Miracle-dz/UniFAR-FTUs huggingface dataset:
Offspring from Reproduction Problems: What Replication Failure Teaches Us

Repeating experiments is an important instrument in the scientific toolbox to validate previous work and build upon existing work. We present two concrete use cases involving key techniques in the NLP domain for which we show that reproducing results is still difficult. We show that the deviation that can be found in reproduction efforts leads to questions about how our results should be interpreted. Moreover, investigating these deviations provides new insights and a deeper understanding of the examined techniques. We identify five aspects that can influence the outcomes of experiments that are typically not addressed in research papers. Our use cases show that these aspects may change the answer to research questions leading us to conclude that more care should be taken in interpreting our results and more research involving systematic testing of methods is required in our field.
Molecular modification of starch during thermomechanical treatment

Macromolecular degradation of starch by heating and shear forces was investigated using a newly developed shear cell. With this equipment, waxy corn starch was subjected to a variety of heat and shear treatments in order to find the key parameter determining the degree of macromolecular degradation. A model based on the maximal shear stress during the treatment gave an improved prediction compared to existing models in literature based on specific mechanical energy input (SME) or shear stress multiplied by time (τ·t). It was concluded that molecular weight reduction of starch at the temperatures investigated (85-110°C) is a timeindependent process, during which the starch molecules are broken down virtually instantaneously by high shear force within time scales investigated. Consequences for design of shear based processes (especially extrusion) are shortly discussed. This chapter was published as: R.M. van den Einde, A. Bolsius, J.J.G. van Soest, L.P.B.M. Janssen, A.J. van der Goot, R.M. Boom, The effect of thermomechanical treatment on starch breakdown and the consequences for process design. (2004). Carbohydrate Polymers, 55(1), 57-63.
A Family of Potent Ru(II) Photosensitizers with Enhanced DNA Intercalation: Bimodal Photokillers

A new family of Ru(II)‐based photosensitizers was synthesized and systematically characterized. The ligands employed to coordinate the ruthenium metal center were the commercially available 2,2′‐bipyridine and a pyridine‐quinoline hybrid bearing an anthracene moiety. The complexes obtained carry either PF6− or Cl− counterions. These counterions determine the complexes' hydrophobic or hydrophilic character, respectively, therefore dictating their solubility in biologically related media. All photosensitizers exhibit characteristic, relatively strong and wide UV–Vis absorption spectral profiles. Their high efficiency in generating cytotoxic singlet oxygen was established (up to ΦΔ ~0.8). Moreover, the interaction of these photosensitizers with double‐stranded DNA was studied fluoro‐ and photospectroscopically and their binding affinities were found to be of the order of 3 × 107 M−1. All complexes are photocytotoxic to DU145 human prostate cancer cells. The highest light‐induced toxicity was conferred by the photosensitizers bearing Cl− counterions, probably due to the looser ionic “chaperoning” of Cl−, in comparison to PF6− , leading to higher cell internalization.
C2C ONLINE AUCTION WEBSITE PERFORMANCE: BUYER’S PERSPECTIVE

Despite the popularity among millions of users around the globe of selling, bidding, and buying products using C2C online auction websites, the existing literature on online auctions provides us with little understanding on important factors of the C2C auctioneer website performance. One way to understand the performance factors of C2C auction websites could be to extend the past theories of end user computing satisfaction from the buyer perspective. The current study develops a research framework for measuring C2C online auction website performance by identifying factors which influences C2C auction buyer’s satisfaction and net benefit. Based on the research framework, we develop measurements and empirically test C2C auction website performance with a sample size of 131 C2C online auction buyers. Our empirical results indicate that the C2C auction website content, user friendliness (a combined measure of C2C auction format and ease of use), timeliness, security, transactions, and product varieties are positively related to the website performance for the auction buyers. Implications of the current study and potential for future studies are also discussed.
Biodegradation of lignocellulose in Bermuda grass by white rot fungi analyzed by solid-state 13C nuclear magnetic resonance

Following the solid-state fermentation of Bermuda grass by two lignin-degrading white rot fungi, compositional changes have been observed in situ by utilization of cross-polarization and magic angle spinning 13C nuclear magnetic resonance difference spectra and interrupted decoupling spectra. Intensity differences in the 13C resonances assigned to specific components of the cell wall were used to observe these changes. Bermuda grass treated with Phanerochaete chrysosporium K-3 exhibited losses primarily in the polysaccharide components, with a smaller proportion of phenolic components also being degraded. In contrast, Ceriporiopsis subvermispora FP 90031-sp removed a proportionate amount of phenolic components compared with polysaccharide components. The results also indicated that C. subvermispora preferentially removes guaiacyl phenolic components relative to syringyl phenolic components, while P. chrysosporium was nonspecific in its attack on phenolic components.
Anti-Inflammatory Effects of Concentrated Ethanol Extracts of Edelweiss (Leontopodium alpinum Cass.) Callus Cultures towards Human Keratinocytes and Endothelial Cells

Edelweiss (Leontopodium alpinum Cass.) is traditionally employed in folk medicine as an anti-inflammatory remedy. In nature, the plant is sparsely available and protected; therefore production of callus cultures was established. A concentrated ethanolic extract of culture homogenate, with leontopodic acid representing 55 ± 2% of the total phenolic fraction (ECC55), was characterized for anti-inflammatory properties in primary human keratinocytes (PHKs) and endotheliocytes (HUVECs). Inflammatory responses were induced by UVA+UVB, lipopolysaccharide (LPS), oxidized low-density lipoprotein (oxLDL), and a mixture of proinflammatory cytokines. Trichostatin A, a sirtuin inhibitor, was used to induce keratinocyte inflammatory senescence. ECC55 (10–50 μg/mL) protected PHK from solar UV-driven damage, by enhancing early intracellular levels of nitric oxide, although not affecting UV-induced expression of inflammatory genes. Comparison of the dose-dependent inhibition of chemokine (IL-8, IP-10, MCP-1) and growth factor (GM-CSF) release from PHK activated by TNFα + IFNγ showed that leontopodic acid was mainly responsible for the inhibitory effects of ECC55. Sirtuin-inhibited cell cycle, proliferation, and apoptosis markers were restored by ECC55. The extract inhibited LPS-induced IL-6 and VCAM1 genes in HUVEC, as well as oxLDL-induced selective VCAM1 overexpression. Conclusion. Edelweiss cell cultures could be a valuable source of anti-inflammatory substances potentially applicable for chronic inflammatory skin diseases and bacterial and atherogenic inflammation.
Stress response genes are suppressed in mouse preimplantation embryos by granulocyte-macrophage colony-stimulating factor (GM-CSF).

BACKGROUND Granulocyte-macrophage colony-stimulating factor (GM-CSF) is known to promote the development and survival of human and mouse preimplantation embryos; however, the mechanism of action of GM-CSF in embryos is not defined. METHODS Mouse blastocysts were cultured from zygote stage in vitro with and without recombinant mouse GM-CSF (rmGM-CSF), and in vivo developed blastocysts were flushed from Csf2 null mutant and wild-type mice. The effect of GM-CSF on blastocyst expression of stress response and apoptosis genes was evaluated by microarray, qPCR and immunochemistry. RESULTS Microarray analysis of the gene transcription profile showed suppression of stress response and apoptosis gene pathways in blastocysts exposed to rmGM-CSF in vitro. qPCR analysis confirmed that rmGM-CSF inhibited expression of heat shock protein (HSP) and apoptosis pathway genes Cbl, Hspa5, Hsp90aa1, Hsp90ab1 and Gas5 in in vitro blastocysts. Immunocytochemical analysis of HSP 1 (HSPA1A/1B; HSP70), BAX, BCL2 and TRP53 (p53) in in vitro blastocysts showed that HSPA1A/1B and BCL2 proteins were less abundant when embryos were cultured with rmGM-CSF. BAX and TRP53 were unchanged at the protein level, but Bax mRNA expression was reduced after GM-CSF treatment. In in vivo developed blastocysts, Csf2 null mutation caused elevated expression of Hsph1 but not other stress response genes. CONCLUSIONS We conclude that GM-CSF inhibits the cellular stress response and apoptosis pathways to facilitate embryo growth and survival, and the protective effects of GM-CSF are particularly evident in in vitro culture media, whereas in vivo other cytokines can partly compensate for absence of GM-CSF.
Typhonium giganteum Lectin Exerts A Pro-Inflammatory Effect on RAW 264.7 via ROS and The NF-κB Signaling Pathway

Typhonii rhizoma, a widely used herb in traditional Chinese medicine, has acute irritating toxicity related to Typhonium giganteum lectin (TGL). TGL exhibits acute inflammatory effects, but the underlying molecular mechanisms are largely unknown. This paper is designed to assess the pro-inflammatory response of TGL on RAW 264.7 cells. RAW 264.7 treated with 6.25, 12.5, 25, and 50 µg/mL TGL showed elevated levels of inflammatory factors (TNF-α, IL-1β) and of p-IκB and p-p65, all dose-dependent, indicating that TGL had a substantial inflammatory effect and mobilized the nuclear factor-κB (NF-κB) pathway. All four TGL treatments also induced the up-regulation of reactive oxygen species (ROS) and cytosolic free Ca2+ and down-regulation of mitochondrial membrane potential (MMP). The production of cytokines and p-IκB, p-p65 were reduced by N-acetylcysteine (NAC), an ROS scavenger, which somewhat abrogated ROS production. The results showed the TGL-activated inflammatory signaling pathway NF-κB to be associated with the overproduction of ROS. Moreover, 50 μg/mL treatment with TGL led to cell apoptosis after 1 h and increased necrosis over time. These results provided potential molecular mechanisms for the observed inflammatory response to TGL including up-regulation of ROS and cytosolic free Ca2+, down-regulation of MMP, the mobilization of the NF-κB pathway, and the subsequent overproduction of pro-inflammatory factors resulting in apoptosis. Long-term stimulation with TGL resulted in strong toxic effects related to inflammation that induced necrosis in macrophages.
Clinical outcome at a minimum of five years after reconstruction of the anterior cruciate ligament.

BACKGROUND We are not aware of any previous studies in which independent measurements of function with validated outcome questionnaires such as the Knee Injury and Osteoarthritis Outcome Score and the International Knee Documentation Committee score were evaluated five years after reconstruction of the anterior cruciate ligament. We hypothesized that patient demographics, mechanism of injury, and intra-articular injuries and their treatment are factors associated with function five years after reconstruction of the anterior cruciate ligament. METHODS A consecutive series of unilateral, arthroscopically assisted primary reconstructions of the anterior cruciate ligament performed by one surgeon using a patellar tendon graft was evaluated. Data on patient demographics, injury variables, and intra-articular lesions noted at the time of surgery were collected prospectively. Multivariable regression analysis was used to identify independent predictors of outcomes as measured with five questionnaires. RESULTS Sixty-nine percent (217) of 314 knees with a reconstruction of the anterior cruciate ligament were followed for an average of 5.4 years. The average age at the time of the operation was twenty-seven years. Independent predictors of a worse outcome, which was measured with the overall Knee Injury and Osteoarthritis Outcome Score, the International Knee Documentation Committee score, the Lysholm score, and the Western Ontario and McMaster Universities Osteoarthritis Index score, included the patient's recollection of hearing or feeling a pop at the time of the injury, a weight gain of >15 lb (6.8 kg), and no change in educational level since the surgery. There was a lack of association between the outcome and either the occurrence or the form of treatment of a meniscal tear or chondromalacia of the articular cartilage. CONCLUSIONS To our knowledge, we performed the first prospective cohort study to evaluate the prognosis following reconstruction of the anterior cruciate ligament by identifying significant associations between multiple variables and clinical outcomes as measured with validated questionnaires. The clinician can counsel patients about the intermediate-term functional outcomes of reconstructions of the anterior cruciate ligament on the basis of these findings. Suggestions regarding weight control and future education may improve intermediate-term outcomes.
Children’s drawings from Seiberg–Witten curves

We consider N = 2 supersymmetric gauge theories perturbed by tree level superpotential terms near isolated singular points in the Coulomb moduli space. We identify the Seiberg-Witten curve at these points with polynomial equations used to construct what Grothendieck called “dessins d’enfants” or “children’s drawings” on the Riemann sphere. From a mathematical point of view, the dessins are important because the absolute Galois group Gal(Q/Q) acts faithfully on them. We argue that the relation between the dessins and Seiberg–Witten theory is useful because gauge theory criteria used to distinguish branches of N = 1 vacua can lead to mathematical invariants that help to distinguish dessins belonging to different Galois orbits. For instance, we show that the confinement index defined in hep-th/0301006 is a Galois invariant. We further make some conjectures on the relation between Grothendieck’s program of classifying dessins into Galois orbits and the physics problem of classifying phases of N = 1 gauge theories.
Complex rearrangement of chromosomes 7q21.13‐q22.1 confirms the ectrodactyly‐deafness locus and suggests new candidate genes

Complex chromosomal rearrangements with more than two breakpoints are rare. We report on a 5‐year‐old girl, evaluated because of psychomotor delay, ectrodactyly of right hand and feet, craniofacial dysmorphic features, cleft palate, deafness, and tetralogy of Fallot. A standard karyotype suggested a small intrachromosomal duplication of chromosome 7q. The chromosomal rearrangement was characterized by mBAND, which disclosed a reciprocal interstitial translocation t(7;8)(q21q22;q23q24). FISH analysis and array‐CGH analysis showed a paracentric inversion of 7q and a microdeletion of 7q21.13. The parents had normal chromosomes. The deletion found in the present patient confirms that candidate region of ectrodactyly‐deafness (OMIM 220600) maps to 7q21 and suggests new candidate genes for that disorder. This patient also had facial features reminiscent of tricho‐rhino‐phalangeal syndrome and one chromosome breakpoint involved band 8q24, a locus for this disorder. In addition, FOG1 gene maps to 8q23 and has been implicated in a subset of subjects with tretralogy of Fallot. We suggest that the aberration of 8q may have contributed to her facial and cardiac findings. © 2007 Wiley‐Liss, Inc.
The Impact of Focused Gene Ontology Curation of Specific Mammalian Systems

The Gene Ontology (GO) resource provides dynamic controlled vocabularies to provide an information-rich resource to aid in the consistent description of the functional attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). System-focused projects, such as the Renal and Cardiovascular GO Annotation Initiatives, aim to provide detailed GO data for proteins implicated in specific organ development and function. Such projects support the rapid evaluation of new experimental data and aid in the generation of novel biological insights to help alleviate human disease. This paper describes the improvement of GO data for renal and cardiovascular research communities and demonstrates that the cardiovascular-focused GO annotations, created over the past three years, have led to an evident improvement of microarray interpretation. The reanalysis of cardiovascular microarray datasets confirms the need to continue to improve the annotation of the human proteome. Availability GO annotation data is freely available from: ftp://ftp.geneontology. org/pub/go/gene-associations/
Gravitational Waves from Neutron Stars: A Review

Abstract Neutron stars are excellent emitters of gravitational waves. Squeezing matter beyond nuclear densities invites exotic physical processes, many of which violently transfer large amounts of mass at relativistic velocities, disrupting spacetime and generating copious quantities of gravitational radiation. I review mechanisms for generating gravitational waves with neutron stars. This includes gravitational waves from radio and millisecond pulsars, magnetars, accreting systems, and newly born neutron stars, with mechanisms including magnetic and thermoelastic deformations, various stellar oscillation modes, and core superfluid turbulence. I also focus on what physics can be learnt from a gravitational wave detection, and where additional research is required to fully understand the dominant physical processes at play.
Factors Associated with Nasal Colonization of Methicillin-Resistant Staphylococcus aureus among Healthy Children in Taiwan

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) has been identified as a major cause of community-associated (CA) S. aureus infections in the past decade. The main reservoir in the community for MRSA and the factors contributing to its worldwide spread remain poorly defined. Between July 2005 and June 2008, a total of 6,057 healthy children 2 to 60 months of age were screened for carriage of S. aureus and Streptococcus pneumoniae in Taiwan. The prevalence and epidemiological factors influencing MRSA carriage were determined. MRSA strains were tested for antimicrobial susceptibility and underwent molecular characterization. The overall prevalences of MRSA and S. aureus carriage were 7.8% and 23.2%, respectively. A majority (88%) of MRSA isolates belonged to a common Asian-Pacific CA-MRSA lineage, multilocus sequence type 59, and were resistant to multiple non-beta-lactam antibiotics. The carriage rate of MRSA was higher among subjects 2 to 6 months old (P < 0.0001), residing in northern Taiwan (P = 0.0003), and enrolled later in the study (P < 0.0001). MRSA colonization was associated with the number of children in the family (adjusted odds ratio [aOR], 1.114; 95% confidence interval [CI], 1.002 to 1.240; P = 0.0463) and day care attendance (aOR, 1.530; 95% CI, 1.201 to 1.949; P = 0.0006). Breast feeding (P < 0.0001) and colonization with S. pneumoniae (P = 0.0170) were protective against MRSA colonization. We concluded that epidemic CA-MRSA strains increasingly colonized Taiwanese children between 2005 and 2008. The carriage rate varied significantly across different demographical features. Crowding was an independent environmental risk factor that might accelerate CA-MRSA transmission in the community.
What motivates the consumer's food choice?

OBJECTIVE The aim of the study was to analyse the psychometric properties of the Food Choice Questionnaire (FCQ) in Spanish population (FCQ-SP), its factor structure and internal consistency. In addition, the relationships between the FCQ-SP and the General Health Questionnaire (GHQ), the Irrational Food Beliefs Scale (IFBS), and the Eating Disorders Inventory-3 (EDI-3) were analysed in order to explore the validity of the FCQSP. Possible gender differences in the food choice pattern were analysed. METHODS The sample comprised 255 women and 50 men, ranged from 25 to 64 years. In order to get a better interpretation of the results associated with changes based on the age, the participants were grouped in four age intervals (25-34, 35-44, 45-54, and 55-64). All the participants were relatives of secondary and high school students in three schools of Seville and Cordoba. RESULTS The factor analysis yields the seven following factors: mood, health and natural content, sensory appeal, weight control, convenience, familiarity, and price. The internal consistency was determined by means of the Cronbach's α coefficients, which ranged from 0.70 to 0.83 for the different components. With regards to the food choice profile, sensory appeal was the most motivating factor to choose food, followed by price and weight control. With respect to gender differences, women showed higher scores than men in all components except in the case of price. DISCUSSION The FCQ-SP has adequate psychometric properties to be applied to Spanish population, and it is useful to explore the consumers' motivation with regards to food choice.
MYH7 gene tail mutation causing myopathic profiles beyond Laing distal myopathy

Objective: To describe a wide range of clinical and pathologic myopathic profiles associated with the p.K1729del mutation in the MYH7 gene, known to cause Laing distal myopathy. Methods: A study conducted in the Safor region (Spain), setting of a large cluster of patients. Clinical, neurophysiologic, muscle imaging, and muscle biopsy studies and MYH7 gene sequencing were investigated in 32 patients from 4 kindreds. Data from 36 deceased or nonexamined patients were collected from hospital records or relatives. Results: Onset ranged from congenital to the 6th decade. All patients presented weakness of great toe/ankle dorsiflexors and many had associated neck flexor, finger extensor, and mild facial weakness. In most cases, involvement of proximal and axial muscles was observed either clinically or by muscle imaging, sometimes giving rise to scapuloperoneal and limb-girdle syndromes. Disabling myalgias, skeletal deformities, and dilated cardiomyopathy in one patient were associated features. Life expectancy was not reduced but the spectrum of disability ranged from asymptomatic to wheelchair confined. Electromyographic neurogenic features were frequently recorded. Muscle fiber type disproportion, core/minicore lesions, and mitochondrial abnormalities were the most relevant pathologic alterations. All patients carried the p.K1729del mutation in MYH7. Conclusions: The p.K1729del mutation in the MYH7 gene expresses notable clinical variability and electromyographic and pathologic features that can lead to the misdiagnosis of neurogenic atrophies, congenital myopathies, or mitochondrial myopathies. Mutations in genes encoding other sarcomeric and reticulo-sarcoplasmic proteins involved in calcium regulation share pathologic characteristics with our patients, suggesting a possible pathogenetic connection.