nils-herrmann/clean_scirepeval huggingface dataset:
Self-Controlled Case Series Analysis With Event-Dependent Observation Periods

The self-controlled case series method may be used to study the association between a time-varying exposure and a health event. It is based only on cases, and it controls for fixed confounders. Exposure and event histories are collected for each case over a predefined observation period. The method requires that observation periods should be independent of event times. This requirement is violated when events increase the mortality rate, since censoring of the observation periods is then event dependent. In this article, the case series method for rare nonrecurrent events is extended to remove this independence assumption, thus introducing an additional term in the likelihood that depends on the censoring process. In order to remain within the case series framework in which only cases are sampled, the model is reparameterized so that this additional term becomes estimable from the distribution of intervals from event to end of observation. The exposure effect of primary interest may be estimated unbiasedly. The age effect, however, takes on a new interpretation, incorporating the effect of censoring. The model may be fitted in standard loglinear modeling software; this yields conservative standard errors. We describe a detailed application to the study of antipsychotics and stroke. The estimates obtained from the standard case series model are shown to be biased when event-dependent observation periods are ignored. When they are allowed for, antipsychotic use remains strongly positively associated with stroke in patients with dementia, but not in patients without dementia. Two detailed simulation studies are included as Supplemental Material.

Field of study: Mathematics
Integration of Undergraduate Education and Field Campaigns: A Case Study from Deep Convective Clouds and Chemistry

An undergraduate course was taught at the University of North Dakota (UND) that examined the objectives and motivation of the Deep Convective Clouds and Chemistry (DC3) field campaign. The course included discussions about particular challenges involved in making chemical transport measurements and field campaign forecasts; hands-on forecasting exercises for all three DC3 regions were also included. Subsequently, UND undergraduate students traveled to the University of Alabama in Huntsville to participate in DC3 campaign operations. While in the field, students actively participated in radiosonde operations (including instrument preparation and launch, field log documentation, and data quality control) as well as mission planning and daily forecast discussions. During the field period, a hands-on internship was held at UND that gave both graduate and undergraduate students a chance to forecast for the campaign (offline) and then listen in on the live forecast discussion. Formal assessment of the undergrad...

Field of study: Environmental science
The Glucocorticoid Dexamethasone Inhibits U937 Cell Adhesion and Neutrophil Release via RhoA/ROCK1-Dependent and Independent Pathways

The aim of the present study was to investigate the role of the Ras homolog family member A (RhoA)/Rho-associated coiled-coil-containing protein kinase 1 (ROCK1) signaling pathway in the inhibition of inflammatory responses by the glucocorticoid dexamethasone (Dex).  The inhibitory effects of Dex and Rho-kinase inhibitor fasudil (Fas) on phorbol ester-induced release of O2- and MPO from neutrophils and on U937 mononuclear cell adhesion were examined along with the expression and activity levels of RhoA and ROCK1.  High doses of Dex rapidly inhibited the release of O2- and myeloperoxidase (MPO) from neutrophils and the adhesion of U937 cells, while Fas was only found to inhibit U937 cell adhesion. Additionally, Dex suppressed ROCK1 activity. However, Dex had no effects on ROCK1 or RhoA expression levels or on RhoA activity. Neither the glucocorticoid receptor antagonist mifepristone (RU-486) nor the protein synthesis inhibitor cycloheximide (CHX) was able to suppress the effects of Dex (p>0.05).  The present findings indicate that Dex suppressed neutrophil release through ROCK1-independent mechanisms and inhibited the adhesion of U937 mononuclear cells through ROCK1-dependent non-genomic mechanisms that did not involve RhoA.

Field of study: Biology, Chemistry
An impairment of antibody production in adoptively restored, lethally irradiated thymectomized mice.

Lethally irradiated, bone marrow protected, normal and thymectomized adult mice were given 140–250 × 106 syngeneic spleen and lymph node cells from normal or sensitized donors. These mice were tested at intervals following irradiation for their ability to reject allogeneic and xenogeneic skin grafts and to produce haemagglutinins. The results show that adoptively restored, thymectomized mice are capable of responding normally to skin homografts of varying antigenic disparity and of producing haemagglutinins to xenogeneic antigens. However, the majority of the mice which received lymphoid cells from normal donors were unable to produce haemagglutinating antibody in response to allogeneic antigens. Both 19S and 7S antibody were produced by the thymectomized mice.

Field of study: Biology, Medicine
BoXHED: Boosted eXact Hazard Estimator with Dynamic covariates

The proliferation of medical monitoring devices makes it possible to track health vitals at high frequency, enabling the development of dynamic health risk scores that change with the underlying readings. Survival analysis, in particular hazard estimation, is well-suited to analyzing this stream of data to predict disease onset as a function of the time-varying vitals. This paper introduces the software package BoXHED (pronounced 'box-head') for nonparametrically estimating hazard functions via gradient boosting. BoXHED 1.0 is a novel tree-based implementation of the generic estimator proposed in Lee et al. (2017), which was designed for handling time-dependent covariates in a fully nonparametric manner. BoXHED is also the first publicly available software implementation for Lee et al. (2017). Applying it to a cardiovascular disease dataset from the Framingham Heart Study reveals novel interaction effects among known risk factors, potentially resolving an open question in clinical literature.

Field of study: Computer science
Does Economic Crisis Reduce Support for Markets and Democracy in Latin America? Some Evidence from Surveys of Public Opinion and Well Being

The severe economic crisis facing several countries in the region over the last couple of years has led many observers to predict a backlash against market policies and even against democracy in the region. An economic crisis of such proportions should also, in theory, have negative effects on subjective well being. Our analysis, based on the Latinobarometro surveys from 2000–2002, finds some unexpected positive trends, as well as notable differences between those countries that suffered from crises and those that did not. Satisfaction with market policies and with the way democracy is working has decreased among all groups except the very wealthy. In contrast, support for democracy as a system of government has increased, suggesting that respondents are increasingly distinguishing between democracy as a system of government, and the manner in which particular governments are performing. We also find evidence of changing attitudes towards redistributive taxation among the wealthy.

Field of study: Political science
T cell receptor usage in patients with non‐progressing HIV infection

It is still unclear why some patients with HIV progress more slowly than others to developing full blown AIDS. In this study using flow cytometry we have investigated the TCRBV repertoire of peripheral blood T lymphocytes in 17 long‐term non‐progressing HIV patients (LTNP) to determine if there is a biased usage of T cell receptor V gene products. Patients were identified from hospital records and entered into the study. Three colour flow cytometry was used to determine the expression of the TCRBV3S5, BV5S1, BV5S2, BV5S3, BV6S1, BV7S1, BV9, BV11, BV12, BV13, BV14, BV16, BV17, BV18, BV20, BV21S3, BV22, and BV23 by CD8 and CD4 positive cells isolated from the peripheral blood of patients and controls. Increases in the absolute numbers of CD8+ T cells expressing TCRBV2 and 8 were observed in the HIV‐LTNP population (P < 0·05 in both cases). No differences were seen in numbers of CD8+ T cells expressing other TCRBV or in any TCRBV within the CD4+ T cell popu‐lation. At follow up (1–2 years later), those patients in which CD4 levels were below 500 × 106/l were those initially found to have lower levels of TCRBV8 +ve CD8 cells. A significant increase in the absolute numbers of T cells coexpressing the gamma delta (γδ) T cell receptor and CD8 were also seen in the HIV‐LTNP patients compared with controls (P = 0·002). The increase in CD8+ T cells in the HIV‐LTNP patients may be interpreted as either an antigen specific, or group of antigen specific responses to viral antigen, or less likely a viral superantigen. A low level of TCRBV8, CD8+ T cells might be predictive of a more rapid disease progression and might indicate a protective role for this population in HIV infected patients. The increase in γδT cells bearing the CD8 coreceptor suggests a role for this cell type in the response to HIV infection.

Field of study: Biology, Medicine
Characteristics and turnover of exopolymeric substances in a hypersaline microbial mat.

The properties and microbial turnover of exopolymeric substances (EPS) were measured in a hypersaline nonlithifying microbial mat (Eleuthera, Bahamas) to investigate their potential role in calcium carbonate (CaCO(3)) precipitation. Depth profiles of EPS abundance and enzyme activities indicated that c. 80% of the EPS were turned over in the upper 15-20 mm. Oxic and anoxic mat homogenates amended with low-molecular-weight (LMW) organic carbon, sugar monomers, and different types of EPS revealed rapid consumption of all substrates. When comparing the consumption of EPS with that of other substrates, only marginally longer lag times and lower rates were observed. EPS (5-8%) were readily consumed during the conversion of labile to refractory EPS. This coincided with a decrease in glucosidase activity and a decrease in the number of acidic functional groups on the EPS. Approximately half of the calcium bound to the EPS remained after 10 dialyses steps. This tightly bound calcium was readily available to precipitate as CaCO(3). We present a conceptual model in which LMW organic carbon complexed with the tightly bound calcium is released upon enzyme activity. This increases alkalinity and creates binding sites for carbonate and allows CaCO(3) to precipitate. Therefore, this model explains interactions between EPS and CaCO(3) precipitation, and underscores the critical role of aerobic and anaerobic microorganisms in early diagenesis and lithification processes.

Field of study: Biology, Environmental science
Analysis of tyrosine hydroxylase and insulin transcripts in human neuroendocrine tissues.

We have previously shown that the mRNA for human tyrosine hydroxylase (TH) exists in one of 4 forms as a result of alternative splicing of intron 1. In order to determine the tissue-specific expression of the multiple human transcripts we have utilized specifically primed polymerase chain reactions (PCR) in combination with reverse-transcribed RNA. Using PCR analysis we determined that many human neuronal tissues express all 4 forms of human TH (hTH-1-4); however, hTH-3 and -4 are generally expressed at less than 1% of the other two. Of all tissues examined, only pancreatic beta-islet cells expressed a single form of human TH mRNA (hTH-2). The mRNA for rat TH is present in only one form, the equivalent of hTH-1. Since we have shown that the human genes for TH and insulin are only 2.7 kb apart and several groups have reported insulin-like expression in neuronal tissues, we looked for insulin transcription in the same central and peripheral nervous system samples. Insulin mRNA was not present within the limits of detection.

Field of study: Biology
Charge trapping correction in Ge spectrometers

A charge-trapping model is developed which does not require the assumption of shallow-level detrapping. The model shows the charge-trapping deficit to be proportional to S/sub 0/t/sup N/, where S/sub 0/ is the peak amplitude of the shaping amplifier pulse, t is the charge collection time for the carrier being trapped, and 1.5 >

Field of study: Physics
Possible eucaryotic algae (Bangiophycidae) among early Proterozoic microfossils

Recent data concerning extant planktonic red algae, chrysophytes, and haptophytes suggest possible reallocation of certain previously described middle and late Precambrian microfossils to one or more of these eucaryotic groups. Both binary fission and budding reproductive methods characterize Huroniospora of the Gunflint Iron Formation and Palaeocryptidium of the Bohemian Proterozoic. Their reproduction, morphology, habitat, and wide geographic distribution, as well as phylogenetic interpretations based on morphology, life cycles, and biochemistry of extant algae, suggest possible assignment of the Precambrian fossils to the unicellular red algal Order Porphyridiales (Subclass Bangiophycidae) rather than to the procaryotic blue-green algae or to the terrestrial fungi as recently suggested. Living Porphyridium may show peripheral multiple budding, with the resultant small cells held in the mucilaginous sheath that surrounds the parent cell, suggesting a similar relationship of Eosphaera tyleri Barghoorn and the Type 4 organism of Hofmann and Jackson. Eucapsis ? from the Paradise Creek Formation also might be referable to the Rhodophyta (spore packets of Bangiales) or Chromophyta (colony stage of Haptophyceae or Chrysophyceae) rather than to the blue-green algae. Reassignment of the Gunflint taxa to the red algal Subclass Bangiophycidae would make this the earliest fossil record of this group; preservation of these unicellular organisms is due to the exceptional nature of the enclosing chert. The suggested reassignment also would date the evolution of the eucaryotic cell and of vegetative mitotic cell division by binary fission and budding by at least 1.9 × 10 9 yr B.P., about the time previously hypothesized as representing the final transition from an anoxic to an oxygenic atmosphere. Genetic recombination resulting from sexual reproduction, with nuclear fusion and meiosis, first appeared in red or green algae at some time within the succeeding 1 b.y.

Field of study: Geology
Absence of covalently linked core protein from newly synthesized hyaluronate.

1. Primary cultures of chondrocytes from the Swarm rat chondrosarcoma were labelled with either [3H]glucosamine or [14C]glucosamine, and hyaluronate synthesized by the cells was isolated from the cell layer. Parallel cultures were labelled with either [3H]serine or [3H]lysine, and identical fractions were isolated from the cell layer. Some cultures were dual-labelled. 2. In cultures labelled with [3H]serine for between 30 min and 24 h and extracted with 4.0 M-guanidine, a procedure that solubilizes predominantly extracellular macromolecules, small amounts of [3H]serine-labelled molecules were found associated with the hyaluronate fraction purified from the extract by dissociative CsCl-density-gradient centrifugation and dissociative Sepharose CL-2B chromatography. About 75% of the [3H]serine-labelled molecules in the fraction were specifically associated with hyaluronate, since they could be removed by prior treatment with proteinase-free Streptomyces hyaluronidase. The association of the [3H]serine-labelled molecules with hyaluronate was non-covalent, since they could be separated from it by further centrifugation in CsCl density gradients containing 4 M-guanidinium chloride and a zwitterionic detergent. 3. In other experiments the cultures were extracted with a sequential zwitterionic-detergent/guanidinium chloride procedure that completely solubilized the cell layer and enabled fractions containing newly synthesized cell-associated hyaluronate to be isolated. Zwitterionic detergent was present throughout. No [3H]lysine was incorporated into these fractions, irrespective of whether the cultures were pulsed concurrently with [3H]lysine and [14C]glucosamine or sequentially with [3H]lysine to prelabel the protein pool (24 h) followed by [14C]-glucosamine to label hyaluronate (1 h). 4. The results show that newly synthesized hyaluronate is not associated with covalently bound protein, and suggest that chain synthesis is initiated by a mechanism other than on to a core protein. Small amounts of [3H]serine-labelled molecules are, however, non-covalently associated with extracellular hyaluronate. Their identity is at present unknown, but they are probably of low molecular weight.

Field of study: Biology, Computer science
SPATIAL CALCULATION FEM FOR SKEW T-BEAM BRIDGE WITH MULTI-RIBBED SLABS

This paper deals with the spatial calculation FEM of skew T-beam bridge with multi-ribbed slabs. Firstly, the bridge floor deck and the ribbed slab of T-beam bridge with multi-ribbed slabs are taken as a skew slab-beam and a general slab-beam, respectively. Then the shear lag and the local bending of the bridge floor deck are considered in constituting the displacement function, and the element rigidity matrix is assembled according to the deformation coordination of T-beam section displacement parameter. Finally, the spatial calculation FEM for skew T-beam bridge with multi-ribbed slabs is proposed.

Field of study: Engineering
Semianalytical thermal analysis of the heat capacity of YAG laser rods.

Based on the theory of semianalytical thermal analysis, we investigate the heat capacity of Nd:YAG laser rods for pumping and cooling. A general expression for the temperature field within Nd:YAG laser rod crystals is obtained for the pumping stage and the relation of the maximum temperature rise with pumping time. We also achieve an expression for the temperature field for the cooling stage and the relation of the maximum temperature rise with cooling time. These results show that, when using the output power of 300 W LD pumped Nd:YAG laser rod crystals for 5 s, the maximum temperature rise in the center of the pump face is 154.79 degrees C. After we stop the pumping for 30 s, the maximum temperature rise drops to 0.8%. These results are in agreement with those reported by others. Our results provide a theoretical basis for the optimized design of a LD end-pumped heat capacity laser.

Field of study: Physics
Poly-ADP-ribosylation of histone proteins of human kidney T1-cells in vitro following gamma-irradiation.

Poly-ADP-ribosylation of cellular proteins is involved with radiation induced damage and its repair. It has been observed that suspension of human kidney T1-cells in vitro attained elevated levels of poly-ADP-ribosylation due to experimental manipulations necessary for preparation of single cell suspension from monolayer cell cultures. These cells in suspension were exposed to various doses of gamma-rays with or without subsequent repair incubation. The PADPR of histones H3, H1 and H2B increased with increasing dose of radiation and decreased after 90 min or repair incubation. Concomitant with these changes, the affinity of histones to DNA in chromatin reduced immediately after irradiation. Normal affinity was reestablished after post-irradiation repair incubation. The results indicate that induction of poly-ADP-ribosylation of histone proteins by radiation and by manipulations to prepare single cell suspension involved different cellular components.

Field of study: Biology, Chemistry, Physics
Dynamics of sustained use and abandonment of clean cooking systems: lessons from rural India

Clean cooking technologies—ranging from efficient cookstoves to clean fuels—are widely deployed to reduce household air pollution and alleviate adverse health and climate consequences. Although much progress has been made on the technical aspects, sustained and proper use of clean cooking technologies by populations with the most need has been problematic. Only by understanding how clean cooking as an intervention is embedded within complex community processes can we ensure its sustained implementation. Using a community-based system dynamics approach, we engaged two rural communities in co-creating a dynamic model to explain the processes influencing the uptake and transition to sustained use of biogas (an anaerobic methane digester), a clean fuel and cooking technology. The two communities provided contrasting cases: one abandoned biogas while the other continues to use it. We present a system dynamics simulation model, associated analyses, and experiments to understand what factors drive transition and sustained use. A central insight of the model is community processes influencing the capacity to solve technical issues. Model analysis shows that families begin to abandon the technology when it takes longer to solve problems. The momentum in the community then shifts from a determination to address issues with the cooking technology toward caution in further adhering to it. We also conducted experiments using the simulation model to understand the impact of interventions aimed at renewing the use of biogas. A combination of theoretical interventions, including repair of non-functioning biogas units and provision of embedded technical support in communities, resulted in a scenario where the community can continue using the technology even after support is retracted. Our study also demonstrates the utility of a systems approach for engaging local stakeholders in delineating complex community processes to derive significant insights into the dynamic feedback mechanisms involved in the sustained use of biogas by the poor.

Field of study: Environmental science
Enhanced dielectric properties of Zr−Sn−Ti oxynitride thin films

Zr0.26Sn0.23Ti0.51OxOy (ZSTON) and Zr0.26Sn0.23Ti0.51O2σ (ZSTO) films have been prepared on Pt coated silicon substrates by pulsed laser deposition technique using a Zr−Sn−Ti oxide target at a substrate temperature of 650°C in N2 and O2 ambient, respectively. TEM observation showed that both kinds of films are amorphous. XPS analysis showed that the N/O ratio in ZSTON is 0.08/0.92. With the help of a comparative study of the dielectric properties of ZSTON and ZSTO films, it has been found that incorporation of nitrogen can increase the dielectric coefficient and decrease the dielectric loss of the multicomponent oxide films remarkably. Optical transmittance measurements showed that incorporation of nitrogen can slightly decrease the width of the bandgap and increase the refractive index of the films. It is proposed that amorphous Zr−Sn−Ti oxynitride stable at 650°C is a potential dielectric material for DRAM applications.

Field of study: Materials science
DENSITY DEPENDENCE, AND VALIDITY OF SEMI-EMPIRICAL FORMULA

5 2 Center for Excellence in Astronomy and Astrophysics (CEAA-RIAAM)-Maragha, P.O. Box 6 55134-441, Maragha 55177-36698, Iran 7 11 clear potential. We have also investigated the temperature and density dependence of 12 asymmetry energy. Our results show that the asymmetry energy of nuclear matter de- 13 pends on both density and temperature. We have also studied the effects of different 14 terms in the asymmetry energy of nuclear matter. These investigations indicate that 15 at different densities and temperatures, the contribution of parabolic term is very sub- 16 stantial with respect to the other terms. Therefore, we can conclude that the parabolic 17 approximation is a relatively good estimation, and our calculated binding energy of 18 asymmetric nuclear matter is in a relatively good agreement with that of semi-empirical 19 mass formula. However, for the accurate calculations, it is better to consider the effects 20 of other terms.

Field of study: Physics