Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent approaches to the prioritization of candidate disease genes

Many efforts are still devoted to the discovery of genes involved with specific phenotypes, in particular, diseases. High‐throughput techniques are thus applied frequently to detect dozens or even hundreds of candidate genes. However, the experimental validation of many candidates is often an expensive and time‐consuming task. Therefore, a great variety of computational approaches has been developed to support the identification of the most promising candidates for follow‐up studies. The biomedical knowledge already available about the disease of interest and related genes is commonly exploited to find new gene–disease associations and to prioritize candidates. In this review, we highlight recent methodological advances in this research field of candidate gene prioritization. We focus on approaches that use network information and integrate heterogeneous data sources. Furthermore, we discuss current benchmarking procedures for evaluating and comparing different prioritization methods. WIREs Syst Biol Med 2012. doi: 10.1002/wsbm.1177
The Sit-and-Wait Hypothesis in Bacterial Pathogens: A Theoretical Study of Durability and Virulence

The intriguing sit-and-wait hypothesis predicts that bacterial durability in the external environment is positively correlated with their virulence. Since its first proposal in 1987, the hypothesis has been spurring debates in terms of its validity in the field of bacterial virulence. As a special case of the vector-borne transmission versus virulence tradeoff, where vector is now replaced by environmental longevity, there are only sporadic studies over the last three decades showing that environmental durability is possibly linked with virulence. However, no systematic study of these works is currently available and epidemiological analysis has not been updated for the sit-and-wait hypothesis since the publication of Walther and Ewald’s (2004) review. In this article, we put experimental evidence, epidemiological data and theoretical analysis together to support the sit-and-wait hypothesis. According to the epidemiological data in terms of gain and loss of virulence (+/-) and durability (+/-) phenotypes, we classify bacteria into four groups, which are: sit-and-wait pathogens (++), vector-borne pathogens (+-), obligate-intracellular bacteria (--), and free-living bacteria (-+). After that, we dive into the abundant bacterial proteomic data with the assistance of bioinformatics techniques in order to investigate the two factors at molecular level thanks to the fast development of high-throughput sequencing technology. Sequences of durability-related genes sourced from Gene Ontology and UniProt databases and virulence factors collected from Virulence Factor Database are used to search 20 corresponding bacterial proteomes in batch mode for homologous sequences via the HMMER software package. Statistical analysis only identified a modest, and not statistically significant correlation between mortality and survival time for eight non-vector-borne bacteria with sit-and-wait potentials. Meanwhile, through between-group comparisons, bacteria with higher host-mortality are significantly more durable in the external environment. The results of bioinformatics analysis correspond well with epidemiological data, that is, non-vector-borne pathogens with sit-and-wait potentials have higher number of virulence and durability genes compared with other bacterial groups. However, the conclusions are constrained by the relatively small bacterial sample size and non-standardized experimental data.
Studying Teachers' Lives as an Educational Issue: Autobiographical Reflections from a Scholarly Journey.

What does it mean to live a teacher’s life? What does it mean to be a teacher, to become a teacher, to stay in teaching, or to leave the profession? Why are teachers doing what they are doing the way they are doing it? These questions have fascinated me throughout my academic career as a researcher as well as in my teaching and my work as a teacher educator, an in-service trainer, and a facilitator of school improvement processes. In my address, I will look back on my career and the ways in which I have tried to understand teachers’ work lives. These autobiographical reflections of my own academic development are the story of an ongoing effort to grasp and unravel the lives of teachers through appropriate conceptualization, empirical grounding, and theory building, which eventually constitute the best possible basis to design interventions and practices. It was and continues to be a
Epidural analgesia and breastfeeding: a randomised controlled trial of epidural techniques with and without fentanyl and a non‐epidural comparison group

We compared breastfeeding initiation and duration in 1054 nulliaparae randomised to bupivacaine Control epidural, Combined Spinal Epidural or Low Dose Infusion and 351 matched non‐epidural comparisons. Women were interviewed after delivery and completed a postal questionnaire at 12 months. Regression analysis determined factors which independently predicted breastfeeding initiation. Breastfeeding duration was subjected to Kaplan–Meier analysis. A similar proportion of women in each epidural group initiated breastfeeding. Women with no epidural did not report a higher initiation rate relative to epidural groups and those who received pethidine reported a lower initiation rate than control epidural (p = 0.002). Older age groups (p < 0.001) and non‐white ethnicity (p < 0.026) were predictive of breastfeeding. Epidural fentanyl dose, delivery mode and trial group were not predictive. Mean duration for breastfeeding was similar across epidural groups (Control 13.3, Combined Spinal Epidural 15.5, Low Dose Infusion 15.0 weeks). Our data do not support an effect of epidural fentanyl on breastfeeding initiation.
Nanoscale void nucleation and growth and crack tip stress evolution ahead of a growing crack in a single crystal

A constrained three-dimensional atomistic model of a cracked aluminum single crystal has been employed to investigate the growth behavior of a nanoscale crack in a single crystal using molecular dynamics simulations with the EAM potential. This study is focused on the stress field around the crack tip and its evolution during fast crack growth. Simulation results of the observed nanoscale fracture behavior are presented in terms of atomistic stresses. Major findings from the simulation results are the following: (a) crack growth is in the form of void nucleation, growth and coalescence ahead of the crack tip, thus resembling that of ductile fracture at the continuum scale; (b) void nucleation occurs at a certain distance ahead of the current crack tip or the forward edge of the leading void ahead of the crack tip; (c) just before void nucleation the mean atomic stress (or equivalently its ratio to the von Mises effective stress, which is called the stress constraint or triaxiality) has a high concentration at the site of void nucleation; and (d) the stress field ahead of the current crack tip or the forward edge of the leading void is more or less self-similar (so that the forward edge of the leading void can be viewed as the effective crack tip).
Seasonal patterns of mortality in relation to social factors

Background New Zealand is a temperate country with substantial excess winter mortality. We investigated whether this excess winter mortality varies with social factors. Methods Records from New Zealand censuses in 1981, 1986, 1991, 1996 and 2001 were each anonymously and probabilistically linked to 3 years of subsequent mortality data creating five cohort studies of the New Zealand adult population (age 30–74 years at census) each with 3 years' follow-up. Logistic regression analysis was used to model the risk of dying in winter compared to summer with winter deaths classified ‘1’ and summer deaths ‘0’. There were 75 138 eligible mortality records with complete data on social variables recorded for 58 683 (78%). Results Adjusting for age, sex, census year, ethnicity and tenure, those in the lowest tertile of income were at increased risk of winter death compared to those in the highest tertile: OR 1.13 (95% CI 1.08 to 1.19). Compared to home owners, people living in rented accommodation were at greater risk of winter death: OR 1.05 (95% CI 1.01 to 1.10). Urban dwellers were also at significantly increased risk. The strongest associations were seen for infectious diseases. Conclusions There was an increased risk of dying in winter for most New Zealanders, but more so among low-income people, those living in rented accommodation and those living in cities. Exact causal mechanisms are not known but possibly include correlated poorer health status, low indoor temperatures and household crowding.
Acute Peritoneal Dialysis in the Newborn Period: A 7-Year Single-Center Experience at Tertiary Neonatal Intensive Care Unit in Turkey

Abstract Objective To evaluate the underlying causes and outcomes of neonates who underwent acute peritoneal dialysis (APD). Study Design This report describes a 7-year experience with APD in 77 neonates. Results Underlying causes requiring APD were acute tubular necrosis (ATN; n = 53), inborn error of metabolism (n = 18), bilateral renal vein thrombosis (n = 3), obstructive uropathy (n = 2; posterior urethral valve and neurogenic bladder), and bilateral renal artery thrombosis (n = 1). Fifteen of the 53 patients developed post–cardiac surgery ATN. The mean dialysis duration was 6.2 ± 10.7 days (range 1 to 90 days). Complications of procedure were hyperglycemia (n = 35), leaking of dialysate (n = 13), peritonitis (n = 10), catheter obstruction (n = 3), bleeding when inserting the catheter (n = 3), exit site infection (n = 2), and bowel perforation (n = 1). There were 57 deaths (74%) in this high-risk group due to underling causes. Of the 20 survivors, 16 patients showed a full renal recovery, but mild chronic renal failure developed in 1 patient and proteinuria with/without hypertension in 3 patients. Conclusion Peritoneal dialysis is an effective means of renal replacement therapy in the neonatal period in the management of metabolic disturbances as well as renal failure. Although major complications of procedure are not so common, these patients have high mortality rates due to the serious nature of the primary causes.
Selection and Validation of Reference Genes for qRT-PCR Expression Analysis of Candidate Genes Involved in Olfactory Communication in the Butterfly Bicyclus anynana

Real-time quantitative reverse transcription PCR (qRT-PCR) is a technique widely used to quantify the transcriptional expression level of candidate genes. qRT-PCR requires the selection of one or several suitable reference genes, whose expression profiles remain stable across conditions, to normalize the qRT-PCR expression profiles of candidate genes. Although several butterfly species (Lepidoptera) have become important models in molecular evolutionary ecology, so far no study aimed at identifying reference genes for accurate data normalization for any butterfly is available. The African bush brown butterfly Bicyclus anynana has drawn considerable attention owing to its suitability as a model for evolutionary ecology, and we here provide a maiden extensive study to identify suitable reference gene in this species. We monitored the expression profile of twelve reference genes: eEF-1α, FK506, UBQL40, RpS8, RpS18, HSP, GAPDH, VATPase, ACT3, TBP, eIF2 and G6PD. We tested the stability of their expression profiles in three different tissues (wings, brains, antennae), two developmental stages (pupal and adult) and two sexes (male and female), all of which were subjected to two food treatments (food stress and control feeding ad libitum). The expression stability and ranking of twelve reference genes was assessed using two algorithm-based methods, NormFinder and geNorm. Both methods identified RpS8 as the best suitable reference gene for expression data normalization. We also showed that the use of two reference genes is sufficient to effectively normalize the qRT-PCR data under varying tissues and experimental conditions that we used in B. anynana. Finally, we tested the effect of choosing reference genes with different stability on the normalization of the transcript abundance of a candidate gene involved in olfactory communication in B. anynana, the Fatty Acyl Reductase 2, and we confirmed that using an unstable reference gene can drastically alter the expression profile of the target candidate genes.
Do Minimum Wages Lead to Job Losses? Evidence from OECD Countries on Low-Skilled and Youth Employment

The author investigates effects of minimum wage rates on low-skilled, female low-skilled, and youth employment. The sample consists of 19 Organisation for Economic Co-operation and Development (OECD) countries from 1997 to 2013 for low-skilled workers and from 1983 to 2013 for young workers. Six different static or dynamic estimation approaches are applied on different versions of the specifications, controlling for up to quadratic time trends. The author further investigates the effects over the long run and over the business cycle as well as the effects of high minimum wages and of institutional complementarities. The findings provide little evidence of substantial disemployment effects for low-skilled, female low-skilled, or young workers. The estimated employment elasticities are small and statistically indistinguishable from zero. The author then considers why his results on youth employment differ from those of Neumark and Wascher (2004), showing that they overstate precision and that small changes in their specifications lead to minimum wage effects close to zero.
Landscape dynamics in Mediterranean oak forests under global change: understanding the role of anthropogenic and environmental drivers across forest types

The Mediterranean region is projected to be extremely vulnerable to global change, which will affect the distribution of typical forest types such as native oak forests. However, our understanding of Mediterranean oak forest responses to future conditions is still very limited by the lack of knowledge on oak forest dynamics and species‐specific responses to multiple drivers. We compared the long‐term (1966–2006) forest persistence and land cover change among evergreen (cork oak and holm oak) and deciduous oak forests and evaluated the importance of anthropogenic and environmental drivers on observed changes for Portugal. We used National Forest Inventories to quantify the changes in oak forests and explored the drivers of change using multinomial logistic regression analysis and an information theoretical approach. We found distinct trends among oak forest types, reflecting the differences in oak economic value, protection status and management schemes: cork oak forests were the most persistent (62%), changing mostly to pines and eucalypt; holm oak forests were less persistent (53.2%), changing mostly to agriculture; and deciduous oak forests were the least persistent (45.7%), changing mostly to shrublands. Drivers of change had distinct importance across oak forest types, but drivers from anthropogenic origin (wildfires, population density, and land accessibility) were always among the most important. Climatic extremes were also important predictors of oak forest changes, namely extreme temperatures for evergreen oak forests and deficit of precipitation for deciduous oak forests. Our results indicate that under increasing human pressure and forecasted climate change, evergreen oak forests will continue declining and deciduous oak forests will be replaced by forests dominated by more xeric species. In the long run, multiple disturbances may change competitive dominance from oak forests to pyrophytic shrublands. A better understanding of forest dynamics and the inclusion of anthropogenic drivers on models of vegetation change will improve predicting the future of Mediterranean oak forests.
Testing Hypotheses for the Success of Different Conservation Strategies

Abstract: Evaluations of the success of different conservation strategies are still in their infancy. We used four different measures of project outcomes—ecological, economic, attitudinal, and behavioral—to test hypotheses derived from the assumptions that underlie contemporary conservation solutions. Our hypotheses concerned the effects of natural resource utilization, market integration, decentralization, and community homogeneity on project success. We reviewed the conservation and development literature and used a specific protocol to extract and code the information in a sample of papers. Although our results are by no means conclusive and suffer from the paucity of high‐quality data and independent monitoring (80% of the original sample of 124 projects provided inadequate information for use in this study), they show that permitted use of natural resources, market access, and greater community involvement in the conservation project are all important factors for a successful outcome. Without better monitoring schemes in place, it is still impossible to provide a systematic evaluation of how different strategies are best suited to different conservation challenges.
Correlation of Cigarette-Induced Increase in Serum Nicotine Levels with Arginine Vasopressin Concentrations in the Syndrome of Self-Induced Water Intoxication and Psychosis (SIWIP)

Ten patients [9 men and 1 woman; mean age 42.4 ± 8.5 (± SD) years] who were smokers and who suffered the complications of self-induced water intoxication and psychosis (SIWIP) (8 patients with schizophrenic disorders, 1 patient with manic-depressive illness, 1 patient with dementia) are reported. Each patient underwent serial determinations of parameters of water metabolism including plasma and urine osmolality and plasma arginine vasopressin (AVP). The syndrome of inappropriate antidiuresis (SIAD) was found in each patient. Because of the reported effect that cigarette smoking has on anti-diuresis, we correlated serum nicotine (NIC) levels with plasma and urine osmolality, AVP, and 24-hour urine volume (24°-UV). We found no relationship between NIC and plasma or urine osmolality, AVP, or 24°-UV. In the presence of SIWIP and SIAD, we infer the limbic-hypothalamic neurotransmitters in these psychotic patients are sufficiently powerful in stimulating both compulsive water drinking and inappropriate release of AVP so as to overshadow any effects that NIC may have on water metabolism.
Input-output analysis and growth theory

This thesis studies a theory for the amplification of technological improvement by the production network structure of the economy. The theory is motivated by the idea that, to the extent that inputs and outputs of industries form a chain, improvements are passed down the chain and accumulate multiplicatively. Under a simple model for technological improvement it is possible to compute the overall improvement factor for the general case where the production network has a complicated structure containing cycles. We call this the trophic depth by analogy with ecology. This leads to testable predictions about GDP growth and its variance. We analyse data for 40 countries and 35 industries from 1995 to 2009 and demonstrate that trophic depths are strongly correlated with economic growth. A regression of GDP growth of countries against their trophic depths has a highly statistically significant R-squared equal to 0.38, and when other standard explanatory variables are added to the regression, the trophic depth remains a robust and statistically significant contributor. We perform some statistical analysis to understand the evolution of trophic depths at different stage of the economic development. We identify two growth paths. Along the first growth path, countries are catching up frontier economies while along the second growth path countries are falling behind. This approach allows us to make some forecasts about the evolution of trophic depths and of the wealth of countries. This provides a comprehensive framework to understand the acceleration and deceleration of economic growth. Then, we study another type of technological progress that corresponds to the adoption of new goods in the production chain. This mechanism is related to the dynamic of the production network and for this purpose we perform a link prediction analysis to determine some key factors for new adoptions. Finally, we analyse the relation between stock return comovement and institutional preferences across stocks of various size. A growing literature highlights the role of investors' common asset holdings on market dynamics. While previous studies focused on large stocks we also include small stocks in the sample in order to acknowledge the shift in institutional preferences towards small stocks over the last decades. Moreover, we add the input-output linkages between firms from different industries to our set of explanatory variables.
Resveratrol nanoformulation for cancer prevention and therapy

Chemoprevention of human cancer(s) is a viable option for cancer control, especially when chemopreventive intervention is involved during the early stages of the carcinogenesis process. Naturally occurring bioactive food components, such as dietary polyphenols, have shown good antioxidant activity and other beneficial activities. In addition, compounds belonging to the polyphenolic chemical class may play promising roles in cancer prevention. Among them, the phytoalexin resveratrol has demonstrated antiproliferative effects, as well as the ability to inhibit initiation and promotion of induced cancer progression in a wide variety of tumor models. However, resveratrol, like other natural polyphenols, is an extremely photosensitive compound with low chemical stability and limited bioavailibility, which limit the therapeutic application of its beneficial effects. In this context, the development of innovative formulation strategies able to overcome physicochemical and pharmacokinetic limitations of this compound could be beneficial. This may be achieved via nanotechnology approaches utilizing suitable carriers that allow slow, sustained, and controlled release of the encapsulated agent. This review focuses on the recent developments of novel nanoformulations used to deliver sustained levels of resveratrol.
Binge ethanol exposure in adult rats causes necrotic cell death.

BACKGROUND Although alcoholics show neurodegeneration after decades of drinking, recent studies with an animal model of binge drinking have found corticolimbic damage after as few as four days. Neurodegeneration can occur through apoptotic or necrotic mechanisms. The goal of this research is to characterize the time course of binge ethanol-induced neurodegeneration and to identify apoptotic or necrotic characteristics of this neurodegeneration. METHODS Histologic methods (e.g., amino cupric silver staining, Fluoro-Jade B, hematoxylin and eosin, transmission electron microscopy) were used to quantify the time course of degeneration and to characterize the ultrastructural changes that occur with binge ethanol-induced neurodegeneration. RESULTS After 2 days of binge ethanol, significant damage was evident in the olfactory bulb. After 4 days of binge ethanol, there was significant damage in the agranular insular cortex, anterior piriform cortex, perirhinal cortex, lateral entorhinal cortex, and the temporal dentate gyrus. Ultrastructural examination revealed shrunken soma, vacuolated cytoplasm, pyknotic nucleus, and irregularly clumped chromatin consistent with dark cell degeneration, a form of necrotic neuronal death. CONCLUSIONS Binge drinking causes necrotic neurodegeneration after 2 days of exposure and increased damage after 4 days but does not increase during withdrawal. These studies indicate that binge drinking induced neurodegeneration is necrotic and occurs during ethanol intoxication and not as a result of ethanol withdrawal.