Miracle-dz/UniFAR-FTUs huggingface dataset:
Straightforward and de Novo Peptide Sequencing by MALDI-MS/MS Using a Lys-N Metalloendopeptidase*S

In this work, we explore the potential of the metalloendopeptidase Lys-N for MALDI-MS/MS proteomics applications. Initially we digested a HEK293 cellular lysate with Lys-N and, for comparison, in parallel with the protease Lys-C. The resulting peptides were separated by strong cation exchange to enrich and isolate peptides containing a single N-terminal lysine. MALDI-MS/MS analysis of these peptides yielded CID spectra with clear and often complete sequence ladders of b-ions. To test the applicability for de novo sequencing we next separated an ostrich muscle tissue protein lysate by one-dimensional SDS-PAGE. A protein band at 42 kDa was in-gel digested with Lys-N. Relatively straightforward sequencing resulted in the de novo identification of the two ostrich proteins creatine kinase and actin. We therefore conclude that this method that combines Lys-N, strong cation exchange enrichment, and MALDI-MS/MS analysis provides a valuable alternative proteomics strategy.
Numerical time‐domain modelling of hoof–ground interaction during the stance phase

BACKGROUND Hoof-ground interaction impacts on the health and performance characteristics of horses. Due to complex interactions between hoof and ground during the stance phase, previous experimentally dominated studies concentrated on subproblems of the phenomena observed. A multidisciplinary methodology with mathematical modelling, material testing and in vivo experimental measurements seems promising. OBJECTIVES With the help of a mathematical approach, this contribution aims to explain from a biomechanical point of view the phenomena observed during experimental investigations (hoof acceleration, interacting forces) and aims to contribute to an overall experimental-mathematical multidisciplinary approach. STUDY DESIGN In silico modelling of hoof-ground interaction (limb, hoof and horizontally unbounded ground). METHODS Hoof-ground interaction is represented by a time-domain finite element model including the limb, the hoof and the unbounded representation of the ground via the scaled boundary finite element method to capture radiation damping during the stance phase. Motoric forces (driving forces) of the horse during locomotion are included. RESULTS Numerical model results for acceleration-time relations (hoof) at different trotting velocities are compared with previously published acceleration-time relations and show qualitative agreement. From the model approach, power loss due to different ground properties and ground damping is computed in combination with the maximum limb force during the stance phase. MAIN LIMITATIONS Intentionally, a simplified model approach for the material and structural representation of the limb, the hoof and the ground in terms of material features and spatial resolution has been used for this study, which might be the basis for a model refinement in terms of contact properties as well as the integration of bone and joint structures. CONCLUSIONS The comparison to experimentally obtained results demonstrates the applicability of the model, which, in turn, enables an insight into the processes taking place during hoof-ground interaction.
Comparative proteomic analysis of low stage and high stage endometrioid ovarian adenocarcinomas

Ovarian cancer, the second most common gynecological malignancy, accounts for 3% of all cancers among women in the United States, and has a high mortality rate, largely because existing therapies for widespread disease are rarely curative. Ovarian endometrioid adenocarcinoma (OEA) accounts for about 20% of the overall incidence of all ovarian cancer. We have used proteomics profiling to characterize low stage (FIGO stage 1 or 2) versus high stage (FIGO stage 3 or 4) human OEAs. In general, the low stage tumors lacked p53 mutations and had frequent CTNNB1, PTEN, and/or PIK3CA mutations. The high stage tumors had mutant p53, were usually high grade, and lacked mutations predicted to deregulate Wnt/β‐catenin and PI3K/Pten/Akt signaling. We utilized 2‐D liquid‐based separation/mass mapping techniques to elucidate molecular weight and pI measurements of the differentially expressed intact proteins. We generated 2‐D protein mass maps to facilitate the analysis of protein expression between both the low stage and high stage tumors. These mass maps (over a pI range of 5.6–4.6) revealed that the low stage OEAs demonstrated protein over‐expression at the lower pI ranges (pI 4.8–4.6) in comparison to the high stage tumors, which demonstrated protein over‐expression in the higher pI ranges (pI 5.4–5.2). These data suggest that both low and high stage OEAs have characteristic pI signatures of abundant protein expression probably reflecting, at least in part, the different signaling pathway defects that characterize each group. In this study, the low stage OEAs were distinguishable from high stage tumors based upon the proteomic profiles. Interestingly, when only high‐grade (grade 2 or 3) OEAs were included in the analysis, the tumors still tended to cluster according to stage, suggesting that the altered protein expression was not solely dependent upon tumor cell differentiation. Further, these protein profiles clearly distinguish OEA from other types of ovarian cancer at the protein level.
Quality of in-home care, long-term care placement, and the survival of persons with dementia

Purpose of the study: Caregivers of persons with dementia living at home adopt a variety of caregiving styles that vary in quality. Three styles of high-quality care and poor-quality care have been identified. The outcomes, however, of varying styles of caregiving are unknown. Our purpose was to investigate the linkage of quality of care to long-term care placement and survival. Design and methods: We used a sample of 148 primary caregivers of a relative living at home and needing assistance due to memory or thinking problems. We used items from four existing scales and five new items to construct measures of high-quality and poor-quality care. Long-term care and survival were determined from two follow-ups. Cox proportional hazards regression was used to estimate the relationship of quality of care to long-term care placement and survival. Results: Poor quality of care increased the risk of long-term care placement, as expected, but high-quality care was not related to placement. Surprisingly, high-quality care increased the risk of death while poor-quality care decreased the risk. Secondary results were: wishful/intrapsychic coping (a dysfunctional type of emotion-focused coping) and long-term care placement shortened the survival; and caregiver personality traits of neuroticism and agreeableness lengthened the survival. Implications: It is premature to recommend caregiver interventions based on our unexpected findings. Further studies are vital and should include care-recipient impairments and the quality of life of the person with dementia as additional outcomes.
Comparison of Treatment Effects Measured by the Hazard Ratio and by the Ratio of Restricted Mean Survival Times in Oncology Randomized Controlled Trials.

PURPOSE We aimed to compare empirically the treatment effects measured by the hazard ratio (HR) and by the difference (and ratio) of restricted mean survival times (RMST) in oncology randomized trials. METHODS We selected oncology randomized controlled trials from five leading journals during the last 6 months of 2014. We reconstructed individual patient data for one time-to-event outcome from each trial, preferably the primary outcome. We reanalyzed each trial and compared the treatment effect estimated by the HR with that by the difference (and ratio) of RMST. We estimated an average ratio of the HR to the ratio of RMST; an average ratio less than one indicates more optimistic assessments with HRs. RESULTS We analyzed 54 randomized controlled trials totaling 33,212 patients. The selected outcome was overall survival in 21 (39%) trials. There was evidence of nonproportionality of hazards in 13 (24%) trials. The HR and RMST-based measures were in agreement regarding the statistical significance of the effect, except in one case. The median HR was 0.84 (Q1 to Q3 range, 0.67 to 0.97) and the median difference in RMST was 1.12 months (range, 0.22 to 2.75 months). The average ratio of the HR to the ratio of RMST was 1.11 (95% CI, 1.07 to 1.15), with substantial between-trial variability (I(2) = 86%). Results were consistent by outcome type (overall survival v other outcomes) and whether the proportional hazard assumption held or not. CONCLUSION On average, the HR provided significantly larger treatment effect estimates than the ratio of RMST. The HR may seem large when the absolute effect is small. RMST-based measures should be routinely reported in randomized trials with time-to-event outcomes.
In Vitro Hepatic Metabolism of Cediranib, a Potent Vascular Endothelial Growth Factor Tyrosine Kinase Inhibitor: Interspecies Comparison and Human Enzymology

The in vitro metabolism of cediranib (4-[(4-fluoro-2-methyl-1H-indol-5-yl)oxy]-6-methoxy-7-[3-(1-pyrrolidinyl)propoxy]quinazoline), a vascular endothelial growth factor (VEGF) tyrosine kinase inhibitor (TKI) of all three VEGF receptors in late-stage development for the treatment of colorectal cancer and recurrent glioblastoma was investigated in hepatic proteins from preclinical species and humans using radiolabeled material. In human hepatocyte cultures, oxidative and conjugative metabolic pathways were identified, with pyrrolidine N+-glucuronidation being the major route. The primary oxidative pathways were di-and trioxidations and pyrrolidine N-oxidation. All metabolites with the exception of the N+-glucuronide metabolite were observed in rat and cynomolgus monkey hepatocyte preparations. Additional metabolism studies in liver microsomes from these or other preclinical species (CD-1 mouse, Han Wistar rat, Dunkin Hartley guinea pig, Göttingen mini-pig, New Zealand White rabbit, beagle dog, and cynomolgus and rhesus monkey) indicated that the N+-glucuronide metabolite was not formed in these additional species. Incubations with recombinant flavin-containing monooxygenase (FMO) and UDP-glucuronosyltransferase (UGT) enzymes and inhibition studies using the nonselective cytochrome P450 (P450) chemical inhibitor 1-aminobenzotriazole in human hepatocytes indicated that FMO1 and FMO3 contributed to cediranib N-oxidation, whereas UGT1A4 had a major role in cediranib N+-glucuronidation. P450 enzymes had only a minor role in the metabolism of cediranib. In conclusion, species differences in the formation of the N+-glucuronide metabolite of cediranib were observed. All other metabolites of cediranib found in humans were also detected in rat and cynomolgus monkey. Non-P450 enzymes are predominantly involved in the metabolism of cediranib, and this suggests that clinical drug interactions involving other coadministered drugs are unlikely.
The serotyping of hospital strains of streptococci belonging to Lancefield group C and group G

SUMMARY A collection of more than 300 strains belonging to either Lancefield group C or group G was made. The cultures had been isolated either sporadically from patients with serious disease or as apparent clusters from various nosocomial outbreaks. T-protein antigens were sought. So far, nine distinct serotypes have been found among the group G streptococci and seven serotypes amongst the Streptococcus equisimilis (group C) strains. Of the sixteen serotypes, four were the original T-types 7, 16, 20 and 21 described by Griffith (1934). Because of the similarities of representatives of the two groups to Lancefield group A streptococci (Griffith, 1934; Maxted & Potter, 1967) a few strains not unexpectedly carried T antigens usually seen in group A streptococci. Using this scheme it has been possible to serotype 76% of S. equisimilis strains of human origin and 82% of group G streptococci from human clinical material. A small collection of group C and group G streptococci of animal origin could not be serotyped with the experimental T-antisera.
Phasor measurement unit placement techniques for complete and incomplete observability

This paper presents techniques for identifying placement sites for phasor measurement units (PMUs) in a power system based on incomplete observability. The novel concept of depth of unobservability is introduced and its impact on the number of PMU placements is explained. Initially, we make use of spanning trees of the power system graph and a tree search technique to find the optimal location of PMUs. We then extend the modeling to recognize limitations in the availability of communication facilities around the network and pose the constrained placement problem within the framework of Simulated Annealing (SA). The SA formulation was further extended to solve the pragmatic phased installation of PMUs. The performance of these methods is tested on two electric utility systems and IEEE test systems. Results show that these techniques provide utilities with systematic approaches for incrementally placing PMUs thereby cushioning their cost impact.
Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile

Porcine Astrovirus (PoAstV) causes mild diarrhea in young pigs and is considered an emerging virus in the swine industry worldwide. PoAstV has high genetic diversity and has been classified into five genetic lineages, PoAstV1–5. In Chile, only human astroviruses have been reported. This study aimed to determine the presence and genetic diversity of PoAstV circulating in intensive pig farms in Chile. Seventeen Chilean intensive swine farms from Valparaíso, Metropolitana, O'Higgins, Ñuble and Araucanía regions were sampled. A selection of oral fluid and fecal material samples from 1–80 days-old pigs were collected and analyzed using next-generation sequencing. The circulation of PoAstV was confirmed in all studied farms. We obtained complete or partial sequences of PoAstV-2 (n = 3), PoAstV-4 (n = 2), and PoAstV-5 (n = 7). In 15 out of 17 farms, we detected more than one lineage co-circulating. Phylogenetic analyses grouped the seven PoAstV-5 strains in a monophyletic cluster, closely related to the United States PoAstV-5 strains. The three PoAstV-2 were located into two separate sub-clusters. PoAstV-4 sequences are also grouped in two different clusters, all related to Japanese strains. Thus, our results indicate that PoAstV circulates in Chile with high frequency and diversity. However, the lack of reference sequences impairs local evolution patterns establishment and regional comparisons. This is the first contribution of PoAstV genomes in Latin America; more studies are needed to understand the diversity and impact of PoAstV on swine health.
Orientation of the Genetic Variance‐Covariance Matrix and the Fitness Surface for Multiple Male Sexually Selected Traits

Stabilizing selection has been predicted to change genetic variances and covariances so that the orientation of the genetic variance‐covariance matrix (G) becomes aligned with the orientation of the fitness surface, but it is less clear how directional selection may change G. Here we develop statistical approaches to the comparison of G with vectors of linear and nonlinear selection. We apply these approaches to a set of male sexually selected cuticular hydrocarbons (CHCs) of Drosophila serrata. Even though male CHCs displayed substantial additive genetic variance, more than 99% of the genetic variance was orientated 74.9° away from the vector of linear sexual selection, suggesting that open‐ended female preferences may greatly reduce genetic variation in male display traits. Although the orientation of G and the fitness surface were found to differ significantly, the similarity present in eigenstructure was a consequence of traits under weak linear selection and strong nonlinear (convex) selection. Associating the eigenstructure of G with vectors of linear and nonlinear selection may provide a way of determining what long‐term changes in G may be generated by the processes of natural and sexual selection.
HPV16 semiquantitative viral load and serologic biomarkers in oral and oropharyngeal squamous cell carcinomas

A considerable subset of oropharyngeal squamous cell carcinomas (SCCs) are positive for human papillomavirus (HPV); however, delineating etiologically‐associated HPV infections from SCCs with concurrent HPV infection unrelated to tumorigenesis is challenging. Viral load assessment in biopsy specimens may help facilitate such differentiation. HPV16 viral load and serologic markers were assessed among oral and oropharyngeal cases from a multinational study conducted by the International Agency for Research on Cancer (IARC). HPV16 viral load, measured semiquantitatively by PCR‐enzyme immunoassay, was dichotomized as high or low based on the median optical density value. Serologic antibodies to HPV16 virus‐like particles (VLPs) and to HPV16 E6 and E7 proteins were measured by ELISA. Compared to HPV DNA‐negative cases (n = 852), HPV16 DNA‐positive cases with high viral load (n = 26) were significantly more likely to originate in the oropharynx (odds ratio [OR], 12.0; 95% confidence interval [CI], 5.2–27.5) and, after adjustment for tumor site (AdjOR), have antibodies against HPV16 VLPs (AdjOR, 14.6; 95% CI, 6.0–35.6), E6 (AdjOR, 57.6; 95% CI, 21.4–155.3) and E7 (AdjOR, 25.6; 95% CI, 9.3–70.8). HPV16 DNA‐positive cases with low viral load (n = 27) were more commonly oropharyngeal (OR, 2.7; 95% CI, 1.1–6.2) and seropositive for HPV16 VLPs (AdjOR, 2.7; 95% CI, 1.1–6.9), E6 (AdjOR, 3.0; 95% CI, 0.7–14.0) and E7 (AdjOR, 3.5; 95% CI, 0.7–16.3), compared to HPV DNA‐negative cases; the associations, however, were neither as strong nor as significant as the associations for high viral load. As there appears to be a strong association between HPV16 serologic markers and viral load, in the absence of data on serologic markers, HPV16 viral load may be used to help delineate the subset of HPV16 DNA‐positive oral and oropharyngeal cancers that may be the consequence of HPV infection. © 2005 Wiley‐Liss, Inc.
Spanish Civil War caves of Asturias in archaeology and memory

Abstract As the Spanish Civil War drew to a close, retreating Republican troops in the northern region of Asturias took refuge in caves in the mountains from the brutal victor’s justice of the Francoist forces. In this paper we examine three of these caves in the context of the Civil War experiences of the rural municipality of Santo Adriano, based on a combination of archaeological recording and oral history interviews. The paper focuses on the role of the La Ponte-Ecomuseum, a grassroots heritage organisation that has worked to preserve and communicate the tangible and intangible heritage of the district. The Civil War heritage presents cultural, political and practical challenges for the museum: nonetheless it has succeeded in establishing an ongoing programme for its communication and protection.
Endovascular Stent Grafts in Urgent Blunt and Penetrating Thoracic Aortic Trauma

A traumatic thoracic aortic injury is fatal in the majority of cases. Surviving the aortic injury in addition to the myriad of associated trauma requires comprehensive medical management from many medical services. Balancing these services and coordinating the medical care requires free and open communication between services. Although one might assume a thoracic aortic injury takes precedence over other injuries, an organized plan of care in which the morbidity of the injury as well as the consequences of treatment of each injury helps provide an appropriate "rank order" in the treatment process. A patient with a thoracic aortic injury can be observed for several days while additional injuries are treated, as long as appropriate blood pressure controls are observed. The treatment order for multiple injuries must be reevaluated on a regular basis to adjust for changes in the overall clinical condition. This rank order to treatment and scheduled treatment plan allows for appropriate imaging, evaluation, and coordination of services in preparation for the placement of a thoracic aortic stent graft. The goal of treatment is to reduce the risk of aortic rupture and subsequent fatal hemorrhage. Choosing an open surgical repair versus an endovascular stent graft depends upon physician expertise and clinical status of the patient. In the appropriate clinical setting, endovascular repair of the thoracic aortic injury has become the treatment of choice at the authors' institution in patients with significant operative risks and extensive comorbid injuries. Specific characteristics of the injured aorta also dictate the type of endovascular device required for repair. Case reviews of a patient with blunt trauma and a patient with penetrating trauma used to demonstrate clinical parameters, imaging options, and details of stent graft choice and placement, are presented followed by a review of the literature.
An econometric approach to crowding in touristic city centres

Using a common property resource conceptualization, this article introduces a new methodology for crowding valuation in touristic city centres. Crowding issues are defined in terms of utility gains or losses through a stated-preference choice experiment, making it possible to quantify crowding disturbances in monetary terms. The proposed method is applied to the case of Antwerp, Belgium, specifically focusing on the effect of use density on local inhabitants. The case study serves to reveal quantitatively the theorized quadratic effects of crowding on the space utility of residents. Potential utility effects of different crowding levels are discussed and compared to actual use levels. The methodology provides new opportunities for threshold optimization in crowding-sensitive urban areas, taking into account a community-based norm development.
Cytochrome P450 2C19 loss-of-function polymorphism, but not CYP3A4 IVS10+12G/A and P2Y12 T744C polymorphisms, is associated with response variability to dual antiplatelet treatment in high-risk vascular patients

Objectives The aim of this study was to evaluate the effect of polymorphisms affecting the clopidogrel metabolism (CYP3A4 IVS10+12G/A and CYP2C19*2) and the P2Y12 receptor (P2Y12 T744C) on modulating platelet function in acute coronary syndrome patients on dual antiplatelet treatment. Background Residual platelet reactivity (RPR) phenomenon on antiplatelet therapy requires clarification. P2Y12 T744C, CYP3A4 IVS10+12G/A and, in healthy individuals only, CYP2C19*2 polymorphisms have been investigated; however, the influence on platelet reactivity in a large population of high-risk vascular patients on dual antiplatelet treatment has not yet been elucidated. Methods A total of 1419 acute coronary syndrome patients on dual antiplatelet treatment were studied. Platelet function was evaluated by platelet-rich plasma aggregation. Electronic nanochips and restriction-fragment length polymorphism were used for analysis of polymorphisms. Results Only CYP2C19*2, out of the three investigated polymorphisms, is associated with higher platelet reactivity. Carriers of the *2 allele had significantly higher platelet aggregation values after arachidonic acid (AA; P=0.043), 2 μmol/l adenosine 5′ diphosphate (ADP; P<0.0001) and 10 μmol/l ADP (P=0.001) stimuli. The genotype distribution of CYP2C19*2 polymorphism significantly differed between patients with and without RPR, as evaluated by 10-μmol/l ADP-induced platelet aggregation (P=0.002) and by AA-induced platelet aggregation (P=0.045). At the multivariate linear regression analysis, the CYP2C19*2 polymorphism remained a significant and independent risk factor for dual antiplatelet treatment variability. Conclusions This study demonstrates, for the first time, that the *2 CYP2C19 allele is associated with higher platelet aggregability and RPR in high-risk vascular patients on dual antiplatelet treatment. These findings can have a significant impact on the future design of pharmacogenetic antiaggregant strategies for high-risk vascular patients on dual antiplatelet treatment.