Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecological niche define the limits of pig agroecology: a comparative review of evidence from early centres of sedentary agriculture

ABSTRACT Change strategies, and the eventual abandonment of semi-domesticated and domesticated Sus scrofa is discussed in regards to increasing regional aridity in both the ancient Levant and what is now northwest China between 8,000 BP and 4,000 BP. A review of literature suggests a changing agroecological role of pigs, from one closely linked to production in the local ecosystem to one closely linked to production in the human social system as drying conditions created more favourable conditions for grain agriculture. The eventual abandonment of pigs as a viable agroecosystem component is discussed.
Contribution of IBD5 Locus to Clinical Features of IBD Patients

AIM:The aim of this study was to investigate the influence of the IBD5 locus on clinical features of inflammatory bowel disease (IBD) patients, and its possible interaction with the CARD15 gene.PATIENTS AND METHODS:A cohort of 1,199 IBD patients (570 with CD and 629 with ulcerative colitis [UC]), and 357 healthy subjects were investigated. Information on clinical features was fully available for 855 IBD patients. Two SNPs in the IBD5 locus (IGR2198a_1 and IGR2096a_1) and the three major variants of CARD15 gene were genotyped in patients and controls.RESULTS:Homozygous carriers of risk alleles were significantly more frequent in CD (22.6% for IGR2198a_1, OR = 1.6, p= 0.015; 21.9% for IGR2096a_1, OR = 1.6, p= 0.012) compared to controls (16.8% and 15.7%, respectively). The homozygote frequency was also increased in UC patients, but not significantly. No significant gene-gene interaction was detected between IBD5 and CARD15. A univariate analysis detected association between IBD5 and steno/fistulizing behavior in CD patients (OR = 1.9; p= 0.004), and presence of more extensive colitis in UC patients (OR = 1.7; p= 0.01). Results from multiple logistic regression, after correction for covariates, showed that the influence of IBD5 on clinical outcome of CD was completely masked by that of CARD15, while the influence on more extensive colitis in UC patients was confirmed.CONCLUSIONS:Our study shows that presence of the IBD5 risk alleles, particularly in the homozygous state, is associated with IBD and especially with CD, without a significant epistasis with CARD15. The contribution of CARD15 risk alleles to CD clinical features is prominent on that of IBD5.
How to describe protein motion without amino acid sequence and atomic coordinates

This paper reports a computational method, the quantized elastic deformational model, that can reliably describe the conformational flexibility of a protein in the absence of the amino acid sequence and atomic coordinates. The essence of this method lies in the fact that, in modeling the functionally important conformational changes such as domain movements, it is possible to abandon the traditional concepts of protein structure (bonds, angles, dihedrals, etc.) and treat the protein as an elastic object. The shape and mass distribution of the object are described by the electron density maps, at various resolutions, from methods such as x-ray diffraction or cryo-electron microscopy. The amplitudes and directionality of the elastic deformational modes of a protein, whose patterns match the biologically relevant conformational changes, can then be derived solely based on the electron density map. The method yields an accurate description of protein dynamics over a wide range of resolutions even as low as 15–20 Å at which there is nearly no visually distinguishable internal structures. Therefore, this method dramatically enhances the capability of studying protein motions in structural biology. It is also expected to have ample applications in related fields such as bioinformatics, structural genomics, and proteomics, in which one's ability to extract functional information from the not-so-well-defined structural models is vitally important.
Emotion recognition on speech signals using machine learning

With the increase in man to machine interaction, speech analysis has become an integral part in reducing the gap between physical and digital world. An important subfield within this domain is the recognition of emotion in speech signals, which was traditionally studied in linguistics and psychology. Speech emotion recognition is a field having diverse applications. The prime objective of this paper is to recognize emotions in speech and classify them in 7 emotion output classes namely, anger, boredom, disgust, anxiety, happiness, sadness and neutral. The proposed approach is based upon the Mel Frequency Cepstral coefficients (MFCC) and energy of the speech signals as feature inputs and uses Berlin database of emotional speech. The features extracted from speech are converted into a feature vector, which in turn are used to train different classification algorithms namely, Support Vector Machine (SVM), Random Decision Forest and Gradient Boosting. Random forest was found to have the highest accuracy and predicted correct emotion 81.05% of the time.
Les Grands Challenges issus des ateliers thématiques des ORPHÉE-RDV’2017

Cette rubrique presente les Grands Challenges identifies lors des ateliers thematiques organises dans le cadre des ORPHEE-RDV’2017. Six ateliers thematiques ont reuni des chercheurs, des praticiens et des entrepreneurs dans le domaine de la e-education. Huit Grands Challenges ont emerge de ce travail collaboratif et interdisciplinaire. Ils posent des questions sur l’integration de nouvelles methodes et technologies dans les dispositifs d’enseignement, sur les moyens de favoriser le developpement de nouvelles competences par l’apprenant, et sur les systemes a mettre en œuvre pour analyser l’activite des apprenants, permettre leur suivi et personnaliser les parcours d’apprentissage.
First-line investigation of acute intracerebral hemorrhage using dynamic magnetic resonance angiography

Purpose: To report the initial experience of magnetic resonance (MR) digital subtraction angiography (MR-DSA) in the dynamic assessment of the cerebral circulation in acute non-traumatic intracerebral hemorrhage (ICH). Material and Methods: Twelve patients with acute ICH were investigated within 6 days of the ictus using a dynamic contrast-enhanced 2-D MR angiogram that produces subtracted images with a temporal resolution of 1–2 frame/s. The MR-DSA examinations were assessed for evidence of an intracranial vascular abnormality and were compared with (i) the routine MR sequences, (ii) non-dynamic time-of-flight MR angiography, and (iii) catheter angiogram performed during the same admission. Results: All 12 MR-DSA examinations were considered to be technically satisfactory. MR-DSA detected an intracranial vascular abnormality in 7 patients (3 arteriovenous malformations, 2 aneurysms, 1 dural arteriovenous fistula, and 1 venous thrombosis). All abnormalities were confirmed by catheter angiography with the exception of one patient with venous sinus thrombosis found on MR imaging that did not undergo catheter angiography. All four arteriovenous shunts were detected by MR-DSA by virtue of early venous filling. Conclusion: MR-DSA can be performed satisfactorily in the setting of acute ICH and provides an alternative method to catheter angiography for identifying shunting vascular abnormalities such as arteriovenous malformations and fistulae, as well as large aneurysms and venous occlusions. MR-DSA is a contrast-medium-based technique that does not suffer from the T1 shortening effects of acute hemorrhage that can obscure abnormalities on conventional flow-based non-dynamic techniques.
Efficacy of subgingival irrigation using herbal extracts on gingival inflammation.

BACKGROUND The aim of the present study was to investigate the efficacy of an herbal-based mouthrinse in combination with an oral irrigator in reducing gingival inflammation. METHODS A total of 89 patients (45 females, 44 males; mean age 49.1 +/- 1.31 years) were included in this prospective, randomized, double-blind clinical study and allocated to 3 treatment groups: group 1 (n = 34), treated with an oral irrigator with subgingival tips and an herbal-based mouthrinse; group 2 (n = 29), the oral irrigator was applied in combination with a conventional mouthwash; and group 3 (n = 26), treated with the conventional mouthwash without subgingival irrigation. Data collected at baseline and after 4, 8, and 12 weeks included gingival index (GI), sulcus bleeding index (SBI), plaque index (PI), and probing depth (PD). RESULTS Over a period of 3 months, GI decreased from 1.80 +/- 0.04 to 1.56 +/- 0.04 in group 1; from 1.79 +/- 0.05 to 1.68 +/- 0.04 in group 2; and remained nearly constant in group 3 (from 1.79 +/- 0.05 to 1.81 +/- 0.04). Differences between the groups were significant (analysis of variance, P < 0.05). SBI values in group 1 were reduced from 2.51 +/- 0.06 to 2.13 +/- 0.06 after 3 months and were significantly lower than in group 2 (P = 0.001) and 3 (P = 0.002), with SBIs of 2.44 +/- 0.06 and 2.42 +/- 0.07, respectively, after 12 weeks. A reduction in PI was noted for all 3 groups throughout the follow-up period, with no statistically significant differences. Probing depths were not reduced significantly in any group. CONCLUSION Subgingival irrigation with an herbal-based mouthrinse led to a significant reduction in both SBI and GI. This regimen can, therefore, be recommended as an adjunctive procedure to reduce gingival inflammation.
Quantifying Financing Needs in the Belt and Road Countries

ABSTRACT This paper provides a thorough analysis to quantify the financing needs in the Belt and Road countries during 2009 and 2014. By examining financial constraints using financial data of firms in the Belt and Road countries, this study constructs a Financing Needs Index for Belt and Road countries and highlights the characteristics of financing needs across 36 countries and 6 years. By further incorporating information from World Bank Enterprise Surveys, this paper builds an Augmented Financing Needs Index for 56 Belt and Road countries. The findings of this paper provide important policy implications by showing that countries can improve their financial liberalization and institutional environment to address the financing needs of their indigenous firms and thus achieve economic growth.
Acquisition of antibodies to various coxsackie and echo viruses and hepatitis A virus in agricultural communal settlements in Israel

A seroepidemiological study was conducted to measure the antibody prevalence for eight different enteric viruses. These include seven “classical” enteroviruses, ie, Coxsackie virus types A9, B1, B3, B4 and three ECHO virus types 4, 7, and 9, as well as hepatitis A virus (HAV), recently classified as enterovirus 72. Sera samples were obtained from 791 residents living in 29 agricultural settlements (kibbutzim) with a total population of 15,950. The results indicated that the acquisition of antibodies to Coxsackie and ECHO viruses occurred at a significantly earlier age than to HAV. Prevalence of antibodies to Coxsackie and ECHO viruses at two to four years of age was 40%–69%, in contrast to 4% for HAV. At age 5–17 years, 85% had antibodies to five or more of the seven “classical” enteroviruses, as compared with 10% to HAV. The latter steeply increased to 63% for age group 18–24 years and reached a peak of 95% for age group 50 years and older. Prevalence of antibodies to ECHO and Coxsackie viruses were often found to be higher in females than in males, within the age group of 18 years and older, but not in age groups 18 years and younger. Prevalence of antibodies to HAV was observed to be much higher in males than in females 18–24 years of age. No significant difference was found in the prevalence of individuals harboring antibodies to three or more and even up to five or more Coxsackie and ECHO viruses between those HAV‐negative versus those HAV positive. This suggests that in addition to the well‐known fecal‐oral mode of transmission in these agents, other factors are involved that are responsible for the significantly different mode of aquisition of infection and immunity to classical enteroviruses and HAV in the community of the kibbutz.
A low phase noise local oscillator module for instrumentation application

In this paper we have developed a novel Local Oscillator Module for down conversion application in Signal Source Analyzer with low phase noise, which covers 3-10 GHz frequency range. The local oscillator is a multi-loop YTO based frequency synthesizer, which is implemented with ultra low phase noise OCXO, low phase noise YIG-tuned oscillator, low conversion loss, and low noise sampling phase detector. In this project in order to have a good phase noise of local oscillator, key circuits have been analyzed, designed and implemented. The output signal of local oscillator has a pretty good phase noise, and the measured phase noise at 10 kHz offset is about -128dBc/Hz at 3.05GHz and -120dBc/Hz at 9.95GHz respectively. The frequency switching time is less than 2 millisecond in the entire operating range.
p38 MAPK activity is stimulated by vascular endothelial growth factor receptor 2 activation and is essential for shear stress‐induced angiogenesis

Increased capillary shear stress induces angiogenesis in skeletal muscle, but the signaling mechanisms underlying this response are not known. We hypothesize that shear stress‐dependent activation of vascular endothelial growth factor receptor 2 (VEGFR2) causes p38 and ERK1/2 phosphorylation, which contribute to shear stress‐induced angiogenesis. Skeletal muscle microvascular endothelial cells were sheared (12 dynes/cm2, 0.5–24 h). VEGFR2‐Y1214 phosphorylation increased in response to elevated shear stress and VEGF stimulation. p38 and ERK1/2 phosphorylation increased at 2 h of shear stress but only p38 remained phosphorylated at 6 and 24 h of shear stress. VEGFR2 inhibition abrogated p38, but not ERK1/2 phosphorylation. VEGF production was increased in response to shear stress at 6 h, and this increased production was abolished by p38 inhibition. Male Sprague–Dawley rats were administered prazosin (50 mg/L drinking water, 1, 2, 4, or 7 days) to induce chronically elevated capillary shear stress in skeletal muscle. In some experiments, mini‐osmotic pumps were used to dispense p38 inhibitor SB203580 or its inactive analog SB202474, to the extensor digitorum longus (EDL) of control and prazosin‐treated rats. Immunostaining and Western blotting showed increases in p38 phosphorylation in capillaries from rats treated with prazosin for 2 days but returned to basal levels at 4 and 7 days. p38 inhibition abolished the increase in capillary to muscle fiber ratio seen after 7 days of prazosin treatment. Our data suggest that p38 activation is necessary for shear stress‐dependent angiogenesis. J. Cell. Physiol. 222:120–126, 2010. © 2009 Wiley‐Liss, Inc.
Molecular Basis of Insulin‐Responsive GLUT4 Trafficking Systems Revealed by Single Molecule Imaging

Development of a ‘static retention’ property of GLUT4, the insulin‐responsive glucose transporter, has emerged as being essential for achieving its maximal insulin‐induced surface exposure. Herein, employing quantum‐dot‐based nanometrology of intracellular GLUT4 behavior, we reveal the molecular basis of its systematization endowed upon adipogenic differentiation of 3T3L1 cells. Specifically, (i) the endosomes‐to‐trans‐Golgi network (TGN) retrieval system specialized for GLUT4 develops in response to sortilin expression, which requires an intricately balanced interplay among retromers, golgin‐97 and syntaxin‐6, the housekeeping vesicle trafficking machinery. (ii) The Golgin‐97‐localizing subdomain of the differentiated TGN apparently serves as an intermediate transit route by which GLUT4 can further proceed to the stationary GLUT4 storage compartment. (iii) AS160/Tbc1d4 then renders the ‘static retention’ property insulin responsive, i.e. insulin liberates GLUT4 from the static state only in the presence of functional AS160/Tbc1d4. (iv) Moreover, sortilin malfunction and the resulting GLUT4 sorting defects along with retarded TGN function might be etiologically related to insulin resistance. Together, these observations provide a conceptual framework for understanding maturation/retardation of the insulin‐responsive GLUT4 trafficking system that relies on the specialized subdomain of differentiated TGN.
Long-term morbidity and mortality in survivors of critical illness: a 5-year observational follow-up study.

INTRODUCTION This prospective observational study over 5 years aimed to quantify long-term morbidity and mortality in a prospectively recruited cohort of Central Australian survivors of critical illness. METHODS Eligible participants are survivors of an intensive care unit (ICU) admission for a critical illness at the Alice Springs Hospital (ASH), prospectively recruited during 2009. The ASH ICU is a 10-bed unit located in Central Australia with approximately 600 admissions annually, 95% of which are emergent, and 65% Indigenous. All-cause mortality, secondary healthcare utilisation and functional outcomes were measured by 6-minute walk distance (an indicator of functional status) and the home and community care (HACC) screening tool at 5 years. RESULTS Sixty eight percent of the cohort had died at 5 years. Median age of death was 53 years with a median time to death of 604 days following ICU admission. There was increased secondary healthcare utilisation measured by emergency department presentations and hospital re-admissions, with a median 5.22 healthcare presentations per year alive. There is evidence of ongoing functional limitation with 6-minute walk distance at 5 years significantly less than that predicted, despite high scores on the HACC screening assessment suggesting virtually full resumption of basic and domestic activities of daily living. CONCLUSIONS A critical illness is not an isolated event, and there is evidence of ongoing high secondary healthcare utilisation, reflecting a high burden of disease. Mortality in this cohort is higher than would be expected from international data, and at a young median age, suggesting significant loss of productive life years. In addition, there is evidence of ongoing morbidity, with higher rates of healthcare utilisation than comparable international studies. This has profound implications for healthcare planners due to the ongoing economic implications, and may suggest a need for increased primary healthcare resources to pre-emptively manage chronic disease and reduce the burden of healthcare utilisation at acute care facilities.
Aberrant Gene Expression in Epithelial Cells of Mixed Odontogenic Tumors

Comparative investigations of odontogenic cells in normally forming teeth and tumors may provide insights into the mechanisms of the differentiation process. The present study is devoted to late phenotypic markers of ameloblast and odontoblast cells, i.e., proteins involved in biomineralization. The in situ expression of amelogenins, keratins, collagens type III and IV, vimentin, fibronectin, osteonectin, and osteocalcin was performed on normal and tumor odontogenic human cells. The pattern of protein expression showed some similarities between ameloblasts and odontoblasts present in normally developing human teeth and cells present in neoplastic tissues of ameloblastic fibroma, ameloblastic fibro-odontomas, and complex odontomas. Amelogenins (for ameloblasts) and osteocalcin (for odontoblasts) were detected in cells with well-organized enamel and dentin, respectively. In contrast, "mixed" cells located in epithelial zones of mixed odontogenic tumors co-expressed amelogenins and osteocalcin, as shown by immunostaining. The presence of osteocalcin transcripts was also demonstrated by in situ hybridization in these cells. Keratins and vimentin were detected in the same epithelial zones. Tumor epithelial cells were associated with various amounts of polymorphic matrix (amelogenin- and osteocalcin-immunoreactive), depending on the types of mixed tumors. No osteocalcin labeling was found in epithelial tumors. This study confirms that the differentiation of normal and tumor odontogenic cells is accompanied by the expression of some common molecules. Furthermore, the gene products present in normal mesenchymal cells were also shown in odontogenic tumor epithelium. These data may be related to a tumor-specific overexpression of the corresponding genes transcribed at an undetectable level during normal development and/or to an epithelial-mesenchymal transition proposed to occur during normal root formation. A plausible explanation for the results is that the odontogenic tumor epithelial cells are recapitulating genetic programs expressed during normal odontogenesis, but the tumor cells demonstrate abnormal expression patterns for these genes.
Molecular epidemiology of multiresistant Escherichia coli isolates from community-onset urinary tract infections in Cornwall, England.

OBJECTIVES To study the clonality of gentamicin-resistant, extended-spectrum beta-lactamase (ESBL)-negative and ESBL-producing Escherichia coli isolated from community-onset urinary tract infections (UTIs) in Cornwall. METHODS Isolates were identified by API, susceptibilities were determined by local disc testing, and MICs were determined at the reference laboratory, both interpreted using BSAC guidelines. bla(CTX-M) genes were sought by PCR, and isolates were compared by PFGE. RESULTS In the years 2004 and 2005, 69 E. coli were submitted by Truro (Cornwall) laboratory for reference laboratory testing: these included 14 gentamicin-resistant, ESBL-negative isolates; 45 with group 1 CTX-M enzymes; seven with group 9 CTX-M enzymes; and three with non-CTX-M ESBLs. By PFGE, nine gentamicin-resistant, ESBL-negative E. coli were distinct (<85% similarity) from all the ESBL producers, but three were related to producers of group 1 CTX-M enzymes, and two isolates were related to a non-CTX-M ESBL producer. An outbreak strain was identified, represented by 11 gentamicin-resistant and one gentamicin-susceptible isolates, all with group 1 CTX-M enzymes, and two gentamicin-resistant, ESBL-negative isolates. This was distinct by PFGE from nationally distributed CTX-M-producing strains. Five of nine patients infected with this strain had been on the same ward in a local hospital; four presented with community-onset UTIs; one inpatient developed a hospital-acquired bacteraemia. Of the other four patients presenting with community-onset UTIs, three were admitted to different hospitals and the fourth had only attended an outpatient clinic. CONCLUSIONS Community-onset, ESBL-producing and non-producing E. coli were diverse. Two ESBL-negative isolates were closely related to a local CTX-M-producing outbreak strain, suggesting gain or loss of a bla(CTX-M)-carrying plasmid. An outbreak strain was linked with prior hospital admission and appeared not to represent genuine community acquisition.