Miracle-dz/UniFAR-FTUs huggingface dataset:
Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines

We describe open, reproducible pipelines that create an integrated genomic profile of a cancer and use the profile to find mutations associated with disease and potentially useful drugs. These pipelines analyze high‐throughput cancer exome and transcriptome sequence data together with public databases to find relevant mutations and drugs. The three pipelines that we have developed are: (1) an exome analysis pipeline, which uses whole or targeted tumor exome sequence data to produce a list of putative variants (no matched normal data are needed); (2) a transcriptome analysis pipeline that processes whole tumor transcriptome sequence (RNA‐seq) data to compute gene expression and find potential gene fusions; and (3) an integrated variant analysis pipeline that uses the tumor variants from the exome pipeline and tumor gene expression from the transcriptome pipeline to identify deleterious and druggable mutations in all genes and in highly expressed genes. These pipelines are integrated into the popular Web platform Galaxy at http://usegalaxy.org/cancer to make them accessible and reproducible, thereby providing an approach for doing standardized, distributed analyses in clinical studies. We have used our pipeline to identify similarities and differences between pancreatic adenocarcinoma cancer cell lines and primary tumors.
Bioethanol production from rice straw residues

A rice straw - cellulose utilizing mold was isolated from rotted rice straw residues. The efficient rice straw degrading microorganism was identified as Trichoderma reesei. The results showed that different carbon sources in liquid culture such as rice straw, carboxymethyl cellulose, filter paper, sugar cane bagasse, cotton stalk and banana stalk induced T. reesei cellulase production whereas glucose or Potato Dextrose repressed the synthesis of cellulase. T. reesei cellulase was produced by the solid state culture on rice straw medium. The optimal pH and temperature for T. reesei cellulase production were 6 and 25 °C, respectively. Rice straw exhibited different susceptibilities towards cellulase to their conversion to reducing sugars. The present study showed also that, the general trend of rice straw bioconversion with cellulase was more than the general trend by T. reesei. This enzyme effectively led to enzymatic conversion of acid, alkali and ultrasonic pretreated cellulose from rice straw into glucose, followed by fermentation into ethanol. The combined method of acid pretreatment with ultrasound and subsequent enzyme treatment resulted the highest conversion of lignocellulose in rice straw to sugar and consequently, highest ethanol concentration after 7 days fermentation with S. cerevisae yeast. The ethanol yield in this study was about 10 and 11 g.L−1.
Rearrangement of the transcription factor gene CHOP in myxoid liposarcomas with t(12;16)(q13;p11)

Most myxoid liposarcomas (MLS) are characterized cytogenetically by a t(12; 16)(q13;p11). It is reasonable to assume that this translocation corresponds to the consistent rearrangement of one or two genes in 12q 13 and/or 16p11, and that the loci thus affected are important in the normal control of fat cell differentiation and proliferation. We have used Southern blot technique to test whether a gene of the CCAAT/enhancer binding protein (C/EBP) family, CHOP, which maps to 12q13 and is assumed to be involved in adipocyte differentiation, could be the 12q gene in question. Using a cDNA probe that spans the CHOP coding region, we detected one rearranged and one wild type allele in nine of nine MLS with t(l2;l6). Using PCR generated, site‐specific probes corresponding to the non‐coding exons 1 and 2 and intron 2 of CHOP, rearrangements in five of seven tumors mapped to the 2.4 and 1.6 kbp Pstl fragments that contain the first two exons and introns of the gene and the upstream promoter region. In contrast to the findings in MLS, no tumor without a t(12;16) exhibited aberrant CHOP restriction digest patterns. These tumors included one highly differentiated liposarcoma with abnormal karyotype but no involvement of 12q 13, seven lipomas with various cytogenetic aberrations of 12q 13–15, two uterine leiomyomas with t( 12; 14) (q 14–15;q23–24), and one hemangiopericytoma and one chondroma, both of which also had 12q 13 changes. These findings demonstrate that the 12q breakpoint of the t( 12;16) in MLS differs from those in the other tumors investigated, even in cases with no cytogenetically visible differences in breakpoint position, that CHOP rearrangement is specific for MLS, and that the breakpoints cluster to the 5′ region of the gene. We assume that the CHOP alteration is an important step in MLS tumorigenesis and speculate that this is achieved by interference with the normal function of the C/EBP family of transcription factors.
sLORETA intracortical lagged coherence during breath counting in meditation-naïve participants

We investigated brain functional connectivity comparing no-task resting to breath counting (a meditation exercise but given as task without referring to meditation). Functional connectivity computed as EEG coherence between head-surface data suffers from localization ambiguity, reference dependence, and overestimation due to volume conduction. Lagged coherence between intracortical model sources addresses these criticisms. With this analysis approach, experienced meditators reportedly showed reduced coherence during meditation, meditation-naïve participants have not yet been investigated. 58-channel EEG from 23 healthy, right-handed, meditation-naïve males during resting [3 runs] and breath counting [2 runs] was computed into sLORETA time series of intracortical electrical activity in 19 regions of interest (ROI) corresponding to the cortex underlying 19 scalp electrode sites, for each of the eight independent EEG frequency bands covering 1.5–44 Hz. Intracortical lagged coherences and head-surface conventional coherences were computed between the 19 regions/sites. During breath counting compared to resting, paired t-tests corrected for multiple testing revealed four significantly lower intracortical lagged coherences, but four significantly higher head-surface conventional coherences. Lowered intracortical lagged coherences involved left BA 10 and right BAs 3, 10, 17, 40. In conclusion, intracortical lagged coherence can yield results that are inverted to those of head-surface conventional coherence. The lowered functional connectivity between cognitive control areas and sensory perception areas during meditation-type breath counting compared to resting conceivably reflects the attention to a bodily percept without cognitive reasoning. The reductions in functional connectivity were similar but not as widespread as the reductions reported during meditation in experienced meditators.
Complex network approach to characterize the statistical features of the sunspot series

Complex network approaches have been recently developed as an alternative framework to study the statistical features of time-series data. We perform a visibility-graph analysis on both the daily and monthly sunspot series. Based on the data, we propose two ways to construct the network: one is from the original observable measurements and the other is from a negative-inverse-transformed series. The degree distribution of the derived networks for the strong maxima has clear non-Gaussian properties, while the degree distribution for minima is bimodal. The long-term variation of the cycles is reflected by hubs in the network that span relatively large time intervals. Based on standard network structural measures, we propose to characterize the long-term correlations by waiting times between two subsequent events. The persistence range of the solar cycles has been identified over 15–1000 days by a power-law regime with scaling exponent γ = 2.04 of the occurrence time of two subsequent strong minima. In contrast, a persistent trend is not present in the maximal numbers, although maxima do have significant deviations from an exponential form. Our results suggest some new insights for evaluating existing models.
Uniqueness for the Vortex-Wave System When the Vorticity Is Constant Near the Point Vortex

We prove uniqueness for the vortex-wave system with a single point vortex introduced by Marchioro and Pulvirenti in the case where the vorticity is initially constant near the point vortex. Our method relies on the Eulerian approach for this problem and in particular on the formulation in terms of the velocity.
Comparison of Physostigmine and Neostigmine for Antagonism of Neuromuscular Block

The ability of physostigmine alone and in combination with neostigmine to reverse d‐tubocurarine‐induced neuromuscular block was evaluated in surgical patients. The relaxation was maintained at a level of90 % twitch suppression during balanced anaesthesia, and antagonism was attempted with physostigmine 1.5 mgX3; neostigmine 0.5 mgX3; neostigmine 1.0 mgX3; or with a combination of physostigmine 0.75 mg and neostigmine 0.5 mg × 3.
Retinopathy and clinical outcomes in patients with type 2 diabetes mellitus, chronic kidney disease, and anemia

Objective Retinopathy is an established microvascular complication of type 2 diabetes mellitus (T2DM), but its independent relationship with macrovascular and other microvascular complications is less well defined across the spectrum of kidney disease in T2DM. We examined the prognostic value of retinopathy in assessing the risk of developing end-stage renal disease (ESRD), cardiovascular morbidity or death among patients in the Trial to Reduce cardiovascular Events with Aranesp Therapy (TREAT). Design TREAT enrolled 4038 patients with T2DM, chronic kidney disease (CKD) and moderate anemia. Patients were grouped by baseline history of retinopathy. Proportional hazards regression models were utilized to assess the association between retinopathy and subsequent ESRD, cardiovascular morbidity or death over an average of 2.4 years. Results Although younger, the 1895 (47%) patients with retinopathy had longer duration of diabetes, lower estimated glomerular filtration rate, more proteinuria, and more microvascular complications. In univariate analysis, retinopathy was associated with a higher rate of ESRD, but not with cardiovascular events or mortality. After adjustment, retinopathy was no longer statistically significant for the prediction of ESRD or any clinical endpoint. Conclusions In a large cohort of patients with T2DM, CKD, and anemia, retinopathy was common but not independently associated with a higher risk of renal or cardiovascular morbidity or death. Trial registration number NCT00093015
Independent associations of physical activity and cardiovascular fitness with cardiovascular risk in adults

Background Uncertainty still exists whether physical activity (PA) and cardiovascular fitness (CF) contribute separately to cardiovascular disease (CVD) risk. This study examined the associations of PA and CF on individual as well as clustered CVD risk factors. Design Cross-sectional. Methods Seven hundred and eighty-one men and 890 women, aged 20–65 years, from two random population-based samples of Swedish women and men were included. PA was assessed by questionnaire and CF was predicted by a submaximal cycle ergometry test. Waist circumference, blood pressure, and fasting levels of blood lipids were assessed and dichotomized by conventional cut-off points. Results Participants reporting high PA level benefited from lower triglycerides and atherogenic cholesterol levels, regardless of CF. Higher CF level was, regardless of PA, associated with lower risk for all risk factors. With regard to clustering of risk factors, each higher CF level was associated with a gradually reduced risk by half or more, independent of PA. Furthermore, being unfit but reporting high PA was associated with a 50% lower risk compared with being unfit and inactive. Furthermore, high reported PA was associated with an additional reduced risk among fit participants. In addition, an excess risk of interaction was found for waist circumference, triglycerides, and the clustered CVD risk between neither being sufficiently active nor being fit. Conclusion This study suggests that both PA and CF are independently associated with lower cardiovascular risk, and that both variables should be taken into account when CVD risk is estimated.
GTI: An Unsupervised Approach for Sentiment Analysis in Twitter

This paper presents the approach of the GTI Research Group to SemEval-2015 task 10 on Sentiment Analysis in Twitter, or more specifically, subtasks A (Contextual Polarity Disambiguation) and B (Message Polarity Classification). We followed an unsupervised dependency parsing-based approach using a sentiment lexicon, created by means of an automatic polarity expansion algorithm and Natural Language Processing techniques. These techniques involve the use of linguistic peculiarities, such as the detection of polarity conflicts or adversative/concessive subordinate clauses. The results obtained confirm the competitive and robust performance of the system.
The Influence of Collective Working Memory Strategies on Agent Teams

Past self-organizing models of collectively moving "particles" (simulated bird flocks, fish schools, etc.) typically have been based on purely reflexive agents that have no significant memory of past movements or environmental obstacles. These agent collectives usually operate in abstract environments, but as these domains take on a greater realism, the collective requires behaviors use not only presently observed stimuli but also remembered information. It is hypothesized that the addition of a limited working memory of the environment, distributed among the collective's individuals can improve efficiency in performing tasks. This is first approached in a more traditional particle system in an abstract environment. Then it is explored for a single agent, and finally a team of agents, operating in a simulated 3-dimensional environment of greater realism. In the abstract environment, a limited distributed working memory produced a significant improvement in travel between locations, in some cases improving performance over time, while in others surprisingly achieving an immediate benefit from the influence of memory. When strategies for accumulating and manipulating memory were subsequently explored for a more realistic single agent in the 3-dimensional environment, if the agent kept a local or a cumulative working memory, its performance improved on different tasks, both when navigating nearby obstacles and, in the case of cumulative memory, when covering previously traversed terrain. When investigating a team of these agents engaged in a pursuit scenario, it was determined that a communicating and coordinating team still benefited from a working memory of the environment distributed among the agents, even with limited memory capacity. This demonstrates that a limited distributed working memory in a multi-agent system improves performance on tasks in domains of increasing complexity. This is true even though individual agents know only a fraction of the collective's entire memory, using this partial memory and interactions with others in the team to perform tasks. These results may prove useful in improving existing methodologies for control of collective movements for robotic teams, computer graphics, particle swarm optimization, and computer games, and in interpreting future experimental research on group movements in biological populations.
On the cubic bottleneck in subtyping and flow analysis

We prove that certain data-flow and control-flow problems are 2NPDA-complete. This means that these problems are in the class 2NPDA and that they are hard for that class. The fact that they are in 2NPDA demonstrates the richness of the class. The fact that they are hard for 2NPDA can be interpreted as evidence they can not be solved in sub-cubic time-the cubic time decision procedure for an arbitrary 2NPDA problem has not been improved since its discovery in 1968.
The assembly factor P17 from bacteriophage PRD1 interacts with positively charged lipid membranes.

The interactions of the assembly factor P17 of bacteriophage PRD1 with liposomes were investigated by static light scattering, fluorescence spectroscopy, and differential scanning calorimetry. Our data show that P17 binds to positively charged large unilamellar vesicles composed of the zwitterionic 1-palmitoyl-2-oleoyl-phosphatidylcholine and sphingosine, whereas only a weak interaction is evident for 1-palmitoyl-2-oleoyl-phosphatidylcholine vesicles. P17 does not bind to negatively charged membranes composed of 1-palmitoyl-2-oleoyl-phosphatidylglycerol and 1-palmitoyl-2-oleoyl-phosphatidylcholine. Our differential scanning calorimetry results reveal that P17 slightly perturbs the phase behaviour of neutral phosphatidylcholine and negatively charged multilamellar vesicles. In contrast, the phase transition temperature of positively charged dimyristoylphosphatidylcholine/sphingosine multilamellar vesicles (molar ratio 9 : 1, respectively) is increased by approximately 2.4 degrees C and the half width of the enthalpy peak broadened from 1.9 to 5.6 degrees C in the presence of P17 (protein : lipid molar ratio 1 : 47). Moreover, the enthalpy peak is asymmetrical, suggesting that lipid phase separation is induced by P17. Based on the far-UV CD spectra, the alpha-helicity of P17 increases upon binding to positively charged micelles composed of Triton X-100 and sphingosine. We propose that P17 can interact with positively charged lipid membranes and that this binding induces a structural change on P17 to a more tightly packed and ordered structure.
The Ecology of ‘Acroporid White Syndrome', a Coral Disease from the Southern Great Barrier Reef

Outbreaks of coral disease have increased worldwide over the last few decades. Despite this, remarkably little is known about the ecology of disease in the Indo-Pacific Region. Here we report the spatiotemporal dynamics of a coral disease termed ‘Acroporid white syndrome’ observed to affect tabular corals of the genus Acropora on the southern Great Barrier Reef. The syndrome is characterised by rapid tissue loss initiating in the basal margins of colonies, and manifests as a distinct lesion boundary between apparently healthy tissue and exposed white skeleton. Surveys of eight sites around Heron Reef in 2004 revealed a mean prevalence of 8.1±0.9%, affecting the three common species (Acropora cytherea, A. hyacinthus, A. clathrata) and nine other tabular Acropora spp. While all sizes of colonies were affected, white syndrome disproportionately affected larger colonies of tabular Acroporids (>80 cm). The prevalence of white syndrome was strongly related to the abundance of tabular Acroporids within transects, yet the incidence of the syndrome appears unaffected by proximity to other colonies, suggesting that while white syndrome is density dependant, it does not exhibit a strongly aggregated spatial pattern consistent with previous coral disease outbreaks. Acroporid white syndrome was not transmitted by either direct contact in the field or by mucus in aquaria experiments. Monitoring of affected colonies revealed highly variable rates of tissue loss ranging from 0 to 1146 cm−2 week−1, amongst the highest documented for a coral disease. Contrary to previous links between temperature and coral disease, rates of tissue loss in affected colonies increased threefold during the winter months. Given the lack of spatial pattern and non-infectious nature of Acroporid white syndrome, further studies are needed to determine causal factors and longer-term implications of disease outbreaks on the Great Barrier Reef.
Spectrum of dyons and black holes in CHL orbifolds using Borcherds lift

The degeneracies of supersymmetric quarter BPS dyons in four dimensions and of spinning black holes in five dimensions in a CHL compactification are computed exactly using Borcherds lift. The Hodge anomaly in the construction has a physical interpretation as the contribution of a single M-theory Kaluza-Klein 6-brane in the 4d-5d lift. Using factorization, it is shown that the resulting formula has a natural interpretation as a two-loop partition function of left-moving heterotic string, consistent with the heuristic picture of dyons in the M-theory lift of string webs.
Disjoint Edges in Complete Topological Graphs

It is shown that every complete $$n$$-vertex simple topological graph has at $$\varOmega (n^{1/3})$$ pairwise disjoint edges, and these edges can be found in polynomial time. This proves a conjecture of Pach and Tóth, which appears as Problem 5 from Chapter 9.5 in Research Problems in Discrete Geometry by Brass, Moser, and Pach.
An Experimental Comparison of Bubble and Sediment Plumes in Stratified Environments

Environmental applications of bubble plumes require experimental data for bubbles smaller than one millimeter in diameter. It is difficult to obtain a steady flow of bubbles this small in the laboratory, so this study investigates the use of negatively buoyant sediment plumes to model positively buoyant bubble plumes. This procedure benefits from the ease with which sediment is measured, obtained and stored at any desired diameter. In trials comparing sediment and bubbles of the same terminal and slip velocity, in plumes with equal and opposite buoyancy fluxes, sediment is shown to be a good model for air bubbles to determine plume peeling heights in stratified environments. Within margins of experimental repeatability, the bubble plumes and sediment plumes peel at the same distance from their starting points. Further experiments with smaller sediment provide data that is used to generate a graph for determining plume peeling heights; the normalized plume peeling height is found to decrease with increasing sediment size. This normalized curve can applied to bubble plumes by matching slip and terminal velocities. A negatively buoyant liquid plume is observed, and its peeling height is compared both to theoretical single-phase peeling heights and to experimental sediment plume peeling heights. The results for the liquid plume match theoretical estimates for single-phase buoyant plumes, but momentum effects distort the comparison between liquid and sediment plumes. Experimental bubble plume results are compared with previous studies; normalized peeling heights in this work are higher than those in one earlier simulation, but lower than those in another. Bubble plume peeling is observed to cause less diverted volume flux than predicted by a simulation in an earlier work. Thesis Supervisor: Dr. E. Eric Adams Title: Senior Research Engineer
Polynomial-Time Algorithms for Multirate Anypath Routing in Wireless Multihop Networks

In this paper, we present a new routing paradigm that generalizes opportunistic routing for wireless multihop networks. In multirate anypath routing, each node uses both a set of next-hops and a selected transmission rate to reach a destination. Using this rate, a packet is broadcast to the nodes in the set, and one of them forwards the packet on to the destination. To date, there is no theory capable of jointly optimizing both the set of next-hops and the transmission rate used by each node. We solve this by introducing two polynomial-time routing algorithms and provide the proof of their optimality. The proposed algorithms have roughly the same running time as regular shortest-path algorithms and are therefore suitable for deployment in routing protocols. We conducted measurements in an 802.11b testbed network, and our trace-driven analysis shows that multirate anypath routing is on average 80% better than 11-Mbps anypath routing, with a factor of 6.4 improvement in the best case. If the rate is fixed at 1 Mbps instead, performance improves by a factor of 5.4 on average.