Miracle-dz/UniFAR-FTUs huggingface dataset:
An Evaluation of Candidate Genes of Inflammation and Thrombosis in Relation to the Risk of Venous Thromboembolism: The Women's Genome Health Study

Background—Although pathways associated with hemostasis and thrombosis are well documented to have an impact on venous thromboembolism (VTE), whether the inflammatory cascade also influences VTE risk is uncertain. Methods and Results—We evaluated 51 polymorphisms from 32 inflammation-related genes (and an additional 19 polymorphisms from 15 thrombosis-related genes) as potential determinants of VTE in a prospective cohort of 22 413 white women followed over a 10-year period. Hazard ratios (HRs) for incident VTE according to the different genotypes were assessed by Cox proportional-hazards models. The false discovery rate (FDR) was used for correction for multiple testing with a 0.20 cut point. During follow-up, 158 idiopathic and 180 secondary VTE events occurred. As anticipated, factor V Leiden (HR, 3.22; 95% CI, 1.92 to 5.40; P<0.0001; FDR=0.004) and the prothrombin mutation (HR, 2.57; 95% CI, 1.64 to 4.02; P<0.0001; FDR=0.004) were both strongly associated with incident idiopathic VTE, as was the rs6046 polymorphism in the factor VII gene (HR, 0.54; 95% CI, 0.35 to 0.86; P=0.008; FDR, 0.12). With regard to polymorphism in the inflammatory genes, variation at rs1143634 in the IL-1β gene was associated with a reduced risk of idiopathic VTE (HR, 0.59; 95% CI, 0.44 to 0.80; P=0.0007; FDR=0.02), whereas variation at rs1800872 in the IL-10 gene was associated with increased risk (HR, 1.42; 95% CI, 1.12 to 1.80; P=0.004; FDR=0.07). By contrast, no significant associations were found for secondary VTE events. Conclusion—In addition to previously reported polymorphisms associated with hemostasis and thrombosis, these prospective cohort data suggest that genetic variation in IL-1 β and IL-10 genes may also influence the risk of idiopathic VTE.
The Effects of Splanchnicectomy on the Blood Pressure in Hypertension: A Controlled Study

The effect of supradiaphragmatic splanchnicectomy on the blood pressure of 294 hypertensive patients followed for 10 to 18 months after surgery is compared with the effects of nonspecific medical management in a control group of 79 patients similarly studied. The data are presented in simple graphic form. It is concluded that 29 per cent of the hypertensive patients had reductions in blood pressure outside the range of spontaneous variation, that the vascular complications of hypertension decreased the likelihood of a good result, and that extension of the sympathetic ganglionectomy upward appeared to increase the frequency of good results without requiring a two-stage operation or producing significant postoperative orthostatic hypotension.
Knowledge-Based Reasoning on Semantic Maps

Robotic systems should have a deep and specific knowledge about the environment they live in to properly interact with people and effectively perform the requested tasks. To this end, a suitable representation of the environment is needed, including both metric spatial information and semantic representations of locations and objects of interest. In this paper a representation of spatial and environmental knowledge, as well as a method for reasoning on it are presented. More specifically, the representation method is designed to properly integrate metric information about the environment and semantic information provided by the user, allowing for an effective knowledge-based reasoning. The result is a qualitative high-level representation of the environment that embodies all the knowledge required by a robot to actually reason on it and execute complex tasks.
A Comprehensive Analytical Model for Wormhole Routng in Multicomputer Systems

An analytical model for obtaining performance measures in multicomputer networks that use wormhole routing is presented. Unlike previous wormhole routing models, the model introduced in this paper is accurate and quite simple. The model is validated through flit-level simulation experiments and is sufficiently general to be extended for several networks, including k-ary n-cubes, and related routing paradigms, such as virtual cut-through, The value of this model is exhibited through its application to current networks to indicate cost-effective augmentations which result in significant performance improvements.
A combinatorial construction of almost-ramanujan graphs using the zig-zag product

Reingold, Vadhan and Wigderson [21] introduced the graph zig-zag product. This product combines a large graph and a small graph into one graph, such that the resulting graph inherits its size from the large graph, its degree from the small graph and its spectral gap from both. Using this product they gave the first fully-explicit combinatorial construction of expander graphs. They showed how to construct D-regular graphs having spectral gap 1-O(D-1/3). In the same paper, they posed the open problem of whether a similar graph product could be used to achieve the almost-optimal spectral gap 1-O(D-1/2). In this paper we propose a generalization of the zig-zag product that combines a large graph and several small graphs. The new product gives a better relation between the degree and the spectral gap of the resulting graph. We use the new product to give a fully-explicit combinatorial construction of D-regular graphs having spectral gap 1-D-1/2 + o(1).
Unorthodox approach toward microscopic shape from image focus using optical microscopy

Shallow depth‐of‐field is an inherent property of optical microscope. Because of this limitation, it is usually impossible to image large three‐dimensional (3D) objects entirely in focus. However, the in‐focus information of the object's surface can be acquired over a range of images by optical sectioning of the object in consideration. These images can then be processed to generate a single in‐focus image and further for 3D shape reconstruction using methods like Shape from focus (SFF). SFF represents a passive technique for recovering object shapes. Although numerous methods for SFF have been recently proposed, all follow similar precedent of focus measure application and depth recovery by maximizing the focus curves. As the conventional techniques assume the presence of prominent texture in the scene, the shape of weak textured surfaces are not recovered properly. In this manuscript, we have followed an unorthodox approach to recover shapes of microscopic objects using SFF. At first, the in‐focus image is obtained, pursued by computing depth along the edges and their neighbors present in scene. Empty spaces in the final depth map are then calculated by surface interpolation. The proposed approach works well even for objects with weak textures. Microsc. Res. Tech., 2013. © 2012 Wiley Periodicals, Inc.
Light Reduction Capabilities of Homemade and Commercial Incubator Covers in NICU

Reduction of high-risk neonates' exposure to aversive light stimulation is an important component of developmentally supportive care. In neonatal intensive care unit (NICU), usually light is reduced by reducing the room's light level or by using incubator covers. Many types of incubator covers are in use, including homemade and commercial covers. A comparative study was used to determine the light reducing capabilities of 19 homemade incubator covers, 2 commercial covers, and 1 receiving blanket. The covers were tested by covering and uncovering an incubator and an oxygen hood in the NICU during daytime and nighttime lightings. The light reducing capabilities value was determined for each cover using an Extech light dosimeter when the cover was placed over and removed from an oxyhood, and an incubator. The study showed that the light reducing capability of the commercial covers was 91.2%, the homemade covers capability was 72.1%, and the receiving blankets capability was 55.1%. A significant difference between the commercial and homemade covers was found (F = 452.50, P < 0.00). Commercial incubator covers are the most effective covers to achieve light reduction; homemade covers can be effective if made large enough so that they completely cover all sides of the incubator.
ExposureSense: Integrating daily activities with air quality using mobile participatory sensing

With an increasing number of rich embedded sensors, like accelerometer and GPS, smartphone becomes a pervasive people-centric sensing platform for inferring user's daily activities and social contexts. Alternatively, wireless sensor network offers a comprehensive platform for capturing the surrounding environmental information using mobile sensing nodes, e.g., the OpenSense project [2] in Switzerland deploying air quality sensors like CO on public transports like buses and trams. The two sensing platforms are typically isolated from each other. In this paper, we build ExposureSense, a rich mobile participatory sensing infrastructure that integrates the two independent sensing paradigms. ExposureSense is able to monitor people's daily activities as well to compute a reasonable estimation of pollution exposure in their daily life. Besides using external sensor networks, ExposureSense also supports pluggable sensors (e.g., O3) to further enrich air quality data using mobile participatory sensing with smartphones.
Craniofacial development in marsupial mammals: Developmental origins of evolutionary change

Biologists have long studied the evolutionary consequences of the differences in reproductive and life history strategies of marsupial and eutherian mammals. Over the past few decades, the impact of these strategies on the development of the marsupial embryo and neonate has received attention. In this review, the differences in development in the craniofacial region in marsupial and eutherian mammals will be discussed. The review will highlight differences at the organogenic and cellular levels, and discuss hypotheses for shifts in the expression of important regulatory genes. The major difference in the organogenic period is a whole‐scale shift in the relative timing of central nervous system structures, in particular those of the forebrain, which are delayed in marsupials, relative to the structures of the oral–facial apparatus. Correlated with the delay in development of nervous system structures, the ossification of the bones of the neurocranium are delayed, while those of the face are accelerated. This study will also review work showing that the neural crest, which provides much of the cellular material to the facial skeleton and may also carry important patterning information, is notably accelerated in its development in marsupials. Potential consequences of these observations for hypotheses on constraint, evolutionary integration, and the existence of developmental modules is discussed. Finally, the implications of these results for hypotheses on the genetic modulation of craniofacial patterning are presented. Developmental Dynamics 235:1181–1193, 2006. © 2006 Wiley‐Liss, Inc.
"New view" of protein folding reconciled with the old through multiple unfolding simulations.

Twenty-four molecular dynamics trajectories of chymotrypsin inhibitor 2 provide a direct demonstration of the diversity of unfolding pathways. Comparison with experiments suggests that the transition state region for folding and unfolding occurs early with only 25 percent of the native contacts and that the root-mean-square deviations between contributing structures can be as large as 15 angstroms. Nevertheless, a statistically preferred unfolding pathway emerges from the simulations; disruption of tertiary interactions between the helix and a two-stranded portion of the beta sheet is the primary unfolding event. The results suggest a synthesis of the "new" and the classical view of protein folding with a preferred pathway on a funnel-like average energy surface.
Specific features of distribution in the World Ocean of some flying fishes of the genera Exocoetus, Hirundichthys and Cypselurus (Exocoetidae)

The paper describes distribution (both seasonal and the average long-term) of the species and subspecies of the three previously taxonomically studied by the author groups of flying fishes: genus Exocoetus , subgenus Hirundichthys s.str. and Cypselurus “ poecilopterus ” species group. Species distribution is compared with oceanographic features (temperature, salinity, water masses, currents, biological productivity). The cases of joint occurrence of species in one sample are analyzed. It is shown that allopatric (and parapatric) species from different groups have different patterns of area partition. In the case of flying fishes of the genus Exocoetus , the main factor determining the boundaries between species is circulation of surface waters, among the representatives of the subgenus Hirundichthys – it is the distance from coasts, and in the "poecilopterus" group – it is the salinity. The boundaries between the ranges of species of the genus Exocoetus pass mainly along the boundaries of ocean currents, in the species of the subgenus Hirundichthys - along the boundary between the far-neritic and oceanic zones, and in the " poecilopterus " group - according to isohaline of ~ 35 ‰. Sympatric species are supposed to have different mechanisms to reduce the interspecies competition: in the genus Exocoetus , there is a division into few-raker and many-raker species, while for the species of the subgenus Hirundichthys it was noticed an alternate use of the Arabian Sea basin and spatial separation of fishes having similar sizes.
Hierarchical image representation via multi-level sparse coding

This paper presents a hierarchical model for robust image representation. We first introduce multi-level sparse coding algorithm and normalized max pooling strategy which are designed to obtain meaningful sparse codes and robust pooled codes, respectively. With the sparse codes and pooled codes, a hierarchical architecture is built and more robust features are extracted at the second layer. The proposed method has been evaluated on two widely used datasets: Caltech-101 and Caltech-256, and experimental results demonstrate that the proposed method is both effective and robust in image representation compared with the state-of-the-art.
Review of a Pivotal Human Factors Article: “Humans and Automation: Use, Misuse, Disuse, Abuse”

Objective: This paper considers the influence of “Humans and Automation: Use, Misuse, Disuse, Abuse” and examines how it relates to the evolving issue of human-automation interaction. Background: Automation presents important practical challenges that can dramatically affect satisfaction, performance, and safety; philosophical challenges also arise as automation changes the nature of work and human cognition. Method: Papers cited by and citing “Humans and Automation” were reviewed to identify enduring and emerging themes in human-automation research. Results: “Humans and Automation” emerges as an important node in the network of automation-related papers, citing many and being cited by many recent influential automation-related papers. In their article, Parasuraman and Riley (1997) integrated previous research and identified differing expectations across designers, managers, and operators regarding the need to support operators as a source of automation problems. They also foresaw and inspired research that addresses problems of overreliance and underreliance on automation. Conclusion: This pivotal article and associated research show that even though automation seems to relieve people of tasks, automation requires more, not less, attention to training, interface design, and interaction design. The original article also alludes to the emergence of vicious cycles and dysfunctional meta-control. These problems reflect the coevolution of automation and humans, in which both adapt to the responses of the other. Application: Understanding this coevolution has important philosophical implications for the nature of human cognition and practical implications for satisfaction, performance, and safety.
Editorial: Improving Working Memory in Learning and Intellectual Disabilities

Working memory (WM) has been defined as a system for temporarily retaining and manipulating information while performing a variety of cognitive tasks (Baddeley, 1986). To date, the crucial role of WM in activities of everyday life (including reading, writing, arithmetic, learning, language-processing, orientation, imagination) has been demonstrated in an impressive body of research. Several studies have shown an impairment in WM in individuals with learning disabilities (LD) or intellectual disabilities (ID, e.g., Lanfranchi et al., 2004; LD, Peng and Fuchs, 2016). Given its core role in cognition, the feasibility of training WM has emerged in the literature as a crucial issue, with efforts focusing on analyzing whether and how improving WM might affect cognitive processes associated with WM as well. The results have been contradictory so far, however, with some studies finding WM training effective in producing improvements in the trained task, but few reporting transfer effects to allied cognitive processes, and even fewer identifying any maintenance effects, when investigated (see Melby-Lervag and Hulme, 2013, for example). Starting from this literature, the aim of the research discussed here is to add new evidence on the direct and transfer effects of WM training in individuals with LD or ID. Several key points have emerged concerning WM training in these particular populations, as summarized in the following paragraphs.
DiANNA: a web server for disulfide connectivity prediction

Correctly predicting the disulfide bond topology in a protein is of crucial importance for the understanding of protein function and can be of great help for tertiary prediction methods. The web server outputs the disulfide connectivity prediction given input of a protein sequence. The following procedure is performed. First, PSIPRED is run to predict the protein's secondary structure, then PSIBLAST is run against the non-redundant SwissProt to obtain a multiple alignment of the input sequence. The predicted secondary structure and the profile arising from this alignment are used in the training phase of our neural network. Next, cysteine oxidation state is predicted, then each pair of cysteines in the protein sequence is assigned a likelihood of forming a disulfide bond—this is performed by means of a novel architecture (diresidue neural network). Finally, Rothberg's implementation of Gabow's maximum weighted matching algorithm is applied to diresidue neural network scores in order to produce the final connectivity prediction. Our novel neural network-based approach achieves results that are comparable and in some cases better than the current state-of-the-art methods.
Identification of novel HXT genes in Saccharomyces cerevisiae reveals the impact of individual hexose transporters on qlycolytic flux

In Saccharomyces cerevisiae, hexose uptake is mediated by HXT proteins which belong to a superfamily of monosaccharide facilitators. We have identified three more genes that encode hexose transporters (HXT5, 6, 7). Genes HXT6 and HXT7 are almost identical and located in tandem 3′ adjacent to HXT3 on chromosome IV. We have constructed a set of congenic strains expressing none or any one of the seven known HXT genes and followed growth and flux rates for glucose utilization. The hxt null strain does not grow on glucose, fructose or mannose, and both glucose uptake and flux rate were below the detection level. Expression of either HXT1, 2, 3, 4, 6 or 7 is basically sufficient for aerobic growth on these sugars. In most of the constructs, glucose was the preferred substrate compared to fructose or mannose. There is a considerable variation in flux and growth rates with 1% glucose, dependent on the expression of the individual HXT genes. Expression of either HXT2, 6 or 7 in the null background is sufficient for growth on 0.1% glucose, while growth of strains with only HXT1, 3 or 4 requires higher (≥1%) glucose concentrations. These results demonstrate that individual HXT proteins can function independently as hexose transporters, and that most of the metabolically relevant HXT transporters from S. cerevisiae have been identified.
Analysis of a simple multihop underwater acoustic network

A multihop underwater acoustic network, which consists of a series of equal-distance hops connected by relay transceivers in a tandem, is considered. Messages are originated as coded packets from a source node at one end, relayed (decoded and re-encoded) sequentially hop by hop, and finally received by a destination node at the other end of the network. Several key characteristics of underwater acoustic channels, namely, frequency-dependent signal attenuation and noise, inter-hop interference, half-duplex constraint, and large propagation delay, are taken into account in the analysis. A simple transmission protocol with spatial reuse is considered, and the transmission schedule is designed to satisfy the half-duplex constraint on relay transceivers in the presence of large propagation delay. To efficiently cope with frequency-dependent channel characteristic and inter-hop interference, the power spectral density function of signaling is analytically optimized in a way analogous to water-filling. Furthermore, the problem of determining the minimum number of hops to support a prespecified rate and reliability with and without a maximum coded packet length constraint is examined. Finally, numerical results are presented to illustrate the analysis.
Dengue Control in North Queensland, Australia: Case Recognition and Selective Indoor Residual Spraying

A large epidemic of dengue in Townsville and Charters Towers, north Queensland, Australia, initiated the development of a Dengue Fever Management Plan for north Queensland (DFMP) in 1994. The DFMP integrated disease surveillance, vector control and health promotion activities to prevent dengue outbreaks. While initially successful in preventing the recurrence of epidemic dengue in north Queensland, a protracted epidemic of DEN-3 in the Cairns area led to a revision of the DFMP in 2000. The revised DFMP placed emphasis on the early recognition of cases and development of a specialized Dengue Action Response Team (DART) to conduct selective indoor residual spraying with pyrethroid insecticides to control the vector, Aedes aegypti. Since the launch of the DFMP 2000, dengue outbreaks have been contained in terms of the areas affected, duration of the outbreak and the total number of cases despite an increase in recognized dengue activity.