nils-herrmann/clean_scirepeval huggingface dataset:
HLA‐DRB1 leprogenic motifs in Nigerian population groups

Amino acid residues involved in the peptide binding groove of HLA‐DRB1 alleles were examined in three Nigerian ethnic groups with leprosy (n = 287) and 170 controls to determine the role of DRB1 alleles in disease outcome with Mycobacterium leprae. Nine positively charged motifs and two others with neutral charge to the binding groove were detected. These motifs occurred more frequently in leprosy (leprogenic) than was expected by chance (P < 0.0001). In contrast, five motifs with net negative or ‘modified’ neutral charges to the pocket were negatively associated with leprosy. We conclude that clinical outcome of infection with M. leprae is largely determined by a shared epitope in DRB1 alleles marked by several motifs. These motifs occur in otherwise normal DRB1 alleles, characterized by net positive or neutral charges in the binding groove. We hypothesize that these polarities cause poor binding of DRB1 to M. leprae. On presentation, the signal via the T cell receptor results in muted cell‐mediated immunity. The resulting response translates to various forms of leprosy depending on degree of charge consonance between M. leprae and host DRB1 allele. Other factors within or without the HLA complex, such as the T cell receptor repertoire, may also influence the resulting disease.

Field of study: Biology, Medicine
Pattern of Juvenile Rheumatoid Arthritis in a Teaching Hospital in Kuwait

Reports on juvenile rheumatoid arthritis (JRA) from developing countries are scarce due to lack of comprehensive epidemiologic surveys. We report our experience with this disease in Kuwait. This study involves 47 children diagnosed with JRA over a period of 3 years. All 47 children satisfied the American College of Rheumatology criteria for the diagnosis of JRA. The results revealed a prevalence of 0.36 cases per 1,000 children at risk, a rate compatible with international figures. Pauciarticular onset, the predominant subtype, accounted for 49% while polyarticular and systemic onset type accounted for 25.5% each. Iridocyclitis was diagnosed in 3 children (6.4%) with positive antinuclear antibody. Although the prevalence of JRA and its subtypes is not different from figures reported for other regions, iridocyclitis appears to be infrequent in the population of Kuwait.

Field of study: Medicine
Peasants and Petty Capitalists in Southern Oaxacan Sugar Cane Production and Processing, 1930–1980

The documented history of Mexican sugar in the twentieth century begins with the introduction of vacuum-pan technology between 1880 and 1910, subsequently chronicling the progressive expansion and concentration of the industry, and the creeping State intervention which eventually resulted in the nationalisation of most private sugar mills during the 1960s and 1970s. 1 Small-scale, labour-intensive rural trapiches producing panela (an unrefined form of semi-crystalline sugar) have largely been left out of this history, despite the fact that trapiches were often predecessors to modern sugar mills and in many areas survived displacement by them. Surveying Oaxaca's Isthmus of Tehuantepec region in 1940, for example, Ybarra recorded three industrialised mills and 37 small, motorised, panela- producing trapiches . 2 In 1947, according to Aragon Calvo and Vargas Comargo, panela accounted for an estimated 25% of Mexican sugar production overall, and consumption of panela exceeded that of refined sugar in the states of Veracruz and Guerrero. 3 Panela continues to be produced and consumed in Mexico today — albeit in reduced quantities. In Panama, Colombia, India and other nations, panela (or the local equivalent) is an even more important sugar source than in Mexico. 4 Nationally the labour-intensive panela industry pales into insignificance next to the modern sugar sector. However, in particular regions and communities, as I shall attempt to demonstrate, it has been an important source of employment and capital, providing rural dwellers with their first experience of disciplined factory work and numerous small entrepreneurs with profits that were invested back into the communities to expand control over local land and businesses.

Field of study: Political science
Design and Implementation of Amphibious Robot for Subsea Cable Maintenance

Due to the complex subsea environment and the effect of various submarine conditions, it is quite often that the subsea cables may be damaged easily. In this paper, an amphibious robot, a kind of remotely operated vehicle (ROV), for subsea cable maintenance is designed. The robot is able to work in two operation modes, which are floating mode and tracked crawling mode. The robot is also equipped with operating tools such as manipulator and shearing machine to repair the cables. Multiple sensors and navigator are applied for robot navigation to ensure the operation stability.

Field of study: Engineering
Total column water vapour retrieval from S-5P/TROPOMI in the visible blue spectral range

Total column water vapour has been retrieved from TROPOMI measurements
in the visible blue spectral range and compared to a variety of different
reference data sets for clear-sky conditions during boreal summer and
winter. The retrieval consists of the common two-step DOAS approach:
first the spectral analysis is performed within a linearized scheme
and then the retrieved slant column densities are converted to vertical
columns using an iterative scheme for the water vapour a priori profile
shape, which is based on an empirical parameterization of the water
vapour scale height. Moreover, a modified albedo map was used
combining the OMI LER albedo and scaled MODIS albedo map. The use of
the alternative albedo is especially important over regions with very
low albedo and high probability of clouds like the Amazon region. The errors of the total column water vapour (TCWV) retrieval have been theoretically estimated considering the contribution of a variety of different uncertainty
sources. For observations during clear-sky conditions, over ocean surface, and at low solar zenith angles the error typically is around values of 10 %–20 %, and during cloudy-sky conditions, over land surface, and
at high solar zenith angles it reaches values around 20 %–50 %. In the framework of a validation study the retrieval demonstrates
that it can well capture the global water vapour distribution:
the retrieved H2O vertical column
densities (VCDs) show very good agreement with the reference data sets over ocean for boreal summer and winter whereby the modified albedo map substantially improves the retrieval's consistency to the
reference data sets, in particular over tropical land masses. However, over land the retrieval underestimates the VCD by about 10 %, particularly
during summertime. Our investigations show that this underestimation
is likely caused by uncertainties within the surface albedo and
the cloud input data: low-level clouds cause an underestimation, but for mid- to high-level clouds good agreement is found.
In addition, our investigations indicate that these
biases can probably be further reduced by the use of improved
cloud input data. For the general purpose we recommend only using VCDs with cloud fraction and AMF >0.1 , which
represents a good compromise between spatial coverage and
retrieval accuracy. The TCWV retrieval can be easily applied to further satellite
sensors (e.g. GOME-2 or OMI) for creating uniform, long-term measurement data sets, which is particularly interesting for climate and trend studies
of water vapour.

Field of study: Environmental science
Counterfactual Contradictions: Interpretive Error in the Analysis of AEDPA

Courts routinely engage in counterfactual analysis—considering what might have been, had things been different—in a variety of legal contexts (such as determining causation for tort claims and establishing damages). But in the last two Terms, the Supreme Court has issued several opinions restricting the use of counterfactual reasoning in the context of federal habeas corpus review of state criminal convictions (under § 2254(d) of the Antiterrorism and Effective Death Penalty Act, or AEDPA). Specifically, the Court has refused to consider what state courts might have done if presented with a slightly different set of facts or law. This practice leaves a group of petitioners without redress for acknowledged constitutional violations. This Note presents a novel framework for categorizing the modes of counterfactual reasoning in which courts engage. It then analyzes the Court’s decision in Cullen v. Pinholster and related opinions, examining them for possible explanations for the Court’s departure in habeas cases from its usual practice of accepting the need for counterfactuals. It concludes that the Court has given no clear reason why it should depart from the usual background principle that counterfactual reasoning is a valid method of analysis. Finally, it proposes a more coherent scheme for addressing counterfactuals in habeas proceedings.

Field of study: Law
Multiple scales and geometric structures: additional sources of randomness

In Jagers (2009), it was stated that “when physicists and mathematicians selfconfidently moved on to biology, they equipped themselves with the arsenal of Applied Mathematics  in an attempt to repeat the same success story, as for Physics. At the beginning of the twentieth century Mathematical Biology became almost equivalent to deterministic approaches in terms of differential equations on the level of biological systems or collectives (typically populations).” In this article, I will reflect on how biology and medicine have exploited existing theoretical frameworks and stimulated the development of new technical weaponry. Until the 1970s, biomathematics and biostatistics, though naïve with respect to modern mathematical and computational methods, developed as bridges between biological data and mathematical modelling (see, e.g. Bailey 1975, and references therein). In contrast, the approach taken by mathematicians between the 1970s and the 1980s was often based on reaction–diffusion systems described in terms of deterministic PDE’s. Unfortunately the motivation for the mathematical modelling had shifted towards an approach that was at best discipline (biology) independent and, at worst, inappropriately trans-disciplinary (Capasso et al. 1985). Anyhow, research in biomathematics has played an important role in identifying relevant biological principles that are responsible for biological patterns, such as animal coating (see, e.g. Murray 2003 and references therein). Due to the high mathematical complexity, what is still missing, towards a full biological understanding, is the link between biological phenomena that occur at different scales; this is fundamental for a realistic control of the relevant phenomena, as required in Medicine, and Bioengineering. Clearly, PDE modelling is essentially macroscopic. Though a good source for insight in biological applications, such models smooth out the discrete and individual

Field of study: Biology, Mathematics
A Model for Predicting Chlorophyll Content in Cassava Based on SPAD Values

In order to investigate a non-destructive and quick measuring method for chlorophyll content in cassava,a model for predicting total chlorophyll content that was based on SPAD values,specific leaf area,chlorophyll content was established.The results indicated that the influence of chlorophyll A to SPAD values was larger than chlorophyll B;specific leaf area and leaf position and SPAD values and chlorophyll content showed significant correlation;added specific leaf area and leaf position,the accuracy of the model for predicting total chlorophyll content was improved;based on SPAD values,specific leaf area and leaf position,the model for predicting total chlorophyll content was established as C=-4.51+0.092 5 Sp+0.039 9 Sa+0.145 0(Lp).

Field of study: Agricultural and Food sciences
Structured Prediction by Conditional Risk Minimization

We propose a general approach for supervised learning with structured output spaces, such as combinatorial and polyhedral sets, that is based on minimizing estimated conditional risk functions. Given a loss function defined over pairs of output labels, we first estimate the conditional risk function by solving a (possibly infinite) collection of regularized least squares problems. A prediction is made by solving an inference problem that minimizes the estimated conditional risk function over the output space. We show that this approach enables, in some cases, efficient training and inference without explicitly introducing a convex surrogate for the original loss function, even when it is discontinuous. Empirical evaluations on real-world and synthetic data sets demonstrate the effectiveness of our method in adapting to a variety of loss functions.

Field of study: Computer science
Patient Experiences of Dietary Management in Chronic Kidney Disease: A Focus Group Study.

People with chronic kidney disease (CKD) contend with complex dietary recommendations. The challenge in practice is for clinicians to provide individualized support with the frequency and consistency required to sustain dietary changes. This study aimed to describe the experiences of patients with managing dietary recommendations, including their perspectives on the potential to use telehealth to support dietary management in CKD.



Focus group study.



Twenty-one adult patients with CKD (nondialysis) and 3 caregivers (total N = 24) purposively sampled to achieve diverse demographic and clinical characteristics, from two nephrology units in Queensland, Australia.



Five focus groups were conducted, audio recorded, and transcribed. Transcripts were analyzed using thematic analysis drawing on the principles of grounded theory.



Themes aligned with the research question.



We identified five themes: exasperating stagnancy (patronized by redundant advice, confused and unprepared for dietary change, inevitability of failure, and barriers to accessing dietetic services); supporting and sustaining change (receiving regular feedback, incremental and comprehendible modification, practical guidance on food, flexibility in monitoring schedule, and valuing peer advice); fostering ownership (seeking kidney diet information, enacting behavior change, making reminders, and tracking progress against targets); motivators and positive learning instruction (relying on reassurance, positive reinforcement, focusing on allowable foods, and involving family); threats and ambiguities of risk (sugar as the culprit, ubiquity of salt, illegible food labeling, avoiding processed foods, and questioning credibility of sources).



Patients with CKD desire a preventative approach to CKD progression and maintaining their health, however, are stymied by dietary restrictions and a lack of reliable dietetic advice. Easy-to-use telehealth options have the potential to overcome the shortcomings in current health service delivery which may be limiting factors to providing these approaches. They provide patients with pragmatic tools, comprehensible and consistent information which fosters ownership and self-monitoring.

Field of study: Medicine
Controlling LEP/SPS accelerator equipment

The pilot project for a new design of the software of CERN`s LEP/SPS control system is described. The main deliverables produced during this project are: (1) an object-oriented design for generic access to LEP/SPS HEP (High-Energy Physics) equipment; and (2) an implementation/specialization of this design for one type of equipment, viz. Beam Loss Monitors. The design follows the OMT method. A generic object model is created which represents a possible accelerator-complex. This model is used (inherited) for the definition of the object model of a subsystem (BLMs) of the SPS/LEP accelerators. The dynamic behavior of the BLMs is modeled with state diagrams.

Field of study: Physics
Chemokine and chemokine receptor gene expression in the mesenteric adipose tissue of KKAy mice.

To investigate chemokines and their receptors gene expression in the intra-abdominal adipose tissue of diabetic/obese mice.



KKAy mice were fed either by a high-fat diet (HFD) or a low-fat diet (LFD) and obese characteristics were analyzed. Various adipose tissues were isolated from HFD-fed obese KKAy mice and from obese controls. We carried out RT-PCR, GeneChip microarray, and real-time PCR analyses on samples derived from the adipose tissues.



The HFD-feded obese KKAy mice had the physiological characteristics of obese animal and had increased levels of the transcripts of several chemokine and chemokine receptor genes, such as CCL5, CCL19, CCL25, CXCL10, CXCL13, CCR6, and CCR7, in their intra-abdominal adipose tissue. The strong expression of CCR6 and CCR7 was verified by microarray and quantitative real-time PCR analysis. The HFD increased CCR6 and CCR7 expression only in mesenteric (ME) adipose tissue, not in subcutaneous (SC) adipose tissue.



Since the enhanced expression of such molecules is likely to contribute to the inflammation in chronic inflammatory disease, our data suggest that the increased levels of CCR6 and CCR7 are involved in the inflammation response in the intra-abdominal adipose tissue of the obese/diabetic mice.

Field of study: Medicine
Relationship Between Cotton Lint Color and Weather Exposure

DATA were taken to quantify the changes in cotton fiber properties when cotton was exposed to different quantifiable weather patterns. Bolls were tagged in the field as they began to open, and subsamples were taken on a weekly basis. Fiber quality change coefficients for colorimeter-reflectance and degree-of-yellowness were calculated for each period. Two pre-diction equations for the quality change coefficients as a function of weather were developed by use of regression analysis. The regression equations account for about 60 percent of the observed variation. The two pre-diction equations were incorporated into a computer simulation routine to give the quality and corresponding grade for a given age of cotton. The computer simulation routine updates the cotton quality each day and is reasonably accurate in its pre-diction of cotton color and grade. The predicted values are generally slightly lower than the observed values.

Field of study: Agricultural and Food sciences
Ignition catalysts for furfuryl alcohol - Red fuming nitric acid bipropellant

References 1 Alien, H. J. and Eggers, A. J., "A Study of the Motion and Aerodynamic Heating of Ballistic Missiles Entering the Earth Atmosphere at High Supersonic Speeds," Rept. 1381, 1958, NACA. 2 Leon, H. I., "Angle of Attack Convergence of a Spinning Missile Descending Through the Atmosphere," Journal of the Aerospace Sciences, Vol. 25, No. 8, 1958, pp. 480-484. 3 Garber, T. B., "On the Rotational Motion of a Body ReEntering the Atmosphere," Journal of the Aerospace Sciences, Vol. 26, No. 7, 1959, pp. 443-449. 4 Coakley, T. J., "Dynamic Stability of Symmetric Spinning Missiles," AIAA Journal, Vol. 5, No. 10, Oct. 1968,  Jaffe, P., "Terminal Dynamics of Atmospheric Entry Capsules," AIAA Journal, Vol. 7, No. 6, June 1969,  Nayfeh, A. H., "A Multiple Time Scaling Analysis of Reentry Body Roll Dynamics," Transactions of the Third Technical Workshop on Dynamic Stability Problems, NASA Ames Research Center, Nov. 1968; also AIAA Journal, Vol. 7, No. 11, Nov. 1969, pp.2155-2157. 7 Flatus, D. H., "Angle-of-Attack Convergence and WindwardMeridian Rotation Rate of Rolling Re-Entry Vehicles," Transactions of the Third Technical Workshop on Dynamic Stability Problems, NASA Ames Research Center, Nov. 1968; also AIAA Journal, Vol. 7, No. 12, Dec. 1969,  "Equilibrium Roll Rate Theory for a Re-entry Vehicle," Document 67SD234, 1967, General Electric Co.

Field of study: Physics
The Great Recession and Mothers' Health

We use longitudinal data from the Fragile Families and Child Well-being Study to investigate the impacts of the Great Recession on the health of mothers. We focus on a wide range of physical and mental health outcomes, as well as health behaviors. We find that increases in the unemployment rate decrease self-reported health status and increase smoking and drug use. We also find evidence of heterogeneous impacts. Disadvantaged mothers-African-American, Hispanic, less educated, and unmarried-experience greater deterioration in their health than advantaged mothers-those who are white, married, and college educated.

Field of study: Economics
FINITE ELEMENT MODELLING OF FRP-REINFORCED MASONRY WALLS UNDER IN-PLANE LOADINGS

In an attempt to capture the features of the masonry walls before and after reinforcement, the finite element meso-scale models of the FRP-reinforced masonry walls with flemish bond are constructed using zero-thickness cohesive elements in ABAQUS. The responses of the finite element models are validated with the experimental results of the cyclic tests and the analytical results of the relative codes for monotonic cases. The results show that the finite element models are capable of simulating the seismic performance of the FRP-reinforced masonry walls accurately, analyzing the effect of FRP reinforcement and calculating the shear bearing capacity of the unreinforced and FRP-reinforced masonry walls under monotonic loadings.

Field of study: Engineering
Chinese coastal seas are facing heavy atmospheric nitrogen deposition

As the amount of reactive nitrogen (N) generated and emitted increases the amount of N deposition and its contribution to eutrophication or harmful algal blooms in the coastal zones are becoming issues of environmental concern. To quantify N deposition in coastal seas of China we selected six typical coastal sites from North to South in 2011. Concentrations of NH3, HNO3, NO2, particulate NH4 (pNH4 ) and pNO3 ranged from 1.97–4.88, 0.46–1.22, 3.03–7.09, 2.24–4.90 and 1.13–2.63 μgNm �3 at Dalian (DL), Changdao (CD), Linshandao (LS), Fenghua (FH), Fuzhou (FZ), and Zhanjiang (ZJ) sites, respectively. Volume-weighted NO3 –N and NH4 –N concentrations in precipitation varied from 0.46 to 1.67 and 0.47 to 1.31 mg N L �1 at the six sites. Dry, wet and total deposition rates of N were 7.8–23.1, 14.2–25.2 and 22.0–44.6 kg N ha �1 yr �1 across the six coastal sites. Average N dry deposition accounted for 45.4% of the total deposition and NH3 and pNH4 contributed to 76.6% of the dry deposition. If we extrapolate our total N deposition of 33.9 kg N ha �1 yr �1 to the whole Chinese coastal sea area (0.40 million km 2 ), total N deposition amounts to 1.36 Tg N yr �1 , a large external N input to

Field of study: Environmental science
ELABORATIVE MAPS FOR ENHANCED LEARNING OF HISTORICAL INFORMATION: UNITING SPATIAL, VERBAL, AND IMAGINAL INFORMATION

Map-like displays containing names of battles of the American Revolution and related battle information were presented to 72 middle school students with learning disabilities (LD). Students were randomly assigned to one of three map conditions that depicted information in a spatial organizational format but varied the symbols used to mark the map. Map symbols included (a) reconstructive elaborations of battle names and associated event information, (b) mnemonic keywords of battle names, and (c) realistic drawings of soldiers, buildings, and so forth. A 3 (organization) by 2 (recall) (location vs. event information) analysis of variance indicated that recall of locations was significantly greater than recall of event information in all conditions, mnemonic encoding resulted in greater recall of locations but not events, and elaborative encoding resulted in greater recall of event information relative to the mnemonic map but greater recall of locations and event information relative to the non-mnemonic map. Student reports of strategy use and implications for instruction of students with LD are discussed.

Field of study: Education