nils-herrmann/clean_scirepeval huggingface dataset:
On the use of Harrell's C for clinical risk prediction via random survival forests

Harrell's C is proposed as a split criterion in random survival forests.Split points of continuous predictor variables differ substantially between Harrell's C and log-rank splitting.The log-rank statistic has a stronger end-cut preference than Harrell'sźC.Harrell's C outperforms log-rank splitting in smaller scale studies.Harrell's C outperforms log-rank splitting if the censoring rate is high. Random survival forests (RSF) are a powerful method for risk prediction of right-censored outcomes in biomedical research. RSF use the log-rank split criterion to form an ensemble of survival trees. The most common approach to evaluate the prediction accuracy of a RSF model is Harrell's concordance index for survival data ('C index'). Conceptually, this strategy implies that the split criterion in RSF is different from the evaluation criterion of interest. This discrepancy can be overcome by using Harrell's C for both node splitting and evaluation. We compare the difference between the two split criteria analytically and in simulation studies with respect to the preference of more unbalanced splits, termed end-cut preference (ECP). Specifically, we show that the log-rank statistic has a stronger ECP compared to the C index. In simulation studies and with the help of two medical data sets we demonstrate that the accuracy of RSF predictions, as measured by Harrell's C, can be improved if the log-rank statistic is replaced by the C index for node splitting. This is especially true in situations where the censoring rate or the fraction of informative continuous predictor variables is high. Conversely, log-rank splitting is preferable in noisy scenarios. Both C-based and log-rank splitting are implemented in the Rźpackage ranger. We recommend Harrell'sźC as split criterion for use in smaller scale clinical studies and the log-rank split criterion for use in large-scale 'omics' studies.

Field of study: Computer science
The clinic of the speaking body

The title of this paper contains the echo of the Meeting of the International of the Forums in Rome in 2010, The Mystery of the Speaking Body. In replacing the word 'mystery' with 'clinic' I'm drawing attention to something essential with regard to both practice and presence: the analyst's embodied response to the analysand in the setting of the consulting room. But I do not want to lose the sense of the mystery in the work we do. In the consulting room, the discourse of the analyst is the condition for crossing into the foreign terrain of the unconscious. Analysis is a practice of speaking and hearing that requires the presence of two bodies; I am arguing that it cannot be conducted effectively by phone or by Skype for there, the real effect of speech on the body is lost. The analysand's desire to explore the unconscious is evident at the level of speech but also in the act of coming to the session. A subject moves his body into the analytic space, actually and in his words. The living body is the body that enjoys, the body that brings with it the dimension of the unconscious Real.

Field of study: Philosophy
Comparison of the early immune responses in mice vaccinated by different kinds of hepatitis B surface antigen

To evaluate the early cellular immune responses to three kinds of hepatitis B surface antigen (HBsAg) in the immunized mice. At day 4,the levels of IFN-γand IL-2 secreted by CD4+ and CD8+T cells which selected from splenic mononuclear cells (MNC) of the vaccinated mice were detected by enzyme-linked immunospot methods (ELISPOT) after stimulation in vitro with HBsAg MHC class Ⅰ peptide S28-39 of HBsAg or recombinant hepatitis B surface antigen(rHBsAg).Results After selected by MACs,the purity of CD3+/CD4+ and CD3+/CD8+T cell was more than 90％.The positive rate of IFN-γsecreted by CD4+T cells induced by HBsAg derived from Hansenula polymorpha(rHP) was higher than that of HBsAg derived from CHO cell (rCHO).Levels of IFN-γ secreted by CD8+T cells and IL-2 secreted by CD4+T cells induced by rHP antigen were significantly higher than those of rCHO( P＜0.05 ).Meanwhile,levels of IFN-γsecreted by CD4+T cells and CD8+T cells induced by rHP were also significantly higher than those of plasma HBsAg(pHB) (P＜0.05).Conclusion At day 4,the cellular immune responses induced by HBsAg could be detected.But the immune responses induced by the three kinds of HBsAg are different in levels.According to early cellular immune response intensity,the rHP HBsAg are superior to the rCHO and pHB,in accordance with the high protection rate interrupting the mother-infant transmission immunized by rHP vaccine in clinical trial.It provides scientific basis for necessity of timely birth dose of HB vaccine and kind of HB vaccine for high risk newborn infants vaccinated. 
 
 
Hepatitis B;  Surface antigen;  Cellular immune response;  Enzyme-linked immunospot ( ELISPOT )

Field of study: Biology
[An effect of valdoxan on the hemostasis in patients with acute coronary syndrome in the combination with anxiety and depressive disorders].

To explore the dynamics of hemostasis in patients with acute coronary syndrome (ACS) in the combination with anxiety and depressive disorders (ADD) during therapy with valdoxan (agomelatine).



We examined 196 male and female patients (mean age 64.2 ± 0.8 years) in the first 24 hours of ACS. The patients were divided into three groups: patients with ACS without ADD (n=88), patients with ACS and ADD without valdoxan therapy (n=58) and patients with ACS and ADD treated with valdoxan (n=50). Coagulation and vascular-platelet hemostasis were studied in the first 24 hours of hospitalization and in the 10th day of hospitalization.



Patients with ACS revealed high levels of fibrinogen, soluble fibrin-monomer complexes, D-dimer at all stages of the study. In patients with ADD, these parameters were significantly higher compared to patients without ADD. The levels of D-dimer in the 10th day were similar in patients with ADD treated with valdoxan and in patients with ACS without ADD. In both groups of patients with ADD, the levels of spontaneous aggregation in the first and 10th days of hospitalization were not significantly higher than in the control group and in patients with ACS without ADD. All patients with ACS had high values of platelet aggregation stimulated by adenosine diphosphate in dose 0.1 uM. In patients with ACS and ADD treated with valdoxan, a significant reduction of these parameters was noted in the 10th day of treatment compared to the first day of hospitalization.



The high procoagulant activity of the hemostatic system was observed during all stages of the study in the patients with ACS and ADD who received a combined antithrombotic therapy without valdoxan.

Field of study: Medicine, Psychology
A lipid-associated acetylcholine receptor as an antigen in diagnosis of myasthenia gravis.

Antibodies to the acetylcholine receptor are detected in over 85% of myasthenic patients' sera when acetylcholine receptors extracted from human muscle are used as the antigen. As recent data have shown the importance of the lipid environment for receptor function, we have used a lipid-associated acetylcholine receptor as the antigen for antibody determination. This fraction was shown to discriminate better between normal human sera and sera from myasthenic patients with low antibody titres. Among 12 sera from myasthenic patients in which antibodies were undetectable with the delipidated receptor as the antigen, seven were positive with the lipid-associated receptor. This lipid-associated fraction could be used beneficially for research and clinical investigation.

Field of study: Biology, Medicine
Interactions between centrally and peripherally generated neuromuscular oscillations

SummaryAn experimentally based model of the mammalian neuromuscular system has been extended to include the interaction of sinusoidal inputs generated within the central nervous system and those produced peripherally by reflex pathways, together with muscle properties and external loads. Multiple reflex pathways and pathways having acceleration as well as velocity and length sensitivity are considered. The responses are analyzed for brief inputs (Dirac δ-functions), sinusoidal driving functions and mixtures of the two over ranges in which the model behaves either linearly or non-linearly. Approximate solutions are derived for the non-linear range, and exact numerical solutions are computed for a few examples within the linear range. The extent to which brief inputs can reset ongoing oscillations and the extent to which sinusoidal inputs can entrain these oscillations are of particular interest.

Field of study: Biology, Mathematics
Patterns of protein carbonylation during Medicago truncatula seed maturation.

Seeds mainly acquire their physiological quality during maturation, whereas oxidative conditions reign within cells triggering protein carbonylation. To better understand the role of this protein modification in legume seeds, we compared by proteomics patterns of carbonylated proteins in maturing seeds of Medicago truncatula naturally desiccated or prematurely dried, a treatment known to impair seed quality acquisition. In both cases, protein carbonylation increased in these seeds, accompanying water removal. We identified several proteins whose extent of carbonylation varied when comparing natural desiccation and premature drying and that could therefore be responsible for the impairment of seed quality acquisition or expression. In particular, we focused on PM34, a protein specific to seeds exhibiting a high sensitivity to carbonylation and of which function in dicotyledons was not known before. PM34 proved to have a cellulase activity presumably associated with cell elongation, a process required for germination and subsequent seedling growth. We discuss the possibility that PM34 (abundance or redox state) could be used to assess crop seed quality.

Field of study: Environmental science
Methods for assessing the cost-effectiveness of public health interventions: key challenges and recommendations.

Increasing attention is being given to the evaluation of public health interventions. Methods for the economic evaluation of clinical interventions are well established. In contrast, the economic evaluation of public health interventions raises additional methodological challenges. The paper identifies these challenges and provides suggestions for overcoming them.



To identify the methodological challenges, five reviews that explored the economics of public health were consulted. From these, four main methodological challenges for the economic evaluation of public health interventions were identified. A review of empirical studies was conducted to explore how the methodological challenges had been approached in practice and an expert workshop convened to discuss how they could be tackled in the future.



The empirical review confirmed that the four methodological challenges were important. In all, 154 empirical studies were identified, covering areas as diverse as alcohol, drug use, obesity and physical activity, and smoking. However, the four methodological challenges were handled badly, or ignored in most of the studies reviewed.



The empirical review offered few insights into ways of addressing the methodological challenges. The expert workshop suggested a number of ways forward for overcoming the methodological challenges.



Although the existing empirical literature offers few insights on how to respond to these challenges, expert opinion suggests a number of ways forward. Much of what is suggested here has not yet been applied in practice, and there is an urgent need both for pilot studies and more methodological research.

Field of study: Medicine, Political science
Simultaneous extraction of optical transport parameters and intrinsic fluorescence of tissue mimicking model media using a spatially resolved fluorescence technique.

We present a method based on spatially resolved fluorescence measurement for the simultaneous estimation of optical transport parameters, namely, the reduced scattering coefficient (micro s'), the absorption coefficient (micro a), and the intrinsic fluorescence spectra from turbid media. The accuracy of this approach was tested by conducting studies on a series of tissue-simulating phantoms with known optical transport properties. The estimated relative error in the values for micro s' and micro a using this technique was found to be < or =10%. Furthermore, the line shape and intensity of the intrinsic fluorescence recovered by using this approach were observed to be free from the distorting effects of the wavelength-dependent absorption and scattering properties of the medium, and they were in excellent agreement with the directly measured intrinsic fluorescence spectra of the fluorophores.

Field of study: Physics
Triggering of Suicidal Erythrocyte Death Following Boswellic Acid Exposure

The antinflammatory natural product boswellic acid is effective against cancer at least in part by inducing tumor cell apoptosis. Similar to apoptosis of nucleated cells erythrocytes may enter eryptosis, a suicidal death characterized by cell shrinkage and cell membrane scrambling with phosphatidylserine translocation to the erythrocyte surface. Stimulators of eryptosis include oxidative stress, increase of cytosolic Ca2+-activity ([Ca2+]i), energy depletion, ceramide formation and p38 kinase activation. The present study tested, whether and how boswellic acid induces eryptosis.  Phosphatidylserine exposure at the cell surface was estimated from annexin V binding, cell volume from forward scatter, hemolysis from hemoglobin release, [Ca2+]i from Fluo3-fluorescence, ceramide abundance utilizing specific antibodies, reactive oxygen species (ROS) from 2′,7′-dichlorodihydrofuorescein diacetate (DCFDA) fluorescence, and cytosolic ATP concentration utilizing a luciferin-luciferase assay kit.  A 24 hours exposure of human erythrocytes to boswellic acid (5 µg/ml) significantly increased the percentage of annexin-V-binding cells (to 9.3 ±0.9 %) and significantly decreased forward scatter. Boswellic acid did not significantly modify [Ca2+]i, cytosolic ATP, ROS, or ceramide abundance. The effect of boswellic acid on annexin-V-binding was significantly blunted, but not abolished by p38 kinase inhibitors skepinone (2 µM) and SB203580 (2 µM).  Boswellic acid stimulates cell shrinkage and phospholipid scrambling of the erythrocyte cell membrane, an effect in part dependent on p38 protein kinase activity.

Field of study: Biology, Chemistry
Li2TiO3 and Li2ZrO3 co-modification LiNi0.8Co0.1Mn0.1O2 cathode material with improved high-voltage cycling performance for lithium-ion batteries

LiNi0.8Co0.1Mn0.1O2 (NCM) materials with surface modification by Li2TiO3 (LTO), Li2ZrO3 (LZO) and Li2TiO3-Li2ZrO3 (LTZO) coatings are successfully synthesized via a simple wet chemical method and proper heat-treatment process. The crystal structure, surface morphology, valence states and electrochemical properties of different modified NCM materials are investigated by the means of X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). The NCM co-modified by Li2TiO3 and Li2ZrO3 composite coatings (LTZO@NCM) shows remarkable improvements in cycling performance and rate capability, the discharge capacity is 190.36 mAh g−1 with high capacity retention of 92.64% at 0.2C after 100 cycles between 2.75 and 4.4 V, compared to 174.83 mAh g−1 with the capacity retention of 87.20% for pristine NCM. Even at a high current density of 1 C, LTZO@NCM still maintains a high discharge capacity of 149.77 mAh g−1 cycled at high cut-off voltage of 4.4 V, with a capacity retention rate of 83.04% at 150th cycle, while bare NCM only delivers 123.92 mAh g−1 with capacity retention of 68.86%. The enhanced electrochemical performance can be ascribed to the modified effect of LTZO nano-coating layer on the NCM surface. LTZO nano-coating layer can not only effectively protect NCM particles, avoid the occurrence of side reaction, but also provide a better Li+ transport channels, improve lithium ion diffusion rate and enhance the structure stability and electrochemical performances of NCM material.

Field of study: Materials science
Palaeoecology and palaeoenvironment of Mississippian coastal lakes and marshes during the early terrestrialisation of tetrapods

The Ballagan Formation of northern Britain provides an exceptional record of Early Mississippian ecosystems that developed as tetrapods emerged onto land. In this paper, we study two 500-metre sections of the formation near Berwick-upon-Tweed, which are characterised by abundant ferroan dolostone beds. Five lithofacies are identified: cemented siltstone and sandstone, homogeneous dolomicrite, mixed dolomite and siltstone, mixed calcite and dolomite, and dolomite with evaporite minerals. Cemented sediments have non-planar to planar subhedral dolomite crystals, up to 40 μm in size, whereas other facies predominantly comprise dolomicrite or planar euhedral dolomite rhombs 15 μm in size, with patches of larger rhombs indicating partial recrystallisation. The macro- and microfossil content of the dolostones is dominated by sarcopterygian (rhizodont) and actinopterygian fish, bivalves, Serpula, ostracods and Chondrites trace fossils; with rarer Spirorbis, chondrichthyans (Ageleodus, hybodonts and ?ctenacanths, xenacanths), non-gyracanth acanthodians, gastropods, eurypterids, brachiopods, plant debris, wood, lycopsid roots, charcoal, megaspores, phycosiphoniform burrows, Zoophycos? and Rhizocorallium. The oxygen and carbon isotope composition of dolomites range from –3.6‰ to –1.7‰ (for δ18O) and –2.6‰ to +1.6‰ (for δ13C) respectively indicating dolomite growth in mixed salinity waters. Frequent marine storm-surge events transported marine waters and animals into floodplain lakes, where evaporation, interstitial sulphate-reducing bacteria, iron reduction and methanogenesis allowed dolomite growth in the shallow sub-surface. Secondary pedogenic modification (by roots, brecciation, desiccation, and soil forming processes) is common and represents lake evaporation with, in some cases, saline marsh development. The dolostone facies are part of a complex environmental mosaic of sub-aerial dry floodplain, wet marshy floodplains, rivers, and lakes ranging in salinity from freshwater to hypersaline. Marine influence is strongest at the base of the formation and decreases over time, as the floodplain became drier, and forested areas became more established. Coastal lakes were an important habitat for animals recovering from the end-Devonian Hangenberg Crisis and may have acted as a pathway for euryhaline fishes, molluscs and arthropods to access freshwater environments.

Field of study: Environmental science, Geography
Pitman Nearness Comparison of the Traditional Estimator of the Coefficient of Determination and Its Adjusted Version in Linear Regression Models

In this article we present formulae for the determination of Pitman Nearness in comparing the coefficient of determination with its adjusted version in regression models for a given sample size. We generalize this finding to compare R2 with a nonnegative parts version of the adjusted R2. We compare our small, medium, and large sample results with the asymptotic results of Kumar and Srivastava (2004).

Field of study: Mathematics
Influence of ultraviolet C bystander effect on inflammatory response in A375 cell on subsequent exposure to ultraviolet C or hydrogen peroxide.

Ultraviolet C (UVC) irradiation (λ: 200-280 nm) causes release of several secretory cytokines responsible for inflammation. Our objective was to investigate whether inflammatory response was also induced in bystander cells. For this purpose, the conditioned medium containing the released factors from UVC irradiated A375 cells was used in this study to evaluate the expression of inflammatory markers, such as tumour necrosis factor alpha (TNFα), nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) and p38 mitogen-activated protein kinase (p38 MAPK) in its bystander cells. Inflammatory responses in bystander cells subjected to further irradiation by UVC or other damaging agent like H2O2 were also examined. It was observed that TNFα, NFκB and p38 MAPK were not induced in UVC-bystander cells, but their expression was suppressed in the UVC-bystander cells treated with UVC or H2O2. This lowering in inflammatory response might be due to smaller depletion in the reduced glutathione (GSH) content present in these treated bystander cells. The study indicated that UVC-induced bystander effect was an intrinsic protective response in cells, capable of suppressing inflammation induced in cells on exposure to damaging agents.

Field of study: Biology, Chemistry, Physics
What "good outcome" means to patients: Understanding recovery and improvement in psychotherapy for major depression from a mixed-methods perspective.

This study explored the meaning of "good outcome" within and beyond the much-used statistical indices of clinical significance in standard outcome research as developed by Jacobson and Truax (1991). Specifically, we examined the experiences of patients marked as "recovered" and "improved" following cognitive-behavioral therapy and psychodynamic therapy for major depression. A mixed-methods study was conducted using data gathered in an RCT, including patients' pre-post outcome scores on the Beck Depression Inventory-II and posttreatment client change interviews. We selected 28 patients who showed recovery and 19 patients who showed improvement in self-reported depression symptoms. A grounded theory analysis was performed on patients' interviews, ultimately resulting in a conceptual model of "good outcome." From patients' perspectives, good outcome can be understood as feeling empowered, finding personal balance and encountering ongoing struggle, indicating an ongoing process and variation in experience. The Jacobson-Truax classification of "good outcome" could not account for the (more pessimistic) nuances in outcome experiences, especially for "improved" patients, and did not grasp the multidimensional nature of outcome as experienced by patients. It is recommended that statistical indications of clinical meaningfulness are interpreted warily and ideally contextualized within personal narratives. Further research on the phenomenon of change and good outcome is required, aiming at integrating multiple perspectives and methods accordingly the multidimensional phenomenon under study.

Field of study: Psychology