Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperature and population density determine reservoir regions of seasonal persistence in highland malaria

A better understanding of malaria persistence in highly seasonal environments such as highlands and desert fringes requires identifying the factors behind the spatial reservoir of the pathogen in the low season. In these ‘unstable’ malaria regions, such reservoirs play a critical role by allowing persistence during the low transmission season and therefore, between seasonal outbreaks. In the highlands of East Africa, the most populated epidemic regions in Africa, temperature is expected to be intimately connected to where in space the disease is able to persist because of pronounced altitudinal gradients. Here, we explore other environmental and demographic factors that may contribute to malaria's highland reservoir. We use an extensive spatio-temporal dataset of confirmed monthly Plasmodium falciparum cases from 1995 to 2005 that finely resolves space in an Ethiopian highland. With a Bayesian approach for parameter estimation and a generalized linear mixed model that includes a spatially structured random effect, we demonstrate that population density is important to disease persistence during the low transmission season. This population effect is not accounted for in typical models for the transmission dynamics of the disease, but is consistent in part with a more complex functional form of the force of infection proposed by theory for vector-borne infections, only during the low season as we discuss. As malaria risk usually decreases in more urban environments with increased human densities, the opposite counterintuitive finding identifies novel control targets during the low transmission season in African highlands.
Midbrain dopaminergic neurogenesis and behavioural recovery in a salamander lesion-induced regeneration model

Death and lack of functional regeneration of midbrain dopaminergic (DA) neurons, decreased DA input in the target striatum and movement anomalies characterise Parkinson's disease (PD). There is currently no cure for PD. One way to promote recovery would be to induce or enhance DA neurogenesis. Whether DA neurogenesis occurs in the adult midbrain is a matter of debate. Here, we describe the creation of a salamander 6-hydroxydopamine model of PD to examine midbrain DA regeneration. We demonstrate a robust and complete regeneration of the mesencephalic and diencephalic DA system after elimination of DA neurons. Regeneration is contributed by DA neurogenesis, leads to histological restoration, and to full recovery of motor behaviour. Molecular analyses of the temporal expression pattern of DA determinants indicate that the regenerating DA neurons mature along a similar developmental program as their mammalian counterparts during embryogenesis. We also find that the adult salamander midbrain can reactivate radial glia-like ependymoglia cells that proliferate. The salamander model provides insights into the mechanisms of DA regeneration/neurogenesis and may contribute to the development of novel regenerative strategies for the mammalian brain.
Craniomandibular Disorders and Mandibular Reference Position in Orthodontic Treatment

The aim of this paper is to bring into focus the literature on the choice of the mandibular reference position in orthodontic treatment; of a particular reference to this paper is intercuspal position, centric relation position, or therapeutic position. To give a comprehensive account of the literature review on craniomandibular disorders (CMD), we have relied on books and articles using both Google Scholar and PubMed. Selection criteria included a combination of Mesh and type of article. Article classification was made by two authors, using the following structure outline: prevalence of craniomandibular disorders, its etiology and pathophysiology, occlusion and craniomandibular disorders, orthodontic treatment and CMD, and the mandibular reference position in orthodontics. An important conclusion that emerged from the present literature review is that CMD do not seem to be directly related to orthodontic treatment, and their appearance cannot be predicted or prevented by any means. Therefore, orthodontists must adopt a mandibular reference suitable to their patients and which best respects the balance existing in the stomatognathic system.
Contribution of hydrogen bonds to protein stability

Our goal was to gain a better understanding of the contribution of the burial of polar groups and their hydrogen bonds to the conformational stability of proteins. We measured the change in stability, Δ(ΔG), for a series of hydrogen bonding mutants in four proteins: villin headpiece subdomain (VHP) containing 36 residues, a surface protein from Borrelia burgdorferi (VlsE) containing 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa (RNase Sa) and T1 (RNase T1). Crystal structures were determined for three of the hydrogen bonding mutants of RNase Sa: S24A, Y51F, and T95A. The structures are very similar to wild type RNase Sa and the hydrogen bonding partners form intermolecular hydrogen bonds to water in all three mutants. We compare our results with previous studies of similar mutants in other proteins and reach the following conclusions. (1) Hydrogen bonds contribute favorably to protein stability. (2) The contribution of hydrogen bonds to protein stability is strongly context dependent. (3) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (4) Polar group burial can make a favorable contribution to protein stability even if the polar groups are not hydrogen bonded. (5) The contribution of hydrogen bonds to protein stability is similar for VHP, a small protein, and VlsE, a large protein.
Effect of Cell Shrinkage on Permeability of Cultured Bovine Aortic Endothelia and Frog Mesenteric Capillaries

1 We have tested the hypothesis that a reduction in endothelial cell volume increases microvessel permeability and that the degree of endothelial cell attachment to their basement membranes determines the magnitude of permeability changes caused by a reduction in endothelial cell volume. 2 A decrease in endothelial cell volume was imposed on both intact microvessels and cultured endothelial monolayers by raising osmolarity by 100 mosmol l−1 3 We found that hypertonic solutions did not increase the hydraulic permeability (Lp) of individually perfused venular microvessels in frog mesentery when the perfusate contained albumin. Hypertonic solutions did increase Lp, however, after we perfused the microvessels with the peptide Gly‐Arg‐Gly‐Asp‐Thr‐Pro (GEGDTP; 0.3 mmol l−1), to disrupt integrin‐dependent endothelial cell (EC) attachment to the extracellular matrix (ECM). 4 After albumin was removed from the perfusate, hypertonic solutions increased Lp of microvessels and the permeability of endothelial monolayers to α‐lactalbumin. 5 Our findings indicate that endothelial cell integrin‐ECM binding plays a role in transducing changes in cell volume and/or shape into changes in permeability. We hypothesize that removal of albumin from the vascular perfusate may compromise EC–ECM interactions via an integrin‐dependent mechanism.
Lexical tone awareness among Chinese children with developmental dyslexia*

ABSTRACT This study examined the extent and nature of lexical tone deficit in Chinese developmental dyslexia. Twenty Cantonese-speaking Chinese dyslexic children (mean age 8 ; 11) were compared to twenty average readers of the same age (CA control group, mean age 8 ; 11), and another twenty younger average readers of the same word reading level (RL control group, mean age 7 ; 4) on different measures of lexical tone awareness, rhyme awareness and visual–verbal paired-associate learning. Results showed that the Chinese dyslexic children performed significantly worse than the CA but not the RL control groups in nearly all the lexical tone and rhyme awareness measures. Analyses of individual performance demonstrated that over one-third of the dyslexic children showed a deficit in some aspects of tone awareness. Tone discrimination and tone production were found to correlate significantly with Chinese word reading. These findings confirm that Chinese dyslexic children show weaknesses in tone awareness.
Evolution of the feline-subgroup parvoviruses and the control of canine host range in vivo

A related group of parvoviruses infects members of many different carnivore families. Some of those viruses differ in host range or antigenic properties, but the true relationships are poorly understood. We examined 24 VP1/VP2 and 8 NS1 gene sequences from various parvovirus isolates to determine the phylogenetic relationships between viruses isolated from cats, dogs, Asiatic raccoon dogs, mink, raccoons, and foxes. There were about 1.3% pairwise sequence differences between the VP1/VP2 genes of viruses collected up to four decades apart. Viruses from cats, mink, foxes, and raccoons were not distinguished from each other phylogenetically, but the canine or Asiatic raccoon dog isolates formed a distinct clade. Characteristic antigenic, tissue culture host range, and other properties of the canine isolates have previously been shown to be determined by differences in the VP1/VP2 gene, and we show here that there are at least 10 nucleotide sequence differences which distinguish all canine isolates from any other virus. The VP1/VP2 gene sequences grouped roughly according to the time of virus isolation, and there were similar rates of sequence divergence among the canine isolates and those from the other species. A smaller number of differences were present in the NS1 gene sequences, but a similar phylogeny was revealed. Inoculation of mutants of a feline virus isolate into dogs showed that three or four CPV-specific differences in the VP1/VP2 gene controlled the in vivo canine host range.
Local and General Markedness

University of California, San Diego The work of Jakobson-and later, of Greenberg-has developed the notion of MORPHOLOGICAL MARKEDNESS. In this view, certain morphological categories (e.g. noun singulars) are considered unmarked or more basic in relation to others (e.g. noun plurals). It is shown here that there are some principled exceptions to the general markedness conventions. One example of such LOCAL MARKEDNESS, as this type of markedness reversal will be called, is that nouns whose referents naturally occur in groups or pairs show many of the effects of being unmarked in the plural. The consequences of such local markedness in terms of language acquisition, paradigm regularization, lexical borrowing, and the formation of double morphology are explored in some detail. *
Generation of Black-Dominant Responses in V1 Cortex

Consistent with human perceptual data, we found many more black-dominant than white-dominant responses in layer 2/3 neurons of the macaque primary visual cortex (V1). Seeking the mechanism of this black dominance of layer 2/3 neurons, we measured the laminar pattern of population responses (multiunit activity and local field potential) and found that a small preference for black is observable in early responses in layer 4Cβ, the parvocellular-input layer, but not in the magnocellular-input layer 4Cα. Surprisingly, further analysis of the dynamics of black-white responses in layers 4Cβ and 2/3 suggested that black-dominant responses in layer 2/3 were not generated simply because of the weak black-dominant inputs from 4Cβ. Instead, our results indicated the neural circuitry in V1 is wired with a preference to strengthen black responses. We hypothesize that this selective wiring could be due to (1) feedforward connectivity from black-dominant neurons in layer 4C to cells in layer 2/3 or (2) recurrent interactions between black-dominant neurons in layer 2/3, or a combination of both.
Protocol implementation on the Nectar Communication Processor

We have built a high-speed local-area network called Nectar that uses programmable communication processors as host interfaces. In contrast to most protocol engines, our communication processors have a flexible runtime system that supports multiple transport protocols as well as application-specific activities. In particular, we have implemented the TCP/IP protocol suite and Nectar-specific communication protocols on the communication processor. The Nectar network currently has 25 hosts and has been in use for over a year. The flexibility of our communication processor design does not compromise its performance. The latency of a remote procedure call between application tasks executing on two Nectar hosts is less than 500 μsec. The same tasks can obtain a throughput of 28 Mbit/sec using either TCP/IP or Nectar-specific transport protocols. This throughput is limited by the VME bus that connects a host and its communication processor. Application tasks executing on two communication processors can obtain 90 Mbit/sec of the possible 100 Mbit/sec physical bandwidth using Nectar-specific transport protocols.
A Multi-Interface DTN-like Communication System

The networking industry is quickly adopting IP as the technology to run all the communication applications people need. Yet, there exists a lot of use cases and deployments, where end-to-end IP is not available. This is the domain Delay Tolerant Networking (DTN) is targeting. The Multi Interface Communications Software (MICS) is a robust DTN-like messaging platform for heterogeneous communications equipment. MICS can provide message delivery in networks that lack essentials required by traditional TCP/IP-solutions, like end-to-end connectivity or compatible addressing methods. MICS abstracts the used communications medium, that is the network and link layer, from applications. Applications and network interfaces connect to MICS core using well known and standardized APIs. Familiar email addresses and APIs are used to interface applications with the MICS system. The high-level operation of MICS resembles DTN since we make use of store-and-forward message delivery and multipath message routing together with flooding. This paper concentrates on the overall concept of the MICS system, software architecture, IPC methods, details design choices, message routing and discusses real world deployment scenarios.
Producing a Large-scale Encyclopedic Corpus over the Web

Encyclopedias, which describe general/technical terms, are valuable language resources (LRs). As with other types of LRs relying on human introspection and supervision, constructing encyclopedias is quite expensive. To resolve this problem, we automatically produced a large-scale encyclopedic corpus over the World Wide Web. We first searched the Web for pages containing a term in question. Then we used linguistic patterns and HTML structures to extract text fragments describing the term. Finally, we organized extracted term descriptions based on domains. The resultant corpus contains approximately 100,000 terms. We also evaluated the quality of 2,000 test terms, and found that correct descriptions were obtained for 65% of test terms.
Linear-time encodable codes meeting the gilbert-varshamov bound and their cryptographic applications

A random linear code has good minimal distance with high probability. The conjectured intractability of decoding random linear codes has recently found many applications in cryptography. One disadvantage of random linear codes is that their encoding complexity grows quadratically with the message length. Motivated by this disadvantage, we present a randomized construction of linear error-correcting codes which can be encoded in linear time and yet enjoy several useful features of random linear codes. Our construction is based on a linear-time computable hash function due to Ishai, Kushilevitz, Ostrovsky and Sahai [25]. We demonstrate the usefulness of these new codes by presenting several applications in coding theory and cryptography. These include the first family of linear-time encodable codes meeting the Gilbert-Varshamov bound, the first nontrivial linear-time secret sharing schemes, and plausible candidates for symmetric encryption and identification schemes which can be conjectured to achieve better asymptotic efficiency/security tradeoffs than all current candidates.
Linking ergonomics simulation to production process development

Production development can conflict with production ergonomics and management of environmental impacts. In this paper, we describe how ergonomics can be assessed in production system design by means of a joint simulation tool. The tool enables ergonomics and environmental impacts assessment in conjunction with production process development. The ergonomics sub-tool is based on a digital human model, which has been improved by introducing an updated data measurement system and neural network processing and inference functionality. The results will extend the new simulation modelling capabilities of the existing digital human model by increasing the motion prediction accuracy and providing freedom to model a multitude of task-related motions in a realistic way.
Diversity-multiplexing tradeoff analysis for wireless multicast systems with Amplify-and-Forward scheme

In this paper, we consider a Amplify-and-Forward (AF) cooperative multicast system in a Rayleigh-fading environment, where two-sources communicate with two destinations assisted by N relays (2 - N - 2 system). We consider two cooperative schemes, i.e., the conventional Round-Robin (RR) Scheme and the proposed relay selection (RS) scheme in the multicast system. The diversity-multiplexing tradeoff (DMT) analysis is performed over the two cooperative schemes, by which we find both cooperative schemes can provide N order diversity. The simulation not only validates the theoretical prediction, but also shows that RR offers better performance than RS in the sense of system outage probability (SOP). But RS just employs one relay in one time frame. This offers a tradeoff between the outage probability and the number of relays in service during one time frame.
Signals Regulating the Expression of the Nuclear Gene Encoding Alternative Oxidase of Plant Mitochondria

Suspension cells of tobacco (Nicotiana tabacum L. cv Bright Yellow) were used to investigate signals regulating the expression of the nuclear gene Aox1 encoding the mitochondrial alternative oxidase (AOX) protein responsible for cyanide-resistant respiration in plants. We found that an increase in the tricarboxylic acid cycle intermediate citrate (either after its exogenous supply to cells or after inhibition of aconitase by monofluoroacetate) caused a rapid and dramatic increase in the steady-state level of Aox1 mRNA and AOX protein. This led to a large increase in the capacity for AOX respiration, defined as the amount of salicylhydroxamic acid-sensitive O2 uptake by cells in the presence of potassium cyanide. The results indicate that citrate may be an important signal metabolite regulating Aox1 gene expression. A number of other treatments were also identified that rapidly induced the level of Aox1 mRNA and AOX capacity. These included short-term incubation of cells with 10 mM acetate, 2 [mu]M antimycin A, 5 mM H2O2, or 1 mM cysteine. For some of these treatments, induction of AOX occurred without an increase in cellular citrate level, indicating that other signals (possibly related to oxidative stress conditions) are also important in regulating Aox1 gene expression. The signals influencing Aox1 gene expression are discussed with regard to the potential function(s) of AOX to modulate tricarboxylic acid cycle metabolism and/or to prevent the generation of active oxygen species by the mitochondrial electron transport chain.
Controlled Natural Languages for Knowledge Representation

This paper presents a survey of research in controlled natural languages that can be used as high-level knowledge representation languages. Over the past 10 years or so, a number of machine-oriented controlled natural languages have emerged that can be used as high-level interface languages to various kinds of knowledge systems. These languages are relevant to the area of computational linguistics since they have two very interesting properties: firstly, they look informal like natural languages and are therefore easier to write and understand by humans than formal languages; secondly, they are precisely defined subsets of natural languages and can be translated automatically (and often deterministically) into a formal target language and then be used for automated reasoning. We present and compare the most mature of these novel languages, show how they can balance the disadvantages of natural languages and formal languages for knowledge representation, and discuss how domain specialists can be supported writing specifications in controlled natural language.
Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling.

Hodgkin lymphoma (HL) is a malignancy of unknown pathogenesis. The malignant Hodgkin and Reed/Sternberg (HRS) cells derive from germinal center B cells (or rarely, T cells) but have a heterogeneous and largely uncharacterized phenotype. Using microarrays, we compared the gene expression profile of four HL cell lines with profiles of the main B cell subsets and B cell non-HLs to find out whether HRS cells, despite their described heterogeneity, show a distinct gene expression, to study their relationship to other normal and malignant B cells, and to identify genes aberrantly or overexpressed by HRS cells. The HL lines indeed clustered as a distinct entity, irrespective of their B or T cell derivation, and their gene expression was most similar to that of EBV-transformed B cells and cell lines derived from diffuse large cell lymphomas showing features of in vitro-activated B cells. Twenty-seven genes, most of which were previously unknown to be expressed by HRS cells, showed aberrant expression specifically in these cells, e.g., the transcription factors GATA-3, ABF1, EAR3, and Nrf3. For five genes, expression in primary HRS cells was confirmed. The newly identified HL-specific genes may play important roles in the pathogenesis of HL, potentially represent novel diagnostic markers, and can be considered for therapeutic targeting.
Application of the Kalman Filters to the High-Performance Drive System With Elastic Coupling

In this paper, issues related to parameter identification and high-performance control of the drive system with an elastic joint are discussed. After a brief introduction, the mathematical model of the drive and the proposed high-performance control structure are presented. The effect of the location of closed-loop poles and cancellation of zeros of the structure is examined. Then, the mathematical models of the Kalman filters used in this study are presented, and the results of the identification procedure are described. The effectiveness of the proposed structure has been examined under simulation and experimental study.
Synthesis-friendly techniques for tightly-coupled integration of hardware accelerators into shared-memory multi-core clusters

Several many-core designs tackle scalability issues by leveraging tightly-coupled clusters as building blocks, where low-latency, high-bandwidth interconnection between a small/medium number of cores and L1 memory achieves high performance/watt. Tight coupling of hardware accelerators into these multicore clusters constitutes a promising approach to further improve performance/area/watt. However, accelerators are often clocked at a lower frequency than processor clusters for energy efficiency reasons. In this paper, we propose a technique to integrate shared-memory accelerators within the tightly-coupled clusters of the STMicroelectronics STHORM architecture. Our methodology significantly relaxes timing constraints for tightly-coupled accelerators, while optimizing data bandwidth. In addition, our technique allows to operate the accelerator at an integer submultiple of the cluster frequency. Experimental results show that the proposed approach allows to recover up to 84% of the slow-down implied by reduced accelerator speed.