nils-herrmann/clean_scirepeval huggingface dataset:
High-Dimensional Mixed Graphical Models

While graphical models for continuous data (Gaussian graphical models) and discrete data (Ising models) have been extensively studied, there is little work on graphical models for datasets with both continuous and discrete variables (mixed data), which are common in many scientific applications. We propose a novel graphical model for mixed data, which is simple enough to be suitable for high-dimensional data, yet flexible enough to represent all possible graph structures. We develop a computationally efficient regression-based algorithm for fitting the model by focusing on the conditional log-likelihood of each variable given the rest. The parameters have a natural group structure, and sparsity in the fitted graph is attained by incorporating a group lasso penalty, approximated by a weighted lasso penalty for computational efficiency. We demonstrate the effectiveness of our method through an extensive simulation study and apply it to a music annotation dataset (CAL500), obtaining a sparse and interpretable graphical model relating the continuous features of the audio signal to binary variables such as genre, emotions, and usage associated with particular songs. While we focus on binary discrete variables for the main presentation, we also show that the proposed methodology can be easily extended to general discrete variables.

Field of study: Computer science
A FAST ANALYTICAL METHOD FOR THE DEFORMATION OF BEAMS WITH VARYING CROSS-SECTIONS

For beams with varying stiffness and complex loads, the common method is unable to obtain analytic solutions. A continuous subsection independently systematic integral method(CSISIM for short) is presented for fast determination of analytical solutions of the deformation of beams with varying sections. In CSISIM, the beam is first separated into segments. A general mechanical model is established for solution of beams with varying stiffness under complex load. The forth-order differential deflection equation of any cross section is derived from the model. Then the general solutions of beam deflection are obtained independently by four-fold integration.Integral constants are determined from the boundary conditions and continuity conditions. It is not necessary to simplify loading and beam structure when establishing a model of continuous curved variable cross-section beam and processing the derivation. The beam deformation analytical solution procedure is programed directly by using symbolic computation software. It realizes an analytic solution by computer for beams with varying stiffness under complex loads. In this paper, there are three engineering examples-a stepped beam, a uniform depth variable width cross-section beam, and a uniform width variable height cross-section beam. Their analytical solutions are obtained by CSISIM. The engineering examples show that it is simple to establish mathematical models using this method. Calculation programming is systematic. Analytical solution can be quickly obtained.

Field of study: Engineering
Neoliberal Europe: Enabling Ethno-Cultural Neutrality or Fueling Neo-Nationalist Sentiment?

Ideologically committed to the neoclassical notion of "market discipline," the neoliberal regime is argued to promote principles of ethno-cultural neutrality and to create a level-playing field for all individuals regardless of race, class, gender, or other marker of minority status. However, in practice, neoliberal policies have increased the incidence of economic marginalization among lower and middle socio-economic classes in Europe, and have contributed to growing tensions between cultural majorities and ethnic minority groups. While similar sentiments associated with the rise of nationalism in nineteenth century Europe clearly predate the neoliberal era, in this paper I argue that neoliberal policies, backed by European Union institutions, have created material conditions which have exposed and widened structural incompatibilities between the notions of state and nation. Since the 1990s, these incompatibilities have legitimized the resurgence of radical nationalist sentiment within European nation-states, creating a favorable terrain for the populist rise of far-right factions. In lieu of promoting ethno-cultural neutrality, neoliberal policies have weakened liberal and social principles of inclusion, and have eroded welfare state provisioning systems in European democracies. They have fueled what Thorstein Veblen (1923, 28) referred to as "unreasoning habits of national conceit, fear, hate, contempt, and servility."

Field of study: Economics
Effects of short‐term ozone fumigation on tobacco plants: response of the scavenging system and expression of the glutathione reductase

The role that the constituents of the ascorbate-glutathione cycle play in the mechanism of contrasting ozone sensitivities was examined in mature and old tobacco leaves after acute ozone-fumigation (150 p.p.b., 5 h). Levels of the enzyme activities associated with the detoxifying system were lower in ozone-sensitive Bel W3 control plants than in unfumigated ozone-tolerant Bel B plants. In particular, the endogenous activities of ascorbate peroxidase (APX) and glutathione reductase (GR), and the metabolites ascorbic acid (AA) and reduced glutathione (GSH) were more abundant in Bel B than Bel W3 control plants. These results suggest that the higher tolerance of Bel B to O 3 is associated with a greater initial content of the antioxidant enzymes or metabolites. Only in the mature leaves of the ozone-tolerant Bel B cv. did fumigation trigger activation of APX and, weakly, of dehydroascorbate reductase (DHAR). The activity of these enzymes was significantly lower after ozone treatment in both mature and old leaves of Bel W3 than in control plants. Fumigation had little effect on the ascorbate content. Its main effects on the glutathione pool were that it boosted the oxidized form and lowered the reduced form, particularly in mature Bel W3 leaves. Extractable GR activity remained unchanged in both Bel B and Bel W3 immediately after fumigation, but increased slightly 24 h later, particularly in mature leaves of Bel W3. Exposure to O 3 caused a sharp decline in chloroplastic GR mRNA levels in both cultivars. However, as Western blot analysis failed to detect any major changes in GR protein content at this time, the protein must be highly stable. There is therefore a good correlation between tolerance to O 3 and high endogenous levels of antioxidant metabolites such as AA and GSH in tobacco. In addition, the degree of inducibility of the system discriminates the two cultivars investigated.

Field of study: Environmental science
Glucose dissimilation in Entamoeba histolytica.

: The endproducts of glucose dissimilation in Entamoeba histolytica were found to be carbon dioxide, acetate and ethanol. This organism possesses the same Embden-Meyerhof intermediates as found in most investigated organisms. In its glucose-to-pyruvate pathway several unusual features were demonstrated. The pyruvate-to-acetate and pyruvate-to-ethanol pathways are also unique as compared with that of other organisms. The distinctive properties of the metabolic enzymes provide the basis for the development of new chemotherapeutic agents against this parasitic protozoa.

Field of study: Biology
J-dependence in the isotope-shift of the 4f75d6s a10D-term in the ground-configuration of Gd II

In order to extend the parametric description of the isotope shift to 5d-electrons in the lanthanides the IS of three GdII transitions (4f75d6pz10F11/2→4f75d6sa10D9/2, 11/2, 13/2) was measured with enriched isotopes and natural composition of Gd in hollow cathodes. The values −99.75(30)mK, −100.15(25)mK and −101.90(50)mK were obtained for the IS (between156Gd and160Gd) from the lines 367.1 nm, 374.4 nm and 385.6 nm resp. From theJ-dependence of the IS found in the a10D multiplet the crossed-second-order parameterz5d=1.40 (35) mK was calculated. After normalization withδ〈r2〉 andζ5d the figurez5d, norm=6.2(1.8)· 10−6 fm−2 agrees fully with the corresponding value from Eu I. This proves that theJ-dependence within a multiplet arises mainly from a crossed-second-order effect, which is originating from the field shift operator and operators of magnetic interactions.

Field of study: Physics
Nephritis in infectious mononucleosis.

Three patients are presented with acute nephritis associated with infectious mononucleosis. Renal biopsy in these patients indicates that an interstitial nephritis or a focal mesangial glomerulonephritis can be present. The condition can be distinguished from post-streptococcal glomerulonephritis, and should be considered in all patients presenting with acute nephritis, particularly if other features such as fever, skin rash ‘hepatitis’ or thrombocytopaenia are present.

Field of study: Medicine
A new methodology incorporating public participation within Cuba's ICZM program

Although public participation (PP) has influenced some integrated coastal zone management (ICZM) programs around the world, researchers have rarely analyzed this component specifically inside an ICZM cycle. Furthermore, the approach for integrating environmental energy planning tools within the ICZM Programs for the Small Island Developing States (SIDS) has presented an ongoing challenge for specialists involved in management issues. In Cuba, plans for coastal development are supported by land use planning activities and environmental planning tools. However, the functions and outputs of those tools are “non-obvious”, precluding sufficient integration among them. As these aforementioned actions have not been systematically carried out in the Cuban territory, and the systems of inter-institutional relationships with local communities have presented some insufficiencies, the national marine-terrestrial interphase has suffered some negative environmental impacts impossible to be solved by the national authorities. Designing a new methodology that incorporates PP and environmental energy planning tools in the stages of an ICZM program is the objective of this article. The methodology was named MePuPa and has improved current tools for land use planning and ICZM in Cuba. Previously selected “Local Indicators of Environmental Sustainability”, applied in two geo-systemic units in the southeastern region of Cuba, were used to demonstrate the methodology. The qualitative and qualitative methods in the proposed MePuPa were also applied. Finally, the MePuPa methodology was tested for four of its five stages. Six advantages and five learned lessons were identified during the Preparation to Proposal stages. MePuPa resulted in a useful local management tool for environmental energy planning, ICZM, economic and agricultural activities, strategic ecosystems recovery, as well as improvements to the governance and decision-making processes in one SIDS.

Field of study: Environmental science
Nonlinear mass transfer and hydrodynamic stability in solubility phenomena

The dissolution of gases, liquids,or solids in liquids is a heterogeneous reaction, and in many cases, the reaction rate is limited by a diffusive transfer of substance in the boundary layer at the face interphase. In modern industry, intensive interphase mass transfer processes are accomplished by large concentration gradients. This can result in a set of nonlinear effects and the difference between experimental data and predictions of the linear mass transfer theory. One of the main nonlinear effects is a result of the induction of a secondary flow at the interface boundary. This can lead to essential changes of the dissolution rate and the hydrodynamic stability of the system.

Field of study: Chemistry
Universal representations of Lie algebras by coderivations

A class of representations of a Lie superalgebra (over a commutative superring) in its symmetric algebra is studied. As an application we get a direct and natural proof of a strong form of the Poincare–Birkhoff–Witt theorem, extending this theorem to a class of nilpotent Lie superalgebras. Other applications are presented. Our results are new already for Lie algebras.

Field of study: Mathematics
On the Potential Static Strength of Hybrid (Bolted/Bonded) Lap Joints with Functionally Graded Adhesives

In this paper, the potential static strength of hybrid (bolted/bonded) – termed HBB – joints with functionally graded adhesives (FGA) is theoretically investigated, in reference to the pure bolted joint, the pure bonded joint and the HBB joint with homogeneous adhesive (HA). The investigation is performed on a particular in-plane tensile loaded single-lap joint made of identical aluminum adherends with two lines of fasteners and three various adhesive symmetrical graduation laws. The stress analysis is performed using the macro-element (ME) technique within 1D-bar framework. Moreover, closed-form expressions for the bolt load transfer rates and maximal adhesive stresses of balanced single-lap HBB joint with two identical fasteners are derived. It is shown that the FGAs allows fort a better load sharing between the adhesive and the fasteners than the HA. Moreover, the use of FGAs instead of HA could lead to a potential static strength benefit for the adhesive layer part rather than for the fastening part.

Field of study: Physics
An informed thought experiment exploring the potential for a paradigm shift in aquatic food production

The Neolithic Revolution began approximately 10,000 years ago and is characterized by the ultimate, nearly complete transition from hunting and gathering to agricultural food production on land. The Neolithic Revolution is thought to have been catalyzed by a combination of local population pressure, cultural diffusion, property rights and climate change. We undertake a thought experiment that examines trends in these key hypothesized catalysts of the Neolithic Revolution and patterns of today to explore whether society could be on a path towards another paradigm shift in food production: away from hunting of wild fish towards a transition to mostly fish farming. We find similar environmental and cultural pressures have driven the rapid rise of aquaculture, during a period that has now been coined the Blue Revolution, providing impetus for such a transition in coming decades to centuries (as opposed to millennia). However, we also highlight the interacting and often mutually reinforcing impacts of 1) technological and scientific advancements, 2) environmental awareness and collective action and 3) globalization and trade influencing the trajectory and momentum of the Blue Revolution from patterns and processes of the Neolithic Revolution. We present two qualitative narratives that broadly fall within two future trajectories of seafood production: 1) a ubiquitous aquaculture transition and 2) commercial aquaculture and fisheries coexistence. Each narrative contains two sub-narratives based on differing management and regulatory strategies for aquaculture and fisheries. This scenarios approach aims to encourage logical, forward thinking, and innovative solutions to complex systems’ dynamics. Scenario-based thought experiments are useful to explore large scale questions, increase the accessibility to a wider readership, and ideally catalyze discussion around proactive governance mechanisms. We argue the future is not fixed and society now has greater foresight and capacity to choose the workable balance between fisheries and aquaculture that supports economic, environmental, cultural and social objectives through combined planning, policies, and management.

Field of study: Environmental science
AERODYNAMIC ROUGHNESS AND SALTATION TRAPPING EFFICIENCY OF TILLAGE RIDGES

A new wind erosion prediction system (WEPS) is being developed by a modeling team to replace the current wind erosion equation. WEPS simulates erosion, as well as soil and biomass conditions that control wind erosion. Parameters for the WEPS erosion submodel are being developed in a series of wind tunnel experiments. Field tillage ridges containing large aggregates are often used to aid in control of wind erosion. Two of the ways armored ridges control erosion are raising the threshold velocity where erosion begins and trapping saltating soil particles. The objectives of this study were to determine:

Field of study: Agricultural and Food sciences
A Model of the Unfolded Protein Response: Pancreatic β-Cell as a Case Study

Pancreatic β-cell failure is increasingly recognized as central to the progression of diabetes mellitus. Different causes are implicated in the onset of β-cell stress, dysfunction or death. Recent genetic and biochemical evidence both in humans and mice shows that failure in modulating the capacity and quality of the endoplasmic reticulum protein-folding machinery leads to β-cell death. The quality control of protein-folding is regulated by several signaling pathways, which are collectively termed the unfolded protein response. In β-cells proinsulin represents up to 50% of the total protein synthesis, and the rate of glucose-stimulated proinsulin translation is approximately 1 million molecules per minute per cell. When proinsulin folding is disrupted, the high burden imposed by proinsulin synthesis on the unfolded protein response is considered the leading cause of certain diabetes phenotypes. We have developed a model of the unfolded protein response to investigate the factors that can prevent misfolded protein accumulation. We also present predictions for therapeutic strategies to ameliorate pancreatic β-cell death in diabetes patients.

Field of study: Biology, Chemistry
Design of all-dielectric three-wavelength non-polarizing parallel plate beam splitter

With the Needle thin film synthesis method and Conjugate graduate refinement method,all-dielectric three-wavelength non-polarizing parallel plate beam splitters are designed.The chosen of materials component and initial stack are based on Costich and Thelen's theory. The results of design and analysis show that it maintains a very low polarization ratio in spectral range of(532±10),(633±10) and(1 315±10) nm.To the requirement for non-polarizing in 532,633 and 1 315 nm,the reasonable angular field of design can be 45°±2°.

Field of study: Physics
A chemical lipid modification of recombinant preS antigen to study the mechanism of HBV attachment to the host cell.

Surface antigen preS of Hepatitis B virus plays fundamental roles in mediating receptor recognition and virus internalization. Myristoylation at N-terminal Gly(2) residue of preS is essential for viral attachment and infectivity. A number of myristoylated proteins have been shown to undergo a conformational change (myristoyl switch) that alters their affinity to cell membrane. However, there is little knowledge about what effect this fatty acylation contributes in virus-host cell interaction. Here we demonstrated a new method for lipid modification of recombinant preS protein at N-terminal residue 2 with alkylating chemicals. Modified preS was able to inhibit HBV penetrating into HepG2 cells with an increased efficiency compared to unmodified form. Flow cytometric analysis indicated that lipid modification enhanced the binding affinity of preS to hepatocytes, but not resulting from hydrophobic interaction. CD analysis further revealed a conformational change of modified preS in the presence of membrane mimetics. These findings imply that the conformation transition induced by fatty acylation is important for efficient attachment of virus to cell receptors, and this method of chemical lipid modification provides a basis for designing therapeutic inhibitors to Hepatitis B virus.

Field of study: Biology, Engineering
Helicity amplitudes and electromagnetic decays of hyperon resonances

We present results for the helicity amplitudes of the lowest-lying hyperon resonances Y*, computed within the framework of the Bonn Constituent-Quark model, which is based on the Bethe-Salpeter approach. The seven parameters entering the model were fitted to the best-known baryon masses. Accordingly, the results for the helicity amplitudes are genuine predictions. Some hyperon resonances are seen to couple more strongly to a virtual photon with finite Q2 than to a real photon. Other Y*'s, such as the S01(1670) Λ-resonance or the S11(1620) Σ-resonance, couple very strongly to real photons. We present a qualitative argument for predicting the behaviour of the helicity asymmetries of baryon resonances at high Q2.-1

Field of study: Physics
Decreased plasma brain-derived neurotrophic factor levels in patients with alcohol dependence.

Many reports have suggested possible relationships between brain-derived neurotrophic factor (BDNF) and alcohol dependence. A protective effect of BDNF against ethanol-induced cell damage has been suggested, and this effect may contribute to the development or maintenance of alcohol dependence. This study was carried out in order to verify the significance of BDNF in alcohol dependence.



Peripheral BDNF levels were measured in alcohol-dependent patients and control subjects using an enzyme-linked immunosorbent assay. A physician's interview and standardized questionnaire were used to obtain information regarding each patient's history of alcohol consumption.



The mean BDNF level was lower in the alcohol dependence group (389.5 +/- 501.7 pg/ml) than in the normal controls (822.5 +/- 420.7 pg/ml) by analysis of covariance (ANCOVA) (F = 25.79, p < 0.01). The mean BDNF level was lower in the alcohol-dependent patients with a positive family history of alcohol dependence (247.6 +/- 289.2 pg/ml) than in those with a negative family history of alcohol dependence (583.9 +/- 652.8 pg/ml) by ANCOVA (F = 6.51, p = 0.01). The BDNF levels did not correlate significantly with any of the variables analyzed in this study, including Beck depression inventory, state and trait anxiety inventory (STAI-S and T), and various drinking behaviors.



Changes in the levels of BDNF might play a role in the pathophysiology and inheritance of alcohol dependence.

Field of study: Medicine
NONLINEAR OPTICS: Theory of an opposed four-wave interaction in arbitrary-intensity fields applied to media with resonant and thermal nonlinearity mechanisms

A system of equations is derived to describe a transient opposed degenerate four-wave interaction (FWI) in fields of arbitrary intensity in gaseous media exhibiting resonant and thermal nonlinearity mechanisms. A system of closed equations describing an opposed degenerate FWI in fields of arbitrary intensity is obtained for the steady-state case. It is found that, unlike linearly absorbing media, the optimal reflection coefficients of a signal wave in nonlinearly absorbing media are only achieved at reference wave intensities comparable with the saturation intensity of the resonant medium. Numerical calculations illustrate a fall in the reflection coefficient as the amplitude of the signal wave is increased.

Field of study: Engineering, Physics
A Simplified Regression Formulation of Tukey's Test.

A simplified regression approach is used for Tukey’s test for multiple comparisons. By constructing k - 1 regression equations (where k is the number of means) in such a way that each mean is being compared to every other mean, the computed t-values that result from testing the significance of each regression weight can be compared to a modified value (q)/√2 from the studentized range statistic.

Field of study: Education