nils-herrmann/clean_scirepeval huggingface dataset:
Quantitative analysis of retroviral and lentiviral gene transfer to murine embryonic stem cells.

The effectiveness of retrovirus or lentivirus transduction of embryonic stem (ES) cells is often limited because transgene expression is silenced or variegated. We wondered if other steps of transduction, in addition to gene expression, were restricted in ES cells. We quantitatively compared (1) the amount of virus binding, (2) the number of integrated transgenes, and (3) the resulting level of gene expression. We found that three- to fourfold fewer retroviruses and lentiviruses bound to R1 mES cells than to NIH 3T3 cells, suggesting that both types of viruses bind less efficiently to mES cells. Retroviruses and lentiviruses differed in the efficiency with which they completed post-binding steps of transduction. In R1 mES cells, we detected 3-fold fewer integrated retrovirus transgenes and 11-fold lower expression levels than in NIH 3T3 cells, which suggests that the primary limitation to retrovirus transduction may be low levels of transgene expression. In contrast, we detected 10-fold fewer integrated lentivirus transgenes and 8-fold lower expression levels in R1 mES cells than in NIH 3T3 cells, which suggests that lentivirus transduction may be limited by inefficient intracellular post-binding steps of transduction. The implications of our findings for developing improved viral vectors for transducing mES cells are discussed.

Field of study: Biology, Engineering
Numerical Simulation of Closed-die Extrusion Process of Oil Drill Stem Joints

Oil drill stem joints are typically hollow shaft parts. Aiming at problems of oil drill stem joints in hot forging, a hot closed-die extrusion forming process of vertical two-way with horizontal parting die was proposed. Combined with floating die technology, the forming process of drill stem joints was simulated by using the finite element software DEFORM-3D. Metal flow law, forming force and clamping force were analyzed. Research results show that vertical extrusion forming process is feasible, which has significant advantages of shortening the process flow and reducing the forming load.

Field of study: Materials science
Drosophila comet assay: insights, uses, and future perspectives

The comet assay, a very useful tool in genotoxicity and DNA repair testing, is being applied to Drosophila melanogaster since around 15 years ago, by several research groups. This organism is a valuable model for all kind of processes related to human health, including DNA damage response. The assay has been performed mainly in vivo using different larvae cell types (from brain, midgut, hemolymph, and imaginal disk), but also in vitro with the S2 cell line. Since its first application, it has been used to analyze the genotoxicity and action mechanisms of different chemicals, demonstrating good sensitivity and proving its usefulness. Moreover, it is the only assay that can be used to analyze DNA repair in somatic cells in vivo, comparing the effects of chemicals in different repair strains, and to quantitate repair activities in vitro. Additionally, the comet assay in Drosophila, in vivo and in vitro, has been applied to study the influence of protein overexpression on genome integrity and degradation. Although the assay is well established, it could benefit from some research to determine optimal experimental design to standardize it, and then to allow comparisons among laboratories independently of the chosen cell type.

Field of study: Biology
Coastal hazards from slope mass movements: Analysis and management approach on the Barlavento Coast, Algarve, Portugal

The Barlavento Coast, Algarve, Portugal, is dominated by rocky sea-cliffs, cut on Miocene calcarenites which evolves through intermittent and discontinuous events of slope mass movements, along a 46 km cliff front. Here, the main coastal geologic hazards result from the conflict between human occupation and sea-cliff recession. Most of the research on the dynamics of the cliffs has been directed to the risk with the aim of defining long term set-back lines, for a preventive planning of the cliff top occupation. Little attention has been given to the hazard associated with mass movements on bathing beaches backed by sea-cliffs. This article presents the results of a field inventory of 244 slope mass movements single events, collected in a rocky shore with tens of touristic pocket beaches, covering an nineteen year time span (1995–2014). Results show that landslides have seasonal pattern with higher incidence in the period between winter and early spring. More than 15% of movements occur during the Easter holidays (April) and 4% of landslides occur during the official bathing season (June–September). The spatial distribution of landslides shows that only 22% of the mass movements occur in capes and headlands, while 78% occur on the beaches, which demonstrates that the beaches are real hot spots of risk. Based on the size distribution of slope mass movements runout ratio (the ratio between the radius of the base of the cone of and the height of the movement) a table of levels of security and hazard on beaches was built. Security levels enable the definition of cartographic hazard areas on beaches which can be provided to the beach users on information boards at the beach entrance.

Field of study: Environmental science
The Treatment of the Voluntary Boarder

1. 1,095 cases were admitted to the Retreat as voluntary boarders between January 1, 1891, and December 31, 1930. 703 cases were admitted once. 71 men and 63 women were admitted twice or more.

2. During the period voluntary admission has been made increasingly easier, on account of a widened outlook on the part of the Commissioners of the Board of Control and of the medical authorities. Since 1925 more voluntary patients than certified patients have annually entered all the registered mental hospitals.

3. Volition at the time of admission, with the likelihood that it will continue for an appreciable period, is the only satisfactory criterion as to whether a patient may be admitted to a mental hospital as a boarder or not.

4. The results of cases staying voluntarily have been: Recovered 40%, relieved 40%, unimproved 20%. In 1,170 cases admitted under certificates, the results have been: Recovered 42%, relieved 31%, unimproved 27%.

5. The conditions under which voluntary patients are received allow a number to leave against advice. 44% of the unrecovered boarders leave in this way. Under conditions of legal detention this number would be likely to be much less, and an approximate figure for the results then is computed to be: Recovered 53%, relieved 30%, unimproved 17%.

6. A number of the voluntary admissions are highly unsatisfactory because of the attitude adopted by the patients' relatives and friends. The tiresome formalities of certification seem to instil into the relatives a profounder appreciation of the seriousness of mental disorder. Knowledge of his ability to leave the hospital of his own choice is a hindrance to the recovery of the vacillating individual, and this attitude handicaps a number of other cases rather different in type, but who are likely to recover under hospital treatment.

7. 170 voluntary cases were certified when their behaviour no longer confirmed their volition. The causes for this step were confusion, stupor, excitement, indecision, querulousness, suicidal attempts. 51% of these cases ultimately recovered. Examples of the alteration in attitude towards the necessity of certification are given.

8. Neither senile nor paranoid cases are at all times unsuitable for voluntary admission.

9. The ease with which a voluntary boarder can leave is especially dangerous for potential suicides. Possibility of suicide is a condition which is not recognized readily by the relatives, and seems sometimes to be purposely overlooked. The causes of this are discussed. Suicide of voluntary boarders within a short time of their leaving hospital care has occurred too frequently: 14 cases are known in this series.

10. Reception of patients as voluntary boarders has enabled alcoholics and psychoneurotics to seek hospital treatment. Such cases were rarely willing to come for treatment when the only mode of admission was certification. Of the 1,095 admissions, 52 were of alcoholics, and 99 were of psychoneurotics.

Field of study: Medicine, Psychology
Numerical study on pollutant removal performance of vortex ventilation with different pollution source locations

This study presents the flow trajectory and pollutant distribution of a vortex ventilation system with different pollution source locations. First, the horizontal flow path and vertical structure of vortex ventilation are analyzed using the Burgers–Rott vortex model to predict the basic flow trajectory of pollutants in vortex ventilation system, and to provide a reference for the layout of pollution source locations in the following research. Thereafter, the flow characteristics of pollutants with different source locations in the vortex ventilation are studied numerically. The results indicate that, owing to the flow characteristics of the column vortex, the pollutant released from different pollution source locations has three flow modes: inflow mode, upward flow mode and downward flow mode, showing that the locations of pollution source have a significant impact on the flow mode and distribution of pollutants. Moreover, the ventilation effectiveness (VE) for pollutant removal and the mean residence time (MRT) of pollutants are used to evaluate the vortex ventilation. The results demonstrate that when the pollution source is located in the vortex tube, the ventilation system shows good performance in both VE and MRT; when the pollution sources are located outside the vortex tube, none of the sources show satisfying VE, whereas the MRT performance is good for severe sources. Finally, vortex ventilation systems are qualitatively divided into five regions for preliminarily predicting the pollutant removal performance for different pollution source locations.

Field of study: Engineering
Compensation of wavelength dependent image shifts in imaging optical interferometry.

In modern interferometers for absolute length measurements, when applying phase stepping interferometry, several different wavelengths are used as light sources, and the interferogram is projected to a CCD-camera array. Such interferometers are equipped with wedged optical components as windows and beam splitters, to prevent additional interferences. The wedged optics causes the position of a test piece within the interferogram related to the camera pixel coordinates to be dependent on the wavelength used. This effect depends on the wedge angles and the thicknesses of optical components as well as on their distances within the interferometer's optical pathway. We give a quantitative analysis and suggest a compensation of this dispersion effect by an additional wedge plate outside the interferometer.

Field of study: Physics
InterPlaNetary Internet: state-of-the-art and research challenges

The developments in the space technologies are enabling the realization of deep space scientific missions such as Mars exploration. InterPlaNetary (IPN) Internet is expected to be the next step in the design and development of deep space networks as the Internet of the deep space planetary networks. However, there exist significant challenges to be addressed for the realization of this objective. Many researchers and several international organizations are currently engaged in defining and addressing these challenges and developing the required technologies for the realization of the InterPlaNetary Internet. In this paper, the current status of the research efforts to realize the InterPlaNetary Internet objective is captured. The communication architecture is presented, and the challenges posed by the several aspects of the InterPlaNetary Internet are introduced. The existing algorithms and protocols developed for each layer and the other related work are explored, and their shortcomings are pointed out along with the open research issues for the realization of the InterPlaNetary Internet. The objective of this survey is to motivate the researchers around the world to tackle these challenging problems and help to realize the InterPlaNetary Internet.

Field of study: Computer science
Graphic study of igneous rock series

Scope of Paper The increasing number of well studied examples of igneous differentiation and comagmatic regions indicates that a compilation of available data may be suggestive to those who are building petrologic theories on the basis of the idea of differentiation. A fairly satisfactory graph has been found for the concise presentation of the data. On this graph are plotted data for 40 rock-masses in which gradational series can be traced, and about 20 series of less definite connection but strong signs of consanguinity. The several series are widely different, showing that different factors may dominate differentiation in different cases. If this compilation of scattered data can be kept in mind in building a petrologic theory for one particular case, its object will be amply fulfilled. Earlier Plots The diagrammatic presentation of rock series has been attempted by several petrologists. 2 Few of these plots are so constructed as to show . . .

Field of study: Geology
The electroplastic effect and phase transformations in amorphous and nanocrystalline alloys under tension with current

Results from studying the effect of the structural and phase features of coarse-grained, ultrafine-grained, nanocrystalline, and amorphous alloys on the electroplastic effect under tension are presented. It is shown that a smaller grain size, the emergence of secondary phases, and amorphization in alloys lead to the reduction or complete disappearance of the electroplastic effect. In alloys with reversible thermoelastic martensite transformation, the shape memory effect can inhibit the manifestation of electroplastic effect.

Field of study: Physics
Abrupt transitions to tumor extinction: a phenotypic quasispecies model

The dynamics of heterogeneous tumor cell populations competing with healthy cells is an important topic in cancer research with deep implications in biomedicine. Multitude of theoretical and computational models have addressed this issue, especially focusing on the nature of the transitions governing tumor clearance as some relevant model parameters are tuned. In this contribution, we analyze a mathematical model of unstable tumor progression using the quasispecies framework. Our aim is to define a minimal model incorporating the dynamics of competition between healthy cells and a heterogeneous population of cancer cell phenotypes involving changes in replication-related genes (i.e., proto-oncogenes and tumor suppressor genes), in genes responsible for genomic stability, and in house-keeping genes. Such mutations or loss of genes result into different phenotypes with increased proliferation rates and/or increased genomic instabilities. Despite bifurcations in the classical deterministic quasispecies model are typically given by smooth, continuous shifts (i.e., transcritical bifurcations), we here identify a novel type of bifurcation causing an abrupt transition to tumor extinction. Such a bifurcation, named as trans-heteroclinic, is characterized by the exchange of stability between two distant fixed points (that do not collide) involving tumor persistence and tumor clearance. The increase of mutation and/or the decrease of the replication rate of tumor cells involves this catastrophic shift of tumor cell populations. The transient times near bifurcation thresholds are also characterized, showing a power law dependence of exponent $$-1$$-1 of the transients as mutation is changed near the bifurcation value. These results are discussed in the context of targeted cancer therapy as a possible therapeutic strategy to force a catastrophic shift by simultaneously delivering mutagenic and cytotoxic drugs inside tumor cells.

Field of study: Biology, Mathematics
In Vitro Regulation of Non-enzymatic Antioxidant Efficiency ofMomordica dioica Roxb by Elicitation and Salt Stress

Antioxidants play an important role in inhibiting the free radicals thereby provides protection against infection and degenerative diseases. Natural antioxidants are scavenging reactive oxygen species (ROS), they are preferred over synthetic antioxidants because of their safety over the synthetic antioxidant chemicals.  In the present investigation sequentially extracts of various plant parts of M. dioica, and its tissue cultures were analyzed for their antioxidant potential. Standard protocols of scavenging effect on the DPPH free radical, Haemoglobin glycosylation Assay, Ferric Reducing Antioxidant Power, Nitric oxide and Lipid Peroxidation Assay were performed with some modifications. The fractionated extractives using different solvents analyzed for their antioxidant potential, the DCF of fruits with DPPH, MF of callus with HG and MF of stem with FRAP assays showed the highest AE. Elicitation increased the AE from 85 to173% in various treated samples. Effect of salt and Vitamin C gave significant blockage that increased with time treatment. Effect of various elicitors (sodium nitroprusside and salicylic acid), ascorbic acid and sodium chloride in different concentrations and time period on AE (antiradical efficiency) was also investigated. Results were expressed as AE, which is 1000/ IC50 in case of DPPH while in FRAP it was expressed as μM/l/g. M. dioica showed that this plant is a potent antioxidant agent. It is able to increase cellular survival by reducing intracellular lipid and protein oxidation levels and ROS scavengers.

Field of study: Agricultural and Food sciences
Pharmacokinetics and safety of calcium L-threonate in healthy volunteers after single and multiple oral administrations

To evaluate the pharmacokinetics of L-threonate after single or multiple oral administrations and its safety profile in healthy Chinese volunteers.This was an open-label, single- and multiple-dose study. The subjects were assigned to receive a single dose, 675, 2025, or 4050 mg, of calcium L-threonate (n=12) or repeated doses of 2025 mg twice daily for 4 d (n=12). Serial plasma and urine samples were analyzed with HPLC-MS/MS. Pharmacokinetic parameters of L-threonate were calculated using non-compartmental analysis with WinNonlin software.In the single dose group, Cmax reached at 2.0 h and the mean t1/2 was approximately 2.5 h. Area under curve (AUC) and Cmax increased with dose escalation, but dose proportionality was not observed over the range of 675 to 4050 mg. AUC and Cmax in the fasted subjects were lower compared with those in the non-fasted subjects. Cumulative urinary excretion of L-threonate over 24 h represented 5.9% of the administered dose with a mean Cl/r of 0.8 L/h. In the multiple-dose study, no accumulation appeared upon repeated doses of 2025 mg twice daily for 4 d. There were no serious adverse events that occurred during this study.Calcium L-threonate was well tolerated in healthy Chinese subjects, with no pattern of dose-related adverse events. Plasma exposure increased with dose escalation, but linear pharmacokinetics were not observed over the studied doses. L-threonate was absorbed rapidly, and its absorption was enhanced by food intake. No systemic accumulation appeared after repeated administrations.

Field of study: Biology, Chemistry, Medicine
The Definition of Leisure

An analysis of the definition of leisure seems to be needed at the present time for at least three reasons: First, significant changes have occurred in the nature of "the job" over the past century. Second, there has been a rising secular trend in per capita incomes. And third, leisure is a concept common to many disciplines. The first two of these factors result from the dynamics of our economic system and the third follows from the multi-disciplinary character of the concept itself.

Field of study: Economics
Present and future status of artisanal fisheries in the Adriatic Sea (western Mediterranean Sea)

Artisanal fisheries represents an important source of employment and income for many Mediterranean coastal communities, as well as an important cultural and traditional identity factor at a regional level. However, despite its importance, it is generally under-studied, in both ecological and socio-economic terms, so hampering the chance of developing sustainable and integrated management measures. At present, on the West coast of the Adriatic Sea, within the three-mile area, artisanal fisheries and hydraulic dredging are the only approved commercial fishing activities. This study confirmed the importance of the artisanal fisheries in this area, representing a multitarget and multigear activity. Despite the 39 exploited species, however, we found high vulnerability both for species (76% of total catches depend upon only three species—cuttlefish, mantis shrimp, and sole) and thermal affinity groups (cold and temperate species contributed to the entire catches). Furthermore, our data showed that fishing effort and CPUE values were greater than those reported at the regional level, and also indicated that the discard rate was lower than in other Adriatic areas. Regarding ecological effects, the two trophodynamic indicators that we applied showed a sustainable situation, but scenarios of possible changes in environmental or fishing effort conditions highlighted the proximity of the stock to the unsustainability threshold. Our findings suggest the need for an adequate management strategy to cope with possible future changes in population boundaries and conditions.

Field of study: Environmental science
Reflective writing, reflecting on identities: The construction of writer identity in student teachers’ reflections

The study focuses on student teachers’ reflective writing as an academic literacies practice. Data are drawn from a combined ethnographic approach to student teachers’ reflective writing on their practicum experience in a Primary Education Department of a Greek University. Ivanic’ (1998) framework on the construction of writer identity is employed in order to explore the resources and the discourses which student teachers deploy to position themselves with or against academic and professional discourses available in the socio-culturally bounded context of Teacher Education in Greece. The discourses under negotiation resonate socially circulating discourses that underpin the formation of student teachers’ professional identity. Given the specifications of the genre and the specifications of the context, reflective writing could possibly call for a transformative approach to academic writing practices.

Field of study: Education, Linguistics
Consciousness-Raising, Error Correction and Proofreading.

The paper discusses the impact of developing a consciousness-raising approach in error correction at the sentence level to improve students' proofreading ability. Learners of English in a foreign language environment often rely on translation as a composing tool and while this may act as a scaffold and provide some support, it frequently leads to predictable and persistent errors. Such fossilization can cause inaccuracies that detract from student composition and that require instruction and repeated practice in order to eradicate the errors. The current paper reports on an experiment in consciousness-raising about specific categories of errors with a group of 30 students in the Faculty of Education in Zayed University, Dubai during the spring semester 2014. Post-test results compared with those on a pre-test indicate a significant improvement in students' performance as a result of structured input (specially prepared grammar materials) and focused instruction (teaching that focuses on each specific grammar point identified as problematic).

Field of study: Education