nils-herrmann/clean_scirepeval huggingface dataset:
High level expression of monomeric and dimeric human α1,3-fucosyltransferase V

α3/4-Fucosyltransferases play a crucial role in inflammatory processes and tumor metastasis. While several human fucosyltransferases (FucTs) with different acceptor substrate specificities have been identified, the design of specific inhibitors for therapeutic approaches is hampered by the lack of structural information. In this study, we evaluated the expression of different constructs of human fucosyltransferase V to generate the large amounts required for structural studies. The truncated constructs lacking the transmembrane region and the cytosolic N-terminus, were expressed in baculovirus-infected Trichoplusia ni (Tn) insect cells and in two non-lytic expression systems, stably transfected human HEK 293 and T. ni cells. Since secretion of some glycosyltransferases is controlled by formation of dimeric molecules via disulfide bonds, one of the fucosyltransferase V constructs contained the N-terminal cysteine residue 64 for dimerization, whereas this residue was replaced in the other construct by serine. In both human and insect cells dimerization did not prove to be essential for efficient expression and secretion. On the basis of enzymatic activity, the yield of secreted fucosyltransferase V was approximately 10-fold higher in stably transfected insect cells than in HEK 293 cells. In particular the monomeric form of the enzyme provides a valuable tool for structural analyses to elucidate the fine specifity of fucosyltransferase V-mediated fucosylation of Lewis type glycans.

Field of study: Biology, Engineering
Shaping diffraction-free Lommel beams with digital binary amplitude masks.

Here, we report on experimental observations of various Lommel modes that possess distinct diffraction-free behaviors. The binary amplitude masks are designed to accurately encode the complex field information with the superpixel method. Then, the generation of the desired beams is demonstrated with these binary patterns projected onto the digital micromirrors device (DMD). Remarkably, we find that the field distribution and orbital angular momentum can be continuously engineered by tuning the beam parameters. Furthermore, the shape-invariant feature of such beams is verified by their far-field ring-like structures. Our observations are in good accordance with the theoretical predictions, and our methods may find potential applications in optical guiding and imaging. Moreover, apart from the DMD, the binary amplitude hologram can also be presented with well-fabricated elements, and thus, our method will also enable new applications for surface plasmon polaritons as well as electron beams.

Field of study: Physics
On the nature of dust clouds in the region towards M81 and NGC3077

There is some controversy on the nature of dust clouds found in direction of the interacting galaxy triplett M81, M82, and NGC3077. Are they associated with the tidal arms seen in HI around those galaxies or are they simply Galactic foreground clouds? Data from the SPIRE instrument onboard HERSCHEL and MIPS onboard of SPITZER are used to derive physical parameters for the dust clouds. These observions are compared to CO clouds previously mapped with the IRAM and the FCRAO radio telescopes.SPIRE and MIPS maps show several dust clouds north of M81 and south of NGC3077. Modelling of the dust emission provides total hydrogen column densities between 1.5 and 5.0 * 10^20 cm^-2. Dust temperatures are between 13 to 17K. No significant difference in the dust emission can be found between individual clouds. It is shown that CO line emission provides the best clues on the origin of those clouds. Most of the clouds seen towards M81 are associated with small-area molecular structures (SAMS), i.e. tiny CO clouds of Galactic origin. The clouds seen towards NGC3077 are partly associated with the tidal arms and are partly in the Galactic foreground associated with SAMS.

Field of study: Physics
Impact of intrauterine hypoxia on adolescent and adult cognitive function in rat offspring: sexual differences and the effects of spermidine intervention

Intrauterine hypoxia (IUH) affects the growth and development of offspring. It remains unclear that how long the impact of IUH on cognitive function lasts and whether sexual differences exist. Spermidine (SPD) has shown to improve cognition, but its effect on the cognitive function of IUH offspring remains unknown. In the present study we investigated the influence of IUH on body weight and neurological, motor and cognitive function and the expression of APP, BACE1 and Tau5 proteins in brain tissues in 2- and 4-month-old IUH rat offspring, as well as the effects of SPD intervention on these parameters. IUH rat model was established by treating pregnant rats with intermittent hypoxia on gestational days 15–21, meanwhile pregnant rats were administered SPD (5 mg·kg−1·d−1;ip) for 7 days. Neurological deficits were assessed in the Longa scoring test; motor and cognitive functions were evaluated in coat hanger test and active avoidance test, respectively. We found that IUH decreased the body weight of rats in both sexes but merely impaired motor and cognitive function in female rats without changing neurological function in the rat offspring of either sex at 2 months of age. For 4-month-old offspring, IUH decreased body weight in males and impaired neurological function and increased cognitive function in both sexes. IUH did not affect APP, BACE1 or Tau5 protein expression in either the hippocampus or cortex of all offspring; however, it increased the cortical Tau5 level in 2-month-old female offspring. Surprisingly, SPD intervention prevented weight loss. SPD intervention reversed the motor and cognitive decline caused by IUH in 2-month-old female rat offspring. Taken together, IUH-induced cognitive decline in rat offspring is sex-dependent during puberty and can be recovered in adult rats. SPD intervention improves IUH-induced cognitive and neural function decline.

Field of study: Biology, Chemistry, Medicine
Team-based comanagement of diabetes in rural primary care.

To explore clinical indicators among patients with diabetes in southern Alberta and assess changes over time, and to compare patients with diabetes attending a reference clinic (RC), which had adapted its service model to address the specific needs of the patient population, with patients with diabetes attending comparison clinics (CCs) in the same region.



Analysis of longitudinal data from the Canadian Primary Care Sentinel Surveillance Network (CPCSSN).



Rural southern Alberta.



A community-based family medicine clinic and the 6 other CPCSSN clinics in the same region at the time of the study.



A range of data elements from patients with diabetes within the RC, as well as from patients with diabetes from the CCs, were analyzed by CPCSSN to compare rates of comorbidity and mean body mass index, hemoglobin A1c levels, and blood pressure, as well as service use and measurement frequency. Rate of change per year was modeled longitudinally for each of the outcomes.



The RC had higher proportions of patients with comorbid conditions and a consistently higher mean body mass index. Mean HbA1c levels varied minimally between the RC and CCs, with both sets worsening slightly. However, the rate of worsening among patients with diabetes in the RC was found to be significantly greater (P < .05) than for those in the CCs. Blood pressure also varied minimally between the RC and the CCs, with both sets improving; however, the RC had a significantly greater (P < .001) rate of improvement than the CCs did. Finally, a greater proportion of patients in the RC had complete data for these 3 outcome measures, and RC patients made a greater number of clinic visits compared with the CC patients (P < .001).



This study describes a team-based comanagement organizational model and might provide useful commentary about organizational effectiveness in primary care. Although improvement in health outcomes cannot be directly attributed to any specific change in clinic organization, some statistically and likely clinically significant benefit was found associated with the service model of the RC in a relatively medically and socially challenged patient population and in a conservative evaluative design.

Field of study: Medicine
Constrained Estimators and Consistency of a Regression Model on a Lexis Diagram

This article considers a regression model on a Lexis diagram of an a × p table with a single response in each cell following a distribution in the exponential family. A regression model on the fixed effects of a rows, p columns, and a + p − 1 diagonals induces a singular design matrix and yields multiple estimators, leading to parameter identifiability problem in age–period–cohort analysis in social sciences, demography, and epidemiology, where assessment of secular trend in age, period, and birth cohort of social events (e.g., violence) and diseases (e.g., cancer) is of interest. Similar problems also exist in other settings, such as in supersaturated designs. In this article, we study the finite sample properties of the multiple estimators, propose a penalized profile likelihood method to study the consistency and asymptotic bias, and demonstrate the results through simulations and data analysis. As a by-product, the identifiability problem is addressed with consistent estimation for model parameters and secular trend. We conclude that consistent estimation can be identified through estimable function and asymptotics studies in regressions with a singular design. Our method provides a novel approach to studying asymptotics of multiple estimators with a diverging number of nuisance parameters.

Field of study: Mathematics
TU‐A‐BRB‐04: Fragmentation Analysis in Heavy Ion Therapy: A Novel Experimental Approach to Measure Lateral Distributions of Secondary Charged Particles

In carbonion beamradiotherapy, nuclear fragmentation in tissue leads to an attenuation of the primary particle flux and the build‐up of lighter projectile fragments. The radio‐biological effectiveness of these secondary particles differs from the primary ions. Therefore, fragmentation has to be considered in physical models used for therapy planning. While until now large apparatus have been used for ion spectroscopic measurements, we developed an experimental technique to measure lateral distributions of charged particles directly within or closely behind phantoms, using a small pixelated detector. Experiments were performed at the Heidelberg Ion‐Beam Therapy Center. A carbon ion pencil beam (∼5mm nominal width, E initial=271MeV/u) was directed towards a 12.7cm thick PMMA phantom. Secondary particles leaving the phantom were detected with the Timepix detector, placed perpendicular to the beam 5cm behind the phantom. The Timepix detector consists of a 300μm thick silicon sensor and a read‐out chip with 256×256 square pixels (55μm pitch). The high spatial resolution and the pixel‐wise energy calibration enable to determine the energy‐loss of individual particles in the sensitive layer. Together with pattern recognition analysis of characteristic particle traces in the detector, we are able to distinguish types of particles and discriminate the ion species.  Lateral distributions of events identified as being induced by hydrogen, helium and boron ions were determined. They show approximately Gaussian shaped profiles with FWHM values of 3.2mm (boron), 6.3mm (helium) and 13.1mm (hydrogen). These results are consistent with the expectation, that lighter fragments show wider distributions.  We present a novel method to determine secondary charged particle distributions in heavy ion therapy directly within phantoms. The main advantage lies in the flexibility of the set‐up. The performance of the method is promising to enable fragment distributions measurements in a wide phase space in the future. Research carried out in frame of the Medipix Collaboration

Field of study: Medicine, Physics
The Effects Of Early Institutional Care On Adolescent Personality

This research resulted from a general in terest in the phenomenon of infant depriva tion and a particular interest in the infant institution as a case in point. In a previous study (4), a comparison was made of 40 children in foster homes, who had each spent about the first two or three years of their lives in an infant institution (institutional children) and 40 children whose total experi ence had been in foster homes (foster home children). It was clearly demonstrated that the children placed in foster homes after babyhood rearing in an institution evidenced greater frequency of problem behavior than did the children with continuous foster home experience. Further, the institution children showed more problems involving the overt expression of anxiety (restlessness, hyper activity, inability to concentrate), the overt expression of aggression (temper display, im pudence, destructiveness, failure to regard privacy rights, cruelty without cause, etc.) and affective impoverishment. It was inferred that the institution children were less secure, more isolated from other people and less capable of entering into meaningful human relationships.

Field of study: Education
Über einen neuen Vakuum-Doppelmonochromator für das Gebiet von ungefähr 0,160 bzw. 0,130 μ bis ins Ultrarot

ZusammenfassungDiese Mitteilung behandelt einen evakuierbaren Doppel-Monochromator, der für Quarz- und Flußspatoptik eingerichtet werden kann und mit Hilfe dessen es möglich ist, Arbeiten bis ins Schumanngebiet auszudehnen.

Field of study: Physics
Fifteen Year Outcome of the Ceraver Hermes Posterior-Stabilized Total Knee Arthroplasty: Safety of the Procedure with Experienced and Inexperienced Surgeons

We wished to determine whether total knee replacement (TKA) performed by young surgeons increased rates of mortality and complications compared with TKA performed by senior surgeons using the same model of arthroplasty. There were no significant pre-operative differences between the groups in terms of age, gender, height, weight, body mass index, diagnosis, comorbidity and duration of follow-up, which was a mean of 15 years in both groups. Hence, we assessed the 15 year survival of the first 150 Ceraver Posterior-Stabilized total knee arthroplasties undertaken by young surgeons (aged of less than 30 years) in formation in a single university hospital setting (Group B). We used survival curve analysis, with strict definitions regarding end-points, and evaluated a number of different endpoint criteria to assess the outcome and to compare the results with those obtained by the two seniors (aged of more than 40 years) with their 50 first implantations (Group A). The clinical results and survival rate of implants at intermediate to long-term follow-up were similar in both Groups. Kaplan-Meier survival analysis, with revision as the endpoint for failure, showed that the rate of survival at ten years was 96% (95% CI, 93 to 100) in both groups. At fifteen years the rate of survival was 91% (95% CI, 85 to 97) in group B, and 92% (95% CI, 90 to 94) in group A. The implant used in this series appears particularly safe since the usual complications observed with posterior stabilized arthroplasties were not observed even with young surgeons.

Field of study: Medicine
Miocene pelagic biogenic sediment production and diagenesis, St. Croix, U.S. Virgin Islands

The Middle Miocene Kingshill Marl of St. Croix, Virgin Islands, affords an opportunity to reconstruct ancient island-margin calcareous plankton communities and to determine their contribution to the accumulation of island-slope sediments. Because of the present outcrop pattern of this unit, both lateral and vertical changes in organism/sediment relationships may be investigated. Subsidence of a NE-SW trending grabenal structure on St. Croix during the latest Early Miocene produced the Kingshill Seaway, which was flanked on the northwest and southeast by island masses of Cretaceous volcanogenic sediments, and on the northeast and southwest by the insular shelf edges. Hydrographic conditions in the shallow Seaway promoted high rates of pelagic biogenic skeletal production, resulting in the accumulation of thick pelagic calcareous oozes composed of a framework of calcitic planktonic foraminiferal tests in a matrix of calcareous nannoplankton, planktonic foraminiferal debris and fine aragonite needles. Minor siliceous components included diatom frustules and sponge spicules. Turbidity currents and debris flows transported terrigenous detritus and reef-tract skeletal rubble into the Seaway from the shallow basin margins. Comparison of the pelagic chalks and marls of the Kingshill Marl with modern sediments accumulating on the northwest St. Croix island slope establishes valuable guidelines to infer the total biogenic composition of the original ooze accumulating on the Kingshill Seaway floor. Comparison of the diagenetic processes affecting island-slope calcareous oozes with those affecting their deep-sea counterparts underscores the necessity of considering the range and intensity of differential solution as a factor in the ooze → chalk diagenetic continuum. The major diagenetic event in the Kingshill Marl ooze → chalk process was the solution of aragonitic skeletal sediment, probably during flushing by fresh water.

Field of study: Environmental science, Geography
Differential expression of the two forms of prolactin receptor mRNA within microdissected hypothalamic nuclei of the rat.

The prolactin receptor (PRL-R) has recently been identified in various hypothalamic nuclei of female rats. In this study, expression of both the short- and long-forms of PRL-R mRNA was investigated in 11 microdissected hypothalamic nuclei of ovariectomized, estrogen-treated rats. Specific nuclei were micropunched from 300-micrometer thick frozen coronal sections with autoclaved stainless steel needles of 300 or 500 micrometer diameter. Total RNA was extracted from the punched tissue, and the two forms of PRL-R mRNA were detected by reverse transcription polymerase chain reaction (RT-PCR) using specific primers. The RT-PCR product was verified by Southern hybridization with a digoxigenin-labelled oligonucleotide probe common to both forms. The results showed that both forms of PRL-R mRNA were expressed to varying degrees in the choroid plexus, cerebral cortex and various hypothalamic nuclei, including: ventromedial preoptic nucleus, ventrolateral preoptic nucleus, medial preoptic nucleus, suprachiasmatic nucleus, supraoptic nucleus, paraventricular hypothalamic nucleus, periventricular hypothalamic nucleus, arcuate nucleus, ventromedial hypothalamic nucleus, and median eminence. Of these brain regions, the choroid plexus expressed the highest level while the suprachiasmatic nucleus contained the lowest level of mRNA. There was no expression detected in the dorsomedial hypothalamic nucleus. The choroid plexus, supraoptic nucleus and paraventricular hypothalamic nucleus had higher levels of the short-form of the PRL-R mRNA than the long-form, whilst other hypothalamic nuclei preferentially expressed the long-form of the PRL-R mRNA. The differential expression of PRL-R gene suggests that the two forms may be differentially regulated in specific brain regions and may mediate different functions of PRL.

Field of study: Biology
Whence the odd-even staggering in nuclear binding?

We explore the systematics of odd-even mass staggering with a view to identifying the physical mechanisms responsible. The BCS pairing and mean-field contributions have A - and number parity dependences which can help disentangle the different contributions. This motivates the two-term parametrization c1 + c2/A as a theoretically based alternative to the inverse-power form traditionally used to fit odd-even mass differences. Assuming that the A -dependence of the BCS pairing is weak, we find that mean-field contributions are dominant below mass number A ∼ 40 while BCS pairing dominates in heavier nuclei.

Field of study: Physics
Possible Temperatures in the Oceanic Upper Mantle and the Formation of Magma

Note: This paper is dedicated to Aaron and Elizabeth Waters on the occasion of Dr. Waters' retirement. 

Horizontal heat transfer, either by plates that cool as they move away from their source at a ridge axis or by convection currents, invalidates all temperature distributions calculated on the assumption of purely radial outward heat transfer. Temperature gradients in the upper mantle in oceanic regions are estimated on the assumptions that (1) the top of the low-velocity zone corresponds to the “wet” solidus of peridotite containing a very small amount of water, and (2) that the seismic discontinuity near 400-km depth corresponds to the olivine-β spinel inversion. The gradients are very low, suggesting that convection is the dominant mode of heat transfer throughout the upper mantle. Possible temperature profiles are accordingly drawn by joining a conduction solution in the lithosphere to an adiabatic (or near-adiabatic) curve below the lithosphere. The temperature profile at any point depends on the local age of the plate; it is impossible to devise a representative average oceanic geotherm that could be used, when superposed on a petrological phase diagram, to predict the depth of formation of magmas or to account for their compositional variations.

Field of study: Geology
Consequences of extensive glanular dissection.

I read with interest the article entitled “TIP hypospadias repair: A pediatric urology indicator operation” by Snodgrass and Bush . The authors state that the increase in glans size does not reduce the likelihood for glans dehiscence, and it is the extent of dissection into the glans wings that effectively reduces dehiscence. A logical extension of this statement is that glans dehiscence is avoided at the expense of a reduced diameter of the glanular urethra, inevitably leading to stenosis. In their unpublished data, the authors do not specifically give the results for urethral stenosis in patients with “extensive” dissection to avoid glans dehiscence. Moreover, the authors’ most recent publication about extensive glans dissection includes a large series of patients, where they prefer to use the indistinct heading “urethroplasty complications,” instead of listing specific complications (stenosis, dehiscence, fistula, etc.) of glans and urethroplasties . In the normal human penis, glans wings merge in the midline ventrally, but are separated by the so-called “septum glandis,” in conjunction with the frenulum . This septum of the glans penis is a median partition within the ventral glans, which extends to the tunica albuginea and is attached to the frenulum and the urethra, and is more prominent after adolescence. The frenulum is also included in the formation of the distal (glanular and subcoronal) urethra . Hence, the approximated glans wings should allow for ventral support of the glanular and subcoronal urethra by a reconstructed neofrenulum. Neither glanular surface enhancement nor extensive dissection of the glans wings and their full-length approximation are anatomically compulsory, and may in fact be counterproductive. According to our experience, the split glans wings should be

Field of study: Medicine
Algorithm of Fractal Image Compression on CUDA

In fractal image compression,the matching procedure between range blocks and domain blocks can be executed in parallel manner.Therefore,in order to accelerate fractal image compression by using GPU,we apply compute unified device architecture CUDA to it.This paper presents a hybrid quad tree compression approach of GPU and CPU,which accelerates the distance calculation that consumes time mostly in GPU side,and handles quad tree division,initialization and so on in CPU side.In GPU part,we discuss two methods,single range block and multiple range blocks.Analysis and experiments show that the latter can achieve better parallel performance than the former.When our approach is compared with traditional pure CPU ones,it can improve fractal compression speed greatly.

Field of study: Computer science