nils-herrmann/clean_scirepeval huggingface dataset:
Flow cytometric and immunohistochemical evaluation of ethanol-induced changes in splenic and thymic lymphoid cell populations.

Ethanol-induced alterations in the immune system are thought to play a major role in increasing the susceptibility of alcoholics to infections and tumors. One important change in the immune system is the noted loss of lymphoid cells from the thymus and spleen. To examine these alterations we used a model system where C57Bl/6 mice were pair-fed either a Leiber-DeCarli diet containing 7% (v/v) ethanol or an isocaloric control diet. Mice receiving ETOH for 7 days showed a loss of cells from the spleen and thymus; this loss was even more severe after withdrawal for 1 day. The most profound changes were seen after 2 weeks of ETOH. Spleen and thymus cell numbers were reduced to 36% and 6.2%, respectively compared to control mice. Staining of thymocytes with monoclonal antibodies to lymphocyte surface markers and evaluation with flow cytometry revealed that immature thymocytes (PNA+, CD4+/CD8+) were most reduced. Mature thymocytes (CD4+/CD8- or CD4-/CD8+) were depleted, and the CD4+ to CD8+ ratio was increased. Sections of thymus stained with hematoxylin and eosin or with immunohistochemical methods showed atrophy and lymphoid cell depletion. No cortex was histologically identifiable after 2 weeks of ETOH. The spleen cells most affected by ETOH were the B cells. They were reduced to 8.2 x 10(6) cells/spleen (31.5% of the lymphocytes), as compared to 38.5 x 10(6) cells/spleen (50.3% of the lymphocytes) in the control mice. The spleen was atrophic, but the immunoarchitecture was preserved. Ethanol causes a depletion of lymphocytes from the spleen and thymus with alterations in lymphocyte subpopulations.(ABSTRACT TRUNCATED AT 250 WORDS)

Field of study: Medicine
The mechanism of substrate-controlled allosteric regulation of SAMHD1 activated by GTP.

SAMHD1 is the only known eukaryotic deoxynucleoside triphosphate triphosphohydrolase (dNTPase) and is a major regulator of intracellular dNTP pools. It has been reported to be a potent inhibitor of retroviruses such as HIV-1 and endogenous retrotransposons. Previous crystal structures have revealed that SAMHD1 is activated by dGTP-dependent tetramer formation. However, recent data have indicated that the primary activator of SAMHD1 is GTP, not dGTP. Therefore, how its dNTPase activity is regulated needs to be further clarified. Here, five crystal structures of the catalytic core of SAMHD1 in complex with different combinations of GTP and dNTPs are reported, including a GTP-bound dimer and four GTP/dNTP-bound tetramers. The data show that human SAMHD1 contains two unique activator-binding sites in the allosteric pocket. The primary activator GTP binds to one site and the substrate dNTP (dATP, dCTP, dUTP or dTTP) occupies the other. Consequently, both GTP and dNTP are required for tetramer activation of the enzyme. In the absence of substrate binding, SAMHD1 adopts an inactive dimer conformation even when complexed with GTP. Furthermore, SAMHD1 activation is regulated by the concentration of dNTP. Thus, the level of dNTP pools is elegantly regulated by the self-sensing ability of SAMHD1 through a novel activation mechanism.

Field of study: Chemistry
Heat balance sap flow gauge for small diameter stems

Applying heat balance sap flow gauges to plant stems <10 mm in diameter has been difficult because a miniature design is needed that can be attached to a range of stem geometries. This report presents a modified gauge design for use on small plant stems of irregular geometry and shows results from Glycine max with stem diameters of 3–4 mm. The gauge was evaluated on container-grown plants by comparing gauge measurements of flow to gravimetric estimates of transpiration. Experiments were conducted in the laboratory and greenhouse, using artificial and natural lighting, respectively. Laboratory comparisons of gauge versus gravimetric water loss measurements indicated that the instrument was accurate to within ±5% when soil water was not limiting. Similar results were obtained from greenhouse tests except when soil water availability was low and cumulative gauge estimates became 30–45% less than gravimetric measurements. Differences may have reflected reduced plant water uptake or errors in sap flow estimates associated with low flow rates. Gauge accuracy was not improved by including the rate change in heat storage (S) in the flow calculations because S was always less then 3% of the total heat balance. Relationships between system temperature and sap flow rate suggested a diagnostic test for determining optimum power input. A time constant of 15 s indicated potential application in many agronomic and physiological studies.

Field of study: Environmental science
Atrial natriuretic peptide in the subfornical organ reduces drinking induced by angiotensin or in response to water deprivation.

Three experiments tested whether the subfornical organ (SFO) could be a site of action for the antidipsogenic effects of atrial natriuretic peptide (ANP) in rats. Pretreatment with 100, 230, or 500 pmol ANP in the SFO reduced drinking induced by 10 pmol angiotensin II in the SFO. Drinking in response to water deprivation was reduced by ANP in rats having cannulas in or near the SFO, but not in rats having cannulas distant from the SFO or in the ventricles. Finally, ANP had no effect on eating or drinking after food deprivation, suggesting that the rats in the other experiments were not acutely incapacitated. The SFO may mediate the central effects of ANP on drinking induced by angiotensin or in response to water deprivation and could play a similar role in the central effects of ANP on salt appetite, diuresis, vasopressin secretion, and blood pressure.

Field of study: Biology, Psychology
Two-dimensional Renewal Function Approximation

Two-dimensional renewal functions, which are naturally extensions of one-dimensional renewal functions, have wide applicability in areas where two random variables are needed to characterize the underlying process. These functions satisfy the renewal equation, which is not amenable for analytical solutions. This paper proposes a simple approximation for the computation of the two- dimensional renewal function based only on the first two moments and the correlation coefficient of the variables. The approximation yields exact values of renewal function for bivariate exponential distribution function. Illustrations are presented to compare our approximation with that of Iskandar (1991) who provided a computational procedure which requires the use of the bivariate distribution function of the two variables. A two-dimensional warranty model is used to illustrate the approximation.

Field of study: Mathematics
A novel Th1‐type T‐cell immunity‐biasing effect of malate dehydrogenase derived from Mycobacterium avium subspecies paratuberculosis via the activation of dendritic cells

HIGHLIGHTSMAP MDH activates DCs with increased expression of TNF‐&agr;, IL‐1&bgr;, IL‐6, and IL‐12p70, but not IL‐10.MAP MDH induces DC maturation by activation of NF‐&kgr;B and MAPK.MAP MDH‐treated DCs induce naïve CD4+/CD8+ T cell proliferation and IFN‐&ggr; secretion in CD4+ T cells.MAP MDH promotes Th1 type immunity via DC activation.  Mycobacterium avium subspecies paratuberculosis (MAP) is the causative pathogen of Johne's disease in ruminants, characterized by chronic granulomatous enteritis; it also has zoonotic potential and is associated with Crohn's disease in humans. A better understanding of the mycobacterial antigens and their roles in the host immune response may facilitate the rational design of control strategies, including the development of effective vaccines and diagnostic tools. However, the functional roles of a large proportion of MAP antigens involved in modulating the host immune response remain unknown. In this study, an immunological role of MAP malate dehydrogenase (MDH, MAP2541c), an antigen that is upregulated in stress culture conditions, such as nutrient starvation and hypoxia, in polarizing naïve CD4+/CD8+ T cells toward Th1‐biased T‐cell immunity via the activation of dendritic cells (DCs) was identified. DCs treated with MAP MDH displayed characteristics of the activated and mature immune status, with augmented expression of cell surface molecules and pro‐inflammatory cytokines, including TNF‐&agr;, IL‐1&bgr;, IL‐6, and IL‐12p70, but not IL‐10, along with a dose‐dependent decrease in the antigen uptake capacity. A mechanistic investigation revealed that the observed DC maturation is mediated by the activation of JNK, ERK, and p38 MAP kinases, and the NF‐&kgr;B signaling pathway. Notably, DCs activated by MAP MDH treatment promoted naïve CD4+/CD8+ T cell proliferation; in particular, they effectively polarized naïve CD4+ T cells to secrete IFN‐&ggr; and IL‐2 and activate T‐bet, but, unlike the LPS control, did not influence IL‐5 and GATA‐3. These results indicated that MAP MDH has the potential to induce the Th1 cell response via DC activation. Collectively, our data demonstrated that MAP MDH is a novel immunostimulatory antigen that drives Th1‐biased T cell polarization via interactions with DCs, suggesting that MDP MDH has the potential to be an effective MAP vaccine antigen target and diagnostic marker.

Field of study: Medicine
Observed long-term greening of alpine vegetation—a case study in the French Alps

We combined imagery from multiple sources (MODIS, Landsat-5, 7, 8) with land cover data to test for long-term (1984–2015) greening or browning trends of vegetation in a temperate alpine area, the Ecrins National Park, in the context of recent climate change and domestic grazing practices. We showed that over half (56%) of the Ecrins National Park displayed significant increases in peak normalized difference vegetation index (NDVImax) over the last 16 years (2000–2015). Importantly, the highest proportional increases in NDVImax occurred in rocky habitats at high elevations (> 2500 m a.s.l.). While spatial agreement in the direction of change in NDVImax as detected by MODIS and Landsat was high (76% overlap), correlations between log-response ratio values were of moderate strength (approx. 0.3). In the context of above treeline habitats, we found that proportional increases in NDVImax were higher between 1984 and 2000 than between 2000 and 2015, suggesting a slowing of greening dynamics during the recent decade. The timing of accelerated greening prior to 2000 coincided with a pronounced increase in the amount of snow-free growing degree-days that occurred during the 1980s and 1990s. In the case of grasslands and low-shrub habitats, we did not find evidence for a negative effect of grazing on greening trends, possibly due to the low grazing intensity typically found in the study area. We propose that the emergence of a longer and warmer growing season enabled high-elevation plant communities to produce more biomass, and also allowed for plant colonization of habitats previously characterized by long-lasting snow cover. Increasing plant productivity in an alpine context has potential implications for biodiversity trajectories and for ecosystem services in mountain landscapes. The presented evidence for long-term greening trends in a representative region of the European Alps provides the basis for further research on mechanisms of greening in alpine landscapes.

Field of study: Environmental science
One-dimensional collimation of laser array outputs.

We consider a computer-generated hologram for the one-dimensional collimation in x of the output from a linear laser-diode array in y. Our concern is to produce one-dimensional pencil beams from each laser diode with small cross talk between the output from the separate laser diodes. Such outputs can be used in matrix-vector, neural net, and interconnection applications. The efficiency and the design of the computer-generated hologram are detailed, and initial optical laboratory results with an electron-beam recorded computer-generated hologram are presented.

Field of study: Physics
On my mind: thoughts about salience, context and figurative language from a second language perspective

This article discusses three claims of the Graded Salience Hypothesis presented in Rachel Giora’s book On our mind. It is argued that these claims may give second language researchers the chance to revise the way they think about word meaning, the literal meaning-figurative meaning dichotomy and the role of context in language processing. Giora’s arguments are related to recent second language research and their relevance is explained through examples. There are also several suggestions made for further research.

Field of study: Linguistics
Practical investigations of two-stage bacon tempering

Bacon has to be tempered (part-frozen) before it can be sliced in a high-speed slicing operation. Traditionally the desired slicing temperature was achieved in a long single-stage process. Increasingly a two-stage process of heat removal followed by temperature equalisation is used to reduce processing time and weight loss. The objectives of the work described in this paper were: 1. To provide practical design data for a two-stage bacon-slicing operation. 2. To provide data that could be used in the development and verification of a model that would help optimise current and new tempering systems.

Field of study: Engineering
Improved Tribological Performance of Amorphous Carbon (a-C) Coating by ZrO2 Nanoparticles

Nanomaterials, such as Graphene, h-BN nanoparticles and MoS2 nanotubes, have shown their ability in improving the tribological performance of amorphous carbon (a-C) coatings. In the current study, the effectiveness of ZrO2 nanoparticles (ZrO2-NPs) in lubricating the self-mated nonhydrogenated a-C contacts was investigated in boundary lubrication regime. The results showed that 13% less friction and 50% less wear compared to the base oil were achieved by employing ZrO2-NPs in the base oil in self-mated a-C contacts. Via analyzing the ZrO2-NPs and the worn a-C surface after tests, it was found that the improved lubrication by ZrO2-NPs was based on “polishing effects”, which is a new phenomenon observed between a-C and nanoparticles. Under the “polishing effect”, micro-plateaus with extremely smooth surface and uniform height were produced on the analyzed a-C surface. The resulting topography of the a-C coating is suitable for ZrO2-NPs to act as nano-bearings between rubbing surfaces. Especially, the ZrO2-NPs exhibited excellent mechanical and chemical stability, even under the severe service condition, suggesting that the combination of nonhydrogenated a-C coating with ZrO2-NPs is an effective, long lasting and environment-friendly lubrication solution.

Field of study: Materials science
Pepsi versus Coke: Labels, Not Tastes, Prevail

60 subjects tasted cola from two cups, one marked L, the other marked S. The same product (either Pepsi or Coke) was placed in both cups. Whether both cups contained Pepsi or Coke, subjects overwhelmingly reported cup S contained the better-tasting product. In Experiment 2, 30 subjects were asked their preference for either Pepsi or Coke. Then they drank from a Pepsi bottle (which contained Coke) and from a Coke bottle (which contained Pepsi). Subjects were significantly influenced by the label of the product they preferred and not by taste differences between these products. It was concluded that a taste comparison of colas should avoid using any labels, even presumably neutral ones like letters of the alphabet, since such labels may have more powerful influences on product comparisons than taste differences.

Field of study: Psychology
Social-spider optimised particle filtering for tracking of targets with discontinuous measurement data

The particle filter (PF), a non-parametric implementation of the Bayes filter, is commonly used to estimate the state of a dynamic non-linear non-Gaussian system. The key idea is to construct a posterior probability satisfying a set of hypotheses representing a potential state of the system. Despite PF's successful applications, it suffers from sample impoverishment in real-world applications. Most of the recent PF-based techniques attempt to improve the functionality of the PF through evolutionary algorithms in the cases of unexpected changes in the system states. However, they have not addressed the discontinuity of observations which is unpreventable in the real world. This study incorporates a recently developed social-spider optimisation technique into PF to overcome the drawback of previous methods in these cases. To avoid premature degeneracy, evolutionary search extends the particle search space when observation is unavailable. The social-spider inspired proposal distribution and the corresponding particle weights are derived to approximate real model states. The experimental results show that the proposed method has superior performance in relation to other evolutionary PF in cases of large changes or discontinuous observations.

Field of study: Computer science
Efeito agudo de diferentes métodos de alongamento sobre o desempenho de força em séries sucessivas

Ainda nao ha consenso sobre a utilizacao de alongamentos antes de exercicios de forca. Sendo assim, o objetivo foi verificar o efeito agudo de dois metodos de alongamento sobre o desempenho da forca no exercicio supino reto. Individuos treinados realizaram 3 series de 8 a 10-RM no supino reto imediatamente apos o alongamento estatico (AE), Facilitacao Neuromuscular Proprioceptiva (FNP) ou condicao controle. Foi encontrada queda significativa das repeticoes na segunda e terceira series em comparacao a primeira em todas as condicoes. Nao houve diferenca significativa no numero de repeticoes ou no volume total entre as condicoes com e sem alongamento. O AE e a FNP nao causaram impacto negativo no desempenho da forca, podendo, assim, serem utilizados previamente a esse exercicio.

Field of study: Education
Operation Experience of the Riken Variable-Frequency Heavy-Ion Linac, Rilac

The RILAC, the variable-frequency heavy-ion linac, which will be used as an injector to the separated sector cyclotron, has provided useful beams to experimental groups. The frequency range available now is 18 - 30 MHz. The upper limit is determined by the parasitics mode at 35 MHz in the rf system. The beam energy can be varied in a wide range by changing the beam phase without degrading the beam quality so much.

Field of study: Physics
Structure of 1-phenyl-3-[o-hydroxy (methoxy) phenyl]-5-benzazolylformazans

A number of benzazolylhydrazones and benzazolylformazans containing an o-hydroxy or o-methoxy group in the phenyl ring attached to the meso-carbon atom were synthesized. The structure of the compounds in various solvents was studied by means of IR and UV spectroscopy and by determination of the ionization constants. The participation of the o-hydroxy group in the formation of an intramolecular hydrogen bond was demonstrated. The interrelationship between the structure and color of the formazans was investigated.

Field of study: Chemistry
Alprazolam and exposure for panic disorder with agoraphobia. Attribution of improvement to medication predicts subsequent relapse.

Patients with panic disorder plus agoraphobia had 8 weeks of drug treatment (alprazolam or placebo) plus psychological treatment (exposure or relaxation). At the end of treatment at week 8, 40 patients who had become much/very much improved rated how much their gains were attributable to medication or to their own efforts. During the tapering-off to week 16, and treatment-free follow-up to week 43, patients who at week 8 had attributed their gains to medication and felt less confident in coping without tablets had more severe withdrawal symptoms and greater loss of gains than did patients who at week 8 had attributed their gains to their own efforts during treatment. Baseline illness severity, greater age, higher expectations from drug treatment, and more side-effects of drugs during treatment all predicted more external attributions (i.e. to the effect of drugs) but did not independently predict relapse. Patients on alprazolam compared with placebo had more drug attributions. Though drug attributions predicted relapse in both alprazolam and placebo groups, predictions were stronger in the alprazolam group.

Field of study: Medicine, Psychology
A stable isotope study of mammal skeletal remains of mid-Pleistocene age, Arago cave, eastern Pyrenees, France. Evidence of taphonomic and diagenetic effects

This study reports a set of 85 oxygen isotope measurements carried out on fossil bones of Cervus elaphus, Ovis sp. and Equus sp. from archaeological excavations in the Arago cave, eastern Pyrenees, south-eastern France, of ages ranging from about 650 to 450 ka. A large section of the thick sediment sequence filling the cave was flushed, for an unknown time, by meteoric water through a large opening in the limestone ceiling caused by karst erosion. Under these conditions, part of the biogenic material underwent partial solution and diagenesis; these processes may have caused considerable effects on the original isotopic composition of bone phosphate. The range of the isotopic values obtained from each stratigraphic level is quite wide, particularly in the case of horse remains whose δ18O(PO3−4) values cover a range of about 5‰ in the same stratigraphic level. However, a few isotopically heavy values were obtained from the three species which suggest the possibility of very warm climatic episods or, alternatively, of climatically dry periods. Altogether, the results clearly show that it is not possible to obtain quantitative palaeoclimatological and palaeoenvironmental information from fossils which underwent taphonomic and diagenetic effects, that these effects may take place readily and that time is one of the less important parameters affecting bone preservation. The uncertainties existing in the case of relatively old fossil bones (not always shared by isotope geochemists) are thus directly confirmed.

Field of study: Environmental science, Geography
Inverse spin glass and related maximum entropy problems.

If we have a system of binary variables and we measure the pairwise correlations among these variables, then the least structured or maximum entropy model for their joint distribution is an Ising model with pairwise interactions among the spins. Here we consider inhomogeneous systems in which we constrain, for example, not the full matrix of correlations, but only the distribution from which these correlations are drawn. In this sense, what we have constructed is an inverse spin glass: rather than choosing coupling constants at random from a distribution and calculating correlations, we choose the correlations from a distribution and infer the coupling constants. We argue that such models generate a block structure in the space of couplings, which provides an explicit solution of the inverse problem. This allows us to generate a phase diagram in the space of (measurable) moments of the distribution of correlations. We expect that these ideas will be most useful in building models for systems that are nonequilibrium statistical mechanics problems, such as networks of real neurons.

Field of study: Physics