Miracle-dz/UniFAR-FTUs huggingface dataset:
Profiling of the Tetraspanin CD151 Web and Conspiracy of CD151/Integrin β1 Complex in the Progression of Hepatocellular Carcinoma

Tetraspanin CD151 has been implicated in metastasis through forming complexes with different molecular partners. In this study, we mapped tetraspanin web proteins centered on CD151, in order to explore the role of CD151 complexes in the progression of hepatocellular carcinoma (HCC). Immunoprecipitation was used to isolate tetraspanin complexes from HCCLM3 cells using a CD151 antibody, and associated proteins were identified by mass spectrometry. The interaction of CD151 and its molecular partners, and their roles in invasiveness and metastasis of HCC cells were assayed through disruption of the CD151 network. Finally, the clinical implication of CD151 complexes in HCC patients was also examined. In this study, we identified 58 proteins, characterized the tetraspanin CD151 web, and chose integrin β1 as a main partner to further investigate. When the CD151/integrin β1 complex in HCC cells was disrupted, migration, invasiveness, secretion of matrix metalloproteinase 9, and metastasis were markedly influenced. However, both CD151 and integrin β1 expression were untouched. HCC patients with high expression of CD151/integrin β1 complex had the poorest prognosis of the whole cohort of patients. Together, our data show that CD151 acts as an important player in the progression of HCC in an integrin β1-dependent manner.
Variations in surface and thermocline conditions of the Western Pacific Warm Pool : Insights from Mg/Ca and stable isotopes in foraminifera tests

ii Globorotalia tumida lower (~230–265 m) thermocline conditions. The newly established multispecies Mg/Ca-temperature calibration (Mg/Ca = 0.24 exp 0.097 * T) is in agreement with published regressions from other areas. The species-specific Mg/Ca-temperature relations of G. ruber, G. elongatus and G. tumida are consistent with previously published equations. However, in comparison to other areas, the calcification temperatures of G. sacculifer, P. obliquiloculata and N. dutertrei are exceptionally warm in the WPWP and underestimated by available calibrations. Their regional Mg/Ca-temperature relations are best described by Mg/Ca = 0.24 exp 0.097 * T for G. sacculifer and by Mg/Ca = 0.21 exp 0.097 * T for P. obliquiloculata and N. dutertrei. The results are of major importance aiming at the reconstruction of the paleoconditions in the WPWP. G. ruber and P. obliquiloculata are chosen as suitable indicators for surface and thermocline conditions, respectively and the regional, species-specific Mg/Ca-temperature calibrations set the basis for accurate paleotemperature estimates. The sediment core records reflect a complex pattern of astronomically driven and glacial–interglacial variations in surface and thermocline temperature, δOSW (salinity) and the water column structure and illustrate the interplay of local and remote forcings on the WPWP. The surface δOSW records from both, the southern and the northern WPWP sites depict cyclic variations of precessional duration that likely reflect variations in precipitaton, with enhanced (reduced) precipitation when precession is high (low). The precipitation variability is most likely related to latitudinal migrations of the Intertropical Convergence Zone (ITCZ) with a more southward (northward) position of the ITCZ under high (low)
Split T Cell Tolerance against a Self/Tumor Antigen: Spontaneous CD4+ but Not CD8+ T Cell Responses against p53 in Cancer Patients and Healthy Donors

Analyses of NY-ESO-1-specific spontaneous immune responses in cancer patients revealed that antibody and both CD4+ and CD8+ T cell responses were induced together in cancer patients. To explore whether such integrated immune responses are also spontaneously induced for other tumor antigens, we have evaluated antibody and T cell responses against self/tumor antigen p53 in ovarian cancer patients and healthy individuals. We found that 21% (64/298) of ovarian cancer patients but no healthy donors showed specific IgG responses against wild-type p53 protein. While none of 12 patients with high titer p53 antibody showed spontaneous p53-specific CD8+ T cell responses following a single in vitro sensitization, significant p53-specific IFN-γ producing CD4+ T cells were detected in 6 patients. Surprisingly, similar levels of p53-specific CD4+ T cells but not CD8+ T cells were also detected in 5/10 seronegative cancer patients and 9/12 healthy donors. Importantly, p53-specific CD4+ T cells in healthy donors originated from a CD45RA− antigen-experienced T cell population and recognized naturally processed wild-type p53 protein. These results raise the possibility that p53-specific CD4+ T cells reflect abnormalities in p53 occurring in normal individuals and that they may play a role in processes of immunosurveillance or immunoregulation of p53-related neoplastic events.
Modeling Macro-Critical Energy Sectors in Low-Income Countries: A General Framework and an Application to Côte D'Ivoire

This paper proposes a general framework for monitoring macro-critical energy sectors in low-income countries, defined as consisting of the three subsectors of crude oil and natural gas production, refinery, and electricity production. It aims to derive consistent information on physical and financial flows in the sector, including on interlinkages between the subsectors. It then applies this framework to Cote d'Ivoire. While being an important source of growth, the Ivoirien energy sector is found to have important shortcomings, in particular as regards transparency, efficiency and contribution to fiscal revenue. Among the key problems are partially intransparent production sharing arrangements for hydrocarbon production, price distortions for natural gas, administered prices for refined petroleum products, underfunding and lack of investment in the electricity sector, and inefficient government subsidies in the latter two subsectors.
Feature Selection and Activity Recognition System Using a Single Triaxial Accelerometer

Activity recognition is required in various applications such as medical monitoring and rehabilitation. Previously developed activity recognition systems utilizing triaxial accelerometers have provided mixed results, with subject-to-subject variability. This paper presents an accurate activity recognition system utilizing a body worn wireless accelerometer, to be used in the real-life application of patient monitoring. The algorithm utilizes data from a single, waist-mounted triaxial accelerometer to classify gait events into six daily living activities and transitional events. The accelerometer can be worn at any location around the circumference of the waist, thereby reducing user training. Feature selection is performed using Relief-F and sequential forward floating search (SFFS) from a range of previously published features, as well as new features introduced in this paper. Relevant and robust features that are insensitive to the positioning of accelerometer around the waist are selected. SFFS selected almost half the number of features in comparison to Relief-F and provided higher accuracy than Relief-F. Activity classification is performed using Naïve Bayes and k-nearest neighbor (k-NN) and the results are compared. Activity recognition results on seven subjects with leave-one-person-out error estimates show an overall accuracy of about 98% for both the classifiers. Accuracy for each of the individual activity is also more than 95%.
Advantages of genomic complexity: bioinformatics opportunities in microRNA cancer signatures

MicroRNAs, small non-coding RNAs, may act as tumor suppressors or oncogenes, and each regulate their own transcription and that of hundreds of genes, often in a tissue-dependent manner. This creates a tightly interwoven network regulating and underlying oncogenesis and cancer biology. Although protein-coding gene signatures and single protein pathway markers have proliferated over the past decade, routine adoption of the former has been hampered by interpretability, reproducibility, and dimensionality, whereas the single molecule–phenotype reductionism of the latter is often overly simplistic to account for complex phenotypes. MicroRNA-derived biomarkers offer a powerful alternative; they have both the flexibility of gene expression signature classifiers and the desirable mechanistic transparency of single protein biomarkers. Furthermore, several advances have recently demonstrated the robust detection of microRNAs from various biofluids, thus providing an additional opportunity for obtaining bioinformatically derived biomarkers to accelerate the identification of individual patients for personalized therapy.
Small Dwarf Galaxies within Larger Dwarfs: Why Some Are Luminous while Most Go Dark

We consider the possibility that the Magellanic Clouds were the largest members of a group of dwarf galaxies that entered the Milky Way (MW) halo at late times. Seven of the eleven brightest satellites of the MW may have been part of this system. The proximity of some dwarfs to the plane of the orbit of the Large Magellanic Cloud (LMC) has been used to argue that they formed from tidal debris from the LMC and Small Magellanic Cloud (SMC). Instead, they may owe to the tidal breakup of the Magellanic group. This can explain the association of many of the dwarf galaxies in the Local Group with the LMC system. It provides a mechanism for lighting up dwarf galaxies and reproduces the bright end of the cumulative circular velocity distribution of the satellites in the MW without invoking a stripping scenario for the subhalos to match the satellite distribution expected according to CDM theory. Finally, our model predicts that other isolated dwarfs will be found to have companions. Evidence for this prediction is provided by nearby, recently discovered dwarf associations.
Clinical development of new prophylactic antimalarial drugs after the 5th Amendment to the Declaration of Helsinki

Malaria is of continuing concern in nonimmune traveling populations. Traditionally, antimalarial drugs have been developed as agents for dual indications (treatment and prophylaxis). However, since 2000, when the 5th Amendment to the Declaration of Helsinki (DH2000) was adopted, development of new malaria prophylaxis drugs in this manner has ceased. As a consequence, there may not be any new drugs licensed for this indication in the foreseeable future. Major pharmaceutical companies have interpreted DH2000 to mean that the traditional development paradigm may be considered unethical because of doubt over the likelihood of benefit to endemic populations participating in clinical studies, the use of placebo, and the sustainability of post-trial access to study medications. In this article, we explore the basis of these concerns and suggest that the traditional development paradigm remains ethical under certain circumstances. We also consider alternative approaches that may be more attractive to sponsors as they either do not use placebo, or utilize populations in endemic countries who may unambiguously benefit. These approaches represent the way forward in the future, but are at present unproven in clinical practice, and face numerous regulatory, logistical and technical challenges. Consequently, in the short term, we argue that the traditional clinical development paradigm remains the most feasible approach and is ethical and consistent with the spirit of DH2000 under the appropriate circumstances.
Sliding Mode Sensorless Control of PM Synchronous Motor for Direct-Driven Washing Machines

The rotor position of PMSM is estimated by a novel sliding mode observer (SMO) operating over a wide speed range including deep flux-weakening region. By properly selecting equivalent control feedback gains, the estimation error of rotor position is reduced in low speeds and fast convergence of SMO guaranteed in high speeds. Compared to other PMSM systems for direct-driven washers using Hall effect sensors, the control scheme features high torque production and fast dynamic response, especially in the deep flux weakening high-speed range. The sensorless control algorithm is robust to the armature reaction that seriously affects Hall effect sensor signals and degrades torque production. The proposed sensorless control algorithm is verified by both computer simulation and experimental testing with a dynamometer as well as a direct-driven washer
Issues in Mapping LOINC Laboratory Tests to SNOMED CT

Comprehensive clinical terminologies such as SNOMED CT tend to overlap with specialized terminologies such as LOINC (e.g., for the domain of laboratory procedures). Terminological systems such as the UMLS are often used to bridge between terminologies. However, the integration of LOINC in the UMLS and with other terminologies remains suboptimal. We mapped concepts for laboratory tests from LOINC to pre-coordinated SNOMED CT concepts, based on shared relations to other concepts. As LOINC is finer-grained than SNOMED CT, several LOINC codes tend to map to the same SNOMED CT concept. However, a large proportion of LOINC codes could not be mapped to SNOMED CT through this approach, because of underspecified definitions in SNOMED CT and a lack of fine-grained, pre-coordinated concepts in SNOMED CT.
TRiCmini^+ -A Telepresence Robot for Interpersonal Communication for Older Adults

Aging is associated with an increased risk of isolation. Information and communication technologies have been utilized to assist homecare of older adults. However, in addition to transmitting vital sign data for healthcare purposes, older adults may expect to share their life experiences and feelings by different forms of interactions with their children and family members. Communication tools did facilitate interpersonal communication in terms of real-time verbal communication. Nevertheless, nonverbal communication, such as facial expression and body language, is more powerful and efficient in conveying ideas, thoughts, and emotions. ”TRiCmini^+” is a telepresence robot for interpersonal communication. It demonstrates extensive capability to provide different levels of ”care delivery” to older adults through vital sign monitoring, interpersonal communication, robotic movements, and social network integration. TRiCmini^+ integrates two distinct applications, the ”Care Delivery Frame (CDF)” and the telepresence robot. CDF is an App designed for older adults as an information channel on the tablet PC, which is also the ”face” of TRiCmini^+. CDF is integrated with social network services, and remote caregivers can share messages, photos or video clips with older adults. Moreover, the tablet is also the control center of the robot. In this innovative control structure, the robot control App can be downloaded and maintained easily through the Internet.The prototype and functional test of TRiCmini^+ have been completed. Currently it is under usability evaluation, including the interface design and operation efficiency for both remote and local users. Finally, the effectiveness of communication will be evaluated in real application scenarios to confirm the ”care delivery” in different forms provided by TRiCmini^+ actually meets the expectation of older adults.
Network vs market relations: The effect of friends in crowdfunding

Crowds offer a new form of efficacious collective decision making, yet knowledge about the mechanisms by which they achieve superior outcomes remains nascent. It has been suggested that crowds work best with market-like relationships when individuals make independent decisions and possess dissimilar information. By contrast, sociological discussions of markets argue that risky decisions are mitigated by network relations that embed economic transactions in social ties that promote trustworthiness and reciprocity. To investigate the role of networks within crowds and their performance effects, we examined the complete record of financial lending decisions on Prosper.com, 1/2006-3/2012, the first U.S. crowdfunding platform and a chief gateway to capital for entrepreneurs and general borrowers that continues to disrupt conventional financial lending structures infusing more than $5.1 billion into the market in 2013. Our study reveals how reciprocity, recurring borrower-lender dyads, and persistent co-lending underpin the dynamics of network lending. Further, we show how network ties influence the evolution of the lending behavior. We find that in the early stage of fundraising, network relations provide larger proportions of loans, typically lending four times more per bid than strangers. They also respond to loan requests on average 59.5% sooner than strangers. The size of the first loan and the time to lending also tend to prompt lending by strangers, suggesting that network relations might move the market, a finding that persists even as fewer lenders dominate more of the market for loans on Prosper. Finally, network relations are associated with greater engagement: when the first loan is underwritten by a friend, 50% of the remaining loans come from friends as well.
An Algebraic Approach for H-matrix Preconditioners ∗ Suely

Hierarchical matrices (H-matrices) approximate matrices in a data-sparse way, and the approximate arithmetic for H-matrices is almost optimal. In this paper we present an algebraic approach to constructing H-matrices which combines multilevel clustering methods with the H-matrix arithmetic to compute the H-inverse, H-LU, and the H-Cholesky factors of a matrix. Then the H-inverse, H-LU or H-Cholesky factors can be used as preconditioners in iterative methods to solve systems of linear equations. The numerical results show that this method is efficient and speeds up convergence greatly against other approaches such as JOR or AMG to solving some large, sparse linear systems, and it is comparable to other H-matrix constructions based on Nested Dissection.
MARF and Opa1 Control Mitochondrial and Cardiac Function in Drosophila

Rationale: Mitochondria interact via actions of outer and inner membrane fusion proteins. The role of mitochondrial fusion in functioning of the heart, where mitochondria comprise ≈30% of cardiomyocyte volume and their intermyofilament spatial arrangement with other mitochondria is highly ordered, is unknown. Objective: Model and analyze mitochondrial fusion defects in Drosophila melanogaster heart tubes with tinc&Dgr;4Gal4-directed expression of RNA interference (RNAi) for mitochondrial assembly regulatory factor (MARF) and optic atrophy (Opa)1. Methods and Results: Live imaging analysis revealed that heart tube–specific knockdown of MARF or Opa1 increases mitochondrial morphometric heterogeneity and induces heart tube dilation with profound contractile impairment. Sarcoplasmic reticular structure was unaffected. Cardiomyocyte expression of human mitofusin (mfn)1 or -2 rescued MARF RNAi cardiomyopathy, demonstrating functional homology between Drosophila MARF and human mitofusins. Suppressing mitochondrial fusion increased compensatory expression of nuclear-encoded mitochondrial genes, indicating mitochondrial biogenesis. The MARF RNAi cardiomyopathy was prevented by transgenic expression of superoxide dismutase 1. Conclusions: Mitochondrial fusion is essential to cardiomyocyte mitochondrial function and regeneration. Reactive oxygen species are key mediators of cardiomyopathy in mitochondrial fusion-defective cardiomyocytes. Postulated mitochondrial–endoplasmic reticulum interactions mediated uniquely by mfn2 appear dispensable to functioning of the fly heart.
OVERVIEW CIRCULAR OVERLAPS : RARE DEMONSTRATIONS OF SPECIATION

THE SPLITTING OF a single species into two or more is a difficult process to observe, because it can take a great deal of time. Evolutionary biologists have recognized that a solution to this problem is to use geographical variation to infer how change in time might occur. Especially interesting in that regard is the phenomenon of ‘‘circular overlaps’’ (Mayr 1942), or ‘‘ring species’’ (Cain 1954), in which two sympatric and clearly distinct forms are connected by a chain of populations through which the characteristics of one form gradually change into those of the other. The possibility that ring species might exist was first suggested about a century ago by Stejneger (as quoted by Jordan 1905), and since then a number of possible examples have generated intense interest among evolutionary biologists. One of the most widely known of the proposed examples of ring species is the series of taxa in the Herring Gull (Larus argentatus) and Lesser Black-backed Gull (L. fuscus) group (Crochet et al. 2002). Ever since Mayr (1940, 1942) described these gulls as a prime example of circular overlap and geographic speciation, they have figured prominently in university course lectures, textbooks (e.g. Ridley 1993), and popular books on evolution (e.g. Schilthuizen 2001). The usual description follows from Mayr’s writings:
Unavoidable Languages, Cuts and Innocent Sets of Words

A language X on an alphabet A is unavoidable iff all but finitely many words in A * have a factor in X. In this paper, cuts (which are basically simplifications of languages in terms of avoidability) and innocent language (those which cannot be cut) are defined. Their properties, most of which are related to unavoidable languages, are studied.
Png‐1, a nervous system‐specific zinc finger gene, identifies regions containing postmitotic neurons during mammalian embryonic development

To identify genes associated with early postmitotic cortical neurons, gene fragments were examined for expression in postmitotic, but not proliferative, zones of the embryonic murine cortex. Through this approach, a novel member of the zinc finger gene family, containing 6 C2HC fingers, was isolated and named postmitotic neural gene‐1, or png‐1. Embryonic png‐1 expression was: 1) nervous system‐specific; 2) restricted to zones containing postmitotic neurons; and 3) detected in all developing neural structures examined. In the cortex, png‐1 expression was first observed on embryonic day 11, correlating temporally and spatially with the known generation of the first cortical neurons. Gradients of png‐1 expression throughout the embryonic central nervous system further correlated temporally and spatially with known gradients of neuron production. With development, expression remained restricted to postmitotic zones, including those containing newly‐postmitotic neurons. Png‐1 was also detected within two days of neural retinoic acid induction in P19 cells, and expression increased with further neuronal differentiation. These data implicate png‐1 as one of the earliest molecular markers for postmitotic neuronal regions and suggest a function as a panneural transcription factor associated with neuronal differentiation. J. Comp. Neurol. 130‐142, 1997. © 1997 Wiley‐Liss, Inc.
A case study of combining compositional and object-oriented software development

We analyze an approach to software development where object-oriented and compositional software specifications are written in separate languages and are only loosely connected. It supports compositional design of software in a domain-specific language and automatic model-driven construction of code from classes written in Java. We justify our approach by giving examples of development of large simulation programs and services on large models. We present also an example of using our method in general purpose software development - this is bootstrapping the essential part of a software tool CoCoViLa, i.e. synthesizing CoCoViLa in CoCoViLa itself.