Miracle-dz/UniFAR-FTUs huggingface dataset:
Sensitive Detection of Mono- and Polyclonal ESR1 Mutations in Primary Tumors, Metastatic Lesions, and Cell-Free DNA of Breast Cancer Patients

Purpose: Given the clinical relevance of ESR1 mutations as potential drivers of resistance to endocrine therapy, this study used sensitive detection methods to determine the frequency of ESR1 mutations in primary and metastatic breast cancer, and in cell-free DNA (cfDNA). Experimental Design: Six ESR1 mutations (K303R, S463P, Y537C, Y537N, Y537S, D538G) were assessed by digital droplet PCR (ddPCR), with lower limits of detection of 0.05% to 0.16%, in primary tumors (n = 43), bone (n = 12) and brain metastases (n = 38), and cfDNA (n = 29). Correlations between ESR1 mutations in metastatic lesions and single (1 patient) or serial blood draws (4 patients) were assessed. Results: ESR1 mutations were detected for D538G (n = 13), Y537S (n = 3), and Y537C (n = 1), and not for K303R, S463P, or Y537N. Mutation rates were 7.0% (3/43 primary tumors), 9.1% (1/11 bone metastases), 12.5% (3/24 brain metastases), and 24.1% (7/29 cfDNA). Two patients showed polyclonal disease with more than one ESR1 mutation. Mutation allele frequencies were 0.07% to 0.2% in primary tumors, 1.4% in bone metastases, 34.3% to 44.9% in brain metastases, and 0.2% to 13.7% in cfDNA. In cases with both cfDNA and metastatic samples (n = 5), mutations were detected in both (n = 3) or in cfDNA only (n = 2). Treatment was associated with changes in ESR1 mutation detection and allele frequency. Conclusions: ESR1 mutations were detected at very low allele frequencies in some primary breast cancers, and at high allele frequency in metastases, suggesting that in some tumors rare ESR1-mutant clones are enriched by endocrine therapy. Further studies should address whether sensitive detection of ESR1 mutations in primary breast cancer and in serial blood draws may be predictive for development of resistant disease. Clin Cancer Res; 22(5); 1130–7. ©2015 AACR. See related commentary by Gu and Fuqua, p. 1034
Asymmetric tooth formation in the permanent dentition of cleft-affected children. An orthopantomographic study.

An investigation was made of asymmetric tooth formation in 54 children with cleft lip and alveolus and in 153 children with cleft palate, after which the findings were compared with the corresponding results obtained in an investigation of a group of 258 children with complete cleft lip and palate. Asymmetric growth was found in all the permanent teeth, but it was observed to occur most frequently in the upper incisors and the upper and lower premolars. In the cleftpalate group, asymmetry was seen to occur with equal frequency in both jaws, whereas in the cleftlip and alveolus and the cleftlip and palate groups, the condition was met with considerably more often in the upper jaw. The asymmetry varied from one to five developmental stages, though the difference registered mostly amounted to only one developmental stage. Certain other dental anomalies and etiological factors are also discussed in this paper.
The (Non)Utility of Predicate-Argument Frequencies for Pronoun Interpretation

State-of-the-art pronoun interpretation systems rely predominantly on morphosyntactic contextual features. While the use of deep knowledge and inference to improve these models would appear technically infeasible, previous work has suggested that predicate-argument statistics mined from naturally-occurring data could provide a useful approximation to such knowledge. We test this idea in several system configurations, and conclude from our results and subsequent error analysis that such statistics offer little or no predictive information above that provided by morphosyntax.
Road boundary detection in range imagery for an autonomous robot

The authors describe a road-following system for an autonomous land vehicle, based on range image analysis. The system is divided into two parts: low-level data-driven analysis, followed by high-level model-directed search. The sequence of steps performed in order to detect three-dimensional (3-D) road boundaries is as follows. Range data are first converted from spherical into Cartesian coordinates. A quadric (or planar) surface is then fitted to the neighborhood of each range pixel, using a least squires fit method. Based on this fit, minimum and maximum principal surface curvatures are computed at each point to detect edges. Next, using Hough transform techniques, 3-D local line segments are extracted. Finally, model-directed reasoning is applied to detect the road boundaries. >
Quantitation of hepatitis C virus RNA in peripheral blood mononuclear cells in HCV‐monoinfection and HIV/HCV‐coinfection

Peripheral blood mononuclear cells (PBMCs) represent an extrahepatic hepatitis C virus (HCV) reservoir, the significance of which is unclear due to limited studies and varying test methodologies. In this study, a commercial viral load assay for measuring cell‐associated PBMC HCV RNA was evaluated. HCV RNA was extracted from PBMCs, sorted CD14+, and CD19+ cells and corresponding plasma samples using the Abbott m2000 and Real‐Time HCV assay. Test performance and influence of HIV seropositivity on plasma and PBMC HCV RNA were studied. Among 51 patients, 67 and 62 unique patient samples had detectable plasma and PBMC HCV viral load, respectively. The median PBMC viral load was 535 IU/1 M cells (range 29–5,190). CD19+ cells had significantly higher viral load than CD14+ cells (median log10 HCV viral load 2.63 vs. 1.50 IU/ml; P< 0.001). Stability of PBMC viral load over time was demonstrated in untreated patients; all patients with an undetectable plasma HCV viral load after HCV treatment also demonstrated undetectable PBMC viral load. Repeated testing in nine samples yielded consistent PBMC viral load, differing by only 1.3‐fold (range 1.0–1.7‐fold). Among samples with detectable plasma HCV RNA, the correlation between PBMC and plasma viral load was moderate (r = 0.66) and was greater among HCV mono‐infected compared to HIV/HCV co‐infected subjects (r = 0.80 vs. 0.52). Measurement of cell‐associated PBMC HCV RNA using a commercial assay demonstrated promising test characteristics. Differences in PBMC HCV viral load based on HIV‐coinfection status and the significance of greater copy number in B‐cells requires further study. J. Med. Virol. 84:431–437, 2012. © 2011 Wiley Periodicals, Inc.
Deleterious genomic mutation rate for viability in Drosophila melanogaster using concomitant sibling controls

New deleterious mutations may reduce health and fitness and are involved in the evolution and maintenance of numerous biological processes. Hence, it is important to estimate the deleterious genomic mutation rate (U) in representative higher organisms. However, these estimated rates vary widely, mainly because of inadequate experimental controls. Here we describe an experimental design (the Binscy assay) with concomitant sibling controls and estimate U for viability in Drosophila melanogaster to be 0.31. This estimate, like most published studies, focuses on viability mutations and the overall deleterious genomic mutation rate would therefore be higher.
Glycosylphosphatidylinositol biosynthetic enzymes are localized to a stable tubular subcompartment of the endoplasmic reticulum in Leishmania mexicana

Glycosylphosphatidylinositols (GPI) are essential components in the plasma membrane of the protozoan parasite Leishmania mexicana, both as membrane anchors for the major surface macromolecules and as the sole class of free glycolipids. We provide evidence that L.mexicana dolichol‐phosphate‐mannose synthase (DPMS), a key enzyme in GPI biosynthesis, is localized to a distinct tubular subdomain of the endoplasmic reticulum (ER), based on the localization of a green fluorescent protein (GFP)–DPMS chimera and subcellular fractionation experiments. This tubular membrane (termed the DPMS tubule) is also enriched in other enzymes involved in GPI biosynthesis, can be specifically stained with the fluorescent lipid, BODIPY‐C5‐ceramide, and appears to be connected to specific subpellicular microtubules that underlie the plasma membrane. Perturbation of microtubules and DPMS tubule structure in vivo results in the selective accumulation of GPI anchor precursors, but not free GPIs. The DPMS tubule is closely associated morphologically with the single Golgi apparatus in non‐dividing and dividing cells, appears to exclude luminal ER resident proteins and is labeled, together with the Golgi apparatus, with another GFP chimera containing the heterologous human Golgi marker β1,2‐N‐acetylglucosaminyltransferase‐I. The possibility that the DPMS‐tubule is a stable transitional ER is discussed.
The renal cell primary cilium functions as a flow sensor.

PURPOSE OF REVIEW To discuss recent reports on the function and importance of the renal primary cilium, a widely distributed organelle. RECENT FINDINGS Most epithelial cells, including those in the kidney, express a solitary primary cilium. The primary cilium functions as a flow sensor in cultured renal epithelial cells (MDCK and mouse collecting tubule) mediating a large increase in intracellular calcium concentration. Flow sensing is shown to reside in the cilium itself and to involve the proteins polycystin 1 and 2, defects in which are associated with the majority of cases of human polycystic kidney disease. The role of the cilium in flow-dependent potassium secretion by the collecting tubule and in sensing of chemical components of the luminal fluid are also described. SUMMARY The primary cilium is mechanically sensitive and serves as a flow sensor in cultured renal epithelia. Bending the cilium by mechanical means or flow causes a large, prolonged transient increase in intracellular calcium. The mechanically sensitive protein in the cilium is a polycystin.
Trading services in open distributed environments

The current development of computing and telecommunication environments aims towards interoperability across separate platforms and organisations in a world-wide fashion. Interoperability means that software components can be exploited from arbitrary computers in such a way that the service semantics is preserved. The mechanisms supporting interoperability at the application level must mask heterogeneity of the compound computing environment. The term ‘open distributed processing’ does not currently have a single, commonly accepted interpretation. Therefore, the main system architecture models are critically analysed in order to contrast the facilities for interoperation in each model. The focus of this dissertation is on the problems arising when the interoperating computing systems are controlled by autonomous organisations, i.e., problems of federated systems. Federations between sovereign systems involve exploitation of open interfaces and run-time information about the system facilities. Open systems, especially federated systems, must be based on a shared, very high level architecture model. The Open Distributed Processing (ODP) framework standard has been developed to enable world-wide computing services to evolve. Among other specifications, the family of ODP standards also identifies a set of fundamental services required from each participating system. The trading service is one of the essential meta-information services of open systems. Trading presents a global mediator for information about available services and their properties. This dissertation presents work on the provision of the trading functionality. It analyses the requirements of trading designs and the ways trading function interacts with the system environment. The focus of this study is on federated trading, but trading problems in traditional distributed environments are also discussed. Furthermore, the design, implementation and performance of the DRYAD trading system is presented. In addition, exploitation scenarios for trading functionality in open distributed environments are analysed. Special attention is given for the use of trading in the explicit exchange, negotiation, and contract establishment required for interoperation in federated environments. The trading functionality is a powerful tool to be used within the open infrastructure to support controlled cooperation between autonomous organisations. It allows construction of a worldwide computing environment that tolerates the constant evolution of services and applications. The exploitation of such a world-wide system requires software engineering tools that are based on the open system services. Therefore, major changes are expected in the areas of application architectures and software development processes within the next few years. Computing Reviews (1998)
[Expression profile analysis of Peptide5 and Peptide6 in Arabidopsis].

Two predicted peptide genes in Arabidopsis thaliana L. , Peptide5 and Peptide6, was confirmed by RT-PCR in mRNA level. The expression profile indicated that both genes were generally expressed at different developmental stages and tissues as constitutive gene expression, and they also responded to six treatments including NaCl, PEG, MeJA (methyl jasmonate), SA (salicylic acid), cold and wound in transcription level. Analysis of the promoter sequence suggests that Peptide5 in Arabidopsis may contribute to the secondary xylem formation.
Characterization of Aspergillus section Nigri species populations in vineyard soil using droplet digital PCR

Identification of populations of Aspergillus section Nigri species in environmental samples using traditional methods is laborious and impractical for large numbers of samples. We developed species‐specific primers and probes for quantitative droplet digital PCR (ddPCR) to improve sample throughput and simultaneously detect multiple species in each sample. The ddPCR method was used to distinguish Aspergillus niger, Aspergillus welwitschiae, Aspergillus tubingensis and Aspergillus carbonarius in mixed samples of total DNA. Relative abundance of each species measured by ddPCR agreed with input ratios of template DNAs. Soil samples were collected at six time points over two growing seasons from two raisin vineyards in Fresno County, California. Aspergillus section Nigri strains were detected in these soils in the range of 102–105 CFU g−1. Relative abundance of each species varied widely among samples, but in 52 of 60 samples, A. niger was the most abundant species, ranging from 38 to 88% of the total population. In combination with total plate counts, this ddPCR method provides a high‐throughput method for describing population dynamics of important potential mycotoxin‐producing species in environmental samples.
The Effectiveness of a two-Layer Neural Network for Recommendations

We present a personalized recommender system using neural network for recommending products, such as eBooks, audio-books, Mobile Apps, Video and Music. It produces recommendations based on customer’s implicit feedback history such as purchases, listens or watches. Our key contribution is to formulate recommendation problem as a model that encodes historical behavior to predict the future behavior using soft data split, combining predictor and auto-encoder models. We introduce convolutional layer for learning the importance (time decay) of the purchases depending on their purchase date and demonstrate that the shape of the time decay function can be well approximated by a parametrical function. We present offline experimental results showing that neural networks with two hidden layers can capture seasonality changes, and at the same time outperform other modeling techniques, including our recommender in production. Most importantly, we demonstrate that our model can be scaled to all digital categories, and we observe significant improvements in an online A/B test. We also discuss key enhancements to the neural network model and describe our production pipeline. Finally we open-sourced our deep learning library which supports multi-gpu model parallel training. This is an important feature in building neural network based recommenders with large dimensionality of input and output data.
Riparian zone as a main determinant of the structure of lizard assemblages in upland Amazonian forests

The use of lizards as model organisms in ecological studies is based on their success in occupying a great diversity of habitats, and some species are closely tied to the environment, which is disadvantaged by the legislation of several countries concerning land use. Our aim was to relate lizard species distribution patterns in rainforest environments to variation in environmental gradients, and provide ecologically based metrics for establishing buffer zones around streams. Lizards were sampled three times in 41 standardised transects near Manaus, Brazil, only in dry season, with Time Limited Visual Search associated with raking through leaf litter. We recorded 20 species from 10 families and used non‐metric multidimensional scaling to reduce the dimensionality of quantitative and qualitative compositions of species. Multiple linear regression models indicated that the environmental gradients distance to nearest stream, extent of canopy openness, vegetation density and slope did not significantly influence assemblage species distribution, with an indication of effect of litter depth. By means of piecewise linear regression, the use of riparian zone was estimated at ~190 m from quantitative species composition and ~211 m from qualitative species composition. Five species occurred only in the riparian zone. Our results suggest that conservation of the entire riparian lizard assemblage in Amazonian rainforest is likely to require protection of at least a 211 m buffer on either side of streams.
An adaptive write word-line pulse width and voltage modulation architecture for bit-interleaved 8T SRAMs

We propose an adaptive WWL pulse width and voltage modulation architecture for low voltage bit-interleaved 8T SRAMs. The 8T bitcell offers improved read/write margins but suffers from write and half select concerns when bit-interleaved [1]. Also, low voltage operation leads to a long-tailed write time distribution, requiring large timing margins and limiting Vmin. To minimize timing margins and reduce Vmin, both WWL pulse width and voltage level are adaptively modulated by monitoring written values through the read path. In a 65nm CMOS prototype chip, Vmin is lowered from 700mV to 500mV using this technique, providing 2.55× leakage power reduction and 2.4× active power reduction.
Blood-based diagnostics of traumatic brain injuries

Traumatic brain injury is a major health and socioeconomic problem that affects all societies. However, traditional approaches to the classification of clinical severity are the subject of debate and are being supplemented with structural and functional neuroimaging, as the need for biomarkers that reflect elements of the pathogenetic process is widely recognized. Basic science research and developments in the field of proteomics have greatly advanced our knowledge of the mechanisms involved in damage and have led to the discovery and rapid detection of new biomarkers that were not available previously. However, translating this research for patients’ benefits remains a challenge. In this article, we summarize new developments, current knowledge and controversies, focusing on the potential role of these biomarkers as diagnostic, prognostic and monitoring tools of brain-injured patients.
Inpatient Characteristics of the Child Admitted With Chronic Pain

OBJECTIVE: To define the demographic, diagnostic, procedural, and episode of care characteristics for children admitted with chronic pain. METHODS: We used the Pediatric Health Information System database to obtain data on demographic characteristics, length of stay, readmission rates, diagnoses, and procedures for children admitted with chronic pain. Patients with sickle cell disease, cancer, burns, cerebral palsy, transplants, and ventilator-dependent children were excluded. RESULTS: A total of 3752 patients with chronic pain were identified from 2004 through 2010. Admissions increased by 831% over this time period. The mean age of these patients was 13.5 years, the most common race was white (79%), and female subjects outnumbered male subjects by 2.41 to 1. The most common admission and principal discharge diagnosis was abdominal pain; comorbid diagnoses were common, with a mean of 10 diagnoses per patient. In total, 65% of patients had a comorbid gastrointestinal diagnosis and 44% had a psychiatric diagnosis. The mean length of stay was 7.32 days, with an expected length of stay of 4.24 days; 12.5% were readmitted at least once within 1 year. They underwent a mean of 3.18 procedures per patient. CONCLUSIONS: The average child admitted with chronic pain is a teenaged female with a wide variety of comorbid conditions, many of which are gastrointestinal and psychiatric in nature. Admissions for chronic pain are rising and account for substantial resource utilization. Future studies should further characterize this population, with the overall objective of improving outcomes and optimizing cost-effective care.
The evolution of learning in a semipresential discipline - Analysis based on data mining concepts / A evolução do aprendizado em uma disciplina semipresencial - Análise baseada em conceitos da mineração de dados

Davenport (2014) stated that the data is extremely broad and electronically generated, and therefore requires specially prepared tools to deal with any and all information that can be found, analyzed and harnessed in a timely manner. To obtain data and use them properly, enables a company to improve a product, create a more efficient marketing strategy, cut costs, increase its production, avoid wastage, overcome a competitor, make services more satisfactory, check the performance of a student, among others. This study aims to analyze the use of 113 students based on their grade and the number of accesses in a virtual learning environment, enrolled in a semipresencial discipline in the first half of 2017. The data were extracted from an AVA installed from of Moodle and initially tabulated in a spreadsheet, with subsequent analysis and implementation in the R software. The results demonstrate an improvement in the students' scores associated with the number of accesses. Indicating that with some adjustments learning can evolve.
Rashba spin–orbit coupling and spin precession in carbon nanotubes

The Rashba spin–orbit coupling in carbon nanotubes and its effect on spin-dependent transport properties are analysed theoretically. We focus on clean non-interacting nanotubes with tunable number of subbands N. The peculiar band structure is shown to allow in principle Datta–Das oscillatory behaviour in the tunnelling magnetoresistance as a function of gate voltage, despite the presence of multiple bands. We discuss the conditions for observing Datta–Das oscillations in carbon nanotubes.
The Great Depression and the Friedman-Schwartz Hypothesis

We evaluate the Friedman-Schwartz hypothesis that a more accommodative monetary policy could have greatly reduced the severity of the Great Depression. To do this, we first estimate a dynamic, general equilibrium model using data from the 1920s and 1930s. Although the model includes eight shocks, the story it tells about the Great Depression turns out to be a simple and familiar one. The contraction phase was primarily a consequence of a shock that induced a shift away from privately intermediated liabilities, such as demand deposits and liabilities that resemble equity, and towards currency. The slowness of the recovery from the Depression was due to a shock that increased the market power of workers. We identify a monetary base rule which responds only to the money demand shocks in the model. We solve the model with this counterfactual monetary policy rule. We then simulate the dynamic response of this model to all the estimated shocks. Based on the model analysis, we conclude that if the counterfactual policy rule had been in place in the 1930s, the Great Depression would have been milder.