Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Network Analysis with Multiply Imputed Lipidomic Data

The importance of lipids for cell function and health has been widely recognized, e.g., a disorder in the lipid composition of cells has been related to atherosclerosis caused cardiovascular disease (CVD). Lipidomics analyses are characterized by large yet not a huge number of mutually correlated variables measured and their associations to outcomes are potentially of a complex nature. Differential network analysis provides a formal statistical method capable of inferential analysis to examine differences in network structures of the lipids under two biological conditions. It also guides us to identify potential relationships requiring further biological investigation. We provide a recipe to conduct permutation test on association scores resulted from partial least square regression with multiple imputed lipidomic data from the LUdwigshafen RIsk and Cardiovascular Health (LURIC) study, particularly paying attention to the left-censored missing values typical for a wide range of data sets in life sciences. Left-censored missing values are low-level concentrations that are known to exist somewhere between zero and a lower limit of quantification. To make full use of the LURIC data with the missing values, we utilize state of the art multiple imputation techniques and propose solutions to the challenges that incomplete data sets bring to differential network analysis. The customized network analysis helps us to understand the complexities of the underlying biological processes by identifying lipids and lipid classes that interact with each other, and by recognizing the most important differentially expressed lipids between two subgroups of coronary artery disease (CAD) patients, the patients that had a fatal CVD event and the ones who remained stable during two year follow-up.
The Development and Assessment of a Model-, Grid-, and Basin-Independent Tropical Cyclone Detection Scheme

AbstractA novel approach to tropical cyclone (TC) detection in coarse-resolution numerical model data is introduced and assessed. This approach differs from traditional detectors in two main ways. First, it was developed and tuned using 20 yr of ECMWF Interim Re-Analysis (ERA-Interim) data, rather than using climate model data. This ensures that the detector is independent of any climate models to which it will later be applied. Second, only relatively large-scale parameters resolvable in climate models are included, in order to minimize any grid-resolution dependence on parameter thresholds. This approach is taken in an attempt to construct a unified TC detection procedure applicable to all climate models without the need for any further tuning or adjustment.Unlike traditional detectors that seek to identify TCs directly, the authors' method seeks to identify conditions favorable for TC formation. Favorable TC formation regions at the center of closed circulations in the lower troposphere to the midtropo.
Development of Multiple Cross Displacement Amplification Label-Based Gold Nanoparticles Lateral Flow Biosensor for Detection of Shigella spp.

Shigella spp. , the etiological agent of shigellosis or “bacillary dysentery,” are responsible for considerable morbidity and mortality in excess of a million deaths globally per year. Although PCR-based techniques (such as PCR-based dipstick biosensors) have been used for the molecular diagnosis of infectious disease, these assays were restricted due to the need for a sophisticated thermal cycling apparatus to denature target templates. To facilitate simple and rapid detection of target pathogens, we successfully devised an inexpensive, reliable and nearly instrument-free molecular technique, which incorporates multiple cross displacement amplification (MCDA) combined with a newly designed lateral flow biosensor (LFB) for visual, sensitive and specific detection of Shigella. The MCDA-LFB assay was conducted at 65°C for only 20 min during the amplification stage, and then products were directly analyzed on the biosensor, alleviating the use of special reagents, electrophoresis equipment and amplicon detection instruments. The entire process, including specimen processing (35 min), amplification (20) and detection (2–5 min), can be finished within 1 h. The MCDA-LFB assay demonstrated high specificity for Shigella detection. The analytical sensitivity of the assay was 10 fg of genomic templates per reaction in pure culture and 5.86 CFU per tube in human fecal samples, which was consistent with MCDA by colorimetric indicator, gel electrophoresis, real time turbidity and fluorescence detection. Hence, the simplicity, rapidity and nearly instrument-free platform of the MCDA-LFB assay make it practical for ‘on-site’ diagnosis, point-of-care testing and more. Moreover, the proof-of-concept approach can be reconfigured to detect a wide variety of target sequences by re-designing the specific MCDA primers.
Cigarette smoking and subtypes of bladder cancer

There is little information regarding associations between suspected bladder cancer risk factors and tumor subtypes at diagnosis. Some, but not all, studies have found that bladder cancer among smokers is often more invasive than it is among nonsmokers. This population‐based case‐control study was conducted in Los Angeles, California, involving 1,586 bladder cancer patients and their individually matched controls. Logistic regression was used to conduct separate analyses according to tumor subtypes defined by stage and grade. Cigarette smoking increased risk of both superficial and invasive bladder cancer, but the more advanced the stage, the stronger the effect. The odds ratios associated with regular smokers were 2.2 (95% confidence intervals, 1.8–2.8), 2.7 (2.1–3.6) and 3.7 (2.5–5.5) for low‐grade superficial, high‐grade superficial and invasive tumors respectively. This pattern was consistently observed regardless of the smoking exposure index under examination. Women had higher risk of invasive bladder cancer than men even they smoked comparable amount of cigarettes as men. There was no gender difference in the association between smoking and risk of low‐grade superficial bladder cancer. The heterogeneous effect of cigarette smoking was attenuated among heavy users of NSAIDs. Our results indicate that cigarette smoking was more strongly associated with increased risk of invasive bladder cancer than with low‐grade superficial bladder cancer.
Observations on dust mites (Acari: Pyroglyphidae) in coastal hospitals in South Africa

AbstractSurveys of houses in South Africa have shown that dust mites and mite-derived antigens are more common along the eastern and southern coastal lowlands than on the central Highveld plateau. The present study extended this research to hospitals in the three major coastal cities, to determine whether or not dust mites were present in ward furnishings and on foors, and if so, at what densities. Sampling, over 22 months, in provincial and private hospitals in Durban, Port Elizabeth and Cape Town recovered 10 mite species, including the cosmopolitan pyroglyphids, Dermatophagoides farinae, D. pteronyssinus, Euroglyphus maynei and Malayoglyphus intermedius. Mites were found in all sampled habitats without any apparent preferences, but mean densities were mostly below 10/m2, lower than found previously in houses along the coast. To characterise mite habitats in these coastal hospitals, preliminary environmental data were collected in wards and from inside mattresses. These showed nearly constant environmen.
Chlamydophila psittaci in Fulmars, the Faroe Islands

Chlamydophila psittaci was detected in 10% of 431 fulmars examined from the Faroe Islands. Analysis of ompA showed a sequence almost identical to that of the type strain. The origin of C. psittaci outbreaks in fulmars is discussed. Despite a high level of exposure, the risk for transmission of C. psittaci to humans is low.
Cloud-Based Grasp Analysis and Planning for Toleranced Parts Using Parallelized Monte Carlo Sampling

This paper considers grasp planning in the presence of shape uncertainty and explores how cloud computing can facilitate parallel Monte Carlo sampling of combination actions and shape perturbations to estimate a lower bound on the probability of achieving force closure. We focus on parallel-jaw push grasping for the class of parts that can be modeled as extruded 2-D polygons with statistical tolerancing. We describe an extension to model part slip and experimental results with an adaptive sampling algorithm that can reduce sample size by 90%. We show how the algorithm can also bound part tolerance for a given grasp quality level and report a sensitivity analysis on algorithm parameters. We test a cloud-based implementation with varying numbers of nodes, obtaining a 515 × speedup with 500 nodes in one case, suggesting the algorithm can scale linearly when all nodes are reliable. Code and data are available at: http://automation.berkeley. edu/cloud-based-grasping.
Runooff ratio as a factor in the empirical modelling of soil erosion by individual rainstorms

A number of factors that influence erosion have separate and differing effects on flow discharge and sediment concentration, depending on local conditions. Empirical erosion models that do not have mechanisms to help account for these separate and differing effects often lack the capacity to predict event erosion adequately in many locations. In this paper, the product of the EI30 index, the erosivity index used in the Universal Soil Loss Equation (USLE) and the revised version (RUSLE), and the runoff ratio (QR) is discussed in relation to its capacity to act as an event erosivity index where sheet and rill erosion occur either separately or together in a rainstorm. An analysis of runoff and soil loss data shows the index to be superior to the EI30 index as an event erosivity index for storms on bare fallow plots at Holly Springs, Mississippi. The inclusion of runoff as an independent term in the USLE/RUSLE results in a need to determine new values for the soil erodibility factor, K. Existing USLE/RUSLE equations for determining L and S (topographic factors), C (a crop and crop management factor), and P (an erosion control practice factor) may be used as first approximations provided that the values of the new index are determined for the unit plot condition. Since many of the factors that determine L, S, C, and P influence runoff, new methods to determine these parameters need to be developed in the future if the new index is to be used most effectively.
MACA-BI (MACA By Invitation)-a receiver oriented access protocol for wireless multihop networks

A novel wireless MAC protocol named MACA-BI (MACA By Invitation) is introduced. MACA-BI is a simplified version of the well known MACA (Multiple Access Collision Avoidance) protocol, which is based on the request to send/clear to send (RTS/CTS) handshake and which has inspired the IEEE 802.11 wireless LAN standard. In MACA-BI, the RTS part of the RTS/CTS handshake is suppressed, leaving only the clear to send a control message which can be viewed as an "invitation" by the receiver to transmit. This reduction greatly improves the efficiency when radio turn-around time is significant with respect to packet transmission time. Yet, it preserves the "data" collision free property of MACA. Simulation results for various multihop topologies show that, when the traffic characteristics are stationary or predictable, MACA-BI outperforms several known multiple access protocols, especially when "hidden terminal" conditions are predominant.
Multipath Wide-Bandwidth CMOS Magnetic Sensors

This paper proposes a multipath multisensor architecture for CMOS magnetic sensors, which effectively extends their bandwidth without compromising either their offset or resolution. Two designs utilizing the proposed architecture were fabricated in a 0.18-<inline-formula> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> standard CMOS process. In the first, the combination of spinning-current Hall sensors and nonspun Hall sensors achieves an offset of 40 <inline-formula> <tex-math notation="LaTeX">$\mu \text{T}$ </tex-math></inline-formula> and a resolution of 272 <inline-formula> <tex-math notation="LaTeX">$\mu \text{T}_{\mathrm {rms}}$ </tex-math></inline-formula> in a bandwidth of 400 kHz, which is 40 times more than previous low-offset CMOS Hall sensors. In the second, the combination of spinning-current Hall sensors and pickup coils achieves the same offset, with a resolution of 210 <inline-formula> <tex-math notation="LaTeX">$\mu \text{T}_{\mathrm {rms}}$ </tex-math></inline-formula> in a further extended bandwidth of 3 MHz, which is the widest bandwidth ever reported for a CMOS magnetic sensor.
Nuevas edades radimétricas para la Formación Toro Negro en la Sierra de los Colorados, Sierras Pampeanas Noroccidentales, provincia de La Rioja

New radiometric ages for the Toro Negro Fromation in the Sierra de los Colorados, northwestern Sierras Pampeanas. New absolute ages derived from whole rock K/Ar dating of two vitric tuffs collected from the upper-middle part of the Toro Negro Formation in the outcrops of the Sierra de Los Colorados, Sierras Pampeanas Noroccidentales (La Rioja Province) are presented herein. The obtained values of 8,6 ± 0,3 Ma and 6,8 ± 0,2 Ma respectively, indicate an Upper Miocene age and challenge the previous Pliocene age proposed for this unit. The results presented here have a high degree of confidence because they do not show evidences of reworking, mixing with terrigenous clastics nor diagenetic alteration. The tuff levels were mapped and georeferenced using GPS coordinates and their close location in the stratigraphic column provides an additional control for the obtained ages.
Effect of Different Nitrogen Rates on Grain Yield and Grain Growth of Bread and Durum Wheat Genotypes

In order to identify the effects of different nitrogen levels on grain yield and grain growth of bread and durum wheat genotypes, a field experiment was conducted in 2010 cropping season in Ahvaz, south west of Iran. The experiment was designed as a splitplot with three replications. The N application rates (50, 100 and 150 kg N ha -1 ) were assigned in the main plots and the sub-plots consisted of six wheat genotypes (Vee/Nak, Star, Atilla, Showa, D-84-5 and D-83-8). Results indicated that the differences traits of grain yield, grain protein percentage, the grain effective filling rate, remobilization and the current photosynthesis in the both nitrogen and genotype treatments and the 1000grain weight and the grain effective filling period between genotypes were significant. The highest and lowest grain filling rate was related to Showa genotype in treatment of using 150 kg N ha -1 , and Vee/Nak in treatment of using 50 kg N ha -1 , respectively. The effect of nitrogen levels on grain effective filling period was not significant. The maximum duration of grain filling was devoted to Vee/Nak genotype and the minimum of this trait was for Showa genotype. Atilla genotype, in treatment of using 150 kg N ha
G1/S Cell Cycle Arrest Provides Anoikis Resistance through Erk-Mediated Bim Suppression

ABSTRACT Proper attachment to the extracellular matrix is essential for cell survival. Detachment from the extracellular matrix results in an apoptotic process termed anoikis. Anoikis induction in MCF-10A mammary epithelial cells is due not only to loss of survival signals following integrin disengagement, but also to consequent downregulation of epidermal growth factor (EGFR) and loss of EGFR-induced survival signals. Here we demonstrate that G1/S arrest by overexpression of the cyclin-dependent kinase inhibitors p16INK4a, p21Cip1, or p27Kip1 or by treatment with mimosine or aphidicolin confers anoikis resistance in MCF-10A cells. G1/S arrest-mediated anoikis resistance involves suppression of the BH3-only protein Bim. Furthermore, in G1/S-arrested cells, Erk phosphorylation is maintained in suspension and is necessary for Bim suppression. Following G1/S arrest, known proteins upstream of Erk, including Raf and Mek, are not activated. However, retained Erk activation under conditions in which Raf and Mek activation is lost is observed, suggesting that G1/S arrest acts at the level of Erk dephosphorylation. Thus, anoikis resistance by G1/S arrest is mediated by a mechanism involving Bim suppression through maintenance of Erk activation. These results provide a novel link between cell cycle arrest and survival, and this mechanism could contribute to the survival of nonreplicating, dormant tumor cells that avert apoptosis during early stages of metastasis.
Masked M-QAM OFDM: A simple approach for enhancing the security of OFDM systems

This paper investigates the secure transmission of Orthogonal Frequency Division Multiplexing (OFDM) signals, masked under non-orthogonal FDM signals of approximately the same overall bandwidth. Carrier orthogonality of traditional OFDM is intentionally violated in order to generate an encrypted signal at the physical layer, without any loss in bandwidth efficiency or extra overhead. A symmetric secret key is used for the modulation of part of the FDM signal while the original information symbol modulates the remaining carriers. The encrypted FDM signal generation takes place in an IFFT stage by simple truncation of part of its output. At the receiver, a straightforward suppression of the induced Inter-Carrier Interference (ICI) is performed before the OFDM demodulator, based on knowledge of the secret key. The key holder subsequently uses the traditional OFDM FFT demodulator to extract the information symbol. We demonstrate that an eavesdropper cannot demodulate the transmitted FDM signal by reduced complexity detection methods due to its severe ill-conditioning. Conversely, they have to rely on vectorial Maximum Likelihood detection of exponential complexity. Furthermore, in real noisy environments the eavesdropper detection capability is further affected by the abrupt shrinking of the FDM demodulator detection regions.
Genome analysis iDoComp : a compression scheme for assembled genomes

Motivation: With the release of the latest next-generation sequencing (NGS) machine, the HiSeq X by Illumina, the cost of sequencing a Human has dropped to a mere $4000. Thus we are approaching a milestone in the sequencing history, known as the $1000 genome era, where the sequencing of individuals is affordable, opening the doors to effective personalized medicine. Massive generation of genomic data, including assembled genomes, is expected in the following years. There is crucial need for compression of genomes guaranteed of performing well simultaneously on different species, from simple bacteria to humans, which will ease their transmission, dissemination and analysis. Further, most of the new genomes to be compressed will correspond to individuals of a species from which a reference already exists on the database. Thus, it is natural to propose compression schemes that assume and exploit the availability of such references. Results: We propose iDoComp, a compressor of assembled genomes presented in FASTA format that compresses an individual genome using a reference genome for both the compression and the decompression. In terms of compression efficiency, iDoComp outperforms previously proposed algorithms in most of the studied cases, with comparable or better running time. For example, we observe compression gains of up to 60% in several cases, including H.sapiens data, when comparing with the best compression performance among the previously proposed algorithms. Availability: iDoComp is written in C and can be downloaded from: http://www.stanford.edu/ ~iochoa/iDoComp.html (We also provide a full explanation on how to run the program and an example with all the necessary files to run it.). Contact: iochoa@stanford.edu Supplementary information: Supplementary data are available at Bioinformatics online.
An evaluation study of the determinants of future perspective and global Quality of Life in Spanish long-term premenopausal early-stage breast cancer survivors

Aim of the study Quality of life (QL) is important in premenopausal long-term breast cancer survivors. In this study we assessed QL and factors associated with future perspective and global QL in premenopausal early-stage long-term breast cancer survivors from Spain. Material and methods 243 premenopausal stage I-IIIA relapse-free breast cancer patients who had received surgery 5–20 years previously completed EORTC QLQ-C30 and QLQ-BR23 questionnaires once during follow-up. Univariate and multivariate logistic regression analyses were performed. Results QL mean scores were high in most areas (> 80 in functioning; < 20 in symptoms). The main factors for future perspective were emotional and social functioning, fatigue, breast symptom, and body image. The main factors for global QL were fatigue, pain and physical functioning, and emotional and social functioning. The best logistic model to explain future perspective associated high emotional and social functioning and low breast symptoms with a lower risk of low future perspective (R2 = 0.56). Higher scores in physical and emotional functioning and lower scores in fatigue were associated with a lower risk of low global QL (R2 = 0.50). Conclusions Psychological, social, and physical factors were found to be possible determinants of global QL and future perspective. QL in premenopausal early-stage long-term breast cancer survivors may benefit from multidisciplinary treatment.
Microphysics parameterization for convective clouds in a global climate model: Description and single‐column model tests

[1] An efficient two-moment microphysics parameterization scheme for convective clouds is developed to improve the representation of convective clouds and its interactions with stratiform clouds and aerosol in global climate models (GCMs). The scheme explicitly treats mass mixing ratio and number concentration of four hydrometeor species (cloud water, cloud ice, rain, and snow) and describes several microphysical processes, including autoconversion, self-collection, collection between hydrometeor species, freezing, cloud ice nucleation, droplet activation, and sedimentation. Thus this physically based scheme is suitable for investigating the interaction between convection and aerosol and the indirect aerosol effect on climate. An evaluation of the scheme in the single-column version of NCAR Community Atmospheric Model version 3.5 (CAM3.5) with the Tropical Warm Pool–International Cloud Experiment (TWP-ICE) data shows that the simulation of cloud microphysical properties in convective core is significantly improved, indicating that the new parameterization describes the microphysical processes in convection reasonably well. The contribution from convective detrainment to large-scale cloud ice and liquid water budgets is enhanced greatly. With more realistic convective cloud microphysical properties and their detrainment, the surface stratiform precipitation, which is seriously underestimated in the model, is increased by a factor of roughly 2.5, and therefore is much closer to the observations. In addition, the simulations of net surface shortwave radiation flux, OLR, specific humidity, and temperature are also improved to some extent. Sensitivity experiments show that the microphysics scheme is moderately sensitive to model vertical resolution, updraft vertical velocity, and numerics, but less so to the lower boundary conditions of hydrometeor budget equations. The experiments with climatological aerosol distribution show that convective precipitation is suppressed with increasing aerosol amount, consistent with some available observations.
DILATIONS AND FULL CORNERS ON FRACTIONAL SKEW MONOID RINGS

In this note we will show that the dilation result obtained for fractional skew monoid rings, in the case of a cancellative left Ore monoid S acting on a unital ring A by corner isomorphisms, holds in full generality. We apply this result to the context of semigroup C � -crossed products.