LLukas22/scidocs huggingface dataset:
Multilayered Omics-Based Analysis of a Head and Neck Cancer Model of Cisplatin Resistance Reveals Intratumoral Heterogeneity and Treatment-Induced Clonal Selection.

Purpose: Platinum-based drugs, in particular cisplatin (cis-diamminedichloridoplatinum(II), CDDP), are used for treatment of squamous cell carcinoma of the head and neck (SCCHN). Despite initial responses, CDDP treatment often results in chemoresistance, leading to therapeutic failure. The role of primary resistance at subclonal level and treatment-induced clonal selection in the development of CDDP resistance remains unknown.Experimental Design: By applying targeted next-generation sequencing, fluorescence in situ hybridization, microarray-based transcriptome, and mass spectrometry-based phosphoproteome analysis to the CDDP-sensitive SCCHN cell line FaDu, a CDDP-resistant subline, and single-cell derived subclones, the molecular basis of CDDP resistance was elucidated. The causal relationship between molecular features and resistant phenotypes was determined by siRNA-based gene silencing. The clinical relevance of molecular findings was validated in patients with SCCHN with recurrence after CDDP-based chemoradiation and the TCGA SCCHN dataset.Results: Evidence of primary resistance at clonal level and clonal selection by long-term CDDP treatment was established in the FaDu model. Resistance was associated with aneuploidy of chromosome 17, increased TP53 copy-numbers and overexpression of the gain-of-function (GOF) mutant variant p53R248L siRNA-mediated knockdown established a causal relationship between mutant p53R248L and CDDP resistance. Resistant clones were also characterized by increased activity of the PI3K-AKT-mTOR pathway. The poor prognostic value of GOF TP53 variants and mTOR pathway upregulation was confirmed in the TCGA SCCHN cohort.Conclusions: Our study demonstrates a link of intratumoral heterogeneity and clonal evolution as important mechanisms of drug resistance in SCCHN and establishes mutant GOF TP53 variants and the PI3K/mTOR pathway as molecular targets for treatment optimization. Clin Cancer Res; 24(1); 158-68. ©2017 AACR.
Wideband High Directive Aperture Coupled Microstrip Antenna Design by Using a FSS Superstrate Layer

In this communication a high directive electromagnetic bandgap (EBG) antenna operating in wide frequency band for both return loss (RL) and directivity is examined. In this EBG antenna an aperture coupled microstrip antenna (ACMA) is used as a feeding source and a frequency selective surface (FSS) is used as a superstrate layer. Suitable use of the superstrate layer, microstrip patch and coupling aperture simultaneously, leads to produce separate resonance frequencies and therefore the wide frequency band for RL. Also, high directivity is achieved only by using the superstrate layer that has been made by the FSS layer with square loop elements. At first, a wideband ACMA is designed to operate in x-band. In this step appropriate design of coupling aperture is of a great importance. Secondly, after the design of optimum superstrate layer by the FSS structure, it is added to the ACMA in order to increase both bandwidth and directivity.
On Solving the Linear Programming Problem Approximately

This paper studies the complexity of some approximate solutions of linear programming problems with real coefficients.
Magnetic Characterisation of Rocks Underlying FUTA Campus, South-Western Nigeria

The Federal University of Technology, Akure Campus is predominantly underlain by the Migmatite-gneiss-quartzite complex of the West African Basement Rocks, which forms part of the Pan-African mobile belt. Geo-magnetic characterisation of the underlying rocks was conducted in order to determine the rock boundaries and geologic features within the near surface and subsurface areas of the Campus. Both qualitative and quantitative interpretations of total magnetic intensity data obtained in the area yielded results in terms of different rock units, linear magnetic fabrics, subsurface features and depth to basement of the rocks. On the basis of magnetic response, four rocks units including Granite, Migmatite gneiss, Charnokite and Quartzite were delineated, with varying degree of fabrics’ alterations. Depth-to-bedrock in the Campus varies from 0 to 98.5 m, while depth to fracture/fault in the area falls between 0.1 m and 149.6 m. Keywords : Geo-magnetic characterisation, depth-to-bedrock,   rock fabric, total magnetic intensity, magnetic response
Comparison of Non-Intrusive Polynomial Chaos and Stochastic Collocation Methods for Uncertainty Quantification

Non-intrusive polynomial chaos expansion (PCE) and stochastic collocation (SC) methods are attractive techniques for uncertainty quantification (UQ) due to their strong mathematical basis and ability to produce functional representations of stochastic variability. PCE estimates coefficients for known orthogonal polynomial basis functions based on a set of response function evaluations, using sampling, linear regression, tensor-product quadrature, or Smolyak sparse grid approaches. SC, on the other hand, forms interpolation functions for known coefficients, and requires the use of structured collocation point sets derived from tensor-products or sparse grids. When tailoring the basis functions or interpolation grids to match the forms of the input uncertainties, exponential convergence rates can be achieved with both techniques for general probabilistic analysis problems. In this paper, we explore relative performance of these methods using a number of simple algebraic test problems, and analyze observed differences. In these computational experiments, performance of PCE and SC is shown to be very similar, although when differences are evident, SC is the consistent winner over traditional PCE formulations. This stems from the practical difficulty of optimally synchronizing the form of the PCE with the integration approach being employed, resulting in slight overor under-integration of prescribed expansion form. With additional nontraditional tailoring of PCE form, it is shown that this performance gap can be reduced, and in some cases, eliminated.
Switching Strategy Based on Model Predictive Control of VSI to Obtain High Efficiency and Balanced Loss Distribution

This paper proposes the switching strategy based on finite control set model predictive control (FCS-MPC) method, to reduce switching losses and obtain balanced loss distribution of the voltage-source inverters (VSIs). Unlike the conventional FCS-MPC method with no explicit information of the reference voltage, the developed voltage-based FCS-MPC scheme produces the future reference voltage vector with the Lyapunov function every sampling period. With information of both the future reference voltage and the future load current vectors, the proposed switching strategy instantaneously determines one optimum clamped phase among the three legs in the VSI every sampling period. By optimally determining the clamping phase and its duration on the basis of every sampling period, the proposed switching strategy can successfully reduce the VSI switching losses. In addition, the proposed switching method can yield a balanced loss distribution among the switches in the VSI, contrary to the conventional FCS-MPC. The balanced loss generation as well as the switching loss reduction by the proposed method, which is optimal at the sampling period scale, is directly incorporated with the platform of the FCS-MPC algorithm, since the FCS-MPC operates on the basis of the sampling period. Thus, the proposed switching operation based on the voltage-based FCS-MPC algorithm enables the future VSI output currents to track the future reference current vector, as well as results in the reduced switching losses and the balanced loss performance.
Analysing and presenting qualitative data

This paper provides a pragmatic approach to analysing qualitative data, using actual data from a qualitative dental public health study for demonstration purposes. The paper also critically explores how computers can be used to facilitate this process, the debate about the verification (validation) of qualitative analyses and how to write up and present qualitative research studies.
ABUNDANCE OF FRANKLINIELLA SCHULTZEI (THYSANOPTERA: THRIPIDAE) IN FLOWERS ON MAJOR VEGETABLE CROPS OF SOUTH FLORIDA

The flower thrips, Frankliniella schultzei (Trybom), has only recently been recognized as a pest of vegetable crops in south Florida. Little is known about its abundance and impact on vegetable crops in this region. Therefore, a field experiment was conducted comparing F. schultzei abundance in blooms of the 5 key fruiting vegetable crops grown in south Florida, i.e., cucumber, pepper, snap bean, squash and tomato. Mean number of F. schultzei larvae was highest in cucumber flowers (78.1 larvae/5 flowers) and lowest in bean flowers (5.1 larvae/5 flowers). However, adults of F. schultzei were most numerous in tomato flowers (27.5 adults/5 flowers) and least numerous in snap bean flowers (3.5 adults/ 5 flowers). Neither larvae nor adults of F. schultzei were found in pepper flowers in the present study. The flower samples collected from 5 vegetable crops were also found to be infested with 3 other thrips species. Amongst these, Thrips palmi Karny was the second most abundant thrips species. Frankliniella occidentalis (Pergande) was found in low numbers on all crops except pepper, and Frankliniella fusca (Hinds) was found only on tomato. The above information should be useful in the development of monitoring programs, design of pest management strategies and in the timely application of preventive or suppressive measures in south Florida.
Building multiclass classifiers for remote homology detection and fold recognition

Protein remote homology detection and fold recognition are central problems in computational biology. Supervised learning algorithms based on support vector machines are currently one of the most effective methods for solving these problems. These methods are primarily used to solve binary classification problems and they have not been extensively used to solve the more general multiclass remote homology prediction and fold recognition problems. We present a comprehensive evaluation of a number of methods for building SVM-based multiclass classification schemes in the context of the SCOP protein classification. These methods include schemes that directly build an SVM-based multiclass model, schemes that employ a second-level learning approach to combine the predictions generated by a set of binary SVM-based classifiers, and schemes that build and combine binary classifiers for various levels of the SCOP hierarchy beyond those defining the target classes. Analyzing the performance achieved by the different approaches on four different datasets we show that most of the proposed multiclass SVM-based classification approaches are quite effective in solving the remote homology prediction and fold recognition problems and that the schemes that use predictions from binary models constructed for ancestral categories within the SCOP hierarchy tend to not only lead to lower error rates but also reduce the number of errors in which a superfamily is assigned to an entirely different fold and a fold is predicted as being from a different SCOP class. Our results also show that the limited size of the training data makes it hard to learn complex second-level models, and that models of moderate complexity lead to consistently better results.
Advantages and applications of vehicle to grid mode of operation in plug-in hybrid electric vehicles

Reduction in green house gas emissions, increase in oil prices and dependency on foreign oil are major incentives to the development and deployment of Plug-in hybrid electric vehicles. The plug-in hybrid electric vehicle fleet is expected to increase the base electric load and add constraints on the reliable operation of a power system. However, equipped with bidirectional battery chargers, plug-in hybrid electric vehicles offer the power grid a flexible load, known as vehicle to grid mode of operation, capable of contributing to power system operations by supplying ancillary services. This paper gives an overview of the state of the art in battery technologies and charger requirements. The advantages and requirement for operating in vehicle to grid mode is presented. Alleviation of wind generation and improvement of short-term voltage stability are some of the potential benefits of the vehicle to grid mode.
On the unusual effectiveness of logic in computer science

In 1960, E.P. Wigner, a joint winner of the 1963 Nobel Prize for Physics, published a paper titled On the Unreasonable Effectiveness of Mathematics in the Natural Sciences [Wig60]. This paper can be construed as an examination and affirmation of Galileo’s tenet that “The book of nature is written in the language of mathematics”. To this effect, Wigner presented a large number of examples that demonstrate the effectiveness of mathematics in accurately describing physical phenomena. Wigner viewed these examples as illustrations of what he called the empirical law of epistemology, which asserts that the mathematical formulation of the laws of nature is both appropriate and accurate, and that mathematics is actually the correct language for formulating the laws of nature. At the same time, Wigner pointed out that the reasons for the success of mathematics in the natural sciences are not completely understood; in fact, he went as far as asserting that “ . . . the enormous usefulness of mathematics in the natural sciences is something bordering on the mysterious and there is no rational explanation for it.” In 1980, R.W. Hamming, winner of the 1968 ACM Turing Award for Computer Science, published a follow-up article, titled The Unreasonable Effectiveness of Mathematics [Ham80]. In this article, Hamming provided further examples manifesting the effectiveness of mathematics in the natural sciences. Moreover, he attempted to answer the “implied question” in Wigner’s article: “Why is mathematics so unreasonably effective?” Although Hamming offered several partial explanations, at the end he concluded that on balance this question remains “essentially unanswered”. Since the time of the publication of Wigner’s article, computer science has undergone a rapid, wideranging, and far-reaching development. Just as in the natural sciences, mathematics has been highly effective in computer science. In particular, several areas of mathematics, including linear algebra, number theory, probability theory, graph theory, and combinatorics, have been instrumental in the development of computer science. Unlike the natural sciences, however, computer science has also benefitted from an extensive and continuous interaction with logic. As a matter of fact, logic has turned out to be significantly more effective in computer science than it has been in mathematics. This is quite remarkable, especially since much of the impetus for the development of logic during the past one hundred years came from mathematics.
FRACTURING TRUSS MODEL: SIZE EFFECT IN SHEAR FAILURE OF REINFORCED CONCRETE

The classical truss model (or strut-and-tie model) for shear failure of reinforced concrete beams is modified to describe fracture phenomena during failure. The failure is assumed to be caused by propagation of a compression fracture across the concrete strut during the portion of the loading history in which the maximum load is reached. The compression fracture may consist of a band of splitting cracks that later interconnect to form a shear crack or a shear fracture band inclined to the strut. The width of the fracture band is assumed to occupy only a portion of the strut length and to represent a fixed material property independent of the beam depth. The energy release from the truss is calculated using two alternative approximate methods: (1) using the potential energy change deduced from the concept of stress relief zones; and (2) using the complementary energy change due to stress redistribution caused by propagation of the fracture band across the compressed concrete strut. Both approaches show that a size effect on the nominal strength of shear failure must exist and that it should approximately follow the size effect law proposed by BaZant in 1984. The physical mechanism of the size effect is also explained in a clear and simple intuitive manner. Finally, it is shown that the applied nominal shear stress that causes large initial diagonal cracks to form also exhibits a size effect.
An Australian translational Study to evaluate the prognostic role of inflammatory markers in patients with metastatic ColorEctal caNcer Treated with bevacizumab (Avastin™) [ASCENT]

The use of bevacizumab in combination with fluoropyrimidine-containing chemotherapy is a well-established first-line and second-line treatment for patients with metastatic colorectal cancer (mCRC). However, there remains a need for reproducible, validated, inexpensive and accessible prognostic markers to aid treatment selection. The optimal treatment duration and the role of bevacizumab in certain patient subgroups, considered at particular risk of bevacizumab-mediated toxicity, also require further investigation. The aim of the ASCENT study [an Australian translational Study to evaluate the prognostic role of inflammatory markers in patients with metastatic ColorEctal caNcer Treated with bevacizumab (Avastin™)] is to evaluate the relationship between the host inflammatory response as measured by neutrophil/lymphocyte ratio (NLR) and treatment outcomes in patients with previously untreated mCRC receiving bevacizumab-based first- and second-line treatment. This open-label, prospective, single arm, phase IV, Australian multi-centre study evaluates the relationship between the host inflammatory response as measured by NLR and treatment outcomes in patients with previously untreated mCRC receiving bevacizumab-based first- and second-line treatment. 150 patients will be recruited from 16 centres around Australia. Patients will receive trial treatments in two phases: Phase A: XELOX or mFOLFOX6 plus bevacizumab administered from study start until first disease progression; and Phase B: FOLFIRI plus bevacizumab administered from first disease progression until second disease progression. The primary analysis will test the association between NLR and progression free survival using a proportional Hazards Model. Secondary analyses will investigate whether the relationship can be improved upon with other prognostic biomarkers, and further characterise the safety of bevacizumab following treatment initiation, and when continued after progression in combination with standard chemotherapy regimens (presented through summary statistics and Kaplan Meier curves). Quantifying the relationship between NLR and PFS will inform decision making on the extent to which this simple metric may be applied clinically. ClinicalTrials.gov: NCT01588990
Standard versus pH-adjusted and lidocaine supplemented radiocolloid for patients undergoing sentinel-lymph-node mapping and biopsy for early breast cancer (PASSION-P trial): a double-blind, randomised controlled trial.

BACKGROUND
Sentinel-lymph-node (SLN) mapping and biopsy maintains staging accuracy in early breast cancer and identifies patients for selective lymphadenectomy. SLN mapping requires injection of technetium-99m-sulfur colloid-an effective but sometimes painful method, for which better pain-management strategies are needed. In this randomised, double-blind trial, we compared degree of pain between standard radiocolloid injection and pH-adjusted and lidocaine-supplemented formulations for patients undergoing SLN mapping for breast cancer.


METHODS
Between Jan 13, 2006, and April 30, 2009, 140 patients with early breast cancer were randomly assigned in a 1:1:1:1 fashion to receive the standard topical 4% lidocaine cream and injection of [(99m)Tc]Tc-sulfur colloid (n=35), or to one of three other study groups: topical placebo cream and injection of Tc-sulfur colloid containing either sodium bicarbonate (n=35), 1% lidocaine (n=35), or sodium bicarbonate and 1% lidocaine (n=35). The randomisation sequence was computer generated, and all patients and investigators were masked to treatment allocation. The primary endpoint was patient-reported breast pain immediately after radioisotope injection, using the Wong-Baker FACES pain rating scale and McGill pain questionnaire, analysed in the per-protocol population. This study is registered with ClinicalTrials.gov, number NCT00940199.


FINDINGS
19 of the 140 patients enrolled were excluded from analysis: nine declined study participation or sought care elsewhere, nine did not undergo SLN mapping because of disease extent or a technical problem, and one had unreliable data. There were no adverse events. Mean pain scores on the Wong-Baker scale (0-10) were: 6.0 (SD 2.6) for those who received standard of practice, 4.7 (3.0) for those who received radiocolloid plus bicarbonate, 1.6 (1.4) for those who received radiocolloid plus 1% lidocaine, and 1.6 (1.3) for those who received radiocolloid plus bicarbonate and 1% lidocaine (p<0.0001). Mean pain rating, according to the McGill questionnaire (0-78), was 17.5 (SD 11.8) for the standard-of-care group, 15.4 (14.4) for the sodium bicarbonate group, 4.6 (4.5) for the 1% lidocaine group, and 3.4 (5.1) for the sodium bicarbonate plus 1% lidocaine group (p<0.0001). SLN identification rates for each group were: 96% for the standard of care, 97% for sodium bicarbonate, 90% for 1% lidocaine, and 90% for sodium bicarbonate plus 1% lidocaine group (p=0.56).


INTERPRETATION
For centres that use radiocolloid injections for SLN mapping in patients with early breast cancer, the addition of 1% lidocaine to the radioisotope solution can improve patient comfort, without compromising SLN identification.


FUNDING
US Military Cancer Institute, the Clinical Breast Care Project, and the Army Regional Anesthesia and Pain Management Initiative.
Development of exchange lists for Mediterranean and Healthy Eating diets: implementation in an intervention trial.

BACKGROUND
There has been little research published on the adaptation of diabetic exchange list diet approaches for the design of intervention diets in health research despite their clinical utility. The exchange list approach can provide clear and precise guidance on multiple dietary changes simultaneously. The present study aimed to develop exchange list diets for Mediterranean and Healthy Eating, and to evaluate adherence, dietary intakes and markers of health risks with each counselling approach in 120 subjects at increased risk for developing colon cancer.


METHODS
A randomised clinical trial was implemented in the USA involving telephone counselling. The Mediterranean diet had 10 dietary goals targeting increases in mono-unsaturated fats, n-3 fats, whole grains and the amount and variety of fruits and vegetables. The Healthy Eating diet had five dietary goals that were based on the US Healthy People 2010 recommendations.


RESULTS
Dietary compliance was similar in both diet arms, with 82-88% of goals being met at 6 months, although subjects took more time to achieve the Mediterranean goals than the Healthy Eating goals. The relatively modest fruit and vegetable goals in the Healthy Eating arm were exceeded, resulting in fruit and vegetable intakes of approximately eight servings per day in each arm after 6 months. A significant (P < 0.05) weight loss and a decrease in serum C-reactive protein concentrations were observed in the overweight/obese subgroup of subjects in the Mediterranean arm in the absence of weight loss goals.


CONCLUSIONS
Counselling for the Mediterranean diet may be useful for both improving diet quality and for achieving a modest weight loss in overweight or obese individuals.