Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding the role of force , mechanics , and biological machinery — the “ mechanome ” — will open the way to new strategies for fighting disease . Lighting Up the Mechanome

biological machinery—the " mechanome " —will open the way to new strategies for fighting disease. Genomics and general " omics " approaches, such as proteomics, inter-actomics, and glycomics, among others, are powerful system-level tools in biology. All of these fields are supported by advances in instrumentation and computation, such as DNA sequencers and mass spectrometers, which were critical in " sequencing " the human genome. Revolutionary advances in biology that have harnessed the machinery of polymerases to copy DNA or used RNA interference to capture and turn off genes have also been critical to the development of these tools. Researchers in biophysics and bio-mechanics have made significant advances in experimental methods, and the development of new microscopes has made higher resolution molecular-and cellular-scale measurements possible. Despite these advances, however, no systems-level " omics " perspective— the " mechanome " —has been developed to describe the general role of force, mechanics, and machinery in biology. Like the genome, the mechanome promises to improve our understanding of biological machinery and ultimately open the way to new strategies and targets for fighting disease. Many disease processes are mechanical in nature. Malaria, which infects 500 million people and causes 2 million deaths each year, works through a number of mechanical processes, including parasite invasion of red blood cells (RBCs), increased RBC adhesions, and overall stiffening of RBCs. As the disease progresses, it impairs the ability of infected cells to squeeze
Ranking Journals in Economics, Management and Political Science by Social Choice Theory Methods

Data on economic, management and political science journals are used to produce quantitative estimates of (in)consistency of evaluations based on seven popular bibliometric indicators. This paper proposes a new approach to the construction of aggregate journal rankings: aggregation is considered to be a multicriteria decision problem and ordinal ranking methods from social choice theory are employed to solve it. We apply either a direct ranking method based on majority rule (e.g. the Copeland rule, the Markovian method) or a multistage procedure of selection and exclusion of the best journals, as determined by a majority rule-based social choice solution concept (tournament solution), such as the uncovered set and the minimal externally stable set. We use the same method to analyze correlations of rankings and demonstrate that aggregate rankings reduce the number of contradictions and represent the set of single-indicator-based rankings better than any of the seven rankings themselves.
Status of Arsenic and Selenium in Some Arsenic Hot Spots of Bangladesh and Its Relevance to Arsenicosis in Human Beings

The present work was conducted to find any relevance to the selenium (Se) content in soil, water and in an edible plant to the incidence of arsenicosis in some arsenic hotspots of the country where arsenicosis patients have been identified and where no arsenicosis patients have yet been reported. Soil, plant and water samples were collected from arsenic hot spots of five localit ies viz. Sonargaon, Manikgonj, Munshigonj, Jessore and Ishwardi. The collected plant was Arum (Colocasia esculenta) – a hyper accumulator of As and a very common edible vegetable all over the country. Soil, plant and water samples were analyzed to determine the content of arsenic and selenium in them. Analyses of soil, plant and water samples reveal that the average concentrations of As in the three niches at the locations where arsenicosis is prevalent are higher (3.56, 3.0 and 0.062 mg/kg respectively) than where the incidence of arsenicosis has not been reported (2.83, 2.66 and 0.053 mg/kg respectively). On the other hand, the Se contents showed a reverse phenomena – lower in the locations where patients are prevalent (0.082, 0.027 mg/kg and bdl respectively in three niches) than where no patients have been reported (0.156, 0.053 mg/kg and bdl respectively). The findings are suggestive of the implication of Se in alleviat ing As toxicity in human beings.
The tenascin family of ECM glycoproteins: Structure, function, and regulation during embryonic development and tissue remodeling

The determination of animal form depends on the coordination of events that lead to the morphological patterning of cells. This epigenetic view of development suggests that embryonic structures arise as a consequence of environmental influences acting on the properties of cells, rather than an unfolding of a completely genetically specified and preexisting invisible pattern. Specialized cells of developing multicellular organisms are surrounded by a complex extracellular matrix (ECM), comprised largely of different collagens, proteoglycans, and glycoproteins. This ECM is a substrate for tissue morphogenesis, lends support and flexibility to mature tissues, and acts as an epigenetic informational entity in the sense that it transduces and integrates intracellular signals via distinct cell surface receptors. Consequently, ECM‐receptor interactions have a profound influence on major cellular programs including growth, differentiation, migration, and survival. In contrast to many other ECM proteins, the tenascin (TN) family of glycoproteins (TN‐C, TN‐R, TN‐W, TN‐X, and TN‐Y) display highly restricted and dynamic patterns of expression in the embryo, particularly during neural development, skeletogenesis, and vasculogenesis. These molecules are reexpressed in the adult during normal processes such as wound healing, nerve regeneration, and tissue involution, and in pathological states including vascular disease, tumorigenesis, and metastasis. In concert with a multitude of associated ECM proteins and cell surface receptors that include members of the integrin family, TN proteins impart contrary cellular functions, depending on their mode of presentation (i.e., soluble or substrate‐bound) and the cell types and differentiation states of the target tissues. Expression of tenascins is regulated by a variety of growth factors, cytokines, vasoactive peptides, ECM proteins, and biomechanical factors. The signals generated by these factors converge on particular combinations of cis‐regulatory elements within the recently identified TN gene promoters via specific transcriptional activators or repressors. Additional complexity in regulating TN gene expression is achieved through alternative splicing, resulting in variants of TN polypeptides that exhibit different combinations of functional protein domains. In this review, we discuss some of the recent advances in TN biology that provide insights into the complex way in which the ECM is regulated and how it functions to regulate tissue morphogenesis and gene expression. Dev Dyn;218:235–259. © 2000 Wiley‐Liss, Inc.
JGrid/FCC: A Tool for Efficient Knowledge Extraction from MRI Scans

MRI (Magnetic Resonance Imaging) allows to display different kinds of soft tissue with highest resolution and has attracted increased interest in the analysis of anatomical differences between normal and pathologic populations in the field of neuroscience. However, to get a deeper insight into complex neurological abnormalities like dementia or somatoform disorder large-scale analysis is indispensable but mostly difficult and time consuming. In this paper, we propose JGrid/FCC, a highly efficient software solution for the analysis of MR images using a combination of several data mining techniques including feature selection, clustering and classification (FCC), in order to provide a concise classification of pathogenous areas in the brain. Using the newly developed distributed computing software JGrid, the time usage of the FCC software was reduced by 80% on a cluster of 10 workstations.
Thermal modeling for 3D-ICs with integrated microchannel cooling

Integrated microchannel liquid-cooling technology is envisioned as a viable solution to alleviate an increasing thermal stress imposed by 3D stacked ICs. Thermal modeling for microchannel cooling is challenging due to its complicated thermal-wake effect, a localized temperature wake phenomenon downstream of a heated source in the flow. This paper presents a fast and accurate thermal-wake aware thermal model for integrated microchannel 3D ICs. Validation results show the proposed thermal model achieves more than 400× speed up and only 2.0% error in comparison with a commercial numerical simulation tool. We also demonstrate the use of the proposed thermal model for thermal optimization during the IC placement stage. We find that due to the thermal-wake effect, tiles are placed in the descending order of power magnitude along the flow direction. We also find that modeling thermal-wakes is critical for generating a thermal-aware placement for integrated microchannel-cooled 3D IC. It could result in up to 25°C peak temperature difference according to our experiments.
Why does the Pirate launch the Copy before the Incumbent launches the Original

We analyze this question in a vertical product differentiation model with price competition. We first show that the monopoly situation never maximizes the social welfare. Second, we find that the government’s role is very important in the market where the chance of pirating exists. Third, the incumbent has a key role to avoid the pirate’s entry through prices. Fourth, the incumbent’s incentives to install an antipiracy system decrease as increases the government’s expense in monitoring the piracy. Fifth, the government not permits the incumbent to install it, since the monopoly gives the worst social welfare. Finally, the pirate’s final decision depends on the government’s expense in monitoring the piracy, which depends on its monitoring technology it, the incumbent’s ability to anticipate the pirate can be leader in prices, and the incumbent’s profit like follower is bigger than leader in price. JEL classification : K42; L13; L86
Familial aggregation of severity of diabetic retinopathy in Mexican Americans from Starr County, Texas.

OBJECTIVE Diabetic retinopathy is a major cause of blindness. To determine whether retinopathy itself or only its severity aggregates in families, we examined the occurrence and severity of diabetic retinopathy in Mexican-American siblings with type 2 diabetes. RESEARCH DESIGN AND METHODS Using stereoscopic fundus photography of seven standard fields, we measured retinopathy in 656 type 2 diabetic patients from 282 Mexican-American families from Starr County, Texas. Retinopathy severity was scored using the Early Treatment of Diabetic Retinopathy Study system and classified as no retinopathy, early nonproliferative diabetic retinopathy (NPDR-E), moderate-to-severe nonproliferative diabetic retinopathy (NPDR-S), or proliferative diabetic retinopathy (PDR). RESULTS Of 249 siblings of randomly selected probands with retinopathy, 169 (67.9%) had retinopathy, compared with 95 of 125 siblings of unaffected probands (76.0%; P = 0.11). Proband retinopathy class was associated (P = 0.03) with sibling retinopathy class, with significant odds ratios (ORs) for NPDR-E versus no retinopathy (OR 0.57 [95% CI 0.35-0.93]) and PDR versus NPDR-E (2.02 [1.13-3.63]); the contrast of NPDR-S versus NPDR-E approached significance (1.78 [0.99-3.20]). With the more severe classes (PDR and NPDR-S) combined in one group and the less severe ones (none and NPDR-E) in another, more severe proband retinopathy was associated with more severe sibling retinopathy (1.72 [1.03-2.88]). CONCLUSIONS More severe diabetic retinopathy showed evidence of familial aggregation, but the occurrence of diabetic retinopathy per se did not. The factors involved in the onset of diabetic retinopathy may differ from those involved in its progression to more severe forms.
Tackling the qualification problem using fluent dependency constraints: preliminary report

The use of causal rules, or fluent dependency constraints, has proven to provide a versatile means of dealing with the ramification problem. In this paper, we show how fluent dependency constraints, together with the use of durational fluents, can be used to deal with problems associated with action qualification. We provide both a weak and a strong form of qualification and demonstrate the approach using an action scenario which combines solutions to the frame, ramification and qualification problems in the context of actions with duration, concurrent actions, nondeterministic actions and the use of both Boolean and non-Boolean fluents. The circumscription policy used for the combined problems is reducible to the first-order case. In addition, we demonstrate the use of a research tool, called VITAL (VIsualization of Temporal Action Logics), for querying and visualizing action scenarios.
Assessing the accuracy of trauma patient prioritization: communication design of the M.I.S.E.R information system protocol and communication channel during crisis communication exchanges

This study sought to investigate the effectiveness of an information exchange protocol (M.I.S.E.R) designed to increase the effectiveness of messages pertaining to rural trauma patients and triage prioritization. Trained coders were randomly assigned to three conditions; audio, transcript, and transcript and audio. Participants coded several hundred actual information exchanges between first responders and medical command operators. Findings confirm the effectiveness of the M.I. S.E. R. information exchange protocol as well as the effectiveness of exchanging crisis messages via two-way radio as compared to having a transcript of the call or both audio recordings and transcripts. Implications for communication design, healthcare practitioners, and effective modes for exchanging crisis communication messages are presented.
The Role of Motion Information in Learning Human-Robot Joint Attention

To realize natural human-robot interactions and investigate the developmental mechanism of human communication, an effective approach is to construct models by which a robot imitates cognitive functions of humans. Focusing on the knowledge that humans utilize motion information of others’ action, this paper presents a learning model that enables a robot to acquire the ability to establish joint attention with a human by utilizing both static and motion information. As the motion information, the robot uses the optical flow detected when observing a human who is shifting his/her gaze from looking at the robot to looking at another object. As the static information, it extracts the edge image of the human face when he/she is gazing at the object. The static and motion information have complementary characteristics. The former gives the exact direction of gaze, even though it is difficult to interpret. On the other hand, the latter provides a rough but easily understandable relationship between the direction of gaze shift and motor output to follow the gaze. The learning model utilizing both static and motion information acquired from observing a human’s gaze shift enables the robot to efficiently acquire joint attention ability and to naturally interact with the human. Experimental results show that the motion information accelerates the learning of joint attention while the static information improves the task performance. The results are discussed in terms of analogy with cognitive development in human infants.
Improved testing of low rank matrices

We study the problem of determining if an input matrix A εRm x n can be well-approximated by a low rank matrix. Specifically, we study the problem of quickly estimating the rank or stable rank of A, the latter often providing a more robust measure of the rank. Since we seek significantly sublinear time algorithms, we cast these problems in the property testing framework. In this framework, A either has low rank or stable rank, or is far from having this property. The algorithm should read only a small number of entries or rows of A and decide which case A is in with high probability. If neither case occurs, the output is allowed to be arbitrary. We consider two notions of being far: (1) A requires changing at least an ε-fraction of its entries, or (2) A requires changing at least an ε-fraction of its rows. We call the former the "entry model" and the latter the "row model". We show: For testing if a matrix has rank at most d in the entry model, we improve the previous number of entries of A that need to be read from O(d2/ε2) (Krauthgamer and Sasson, SODA 2003) to O(d2/ε). Our algorithm is the first to adaptively query the entries of A, which for constant d we show is necessary to achieve O(1/ε) queries. For the important case of d = 1 we also give a new non-adaptive algorithm, improving the previous O(1/ε2) queries to O(log2(1/ε) / ε). For testing if a matrix has rank at most d in the row model, we prove an Ω(d/ε) lower bound on the number of rows that need to be read, even for adaptive algorithms. Our lower bound matches a non-adaptive upper bound of Krauthgamer and Sasson. For testing if a matrix has stable rank at most d in the row model or requires changing an ε/d-fraction of its rows in order to have stable rank at most d, we prove that reading θ(d/ε2) rows is necessary and sufficient. We also give an empirical evaluation of our rank and stable rank algorithms on real and synthetic datasets.
Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China

Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into “Yuanjiang-Nanhun” basin and “Ejia-Jiepai” basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.
A model for classical spacetime coordinates

Field equations with general covariance are interpreted as equations for a target space describing physical spacetime co-ordinates, in terms of an underlying base space with conformal invariance. These equations admit an infinite number of inequivalent Lagrangian descriptions. A model for reparametrization invariant membranes is obtained by reversing the roles of base and target space variables in these considerations.
A framework for Green Supply Chain Management complying with RoHS directive

The enforcement of the RoHS (Restrictions of the use of Hazardous Substances) Directive on 1 st July 2006 requires all new Electrical and Electronic Equipment (EEE) entering the European Union (EU) market to be free of six toxic chemicals, including lead and cadmium. The RoHS Directive prevents the use and presence of these chemicals in all EEE. In recent years in Japan, EEE manufacturers exporting products into the EU have enhanced the Green Supply Chain Management (GSCM) as an effort to comply with the RoHS directive and to subsequently gain a competitive position in the EU market. Considering the future implications of the RoHS Directive, they have implemented new environmental programs and policies into their suppliers. This paper describes a case study on GSCM in the Shimadzu Corporation, a Japanese EEE manufacturer. GSCM is illustrated as managing collaborative relationships between manufacturers and suppliers to comply with the directive by considering an overview of the literature on GSCM and the RoHS directive. Based on this review of theory, a conceptual framework for GSCM is initially proposed to improve the collaborative relationships between EEE manufacturers and suppliers. Secondly, we explore the gaps between the framework and the present state of GSCM that have been implemented between an EEE manufacturer and a supplier. The paper concludes with discussion regarding the application and possible further development of the proposed framework for GSCM.
DNA 3′-Phosphatase Activity Is Critical for Rapid Global Rates of Single-Strand Break Repair following Oxidative Stress

ABSTRACT Oxidative stress is a major source of chromosome single-strand breaks (SSBs), and the repair of these lesions is retarded in neurodegenerative disease. The rate of the repair of oxidative SSBs is accelerated by XRCC1, a scaffold protein that is essential for embryonic viability and that interacts with multiple DNA repair proteins. However, the relative importance of the interactions mediated by XRCC1 during oxidative stress in vivo is unknown. We show that mutations that disrupt the XRCC1 interaction with DNA polymerase β or DNA ligase III fail to slow SSB repair in proliferating CHO cells following oxidative stress. In contrast, mutation of the domain that interacts with polynucleotide kinase/phosphatase (PNK) and Aprataxin retards repair, and truncated XRCC1 encoding this domain fully supports this process. Importantly, the impact of mutating the protein domain in XRCC1 that binds these end-processing factors is circumvented by the overexpression of wild-type PNK but not by the overexpression of PNK harboring a mutated DNA 3′-phosphatase domain. These data suggest that DNA 3′-phosphatase activity is critical for rapid rates of chromosomal SSB repair following oxidative stress, and that the XRCC1-PNK interaction ensures that this activity is not rate limiting in vivo.
Parallel K-means Clustering Algorithm on NOWs

Despite its simplicity and its linear time, a serial K-means algorithm's time complexity remains expensive when it is applied to a problem of large size of multidimensional vectors. In this paper we show an improvement by a factor of O(K/2), where K is the number of desired clusters, by applying theories of parallel computing to the algorithm. In addition to time improvement, the parallel version of K-means algorithm also enables the algorithm to run on larger collective memory of multiple machines when the memory of a single machine is insufficient to solve a problem. We show that a problem size can be scaled up to O(K) times a problem size on a single machine.