nils-herrmann/clean_scirepeval huggingface dataset:
An evaluation of multiplex bead based analysis of cytokines and soluble proteins in archived lithium heparin plasma, EDTA plasma and serum samples
Venue: Scandinavian journal of clinical and laboratory investigation

To assess the usability of archived plasma and serum by multiplex (Luminex) analysis of circulating proteins (analytes) by evaluating the day to day variation, the effect of several freeze thaw cycles, and the influence of the media and choice of anticoagulant.  Nineteen analytes in plasma and serum from 86 head and neck cancer patients and 33 controls were evaluated: EGFR, leptin, OPN, VEGFR 1, VEGFR 2, IL 2, IL 13, PDGF bb, TNF, PAI 1, SDF 1a, IL 4, IL 6, IL 8, eotaxin, G CSF, VEGF, GRO a, and HGF.  The correlation between measurements of the same samples analyzed on different dates was reasonable. However, samples run on different dates could exhibit different absolute values. The 75th percentile of the fold differences for samples run on different dates was 2.2. No significant difference was found between one and four freeze thaw cycles (except for HGF) and the correlation was high. We found significant differences in mean concentrations of the majority of analytes in different media and with different anticoagulants. Only the following analytes did not show difference in mean concentrations: EDTA plasma vs. serum: leptin and VEGFR 2, LH plasma vs. serum: IL 2, IL 13, and VEGF, LH plasma levels vs. EDTA plasma: IL 2 and IL 4.  Stored serum, LH plasma, and EDTA plasma from clinical trials can be used for analysis of circulating cytokines and proteins. Variations in measurements occur, but are within reasonable ranges. The optimal type of media depends on the analytes, as different analytes have low number of measurements below the lower limit of quantification and higher dynamic ranges in different media.
Development and validation of a multi analyte LC MS/MS approach for quantification of neuroleptics in whole blood, plasma, and serum.
Venue: Drug testing and analysis

Based on a similar approach for quantification of antidepressants, benzodiazepines, and z drugs, a liquid chromatography tandem mass spectrometry (LC MS/MS) multi analyte approach with simple liquid liquid extraction was extended for fast target screening and quantification of neuroleptics in whole blood, plasma, and serum. As this method is part of a multi analyte procedure for over 100 analytes from different drug classes and as the extracts were additionally used in the authors' laboratory for gas chromatography mass spectrometry (GC MS) analysis, one universal stable isotope labelled internal standard (SIL IS) was used to save time and resource. The method was validated with respect to international guidelines. For accuracy and precision, full calibration was performed with ranges from subtherapeutic to toxic concentrations. Selectivity problems could not be observed, but matrix effects ranged from 68 to 211% in all samples. For the low quality control (QC) recovery ranged from 32 to 112% process efficiency from 31 to 165% and for the high QC recovery from 42 to 141% process efficiency from 29 to 154% In addition statistical data evaluation of the variances of the recovery, matrix effects, and process efficiency data between whole blood vs. plasma, whole blood vs. serum, and plasma vs. serum were done. The presented LC MS/MS approach was applicable for selective detection of 33 neuroleptics as well as accurate and precise quantification of 25 neuroleptics in whole blood, 19 in plasma, and 17 in serum. More significant matrix effects (ME) for neuropletic drugs overall in plasma and serum as compared with whole blood were detected.
Language competence in forensic interviews for suspected child sexual abuse.
Venue: Child abuse neglect

Forensic interviews with children for suspected child sexual abuse require meeting children "where they are" in terms of their developmental level, readiness to disclose, culture, and language. The field lacks research indicating how to accommodate children's diverse cultural and linguistic backgrounds. This article focuses on language competence, defined here as the ability of an organization and its personnel (in this case, Child Advocacy Centers and forensic interviewers) to communicate effectively with clients regardless of their preferred language(s) In this qualitative study, 39 U.S. child forensic interviewers and child advocacy center directors discussed their experiences, practices, and opinions regarding interviews with children and families who are not native speakers of English. Topics include the importance of interviewing children in their preferred language, problems in interpreted interviews, bilingual interviews, and current and recommended procedures. Recommendations for practice and further research are included.
Comparative investigation on nanomechanical properties of hardened cement paste

Three types of nanomechanical methods including static nanoindentation, modulus mapping and peak force quantitative nanomechanical mapping (QNM) were applied to investigate the quantitative nanomechanical properties of the same indent location in hardened cement paste. Compared to the nanoindentation, modulus mapping and peak force QNM allow for evaluating local mechanical properties of a smaller area with higher resolution. Beside, the ranges of elastic modulus distribution measured by modulus mapping and peak force QNM are relatively greater than that obtained from nanoindentation, which may be due to a result of the shaper probe and local confinement effect between multiple phases. Moreover, the average value of elastic modulus obtained using peak force QNM were consistent with those obtained by modulus mapping, while the different in modulus probability distribution could be related to the different nanomechancial theories and contact forces. The probability distributions of elastic modulus measured using nanomechanical methods to provide a basis for the different types of phases existing in cement paste. Based on the observation with high spatial resolution, cement paste can be likely found as nanocalse granular material, in which different submicron scale or basic nanoscale grain units pack together. It indicates that the peak force QNM can effectively provide an effective insight into the nanostructure characteristic and corresponding nanomechanical properties of cement paste.
Early emerging system for reasoning about the social nature of food
Venue: Proceedings of the National Academy of Sciences

Food choice can serve as a social shibboleth, whereby information about what an individual eats affords insight into her cultural background and social relationships. We provide evidence for an early emerging system linking food preferences to social identity. Infants expect people to share food preferences, unless those people belong to different groups, suggesting human reasoning about food preferences is fundamentally social. However, infants generalize disgust toward a food even across people who belong to different groups, suggesting that infants are particularly vigilant to social information that might signal danger. This research opens new lines of investigation regarding infant social cognition and food selection across the lifespan, and has implications for social policy surrounding nutrition, heath, and obesity. Selecting appropriate foods is a complex and evolutionarily ancient problem, yet past studies have revealed little evidence of adaptations present in infancy that support sophisticated reasoning about perceptual properties of food. We propose that humans have an early emerging system for reasoning about the social nature of food selection. Specifically, infants' reasoning about food choice is tied to their thinking about agents' intentions and social relationships. Whereas infants do not expect people to like the same objects, infants view food preferences as meaningfully shared across individuals. Infants' reasoning about food preferences is fundamentally social: They generalize food preferences across individuals who affiliate, or who speak a common language, but not across individuals who socially disengage or who speak different languages. Importantly, infants' reasoning about food preferences is flexibly calibrated to their own experiences: Tests of bilingual babies reveal that an infant's sociolinguistic background influences whether she will constrain her generalization of food preferences to people who speak the same language. Additionally, infants' systems for reasoning about food is differentially responsive to positive and negative information. Infants generalize information about food disgust across all people, regardless of those people's social identities. Thus, whereas food preferences are seen as embedded within social groups, disgust is interpreted as socially universal, which could help infants avoid potentially dangerous foods. These studies reveal an early emerging system for thinking about food that incorporates social reasoning about agents and their relationships, and allows infants to make abstract, flexible, adaptive inferences to interpret others' food choices.
"The Dose Makes the Poison" Informing Consumers About the Scientific Risk Assessment of Food Additives.
Venue: Risk analysis an official publication of the Society for Risk Analysis

Intensive risk assessment is required before the approval of food additives. During this process, based on the toxicological principle of "the dose makes the poison," maximum usage doses are assessed. However, most consumers are not aware of these efforts to ensure the safety of food additives and are therefore sceptical, even though food additives bring certain benefits to consumers. This study investigated the effect of a short video, which explains the scientific risk assessment and regulation of food additives, on consumers' perceptions and acceptance of food additives. The primary goal of this study was to inform consumers and enable them to construct their own risk benefit assessment and make informed decisions about food additives. The secondary goal was to investigate whether people have different perceptions of food additives of artificial (i.e. aspartame) or natural origin (i.e. steviolglycoside) To attain these research goals, an online experiment was conducted on 185 Swiss consumers. Participants were randomly assigned to either the experimental group, which was shown a video about the scientific risk assessment of food additives, or the control group, which was shown a video about a topic irrelevant to the study. After watching the video, the respondents knew significantly more, expressed more positive thoughts and feelings, had less risk perception, and more acceptance than prior to watching the video. Thus, it appears that informing consumers about complex food safety topics, such as the scientific risk assessment of food additives, is possible, and using a carefully developed information video is a successful strategy for informing consumers.
Industry Dynamics and the Minimum Wage: A Putty Clay Approach

We document three new findings about the industry level response to minimum wage hikes. First, restaurant exit and entry both rise following a hike. Second, the rise in entry and exit is concentrated in chains. Third, there is no change in employment among continuing restaurants. We develop a model of industry dynamics based on putty clay technology and show that it is consistent with these findings. In the model, continuing restaurants cannot change employment, and thus industry level adjustment occurs through exit of labor intensive restaurants and entry of capital intensive ones. We show these three findings are inconsistent with other models of industry dynamics.
Type aware transactions for faster concurrent code
Venue: EuroSys

It is often possible to improve a concurrent system's performance by leveraging the semantics of its datatypes. We build a new software transactional memory (STM) around this observation. A conventional STM tracks read and write sets of memory words; even simple operations can generate large sets. Our STM, which we call STO, tracks abstract operations on transactional datatypes instead. Parts of the transactional commit protocol are delegated to these datatypes' implementations, which can use datatype semantics, and new commit protocol features, to reduce bookkeeping, limit false conflicts, and implement efficient concurrency control. We test these ideas on the STAMP benchmark suite for STM applications and on our own prior work, the Silo high performance in memory database, observing large performance improvements in both systems.
Reducing Opacity to Linearizability: A Sound and Complete Method
Venue: ArXiv

Transactional memory is a mechanism that manages thread synchronisation on behalf of a programmer so that blocks of code execute with an illusion of atomicity. The main safety criterion for transactional memory is opacity, which defines conditions for serialising concurrent transactions. Proving opacity is complicated because it allows concurrent transactions to observe distinct memory states, while TM implementations are typically based on one single shared store. This paper presents a sound and complete method, based on coarse grained abstraction, for reducing proofs of opacity to the relatively simpler correctness condition: linearizability. We use our methods to verify TML and NORec from the literature and show our techniques extend to relaxed memory models by showing that both are opaque under TSO without requiring additional fences. Our methods also elucidate TM designs at higher level of abstraction; as an application, we develop a variation of NORec with fast path reads transactions. All our proofs have been mechanised, either in the Isabelle theorem prover or the PAT model checker.
Implementing sustainability in multi tier supply chains: Strategies and contingencies in managing sub suppliers

Buying firms must pay increased attention to supply chain sustainability issues, as stakeholders might hold them responsible for non sustainable supply chain activities. Frequently, sustainability problems occur upstream at the sub supplier level. Building on the literature on multi tier supply chains (MSCs) we investigated the sustainability management strategies of buying firms in the food, apparel, packaging, and consumer electronics with regard to second tier suppliers and beyond. In particular, we analyzed seven cases of global MSCs and found four different characteristic MSC types open, closed, third party, and "don't bother" We identified three main factors supply chain complexity, the sustainability management capabilities of the first tier supplier, and the type of sustainability in focus (i.e. environmental or social sustainability) that determine when and how buying firms actually extend their sustainability strategies to their sub suppliers.
Bitter apricot essential oil induces apoptosis of human HaCaT keratinocytes.
Venue: International immunopharmacology

Psoriasis is a chronic skin disease that affects approximately 2% of the world's population. Conventional therapeutic approaches are not effective or necessarily safe for treating symptoms due to the serious side effects and resistance to currently prescribed drugs. Traditionally, in oriental medicine, apricot seed (Semen Armeniacae amarum) is used to treat skin diseases. However, the underlying mechanism of action has not been systematically elucidated. In the present study, the anti proliferative effect of bitter apricot essential oil (BAEO) on cultured HaCaT cells was evaluated and the mechanism of action investigated. BAEO was isolated by hydrodistillation, and gas chromatography mass spectrometry (GC MS) analysis identified benzaldehyde (75.35% benzoic acid (6.21% and mandelonitrile (5.38% HaCaT cell growth, measured by sulforhodamine B assay (SRB) was inhibited by BAEO with an IC50 value of 142.45 mg/ml. Apoptosis of HaCaT cells treated with BAEO was detected by cell cycle, flow cytometry, and western blot analyses. These measurements revealed G0/G1 cell cycle arrest, elevated numbers of early and late stage apoptotic cells, and caspases 3/8/9 and PARP activation. Z VAD FMK, a broad spectrum caspase inhibitor, attenuated BAEO induced apoptosis. Also, increased Bax and decreased Bcl 2 levels suggest that BAEO induced apoptosis is mediated through both death receptor and mitochondrial pathways. Moreover, reduced Rel/NF kB levels suggest that BAEO mediated apoptosis is also associated with inhibition of the NF kB pathway. These data suggest that BAEO is a naturally occurring material that functions as a potent pro apoptotic factor for human keratinocytes. Thus, it is a promising candidate to treat psoriasis.
Blood plasma levels of anterior pituitary hormones of rabbits after apricot seed exposure in vivo

The present study describes possible changes in plasma levels of anterior pituitary hormones induced by bitter apricot (Prunus armeniaca L. seeds in young female rabbits in vivo. Prunus armeniaca L. is an important medicinal edible plant species commonly known as "apricot" The apricot is a member of the Rosaceae and subfamily Prunoideae. It is one of the most delicious and commercially traded fruits in the world. Apricot kernel is the inner part of the seed of the apricot fruit. The kernel is used to produce oil and other chemicals used for medicinal purposes. The seeds are potentially useful in human nutrition and for treatment several diseases especially cancer. In the present study apricot seeds were mixed with feed at different doses 0, 60, 300, 420 mg*kg 1 of body weight. ELISA was used to determine the levels of follicle stimulating hormone (FSH) luteinizing hormone (LH) and prolactin (PRL) 58 days application of apricot seeds did not affect the concentration (P>=0.05) of PRL, LH in blood plasma. Significant (P<=0.01) inhibition of FSH levels induced by the seeds was found at the dose of 420 mg*kg 1 but not at 60 and 300 mg*kg 1 of body weight. These results are suggesting that the natural substances present in apricot seeds may be involved in mechanisms of ovarian folliculogenesis.
The Development and Refinement of an e Health Screening, Brief Intervention, and Referral to Treatment for Parents to Prevent Childhood Obesity in Primary Care.
Venue: Telemedicine journal and e health the official journal of the American Telemedicine Association

Nearly one third of Canadian children can be categorized as overweight or obese. There is a growing interest in applying e health approaches to prevent unhealthy weight gain in children, especially in settings that families access regularly. Our objective was to develop and refine an e health screening, brief intervention, and referral to treatment (SBIRT) for parents to help prevent childhood obesity in primary care.  Our SBIRT, titled the Resource Information Program for Parents on Lifestyle and Education (RIPPLE) was developed by our research team and an e health intervention development company. RIPPLE was based on existing SBIRT models and contemporary literature on children's lifestyle behaviors. Refinements to RIPPLE were guided by feedback from five focus groups (6 10 participants per group) that documented perceptions of the SBIRT by participants (healthcare professionals [n 20] parents [n 10] and researchers and graduate trainees [n 8] Focus group commentaries were transcribed in real time using a court reporter. Data were analyzed thematically.  Participants viewed RIPPLE as a practical, well designed, and novel tool to facilitate the prevention of childhood obesity in primary care. However, they also perceived that RIPPLE may elicit negative reactions from some parents and suggested improvements to specific elements (e.g. weight related terms) CONCLUSIONS RIPPLE may enhance parents' awareness of children's weight status and motivation to change their children's lifestyle behaviors but should be improved prior to implementation. Findings from this research directly informed revisions to our SBIRT, which will undergo preliminary testing in a randomized controlled trial.
Stocks and fisheries of asari in Japan

Asari clam is one of the most important fishery resources in Japan. The clam has been utilized as not only a food but also a recreational harvestable species. Main habitat of the asari extends from tidal area to shallow subtidal area of sandy soft bottom. Asari is harvested by hand raking or short handled basket raking in tidal areas and long handled basket raking, dredging, helmet diving in subtidal areas. Major areas of asari harvest are Tokyo Bay, Mikawa Bay, Ise Bay, Suo Nada and Ariake Bay. Annual harvest of the asari in the major areas, however, decreased largely after late 1980s except Mikawa Bay. Stock decline of natural asari is remarkable and seriously problematic for coastal fisheries in Japan. Along with application of the various countermeasures intended to restore the natural stocks of asari, a number of factors have been discussed to be responsible for the asari decline. Some of these are decrease of suitable habitat areas, deterioration of water and substrate quality, erosion of the clams by strong wave disturbance, new predators and parasites, oligotrophication, and excess harvesting. We still have not determined significant factors responsible for the asari decline in Japan. In the discussed factors, we compared the effect of five factors; blue tide, river flood, strong wave disturbance, infection of sea spider, and hypoxia on clam larvae, based on the studies in Tokyo Bay. The impacts (mortalities) of the factors for the total asari stock by the blue tide in Sanbanze in 2008, the river flood in Sanbanze in 2007, winter wave mortality in the three areas in 2009 2010, and infection of sea spider in Kisarazu in 2009 were calculated to be 0.16,0.07,0.95,0.30, respectively. Among these factors, winter wave mortality showed the most significant effect on the asari stock in Tokyo Bay. Comparing the properties of the estimated factors, the factors that affected wider areas and longer period with higher mortality were supposed to give severer impact for the asari stock. In order to take effective countermeasures for the decline of asari stock in Japan, further assessment of the impact of the suspected factors is required to be progressed.
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