Miracle-dz/UniFAR-FTUs huggingface dataset:
Lifecourse predictors of adult respiratory function: results from the Newcastle Thousand Families Study

Background: Impaired development in utero is suggested to increase the risk of poor respiratory health in adulthood, although a consensus has not been reached. A possible explanation for discrepancies between previous studies is inconsistent controlling for potential confounding factors, particularly childhood infections. Also, little is known regarding the relative importance of factors operating at different stages of the lifecourse. We have used detailed longitudinal data from the Newcastle Thousand Families cohort to assess the impact of birth weight, and various other factors acting throughout the lifecourse, on predicting forced expiratory volume in 1 s (FEV1). Methods: Detailed information was collected prospectively during childhood, including birth weight, childhood infections and socioeconomic circumstances. At age 49–51 years, 412 study members attended for clinical examination and measurement of FEV1. These data were analysed in relation to a range of factors from across the lifecourse using linear regression models. Results: After adjustment for all other significant variables, increasing birth weight, standardised for sex and gestational age (p = 0.011), being breast fed for more than 4 weeks (p = 0.017), less frequent childhood lower respiratory tract infections (LRTI) (p = 0.015), non- smoking (p<0.001), lower body fat percentage (p = 0.010), male sex (p<0.001), no history of asthma (p = 0.013) and greater adult height (p<0.001) were all independently associated with higher adult FEV1. Conclusion: Adult lung function is influenced by numerous factors during an individual’s lifetime, acting both directly and indirectly throughout the lifecourse. As expected, sex, height and smoking were the most important predictors of FEV1, but birth weight, breast feeding and childhood LRTIs also contributed significantly.
Approximating optimal multicast trees in wireless multihop networks

We study the problem of computing minimal cost multicast trees in multi-hop wireless mesh networks. This problem is known as the Steiner tree problem, and it has been widely studied in fixed networks. However, we show in this paper that in multi-hop wireless mesh networks, a Steiner tree is no longer offering the lowest bandwidth consumption. So, we re-formulate the problem in terms of minimizing the number of transmissions. We show that the new problem is also NP-complete and propose heuristics to approximate such trees. Our simulations results show that the proposed heuristics offer a lower cost than Steiner trees over a variety of scenarios.
Early goal-directed therapy: Sorting through confusion

435 ProCESS trial, as stated by the authors, “all other care was consistent with the Surviving Sepsis Guidelines. ”[6] Taken together, all of these factors contribute to the accuracy of the point, made by Dhooria and Agarwal, that the “usual care” group in all three recent RCTs was delivered by “a very experienced physician population” which may not be the case in the “real world” in which sicker patients are cared for by less experienced physicians who are not operating under the rigor of a randomized, controlled trial. Thus, population severity, administration of fluids prior to randomization, the overall mortality rate, and the physicians providing care provoke concerns about comparing these three trials to the original Rivers study. [5]
High prevalence of hepatitis C virus infection and predominance of genotype 4 in rural gabon

Hepatitis C (HCV) molecular epidemiology is documented poorly in central African countries. In response to this, a population‐based study of 319 consenting adults resident in a remote village of Gabon was undertaken (mean age: 38 years; age range: 13–85+; sex ratio: 0.74). Screening for anti‐HCV antibodies was performed using ELISA and recombinant immunoblot assay. Seropositive samples were assessed further with viral load and genotyping techniques. Sixty‐six (20.7%) individuals were HCV seropositive. Viral loads ranged from 600 to 24.9 million IU/ml (median: 372,500). Seroprevalence and viral loads increased significantly with age (P < 10−5 and P < 0.003, respectively). HCV sequences of the 5′UTR genome region were obtained from 60 (90.9%) samples and NS5B region sequences were obtained from 22 (36.6%) samples. All strains belonged to subtypes of genotype 4: 4e (72.7%), 4c (13.6%), 4p (4.5%), 4r (4.5%) and one unclassified genotype 4 strain. Evolutionary analysis of the subtype 4e sequences indicates a period of raised transmission during the early twentieth century. J. Med. Virol. 80:1581–1587, 2008. © 2008 Wiley‐Liss, Inc.
Contour-based object tracking with occlusion handling in video acquired using mobile cameras

We propose a tracking method which tracks the complete object regions, adapts to changing visual features, and handles occlusions. Tracking is achieved by evolving the contour from frame to frame by minimizing some energy functional evaluated in the contour vicinity defined by a band. Our approach has two major components related to the visual features and the object shape. Visual features (color, texture) are modeled by semiparametric models and are fused using independent opinion polling. Shape priors consist of shape level sets and are used to recover the missing object regions during occlusion. We demonstrate the performance of our method in real sequences with and without object occlusions.
A nomogram for predicting the risk of neck node metastasis in pathologically node-negative oral cavity carcinoma.

OBJECTIVE To generate a nomogram for predicting the risk of neck node metastasis in pathologically node-negative patients using a combination of variables comprising of protein expression, ultrastructural alterations and clinicopathological parameters. MATERIALS AND METHODS Surgically removed oral tumours (n = 103) were analysed for the expression of desmosomal and hemidesmosomal assembly proteins by immunohistochemistry and ultrastructural alterations by transmission electron microscopy (TEM). Protein expression, ultrastructural alterations and clinicopathological variables were used to construct nomogram from the training set in 75 patients. Clinical utility of the nomogram was validated in a discrete set of 28 patients. RESULTS Univariate and multivariate analyses were performed on the training set, and obtained significant variables comprising of integrin β4 expression (p = .027), number of hemidesmosomes (p = .027)/desmosomes (p = .046), tumour differentiation grade (p = .033) and tumour thickness (p = .024) were used for construction of the nomogram. The area under the curve was calculated for both training 0.821 (95% CI 0.725-0.918) and validation sets 0.880 (95% CI 0.743-1.000). The nomogram demonstrated a predictive accuracy of 73.3% and 78.6% with the sensitivity of 81.4% and 83.3% in the training and validation sets, respectively. CONCLUSIONS The nomogram constructed on postsurgical tumour samples will be a value addition to histopathology for the detection of neck node metastasis in pathologically node-negative patients.
Differences in Cognitive Processes Among Handicapped and Average Children

This study investigated the ability of LD, slow learning and average children to adapt learning strategies to different stimulus demands. Small group learning situations were used to encourage subjects to verbalize their strategies to each other and to create the expectation that, since other children have different approaches, the process of strategy selection is critical. Findings demonstrated a distinctly different pattern of strategy usage associated with performance in each of the three diagnostic categories as well as an ability in all three groups to differentiate among stimulus demands.
Effects of Chemotherapy on the Cytogenetic Constitution of Wilms' Tumor

The management of Wilms' tumors consists of a combination of surgery, chemotherapy, and possibly radiotherapy. To date, chemotherapy is being risk stratified according to histologic subtype and stage. Although the cytogenetic characteristics of Wilms' tumors are well established, the cytogenetic effects related to chemotherapy are widely unknown. We herein report on comparative genomic hybridization findings in 41 primary Wilms' tumors of blastemal type, of which 19 had received preoperative chemotherapy (PCT group) and 22 did not (non-PCT group). Overall, imbalances could be detected in 32 tumors, with +1q (17 cases), +7q (10 cases), +7p (6 cases), and −7p (6 cases) as the most common changes. Among these, +7q and −7p were both significantly associated with metastatic disease at the time of surgery (P = 0.002 and 0.007, respectively), and +7q was also associated with higher stage (stages III + IV; P = 0.003). There were significant differences in the cytogenetic constitution of tumors between the two treatment groups. As a trend, tumors in the preoperative-chemotheraphy group had fewer changes (mean, 2.7) than those in the non-preoperative-chemotheraphy group (mean, 3.8), and the frequencies of imbalances at 7p or +7q, respectively, were significantly lower compared with tumors in the non-preoperative-chemotheraphy group (2 of 19 versus 10 of 22, P = 0.019; 1 of 19 versus 9 of 22, P = 0.011). In contrast, −1q was common in both the preop-CT group (10 of 19) and the non-preop-CT group (7 of 22). The results suggest that Wilms' tumor clones with +1q are not obliterated by preoperative chemotherapy, whereas cytogenetically more complex clones with +7q and/or imbalances at 7p seem more responsive and are more likely to be eliminated by chemotherapeutic treatment.
Artificial agents learning human fairness

Recent advances in technology allow multi-agent systems to be deployed in cooperation with or as a service for humans. Typically, those systems are designed assuming individually rational agents, according to the principles of classical game theory. However, research in the field of behavioral economics has shown that humans are not purely self-interested: they strongly care about fairness. Therefore, multi-agent systems that fail to take fairness into account, may not be sufficiently aligned with human expectations and may not reach intended goals. In this paper, we present a computational model for achieving fairness in adaptive multi-agent systems. The model uses a combination of Continuous Action Learning Automata and the Homo Egualis utility function. The novel contribution of our work is that this function is used in an explicit, computational manner. We show that results obtained by agents using this model are compatible with experimental and analytical results on human fairness, obtained in the field of behavioral economics.
Non-redundant coding for deep sub-micron address buses

A coding technique for deep submicron address buses with interwire capacitances dominating the wire-to-ground capacitances is presented. This code is similar to Gray codes, in the sense that it defines an ordering of the binary space, such that adjacent codewords dissipate little energy when sent consecutively. The ordering is shown to be close to optimal, as to the energy dissipation, when sending the whole sequence in order. A circuit diagram realizing the coder is presented, using only n-1 two-input gates, where n is the bus width. Simulations show an improvement in energy dissipation of more than 50% over an uncoded bus in several cases, depending on the data being coded.
A Study on the Evolution of Fuzzy Sets Based Research in Spain Based on Bibliometric Maps 1

In this paper, a bibliometric study of the fuzzy sets theory fleld in Spain is presented. Bibliometric maps showing the associations between the main concepts in the fleld are provided for the periods 1978-1992, 1993- 1997, 1998-2002 and 2003-2007. The maps provide insight into the structure of the fuzzy sets theory fleld in fuzzy Spanish community. They visualize the division of the fleld into several subflelds, and they indicate the rela- tions between these subflelds. The maps are created by the co-word analysis. In this paper, a bibliometric study of the fuzzy sets theory in Spain is presented. It is done by means of bibliometric maps that show the associations between the main concepts studied in Spanish fuzzy commu- nity. The maps provide insight into the structure of the fuzzy sets theory fleld, visualize the division of the fleld into several subflelds and indicate the rela- tions between these subflelds. More concretely, we will study the Spanish fuzzy sets theory fleld using the con- cept of longitudinal mapping, introduced by Garfleld (5). In longitudinal mapping, a series of chronologically sequential maps can be used to detect the advances of scientiflc knowledge and the evolution of the fleld over the last years. While maps of current data alone can- not predict where research will go, longitudinal maps can be useful indicators in the hands of informed an- alysts and domain experts. Analysts and domain ex- perts can use longitudinal maps to forecast emerging trends for a subject domain. Since domain visualiza- tions typically reference key works in a fleld, they are a good tool to enable the novice to become instantly familiar with a fleld through easy identiflcation of key topics and theirs relationships. The bibliometric maps are created by the co-word analysis (2, 9).
The Effect of Automatic Tokenization, Vocalization, Stemming, and POS Tagging on Arabic Dependency Parsing

We use an automatic pipeline of word tokenization, stemming, POS tagging, and vocalization to perform real-world Arabic dependency parsing. In spite of the high accuracy on the modules, the very few errors in tokenization, which reaches an accuracy of 99.34%, lead to a drop of more than 10% in parsing, indicating that no high quality dependency parsing of Arabic, and possibly other morphologically rich languages, can be reached without (semi-)perfect tokenization. The other module components, stemming, vocalization, and part of speech tagging, do not have the same profound effect on the dependency parsing process.
Maximising the impact of remittances on development outcomes: the case of SADC

This paper investigates how remittances from South Africa to 10 countries in the Southern African Development Cooperation (SADC) region could be directed through formal channels to impact on development outcomes. Using annual data from 1994 to 2008, two-step system GMM by Arellano and Bover (1995) and seemingly unrelated regressions by Zellner (1962), we find that when spatial and individual effects are controlled for, different factors drive remittances to the SADC countries in the panel. Whiles altruism prevails in some, self interest prevails in others. This implies that the optimal policy pathway aimed at mitigating the use of informal channels or maximising the impact of remittances on development outcomes would differ between countries. Overall, the level of financial deepening in the home country is also crucial to the use of formal channels and the ability of countries to harness remittances for development purposes.
Prdm1 acts downstream of a sequential RA, Wnt and Fgf signaling cascade during zebrafish forelimb induction

Vertebrate limb induction is triggered in the lateral plate mesoderm (LPM) by a cascade of signaling events originating in the axial mesoderm. While it is known that Fgf, Wnt and retinoic acid (RA) signals are involved in this cascade, their precise regulatory hierarchy has not been determined in any species. tbx5 is the earliest gene expressed in the limb bud mesenchyme. Recently, another transcription factor, Prdm1, has been shown to be crucial for zebrafish forelimb development. Here, we show that Prdm1 is downstream of RA, Wnt2b and Tbx5 activity. We find that RA activity, but not Fgf signaling, is necessary for wnt2b expression. Fgf signaling is required for prdm1 expression in the fin bud, but is not necessary for the initiation of tbx5 expression. We propose a model in which RA signaling from the somitic mesoderm leads to activation of wnt2b expression in the intermediate mesoderm, which then signals to the LPM to trigger tbx5 expression. tbx5 is required for Fgf signaling in the limb bud leading to activation of prdm1 expression, which in turn is required for downstream activation of fgf10 expression.
Molecular and spatial epidemiology of human campylobacteriosis: source association and genotype-related risk factors

SUMMARY The epidemiology of human campylobacteriosis is complex but in recent years understanding of this disease has advanced considerably. Despite being a major public health concern in many countries, the presence of multiple hosts, genotypes and transmission pathways has made it difficult to identify and quantify the determinants of human infection and disease. This has delayed the development of successful intervention programmes for this disease in many countries including New Zealand, a country with a comparatively high, yet until recently poorly understood, rate of notified disease. This study investigated the epidemiology of Campylobacter jejuni at the genotype-level over a 3-year period between 2005 and 2008 using multilocus sequence typing. By combining epidemiological surveillance and population genetics, a dominant, internationally rare strain of C. jejuni (ST474) was identified, and most human cases (65·7%) were found to be caused by only seven different genotypes. Source association of genotypes was used to identify risk factors at the genotype-level through multivariable logistic regression and a spatial model. Poultry-associated cases were more likely to be found in urban areas compared to rural areas. In particular young children in rural areas had a higher risk of infection with ruminant strains than their urban counterparts. These findings provide important information for the implementation of pathway-specific control strategies.
Physical Proximity and Spreading in Dynamic Social Networks

Most infectious diseases spread on a dynamic network of human interactions. Recent studies of social dynamics have provided evidence that spreading patterns may depend strongly on detailed micro-dynamics of the social system. We have recorded every single interaction within a large population, mapping out---for the first time at scale---the complete proximity network for a densely-connected system. Here we show the striking impact of interaction-distance on the network structure and dynamics of spreading processes. We create networks supporting close (intimate network, up to ~1m) and longer distance (ambient network, up to ~10m) modes of transmission. The intimate network is fragmented, with weak ties bridging densely-connected neighborhoods, whereas the ambient network supports spread driven by random contacts between strangers. While there is no trivial mapping from the micro-dynamics of proximity networks to empirical epidemics, these networks provide a telling approximation of droplet and airborne modes of pathogen spreading. The dramatic difference in outbreak dynamics has implications for public policy and methodology of data collection and modeling.
A Gestational High Protein Diet Affects the Abundance of Muscle Transcripts Related to Cell Cycle Regulation throughout Development in Porcine Progeny

Background In various animal models pregnancy diets have been shown to affect offspring phenotype. Indeed, the underlying programming of development is associated with modulations in birth weight, body composition, and continual diet-dependent modifications of offspring metabolism until adulthood, producing the hypothesis that the offspring's transcriptome is permanently altered depending on maternal diet. Methodology/Principal Findings To assess alterations of the offspring's transcriptome due to gestational protein supply, German Landrace sows were fed isoenergetic diets containing protein levels of either 30% (high protein - HP) or 12% (adequate protein - AP) throughout their pregnancy. Offspring muscle tissue (M. longissimus dorsi) was collected at 94 days post conception (dpc), and 1, 28, and 188 days post natum (dpn) for use with Affymetrix GeneChip Porcine Genome Arrays and subsequent statistical and Ingenuity pathway analyses. Numerous transcripts were found to have altered abundance at 94 dpc and 1 dpn; at 28 dpn no transcripts were altered, and at 188 dpn only a few transcripts showed a different abundance between diet groups. However, when assessing transcriptional changes across developmental time points, marked differences were obvious among the dietary groups. Depending on the gestational dietary exposure, short- and long-term effects were observed for mRNA expression of genes related to cell cycle regulation, energy metabolism, growth factor signaling pathways, and nucleic acid metabolism. In particular, the abundance of transcripts related to cell cycle remained divergent among the groups during development. Conclusion Expression analysis indicates that maternal protein supply induced programming of the offspring's genome; early postnatal compensation of the slight growth retardation obvious at birth in HP piglets resulted, as did a permanently different developmental alteration and responsiveness to the common environment of the transcriptome. The transcriptome modulations are interpreted as the molecular equivalent of developmental plasticity of the offspring that necessitates adaptation and maintenance of the organismal phenotype.
Quantifying and Comparing Bipolar Versus Freehand Flake Morphologies, Production Currencies, and Reduction Energetics During Lithic Miniaturization

ABSTRACT Recognized by archaeologists for over a century, and practiced by hominins in nearly every archaeological context in which flaked stone is used, bipolar technology involves the coordination of at least three components (hammer, anvil, and core). Archaeologists are increasingly aware of the variability within bipolar reduction, such that it can hardly be considered a single unified reduction strategy. Our experiments investigate the role of axial bipolar reduction versus freehand reduction as strategies for lithic miniaturization on flint. The results provide clear, probabilistic, and quantifiable methods for identifying bipolar reduction in archaeological assemblages. They also show the time and energetic benefits of bipolar reduction over freehand reduction in contexts involving small, elongated flake production. Our results have wide applicability for interpreting archaeological assemblages across Africa, Europe, North America, and Australia.
Site-Specific Cassette Exchange Systems in the Aedes aegypti Mosquito and the Plutella xylostella Moth

Genetically engineered insects are being evaluated as potential tools to decrease the economic and public health burden of mosquitoes and agricultural pest insects. Here we describe a new tool for the reliable and targeted genome manipulation of pest insects for research and field release using recombinase mediated cassette exchange (RMCE) mechanisms. We successfully demonstrated the established ΦC31-RMCE method in the yellow fever mosquito, Aedes aegypti, which is the first report of RMCE in mosquitoes. A new variant of this RMCE system, called iRMCE, combines the ΦC31-att integration system and Cre or FLP-mediated excision to remove extraneous sequences introduced as part of the site-specific integration process. Complete iRMCE was achieved in two important insect pests, Aedes aegypti and the diamondback moth, Plutella xylostella, demonstrating the transferability of the system across a wide phylogenetic range of insect pests.