Miracle-dz/UniFAR-FTUs huggingface dataset:
The Bilingual Bioprogram : Evidence for Child Bilingualism in the Formation of Creoles

Studies concerning the emergence of creole languages are largely based on assumptions related to the monolingual speaker, with little discussion of the role that bilingualism may play in creole formation. For instance, the Language Bioprogram Hypothesis argues that creoles arise within one generation when children create a novel first language as a result of exposure to their immigrant parents' degenerate L2 (pidgin) speech. A contrasting view argues that creole grammar is manifested through a prolonged process carried out by adults whose unsuccessful attempts at second language acquisition converge to a new code over the span of several generations. Until recently, no method existed for reliably testing claims put forth in creole genesis proposals. By designing computergenerated "artificial societies," it becomes possible to reconstruct historical and linguistic contexts, with an eye towards better understanding the complex factors involved in language acquisition. To this end, the current work draws from recent psycholinguistic research on language development. Additionally, we employ historical records of sugarcane plantations in Surinam (Arends 1995, Bruyn 1995, Van den Berg 2000), using the emergence of the creole Sranan Tongo as a case study. Preliminary findings from three computer simulations suggest that under the scenarios tested, bilingual competence is a necessary, and indeed adequate, component for the formation of a creole grammar. Specifically, locally-born bilingual children over time appear to be the primary contributors in the emerging creole. The rest of the paper is organized as follows: Section 2 provides a brief overview of creole genesis and also sketches the recent theoretical formulations advanced with respect to language acquisition. We then focus on the internal workings of the computational model of the “artificial society” in Section 3, discussing in detail the linguistic and social elements encoded into the simulation. Next we profile the emergence of a real-world creole, using evidence from Sranan as a base. In Section 5, three computer simulations are described, comparing the results to Sranan data and to proposals in wellknown accounts where conditions for creole emergence may hinge on a) populations of children in the early plantation setting and b) the degree of language contact required between speakers of different grammars. The final sections of the paper offer some additional implications for bilingualism and ends with concluding remarks.
Automated Tuberculosis screening using image processing tools

We present a preliminary work as a proof of concept on how image processing algorithms can be applied to detect and diagnose Tuberculosis in microscopic images of sputum samples stained with the Ziehl-Neelsen method. 300 images were acquired at the Hospital Nacional Dos de Mayo and processed using edge detection and mathematical morphology to extract objects of interest. Bacilli are discriminated from these objects applying a classifier based on the Mahalanobis distance and using shape characteristics as features. Results show a specificity value over 90% which is close to previously reported attempts on samples processed with Auramine.
Design of arbitrary waveform generator based on SDRAM

To solve the problems of the difficulty to generate long period waveform, of the complicated operation and inconvenient control, a scheme that is based on the combination of large capacity storage and virtual instruments technique of arbitrary waveform generator (AWG), is proposed. The storage capacity has been raised up to 8M by utilizing Synchronous DRAM (SDRAM) as a waveform data memory; in the meantime, a friendly and easy control instrument interface is finished with the help of LabVIEW. Because of hard control of SDRAM, the FPGA is especially employed to solve the problem of SDRAM control and timing-logical control of the whole system; it not only improves data access speed but also enhances the whole system's integration capability, as well as anti-interference ability. The design of SDRAM controller and instrument interface is given in detail. Testing data of experimental prototype can meet the design targets. It has great practical value.
Notice of RetractionSilent Mutation Effects on Translation Efficiency in Human Cancer Genome

We analyzed translation efficiency changes of 2,437 silent substitutions in human cancers. We observed selections acting on silent sites in cancer genes to increase or decrease gene translation efficiency. By comparing the selection pressures in different cancer types, we found tissue specific translation efficiency changes of cancer synonymous substitutions. We also found that substitutions in oncogenes generally tended to increase the translation efficiency. On the contrary, substitutions in tumor suppressor genes had a tendency to decrease gene expression. The results we showed here shed lights on the importance of silent mutations in cancer, which will help us understand the genetic causes of cancer.
Targets of transcriptional regulation by two distinct type I receptors for transforming growth factor‐β in human umbilical vein endothelial cells

Transforming growth factor‐β (TGF‐β) plays a crucial role in vascular development and homeostasis by regulating many transcriptional targets. Activin receptor‐like kinase 5 (ALK‐5) is a TGF‐β type I receptor expressed in various TGF‐β‐responsive cells. In contrast, ALK‐1 functions as a TGF‐β type I receptor in endothelial cells, and is responsible for human hereditary hemorrhagic telangiectasia (HHT) type II. ALK‐5 and ALK‐1 mediate TGF‐β signals through distinct Smad proteins, i.e., Smad2/Smad3 and Smad1/Smad5, respectively. To identify target genes of ALK‐1 and ALK‐5 in endothelial cells, we conducted oligonucleotide microarray analysis. Human umbilical vein endothelial cells (HUVEC) were infected with recombinant adenoviruses carrying a constitutively active form of ALK‐1 or ALK‐5. ALK‐5 inhibited the proliferation, network formation, and tube formation of HUVEC and induced their apoptosis, whereas ALK‐1 did not exhibit significant effects on HUVEC in vitro. mRNAs were extracted from HUVEC and used for hybridization of oligonucleotide arrays representing approximately 7,000 human genes. Northern blot and quantitative real‐time polymerase chain reaction (PCR) analyses were also performed for some of these genes, confirming the validity of this microarray analysis. We found that ALK‐1 specifically upregulated Smad6, Smad7, Id1, Id2, endoglin, STAT1, and interleukin 1 receptor‐like 1. ALK‐5, in contrast, upregulated PlGF, SM22α, connexin 37, βIG‐H3, and LTBP1. ALK‐1 downregulated Smad1, CXCR4, Ephrin‐A1, and plakoglobin, whereas ALK‐5 downregulated claudin 5 and integrin β5. These results revealed some new targets of TGF‐β in endothelial cells, and differences in transcriptional regulation patterns between ALK‐1 and ALK‐5. J. Cell. Physiol. 193: 299–318, 2002. © 2002 Wiley‐Liss, Inc.
Neuron Density in the Molecular Layer of the Frontal Cortex in Primary Generalized Epilepsy

Summary: Developmental disturbance of the brain as a factor in the causation of epilepsies has been suspected for a long time. An increase of nerve cells in the stratum moleculare, which is qualitatively observed in primary generalized epilepsy, is thought to be an indicator for slight maldevelopment. In this morphometric study, the neuron density of layer I in the frontal lobe in primary generalized epilepsy is measured. Compared with age‐matched controls, the neuron density in primary generalized epilepsy is significantly increased. Thus, neuron density could be a significant index for the disturbance of regional maturation of the cortex.
Stable Adaptive Schemes for System Identification and Control-Part I

Abstract : In another paper, schemes were developed for the identification and control of multivariable systems when all the state variables are accessible. In this report, the main attempt has been to remove this stringent requirement. For a single-input single-output system a unified procedure is developed for designing and adaptive observer which simultaneously estimates the state of the system as well as its parameters. These estimates can then be used to determine suitable feed-forward and feedback controllers for the system.
Collaborative Researching Mode of Implicit Knowledge in Organizational Learning and its Network Implementation

Compared with explicit knowledge, the learning content of implicit knowledge is more plentiful, the nature of learning is more complicated, and learning process is more special. Completed with personal learning, implicit knowledge in organizational learning is more efficient, the results are more profound, the methods are more intense, and most important its network can be implemented. Based on the analysis of characteristics and process of organizational learning of implicit knowledge, combined with collaborative learning mode of e-learning and research-driven organization mode, we design collaborative researching mode of implicit knowledge in organizational learning. In addition, we put forward its network implementation form network support, Learning Environment and means of communication.
Annotation and indexing in the video management system VOM

This paper presents mechanisms for annotating and indexing video by keywords in the Video Object Management system, called VOM. In order to annotate video, an entire video is divided into its video clips, and keywords are assigned to them. These clips are represented in objects, and the objects are organized into a hierarchical data structure in sense of their playback order. Moreover, such objects include a collection of keywords for specifying each object. Then, one object is defined to concatenate several short clips. Keywords assigned to lower positioned objects are abstracted in proportion as this concatenation. The keywords of higher positioned objects are chosen from a collection of the keywords that are assigned into lower ones, or are associated from a set of existing keywords. VOM provides a mechanism to assist in keyword abstraction based on classification of keywords and objects. A collection of them is classified by latent semantic indexing. In addition, the classes consisting of the objects and their keywords are reflected the playback order of the objects.
Detection of prosthetic-hip infections using real-time PCR

Diagnosis of infection after total hip replacement is known to be difficult. Isolation of the bacterial pathogen can give false negative results with current culture methods. Molecularbased methods, as Polymerase Chain Reaction (PCR), may help detect bacteria where culture fails; however, contamination with bacterial DNA when using universal bacterial primers has for a long time been a recognized problem. In this study we describe our attempts of designing a new, rapid PCR method for detection of bacteria in synovial fluid. During the development of this method both the QIAamp® DNA Mini Kit and the MagNA Pure LC Microbiology Kit M was tested for its extraction reliability. Hundred and fifteen synovial fluid samples were analysed for Staphylococcus aureus and methicillin-resistant staphylococci DNA, using the nuc and mecA gene respectively. The synovial fluids were also tested with universal bacterial primers and probe. The PCR results were then compared to the standard culture results. This study shows that culture for S.aureus and methicillin-resistant staphylococci was concordant with the results for nuc and mecA PCR. The universal PCR protocol detects more bacteria (58%) than the culturing method, but also presents many inconclusive results difficult to interpret. In our protocol the MagNA Pure LC Microbiology Kit M showed to be more reliable as DNA-extraction method. Our goal in this study was to develop a better and more reliable diagnostic method for the complicated hip replacement infections. The protocol shows the high potentials of the molecular-based methods, but the bacterial DNA contamination issues using broad-range PCR still remain a problem, and more research is needed to overcome this obstacle.
Community shifts under climate change: mechanisms at multiple scales.

PREMISE OF THE STUDY Processes that drive ecological dynamics differ across spatial scales. Therefore, the pathways through which plant communities and plant-insect relationships respond to changing environmental conditions are also expected to be scale-dependent. Furthermore, the processes that affect individual species or interactions at single sites may differ from those affecting communities across multiple sites. METHODS We reviewed and synthesized peer-reviewed literature to identify patterns in biotic or abiotic pathways underpinning changes in the composition and diversity of plant communities under three components of climate change (increasing temperature, CO2, and changes in precipitation) and how these differ across spatial scales. We also explored how these changes to plants affect plant-insect interactions. KEY RESULTS The relative frequency of biotic vs. abiotic pathways of climate effects at larger spatial scales often differ from those at smaller scales. Local-scale studies show variable responses to climate drivers, often driven by biotic factors. However, larger scale studies identify changes to species composition and/or reduced diversity as a result of abiotic factors. Differing pathways of climate effects can result from different responses of multiple species, habitat effects, and differing effects of invasions at local vs. regional to global scales. Plant community changes can affect higher trophic levels as a result of spatial or phenological mismatch, foliar quality changes, and plant abundance changes, though studies on plant-insect interactions at larger scales are rare. CONCLUSIONS Climate-induced changes to plant communities will have considerable effects on community-scale trophic exchanges, which may differ from the responses of individual species or pairwise interactions.
Antigenic variation of a relapsing fever Borrelia species.

INTRODUCTION . 155 IMMUNOLOGY OF RELAPSING FEVER . 156 THE VARIABLE ANTIGENS ARE OUTER MEMBRANE PROTEINS . 161 ANTIGENIC V ARIA TION IS THE CONSEQUENCE OF DNA REARRANGEMENTS 162 Vrnp GENES ARE ON LINEAR PLASMIDS 163 RECOMBINATION BETWEEN LINEAR PLASMIDS 164 CONCLUDING REMARKS 168
Instructional strategies in the EGRET course: an international graduate forum on becoming a researcher

In today's knowledge economy, graduate students in the field of Computer Science are increasingly required to develop sophisticated, multi-faceted knowledge of conducting research across multiple contexts and countries. This paper reports the experience of teaching a course to prepare Computer Science graduate students for conducting research in the international community. The course emphasized development of skills critical for a successful research career in computer science, and included construction of knowledge as well as hands-on application of instructional content. The intended learning outcomes included (a) gaining familiarity with research design and methodologies in computer science, (b) preparing and delivering research presentations, (c) reviewing the literature, (d) reading and writing research papers, (e) writing and evaluating research proposals, and (f) networking in the international research community. In this paper, we describe an innovative instructional design that emphasized international collaboration with graduate students from another university on a different continent, namely the Open University in the UK. Our instructional strategies included (a) remote participation of graduate students across universities and countries using technologies for computer mediated communication, (b) incorporation of collaborative activities using online tools scaffolding students' construction of sophisticated knowledge of key research activities, and (c) providing students with opportunities for hands-on practical application of concepts in collaborative research activities.
Reducing Inter-subject Anatomical Variation : Analysis of the Functional Activity in Auditory Cortex and Superior Temporal Region using HAMMER

Conventional group analysis of functional MRI (fMRI) data often involves spatial matching of individual data by registering every subject to an anatomical reference. Due to the high degree of intersubject anatomical variability, a low-resolution average anatomical model is typically used as the target template, and/or smoothing kernels are applied to the fMRI data to spatially blur images. However, such smoothing can make it difficult to detect small regions such as auditory cortex when anatomical morphology varies among subjects. Here, we investigate the impact of using a high-dimensional (high-d) registration technique (HAMMER) on fMRI data analysis. It is shown that HAMMERbased analysis results in an enhanced functional signal-to-noise ratio (fSNR) with more localized activation patterns. The technique is validated against a commonly used low-dimensional (low-d) normalization (SPM2). The comparison also includes the effect of template spatial resolution, and the effect of smoothing on fSNR and on activation localization accuracy. The results demonstrate significant improvement in fSNR using HAMMER compared to conventional analysis using SPM, with more precisely localized activation foci.
Characterization of HOG1 homologue, CpMK1, from Cryphonectria parasitica and evidence for hypovirus‐mediated perturbation of its phosphorylation in response to hypertonic stress

We examined the biological function of cpmk1, which encodes a MAPK of Cryphonectria parasitica, and its regulation by mycovirus. Sequence comparisons revealed that cpmk1 had highest homology with osm1, a hog1‐homologue from Magnaporthe grisea. A growth defect was observed in the cpmk1‐null mutant under hyperosmotic conditions, indicating that cpmk1 functionally belongs to a hog1 subfamily. Immunoblot analyses indicated that the CpMK1 pathway was affected specifically in hyperosmotic conditions by the hypovirus CHV1‐EP713. Moreover, the virus‐infected hypovirulent UEP1 strain also exhibited severe osmosensitivity compared to the virus‐free isogenic strain EP155/2, thus providing additional evidence for viral regulation of cpmk1 in response to a hypertonic stress. Besides osmosensitivity, disruption of cpmk1 resulted in several, but not all, hypovirulence‐associated changes, such as reduced pigmentation, conidiation, laccase production and cryparin expression. However, the cpmk1‐null mutant exhibited an increased accumulation of pheromone gene transcripts. Virulence assays of the cpmk1‐null mutant revealed reduced canker area, but not as severe as that of UEP1. These results suggest that mycoviruses modulate the MAPK and thereby provoke the aberrant expression of target genes, some of which are likely to be implicated in viral symptom development.
Learning Deep Representation Without Parameter Inference for Nonlinear Dimensionality Reduction

Unsupervised deep learning is one of the most powerful representation learning techniques. Restricted Boltzman machine, sparse coding, regularized auto-encoders, and convolutional neural networks are pioneering building blocks of deep learning. In this paper, we propose a new building block -- distributed random models. The proposed method is a special full implementation of the product of experts: (i) each expert owns multiple hidden units and different experts have different numbers of hidden units; (ii) the model of each expert is a k-center clustering, whose k-centers are only uniformly sampled examples, and whose output (i.e. the hidden units) is a sparse code that only the similarity values from a few nearest neighbors are reserved. The relationship between the pioneering building blocks, several notable research branches and the proposed method is analyzed. Experimental results show that the proposed deep model can learn better representations than deep belief networks and meanwhile can train a much larger network with much less time than deep belief networks.
Prevalence and Correlates of Metabolic Syndrome in Young Population: A Cross Sectional Study

Background: The Metabolic Syndrome (MS) is emerging as one of the major public health problem all over the world including India. It confers increased risk of Cardiovascular Disease (CVD) and Diabetes Mellitus (DM), both of which pose a huge burden over the society and economics. This study was conducted to assess the prevalence and correlates of MS in young population. Settings and design: A cross-sectional study was performed in Department of Medicine of a rural teaching tertiary care hospital in central India. Materials and methods: In all consecutive study subjects, a National Cholesterol Education Programme Adult Treatment Panel (NCEP ATP – III) criteria was applied to assess the magnitude of MS. Statistical analysis: Prevalence of MS was expressed in percentage. For determining the association of risk factors with MS, we used Student’s t-test to test for continuous variables Chi square for categorical variables and Fisher exact test in the case of small cell sizes (expected value<5). Association was considered statistical significant when P value was ≤ 0.05. Results: The magnitude of MS was 11.2%. Conclusion: Metabolic syndrome exists in significant number of young student population. The early identification of MS and associated risk factors can help to prevent or delay MS, diabetes and CVD by modifying their lifestyle.
The Importance of Being Exhaustive. Optimization of Bridging Structural Water Molecules and Water Networks in Models of Biological Systems

Algorithms and protocols are described for the optimization for H‐bonding of isolated singular H2O molecules and entire networks of H2O molecules. Unlike other approaches that are prone to being trapped in local energy minima, these methods rely on exhaustive searches of orientation space for the H2O molecules. The results are scored with the HINT hydropathic interaction model, but the algorithms should be general for any energy‐scoring computation. Two examples are provided: 1) the tightly‐bound H2O molecule 301 of HIV‐1 protease is shown to be more reasonably oriented in terms of forming H‐bonds with this method than with a molecular mechanics energy minimization method; and 2) the H2O network surrounding carbonmonoxymyoglobin is constructed and analyzed for a 1.80‐Å neutron‐diffraction structure. The H‐atom positions calculated with this method show a somewhat better agreement with the experimental results than do the H‐atom positions calculated with molecular mechanics, and both are considerably better than random.