Miracle-dz/UniFAR-FTUs huggingface dataset:
Annotated Compendium of 102 Breast Cancer Gene-Expression Datasets

Transcriptomic data from breast-cancer patients are widely available in public repositories. However, before a researcher can perform statistical inferences or make biological interpretations from such data, they must find relevant datasets, download the data, and perform quality checks. In many cases, it is also useful to normalize and standardize the data for consistency and to use updated genome annotations. Additionally, researchers need to parse and interpret metadata: clinical and demographic characteristics of patients. Each of these steps requires computational and/or biomedical expertise, thus imposing a barrier to reuse for many researchers. We have identified and curated 102 publicly available, breast-cancer datasets representing 17,151 patients. We created a reproducible, computational pipeline to download the data, perform quality checks, renormalize the raw gene-expression measurements (when available), assign gene identifiers from multiple databases, and annotate the metadata against the National Cancer Institute Thesaurus, thus making it easier to infer semantic meaning and compare insights across datasets. We have made the curated data and pipeline freely available for other researchers to use. Having these resources in one place promises to accelerate breast-cancer research, enabling researchers to address diverse types of questions, using data from a variety of patient populations and study contexts.
Can You Ear Me?

The earlobe is a well-known location for wearing jewelry, but might also be promising for electronic output, such as presenting notifications. This work elaborates the pros and cons of different notification channels for the earlobe. Notifications on the earlobe can be private (only noticeable by the wearer) as well as public (noticeable in the immediate vicinity in a given social situation). A user study with 18 participants showed that the reaction times for the private channels (Poke, Vibration, Private Sound, Electrotactile) were on average less than 1 s with an error rate (missed notifications) of less than 1 %. Thermal Warm and Cold took significantly longer and Cold was least reliable (26 % error rate). The participants preferred Electrotactile and Vibration. Among the public channels the recognition time did not differ significantly between Sound (738 ms) and LED (828 ms), but Display took much longer (3175 ms). At 22 % the error rate of Display was highest. The participants generally felt comfortable wearing notification devices on their earlobe. The results show that the earlobe indeed is a suitable location for wearable technology, if properly miniaturized, which is possible for Electrotactile and LED. We present application scenarios and discuss design considerations. A small field study in a fitness center demonstrates the suitability of the earlobe notification concept in a sports context.
Detecting Social Contexts from Mobile Sensing Indicators in Virtual Interactions with Socially Anxious Individuals

Mobile sensing is a ubiquitous and useful tool to make inferences about individuals' mental health based on physiology and behavior patterns. Along with sensing features directly associated with mental health, it can be valuable to detect different features of social contexts to learn about social interaction patterns over time and across different environments. This can provide insight into diverse communities' academic, work and social lives, and their social networks. We posit that passively detecting social contexts can be particularly useful for social anxiety research, as it may ultimately help identify changes in social anxiety status and patterns of social avoidance and withdrawal. To this end, we recruited a sample of highly socially anxious undergraduate students (N=46) to examine whether we could detect the presence of experimentally manipulated virtual social contexts via wristband sensors. Using a multitask machine learning pipeline, we leveraged passively sensed biobehavioral streams to detect contexts relevant to social anxiety, including (1) whether people were in a social situation, (2) size of the social group, (3) degree of social evaluation, and (4) phase of social situation (anticipating, actively experiencing, or had just participated in an experience). Results demonstrated the feasibility of detecting most virtual social contexts, with stronger predictive accuracy when detecting whether individuals were in a social situation or not and the phase of the situation, and weaker predictive accuracy when detecting the level of social evaluation. They also indicated that sensing streams are differentially important to prediction based on the context being predicted. Our findings also provide useful information regarding design elements relevant to passive context detection, including optimal sensing duration, the utility of different sensing modalities, and the need for personalization. We discuss implications of these findings for future work on context detection (e.g., just-in-time adaptive intervention development).
The real-time display of interferometry data for Goldstone radar astronomy data acquisition

A method for visualizing radar interferometry data in real time has been developed for the Goldstone radar astronomy ranging data-acquisition system. The presentation is similar in appearance to a vector field display or data-based grid. This form was selected to facilitate the recognition of characteristic patterns of local variation in the phase and magnitude of complex elements in a two-dimensional data array. The design emphasized efficiency under the demands of real-time processing and remote monitoring. The interferometry 'phase-magnitude' presentation, as it has come to be called, has been used to monitor radar interferometry experiments on three targets, beginning with the asteroid 4179 Toutatis, and continuing with Mars and Mercury.
The lactonase BxdA mediates metabolic adaptation of maize root bacteria to benzoxazinoids

Root exudates contain secondary metabolites that affect the plant’s root microbiome. How microbes cope with these bioactive compounds, and how this ability shapes root microbiomes remain largely unknown. We investigated how maize root bacteria metabolise benzoxazinoids, the main specialised metabolites of maize. Diverse and abundant bacteria metabolised the major compound (6-methoxy-benzoxazolin-2-one, MBOA) in the maize rhizosphere to 2-amino-7-methoxyphenoxazin-3-one (AMPO). By contrast, bacteria isolated from Arabidopsis, which does not produce benzoxazinoids, were unable to metabolise MBOA. Among Microbacteria strains, this differential metabolisation allowed to identify a conserved gene cluster containing the lactonase bxdA. BxdA converts MBOA to AMPO in vitro and we show that this capacity provided bacteria a growth benefit under carbon-limiting conditions. Together these results reveal that maize root bacteria - through BxdA - are metabolically adapted to the benzoxazinoids of their host. We propose that metabolic adaptation to plant-specialised compounds shapes root bacterial communities across the plant kingdom.
Impact of improved soil moisture on the ECMWF precipitation forecast in West Africa

West Africa is a region of strong coupling between soil moisture and precipitation and where numerical weather prediction of precipitation generally exhibits poor skill. This region has been the focus of the African Monsoon Multidisciplinary Analysis ‐ Land‐surface Model Intercomparison Project in which the European Medium‐Range Weather Forecasts (ECMWF) land surface scheme—among others—has been driven offline by accurate meteorological forcing in order to produce improved soil moisture estimates. The impact of these improved initial conditions for soil moisture on the short‐range precipitation forecast is examined with the ECMWF Integrated Forecast System. While direct and beneficial impact of a more realistic soil moisture is obtained for accumulated precipitation in the regions over the coast of the Gulf of Guinea and eastern Sahel, over the rest of the Sahel the impact is detrimental or neutral.
English in the world : history, diversity, change

English in the World: History, Diversity, Change examines the English language as it has developed through history and is used across the globe today. The first half of the book outlines the history of the language from its fifth-century roots through its development as a national, a colonial, and now a global language. In the second half, the focus shifts to the diversity of the language today. The book explores varieties of English across the English-speaking world, as well as English-related varieties such as pidgins and creoles. It also examines complex processes of variation, hybridity and change in English, and in the shifting styles of individual speakers. Throughout, the focus is on the international nature of English and its use alongside other languages in a diverse range of communities.
Resource Management In Cloud And Big Data Systems

RESOURCE MANAGEMENT IN CLOUD AND BIG DATA SYSTEMS by LENA MASHAYEKHY August 2015 Advisor: Dr. Daniel Grosu Major: Computer Science Degree: Doctor of Philosophy Cloud computing is a paradigm shift in computing, where services are offered and ac- quired on demand in a cost-effective way. These services are often virtualized, and they can handle the computing needs of big data analytics. The ever-growing demand for cloud services arises in many areas including healthcare, transportation, energy systems, and manufacturing. However, cloud resources such as computing power, storage, energy, dol- lars for infrastructure, and dollars for operations, are limited. Effective use of the existing resources raises several fundamental challenges that place the cloud resource management at the heart of the cloud providers’ decision-making process. One of these challenges faced by the cloud providers is to provision, allocate, and price the resources such that their profit is maximized and the resources are utilized efficiently. In addition, executing large-scale ap- plications in clouds may require resources from several cloud providers. Another challenge when processing data intensive applications is minimizing their energy costs. Electricity used in US data centers in 2010 accounted for about 2% of total electricity used nationwide. In addition, the energy consumed by the data centers is growing at over 15% annually, and the energy costs make up about 42% of the data centers’ operating costs. Therefore, it is critical for the data centers to minimize their energy consumption when offering services to customers. In this Ph.D. dissertation, we address these challenges by designing, developing, and analyzing mechanisms for resource management in cloud computing systems and data centers. The goal is to allocate resources efficiently while optimizing a global performance
Detection of Parkinson’s disease using blood and brain cells transcript proﬁles

Identiﬁcation of genes whose regulation of expression is similar in both brain and blood cells could enable monitoring of signiﬁcant neurological traits and disorders by analysis of blood samples. We thus employed transcriptional analysis of pathologically aﬀected tissues, using agnostic approaches to identify overlapping gene functions and integrating this transcriptomic information with expression quantitative trait loci (eQTL) data. Here, we estimate the correlation of genetic expression in the top-associated cis-eQTLs of brain tissue and blood cells in Parkinson’s (PD). We introduced quantitative frameworks to reveal the complex relationship of various biasing genetic factors in PD, a neurodegenerative disease. We examined gene expression microarray and RNA-Seq datasets from human brain and blood tissues from PD-aﬀected and control individuals. Diﬀerentially expressed genes (DEG) were identiﬁed for both brain and blood cells to determine common DEG overlaps. Based on neighborhood-based benchmarking and multilayer network topology aproaches we then developed genetic associations of factors with PD.
Management of Severe Pregnancy-Induced Hypertension, or Gestosis, with Sodium Nitroprusside

Eclampsia continues to be a serious complication of pregnancy with deaths reported by Maternal Mortality Committees. The approximate incidence of eclampsia and the factors associated with this syndrome are listed in Table 1. Preeclampsia with high blood pressure, increased reflexes, clonus and headache is an equally serious complication because this condition frequently leads on to eclampsia. The management of these serious conditions has been controversial for many years. The main approach to therapy has been the emphasis on lowering of the blood pressure. This approach ignores the other manifestations of the disease such as thrombocytopenia, oedema, proteinuria and oliguria, hypovolaemia and often other major organ imbalance induced by the disease. Table 2 lists the maternal organ dysfunction which may accompany this pregnancy disorder. The current name for this condition is Pregnancy-Induced Hypertension (PIH) which has tended to replace Pre-eclampsia or Pre-eclamptic Toxaemia (PET). This name of PIH does not effectively describe the problem· because hypertension may be absent, or only minor, and probably is reactive rather than causative. Goodlin2 has recommended the term Gestosis for this pregnancy complication and this has some merit as the fundamental problem would appear to be the imbalance between prostacyclin (or PGI2) and thromboxane A2 (TXAf ) such that in the more severe forms of the conditIOn TXA2: PGI2 ratios are 8: 1 rather than the more normal 1: 1. 3 The aetiology of this abnormality would appear to be associated with placental implantation, and there
In vitro interactions between Blautia hydrogenotrophica, Desulfovibrio piger and Methanobrevibacter smithii under hydrogenotrophic conditions

ABSTRACT Methanogens, reductive acetogens and sulfate-reducing bacteria play an important role in disposing of hydrogen in gut ecosystems. However, how they interact with each other remains largely unknown. This in vitro study cocultured Blautia hydrogenotrophica (reductive acetogen), Desulfovibrio piger (sulfate reducer) and Methanobrevibacter smithii (methanogen). Results revealed that these three species coexisted and did not compete for hydrogen in the early phase of incubations. Sulfate reduction was not affected by B. hydrogenotrophica and M. smithii. D. piger inhibited the growth of B. hydrogenotrophica and M. smithii after 10 h incubations, and the inhibition on M. smithii was associated with increased sulfide concentration. Remarkably, M. smithii growth lag phase was shortened by coculturing with B. hydrogenotrophica and D. piger. Formate was rapidly used by M. smithii under high acetate concentration. Overall, these findings indicated that the interactions of the hydrogenotrophic microbes are condition-dependent, suggesting their interactions may vary in gut ecosystems.
The Tropospheric Ozone Production about the Spring Equinox (TOPSE) Experiment: Introduction and Overview

[1] The Tropospheric Ozone Production about the Spring Equinox (TOPSE) experiment was conducted during February–March, 2000 to study the evolution of tropospheric chemistry at mid to high latitudes over North America. The experiment used airborne in situ and remote sensing measurements of trace gases, radiation, and aerosols, combined with model simulations, to describe the major processes that control evolution of ozone and oxidants during the winter-spring transition. This paper introduces the major scientific questions of the TOPSE experiment, describes the conduct of the mission, and introduces the scientific results discussed in a series of companion papers in this special section. Among the significant findings of the experiment was that tropospheric ozone increases from winter to spring were dominated by in situ photochemical production in the troposphere, rather than by transport from the stratosphere. Also unique observations of widespread surface ozone depletion events, and of seasonal evolution of trace gases and aerosols as a function of latitude and altitude, were obtained over the course of the mission.
Reconfigurable Bandwidth Bandpass Filter With Enhanced Out-of- Band Rejection Using -Section-Loaded Ring Resonator

A novel ring resonator bandpass filter (BPF) with reconfigurable bandwidth with central frequency at 2.4 GHz is demonstrated. Theoretical analysis for computing the resonant frequencies is shown, and the design approach of implementing π-section stubs connected to the ring to obtain the bandwidth reconfigurability is explained. The use of reconfigurable π-section allows the alteration of the stub’s effective width and therefore the filter’s bandwidth reconfigurability. PIN diodes are used as switching elements to achieve the narrowband and wideband response. Coupled line sections are used for suppressing the higher modes by generating out-of-band transmission zeros, resulting in a significantly enhanced out-of-band rejection. Measurements indicate that the 3 dB fractional bandwidth (FBW) can be switched from 58.5 % to 75% at a fixed center frequency of 2.4 GHz with an insertion loss (IL) better than 1.1 dB. Moreover the -20 dB stopband performance is extended to 2.7f0.
Along‐strike variations in short‐term slow slip events in the southwest Japan subduction zone

[1] Short-term slow slip events accompanied by nonvolcanic deep low-frequency tremors and deep very low frequency earthquakes in southwest Japan were investigated systematically by means of ground tilting studies. The change in tilt usually lasts for several days. By using a genetic algorithm and a least squares method, we inverted the data for tilt steps that were caused by slow slip events and were detected by at least four stations situated near the source of the tremor. Fault parameters were estimated for 54 slow slip episodes that occurred mainly in the western Shikoku, northeastern Kii, and Tokai regions from 2001 to 2008. In eastern Shikoku, two slow slip episodes were detected quantitatively for the first time. The fault geometries of all the slow slip events were located within the belt-like distribution of tremors in the transition zone between the locked and aseismic slip zones at the plate interface of the subducting Philippine Sea Plate. The spatial extent of the fault geometry corresponds roughly to the distribution of clusters of nonvolcanic tremors and very low frequency earthquakes. The moment magnitudes ranged from 5.4 to 6.2, and the slip was ∼1 cm for each slow slip event. The rate of moment release by the detected slow slip events was 40–60% of the moment accumulation expected from the relative plate motion, and it showed regional differences. They may reflect the along-strike variations in plate convergence and/or the characteristic size of the slow slip fault plane on the plate interface.
Laboratory Component of Next-Generation Liquefaction Project Database

S oil liquefaction and resulting ground failure due to earthquakes presents a significant hazard to distributed infrastructure systems and structures around the world. Currently there is no consensus in liquefaction susceptibility or triggering models. The disagreements between models is a result of incomplete datasets and parameter spaces for model development. The Next Generation Liq-uefaction (NGL) Project was created to provide a database for advancing lique-faction research and to develop models for the prediction of liquefaction and its effects, derived in part from that database in a transparent and peer-reviewed manner, that provide end users with a consensus approach to assess liquefaction potential within a probabilistic framework. An online relational database was created for organizing and storing case histories which is available at http://nextgen-erationliquefaction.org/ (https://www.doi.org/10.21222/C2J040, [1]). The NGL field case history database was recently expanded to include the results of laboratory testing programs because such results can inform aspects of liquefaction models that are poorly constrained by case histories alone. Data are organized by a schema describing tables, fields, and relationships among the tables. The types of information available in the database are test-specific and include processed-data quantities such as stress and strain rather than raw data such as load and displacement. The database is replicated in DesignSafe-CI [2] where users can write queries in Python scripts within Jupyter notebooks to interact with the data.
Pseudogenization of
 Mc1r
 gene associated with transcriptional changes related to melanogenesis explains leucistic phenotypes in
 Oreonectes
 cavefish (Cypriniformes, Nemacheilidae)

Organisms that have colonized underground caves encounter vastly different selective pressures than their relatives in above‐ground habitats. While disruption of certain pigmentation genes has been documented in various cave‐dwelling taxa, little is known about wider impacts across pigmentation and other gene pathways. We here study the timeframe and transcriptional landscape of a leucistic and blind cypriniform fish (Oreonectes daqikongensis, Nemacheilidae) that inhabits karst caves in Guizhou, China. Based on data from the mitochondrial ND4, ND5, and Cytb genes, we show that the divergence between O. daqikongensis and its most closely related pigmented species occurred ca. 6.82 million years ago (95% HPD, 5.12–9.01), providing ample time for widespread phenotypic change. Indeed, we found that the DNA sequence of Mc1r (melanocortin‐1 receptor), a key gene regulating the biosynthesis of melanin in most vertebrates, is pseudogenized in O. daqikongensis, caused by a 29 bp deletion in the protein‐coding region. Furthermore, 99,305 unigenes were annotated based on the transcriptome of skin tissue of Oreonectes fish. Among the differentially expressed unigenes, 7,326 (7.4% of the total unigenes) had decreased expression and 2,530 (2.5% of the total unigenes) had increased expression in O. daqikongensis skin. As predicted, the expression of Mc1r and 18 additional genes associated with melanin biosynthesis was significantly downregulated in the skin tissue of O. daqikongensis, but not in its congener. Our results, integrating with other studies on cavefishes, suggest that loss of pigmentation was caused by coding region loss‐of‐function mutations along with widespread transcriptional changes, resulting from extended evolutionary time as a cave‐dwelling form.
Matrix Metalloproteinase-28 Deletion Exacerbates Cardiac Dysfunction and Rupture Following Myocardial Infarction in Mice by Inhibiting M 2 Macrophage Activation

San Antonio Cardiovascular Proteomics Center, Barshop Institute for Longevity and Aging Studies, and Division of Geriatrics, Gerontology and Palliative Medicine, Department of Medicine, The University of Texas Health Science Center at San Antonio; Department of Mechanical Engineering, The University of Texas at San Antonio; Department of Electrical and Computer Engineering, The University of Texas at San Antonio; Center for Lung Biology and Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, WA.
Some Perspectives on Similarity Learning for Case-Based Reasoning and Analogical Transfer

In this paper we investigate interactions between recent advances in the modeling of analogical transfer and similarity learning. Indeed, a unifying principle of case-based prediction methods was recently established, according to which the plausible inference principle of analogical transfer can be interpreted as a transfer of similarity knowledge from a situation space to an outcome space. Following this principle, the task of analogical transfer can be addressed using a global indicator of the compatibility between two similarity measures. Such an indicator can also be used to assess the quality of the situation space similarity measure with respect to the case-based prediction task. We discuss several perspectives opened by such an interpretation of the task of analogical transfer as the optimisation of the compatibility criterion: we explore interactions with similarity learning, as well as with energy function optimisation.