Miracle-dz/UniFAR-FTUs huggingface dataset:
Survey on the Use of Whole-Genome Sequencing for Infectious Diseases Surveillance: Rapid Expansion of European National Capacities, 2015–2016

Whole-genome sequencing (WGS) has become an essential tool for public health surveillance and molecular epidemiology of infectious diseases and antimicrobial drug resistance. It provides precise geographical delineation of spread and enables incidence monitoring of pathogens at genotype level. Coupled with epidemiological and environmental investigations, it delivers ultimate resolution for tracing sources of epidemic infections. To ascertain the level of implementation of WGS-based typing for national public health surveillance and investigation of prioritized diseases in the European Union (EU)/European Economic Area (EEA), two surveys were conducted in 2015 and 2016. The surveys were designed to determine the national public health reference laboratories’ access to WGS and operational WGS-based typing capacity for national surveillance of selected foodborne pathogens, antimicrobial-resistant pathogens, and vaccine-preventable diseases identified as priorities for European genomic surveillance. Twenty-eight and twenty-nine out of the 30 EU/EEA countries participated in the survey in 2015 and 2016, respectively. National public health reference laboratories in 22 and 25 countries had access to WGS-based typing for public health applications in 2015 and 2016, respectively. Reported reasons for limited or no access were lack of funding, staff, and expertise. Illumina technology was the most frequently used followed by Ion Torrent technology. The access to bioinformatics expertise and competence for routine WGS data analysis was limited. By mid-2016, half of the EU/EEA countries were using WGS analysis either as first- or second-line typing method for surveillance of the pathogens and antibiotic resistance issues identified as EU priorities. The sampling frame as well as bioinformatics analysis varied by pathogen/resistance issue and country. Core genome multilocus allelic profiling, also called cgMLST, was the most frequently used annotation approach for typing bacterial genomes suggesting potential bioinformatics pipeline compatibility. Further capacity development for WGS-based typing is ongoing in many countries and upon consolidation and harmonization of methods should enable pan-EU data exchange for genomic surveillance in the medium-term subject to the development of suitable data management systems and appropriate agreements for data sharing.
Line-1 hypomethylation in multistage carcinogenesis of the uterine cervix.

OBJECTIVE To evaluate characteristics of global hypomethylation in evolution of cervical cancer. MATERIALS AND METHODS Eight cases of squamous cell carcinoma (SCC) and seven cases of carcinoma in situ (CIS) were studied. Each of the SCC samples contained CIS, and all SCC and CIS samples contained normal ectocervical epithelium. Microdissection was performed to separate normal epithelium, CIS and SCC prior to DNA extraction. Hypomethylation levels of long interspersed nuclear elements (LINE-1 or L1) were measured with a combined bisulfite restriction analysis (COBRA) PCR (polymerase chain reaction) protocol. The percentage of L1 hypomethylation for SCC, CIS and normal epithelium was compared. RESULTS In the SCC cohort, the L1 hypomethylation level showed progressive increase comparing normal epithelium (59.4 +/- 8.86%) to CIS (64.37 +/- 7.32%) and SCC (66.3 +/- 7.26%) (repeated measurement ANOVA, P = 0.005). A significantly greater L1 hypomethylation level was found in CIS (62.06 +/- 3.44 %) compared to normal epithelium (60.03 +/- 3.69 %) (paired t-Test, P = 0.03). No significant difference in L1 hypomethylation level was noted between CIS of the two sample groups (unpaired t-Test, P = 0.2). CONCLUSIONS In our study, there was a significant correlation between the degree of hypomethylation and progression from normal ectocervical mucosa to CIS and invasive cancer. Laboratory assessment of biopsies for this molecular event may have clinical significance.
Managing time-storage complexity in point location problem: Application to explicit model predictive control

The online computational burden of linear model predictive control (MPC) can be moved offline by using multi-parametric programming, so called explicit MPC. The explicit MPC is a piecewise affine (PWA) function defined over a polyhedral subdivision of the set of feasible states. The online evaluation of such a control law needs to determine the polyhedral region in which the current state lies. This procedure is called the point location problem and its computational complexity is challenging. In this paper a new flexible algorithm is proposed which enables the designer to tradeoff between time and storage complexities. Utilizing the concept of hash tables and the associate hash functions the proposed method is modified to solve an aggregated point location problem in processing complexity independent of the number of polyhedral regions while the storage needs remains tractable. The effectiveness of this approach is supported by several numerical examples.
Low-Fat Versus Low-Carbohydrate Weight Reduction Diets

OBJECTIVE Low-fat hypocaloric diets reduce insulin resistance and prevent type 2 diabetes in those at risk. Low-carbohydrate, high-fat diets are advocated as an alternative, but reciprocal increases in dietary fat may have detrimental effects on insulin resistance and offset the benefits of weight reduction. RESEARCH DESIGN AND METHODS We investigated a low-fat (20% fat, 60% carbohydrate) versus a low-carbohydrate (60% fat, 20% carbohydrate) weight reduction diet in 24 overweight/obese subjects ([mean ± SD] BMI 33.6 ± 3.7 kg/m2, aged 39 ± 10 years) in an 8-week randomized controlled trial. All food was weighed and distributed, and intake was calculated to produce a 500 kcal/day energy deficit. Insulin action was assessed by the euglycemic clamp and insulin secretion by meal tolerance test. Body composition, adipokine levels, and vascular compliance by pulse-wave analysis were also measured. RESULTS Significant weight loss occurred in both groups (P < 0.01), with no difference between groups (P = 0.40). Peripheral glucose uptake increased, but there was no difference between groups (P = 0.28), and suppression of endogenous glucose production was also similar between groups. Meal tolerance–related insulin secretion decreased with weight loss with no difference between groups (P = 0.71). The change in overall systemic arterial stiffness was, however, significantly different between diets (P = 0.04); this reflected a significant decrease in augmentation index following the low-fat diet, compared with a nonsignificant increase within the low-carbohydrate group. CONCLUSIONS This study demonstrates comparable effects on insulin resistance of low-fat and low-carbohydrate diets independent of macronutrient content. The difference in augmentation index may imply a negative effect of low-carbohydrate diets on vascular risk.
Haplotype Inference Constrained by Plausible Haplotype Data

The haplotype inference problem (HIP) asks to find a set of haplotypes which resolve a given set of genotypes. This problem is important in practical fields such as the investigation of diseases or other types of genetic mutations. In order to find the haplotypes which are as close as possible to the real set of haplotypes that comprise the genotypes, two models have been suggested which are by now well-studied: The perfect phylogeny model and the pure parsimony model. All known algorithms up till now for haplotype inference may find haplotypes that are not necessarily plausible, i.e., very rare haplotypes or haplotypes that were never observed in the population. In order to overcome this disadvantage, we study in this paper, a new constrained version of HIP under the above-mentioned models. In this new version, a pool of plausible haplotypes H̃ is given together with the set of genotypes G, and the goal is to find a subset H ⊆ H̃ that resolves G. For constrained perfect phylogeny haplotyping (CPPH), we provide initial insights and polynomial-time algorithms for some restricted cases of the problem. For constrained parsimony haplotyping (CPH), we show that the problem is fixed parameter tractable when parameterized by the size of the solution set of haplotypes.
OD Exce tional c ildren Practical Questions About Collaboration Between General and Special Educators

Collaboration between general and special educators has become one of the most popular topics in the special education field. What are the reasons for this emphasis on collaboration and a number of closely related areas--e.g., consultation, inclusion, and the merging of general and special education? Historically speaking, implementation of the Education for All Handicapped Children Act (PL 94-142) in 1975 has been influential. During initial implementation of the act (now known as the Individuals with Disabilities Education Act, IDEA), school systems focused on establishing self-contained programs for students with disabilities, a service delivery model popular in the 1960s. During the 1970s and early 1980s, this emphasis changed when professionals thought the principles of normalization emphasized in IDEA were better served by the resource model of service delivery (Deno, 1970). Most recently, the calls for educational reform, special education restructuring, and full inclusion have provided further impetus for advocates of collaboration between general and special educators. Given that collaboration has been a popular subject of workshops and of many articles, even entire issues of journals, one would think that we now have a rich research base upon which to draw for recommendations concerning best practices. Unfortunately, this is not the case. Too few researchers have addressed even the most fundamental questions pertaining to the effectiveness of collaboration. Interestingly, we tend to know more about the process of collaboration than its outcomes. This focus on the interactions between collaborators rather than outcomes for students has been branded as a "feel-good approach" to collaboration (Fuchs & Fuchs, 1992). We agree wholeheartedly with the Fuchs's call for more research directed toward the efficacy of collaboration. Unfortunately, as with so many current educational initiatives for students with disabilities (e.g., full inclusion, facilitated communication), the proverbial cart (containing prescriptions for practice) is considerably ahead of the horse (forged from research).
Molecular and cellular characterization of SEL‐OB/SVEP1 in osteogenic cells in vivo and in vitro

We describe a novel human gene, named SEL‐OB/SVEP1, expressed by skeletal tissues in vivo and by cultured osteogenic cells. The mRNA expression was analyzed on frozen tissues retrieved by laser‐capture microscope dissection (LCM) and was detected in osteogenic tissues (periosteum and bone) but not in cartilage or skeletal muscle. The SEL‐OB/SVEP1 cDNA of 11,139 bp was in silico translated into a 3574AA protein with expected molecular weight of 370 kDa. The protein is composed of multiple domains including complement control protein (CCP) modules with selectin superfamily signature; sushi and other domains, such as vWA, EGF, PTX, and HYR. Stromal osteogenic cells were analyzed for the protein expression using anti‐SEL‐OB/SVEP1 for immuno‐precipitation and Western blot application confirm the presence of high molecular weight protein. Immuno‐histochemistry and fluorescence‐activated cell sorting (FACS) were applied to detect SEL‐OB/SVEP1 on the surface of stromal cells. ELISA quantified the dependence of protein expression on cell density. Bioinformatic analysis of SEL‐OB/SVEP1 revealed domains compositions recognized in cell surface molecules and suggested its role in cell adhesion. Analysis of mesechymal osteogenic cells' adhesion in presence of anti‐SEL‐OB/SVEP1 antibody demonstrated its interference with initial adhesion stages. In summary, present study describes novel SEL‐OB/SVEP1 protein with a unique composition of functional domains, restricted pattern of expression in skeletal cells and demonstrated involvement in attachment of mesenchymal cells. The unusual composition of functional domains puts SEL‐OB/SVEP1 in the discrete new group of membrane proteins involved in cell adhesion processes. All together makes SEL‐OB/SVEP1 an attractive marker for studying the role of stromal osteogenic cells and their interactions within the bone marrow microenvironment creating a network that regulates the skeletal homeostasis. J. Cell. Physiol. 206: 420–427, 2006. © 2005 Wiley‐Liss, Inc.
Individual reactions to organizational ethical failures and recovery attempts: A recovery paradox?

The vast majority of behavioral ethical research focuses on the antecedents of unethical behavior. Consequently, questions involving the consequences of organizational unethical behavior remain largely unanswered. Therefore, extant business ethics research largely neglects the impacts of organizational unethical behavior on individuals. Moreover, questions involving what organizations can do to correct or recover from having engaged in unethical behavior as well as individual responses to those efforts are also mostly ignored. Therefore, the purpose of this study is to investigate the impact of unethical activity on employees and explore organizations that have failed ethically and their attempts at recovery. This study explores two issues. First, how do employees react to organizational unethical behavior (OUB) and to what extent are those reactions dependent on contextual and individual factors? Second, to what extent can organizations recover from the negative impacts of ethical failure? More specifically, is it possible for organizations that fail in their ethical responsibilities to recover such that they are paradoxically “better-off” than their counterparts that never failed in the first place? To explore these issues I review, integrate and draw upon the ethical decision-making and service failure recovery literatures for theoretical support. Empirical testing included two studies. The first was a field study using survey data acquired from the Ethics Resource Center (ERC) in which over 29,000 participants were asked about their perceptions of ethics at work. Second, a supplemental field study was conducted in which 100 employees rated the characteristics of unethical acts (e.g. severity). Results revealed a negative direct effect of severity and controllability of the OUB on perceptions of organizational ethicality and a negative direct effect of controllability of the OUB on organizational satisfaction. Ethical context moderated the relationship between OUB controllability and perceived organizational ethicality. Partial support was found for the moderating effects of ethical context on the relationship between OUB severity and perceived organizational ethicality. Results also supported an ethical failure recovery
Chemical Composition and Anti-Inflammatory, Cytotoxic and Antioxidant Activities of Essential Oil from Leaves of Mentha piperita Grown in China

The chemical composition, anti-inflammatory, cytotoxic and antioxidant activities of essential oil from leaves of Mentha piperita (MEO) grown in China were investigated. Using GC-MS analysis, the chemical composition of MEO was characterized, showing that it was mainly composed of menthol, menthone and menthy acetate. MEO exhibited potent anti-inflammatory activities in a croton oil-induced mouse ear edema model. It could also effectively inhibit nitric oxide (NO) and prostaglandin E2 (PGE2) production in lipopolysaccharide (LPS)-activated RAW 264.7 macrophages. The cytotoxic effect was assessed against four human cancer cells. MEO was found to be significantly active against human lung carcinoma SPC-A1, human leukemia K562 and human gastric cancer SGC-7901 cells, with an IC50 value of 10.89, 16.16 and 38.76 µg/ml, respectively. In addition, MEO had moderate antioxidant activity. The results of this study may provide an experimental basis for further systematic research, rational development and clinical utilization of peppermint resources.
Beyond Gist

Research on scene categorization generally concentrates on gist processing, particularly the speed and minimal features with which the “story” of a scene can be extracted. However, this focus has led to a paucity of research into how scenes are categorized at specific hierarchical levels (e.g., a scene could be a road or more specifically a highway); consequently, research has disregarded a potential diagnostically driven feedback process. We presented participants with scenes that were low-pass filtered so only their gist was revealed, while a gaze-contingent window provided the fovea with full-resolution details. By recording where in a scene participants fixated prior to making a basic- or subordinate-level judgment, we identified the scene information accrued when participants made either categorization. We observed a feedback process, dependent on categorization level, that systematically accrues sufficient and detailed diagnostic information from the same scene. Our results demonstrate that during scene processing, a diagnostically driven bidirectional interplay between top-down and bottom-up information facilitates relevant category processing.
Hygienic behaviour in Brazilian stingless bees

ABSTRACT Social insects have many defence mechanisms against pests and pathogens. One of these is hygienic behaviour, which has been studied in detail in the honey bee, Apis mellifera. Hygienic honey bee workers remove dead and diseased larvae and pupae from sealed brood cells, thereby reducing disease transfer within the colony. Stingless bees, Meliponini, also rear broods in sealed cells. We investigated hygienic behaviour in three species of Brazilian stingless bees (Melipona scutellaris, Scaptotrigona depilis, Tetragonisca angustula) in response to freeze-killed brood. All three species had high mean levels of freeze-killed brood removal after 48 h ∼99% in M. scutellaris, 80% in S. depilis and 62% in T. angustula (N=8 colonies per species; three trials per colony). These levels are greater than in unselected honey bee populations, ∼46%. In S. depilis there was also considerable intercolony variation, ranging from 27% to 100% removal after 2 days. Interestingly, in the S. depilis colony with the slowest removal of freeze-killed brood, 15% of the adult bees emerging from their cells had shrivelled wings indicating a disease or disorder, which is as yet unidentified. Although the gross symptoms resembled the effects of deformed wing virus in the honey bee, this virus was not detected in the samples. When brood comb from the diseased colony was introduced to the other S. depilis colonies, there was a significant negative correlation between freeze-killed brood removal and the emergence of deformed worker bees (P=0.001), and a positive correlation with the cleaning out of brood cells (P=0.0008). This shows that the more hygienic colonies were detecting and removing unhealthy brood prior to adult emergence. Our results indicate that hygienic behaviour may play an important role in colony health in stingless bees. The low levels of disease normally seen in stingless bees may be because they have effective mechanisms of disease management, not because they lack diseases. Summary: Hygienic behaviour such as the removal of dead and diseased larvae and pupae has an important role in colony health in stingless bees, and it is greater than in unselected honey bee populations
Impairments of movement initiation and execution in unilateral neglect. Directional hypokinesia and bradykinesia.

Patients with unilateral neglect may exhibit slowness in the initiation of contralesionally directed movements in peripersonal space (directional hypokinesia). The present study used a sequential movement task to characterize any such impairment in a group of 24 patients with right hemisphere lesions, 18 of whom had left neglect. A further five patients with left hemisphere lesions, one of whom had right neglect, were also tested. We measured movement initiation and execution times for leftward and rightward movements in either hemispace and across the body midline. Most left neglect patients, particularly those with lesions involving posterior cortex, showed directional hypokinesia. Left neglect patients with anterior and/or subcortical lesions also showed directional bradykinesia, i.e. a slowing in the execution phase of contralesionally directed movements. This impairment occurred regardless of the spatial location of the apparatus and was exacerbated as patients moved closer to their neglected side. The patient with right neglect showed directional hypokinesia but not directional bradykinesia. Right hemisphere and left hemisphere lesion patients without neglect performed in a manner comparable to controls, who did not exhibit directional hypokinesia or directional bradykinesia. These results suggest that directional hypokinesia is associated with both left hemisphere and right hemisphere damage, but only in the context of unilateral neglect. Moreover, the site of hemispheric lesion may determine the temporal characteristics of movement impairments in neglect. Damage to posterior cortex produces deficits in detecting contralesional targets and initiating movements toward them, while damage to anterior or subcortical structures may disrupt the internal representation of an intended trajectory.
Health problems and psychosocial work environment as predictors of long term sickness absence in employees who visited the occupational physician and/or general practitioner in relation to work: a prospective study

Aims: To determine whether psychosocial work environment and indicators of health problems are prospectively related to incident long term sickness absence in employees who visited the occupational physician (OP) and/or general practitioner (GP) in relation to work. Methods: The baseline measurement (May 1998) of the Maastricht Cohort Study, a prospective cohort study among 45 companies and organisations, was used to select employees at work who indicated having visited the OP and/or GP in relation to work. Self report questionnaires were used to measure indicators of health problems (presence of at least one long term disease, likeliness of having a mental illness, fatigue) and psychosocial work environment (job demands, decision latitude, social support, job satisfaction) as predictors of subsequent sickness absence. Sickness absence data regarding total numbers of sickness absence days were obtained from the companies and occupational health services during an 18 month period (between 1 July 1998 and 31 December 1999). Complete data were available from 1271 employees. Results: After adjustment for demographics and the other predictors, presence of at least one long term disease (OR 2.36; 95% CI 1.29 to 4.29) and lower level of decision latitude (OR 1.69; 95% CI 1.22 to 2.38) were the strongest predictors for sickness absence of at least one month. A higher likelihood of having a mental illness, a higher level of fatigue, a lower level of social support at work, and low job satisfaction were also significant predictors for long term sickness absence, but their effect was less strong. Conclusion: In detecting employees at work but at risk for long term sickness absence, OPs and GPs should take into account not only influence of the psychosocial work environment in general and level of decision latitude in particular, but also influence of indicators of health problems, especially in the form of long term diseases.