nils-herrmann/clean_scirepeval huggingface dataset:
Quality Control Strategy for CRISPR-Cas9-Based Gene Editing Complicated by a Pseudogene

CRISPR-Cas9 mediated gene editing in induced pluripotent stem cells became an efficient tool to investigate biological mechanisms underlying genetic-driven diseases while accounting for the respective genetic background. This technique relies on the targeting of a specific nucleotide sequence present in the gene of interest. Therefore, the gene editing of some genes can be complicated by non-coding pseudogenes presenting a high homology of sequence with their respective genes. Among them, GBA is raising special interest because of its implication as the most common genetic risk factor for Parkinson’s disease. In this study, we present an easy-to-use CRISPR-Cas9 gene editing strategy allowing for specific editing of point mutations in a gene without genetic alteration of its pseudogene exemplified by the correction or insertion of the common N370S mutation in GBA. A quality control strategy by combined fluorescence and PCR-based screening allows the early identification of correctly edited clones with unambiguous identification of the status of its pseudogene, GBAP1. Successful gene editing was confirmed by functional validation. Our work presents the first CRISPR-Cas9 based editing of a point mutation in GBA and paves the way for technically demanding gene engineering due to the presence of pseudogenes.

Field of study: Biology
The effects of physics-based data augmentation on the generalizability of deep neural networks: demonstration on nodule false positive reduction.

An important challenge for deep learning models is generalizing to new datasets that may be acquired with acquisition protocols different from the training set. It is not always feasible to expand training data to the range encountered in clinical practice. We introduce a new technique, physics-based data augmentation (PBDA), that can emulate new CT data acquisition protocols. We demonstrate two forms of PBDA, emulating increases in slice thickness and reductions of dose, on the specific problem of false positive reduction in the automatic detection of lung nodules.



We worked with CT images from the Lung Image Database Consortium (LIDC) collection. We employed a hybrid ensemble convolutional neural network (CNN), developed by Shen1 and which consists of multiple CNN modules (VGG, DenseNet, ResNet), for a classification task of determining whether an image patch was a suspicious nodule or a false positive. To emulate a reduction in tube current, we injected noise by simulating forward projection, noise addition, and backprojection corresponding to 1.5 mAs (a "chest x-ray" dose). To simulate thick slice CT scans from thin slice CT scans, we grouped and averaged spatially contiguous CT within thin slice data. The neural network was trained with 10% of the LIDC dataset that was selected to have either the highest tube current or the thinnest slices. The network was tested on the remaining data. We compared PBDA to a baseline with standard geometric augmentations (such as shifts and rotations) and Gaussian noise addition.



PBDA improved the performance of the networks when generalizing to the test dataset in a limited number of cases. We found that the best performance was obtained by applying augmentation at very low doses (1.5 mAs), about an order of magnitude less than most screening protocols. In the baseline augmentation, a comparable level of Gaussian noise was injected. For dose reduction PBDA, the average sensitivity of 0.931 for the hybrid ensemble network was not statistically different from the average sensitivity of 0.935 without PBDA. Similarly for slice thickness PBDA, the average sensitivity of 0.900 when augmenting with doubled simulated slice thicknesses was not statistically different from the average sensitivity of 0.895 without PBDA. While there were cases detailed in this paper in which we observed improvements, the overall picture was one that suggests PBDA may not be an effective data enrichment tool.



PBDA is a newly proposed strategy for mitigating the performance loss of neural networks related to the variation of acquisition protocol between the training dataset and the data that is encountered in deployment or testing. We found that PBDA does not provide robust improvements with the four neural networks (three modules and the ensemble) tested and for the specific task of false positive reduction in nodule detection. This article is protected by copyright. All rights reserved.

Field of study: Medicine, Physics
Design of Data Terminal Processing Software of WP3103 Automatic Weather Station

For WP3103 automatic weather station,designs a composite application platform which integrates functions of data reception,display,processing,monitor and equipment maintenance.Based on the analysis of the system functional requirements,mainly introduces the design concept of system structure,and describes the function of the major subsystems and flow char.The system has been used within the Guangdong Province,the actual running result shows that the system in real-time data processing of automatic weather stations processes is timely and accurately,operates steadily and reliably.

Field of study: Computer science
The Challenge of Producing Fiber-Based Organic Electronic Devices

The implementation of organic electronic devices on fibers is a challenging task, not yet investigated in detail. As was shown earlier, a direct transition from a flat device structure to a fiber substrate is in principle possible. However, a more detailed investigation of the process reveals additional complexities than just the transition in geometry. It will be shown, that the layer formation of evaporated materials behaves differently due to the multi-angled incidence on the fibers surface. In order to achieve homogenous layers the evaporation process has to be adapted. Additionally, the fiber geometry itself facilitates damaging of its surface due to mechanical impact and leads to a high surface roughness, thereby often hindering commercial fibers to be used as substrates. In this article, a treatment of commercial polymer-coated glass fibers will be demonstrated that allows for the fabrication of rather flexible organic light-emitting diodes (OLEDs) with cylindrical emission characteristics. Since OLEDs rely the most on a smooth substrate, fibers undergoing the proposed treatment are applicable for other organic electronic devices such as transistors and solar cells. Finally, the technique also supports the future fabrication of organic electronics not only in smart textiles and woven electronics but also in bent surfaces, which opens a wide range of applications.

Field of study: Materials science
Application of quantitative RT-PCR to the analysis of dopamine receptor mRNA levels in rat striatum.

A quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) procedure has been developed which selectively amplifies and quantifies the two isoforms of the dopamine D2 receptor. Variability is corrected by the inclusion of a D2 dopamine receptor mRNA standard within each reaction. The internal standard was generated by introducing a point mutation within a D2 cDNA clone that created a unique restriction site within the amplified region. An in vitro transcribed RNA for the internal mutant control is added to the RNA isolated from brain tissue and the mixture is subjected to RT-PCR, digestion with the restriction enzyme, separation of the products by PAGE, and quantification by direct analysis of radioactivity incorporated during the PCR step. The standard is amplified, in the same reaction as the experimental RNA, using the same primers and RT-PCR conditions. In this manner, the effects of contaminants of the RNA preparation which could affect the amplification procedure are assessed. To insure that the amplification is linear, the number of PCR cycles is minimized. This adaptation avoids 'competitive PCR' and provides for a linear response. Moreover, to obviate non-specific co-amplification, primer annealing steps are performed at or above the melting temperature for the primers, thus increasing signal-to-noise ratios. Finally, primer pairs have been designed which permit amplification of specific fragments for each of the five rat dopamine receptor subtypes. These fragments have unique sizes and so can be differentiated when simultaneously amplified in the same RNA preparations.

Field of study: Biology
Taphonomic degradation of molluscan remains during thirteen years on the continental shelf and slope of the northwestern Gulf of Mexico

In 1993, SSETI (Shelf and Slope Experimental Taphonomy Initiative) deployed shells of a suite of molluscan species in a variety of environments of preservation (EOPs) covering a range of depths and sediment types on the Gulf of Mexico continental shelf and upper slope, with the goal of measuring taphonomic rates over an extended period of time. SSETI retrieved shells from these EOPs after 2, 8, and 13 years. The degree of shell degradation was significantly influenced by species, elapsed time-since-deployment, and EOP. A suite of ‘physical’ taphonomic processes, such as dissolution, abrasion, discoloration, and edge alteration, increased in severity over the 13 years; fragmentation occurred in some species. Dissolution proceeded apace; however the incidence of chalkiness declined from high levels observed after a few years while the more extreme levels of dissolution, such as the development of a soft or deeply-dissolved surface, rose significantly in frequency. The incidence of original color declined, while fading of original color increased. Brown-to-red and green discoloration rose rapidly in the first eight years and then declined, leaving a faded shell surface. Between-habitat differences in degradation rate were significant for most taphonomic attributes. Between-species differences were minor in comparison. Thus, taphofacies, the product of the independent actions of a suite of taphonomic processes, originate from and provide information on environmental conditions. Species composition has a lesser inherent influence on the outcome. Not uncommonly, the rates of change in shell condition differed significantly between EOPs although the direction of change was coincident. This was particularly true of the summary indices such as maximum discoloration or the average degree of dissolution. The taphonomic process is nonlinear in time. Nonlinearity is EOP-dependent, becoming a defining attribute leading to disparate taphofacies types. Some taphonomic processes cannot proceed expeditiously without prior alteration of the shell through other taphonomic means. Some taphonomic conditions such as chalkiness can be intermediate states. The presumption that similar taphonomic characteristics between EOPs indicate similar environmental processes operating at similar rates is falsified by SSETI sites in which similar taphonomic indices at Year 13 accrued from different time-varying degradational rates during the preceding years.

Field of study: Environmental science, Geography
Catholic Teaching on Life and the Challenge of the HIV/AIDS Crisis in Sub-Saharan Africa

Drawing from Catholic teaching this paper acknowledges that these communities are obliged to provide pain relief for these victims. For reasons that will be studied in detail treatments beyond this should be regarded as extraordinary and therefore not an obligation. This is based on the fact that ordinary means of treatment are relative to the availability of resources. The resources in the sub-Saharan region are not sufficient to provide any treatment beyond pain relief. This papers focus is on Catholic teaching pertaining to morally necessary measures to prolong life in the HIV/AIDS epidemic in sub- Saharan Africa. The discussion will begin with the development of Catholic teaching on prolonging life and will continue with the principles of ordinary and extraordinary means. Then these principles will be applied to the socioeconomic conditions in sSA. (excerpt)

Field of study: Medicine, Philosophy
Ordering Lusztig’s families in type Bn

Let W be a finite Coxeter group and L be a weight function on W in the sense of Lusztig. We have recently introduced a pre-order relation ⪯L on the set of irreducible characters of W which extends Lusztig’s definition of “families” and which, conjecturally, corresponds to the ordering given by Kazhdan–Lusztig cells. Here, we give an explicit description of ⪯L for W of type Bn and any L. (All other cases are known from previous work.) This crucially relies on some new combinatorial constructions around Lusztig’s “symbols”. Combined with previous work, we deduce general compatibility results between ⪯L and Lusztig’s a-function, valid for any W,L.

Field of study: Mathematics
Hyperfine structure and isotope shifts of neutron-rich138–146Cs

The 6s2S1/2-7p2P3/2 transition in138–142Cs (λ=455.5 nm) has been investigated by high-resolution collinear laser spectroscopy in a fast atomic beam. The isotopes are obtained by on-line mass separation of fission products. Nuclear moments and changes of mean-square charge radii are derived from hyperfine structure and isotope shift.

Field of study: Physics
Low-Noise Wide-Band Amplifier System for Stochastic Beam Cooling Experiments

A new low-noise wide-band power amplifier system has been developed for stochastic beam cooling experiments. The system incorporates a low-noise preamplifier with a noise figure of 1.9 dB over a bandwidth range of 20 to 300 MHz, wide-band driver and buffer stages, a frequency characteristics shaping network, a remotely controlled wide-band attenuator with 0.1 dB resolution, a remotely controlled high resolution adjustable delay line, and a wide-band solid-state output power amplifier. The amplifier system has a maximum voltage gain of 140 dB over a bandwidth from 1.5 to 310 MHz, a signal group delay of 55.5 ns, and a c. w. output power level of 75 W. Particular attention was paid to minimizing the signal propagation time delay of the amplifier system, the propagation time delay change as a function of the system gain, and harmonic and intermodulation distortions. Using a new wide-band electron bombarded semiconductor output amplifier, the system will have a bandwidth from 30 to 400 MHz, a signal group delay of 37 ns and an output power of 100 W.

Field of study: Physics
DISCUSSIONS ON PROBABILISTIC SEISMIC DEMAND MODELS

As an important element of seismic fragility and risk analysis,the probabilistic seismic demand analysis has become a main component of the new-generation of performance-based earthquake engineering(PBEE).The key issue of probabilistic seismic demand analysis is to derive a probabilistic seismic demand model,that denotes the probabilistic relationship between earthquake intensity and seismic demand.Given a specified level of earthquake intensity,seismic demand is generally assumed to submit to a lognormal distribution.A log-line relationship is assumed between earthquake intensity and the median value of seismic demand,while the logarithm standard deviation of seismic demand is assumed invariant.In order to examine the validity of the above assumptions adopted in the probabilistic seismic demand model,four RC frame buildings of various heights and fortification levels are taken as test beds,and one hundred real ground motions are selected as inputs.The results show that the assumptions of the median and logarithm standard deviation of seismic demand are adequate for a probabilistic seismic demand model considering the balance of accuracy and efficiency.However,the conventional lognormal model for seismic demand cannot incorporate the case of collapse,thus it should be modified.

Field of study: Engineering
The thickness of Neogene and Quaternary cover across the central Interior Plateau, British Columbia: analysis of water-well drill records and implications for mineral exploration potential

Analysis of over 10 000 water-well records has been used to produce new depth-to-bedrock maps for areas around five cities on the central Interior Plateau of central British Columbia: 100 Mile House, Prince George, Quesnel, Vanderhoof, and Williams Lake. Hitherto, exploration for mineral and hydrocarbon resources has been hampered by a lack of basic knowledge of the thickness of Neogene and Quaternary lithologies. Interpretation of these new maps provides first-order constraints on the localization of thick drift in pre-Late Wisconsinan bedrock paleovalleys, some of which are now buried. Basalt lavas of the Chilcotin Group are restricted to erosional remnants of previously extensive sheets emplaced onto an older peneplain. Our results confirm that the Neogene and Quaternary cover is primarily controlled by paleotopography and is generally thin and patchy across much of the region. Increased understanding of the three-dimensional distribution of cover produces a corresponding increase in the utility of geological, geochemical, and geophysical exploration techniques, and a reduction in the risk for future mineral exploration activities, especially when combined with more sophisticated data sets.

Field of study: Environmental science
Quaternary palaeolakes in the evolution of semidesert basins, with special emphasis on Lake Bonneville and the Great Basin, U.S.A.

This paper reviews attributes of Quaternary lakes and lake basins which are often important in the environmental prehistory of semideserts. Basin-floor and basin-closure morphometry have set limits on palaeolake sizes; lake morphometry and basin drainage patterns have influenced lacustrine processes; and water and sediment loads have influenced basin neotectonics. Information regarding inundated, runoff-producing, and extra-basin spatial domains is acquired directly from the palaeolake record, including the littoral morphostratigraphic record, and indirectly by reconstruction. Increasingly detailed hypotheses regarding Lake Bonneville, the largest late Pleistocene palaeolake in the Great Basin, are subjects for further testing and refinement. Oscillating transgression of Lake Bonneville began about 28 ka, the highest stage occurred about 15 ka, and termination occurred abruptly about 13 ka. A final resurgence of perennial lakes probably occurred in many subbasins of the Great Basin between 11 and 10 ka, when the highest stage of Great Salt Lake (successor to Lake Bonneville) developed the Gilbert shoreline — and when the Russell shoreline formed 500–600 km away, in the Carson Desert of the Lake Lahontan basin. The highest post-Gilbert stage of Great Salt Lake, which has been one of the few permanent lakes in the Great Basin during Holocene time, probably occurred between 3 and 2 ka. A set of eighteen general observations regarding geologic aspects of the palaeolake record in semidesert basins is helping to guide Quaternary studies in the Great Basin.

Field of study: Environmental science, Geography
Determination of N-Methylcarbamate Insecticide Metolcarb by Enzyme-Linked Immunosorbent Assay

The hapten of the N -methylcarbamate insecticide metolcarb, 3-{[1-(3-(methyl)phenyloxy)carbonyl]amino}propanoic acid (HOM), was synthesized and conjugated with the carrier proteins bovine serum albumin (BSA) and ovalbumin (OVA), respectively, by the active ester method. The conjugate of HOM-BSA was used as immunogen, and we prepared rabbits' anti-metolcarb serum, the titres of which were determined by noncompetitive indirect ELISA procedures and reached 1.28×10 6 . The results of the cross reaction indicate that the antiserum produced could specially recognize the insecticide metolcarb. After optimization of the ELISA conditions, such as ionic strengths, organic solvents, pH values, blocking agents, and so on, the proper parameters of ELISA procedure were determined, and an assay protolcol for the N -methylcarbamate insecticide metolcarb was established. On the basis of statistical analysis, the linear range of determination was from 1 to 104 ng/mL, IC50 was 40.74 ng/mL, limit detection was 0.08–0.10 ng/mL, intra-assay coefficient of variation (CV) reached 2.9%, and inter-assay CV reached 4.6%. The recoveries obtained by standard metolcarb addition to different samples such as rice, water, and soil were 80, 93.4, and 107%, respectively. This is the first time that polyclonal antibodies to the N -methylcarbamate insecticide metolcarb are produced, and the ELISA, used here for efficient and available detection of metolcarb, may become a convenient and satisfied analytical tool for monitoring metolcarb residues in environmental and agricultural samples.

Field of study: Chemistry
Students’ Self-Efficacy and Self-Rating Scores as Predictors of Their Academic Achievement

This study set out to establish the predictive power of students’ self-efficacy and self-rating scores on undergraduate students’ academic achievement in a Psychology course (psychology of Learning). The correlational research design was adopted and all the 133 sophomores in the Continuing Education Programme (CEP) of the Nnamdi Azikiwe University, Awka, Nigeria who registered the course were sampled for the study. The instruments used were a domain-specific self-efficacy questionnaire and a semester examination developed by the researchers. The regression analysis showed that self-efficacy and self-rating did not combine to predict students’ achievement; however, considering their relative contribution, students’ self-rating scores predicted their academic performance more than their self-efficacy. Furthermore, students’ self-efficacy and self-rating scores were related, but only students’ self-rating scores were related to their academic achievement. It was concluded that large self-efficacy is not enough to counter limited knowledge and competence. DOI: 10.5901/jesr.2014.v4n3p223

Field of study: Education, Sociology
The Growth of Bureaucracy in Brazil, 1808–1821

In late November of 1807 the Portuguese government was loaded on to a fleet of naval and merchant vessels, transported across the South Atlantic and deposited in Rio de Janeiro.1 On board were fourteen members of the Royal Family; the Counsellors of State; ministers; Justices of the Court of Appeals and the High Court; the upper echelons of the army and navy; the hierarchy of the church; a full quota of high society; a respectable contingent of the professional, scientific, literary, artistic and business elements; a horde of bureaucrats; and as many rank and file citizens as could secure passage. Also on board were the contents of the royal treasury; the store of diamonds derived from the crown monopoly; silver plate, jewels, books, cash and other portable assets; furnishings for a royal chapel; the royal library; a printing press; and a mass of government records. When John, the Prince Regent, set up shop in Rio de Janeiro, he had readily available the personnel and the files of a bureaucracy for the administration of a national state.2 The bureaucracy was abundantly supplied with candidates. The personnel 3 who accompanied the Court were augmented by a flow of emigres 4 which continued unabated as long as the Court remained in Rio. Many of both groups looked to the Crown for support. In some instances the Court

Field of study: Political science