Miracle-dz/UniFAR-FTUs huggingface dataset:
The burden of HPV‐related diseases in Italy, 2001‐12

Background Human papillomavirus (HPV) infection is the main cause of cervical cancer and plays a relevant role in the development of genital warts and of the cancer of penis and anus, head/neck, oropharynx and genitourinary system. The aim of this study is the evaluation of hospitalizations due to HPV‐related pathologies in 2001‐12 in Italy. Methods The national hospital discharge forms were provided by the Ministry of Health. The HPV‐related hospitalizations were identified using specific diagnostic codes, accordingly to the ICD‐9‐CM coding system. The proportion of hospitalizations of potentially HPV‐related pathologies, obtained from the literature, was evaluated as well as the hospitalization rates (hr) and their trend over time. Results Uterine cervical cancer and CIN III accounted for 40% of hospitalizations (hr: 15.6/100 000 and 17.6/100 000, respectively). Head/neck and oropharynx pathologies accounted for 24.5% of cases (hr: 16/100 000 and 3.9/100 000, in males and females, respectively), followed by genital warts (17.3% of hospitalizations; hr: 7.5/100 000 in males and 8.52/100 000 in females), anal (8.1% of hospitalizations), genitourinary (7.7%) and penis cancers (2.2%). Conclusions The study, even if limited to the evaluation of hospitalizations, points out how HPV‐related pathologies continue to be a relevant public health issue in Italy with a high impact on population.
CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes

Motivation Codon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes. These tools can only analyze a single genome at a time and are often not followed by a validation procedure, resulting in a high rate of false positives. Results We present CoreTracker, a new algorithm for the inference of sense‐to‐sense codon reassignments. CoreTracker identifies potential codon reassignments in a set of related genomes, then uses statistical evaluations and a random forest classifier to predict those that are the most likely to be correct. Predicted reassignments are then validated through a phylogeny‐aware step that evaluates the impact of the new genetic code on the protein alignment. Handling simultaneously a set of genomes in a phylogenetic framework, allows tracing back the evolution of each reassignment, which provides information on its underlying mechanism. Applied to metazoan and yeast genomes, CoreTracker significantly outperforms existing methods on both precision and sensitivity. Availability and implementation CoreTracker is written in Python and available at https://github.com/UdeM‐LBIT/CoreTracker. Contact mabrouk@iro.umontreal. ca Supplementary information Supplementary data are available at Bioinformatics online.
Interaction of run-in edge dislocations with twist grain boundaries in Al-a molecular dynamics study

Grain boundaries play an important role in outlining the mechanical properties of crystalline materials. They act as sites for absorption/nucleation of dislocations, which are the main carriers of plastic deformation. In view of this, the interactions between edge dislocations and twist grain boundaries-dislocation pileup, dislocation absorption and dislocation emission were explored by performing molecular dynamics simulations in face-centered cubic Al using embedded atom method. The 1 1 0 twist grain boundaries with various misorientation angles were selected for this purpose. It was found that the misorientation angle of boundary and stress anomalies arising from repeated dislocation absorption at the grain boundaries are the important parameters in determining the ability of the boundary to emit dislocations. Complex network of dislocations results in later stages of deformation, which may have a significant effect on the mechanical properties of the material. The peculiarities of dislocation nucleation, their emission from twist grain boundaries and the ramifications of this study towards development of higher length scale material models are discussed.
Significance of FGF9 gene in resistance to anti‐EGFR therapies targeting colorectal cancer: A subset of colorectal cancer patients with FGF9 upregulation may be resistant to anti‐EGFR therapies

Although fibroblast growth factor (FGF) signals are strongly associated with malignancy, limited information is available regarding the role of the FGF9 signal in colorectal cancer (CRC). In this study, we investigated the frequency of FGF9 amplification in CRC clinical specimens and the association between the FGF9 gene and resistance to anti‐EGFR therapies. In clinical samples, an FGF9 copy number gain of >5 copies was observed at a frequency of 8/145 (5.5%) and tended to be related to wild‐type KRAS (7/96, 7.3%). Furthermore, FGF9 amplification was not observed in any of the samples from the 15 responders to anti‐EGFR therapies but was observed in one sample from the seven non‐responders with wild‐type KRAS, and two samples from non‐responders also had high FGF9 mRNA expression levels. FGF9 amplification was validated using a fluorescence in situ hybridization (FISH) analysis, and FGF9‐amplified sections showed readily detectable signals originating from FGF9 protein when examined using immunohistochemistry. In both the in vitro and in vivo experiments using FGF9‐overexpressing CRC cell lines, FGF9 overexpression induced strong resistance to anti‐EGFR therapies via the enforced FGFR signal, and this resistance was cancelled by the application of an FGFR inhibitor. Considering these results, the FGF9 gene may play an important role in resistance to anti‐EGFR therapies in patients with CRC, and such resistance might be overcome by combined treatment with an anti‐FGFR inhibitor. These findings strongly encourage the development of FGFR‐targeted therapy for CRC patients with FGF9 gene upregulation. © 2016 Wiley Periodicals, Inc.
Effect of Processing Variables on Compaction and Relaxation Ratio of Water Hyacinth Briquettes

Fuel wood collection has grave consequences on environment resulting in greenhouse gas emissions (GHG), forest conservation and sustainable forest resources management. The selection of water hyacinth as alternative source of energy is an important way of managing the weed problem and contributing to environment management. The water hyacinth and plantain peels were milled into three particle sizes 0.5, 1.6 and 4.0mm, five binder levels 10, 20, 30, 40, 50% and four pressure levels 3, 5, 7 and 9MPa were used. Manually operated hydraulic press was used for the production of briquettes. The experimental design for this study was 5 x 3 x 4 Randomized Complete Block Design. ASABE standard methods were used to determine the moisture contents, compaction ratio and relaxation ratio of the briquettes. The minimum compaction ratio was obtained at pressure P1 (5.19±0.27) and the maximum at pressure P4 (6.80±0.36). The effect of binder on the compaction ratio ranged from 5.87±0.31 (B3) to 6.04±0.25 (B4) for all the five binder proportions utilized. The ANOVA revealed that there was significant difference among all the values obtained for compaction ratio at the various binder levels (P<0.001). The values of compaction ratio obtained indicated more void in the compressed materials. This signifies more volume displacement which is good for packaging, storage and transportation and above all, it is an indication of good quality briquettes. Key word: Bulk density, compression, plantain peels, particle size, Niger Delta
Study on the Corresponding Relationship Between Dynamics System and System Structural Configurations—Develop a Universal Analysis Method for Eliminating the RHP-Zeros of System

The purpose of this paper is to use bond graphs to retain system structures, linking dynamic models and the transfer functions of control systems, and develop a universal analysis method for eliminating the right-half-plane zeros (RHP-zeros) of systems. Although previous literature has investigated RHP-zero elimination, their findings were only applicable to specific systems. When such a system is modified, only a trial-and-error method can be applied to eliminate the RHP-zeros of systems. The main feature of the proposed method involves the analysis of the causal paths contained in bond graphs. Analysis results then serve as a guideline for RHP-zero elimination, which can involve processes including modification of model structures or changes to paths. This method improves the system to get a better performance, instead of using the trial-and-error methods. Finally, a boost converter with an RHP-zero is applied to various examples of RHP-zero elimination, verifying that the proposed methodology can be used to eliminate the RHP-zeros of systems without the need of a trial-and-error process.
The Generation of Forces and Moments during Visual-Evoked Steering Maneuvers in Flying Drosophila

Sideslip force, longitudinal force, rolling moment, and pitching moment generated by tethered fruit flies, Drosophila melanogaster, were measured during optomotor reactions within an electronic flight simulator. Forces and torques were acquired by optically measuring the angular deflections of the beam to which the flies were tethered using a laser and a photodiode. Our results indicate that fruit flies actively generate both sideslip and roll in response to a lateral focus of expansion (FOE). The polarity of this behavior was such that the animal's aerodynamic response would carry it away from the expanding pattern, suggesting that it constitutes an avoidance reflex or centering response. Sideslip forces and rolling moments were sinusoidal functions of FOE position, whereas longitudinal force was proportional to the absolute value of the sine of FOE position. Pitching moments remained nearly constant irrespective of stimulus position or strength, with a direction indicating a tonic nose-down pitch under tethered conditions. These experiments expand our understanding of the degrees of freedom that a fruit fly can actually control in flight.
Are non-ST-segment elevation myocardial infarctions missing in China?

Aims ST-segment elevation myocardial infarctions (STEMI) in China and other low- and middle-income countries outnumber non-ST-segment elevation myocardial infarctions (NSTEMI). We hypothesized that the STEMI predominance was associated with lower biomarker use and would vary with hospital characteristics. Methods and results We hypothesized that the STEMI predominance was associated with lower biomarker use and would vary with hospital characteristics. Using data from the nationally representative China PEACE-Retrospective AMI Study during 2001, 2006, and 2011, we compared hospital NSTEMI proportion across categories of use of any cardiac biomarker (CK, CK-MB, or troponin) and troponin, as well as across region, location, level, and teaching status. Among 15 416 acute myocardial infarction (AMI) patients, 14% had NSTEMI. NSTEMI patients were older, more likely female, and to have comorbidities. Median hospital NSTEMI proportion in each study year was similar across categories of any cardiac biomarker use, troponin, region, location, level, and teaching status. For instance, in 2011 the NSTEMI proportion at hospitals without troponin testing was 11.2% [inter quartile range (IQR) 4.4-16.7%], similar to those with ≥ 75% troponin use (13.0% [IQR 8.7-23.7%]) (P-value for difference 0.77). Analysed as continuous variables there was no relationship between hospital NSTEMI proportion and proportion biomarker use. With troponin use there was no relationship in 2001 and 2006, but a modest correlation in 2011 (R = 0.16, P = 0.043). Admissions for NSTEMI increased from 0.3/100 000 people in 2001 to 3.3/100 000 people in 2011 (P-value for trend < 0.001). Conclusion STEMI is the dominant presentation of AMI in China, but the proportion of NSTEMI is increasing. Biomarker use and hospital characteristics did not account for the low NSTEMI rate. Clinical trial registration www.clinicaltrials. gov (NCT01624883).
Short- and long-term outcomes of intramyocardial implantation of autologous bone marrow-derived cells for the treatment of ischaemic heart disease

OBJECTIVES: Ischaemic heart disease remains a major cause of death in Japan. We have implanted autologous bone marrow-derived cells locally into the ischaemic region as a therapy in addition to coronary artery bypass grafting since 1999. We describe the outcomes of our cell therapy for ischaemic heart disease. METHODS: Eleven patients underwent local implantation of bone marrow-derived cells into the ischaemic region during coronary artery bypass grafting. Clinical outcomes during the acute and chronic phases were recorded. RESULTS: In the acute phase, no adverse effects were observed. Left ventricular ejection fraction values were not signiﬁcantly different before and after treatment. Seven of the 11 patients showed improved blood perfusion in the area of cell therapy 1 month after treatment. In the chronic phase, 5 of 11 patients exhibited improved regional blood ﬂow 1 year after treatment. Overall survival at 1, 5 and 10 years was 100%, 83.3% and 83.3%, respectively. Freedom from major adverse cardiac and cerebrovascular events at 1, 5 and 10 years was 100%, 80.8% and 80.8%, respectively. Death from all causes or freedom from major adverse cardiac and cerebrovascular events at 1, 5 and 10 years was 100%, 64.6% and 64.6%, respectively. CONCLUSIONS: Local implantation of bone marrow-derived cells in patients with ischaemic heart disease is safe and feasible. Cell therapy is a therapeutic option for otherwise untreatable ischaemic heart disease.
Estimating Genetic Variability in Non-Model Taxa: A General Procedure for Discriminating Sequence Errors from Actual Variation

Genetic variation is the driving force of evolution and as such is of central interest for biologists. However, inadequate discrimination of errors from true genetic variation could lead to incorrect estimates of gene copy number, population genetic parameters, phylogenetic relationships and the deposition of gene and protein sequences in databases that are not actually present in any organism. Misincorporation errors in multi-template PCR cloning methods, still commonly used for obtaining novel gene sequences in non-model species, are difficult to detect, as no previous information may be available about the number of expected copies of genes belonging to multi-gene families. However, studies employing these techniques rarely describe in any great detail how errors arising in the amplification process were detected and accounted for. Here, we estimated the rate of base misincorporation of a widely-used PCR-cloning method, using a single copy mitochondrial gene from a single individual to minimise variation in the template DNA, as 1.62×10−3 errors per site, or 9.26×10−5 per site per duplication. The distribution of errors among sequences closely matched that predicted by a binomial distribution function. The empirically estimated error rate was applied to data, obtained using the same methods, from the Phospholipase A2 toxin family from the pitviper Ovophis monticola. The distribution of differences detected closely matched the expected distribution of errors and we conclude that, when undertaking gene discovery or assessment of genetic diversity using this error-prone method, it will be informative to empirically determine the rate of base misincorporation.
Fore-arc deformation and underplating at the northern Hikurangi margin, New Zealand

Geophysical investigations of the northern Hikurangi subduction zone northeast of New Zealand, image fore‐arc and surrounding upper lithospheric structures. A seismic velocity (Vp) field is determined from seismic wide‐angle data, and our structural interpretation is supported by multichannel seismic reflection stratigraphy and gravity and magnetic modeling. We found that the subducting Hikurangi Plateau carries about 2 km of sediments above a 2 km mixed layer of volcaniclastics, limestone, and chert. The upper plateau crust is characterized by Vp = 4.9–6.7 km/s overlying the lower crust with Vp > 7.1 km/s. Gravity modeling yields a plateau thickness around 10 km. The reactivated Raukumara fore‐arc basin is >10 km deep, deposited on 5–10 km thick Australian crust. The fore‐arc mantle of Vp > 8 km/s appears unaffected by subduction hydration processes. The East Cape Ridge fore‐arc high is underlain by a 3.5 km deep strongly magnetic (3.3 A/m) high‐velocity zone, interpreted as part of the onshore Matakaoa volcanic allochthon and/or uplifted Raukumara Basin basement of probable oceanic crustal origin. Beneath the trench slope, we interpret low‐seismic‐velocity, high‐attenuation, low‐density fore‐arc material as accreted and recycled, suggesting that underplating and uplift destabilizes East Cape Ridge, triggering two‐sided mass wasting. Mass balance calculations indicate that the proposed accreted and recycled material represents 25–100% of all incoming sediment, and any remainder could be accounted for through erosion of older accreted material into surrounding basins. We suggest that continental mass flux into the mantle at subduction zones may be significantly overestimated because crustal underplating beneath fore‐arc highs have not properly been accounted for.
Young Children's Participation and Environment Measure: Swedish Cultural Adaptation

ABSTRACT Aim: To culturally adapt and evaluate the psychometric properties of the Young Children's Participation and Environment Measure (YC-PEM) for use by caregivers of Swedish children with and without disabilities, aged 2–5 years. Methods: Thirteen cognitive interviews and two focus groups with caregivers of children with and without disabilities were conducted to evaluate the cultural relevance of YC-PEM content for use in Sweden. Per participant feedback, a revised version of the Swedish YC-PEM was created and pilot tested with caregivers of children with disabilities (n = 11) and children with typical development (n = 22). Results: User feedback informed content revisions to 7% of items. Internal consistency estimates of the Swedish YC-PEM pilot version were acceptable and ranged from . 70 to . 92 for all but two of the YC-PEM scales. Mean percentage agreement between raters ranged from 47% to 93% across YC-PEM scales for inter-rater, and 44% to 86% for test-retest. One of twelve YC-PEM scales revealed significant group differences between young children with and without disabilities. Conclusions: This study contributes preliminary evidence for the use of some scales within a culturally adapted YC-PEM in Sweden. Further validation with larger samples will allow for parametric testing to evaluate its psychometric properties.
Single coronary artery and neonatal arterial switch operation: early and long-term outcomes†

OBJECTIVES The presence of single coronary artery (CA) in the arterial switch operation (ASO) for neonatal treatment with transposition of the great arteries (TGA) has been reported to be an independent risk factor for early death after surgical repair and late reintervention. The study objective was to evaluate the mortality and the CA stenosis risk at early and long term in neonatal ASO for TGA and single CA. METHODS Between January 1987 and January 2010, 979 neonates underwent an ASO, of which 73 had a single CA (7.5% of all cohort): right ostium with posterior left CA loop was the most frequent pattern (63%), followed by left ostium with an anterior right CA loop (26%). Mean age at operation was 9.3 ± 5.7 days. Mean follow-up was 9.8 years (range: 1-20 years). RESULTS Eight patients (11%) died, 6 of coronary-related death. Overall, survival was 90.1 ± 1.9% at 1 year and 88.6% ± 3.8% at 2, 5, 10 and 15 years, respectively. Independent risk factor for mortality was associated surgery before 2001. Freedom from coronary events was 91.6 ± 3.3% at 1 year and 88.7 ± 3.8% at 5, 10 and 15 years respectively. No patients required late reintervention for CA surgery or angioplasty. CONCLUSIONS All coronary-related death occurred within the first 6 months after ASO, and all patients but 1 were operated before 2001. In our experience, it appears that a single CA is not any more a risk factor for early and late mortality after ASO for TGA. Mortality has drastically reduced since 2001 and is now close to that found in TGA with standard coronary patterns. The acquired experience shared between the surgeons and the institution offsets the undeniable surgical difficulty.
Profoundly Expanded T-cell Clones in the Inflamed and Uninflamed Intestine of Patients With Crohn’s Disease

Background and Aim T cells are key players in the chronic intestinal inflammation that characterises Crohn's disease. Here we aim to map the intestinal T-cell receptor [TCR] repertoire in patients with Crohn's disease, using next-generation sequencing technology to examine the clonality of the T-cell compartment in relation to mucosal inflammation and response to therapy. Methods Biopsies were taken from endoscopically inflamed and uninflamed ileum and colon of 19 patients with Crohn's disease. From this cohort, additional biopsies were taken after 8 weeks of remission induction therapy from eight responders and eight non-responders. Control biopsies from 11 patients without inflammatory bowel disease [IBD] were included. The TCRβ repertoire was analysed by next-generation sequencing of biopsy RNA. Results Both in Crohn's disease patients and in non-IBD controls, a broad intestinal T-cell repertoire was found, with a considerable part consisting of expanded clones. Clones in Crohn's disease were more expanded [p = 0.008], with the largest clones representing up to as much as 58% of the total repertoire. There was a substantial overlap of the repertoire between inflamed and uninflamed tissue and between ileum and colon. Following therapy, responders showed larger changes in the T-cell repertoire than non-responders, although a considerable part of the repertoire remained unchanged in both groups. Conclusions The intestinal T-cell repertoire distribution in Crohn's disease is different from that in the normal gut, containing profoundly expanded T-cell clones that take up a large part of the repertoire. The T-cell repertoire is fairly stable regardless of endoscopic mucosal inflammation or response to therapy.