gebhart/patrepeval huggingface dataset:
Protein Quantitation through Targeted Mass Spectrometry: The Way Out of Biomarker Purgatory? (2008)

The enormous potential of biomarkers to revolutionize clinical practice and improve patient care has been well documented (1)(2). Molecular-based diagnostic and prognostic tests, particularly those aimed at protein analytes, could be used to detect disease earlier, enabling treatment to start sooner and possibly cure rather than to merely delay further injury or death. These tools could also be used to stage disease more accurately and to predict response to therapy, thereby helping to select the correct treatment. Biomarkers can also be used to stratify patients for the assessment of new drug therapies and to serve as surrogate endpoints in early-phase drug trials, thereby lowering the overall cost of drug development and producing more effective treatments. Given their high potential therapeutic and financial impacts, that so few new protein biomarkers have been introduced into widespread clinical use recently is, on the surface, surprising. In fact, only 5 new protein markers have been approved by the US Food and Drug Administration in the last 5 years for measurement in plasma or serum \[the information on protein markers in Anderson and Anderson, 2002, has been updated with information from the Center for Devices and Radiological Health, US Food and Drug Administration\] (3)(4).

The reasons for the dearth of new protein biomarkers are gradually becoming clearer. They are related to the high false-discovery rate of “omics” methods (regardless of the technology used), combined with a lack of robust methods for biomarker verification in large clinical sample sets (5)(6)(7)(8). It is now common for differential analyses of tissue or plasma samples by multidimensional liquid chromatography–tandem mass spectrometry (LC-MS/MS)1 (the workhorse tool for unbiased discovery) to confidently identify thousands of proteins, hundreds of which can vary in concentration by 5-fold or more between case …
Feature Selection for multi-labeled variables via Dependency Maximization (2019)

Feature selection and reducing the dimensionality of data is an essential step in data analysis. In this work, we propose a new criterion for feature selection that is formulated as conditional information between features given the labeled variable. Instead of using the standard mutual information measure based on Kullback-Leibler divergence, we use our proposed criterion to filter out redundant features for the purpose of multiclass classification. This approach results in an efficient and fast non-parametric implementation of feature selection as it can be directly estimated using a geometric measure of dependency, the global Friedman-Rafsky (FR) multivariate run test statistic constructed by a global minimal spanning tree (MST). We demonstrate the advantages of our proposed feature selection approach through simulation. In addition the proposed feature selection method is applied to the MNIST data set.
New developments in Ricci flow with surgery (2020)

We give a survey of the developments surrounding Ricci flow in dimension 3 after Perelman's work and explain the connection with the partial resolution of the Generalized Smale Conjecture.
Evidence implicating nonmuscle myosin in restenosis. Use of in situ hybridization to analyze human vascular lesions obtained by directional atherectomy. (1992)

These findings demonstrate that 1) human vascular tissue obtained by percutaneous directional atherectomy constitutes appropriate biopsy material for gene expression studies at the mRNA level, and 2) nonmuscle MHC-B mRNA is present in greater abundance among restenotic versus primary vascular stenoses. These observations thus provide a rational basis to explore restenotic lesions on a larger scale to identify genes that are activated in these lesions and establish potential targets for future gene therapy.
Smithson Tennant (2015)

Smithson Tennant (1761---1815), a British physician turned chemist and chemical engineer, published very few papers but they were signiﬁcant enough as to leave a mark in science and technology. He proved that diamond is a pure allotropic form of carbon, established that carbon dioxide was composed of only carbon and oxygen, discovered iridium and osmium in the residue of platinum ore, invented a simple procedure for producing potassium in large quantities, and established the basis of multiple effect evaporation. In addition, he proved the deleterious effect of magnesium oxide and carbonate in agriculture, emery was a variety of corundum, and that potassium nitrate reacted with gold.
Compressive hyperspectral imaging by random separable projections in both the spatial and the spectral domains (2013)

An efficient method and system for compressive sensing of hyperspectral data is presented. Compression efficiency is achieved by randomly encoding both the spatial and the spectral domains of the hyperspectral datacube. Separable sensing architecture is used to reduce the computational complexity associated with the compressive sensing of a large volume of data, which is typical of hyperspectral imaging. The system enables optimizing the ratio between the spatial and the spectral compression sensing ratios. The method is demonstrated by simulations performed on real hyperspectral data.
DSP for Coherent Single-Carrier Receivers (2009)

In this paper, we outline the design of signal processing (DSP) algorithms with blind estimation for 100-G coherent optical polarization-diversity receivers in single-carrier systems. As main degrading optical propagation effects, we considered chromatic dispersion (CD), polarization-mode dispersion (PMD), polarization-dependent loss (PDL), and cross-phase modulation (XPM). In the context of this work, we developed algorithms to increase the robustness of the single DSP receiver modules against the aforesaid propagation effects. In particular, we first present a new and fast algorithm to perform blind adaptive CD compensation through frequency-domain equalization. This low complexity equalizer component inherits a highly precise estimation of residual dispersion independent from previous or subsequent blocks. Next, we introduce an original dispersion-tolerant timing recovery and illustrate the derivation of blind polarization demultiplexing, capable to operate also in condition of high PDL. At last, we propose an XPM-mitigating carrier phase recovery as an extension of the standard Viterbi-Viterbi algorithm.
Mast cell infiltration correlates with poor prognosis in Hodgkin's lymphoma (2002)

Hodgkin's lymphoma (HL) is characterized by a few Hodgkin, Reed-Sternberg cells (HRS) surrounded by benign cells. We recently reported that mast cells were the predominant CD30L-positive cells in HL tumours, and that they activate HRS in vitro through CD30L-CD30 interaction. Here, we investigated the clinical importance of mast cell infiltration in the tumours of 123 patients. Tumour specimens were stained with a mast-cell-specific antibody that detects tryptase. Mast cells were detected in virtually every case and increasing numbers of mast cells correlated to nodular sclerosis histology (P = 0.008). Patients with higher mast cell infiltration had a worse relapse-free survival (P = 0.01).
Hepatitis C virus early kinetics and resistance‐associated substitution dynamics during antiviral therapy with direct‐acting antivirals (2018)

The emergence of resistance-associated substitutions (RASs) can compromise the high efficacy of direct-acting antivirals (DAAs). Little is known about RASs selection at very early time points during DAA treatment. Therefore, we analyzed the potential emergence of RASs immediately after therapy initiation. Samples of 71 patients treated with different DAAs were collected at baseline, during therapy (hours 4 and 8; days 1-7; weeks 2-4) or until target not detected. HCV-RNA levels were determined by qPCR, and RASs were detected by deep sequencing. Sixty-three (89%) patients achieved a sustained virological response (SVR), 7 (10%) relapsed, and 1 (1%) experienced a breakthrough. Almost all non-SVR (7/8, 88%) showed RASs either at baseline or relapse. High-frequency RASs detected at baseline (Y93H and L159F+C316N) remained detectable at early time points during therapy and reappeared as most prevalent substitutions at relapse. Conversely, emergent RASs at relapse (Q80R, D168E/V, R155K and L31V) were not observed during the first hours-days, before HCV-RNA became undetectable. HCV-RNA decay and genetic evolution of the quasispecies followed a similar pattern during the first hours of therapy in SVR and non-SVR patients. In conclusion, the absence of early RASs selection and the similar dynamics of HCV kinetics and quasispecies in SVR and non-SVR patients after therapy initiation suggest that RASs selection may occur at later stages in the remaining reservoir, where viral populations persist hidden at very low replication levels. Nevertheless, we cannot completely exclude very early selection, when RASs are present below the sensitivity limit of deep sequencing.
Investigation of coercive squareness in TbFeCo films (1991)

TbFeCo is one of the most promising magnetooptical recording media because it shows a high uniaxial anisotropy and a fairly good Kerr effect, and its composition can be tailored to achieve a large room temperature coercivity. A basic study was carried out to determine the factors affecting the mechanisms of magnetization reversal and the regularity of domain growth at room temperature in TbFeCo films. A technique has been established to quantify the regularity of domain growth in terms of coercive squareness. It has been observed that intrinsic magnetization and uniaxial anisotropy are the two most significant parameters to affect coercive squareness. Deposition processes and conditions have a very slight influence on coercive squareness.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Building Data Mining Applications for CRM (1999)

From the Publisher:
How data mining delivers a powerful competitive advantage!
Are you fully harnessing the power of information to support management and marketing decisions? You will,with this one-stop guide to choosing the right tools and technologies for a state-of-the-art data management strategy built on a Customer Relationship Management (CRM) framework. 
Authors Alex Berson,Stephen Smith,and Kurt Thearling help you understand the principles of data warehousing and data mining systems,and carefully spell out techniques for applying them so that your business gets the biggest pay-off possible. 
Find out about Online Analytical Processing (OLAP) tools that quickly navigate within your collected data. Explore privacy and legal issues. . . evaluate current data mining application packages. . . and let real-world examples show you how data mining can impact  and improve  all of your key business processes. Start uncovering your best prospects and offering them the products they really want (not what you think they want)!
How data mining delivers a powerful competitive advantage! 
Are you fully harnessing the power of information to support management and marketing decisions? 
You will,with this one-stop guide to choosing the right tools and technologies for a state-of-the-art data management strategy built on a Customer Relationship Management (CRM) framework. Authors Alex Berson,Stephen Smith,and Kurt Thearling help you understand the principles of data warehousing and data mining systems,and carefully spell out techniques for applying them so that your business gets the biggest pay-off possible. 
Find out about Online Analytical Processing (OLAP) tools thatquickly navigate within your collected data. Explore privacy and legal issues. . . evaluate current data mining application packages. . . and let real-world examples show you how data mining can impact  and improve  all of your key business processes. Start uncovering your best prospects and offering them the products they really want (not what you think they want)!
Effects of physically effective neutral detergent fibre content on dry-matter intake, digestibility and chewing activity in beef cattle fed total mixed ration (2014)

Our aim in this study was to determine the effects of physically effective neutral detergent fibre (peNDF) in a total mixed ration (TMR) on feed intake, digestibility and chewing activity in beef cattle. The experiment had a replicated 3 × 3 Latin square desig, using three fattening Hanwoo (Bos taurus coreanae) steers with ruminal cannulas. Steers were offered one of three diets (high, medium or low peNDF content) obtained by mixing the same TMR for different periods of time (5, 13 and 25 min). peNDF content of TMR was calculated as [total chewing time/NDF intake (kg)] × dietary NDF content, and the proportion of sample dry matter (DM) collected in a =1.18-mm sieve is commonly used as the physical effectiveness factor in the equation. The peNDF1.18 contents of the high, medium and low diets were 25.97%, 21.10% and 17.94% (P &amp;lt; 0.05). In addition, the proportion of particles collected on the 19-mm, 1.18-mm, and pan sieves changed linearly with an increase of TMR mixing time. Mean particle-size distributions of diets were 11.43, 24.11, 30.70 and 33.68 for 19 mm, 8 mm, 1.18 mm and pan, respectively. Eating rate and ruminating and chewing efficiencies were significantly decreased with reduced peNDF content, and DM intake was increased significantly (P &amp;lt; 0.05). Lower peNDF content reduced the total number of chews significantly (P &amp;lt; 0.05). Total time spent chewing associated with eating was not affected by peNDF contents. Digestibility of DM, crude protein and crude fat decreased with reducing peNDF content in the diet, but there was no significant difference among the three groups. These results indicated that peNDF affects intake, digestibility and chewing activity in beef cattle. Therefore, high levels of peNDF appears to improve TMR, as it can increase efficiency and may prevent ruminal disorders in Hanwoo steer.
Nested parallelism in transactional memory (2008)

This paper investigates adding transactions with nested parallelism and nested transactions to a dynamically multithreaded parallel programming language that generates only series-parallel programs. We describe XConflict, a data structure that facilitates conflict detection for a software transactional memory system which supports transactions with nested parallelism and unbounded nesting depth. For languages that use a Cilk-like work-stealing scheduler, XConflict answers concurrent conflict queries in O(1) time and can be maintained efficiently. In particular, for a program with T1 work and a span (or critical-path length) of T∞, the running time on p processors of the program augmented with XConflict is only O(T1/p + pT∞).
Motor and cognitive function in Lewy body dementia: comparison with Alzheimer's and Parkinson's diseases. (1997)

EPS in Lewy body dementia resemble those seen in idiopathic Parkinson's disease, although less rest tremor and left/right asymmetry but more severe rigidity favours a diagnosis of Lewy body dementia. The unique profile of patients with Lewy body dementia seen in the clock face test suggests that this simple and easy to administer test may be useful in the clinical setting to differentiate Lewy body dementia and Alzheimer's disease.
Lexical statistical machine translation for language migration (2013)

Prior research has shown that source code also exhibits naturalness, i.e. it is written by humans and is likely to be repetitive. The researchers also showed that the n-gram language model is useful in predicting the next token in a source file given a large corpus of existing source code. In this paper, we investigate how well statistical machine translation (SMT) models for natural languages could help in migrating source code from one programming language to another. We treat source code as a sequence of lexical tokens and apply a phrase-based SMT model on the lexemes of those tokens. Our empirical evaluation on migrating two Java projects into C# showed that lexical, phrase-based SMT could achieve high lexical translation accuracy (BLEU from 81.3-82.6%). Users would have to manually edit only 11.9-15.8% of the total number of tokens in the resulting code to correct it. However, a high percentage of total translation methods (49.5-58.6%) is syntactically incorrect. Therefore, our result calls for a more program-oriented SMT model that is capable of better integrating the syntactic and semantic information of a program to support language migration.
The impact of variability on the reliability of long on-chip interconnect in the presence of crosstalk (2008)

With deep submicron technologies, the importance of interconnect parasitics on delay and noise has been an ever increasing trend. Consequently the variation in interconnect parameters have a larger impact on final timing and functional yield of the product. We present a comprehensive analysis to quantify the impact of parametric variations on the reliability of global interconnect links in the presence of crosstalk. The impact of parametric variations on wire delay and crosstalk noise is studied for a global interconnect structure in 90nm UMC technology, followed by a novel technique to estimate the bit error rate (BER) of such links. This methodology is employed to explore the design space of interconnect channels in order to mitigate the impact of variability.
Enduracidin Analogues with Altered Halogenation Patterns Produced by Genetically Engineered Strains of Streptomyces fungicidicus (2010)

Enduracidins (1, 2) and ramoplanin (3) are structurally and functionally closely related lipodepsipeptide antibiotics. They are active against multi-drug-resistant Gram-positive pathogens, including MRSA. Each peptide contains one chlorinated non-proteinogenic amino acid residue, Cl(2)-Hpg or Cl-Hpg. To investigate the timing of halogenation and the importance of chlorination on bioactivity and bioavailability of enduracidin, and to probe the substrate specificity and portability of the ramoplanin halogenase, we constructed the mutant strain SfDelta30 in which the enduracidin halogenase gene orf30 had been deleted and complemented it with the ramoplanin counterpart orf20. We also expressed orf20 in the enduracidin wild-type producer. Metabolite analysis revealed SfDelta30 produced the novel analogues dideschloroenduracidins A (4) and B (5), while the recombinant strains SfDelta30R20 and SfR20 produced monodeschloroenduracidins A (6) and B (7) and a trichlorinated enduracidin (8), respectively. In addition, orf30 self-complementation yielded the strain SfDelta30E30, which is capable of producing six peptides including 6 and 7. MS/MS analysis positioned the single chlorine atom in 6 at Hpg(13) and localized the third chlorine atom in 8 to Hpg(11). Biological evaluation of these enduracidin analogues indicated that all retained activity against Staphylococcus aureus. Our findings lay the foundation for further utilization of enduracidin and ramoplanin halogenases in combinatorial biosynthesis.
Approches spontanées et expressions vocales d’un jeune enfant autiste non verbal en musicothérapie active incluant des couplages voix-gestuelle: étude de cas unique (2018)

Soumission à Epi-revel Early disorders of social communication can have a significant impact on the lives of people with Autism Spectrum Disorders (ASD). They do not only concern language difficulties but encompass several aspects of nonverbal communication, and are identifiable from early childhood, in the sensorimotor period, namely before expected entry into language. The communication of the bodies mixed with the vocal exchanges between the baby and his parents are essential for his good motor and psychic development. It is precisely on these aspects that the baby to become autistic encounters difficulties. In this unique case study, we propose to evaluate the impact of weekly music therapy sessions on the evolution of approach behaviors and vocal expressions of a young non-verbal child diagnosed with autism, aged three, during a school year. The proposals of voice-gesture couplings seem to allow an increase of these behaviors. International audience Les troubles précoces de la communication sociale peuvent impacter fortement la vie des personnes ayant des troubles du spectre autistique (TSA). Ils ne concernent pas uniquement les difficultés de langage mais englobent plusieurs aspects de la communication non verbale, et sont repérables dès la petite enfance, dans la période sensori-motrice, à savoir avant l’entrée attendue dans le langage. La communication des corps, mêlée aux échanges vocaux entre le bébé et ses parents sont essentiels pour son bon développement moteur et psychique. C’est précisément sur ces aspects que le bébé à devenir autistique rencontre des difficultés. Dans cette étude de cas unique, nous proposons d’évaluer l’impact de séances de musicothérapie hebdomadaires sur l’évolution des comportements d’approche et des manifestations vocales d’un jeune enfant non verbal diagnostiqué autiste, âgé de trois ans, pendant une année scolaire. Les propositions de couplages voix-gestuelle semblent permettre une augmentation de ces comportements.
Analysis and Modeling of Semantic Relationships in e-Catalog Domain (2004)

Building a domain-suited ontology, as a means to implement the Semantic Web, is widely believed to offer users the benefit of exploiting the semantic knowledge constrained in the application. Electronic Catalog, shortly e-Catalog, manages the information about the goods or conditions play an important role in e-commerce domain. Consequently, semantically enriched yet precise information by the ontology may elaborate the business transactions. In this paper, we analyze the semantic relationships embodied within the catalog domain, as the first step towards the ontological modeling of e-catalog. Exploring ontology should leverage not only the representation of semantic knowledge but also provide the inferencing capability for the model. We employ the EER(extended Entity Relationships) for the basic model. Each modeling construct can be directly translated by DL(Description Logics). Semantic constraints that can be hardly represented in EER are directly modeled in DL.
Complexation of Al(iii) with gluconate in alkaline to hyperalkaline solutions: formation, stability and structure (2013)

Contrary to suggestions in the literature, it has been proven that Al(III) forms a 1 : 1 complex with gluconate (hereafter Gluc(-)) in strongly alkaline (pH > 12) aqueous solutions. The complex formation was proven via(27)Al and (1)H NMR, freezing-point depression, polarimetric measurements as well as potentiometric and conductometric titrations. This complexation is a pH independent process, i.e., a condensation reaction takes place. The stability constant of the complex formed was derived from (1)H NMR and polarimetric measurements, and was found to be log K = 2.4 ± 0.4. In the complex formed, Al(III) has a tetrahedral geometry, and the Al(OH)4(-) is most probably statistically distributed between the alcoholate groups of the Gluc(-).
Significantly reduced lymphadenopathy, salivary gland infiltrates and proteinuria in MRL-lpr/lpr mice treated with ultrasoluble curcumin/turmeric: increased survival with curcumin treatment (2015)

These studies show that UsC/UsT could prove useful as a therapeutic intervention in SLE/SS.