepatitis C patients compared to subjects without HCV infection. These results suggest that HCV may affect a specific pathway in the lipid metabolism and cause steatosis in the liver.
Corrosion behavior of friction stir welded lap joints of AA6061-T6 aluminum alloy

In this work, the corrosion behaviors of friction-stir lap welding of 6061-T6 Al-alloy are studied. The friction-stir lap welding was performed under different welding conditions (rotation speed and welding speed). The corrosion behavior of the parent alloy, the weld nugget zone (WNZ), and the heat affected zone (HAZ) of each welded sample working as an electrode, were investigated by the Tafel polarization test in 3.5 wt. (%) NaCl at ambient temperature. The morphology of the corroded surface of each region was analyzed by scanning electron microscopy together with energy dispersive spectroscopy (SEM-EDS). The results showed that the corrosion resistance of the parent alloy was better than the WNZ and the HAZ in both welding conditions. Localized pit dissolution and intergranular corrosion were the dominant corrosion types observed in the parent alloy, WNZ, and HAZ. The parent alloy, WNZ, and HAZ exhibited similar corrosion potentials (Ecorr) after T6 heat treatment. This treatment had a better effect on the corrosion resistance of the welded regions than the parent alloy.