nils-herrmann/clean_scirepeval huggingface dataset:
Genetic investigation of breast ductal carcinoma In situ: A literature review

The incidence of ductal carcinoma in situ (DCIS) of the breast has greatly increased in countries with breast cancer early detection programs. However, uncertainty remains about its natural history and precise implication of its diagnosis with growing concern in some quarters about possible overdiagnosis and overtreatment. Various molecular techniques have been applied to the investigation of DCIS in an attempt to clarify its biology in relation to invasive breast cancer. The following is a historical tour of some of those molecular studies and the contributions they have made to our understanding of DCIS. It is preceded by a recap of the DCIS conundrum and the uncertainties surrounding its natural history. Peer-reviewed scientific publications on the subject were retrieved by search of PubMed databases. The search was conducted with the following string of keywords: “breast carcinoma in situ genetics,” “breast carcinoma in situ molecular biology,” and “ductal carcinoma in situ molecular method technique.” Reference lists of retrieved articles were scrutinized for additional, relevant publications.

Field of study: Medicine
Effects of 'Queen' and 'Smooth cayenne' pineapple fruit core extracts on browning inhibition of fresh-cut wax apple fruit during storage.

The purpose was to investigate the browning inhibitory effect of ‘Queen’ and ‘Smooth cayenne’ pineapple fruit core extracts (PE) on fresh-cut wax apple fruit cv. ‘Taaptipjan’ during storage. Bromelain yield, pH and total phenols content of both pineapple fruits core and pulp extracts and superficial colour and overall acceptability score of the fresh-cut fruit were determined. ‘Queen’ pineapple fruit had bromelain yield, pH and total phenols content higher than ‘Smooth cayenne’ pineapple fruit. Both ‘Queen’ and ‘Smooth cayenne’ PE contained higher bromelain yield and pH and lower total phenols content than the both fruit pulp extracts. The 50% (v/v) of ‘Queen’ PE dip maintained lightness (L*) value and whiteness index (WI), lowered colour difference, browning index (BI) and browning score (BC) when compared to the 50% (v/v) of ‘Smooth cayenne’ PE dip and control, respectively. The overall acceptability score of the freshcut fruit dipped in ‘Queen” PE was also higher than that of fruit dipped in ‘Smooth cayenne’ PE and control, respectively. In conclusion, both ‘Queen’ and ‘Smooth cayenne’ PE could prevent browning of fresh-cut wax apple fruit during storage which the browning inhibition effect might due to the bromelain yield content. ‘Queen’ PE had higher bromelain yield content and browning inhibitory property than ‘Smooth cayenne’ PE.

Field of study: Agricultural and Food sciences
Lattice dynamics and baric behavior of phonons in Hg2Cl2 crystals at high hydrostatic pressures

A theoretical model based on long-range dispersion corrections of the charge density functional is proposed for model Hg2Cl2 calomel crystals, typical representatives of molecular inorganic compounds where the intermolecular interaction is found to play an important role. This model successfully describes the electronic state and the phonon spectrum of the above crystal, predicts the earlier unstudied phase transition at high hydrostatic pressure. Study of the baric behavior of the phonon spectrum with Raman spectroscopy observes the soft mode in the low-symmetry orthorhombic phase with the frequency softening as the pressure rises. Pressures above 9 GPa considerably transform the Raman spectra, indicating a structural phase transition.

Field of study: Physics
SAMPLING IN BIOGEOCHEMISTRY

Sampling is of vital importance in biogeochemical investigations. In particular:

(1) Only organs of the same age should be compared.

(2) Preferably that organ of a tree which responds best to the element being investigated should be selected.

(3) Second-year twigs give more reproducible results than do first-year twigs.

(4) Lower and top branches may not contain the same amounts of a metal.

(5) A few specific elements are concentrated in larger amounts in particular plants: where practicable the use of these accumulator plants simplifies operations and provides better contrast between normal and anomalous samples.

(6) Anomalies are better detected when results are expressed in p.p.m. of ash rather than of dry plant.

Analyses of plants collected on the property of the Graham Bosquet Mines near Vancouver, B. C. graphically illustrate some of the above points.

Field of study: Geology
Establishment of Atmosphere Pressure-Temperature Programmed Pyrolysis-Mass Spectrometric System and Its Application on Decarboxylation of Coal

A quartz tube reactor was designed to combine with a commercial mass spectrometer for on-line detecting the gases evolved during pyrolysis of coal and other samples with high volatile. The reliability and repeatability of this atmosphere pressure-temperature programmed pyrolysis-mass spectrum ( AP-TPP-MS) system were tested by model compound and real coal sample. The results show that pyrolysis of model compound can give good response,less overlap or tailing gases evolution curves; and multi-peaks can be observed from the same gas curve of real sample. The reliability and repeatability of this system are perfect and the system can be applied to study the coals decarboxylation by comparing the CO2 evolution curves.

Field of study: Chemistry
Beijerinck and the bioluminescent bacteria: microbiological experiments in the late 19th and early 20th centuries.

Microbiological research in the days before specialized equipment, or even electricity, required a great deal of ingenuity. The revival of 90-year-old bioluminescent bacteria from Beijerinck's laboratory in Delft prompted a review of his work with these microorganisms and revealed their use in simple techniques for the investigation of, among other things, sugar metabolism in yeasts, oxygen generation and uptake and even the survival of microorganisms in liquid hydrogen. He used variant strains of bioluminescent bacteria in an attempt to study heredity and variation in biological systems and described one of the earliest examples of enzyme induction.

Field of study: Biology, Environmental science
Drug seeking under a second-order schedule of reinforcement depends on dopamine D3 receptors in the basolateral amygdala.

Drug seeking under the control of drug-associated stimuli and its reinstatement after extinction can be decreased by systemic administration of dopamine D3 receptor antagonists. It is demonstrated that responding by rats on the active lever for cocaine under a 2nd-order schedule of reinforcement, under which responding is maintained by response-contingent cocaine-paired conditioned reinforcers, is markedly attenuated by infusion of the dopamine D3 receptor antagonist SB-277011-A into the amygdala (2 and 4 microg/0.3 microl). By contrast, infusions of SB-277011-A into the shell subregion of the nucleus accumbens and also into the dorsal striatum were without effect. These results show that the control over drug seeking by conditioned reinforcers depends on D3 receptor-dependent dopamine transmission in the amygdala.

Field of study: Biology, Psychology
[Antithrombin activity and platelet aggregation by acid mucopolysaccharides isolated from Stichopus japonicus Selenka].

Human and rabbit’s platelet aggregations were induced by a kind of acid mucopolysaccharide isolated from Stichopus japonicus Selenka(Sjamp). The platelet aggregation curve induced by Sjamp was similar to that induced by ADP. The activity of Sjamp inducing platelet aggregation was dependent on the presence of Ca2+ in the medium, but not affected by aspirin. The antithrombin activity of Sjamp was weaker than that of heparin. The mode of action is different since it was neither dependent upon the antithrombin-III nor inhibited by platelet factor 4.

Field of study: Biology, Chemistry, Medicine
Systematics and taxonomy of soft-shelled turtles (Family Trionychidae) from the Judith River Group (mid-Campanian) of

Four valid species of trionychine trionychid turtles are recognized from the Upper Cretaceous (mid-Campanian; Judithian) Judith River Group, western North America. Cladistic analysis of extant and Judith River Group trionychines supports referral of three fossil species to Aspideretoides gen. nov. and one fossil species to Apalone, the genus of extant North American trionychines. The taxonomic diversity of Judith River Group trionychids is less than that of younger Maastrichtian and Paleocene assemblages from the Western Interior, largely because of the absence of plastomenine trionychids in the Judith River Group assemblage.

Field of study: Environmental science
Quantitative versus subjective evaluation of mammography accreditation phantom images.

The precision of quantitative and subjective evaluations of phantom image quality has been studied. Twenty-seven images of the American College of Radiology (ACR) mammography accreditation phantom were acquired under different x-ray techniques and digitized. Several quantitative image quality measures were obtained from each image by analyzing microcalcification and nodule target objects in the phantom. All images were also scored subjectively by 8 observers, each of whom provided a count of the number of objects seen in each target class (fibrils, microcalcifications, and nodules). An analysis was performed to predict the subjective measurements from the quantitative measurements and to estimate their variabilities. It was found that the subjective measures could be well predicted by the quantitative measures and that the variance of the quantitative measures was significantly smaller than that of the subjective measure, by almost a factor of 10. The implication for the ACR accreditation program for mammography is that a substantial improvement is possible in the image quality evaluation process by performing computerized analysis of the phantom images in addition to subjective analysis.

Field of study: Medicine, Physics
Different bacterial communities associated with the roots and bulk sediment of the seagrass Zostera marina.

The bacterial community of Zostera marina-inhabited bulk sediment vs. root-associated bacteria was investigated by terminal restriction fragment length polymorphism and sequencing, and the spatial extension of the oxygen loss from roots was determined by oxygen microsensors. Extensive oxygen loss was found in the tip region of the youngest roots, and most of the rhizoplane of Z. marina roots was thus anoxic. A significant difference between the bacterial communities associated with the roots and bulk sediment was found. No significant differences were found between differently aged root-bundles. Terminal restriction fragments (TRFs) assigned to sulfate-reducing Deltaproteobacteria showed a relative mean distribution of 12% and 23% of the PCR-amplified bacterial community in the bulk-sediment at the two sites, but only contributed <2% to the root-associated communities. TRFs assigned to Epsilonproteobacteria showed a relative mean distribution of between 5% and 11% in the root-associated communities of the youngest root bundle, in contrast to the bulk-sediment where this TRF only contributed <1.3%. TRFs assigned to Actinobacteria and Gammaproteobacteria also seemed important first root-colonizers, whereas TRFs assigned to Deltaproteobacteria became increasingly important in the root-associated community of the older root bundles. The presence of the roots thus apparently selects for a distinct bacterial community, stimulating the growth of potential symbiotic Epsilon- and Gammaproteobacteria and/or inhibiting the growth of sulfate-reducing Deltaproteobacteria.

Field of study: Biology, Environmental science
Novel programs of food anaphylactogen and the importance of anaphylactogen in food security

Anaphylactogen can stimulate bodies and force the body to response. Anaphylactogen from foods can also bring diseases, it becomes an important problem in society. The problem caused by anaphylactogen from foods belongs to a respect of food secureity it also involves the field of clinical medicine. This article explans the detection methods of anaphylactogen and anaphylactogen in food security.

Field of study: Agricultural and Food sciences
Monte Carlo and experimental derivation of TG43 dosimetric parameters for CSM-type Cs-137 sources.

In this study, complete dosimetric datasets for the CSM2 and CSM3 Cs-137 sources were obtained using the Monte Carlo GEANT4 code. The application of this calculation method was experimentally validated with thermoluminescent dosimetry (TLD). Functions and parameters following the TG43 formalism are presented: the dose rate constant, the radial dose functional, and the anisotropy function. In addition, to aid the quality control process on treatment planning systems, a two-dimensional (2D) rectangular dose rate table (the traditional along-away table), coherent with the TG43 dose calculation formalism, is given. The data given in this study complement existing information for both sources on the following aspects: (i) the source asymmetries were considered explicitly in the Monte Carlo calculations, (ii) TG43 data were derived directly from Monte Carlo calculations, (iii) the radial range of the different tables was increased as well as the angular resolution in the anisotropy function, including angles close to the longitudinal source axis. The CSM2 source TG-43 data of Liu et al.  are not consistent with the Williamson 2D along-away data [ (1988)] at distances closer than approximately 2 cm from the source. The data presented here for this source are consistent with this 2D along-away table, and are suitable for use in clinical practice.

Field of study: Medicine, Physics
MIEC (mixed-ionic-electronic-conduction)-based access devices for non-volatile crossbar memory arrays

Several attractive applications call for the organization of memristive devices (or other resistive non-volatile memory (NVM)) into large, densely-packed crossbar arrays. While resistive-NVM devices frequently possess some degree of inherent nonlinearity (typically 3?30? contrast), the operation of large ( 1000?1000 device) arrays at low power tends to require quite large ( 1e7) ON-to-OFF ratios (between the currents passed at high and at low voltages). One path to such large nonlinearities is the inclusion of a distinct access device (AD) together with each of the state-bearing resistive-NVM elements. While such an AD need not store data, its list of requirements is almost as challenging as the specifications demanded of the memory device. Several candidate ADs have been proposed, but obtaining high performance without requiring single-crystal silicon and/or the high processing temperatures of the front-end-of-the-line?which would eliminate any opportunity for 3D stacking?has been difficult.We review our work at IBM Research?Almaden on high-performance ADs based on Cu-containing mixed-ionic-electronic conduction (MIEC) materials [1?7]. These devices require only the low processing temperatures of the back-end-of-the-line, making them highly suitable for implementing multi-layer cross-bar arrays. MIEC-based ADs offer large ON/OFF ratios (), a significant voltage margin (over which current nA), and ultra-low leakage ( 10 pA), while also offering the high current densities needed for phase-change memory and the fully bipolar operation needed for high-performance RRAM. Scalability to critical lateral dimensions 30 nm and thicknesses 15 nm, tight distributions and 100% yield in large (512 kBit) arrays, long-term stability of the ultra-low leakage states, and sub-50 ns turn-ON times have all been demonstrated. Numerical modeling of these MIEC-based ADs shows that their operation depends on mediated hole conduction. Circuit simulations reveal that while scaled MIEC devices are suitable for large crossbar arrays of resistive-NVM devices with low ( 1.2 V) switching voltages, stacking two MIEC devices can support large crossbar arrays for switching voltages up to 2.5 V.

Field of study: Materials science
The Dattoli-Srivastava conjectures concerning generating functions involving the harmonic numbers

In a recent paper Dattoli and Srivastava , by resorting to umbral calculus, conjectured several generating functions involving harmonic numbers. In this sequel to their work our aim is to rigorously demonstrate the truth of the Dattoli-Srivastava conjectures by making use of simple analytical arguments. In addition, one of these conjectures is stated and proved in more general form.

Field of study: Mathematics
Foundations for measuring IT-outsourcing success and failure

We implemented five easy-to-complete questionnaires in Excel, which could serve as early warning signals for practitioners interested in the odds of their IT-outsourcing deals and could serve to redirect their course when still possible. The questionnaires are based on our earlier published longitudinal, observational study on 30 representative ITO-deals in the Netherlands, of which we know whether they failed or not. Our questionnaires predicted their outcome correctly. To help redirect the course of a dubious deal, we developed a questionnaire estimating the odds in relation to boosting strongly significant critical success determinants. Another questionnaire guides practitioners how to further improve on less critical factors. There are no specific reasons that limit our results to the Dutch situation, which makes it promising, therefore, to apply the Excel as an aid in improving ITO deals in other contexts.

Field of study: Computer science, Engineering
Time delay estimation of soft-sensor model based on hybrid differential evolution algorithm

Time delay estimation is one of the most important issues in system control and signal processing.Through establishing an appropriate fitness function,the time delay estimation of soft-sensor model could be formulated as a multi-dimension nonlinear functional optimization problem,which could be solved by hybrid differential evolution(HDE)algorithm.Numerical simulation results on two benchmarks demonstrated the effectiveness and robustness of HDE.Taking a crude atmospheric distillation unit in oil refinery as an example,a numerical application of the soft-sensor model for the kerosene flash point was made.The application results demonstrated that the accuracy of soft-sensor model was greatly improved with the introduction of time delay estimation.Besides,the effectiveness of the proposed HDE was confirmed.

Field of study: Chemistry, Environmental science
Transport across a topoelectrical Weyl semimetal heterojunction

We propose a general method to realize and calculate the transmission in a Weyl semimetal (WSM) heterostructure by employing a periodic three-dimensional topoelectrical (TE) circuit network. By drawing the analogy between inductor-capacitor circuit lattices and quantum mechanical tight-binding (TB) models, we show that the energy flux in a TE network is analogous to the probability flux in a TB Hamiltonian. TE systems offer a key advantage in that they can be easily tuned to achieve different topological WSM phases simply by varying the capacitances and inductances. The above analogy opens the way to the study of tunneling across heterojunctions separating different types of WSMs in TE circuits, a situation which is virtually impossible to realize in physical WSM materials. We show that the energy flux transmission in a WSM heterostructure depends highly on the relative orientation of the transport direction and the $k$-space tilt direction. For the transmission from a Type I WSM source lead to a Type II WSM drain lead, all valleys transmit equally when the tilt and transmission directions are perpendicular to each other. In contrast, large inter-valley scattering is required for transmission when the tilt and transport directions are parallel to each other, leading to valley-dependent transmission. We describe a Type III WSM phase intermediate between the Type I and Type II phases. An `anti-Klein' tunneling occurs between a Type I source and Type III drain where the transmission is totally suppressed for some valleys at normal incidence. This is in direct contrast to the usual Klein tunneling in Dirac materials where normally incident flux is perfectly transmitted. Owing to the ease of fabrication and experimental accessibility, TE circuits offer an excellent testbed to study the extraordinary transport phenomena in WSM based heterostructures.

Field of study: Physics
Combining Landscape Genomics and Ecological Modelling to Investigate Local Adaptation of Indigenous Ugandan Cattle to East Coast Fever

East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were investigated using molecular data and epidemiological information from 823 indigenous cattle from Uganda. Vector distribution and host infection risk were estimated over the study area and subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. PRKG1 was already described as associated with tick resistance in indigenous South African cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways involved into lymphocytes' proliferation. Additionally, local ancestry analysis suggested the zebuine origin of the genomic region candidate for tick resistance.

Field of study: Biology
The Double Dutch Technique: Split Ileal Graft and Double Monti Tube in Ileocystoplasty

We introduce a modification of ileocystoplasty combined with double Monti tube. This modification prevents the dog ear of the ileum during detuberalisation and also the Monti tube is supported by the surrounding mesenterium of the ileal augment.  In 5 patients that needed ileocystoplasty the new technique has been used. Four patients had a small neuropathic bladder, one patient had a small contracted bladder without neurological disorder. The surgical technique is as follows: 30 or 40 cm ileum is isolated and plicated in a U shape and completely divided in the middle. A 16 mm wide strip of ileum is then cut from the top of the right ileal part, and a similar strip is cut from the bottom of the left ileal part. The strips are cut near the mesentery to form the Monti tubes. The small strips are tubelarised and joined in the middle to form a catheterisable tube. The ileal segments are opened antimesenterially. These ileal flaps are closed over the Monti tube in the middle. The lower part of the Monti tube is implanted with a submucosal tunnel in the bladder wall and the ileal patch is then anastomosed with the bladder. The Monti tube is anastomosed to the umbilicus in an ordinary way without any traction.  All patients have umbilical stoma's without leakage or strictures. Intermittend cathetrisation is very easy. It seems that the Monti tubes are strait and well supported by the surrounding tissues so that kinking is not possible. The augmented bladders show excellent volume and compliance.  Although we treated only a small number of patients we are convinced that this modification provides advantages during the procedure and produces better results in the future.

Field of study: Medicine