nils-herrmann/clean_scirepeval huggingface dataset:
Lack of Prenylated Proteins, Autophagy Impairment and Apoptosis in SH-SY5Y Neuronal Cell Model of Mevalonate Kinase Deficiency

Mevalonate Kinase Deficiency (MKD), is a hereditary disease due to mutations in mevalonate kinase gene (MVK). MKD has heterogeneous clinical phenotypes: the correlation between MVK mutations and MKD clinical phenotype is still to be fully elucidated. Deficiency of prenylated proteins has been hypothesized as possible MKD pathogenic mechanism. Based on this hypothesis and considering that neurologic impairment characterizes Mevalonic Aciduria (MA), the most severe form of MKD, we studied the effects of I268T and N301T MVK mutations on protein prenylation, autophagy and programmed cell death in SH-SY5Y neuroblastoma cell lines.  SH-SY5Y cells were transiently transfected, with the pCMV-6 plasmid containing MVK wild type and the two mutated sequences. Protein prenylation levels were evaluated using GFP-RhoA-F to assess farnesylation, and GFP-RhoA to evaluate geranylgeranylation; autophagy was measured by evaluating LC3 and p62 protein levels, while Annexin V-FITC and Propidium Iodide staining allowed apoptosis detection.  MVK mutants’ over-expression causes decreased levels of farnesylation and geranylgeranylation, and also increased LC3 lipidation in SH-SY5Y, with concomitant p62 accumulation. Treatment with bafilomycin A1 (an inhibitor of vacuolar H+-ATPase, a late autophagy inhibitor) further increase LC3-II and p62 levels, suggesting that degradation of autophagolysosome could be impaired. SH-SY5Y, with both MVK mutants, showed apoptosis increase; the presence of N301T associated with augmented cell death.  We hypothesize that mevalonate pathway impairment causes alteration of farnesylation and geranylgeranylation proteins and alteration of the autophagic flux; these changes can induce apoptosis, possibly more relevant in the presence of N301T mutation.

Field of study: Biology, Chemistry
The Wathaman batholith: An Early Proterozoic continental arc in the Trans-Hudson orogenic belt, Canada

The Wathaman batholith, a major element of the Trans-Hudson orogenic belt in northern Saskatchewan and Manitoba, has an exposed strike length of 900 km. This immense body separates dominantly Archean (Rae-Hearne) provinces to the northwest from Early Proterozoic, arc-related terranes of the orogen to the southeast. Major- and trace-element data for 42 samples from the Saskatchewan part of the batholith are similar to those of Phanerozoic arc batboliths (for example, Sierra Nevada and Andean batholiths). Data plotted on trace-element discrimination diagrams show that the batholith has continental-arc affinities. U-Pb zircon geochronology of five main-phase granite samples suggests that most of the batholith formed between 1865 and 1850 Ma and is coeval with smaller plutons of the La Rouge arc. The main deformation of the batholith is limited by the 1830 Ma age of a late granite sheet that crosscuts folds and foliation of main-phase granites. The 15- to 25-m.y. crystallization span of the batholith is similar to the histories of many more recent continental magmatic arcs.

Field of study: Geology
[Cognitive control impairment in adult with attention deficit/hyperactivity disorder].

To study cognitive impairment in adults with attention deficit hyperactivity disorder (ADHD) and assess the efficacy of cerebrolysin in the treatment of such patients.



Thirty-eight patients with ADHD, aged from 18 to 45 years were enrolled in the study. Along with general neurological examination, several ADHA-specific scales and tests (ASRS-V1-1, SFQ, BIS, the Emotional Intelligence Self-Evaluation, TOVA) were administered.



There was a significant increase in inattention and impulsivity in comparison with the control group, which can be regarded as a decrease in cognitive control. The results of the study showed that cerebrolysin was an effective tool for improving cognitive control in adult patients with ADHD (a significant improvement was noted in 42.1% of patients, improvement in 31.6% of patients).

Field of study: Medicine, Psychology
Evidence of early C 4 grasses, habitat heterogeneity, and faunal response during the Miocene Climatic Optimum in the Mojave Region

Major changes to landscapes, climate, and mammalian faunas occurred at the regional scale in western North America during the Miocene Climatic Optimum (MCO) between ~17 and 14 Ma, but few studies have looked at how the MCO affected basin-scale environments. Paleoenvironmental reconstructions coupled with mammalian fossil assemblages from the Crowder and Cajon Valley formations in the Mojave Desert, California, contribute insights into local-scale (10s of kilometers) responses to warming during the Hemingfordian and Barstovian North American Land Mammal Ages. By integrating lithological descriptions, phytolith analyses, carbon isotope composition of preserved soil organic matter (δ13CSOM), and elemental geochemistry of paleosols, we provide reconstructions of depositional environments, vegetation, and precipitation through the MCO. Phytolith and δ13CSOM evidence suggest that paleoenvironments were predominately C3 grasslands, with the earliest potential presence of C4 grasses in the region found within the Crowder Formation at ~17 Ma. Based on elemental geochemistry of paleosols, mean annual precipitation estimates are 807 (±182) mm yr− 1 at 17 Ma in the Crowder Formation and 740–800 (±182) mm yr− 1 from 16 to 15 Ma in the Cajon Valley Formation. Our multiproxy approach indicates that the Crowder and Cajon Valley basins were stable, large-scale braided stream and floodplain systems with intermittent paleosol development and heterogeneity in vegetation and moisture conditions across spatial scales. Overall, we find a signal of local paleoenvironmental stability during the MCO; however, a significant drying trend in the Crowder Formation does correspond with faunal turnover and reduction in the number of taxa present. High species diversity within faunal assemblages, especially among small mammals, and fewer shared species between the Crowder and Cajon Valley assemblages than expected based on bootstrap analysis indicate that peak mammal diversity was accommodated at both local and regional scales during sustained tectonic activity and the MCO in western North America.

Field of study: Environmental science, Geography
SPICE in retrospect: Developing a standard for process assessment

The SPICE Project was established in 1993 to support the development, validation and transition into use of an International Standard for software process assessment. Its efforts have resulted in the publication of a five-part Standard for Process Assessment, ISO/IEC 15504. This paper reviews the evolution of the Standard, and reflects on the parallel achievements of the SPICE Project and the standardisation effort in advancing the state of the art in process assessment and improvement.

Field of study: Computer science, Engineering
Electrohydrodynamic Thrust for In-Atmosphere Propulsion

The electrohydrodynamic thrust generated by wire–cylinder electrodes under high dc voltage is experimentally analyzed. Some recent experimental studies have shown that electrohydrodynamic thrusters produced by corona discharge and ionic wind are able to deliver high thrust-to-power ratio, which reopens prospects for electrohydrodynamic propulsion. From simple considerations based on ultralight aircraft mass, aerodynamics, battery mass, and experimental electrohydrodynamic thrust densities, their potential for applications is showcased. Furthermore, an experimental study is performed, for which the experimental observations are presented in terms of electric field and thrust density. This allows a simplified and synthetic presentation of propulsive properties. Various experimental biases have been identified and corrected. The measure of time-periodic oscillations of the airflow in the back of the thruster pinpoints a possible wake effect due to the impact of ionic wind on electrodes. The variations of the associated drag are studied when varying the position of the collecting electrodes. It is shown that aerodynamic losses can be significant in experimental electrohydrodynamic thrusters.

Field of study: Physics
A Permian Hydrozoan Mound, Yukon Territory

A carbonate mound built by the hydrozoan Palaeoaplysina has been found in a poorly-exposed sequence of Lower Permian rocks in the northern Richardson Mountains of the Yukon Territory. Similar hydrozoan mounds have been described from Russia and northwestern United States. The Yukon mound is 12 ft (3.7 m) thick and at least 70 ft (21 m) long. It is underlain by marine siltstones and sandstones, and probably shale. The main mound rock is composed of curved hydrozoan plates enclosed in a bioclastic wackestone matrix, and is overlain successively by tubular–foram packstone and oolitic grainstone. Palaeoaplysina is characterized by a plate-like, laterally-expanding growth form, an internal canal system, a cellular calcareous skeleton, and 'mamelons' on the upper surface of well-preserved plates; 'mamelons' are the principal criterion for placing Palaeoaplysina in the Class Hydrozoa of the coelenterates.The Yukon mound is part of a thick sequence of Lower Permian terrigenous clastic and carbonate rocks deposite...

Field of study: Environmental science
The current state of surgical practice for neonatal torsion: a survey of pediatric urologists.

The evaluation and treatment of perinatal testicular torsion is controversial. We performed a survey to assess practice patterns among pediatric urologists regarding treatment of perinatal torsion.



An internet survey was administered to members of two pediatric urology societies. Cases of prenatal, postnatal and bilateral prenatal torsion were outlined. Respondents were asked about use of ultrasound, timing of surgery, incision, and management of the contralateral testicle. A case with a non-palpable testicle and blind ending vessels was also presented.



We had 121 respondents. In a neonate with prenatal torsion, 34% percent would operate immediately, 26% urgently within 72 h, 28% electively and 12% would not explore; 93% would perform a contralateral orchiopexy. In a neonate with postnatal torsion, 93% would operate immediately, 5% urgently, 1% electively and 1% would not explore; 96% would perform a contralateral orchiopexy. In both cases, 75% would use a scrotal incision and 25% would use an inguinal incision. When presented with bilateral prenatal torsion, 90% would operate immediately, 1% urgently, 2% electively and 7% would not operate. In the case of a non-palpable testicle with blind ending vessels 28% would perform a contralateral orchiopexy, 12% would explore the ipsilateral canal for a "nubbin", 56% would perform no intervention and 4% would perform some other form of management.



We documented variability of timing for intervention of prenatal torsion and confirmed that most view postnatal torsion as a surgical emergency. Most perform a contralateral orchiopexy for prenatal torsion despite the fact that most cases are extravaginal. The surgical approach via a scrotal incision appears to be preferred at this time.

Field of study: Medicine
Effect of thermal and ultraviolet treatments on the stability of antioxidant compounds in single strength pineapple juice throughout refrigerated storage

Thermal treatment is commonly applied in juice manufacturing as a method to pasteurize juices. However the heat may deteriorate some of the essential compounds in the juice, especially heat-sensitive antioxidants. Therefore non-thermal treatment such as ultraviolet (UV) ray has been proposed as an alternative for pasteurization. The objective of this study was to compare the effect of thermal and UV treatments on the content of antioxidants (phenolic acids, flavonoids, carotenoids, ascorbic acids) and antioxidant capacity of single strength pineapple juice. The antioxidants stability of juices throughout 14 days of refrigerated storage was also studied. Ultraviolet treatment shows higher ascorbic acid content after treatment as compared to thermally treated single strength pineapple juice. Storage time affected the studied antioxidants, where UV treatment provided better stability to ascorbic acid content while thermal treatment provided better stability to flavonoids and carotenoids.

Field of study: Agricultural and Food sciences
Observation of amplitude squeezing in a constant-current-driven semiconductor laser.

Electromagnetic fields with photon-number fluctuation reduced below the standard quantum limit have been generated in a constant-current\char21{}driven semiconductor laser. The generation is based on a new principle of high impedance suppression for pump-amplitude fluctuation in a highly saturated laser oscillator. The observed noise level is 7.3% (31% after correction for detection quantum efficiency) in power below the standard quantum limit in the entire frequency range between 350 and 450 MHz.

Field of study: Physics
Cenozoic environmental evolution of the Qaidam Basin and its implications for the uplift of the Tibetan Plateau and the drying of central Asia

A complete Cenozoic pollen sequence of the Qaidam Basin has been constructed with absolute age control. The Cenozoic environmental evolution of the Qaidam Basin, and its implications for the uplift of the Tibetan Plateau and the drying of central Asia during the Cenozoic Era is discussed, based on the interpretation of the pollen sequence, the commencement of eolian deposition in central China and the change of climatic distribution pattern of China. The results suggest that in the Qaidam Basin relatively dry climates prevailed in the Eocene–Oligocene and Pliocene–Pleistocene. These dry periods resulted from the effects of a Subtropical High Pressure Zone, and the uplift of the surrounding mountains and the Tibetan Plateau, respectively. About a 600 km northward drift of western China has probably occurred during the late Cenozoic, resulting in the Eocene–Oligocene Arid Climate Belt twisting about six degrees of latitude. The Tibetan Plateau reached probably 1500 m elevation by the latest Miocene (8–5 Ma), not as high as it was thought previously. The Cenozoic environmental evolution of northwest China does not support the idea that the retreat of the Paratethys Sea played an important role in the late Cenozoic drying of central Asia, at least not in northwest China.

Field of study: Environmental science, Geography
Rapid leaf development drives the seasonal pattern of volatile organic compound (VOC) fluxes in a 'coppiced' bioenergy poplar plantation.

Leaves of fast-growing, woody bioenergy crops often emit volatile organic compounds (VOC). Some reactive VOC (especially isoprene) play a key role in climate forcing and may negatively affect local air quality. We monitored the seasonal exchange of VOC using the eddy covariance technique in a 'coppiced' poplar plantation. The complex interactions of VOC fluxes with climatic and physiological variables were also explored by using an artificial neural network (Self Organizing Map). Isoprene and methanol were the most abundant VOC emitted by the plantation. Rapid development of the canopy (and thus of the leaf area index, LAI) was associated with high methanol emissions and high rates of gross primary production (GPP) since the beginning of the growing season, while the onset of isoprene emission was delayed. The highest emissions of isoprene, and of isoprene photo-oxidation products (Methyl Vinyl Ketone and Methacrolein, iox ), occurred on the hottest and sunniest days, when GPP and evapotranspiration were highest, and formaldehyde was significantly deposited. Canopy senescence enhanced the exchange of oxygenated VOC. The accuracy of methanol and isoprene emission simulations with the Model of Emissions of Gases and Aerosols from Nature increased by applying a function to modify their basal emission factors, accounting for seasonality of GPP or LAI.

Field of study: Environmental science
Oxygen content and structure of Ba2YCu3Ox below 525°C

The relationship between the crystal structure and oxygen content was established for Ba 2 YCu 3 O x ceramic. Samples whose initial values of x were either 6.98 (orthorhombic structure) or 6.16 (tetragonal structure) were annealed side by side at 380 to 525°C in flowing nitrogen containing a fixed, small amount of oxygen. The powders were heated until their weightd stabilized and this required very long times at the lower temperatures. The room temperature structure and x were obtained for these samples. X-ray diffraction was also used to determine the structure of powders with intermediate x while the samples were heated using conditions which prevented any change in oxygen content. At room temperature samples with x ⩽6.40 are tetragonal, those with ⩾6.42 have the orthorhombic structure, while samples with 6.42⩽ x ⩽6.55 transform to tetragonal as the temperature raised. The effect of metastability, the kinetics of oxidation and temperature influence are discussed. The 25°C lattice parameters as a function of x are reported for the annealed samples.

Field of study: Materials science
One-Dimensional Alignment of Nanoparticles Via Magnetic Sorting

Near room temperature, thin films of MnAs spontaneously align into two phases, one ferromagnetic and the other paramagnetic. These two phases take the intriguing form of nanoscale "wires." In this experiment, we investigate the spontaneous formation of ordered linear arrays of magnetite nanoparticles on MnAs thin films using scanning probe microscopy.

Field of study: Physics
Prospecting And Testing Of Clay For Schools Offering Ceramics In The Sekondi- Takoradi Metropolis, Ghana

Clay, which is a natural mineral in the earth remains the major ceramic raw material since time immemorial.  With the introduction of the new Educational Reform in 1987, many second and some third cycle institutions have taken ceramics as one of the vocational subjects in Ghana.  Clay, which is the main raw material, is difficult to come by within the Sekondi-Takoradi Metropolis.  This has somehow affected the performance of institutions offering ceramics including St. John’s Senior High School, Ahantaman Senior High School and Takoradi Polytechnic, all in the Metropolis.  To find a solution to this problem, the researchers had made effort to prospect and test for varieties of clay from areas closer to the metropolis.  Literature related to the topic had been reviewed. The experimental research method was employed. The purposive sampling technique was used to select the proposed clay deposits in the selected districts.  All the general procedures and processes used in prospecting and testing for clay were followed.  For example, water of plasticity test, presence of lime test, dry shrinkage test, fired shrinkage test and porosity test.  From the findings, it was realized that these clay deposits could be very useful to schools offering ceramics in the Metropolis.  It was recommended among other things that institutions offering ceramics should patronize clay from these areas, and the district assemblies should try to construct roads to the various clay sites, so as to make them motorable to people who might need the clay.  Clay, Prospecting, Plasticity, Testing, Shrinkage

Field of study: Education
Experimental correlation of falling film absorption heat transfer on micro-scale hatched tubes.

The objectives of this paper are to investigate the effect of surface roughness of micro-hatching tubes on the absorption performance and to develop an experimental correlation of Nusselt number as a function of the roughness. Two different micro-scale hatched tubes and a bare tube are tested to quantify the effect of the surface roughness on the absorption performance. The roughness of the micro-scale hatched tubes ranges 0.386–11.359 μm. The working fluid is H2O/LiBr solution with inlet concentration of 55, 58 and 61 wt.% of LiBr. The absorber heat exchanger consists of 24 horizontal tubes in a column, liquid distributor at the liquid inlet and the liquid reservoir at the bottom of the absorber. It was found that absorption performance of micro-hatching tubes was improved up to two times compared with the bare tube. An experimental correlation of Nusselt number was developed as a function of the film Reynolds number and the roughness with an error band of ±25%.

Field of study: Engineering
Basin architecture and density structure beneath the Strait of Georgia, British Columbia

Georgia Basin is located within one of the most seismically active and populated areas on Canada's west coast. Over the last decade, geological investigations have resolved important details concerning the basin's shallow structure and composition. Yet, until recently, relatively little was known about deeper portions of the basin. In this study, new seismic velocity information is employed to develop a 3-dimensional density model of the basin. Comparison of the calculated gravity response of this model with the observed gravity field validates the velocity model at large scales. At smaller scales, several differences between model and observed gravity fields are recognized. Analysis of these differences and correlation with independent geoscience data provide new insights into the structure and composition of the basin-fill and underlying basement. Specifically, four regions with thick accumulations of unconsolidated Pleistocene and younger sediments, which were not resolved in the velocity model, are id...

Field of study: Environmental science
Birth Control Pill: Abortifacient and Contraceptive

Dear s iste r and brothe r s ignator ies of the document e ntitled Birth Control Pills: Contraceptive or Abortifacient . We love you. We recognize our own s inful natures and are not insens itive to the rea l difficulty of admitting that o ne might poss ibly be wrong. One o f us ( WFC., Jr.) was for several yea rs convinced that labe ling birth control pill s as abortifac ient was the work of an extremist right wing medical conspiracy. O nly on entering into a se rious study of the matte r did he become convinced of the error of hi s ways. We also believe that we have a God whose love for all of us is immeasurable, unqualifi ed, and unchang in g. If you are good enough for Him, you sure ly must qualify fo r o ur love. At the 1998 midwinte r meeting of the American Assoc iation o f ProLife Obstetricians and Gyneco logists (AA PLOG), Pamela Smith, M.D., pres ident of the organization, ca lled for the producti on of a Principles of Pro-Life Medical and Public Health Practice manua l. When do ing thi s she sa id :

Field of study: Medicine, Philosophy
On the nature of non-responding in discrimination learning with and without errors.

In human subjects, discrimination learning with errors results in active responding incompatible with the reinforced response. The direction of such incompatible behavior is opposite to that of the reinforced response. Responding occurs only during the stimulus correlated with extinction. The frequency of active non-responding is maximal shortly after the start of discrimination training (the time at which the frequency of errors decreases most rapidly) and approaches zero as discrimination training continues. The magnitude of behavioral contrast is not related systematically to the number of errors. Instead it is related directly to the frequency of active non-responding. Active non-responding appears to be motivated by the aversiveness of self-produced frustration, in the sense that active non-responding allows the subject to avoid the aversiveness of non-reinforced responding.

Field of study: Biology, Psychology